logoC.briggsae small RNAs

miR-Intess™


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Composition

miR classification
miR expression
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Table
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Clusters

Alignments

confident miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK (19 loci)

cbr-mir-57

Cloning frequencies
absoluteAF16
cbr-mir-57 5arm37
cbr-mir-57 3arm1
normalizedAF16
cbr-mir-57 5arm0.096
cbr-mir-57 3arm0.003
cbr-mir-57 relative cloning frequencies

sblock12 (miRBase cbr-mir-57) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-570.003nono0.48/0.5020/25/0.900.0
0.0
0.0
0.0
31
1
0
0
1
1
0
0
14
17
5
6
5arm
3arm
1
1
nd
nd
0.25
0.20
2
2
38120
sblock12 hairpin
  readsmiRBase family seed
seed     -----------------------------------ACCCUGU-------------------------------------------------------------------------------------------     36miR-57
seed     ----------------------------------------------------------------------------------CGAGCUA--------------------------------------------     1novel
seed     ---------------------------------------UGUAGAU---------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-57     ----------------------------------TACCCTGTAGATCGAGCTGTGTG-------T--------------------------------------------------------------------     2431
      ----------------------------------TACCCTGTAGATCGAGCTGTGTG-------TT-------------------------------------------------------------------     254
      --------------------------------------CTGTAGATCGAGCTGTGTG-------TT-------------------------------------------------------------------     211
      ----------------------------------TACCCTGTAGATCGAGCTGTGT-----------------------------------------------------------------------------     221
      ---------------------------------------------------------------------------------ACGAGCTAGACTACTAGGTG--------------------------------     201
cbriggsae     --------------------GCTCTGAGTTCGTCTACCCTGTAGATCGAGCTGTGTG-------TTCTGAAGT-ATCATACACGAGCTAGACTACTAGGTGAACGATGGAA---TGGAGCA------------      
cremanei     ACGTAAGTTTGAATATCTCATGACTGTTTTCGTCTACCCTGTAGATCGAGCTGTGTG-------TTTTGAAGTGTTCATACACAAGCTAGACTGCAAGGTGAACGACAAAA---TGAGAGAGCTTCTTTATGT      
celegans     -------GTATGTGAACTCATCGACATGCTCGTCTACCCTGTAGATCGAGCTGTGTG--------TTTGAAACAATCATACACGAGCTAGACTACAAGGTGCACGAACAAA---CCGAAGATTTATGAATAT-      
cbrenneri     ----------------------------------TACCCTGTAGATAGAGCTGTGTG-------TTTGGAATATACCGTACACAAGCTAGACTACAAGGTGAACGACTTAT--------GAGCTTTAATTTTA      
cjaponica     -------GTTGATCTGCTCGATCCGAACATCGTCTACCCTGTAGATCGAGCTGTGTGTGTGCTATTTCGAAATGATAGAACACACGCTAGACTTCAGGGTGAACGAGATGGATTTGAGAGAAGGTTGGC----      
                                        ************ **********        *  ***        ****  ******** *  **** ****              *                  
 +++++                    +++++++++++++++++++++++++++++++++++++       +++++++++ +++++++++++++++++++++++++++++++++++++   +++++++            +++++NM_001011629
 -----                    -------------------------------------       --------- -------------------------------------   -------            -----NM_001791
 -----                    -------------------------------------       --------- -------------------------------------   -------            -----NM_001039802
 -----                    -------------------------------------       --------- -------------------------------------   -------            -----NM_001007799
cbriggsae                         (((((...((((((((((..((((.((.((((.((((       (..(((... .))).))))))))).))))))..))))...)))))).   .))))).                 1.000 -33.90
cremanei     (((((((...(((..((((((.....((.((((.((((.(((((.((.((((.((((       (..(((.....))).))))))))).))))))).)))).)))).)).)   )))))....))))))))))     0.987 -37.60
celegans            ....(((((.((.(((...((.((((.((((.(((((.((.((((.((((        (.(((.....))).))))))))).))))))).)))).)))).))..   .))).)))))))......      0.972 -35.50
cbrenneri                                       ((((.(((((....((((.((((       (.(((......))).)))))))))...))))).))))..........        ..............     0.887 -23.10
cjaponica            ((..((((.(((((((((....((((.(((((((.((.((.(((.((((((...(((((.......))))).))))))))).)))).))))))).))))..)))))).)))...))))..))         1.000 -51.90

cbriggsaechromosome:chrII:5768347:5768436:-1Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_001791|CDC42 ## Opposite_strand|Intronic_coding|NM_001007799|Cir ## {Repeats: no} ## {MIR: cbr-mir-57}
cremaneichromosome:chrUn:19014083:19014205:-1Opposite_strand|Intronic_coding|NM_001009825
celeganschromosome:chrII:7850426:7850539:-1intergenic ## {MIR: cel-mir-57}
cbrennerichromosome:chrUn:125714261:125714344:-1intergenic
cjaponicachromosome:chrUn:29105267:29105388:-1intergenic


cbr-mir-44

Cloning frequencies
absoluteAF16
cbr-mir-44 5arm2
cbr-mir-44 3arm63
normalizedAF16
cbr-mir-44 5arm0.005
cbr-mir-44 3arm0.164
cbr-mir-44 relative cloning frequencies

sblock13 (miRBase cbr-mir-44) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-440.001nono0.41/0.4819/22/0.960.0
0.0
0.0
0.0
4
166
0
0
1
1
0
0
13
14
10
12
5arm
3arm
2
3
nd
nd
0.10
0.10
2
1
193112
Clusters
Located in cluster 2: cbr-mir-44, cbr-mir-43, cbr-mir-42
Families
Member of family miR-44/45/61 (seed GACUAGA): cbr-mir-44, cbr-mir-45, cbr-mir-45, cbr-mir-61, block4958_cand
sblock13 hairpin
  readsmiRBase family seed
seed     --------------------------------------------------------------------------------GACUAGA----------------------------------------     188miR-44/45/61
seed     ----------------------------UGGAUGU--------------------------------------------------------------------------------------------     4novel
seed     ---------------------------------------------------------------------------------ACUAGAG---------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-44     -------------------------------------------------------------------------------TGACTAGAGACACATTCAGCT---------------------------     21166
      -------------------------------------------------------------------------------TGACTAGAGACACATTCAG-----------------------------     198
      -------------------------------------------------------------------------------TGACTAGAGACACATTCAGC----------------------------     208
      -------------------------------------------------------------------------------TGACTAGAGACACATTCAGCTT--------------------------     226
      ---------------------------CTGGATGTGCTCGTTAGTCAT-------------------------------------------------------------------------------     214
      --------------------------------------------------------------------------------GACTAGAGACACATTCAGCT---------------------------     201
cbriggsae     --------------GAGAAGGGCCGATCTGGATGTGCTCGTTAGTCATAGACGAATCACACTTGAAAGGTCA-----TATGACTAGAGACACATTCAGCTTGGCCTGGATCTCA-------------      
cremanei     GAGTTAGAGAGTGAGAGAATGGCCGATCTGGATGTGCTCGTTAGTCATAGACGAATCACAGA-AAACAGTCA-----TATGACTAGAGACACATTCAGCTTGGCCTGGATCTCAAATTGAAGAATTT      
celegans     -------------------------ATCTGGATGTGCTCGTTGGTCATAGACGTCAA-CACG-AACTGTTCA-----TATGACTAGAGACACATTCAGCT---------------------------      
cbrenneri     ------------GAGAGAATGGCCGATCTGGATGTGCTCGTTAGTCATAGACGATACACAGA-GAACGGTCA-----TATGACTAGAGACACATTCAGCTTGGCCTGGATCTC--------------      
cjaponica     -------------------------ATCTGGGTGTGCTCGTTAGTCATA---------TATCCGCACGGCTA-TGAGTATGACTAGAGACACATTCAGCT---------------------------      
ppacificus     -----------GAGTCGCAGCCCCGCTCTGGATGTG-----TGATCTTGGTCGTATC-CGCGCAAATGCTCAATGATTATGACTAGAGACACATTCAGCTTGGGGCCGGCTC---------------      
                                ***** ****     *  ** *                       *     ***********************                                 
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_001047975
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_214509
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_001034039
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_001033832
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_214466
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_080679
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_080681
 +++++              ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++             +++++NM_080680
 -----              ----------------------------------------------------------     -------------------------------------             -----NM_133464
cbriggsae                   ((((.(((((((.((((((((((((..(((((((((((...(((....)))...))).     ))))))))))).))))))))).)))))))...)))).                  1.000 -46.40
cremanei     (((((.((...(((((....((((((.((((((((((((..(((((((((((.......... .....))).     ))))))))))).))))))))).))))))....)))))..))....)))))     0.996 -46.36
celegans                              ..((((((((((((...((((((((((.((.. ...) )...)))..     ))))))).))).)))))))))..                                1.000 -23.70
cbrenneri                 ((((....((((((.((((((((((((..(((((((((((.......... .....))).     ))))))))))).))))))))).))))))....))))                   1.000 -42.66
cjaponica                              ..((((((((((((..((((((((         (..((....))... ...)))))))))))).)))))))))..                                1.000 -23.90
ppacificus                ((((((..((((((..(((((((((     (..((.((((((((.. ((.((....))....))..)))))))))).))))))))))..))))))))))))                    0.999 -44.40

cbriggsaechromosome:chrII:8049267:8049361:-1Same_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_133464|ZNF483 ## {Repeats: no} ## {MIR: cbr-mir-44}
cremaneichromosome:chrUn:8362354:8362474:1intergenic
celeganschromosome:chrII:11889919:11890053:1intergenic ## {MIR: cel-mir-44}
cbrennerichromosome:chrUn:172696460:172696554:1intergenic
cjaponicachromosome:chrUn:98918996:98919130:-1intergenic
ppacificuschromosome:chrUn:21366498:21366592:-1Opposite_strand|Intronic_coding|NM_001032504 ## Same_strand|Intronic_coding|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}


cbr-mir-45

Cloning frequencies
absoluteAF16
cbr-mir-45 5arm6
cbr-mir-45 3arm126
normalizedAF16
cbr-mir-45 5arm0.016
cbr-mir-45 3arm0.328
cbr-mir-45 relative cloning frequencies

sblock15 (miRBase cbr-mir-45-1) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-45-10.001nono0.41/0.4819/22/0.960.0
0.0
0.0
0.0
4
166
0
0
1
1
0
0
9
7
10
9
5arm
3arm
2
3
nd
nd
0.10
0.10
2
1
193112
Families
Member of family miR-44/45/61 (seed GACUAGA): cbr-mir-44, cbr-mir-45, cbr-mir-45, cbr-mir-61, block4958_cand
sblock15 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------GACUAGA-----------------------------------     188miR-44/45/61
seed     -----------------------UGGAUGU-----------------------------------------------------------------------------------     4novel
seed     ------------------------------------------------------------------------ACUAGAG----------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-44     ----------------------------------------------------------------------TGACTAGAGACACATTCAGCT----------------------     21166
      ----------------------------------------------------------------------TGACTAGAGACACATTCAGC-----------------------     208
      ----------------------------------------------------------------------TGACTAGAGACACATTCAG------------------------     198
      ----------------------------------------------------------------------TGACTAGAGACACATTCAGCTT---------------------     226
      ----------------------CTGGATGTGC--TCGTTAGTCAT--------------------------------------------------------------------     214
      -----------------------------------------------------------------------GACTAGAGACACATTCAGCT----------------------     201
cbriggsae     ------------A-GTGCCACGCTGGATGTGC--TCGTTAGTCATAGTAACCT-CATCAATTCAGGCTTATGACTAGAGACACATTCAGCTTGGCGCC---------------      
cremanei     ACTGTACCAAAAC-GTGCCACGCTGGATGTGC--TCGTTAGTCATAATAACCT-CATTTAGTAAGGCTTATGACTAGAGACACATTCAGCTTGGCGCCGAACTATAA-ACAGT      
celegans     -----ATGCACCATGTGCCACGCTGGATGTGC--TCGTTAGTCATAATATCCTCCACAAAGCAAGGACTATGACTAGAGACACATTCAGCTTGGCGCCGAATGCAT-------      
cbrenneri     ACTGTTCGGGAAA-CTGCCACGCTGGATGTGC--TCGTTAGTCATAGTAGCCT--ATCCTGAACGGCCTATGACTAGAGACACATTCAGCTTGGCTCCGATATCAATTACAGT      
cjaponica     -----CTGAAATC-TTGCCACGCTGAATGTGC--TCGTTAGTCATAACCACCCATATCGTCAAGGGCATATGACTAGAGACACATTCAGCTTGGCTCACATTTTCAG------      
ppacificus     -----GAGTCGCA-GCCCCGCTCTGGATGTGTGATC-TTGGTCGTATCCGCGCAAATGCTCAATGA-TTATGACTAGAGACACATTCAGCTTGGGGCCGGCTC----------      
                       ** * *** *****   ** ** *** **    *    *        *   **************************  *                      
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001047975
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_214509
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001034039
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001033832
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_214466
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_080679
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_080681
 +++++            + ++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_080680
 -----            - ------------------  ------------------- --------------------------------------------               -----NM_133464
cbriggsae                 . ((((((.(((((((((((  ((..(((((((((...((( .(.....).))).)))))))))))).)))))))))).)))))).                    1.000 -40.20
cremanei     (((((........ ((((((.(((((((((((  ((..(((((((((...((( .........))).)))))))))))).)))))))))).)))))).......... )))))     0.994 -42.77
celegans          (((((....((((((.(((((((((((  ((..((((((((...((((..........)))).))))))))))).)))))))))).))))))....)))))            1.000 -45.40
cbrenneri     ((((((((((... ..((((.(((((((((((  ((..(((((((((..(((.  .........))))))))))))))).)))))))))).)))))))))........)))))     0.902 -47.30
cjaponica          ((((((.. ..((((.(((((((((((  ((..((((((((....(((..........)))..))))))))))).)))))))))).))))......))))))           1.000 -42.90
ppacificus          ((((((.. ((((((..((((((((((..(( .((((((((..((.((....))....)). .)))))))))).))))))))))..))))))))))))               0.999 -44.40

cbriggsaechromosome:chrII:8058565:8058646:-1Same_strand|Intronic_coding|NM_001047975|LOC683871 ## Opposite_strand|Intronic_non-coding|NM_133464|ZNF483 ## {Repeats: no} ## {MIR: cbr-mir-45-1}
cremaneichromosome:chrUn:8356876:8356983:-1intergenic
celeganschromosome:chrII:11880860:11880958:-1intergenic ## {Repeats: AT_rich 1 28 -1 class=Low_complexity} ## {MIR: cel-mir-45}
cbrennerichromosome:chrUn:101670635:101670742:-1Same_strand|Intronic_coding|NM_007742 ## Opposite_strand|Intronic_coding|NM_138591
cjaponicachromosome:chrUn:98930666:98930764:1intergenic
ppacificuschromosome:chrUn:21366498:21366592:-1Opposite_strand|Intronic_coding|NM_001032504 ## Same_strand|Intronic_coding|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}


cbr-mir-36

Cloning frequencies
absoluteAF16
cbr-mir-36 5arm6
cbr-mir-36 3arm415
normalizedAF16
cbr-mir-36 5arm0.016
cbr-mir-36 3arm1.082
cbr-mir-36 relative cloning frequencies

sblock20 (miRBase cbr-mir-36) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-360.001nono0.40/0.5318/23/0.710.0
0.0
0.0
0.0
5
283
0
0
1
1
0
0
25
22
3
4
5arm
3arm
1
1
nd
nd
0.18
0.09
2
2
421112
Clusters
Located in cluster 3: cbr-mir-36, cbr-mir-38, cbr-mir-39, cbr-mir-40, block969_novel, cel-mir-35, cbr-mir-41, cbr-mir-35
Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand
sblock20 hairpin
  readsmiRBase family seed
seed     -------------------------------------------------------------------------------CACCGGG-----------------------------------------------------     407miR-35/36/38/39/40/41
seed     -----------------------------------------------------------------------------------GGGUGAA-------------------------------------------------     7novel
seed     --------------------------------------GUGAAUU----------------------------------------------------------------------------------------------     5novel
seed     ------------------------------------------------------------------------------UCACCGG------------------------------------------------------     1novel
seed     ------------------------------------UUGUGAA------------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-36     ------------------------------------------------------------------------------TCACCGGGTGAAAATTCGCAAT---------------------------------------     22283
      ------------------------------------------------------------------------------TCACCGGGTGAAAATTCGC------------------------------------------     19113
      ----------------------------------------------------------------------------------CGGGTGAAAATTCGCAAT---------------------------------------     187
      ------------------------------------------------------------------------------TCACCGGGTGAAAATTCGCAA----------------------------------------     217
      -------------------------------------TGTGAATTT-TTGCTGCGGTGTT-------------------------------------------------------------------------------     225
      ------------------------------------------------------------------------------TCACCGGGTGAAAATTCG-------------------------------------------     184
      -----------------------------------------------------------------------------ATCACCGGGTGAAAATTCGCAAT---------------------------------------     231
      -----------------------------------ATTGTGAATTT-TTGCTGCGG-----------------------------------------------------------------------------------     201
cbriggsae     ATTCCAATT------------GAAACCTTCGGACCATTGTGAATTT-TTGCTGCGGTGTTACAACTAA--CATCTGTATCACCGGGTGAAAATTCGCAATGGTCCGATGGGTATTCATGTGG-----------------      
cremanei     --------------------------------------GCCAATTC-TTACCGCGGTAATAGAACTGCATAGTTTCTATCACCGGGTGAAAATTCGGCTCGGATC--T-------------------------------      
celegans     --------------------AGAAACCCTTGGACCAGTGTGGGTGT-CCGTTGCGGTGCTAC-ATTCTCTAATCTGTATCACCGGGTGAACACTTGCAGTGGTCC--TCGTGGTTTCT---------------------      
cbrenneri     GTTCATATTTTTCATATTCAGGGGTGGATCGGGCCTGTGCTGATTT-TTGCCGCTGTGATATTTCTAAGCCATGATTATCACCGGGCGAAAATTTGGCACAGGCC--TCGTCCGCCCT---------------------      
cjaponica     -TGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGTTTCTTTCCGCGGTAATA--AATAATACATTATTATCACCGGGAGAAAAACTGGAGTAGGAC--CTGCGACTCGACTCGACCTTTATTCCGCTGTA      
ppacificus     -----------------------------------GGGATGCATATTCTAACCCGGTGACTC-AATAAACAATGA--GTCACCGGGTTAGAATATG------------------TCCA---------------------      
                                                 *         * **        *      *     ********  *  *   *                                                 
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_177732
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_214509
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_001030843
 ++++++++++++++            +++++++++++++++++++++++++ +++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++++++                 +++++NM_001101718
 ++++++++++++++            +++++++++++++++++++++++++ +++++++++++++++++++++  ++++++++++++++++++++++++++++++++++++++++++++++++++++                 +++++NM_001011629
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_207243
 --------------            ------------------------- ---------------------  ----------------------------------------------------                 -----NM_171042
cbriggsae     ...(((..(            ((((((((((((((((((((((((( (..((.(((((.((((.....  ....)))).)))))))..))))))))))))))))))).)))).))))..)))                      1.000 -55.80
cremanei                                           (((((((. (((((.((((.((((((((....)))).)))).))))))))).)))).))).......  .                                    1.000 -23.80
celegans                         (((((((...((((((.((..((((( .((...(((((.((( (..........)))).)))))..)).)))))..)).))))))  ....)))))))                          1.000 -43.20
cbrenneri     ....................(((((((((.(((((((((((((((( (((((...((((((..((........)).))))))..)))))))))).))))))))))  ).)))))))))                          0.944 -57.20
cjaponica      ((((((((......((((..((.(((.((((.(((((..((((((.(((((.((((.((.  (((((....))))))).))))))))).))))))..))))).)  )))...)))...))..))))....))))))))     0.964 -52.50
ppacificus                                        .((..(((((((((((((((((((((( (........)))  )))))))))))))))))))                  ))).                          1.000 -42.10

cbriggsaechromosome:chrII:7535762:7535868:1Opposite_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Opposite_strand|Intronic_coding|NM_214509|COLP1alpha ## Same_strand|Intronic_coding|NM_001101718|LOC100009540 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-36}
cremaneichromosome:chrUn:26786598:26786664:-1intergenic
celeganschromosome:chrII:11537753:11537846:1Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-37}
cbrennerichromosome:chrUn:47821556:47821670:-1intergenic ## {SimpF: trf}
cjaponicachromosome:chrUn:117591701:117591834:-1Opposite_strand|Intronic_coding|NM_171042
ppacificuschromosome:chrUn:47519694:47519840:1Same_strand|Intronic_coding|NM_001003336


cbr-mir-40

Cloning frequencies
absoluteAF16
cbr-mir-40 5arm7
cbr-mir-40 3arm309
normalizedAF16
cbr-mir-40 5arm0.018
cbr-mir-40 3arm0.805
cbr-mir-40 relative cloning frequencies

sblock22 (miRBase cbr-mir-40) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-400.001nono0.50/0.5718/23/0.950.0
0.0
0.0
0.0
7
263
0
0
1
1
0
0
24
24
4
5
5arm
3arm
1
1
nd
nd
0.23
0.23
2
2
316112
Clusters
Located in cluster 3: cbr-mir-36, cbr-mir-38, cbr-mir-39, cbr-mir-40, block969_novel, cel-mir-35, cbr-mir-41, cbr-mir-35
Families
Member of family miR-35/36/38/39/40/41 (seed CACCGGG): cel-mir-35, cel-mir-35, cel-mir-36, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cel-mir-35, cbr-mir-39, cbr-mir-35, cbr-mir-36, cbr-mir-40, cbr-mir-41, cbr-mir-38, block969_novel, block5129_cand
sblock22 hairpin
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------------------------CACCGGG------------------------------------------------------------------     297miR-35/36/38/39/40/41
seed     ----------------------------------------------------------------------------------------------------GGGUGUC--------------------------------------------------------------     11novel
seed     --------------------------------------------------GCGGGUU----------------------------------------------------------------------------------------------------------------     7novel
seed     -----------------------------------------------------------------------------------------------UCACCGG-------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-40     -----------------------------------------------------------------------------------------------TCACCGGGTGTCAATCAGCTAG----------------------------------------------------     22263
      -----------------------------------------------------------------------------------------------TCACCGGGTGTCAATCAGCT------------------------------------------------------     2017
      -----------------------------------------------------------------------------------------------TCACCGGGTGTCAATCAGCTA-----------------------------------------------------     2112
      ---------------------------------------------------------------------------------------------------CGGGTGTCAATCAGCTAG----------------------------------------------------     1811
      -------------------------------------------------AGCGGGTTTTCATCGCAGTGAT--------------------------------------------------------------------------------------------------     227
      -----------------------------------------------------------------------------------------------TCACCGGGTGTCAATCAG--------------------------------------------------------     184
      ----------------------------------------------------------------------------------------------ATCACCGGGTGTCAATCAGCT------------------------------------------------------     211
      -----------------------------------------------------------------------------------------------TCACCGGGTGTCAATCAGCTAGG---------------------------------------------------     231
cbriggsae     -------------------------CTCTGTATCCCCTGCCCTCACCCCAGCGGGTTTTCATCGCAGTGATATGACGCATTCAAACCATTTCTTATCACCGGGTGTCAATCAGCTAGGGTGTGGGCGCGGGTATCCACAGA----------------------------      
cremanei     -----------------TCCGATTGGTTGAAAGAGCCAGAACCTATACCGGT---TTAACTTCGTGGTGATATGACACATATTA--CATTCTTTATCACCGGGAGTAAAAC-----TGGTATAGGATCTGCGACTCGCTGATTGGA-----------------------      
celegans     ---------AGCTTGGCTCTGGTGTCTCCGAACCTCCTGTCCGCACCTCAGTGGATGTATGCCATGATGATAAGATATCAGAAA------TCCTATCACCGGGTGTACATCAGCTAAGGTGCGGGTACAGGTGCATTTGATATCAAGGTGAGTT---------------      
cjaponica     GTGAACACTTGCAGTGGTCCCTCGGGGCAGAAGAGCCAGGACCTACATCAGT---TTCTTTCCGCGGTAATAAATAATACATTA--------TTATCACCGGGAGAAAAAC-----TGGAGTAGGACCTGCGACTC---GACTCGACCTTTATTCCGCTGTATTTTTGC      
                                     *   ** *  *  *   * *    *      *    * ***           *         ********** *   * *      **    **  * *                                             
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_177732
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_214509
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_001030843
 +++++                         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                            +++++NM_001101718
 +++++                         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++                            +++++NM_001011629
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_207243
 -----                         --------------------------------------------------------------------------------------------------------------------                            -----NM_171042
cbriggsae                              .(((((..(((.(((((.(((((.(((.((((..((((.(.((((((.((...............)).)))))).)))))..)))).))).))))).))))).))).....)))))                                 1.000 -47.26
cremanei                      ((((((..((.....(((.((((.(((((((((((   ((.(((((.((((((((............  .......))))))))))))).))))     ))))))))).))))...)))))..))))))                            1.000 -51.31
celegans              ((((((.((.(((((((.........(((((((((((((.(((.((((((((((.((.(((((.(((.......)      )).))))).)))))))))))).))).))))))))..))))).......))))))))).))))))                    1.000 -58.59
cjaponica     (((((....((((((((......((((..((.(((.((((.(((((..((((   ((.(((((.((((.((.(((((....)))        )))).))))))))).))))     ))..))))).))))...)))   ...))..))))....))))))))..)))))     0.921 -53.70

cbriggsaechromosome:chrII:7536135:7536250:1Opposite_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Opposite_strand|Intronic_coding|NM_214509|COLP1alpha ## Same_strand|Intronic_coding|NM_001101718|LOC100009540 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no} ## {MIR: cbr-mir-40}
cremaneichromosome:chrUn:8778754:8778872:-1Same_strand|Intronic_coding|NM_001011005 ## Opposite_strand|Intronic_coding|NM_171042
celeganschromosome:chrII:11538075:11538213:1Opposite_strand|Intronic_coding|Y62F5A.9 ## {MIR: cel-mir-40}
cjaponicachromosome:chrUn:117591694:117591843:-1Opposite_strand|Intronic_coding|NM_171042


sblock24 (miRBase cbr-mir-45-2) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-45-20.001nono0.41/0.4519/22/0.960.0
0.0
0.0
0.0
4
166
0
0
1
1
0
0
9
7
10
9
5arm
3arm
1
3
nd
nd
0.10
0.10
2
1
193112
Families
Member of family miR-44/45/61 (seed GACUAGA): cbr-mir-44, cbr-mir-45, cbr-mir-45, cbr-mir-61, block4958_cand
sblock24 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------------GACUAGA-----------------------------------     188miR-44/45/61
seed     ----------------------UGGAUGU-----------------------------------------------------------------------------------     4novel
seed     -----------------------------------------------------------------------ACUAGAG----------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-44     ---------------------------------------------------------------------TGACTAGAGACACATTCAGCT----------------------     21166
      ---------------------------------------------------------------------TGACTAGAGACACATTCAGC-----------------------     208
      ---------------------------------------------------------------------TGACTAGAGACACATTCAG------------------------     198
      ---------------------------------------------------------------------TGACTAGAGACACATTCAGCTT---------------------     226
      ---------------------CTGGATGTGT--TCGTTAGTCAT--------------------------------------------------------------------     214
      ----------------------------------------------------------------------GACTAGAGACACATTCAGCT----------------------     201
cbriggsae     ------------AGTGCCACGCTGGATGTGT--TCGTTAGTCATAGTAACCT-CATCAATTCAGGCTTATGACTAGAGACACATTCAGCTTGGCGCC---------------      
cremanei     ACTGTACCAAAACGTGCCACGCTGGATGTGC--TCGTTAGTCATAATAACCT-CATTTAGTAAGGCTTATGACTAGAGACACATTCAGCTTGGCGCCGAACTATAA-ACAGT      
celegans     ----ATGCACCATGTGCCACGCTGGATGTGC--TCGTTAGTCATAATATCCTCCACAAAGCAAGGACTATGACTAGAGACACATTCAGCTTGGCGCCGAATGCAT-------      
cbrenneri     ACTGTTCGGGAAACTGCCACGCTGGATGTGC--TCGTTAGTCATAGTAGCCT--ATCCTGAACGGCCTATGACTAGAGACACATTCAGCTTGGCTCCGATATCAATTACAGT      
cjaponica     -----CTGAAATCTTGCCACGCTGAATGTGC--TCGTTAGTCATAACCACCCATATCGTCAAGGGCATATGACTAGAGACACATTCAGCTTGGCTCACATTTTCAG------      
ppacificus     -----GAGTCGCAGCCCCGCTCTGGATGTGTGATC-TTGGTCGTATCCGCGCAAAT-GCTCAATGATTATGACTAGAGACACATTCAGCTTGGGGCCGGCTC----------      
                      ** * *** *****   ** ** *** **    *    *         *  **************************  *                      
 -----            -------------------  ------------------- --------------------------------------------               -----NM_001047975
 -----            -------------------  ------------------- --------------------------------------------               -----NM_214509
 -----            -------------------  ------------------- --------------------------------------------               -----NM_001034039
 -----            -------------------  ------------------- --------------------------------------------               -----NM_001033832
 -----            -------------------  ------------------- --------------------------------------------               -----NM_214466
 -----            -------------------  ------------------- --------------------------------------------               -----NM_080679
 -----            -------------------  ------------------- --------------------------------------------               -----NM_080681
 -----            -------------------  ------------------- --------------------------------------------               -----NM_080680
 +++++            +++++++++++++++++++  +++++++++++++++++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_133464
cbriggsae                 .((((((.(((((((((((  (..((((((((((...((( .(.....).))).)))))))))).)))))))))))).)))))).                    1.000 -40.40
cremanei     (((((........((((((.(((((((((((  ((..(((((((((...((( .........))).)))))))))))).)))))))))).)))))).......... )))))     0.994 -42.77
celegans         (((((....((((((.(((((((((((  ((..((((((((...((((..........)))).))))))))))).)))))))))).))))))....)))))            1.000 -45.40
cbrenneri     ((((((((((.....((((.(((((((((((  ((..(((((((((..(((.  .........))))))))))))))).)))))))))).)))))))))........)))))     0.902 -47.30
cjaponica          ((((((....((((.(((((((((((  ((..((((((((....(((..........)))..))))))))))).)))))))))).))))......))))))           1.000 -42.90
ppacificus          ((((((..((((((..((((((((((..(( .((((((((..((.((.... ))....))..)))))))))).))))))))))..))))))))))))               0.999 -44.40

cbriggsaechromosome:chrII:8061358:8061439:1Opposite_strand|Intronic_coding|NM_001047975|LOC683871 ## Same_strand|Intronic_non-coding|NM_133464|ZNF483 ## {Repeats: no} ## {MIR: cbr-mir-45-2}
cremaneichromosome:chrUn:8356876:8356983:-1intergenic
celeganschromosome:chrII:11880860:11880958:-1intergenic ## {Repeats: AT_rich 1 28 -1 class=Low_complexity} ## {MIR: cel-mir-45}
cbrennerichromosome:chrUn:101670635:101670742:-1Same_strand|Intronic_coding|NM_007742 ## Opposite_strand|Intronic_coding|NM_138591
cjaponicachromosome:chrUn:98930666:98930764:1intergenic
ppacificuschromosome:chrUn:21366498:21366592:-1Opposite_strand|Intronic_coding|NM_001032504 ## Same_strand|Intronic_coding|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity}


cbr-mir-86

Cloning frequencies
absoluteAF16
cbr-mir-86 5arm1339
cbr-mir-86 3arm4
normalizedAF16
cbr-mir-86 5arm3.490
cbr-mir-86 3arm0.010
cbr-mir-86 relative cloning frequencies

sblock29 (miRBase cbr-mir-86) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-860.001nono0.39/0.5018/25/0.970.0
0.0
0.4
0.0
1178
3
0
0
1
1
0
0
14
17
4
6
5arm
3arm
1
1
nd
nd
0.22
0.14
2
2
1343123
sblock29 hairpin
  readsmiRBase family seed
seed     ---------------------------------------AAGUGAA--------------------------------------------------------------------------------------------------------     1328miR-785/86
seed     -------------------------------------------GAAUGCU----------------------------------------------------------------------------------------------------     7novel
seed     ---------------------------------------------------------------------------------------UGGGC-UU-------------------------------------------------------     4novel
seed     ----------------------------------------AGUGAAU-------------------------------------------------------------------------------------------------------     3novel
seed     --------------------------------------------AAUGCUU---------------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-86     --------------------------------------TAAGTGAATGCTTTGCCACAGTC-----------------------------------------------------------------------------------------     23764
      --------------------------------------TAAGTGAATGCTTTGCCACAGT------------------------------------------------------------------------------------------     22414
      --------------------------------------TAAGTGAATGCTTTGCCACAGTCT----------------------------------------------------------------------------------------     2486
      --------------------------------------TAAGTGAATGCTTTGCCACAG-------------------------------------------------------------------------------------------     2128
      --------------------------------------TAAGTGAATGCTTTGCCAC---------------------------------------------------------------------------------------------     1915
      --------------------------------------TAAGTGAATGCTTTGCCA----------------------------------------------------------------------------------------------     1815
      ------------------------------------------TGAATGCTTTGCCACAGTC-----------------------------------------------------------------------------------------     195
      --------------------------------------TAAGTGAATGCTTTGCCACAGTCTT---------------------------------------------------------------------------------------     253
      --------------------------------------------------------------------------------------CTGGGC-TTAGATTCACTTAGGC-----------------------------------------     223
      --------------------------------------TAAGTGAATGCTTTGCCACA--------------------------------------------------------------------------------------------     203
      ---------------------------------------AAGTGAATGCTTTGCCACAGTC-----------------------------------------------------------------------------------------     222
      --------------------------------------------------------------------------------------CTGGGC-TTAGATTCACTTAG-------------------------------------------     201
      ------------------------------------------TGAATGCTTTGCCACAGT------------------------------------------------------------------------------------------     181
      -------------------------------------------GAATGCTTTGCCACAGTCTT---------------------------------------------------------------------------------------     201
      ---------------------------------------AAGTGAATGCTTTGCCACAGT------------------------------------------------------------------------------------------     211
      ------------------------------------------TGAATGCTTTGCCACAGTCT----------------------------------------------------------------------------------------     201
cbriggsae     ------------------------GAGTCAATGCCGTTTAAGTGAATGCTTTGCCACAGTCTTC--GATCATGTCACA--TGAAGCCTGGGC-TTAGATTCACTTAGGCCGGCGTTCCTTGACTCA------------------------      
cremanei     TCCCATACTTTTCA-------AACGAGTCGGCGCCGTCTAAGTGAATGCTTTGCCACAGTCTTC--GACCATGTCAAA--TGAAGCCTGGGC-TAAGATTCGCTTAGGCCGGCGTTTTTCGACACGGATCTT------CAACTTTGGTGA      
celegans     -----------------------CGTGTCCACGCCGTCTAAGTGAATGCTTTGCCACAGTCTTC--GATGTTCTGAAA--TGAAGCCTGGGC-TCAGATTCGCTTAGGCCGGAG---TTTGACACG------------------------      
cbrenneri     CCC----CTTTTTAAAAATACAACGAGTCGGCGCCGTCTAAGTGAATGCTTTGCCACAGTCTTC--GACCATGTCAAA--GGAAGCCTGGGC-TCAGATTCGCTTAGGCCGGCG---TTCGACACGTTTCTTTGTGGGCTGCTTTGGGG-      
ppacificus     --------------------------------------TAAGTGAATTTCTTGCCACAGTCTTA--GCCTAATTCACA-----AGGCTGGGCAATACTTTCGCTTG--------------------------------------------      
cjaponica     --------------------------------------TAAGTGAATGCTTTGCCACAGTCTTCCGATCTCTGTCGAATGTGAAGCCTGGGT-CGAGATTCGCTTA--------------------------------------------      
                                            *********   *************          *   *     ** *****    *  *** ***                                                   
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_177732
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_001016781
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_001005609
 -----                        ----------------------------------------  ------------  ------------ ---------------------------------                        -----NM_001043354
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_111431
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_001399
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_001109404
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_061520
 +++++                        ++++++++++++++++++++++++++++++++++++++++  ++++++++++++  ++++++++++++ +++++++++++++++++++++++++++++++++                        +++++NM_136816
cbriggsae                             (((((((((((((((((((((((.((..(((.(((.((((  (...........  ))))).)))))) ..)))))))))))))).)))))....)))))).                             1.000 -43.40
cremanei     (((((.........       ..((.(((((((((((((((((((((.(((.(((.(((.((((  (((...)))...  .)))).)))))) .))))))))))))))).)))))....)))).))......      ......))).))     0.908 -49.00
celegans                            ((((((.((.((((((((((((((.((..(((.(((.((((  .((........)  ))))).)))))) ..)))))))))))))).)).)   )..))))))                             1.000 -41.30
cbrenneri     (((    (..........(((((((.(((((((((((((((((((((.((..(((.(((.((((  (((...)))...  .)))).)))))) ..)))))))))))))).))))   ).)))).))).....)))).........))))      0.824 -55.61
ppacificus                                           ((((((((....(((((.(((((((.  ...........)     )))))))))))....))))))))                                                 1.000 -21.70
cjaponica                                           (((((((((.(((.(((.(((.((((((.((......)).)).)))).)))))) .))))))))))))                                                 1.000 -24.50

cbriggsaechromosome:chrIII:4132902:4132998:-1Same_strand|Intronic_non-coding|NM_177732|Slc35d1 ## Same_strand|Intronic_coding|NM_001016781|LOC549535 ## Opposite_strand|Intronic_non-coding|NM_001043354|Rorb ## {Repeats: no} ## {MIR: cbr-mir-86}
cremaneichromosome:chrUn:4696101:4696232:1intergenic
celeganschromosome:chrIII:11936521:11936615:-1Same_strand|Intronic_coding|Y56A3A.7a ## {MIR: cel-mir-86}
cbrennerichromosome:chrUn:102433287:102433423:1Same_strand|Intronic_coding|NM_211666
ppacificuschromosome:chrUn:143169699:143169835:-1Opposite_strand|Intronic_coding|NM_182968 ## Same_strand|Intronic_coding|NM_058793
cjaponicachromosome:chrUn:58779719:58779855:1intergenic


cbr-mir-46

Cloning frequencies
absoluteAF16
cbr-mir-46 5arm71
cbr-mir-46 3arm131
normalizedAF16
cbr-mir-46 5arm0.185
cbr-mir-46 3arm0.341
cbr-mir-46 relative cloning frequencies

sblock38 (miRBase cbr-mir-46) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-460.001nono0.45/0.5319/22/0.980.0
0.0
0.0
0.0
70
111
0
0
1
1
0
0
17
16
4
4
5arm
3arm
1
1
nd
nd
0.18
0.14
2
3
202121
Families
Member of family miR-46/47 (seed GUCAUGG): cbr-mir-47, cbr-mir-46
sblock38 hairpin
  readsmiRBase family seed
seed     --------------------------------------------------------------------------------------GUCAUGG----------------------------------------------------     131miR-46/47
seed     ---------------------------------------AGAGAGC---------------------------------------------------------------------------------------------------     71novel
  lencloning frequencies
   AF16
      -------------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTTC---------------------------------------     21111
      --------------------------------------AAGAGAGCCGTCTATTGACAGT-------------------------------------------------------------------------------------     2270
      -------------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTT----------------------------------------     2017
      -------------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCT-----------------------------------------     193
      --------------------------------------AAGAGAGCCGTCTATTGAC----------------------------------------------------------------------------------------     191
cbr-miR-46     -------------------------------------------------------------------------------------TGTCATGGAGTCGCTCTCTTCA--------------------------------------     22-
cbriggsae     ---------------------AGATACAAGTGAAGCTGAAGAGAGCCGTCTATTGACAGTTC--GCTTGTT-----TCATG-TGCTGTCATGGAGTCGCTCTCTTCAG----ATGATC----------------TGAATCTA---      
cremanei     -----AAGTTTTCAACCGAATAAGAGGAGGTAAAGCTGAAGAGAGCCGTCTATTGACAGTTC--GTTTCTA--TACTTATG-TACTGTCATGGAGTCGCTCTCTTCAG----ATGATC-----CTTTCAAGGTTTTTATCTT---      
celegans     -----AGGGTCCAAA------CTGCTGAGGTGAAGCTGAAGAGAGCCGTCTATTGACAGTTCAAGACCACGAGTCGTTGTG-TGCTGTCATGGAGTCGCTCTCTTCAG----ATGATC----CGGTCAATGGTATTTT-------      
cbrenneri     -----------------------------------CTGAAGAGAGCCGTCTATTGACAGTTC--GTCTCTGTTCAGTCAGG-TACTGTCATGGAGTCGCTCTCTTCAG----ATGATC--------------------TCTTGCC      
cjaponica     CGGTAAGTTGGCCAA------AAGACCGGGTGAAGCTGAAGAGAGCCGTCCTTTGACAGTTC--GTCCACGTGGAATATCG-TGCTGTCATGGAGTCGCTCTCTTCAG----ATGACCACGGTCTTTCTTGGTTTTTTCTTTTTG      
ppacificus     --ACCAGGACCCCCG------GCACCACGCAGAGACCGAAGAGAGCCTTCTGTTGACAGTGC-GGGCCGTTGGTGCTAATGCTATTGTCATGGAGTCGCTCTCTTCAGGCTTGTGGTC-------CTCAGGGTACGGT-------      
                                         * ********** **  ******** *  *           *   * *  ***********************     **  *                                 
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_005249
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_068288
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_059518
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_067241
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_001021511
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_001086163
 +++++                     +++++++++++++++++++++++++++++++++++++++++  +++++++     +++++ ++++++++++++++++++++++++++    ++++++                ++++++++   +++++NM_001110403
cbriggsae                          ((((...((.....(((((((((((..((((.(((((((..  ((.....     ....) ))))))))))))...)))))))))))    .....)                )..)))).        1.000 -34.10
cremanei          (((.....((((.....((((((.......(((((((((((..((((.(((((((.(  ((.....  .....))) .)))))))))))...)))))))))))    ....))     ))))...)))).....)))        0.968 -41.50
celegans          ((((((((..      ..((((.(((....(((((((((((..((((.(((((((.((((((.....))).))).. .)))))))))))...)))))))))))    ...)))    ))))...))).)))))            0.851 -43.00
cbrenneri                                        (((((((((((..((((.(((((((..  ...((((......)))) .)))))))))))...)))))))))))    ......                    .......     0.995 -33.10
cjaponica     (((.(((..((((((      ((((((((((....(((((((((((..(((..(((((((.(  ((((....)))....)) .))))))).)))...)))))))))))    ...))).))))))))..)))))....))).)))     0.998 -57.60
ppacificus       (((...((((..(      (.(((((...(((.(((((((((((((((...((((((((( .(((.......)))...)).))))))).))))..))))))))).)))))))))))       )...))))..)))            0.996 -51.00

cbriggsaechromosome:chrIII:7878494:7878586:1Same_strand|Intronic_coding|NM_005249|FOXG1 ## Same_strand|Intronic_non-coding|NM_067241|epc-1 ## {Repeats: no} ## {MIR: cbr-mir-46}
cremaneichromosome:chrUn:22211368:22211490:-1Same_strand|Intronic_coding|NM_001104800
celeganschromosome:chrIII:13660382:13660499:1intergenic ## {MIR: cel-mir-46}
cbrennerichromosome:chrUn:26379438:26379520:-1Same_strand|Intronic_coding|NM_001043931
cjaponicachromosome:chrUn:55670811:55670942:1Same_strand|Intronic_coding|NM_137355
ppacificuschromosome:chrUn:163065262:163065383:1intergenic


cbr-mir-52

Cloning frequencies
absoluteAF16
cbr-mir-52 5arm1408
cbr-mir-52 3arm16
normalizedAF16
cbr-mir-52 5arm3.670
cbr-mir-52 3arm0.042
cbr-mir-52 relative cloning frequencies

sblock42 (miRBase cbr-mir-52) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-520.006nono0.45/0.5518/25/0.980.0
0.0
0.0
0.0
1314
12
0
0
1
1
0
0
17
17
3
5
5arm
3arm
1
1
nd
nd
0.25
0.32
3
4
1424122
Families
Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-56, cel-mir-54, cbr-mir-55, cbr-mir-52, cbr-mir-51, block4665_novel, block4666_novel
sblock42 hairpin
  readsmiRBase family seed
seed     ----------------------------------ACCCGUA---------------------------------------------------------------------------------------------     1357miR-51/52/55
seed     --------------------------------------GUACAUA-----------------------------------------------------------------------------------------     42novel
seed     ---------------------------------------------------------------------------ACGAU-AC---------------------------------------------------     14novel
seed     ---------------------------------CACCCGU----------------------------------------------------------------------------------------------     7novel
seed     -------------------------------------------------------------------------------U-ACAAUG-----------------------------------------------     2novel
seed     -----------------------------------CCCGUAC--------------------------------------------------------------------------------------------     2novel
  lencloning frequencies
   AF16
cbr-miR-52     ---------------------------------CACCCGTACATATGTTTCCGTGCT-----------------------------------------------------------------------------     241314
      -------------------------------------CGTACATATGTTTCCGTGCT-----------------------------------------------------------------------------     2042
      ---------------------------------CACCCGTACATATGTTTCCGTGCTT----------------------------------------------------------------------------     2523
      --------------------------------------------------------------------------CACGAT-ACAATGAGCGGGTAGC-------------------------------------     2212
      ---------------------------------CACCCGTACATATGTTTCCGTGC------------------------------------------------------------------------------     2311
      --------------------------------CCACCCGTACATATGTTTCCGTGCT-----------------------------------------------------------------------------     257
      ---------------------------------CACCCGTACATATGTTTCCGTG-------------------------------------------------------------------------------     226
      ------------------------------------------------------------------------------AT-ACAATGAGCGGGTAGC-------------------------------------     182
      ----------------------------------ACCCGTACATATGTTTCCGTGC------------------------------------------------------------------------------     222
      --------------------------------------------------------------------------CACGAT-ACAATGAGCGGGTAG--------------------------------------     212
      ---------------------------------CACCCGTACATATGTTTCCG---------------------------------------------------------------------------------     201
      ---------------------------------CACCCGTACATATGTTTCCGT--------------------------------------------------------------------------------     211
      ---------------------------------CACCCGTACATATGTTTCC----------------------------------------------------------------------------------     191
cbriggsae     ----------------TTCCCGCTCTGACAGTCCACCCGTACATATGTTTCCGTGCTTGACATA-GAGCTCAATCACGAT-ACAATGAGCGGGTAGCCGGTCATCG-AGTCGGAA-------------------      
cremanei     ---------------GTACCCTCTACTACCGTCCACCCGTACATATGTTTCCGTGCTTGACATT-GTGCTCAATCACGTT-ACAATATATGGGTCGCCGGTCTT---AGGCGGTTC------------------      
celegans     ------------------CCGATTCTGACAGTCCACCCGTACATTTGTTTCCGTGCTTGACTTCAAAGCTCAATCACGGC-ACAATATATGGGTCGCCAGTCATTGTAGTCGG---------------------      
cbrenneri     TATTGGCTAGTATTCTTTTCGGCTCTGACAGTCCACCCGTACATATGTTTCCGTGCTTGACAAT-GAGTTCAATCACGTC-ACAATTTATGGGTCGCCGGTCATTG-AGTTGAACATTTGAACCAGATCTAATA      
cjaponica     ------TATTTCGACGCTCCTCCAACGACAGACCACCCGTACATATGTTTCCGTGCTTGACTCTACGCCTCAATCACGTTAACAATTTATGGTTCGCCGGTCACG--AGTTGAGCTTTTGCGTTTGATG-----      
ppacificus     ---------------------------------TACCCGTACATAT------TCACATTACATTCTGACT--ATCAGAAT-ACAATAGAGGGGGCGG----------AGTG-----------------------      
                                        ********** *         * * **        *  ****     *****    **   *           **                               
 +++++                ++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++ +++++++++++++++++++++++++ ++++++++                   +++++NM_001106790
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_001128722
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_069625
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_069625
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_069822
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_069822
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_171311
 +++++                ++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++ +++++++++++++++++++++++++ ++++++++                   +++++NM_025685
 +++++                ++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++++++ +++++++++++++++++++++++++ ++++++++                   +++++NM_001011629
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_135592
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_205170
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_171312
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_000692
 -----                ------------------------------------------------ --------------- ------------------------- --------                   -----NM_171903
cbriggsae                     .(((.((((((((.....((((((.(((.(((...((((.((((.... ....)))).)))).. )))))).)))))).....))))..) ))).))).                        1.000 -33.90
cremanei                    ..(((.((((..((((...(((((((.((.(((...((((.((((.... ....)))).)))).. ))))).)))))))...))))..)   ))).)))..                       1.000 -29.10
celegans                       ((((((.((((.....(((((((...((((..(((((.((((((....)).)))).))))). ))))..))))))).....))))....))))))                          1.000 -30.50
cbrenneri     ((((((......(((..((((((((((((.....(((((((.((.(((...((((.((((.... ....)))).)))).. ))))).))))))).....))))..) ))))))).....)))......))))))     0.838 -31.90
cjaponica           ....(((((((..((.((((....((((...((..((((((((..((((.((((.........)))).))))..))))...))))...))..))))...  .)))))).....))))).))..          0.979 -29.10
ppacificus                                      (((((((.....(      ((..(((..((((((...  ..)))))) ..))).)))...))))          .)))                            0.996 -12.20

cbriggsaechromosome:chrIV:5731131:5731226:1Same_strand|Intronic_coding|NM_001106790|Kif21a ## Opposite_strand|Intronic_non-coding|NM_001128722|LOC565233 ## Opposite_strand|Intronic_coding|NM_069625|ZK596.1 ## Same_strand|Intronic_non-coding|NM_025685|Col27a1 ## {Repeats: no} ## {MIR: cbr-mir-52}
cremaneichromosome:chrUn:62355770:62355865:1intergenic
celeganschromosome:chrIV:11027568:11027661:-1intergenic ## {MIR: cel-mir-53}
cbrennerichromosome:chrUn:136910867:136910997:1intergenic
cjaponicachromosome:chrUn:11282764:11282884:1intergenic
ppacificuschromosome:chrUn:53882569:53882704:-1Opposite_strand|Intronic_coding|NM_020706


cbr-mir-51

Cloning frequencies
absoluteAF16
cbr-mir-51 5arm645
cbr-mir-51 3arm9
normalizedAF16
cbr-mir-51 5arm1.681
cbr-mir-51 3arm0.023
cbr-mir-51 relative cloning frequencies

sblock43 (miRBase cbr-mir-51) [miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-510.005nono0.50/0.5819/23/0.990.0
0.0
0.0
0.0
613
9
0
0
1
1
0
0
16
13
3
6
5arm
3arm
1
1
nd
nd
0.17
0.19
2
2
654121
Families
Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-56, cel-mir-54, cbr-mir-55, cbr-mir-52, cbr-mir-51, block4665_novel, block4666_novel
sblock43 hairpin
  readsmiRBase family seed
seed     -----------------ACCCGUA------------------------------------------------------------------------------------     642miR-51/52/55
seed     ---------------------------------------------------------------A----UGGAAG----------------------------------     9novel
seed     ---------------------GUAGCUC--------------------------------------------------------------------------------     2novel
seed     ------------------CCCGUAG-----------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-51     ----------------TACCCGTAGCTCCTTGCCATGTT---------------------------------------------------------------------     23613
      ----------------TACCCGTAGCTCCTTGCCATGT----------------------------------------------------------------------     2215
      ----------------TACCCGTAGCTCCTTGCCAT------------------------------------------------------------------------     209
      --------------------------------------------------------------CA----TGGAAGTTGGTCCGGGTAC---------------------     219
      ----------------TACCCGTAGCTCCTTGCCA-------------------------------------------------------------------------     195
      --------------------CGTAGCTCCTTGCCATGTT-----A---------------------------------------------------------------     202
      -----------------ACCCGTAGCTCCTTGCCATGTT---------------------------------------------------------------------     221
cbriggsae     TCCGAAGACGTCCATCTACCCGTAGCTCCTTGCCATGTT-----ACTGGTAAA---AGTGAACA----TGGAAGTTGGTCCGGGTACATGGCCAGTAGGA--------      
cremanei     ----------------TACCCGTAGCTCCTATCCATGTT-----ACTAGCAGATAGAGTGAACA----TGGAAGTTGGTACAGGTG----------------------      
celegans     ----------------TACCCGTAGCTCCTATCCATGTT-----ACTGGTCAA-AAAGTGAACA----TGGAAGCAGGTACAGGTG----------------------      
cbrenneri     ----------------TACCCGTAGCTCCTATCCATGTT-----GTTATCAAA-GAAGTCAACA----TGGAAGTTGGTACTGGTG----------------------      
cjaponica     ----AAGCCCGCCGTCTACCCGTAGCTCCTATCCATGTTGATAAGTTATCACA--ATGCCAACA----TGGAAGCAGGTACTGGTGTACGGTGTTAGTACGGAGGTTT      
ppacificus     ----------------GACCCGTATTGCGCAGTCTAGAG-----ATTAGTAGT---------CATTTCTGGTTGCAGGATCGGGGG----------------------      
                       *******   *     *  *         *               **    ***  *  **  * **                              
 ++++++++++++++++++++++++++++++++++++++++++++     +++++++++   ++++++++    ++++++++++++++++++++++++++++++++        +++++NM_001106790
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_001128722
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_069625
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_069625
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_069822
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_069822
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_171311
 ++++++++++++++++++++++++++++++++++++++++++++     +++++++++   ++++++++    ++++++++++++++++++++++++++++++++        +++++NM_025685
 ++++++++++++++++++++++++++++++++++++++++++++     +++++++++   ++++++++    ++++++++++++++++++++++++++++++++        +++++NM_001011629
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_135592
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_205170
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_171312
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_000692
 --------------------------------------------     ---------   --------    --------------------------------        -----NM_171903
cbriggsae     (((....((..((((.((((((..(((.(((.(((((((     (((......   ))))).))    ))))))..))).)))))).))))...)).)))             1.000 -31.20
cremanei                     ((((.((.(((....((((((((     (((.........))))).))    ))))....))))).))))                           1.000 -16.10
celegans                     ((((.(((.((.((.((((((((     (((...... ..))))).))    )))))).)).))).))))                           1.000 -22.10
cbrenneri                     ((((.((.(((....((((((((     (........ .....)))))    ))))....))))).))))                           1.000 -16.82
cjaponica         (((((((((((.((((.(((.((.((.(((((((((.............  ....)))))    )))))).)).))).)))).))))))..........)))))     0.926 -33.43
ppacificus                     ..((((.(((..((((.((((((     ((.......         .))))))))))))..)))))))..                           1.000 -20.00

cbriggsaechromosome:chrIV:5734733:5734820:1Same_strand|Intronic_coding|NM_001106790|Kif21a ## Opposite_strand|Intronic_non-coding|NM_001128722|LOC565233 ## Opposite_strand|Intronic_coding|NM_069625|ZK596.1 ## Same_strand|Intronic_non-coding|NM_025685|Col27a1 ## {Repeats: no} ## {MIR: cbr-mir-51}
cremaneichromosome:chrUn:62359051:62359178:1intergenic
celeganschromosome:chrIV:11025975:11026102:-1intergenic ## {MIR: cel-mir-51}
cbrennerichromosome:chrUn:136914859:136914986:1Same_strand|Intronic_coding|NM_031749
cjaponicachromosome:chrUn:59536097:59536194:-1Opposite_strand|Intronic_coding|NM_059487
ppacificuschromosome:chrUn:12762076:12762203:1intergenic


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