logoC.briggsae small RNAs

miR-Intess™


Summary
Preprocessing
Mapping
Composition

miR classification
miR expression
Downloads
Table
Thresholds
Families
Clusters

Alignments

confident miRBase miRNAs

miRNAknown_cloningHIGH_multiarm_DicerOK_randfoldOK (19 loci)

cbr-mir-250

Cloning frequencies
absoluteAF16
cbr-mir-250 5arm8
cbr-mir-250 3arm205
normalizedAF16
cbr-mir-250 5arm0.021
cbr-mir-250 3arm0.534
cbr-mir-250 relative cloning frequencies

sblock58 (miRBase cbr-mir-250) [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-2500.001nono0.42/0.5919/22/0.900.0
0.0
0.0
0.0
7
165
0
0
1
1
0
0
13
14
3
6
5arm
3arm
1
1
nd
nd
0.23
0.20
2
2
213121
Clusters
Located in cluster 8: cbr-mir-250, cbr-mir-61
sblock58 hairpin
  readsmiRBase family seed
seed     --------------------------------------------------------------------------AUCACAG-------------------------------------------     205miR-43
seed     --------------------------------CUUCAGU-------------------------------------------------------------------------------------     8novel
seed     ----------------------------------------------------------------------------CACAGUC-----------------------------------------     0miR-250
  lencloning frequencies
   AF16
      -------------------------------------------------------------------------AATCACAGTCAACTGTTGGC-------------------------------     20165
      -------------------------------------------------------------------------AATCACAGTCAACTGTTGG--------------------------------     1922
      -------------------------------------------------------------------------AATCACAGTCAACTGTTGGCA------------------------------     2118
      -------------------------------CCTTCAGTTGCCTCGTGATCCG-----------------------------------------------------------------------     227
      -------------------------------CCTTCAGTTGCCTCGTGATCC------------------------------------------------------------------------     211
cbr-miR-250     ---------------------------------------------------------------------------TCACAGTCAACTGTTGGCACGG---------------------------     22-
cbriggsae     ----------------TCTTCG--GACCACGCCTTCAGTTGCCTCGTGATCCGCCGAATCTG--TAATGGACGAATCACAGTCAACTGTTGGCACGGTCCTTGAA-------GT----------      
cremanei     TGCTGTTATTCGAAGGTCTTCG--GACCGCCCCTTCAGTTGACTCGTGATCCGCCGACTTTGATATATGGACGAATCACAGTCACCTGATGGTACGGTCTTTGAATTCCTATATTATTATGGTA      
celegans     ------------------------------GCCTTCAGTTGCCTCGTGATCCGCCAAACACAATAAATGGACGAATCACAGTCAACTGTTGGC-------------------------------      
cbrenneri     ------------------------------GCCGGCAGTTGCCTGTTGATCCGCCGCAATTA--TGATGGACGAATCACAGTCAACTGTTGGC-------------------------------      
cjaponica     --------TTTATTGGTCTTCATTGACCATTCCTTCAGTTTTCTCGTGATCCGCCAATCTT---CCATGGACGAATCACAGTCAACTGTTGGCCTGGTCCATGTC-------GAGACGATTGGA      
                                     **  *****  **  *********           ****************** *** ***                                      
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_007734
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_001122952
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_001122953
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_059770
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_059769
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_010905
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_000092
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_078262
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_001029071
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_001029072
 +++++                ++++++  ++++++++++++++++++++++++++++++++++++++  +++++++++++++++++++++++++++++++++++++++++       ++          +++++NM_000945
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_079093
 +++++                ++++++  ++++++++++++++++++++++++++++++++++++++  +++++++++++++++++++++++++++++++++++++++++       ++          +++++NM_001089577
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_117764
 +++++                ++++++  ++++++++++++++++++++++++++++++++++++++  +++++++++++++++++++++++++++++++++++++++++       ++          +++++NM_153093
 -----                ------  --------------------------------------  -----------------------------------------       --          -----NM_001085355
cbriggsae                     .(((((  ((((..(((..((((((.((.(((((.(((((......  ...))).)).))))))).))))))..)))..)))))..)))       ).               1.000 -34.80
cremanei     ((((((.......(((..((((  (((((..((.((((.(((((.(((((.(((((...........))).)).)))))))))).)))).))..))))))..)))..)))........))))))     0.984 -40.46
celegans                                   (((..((((((.((.(((((.(((((...........))).)).))))))).))))))..)))                                    1.000 -23.30
cbrenneri                                   (((((((((((.(((.((((.(((((((....  )).))).)).))))))).)))))))))))                                    1.000 -29.40
cjaponica             .......((((((((.(((((..((..(((((..((.(((((.(((((.....   ...))).)).)))))))..)))))..))..))))).)))..       ))))).......     0.985 -35.00

cbriggsaechromosome:chrV:6755121:6755207:-1Opposite_strand|Intronic_coding|NM_007734|Col4a3 ## Opposite_strand|Intronic_non-coding|NM_001122952|Nfia ## Same_strand|Intronic_non-coding|NM_000945|PPP3R1 ## Same_strand|Intronic_coding|NM_001089577|zgc:162132 ## {Repeats: no} ## {MIR: cbr-mir-250}
cremaneichromosome:chrUn:126692870:126692991:-1Opposite_strand|Intronic_coding|NM_073652 ## Same_strand|Intronic_coding|NM_067460
celeganschromosome:chrV:11769881:11770007:-1intergenic ## {MIR: cel-mir-250}
cbrennerichromosome:chrUn:84265177:84265303:1intergenic
cjaponicachromosome:chrUn:133810902:133811007:-1intergenic


cbr-mir-61

Cloning frequencies
absoluteAF16
cbr-mir-61 5arm1
cbr-mir-61 3arm81
normalizedAF16
cbr-mir-61 5arm0.003
cbr-mir-61 3arm0.211
cbr-mir-61 relative cloning frequencies

sblock59 (miRBase cbr-mir-61) [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-610.001nono0.41/0.4819/23/0.990.0
0.0
0.0
0.0
1
74
0
0
1
1
0
0
14
13
3
6
5arm
3arm
1
1
nd
nd
0.23
0.19
4
3
82122
Clusters
Located in cluster 8: cbr-mir-250, cbr-mir-61
Families
Member of family miR-44/45/61 (seed GACUAGA): cbr-mir-44, cbr-mir-45, cbr-mir-45, cbr-mir-61, block4958_cand
sblock59 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------------------------GACUAGA---------------------------------------     81miR-44/45/61
seed     ----------------------------------------GAGU-UAA--------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      ---------------------------------------------------------------------------------TGACTAGAACCTTGACTCTGC--------------------------     2174
      ---------------------------------------------------------------------------------TGACTAGAACCTTGACTCTG---------------------------     206
      ---------------------------------------CGAGT-TAAGGCTAATAGTCCTT------------------------------------------------------------------     221
      ---------------------------------------------------------------------------------TGACTAGAACCTTGACTCT----------------------------     191
cbr-miR-61     ---------------------------------------------------------------------------------TGACTAGAACCTTGACTCTGCTC------------------------     23-
cbriggsae     --------TCGGTG-----------------TCTCGAGCCGAGT-TAAGGCTAATAGTCCTTCCGGTGT-----ATGGTAATGACTAGAACCTTGACTCTGCTCGAGTTACTGAG-------------      
cremanei     GCGTAATATCGGTC-----------------TTCCGAGTTGGGT-CACGGCGCTTAGTCCTTCCGACAT-----ATGGCAATGACTAGAACCTTGGCTCAGCTCGGGACTCCGATGAGC---------      
celegans     -----------ATC-----------GCTGAACCTCGAGATGGGT-TACGGGGCTTAGTCCTTCCTCCGT-----ATGGCAATGACTAGAACCGTTACTCATCTCGAGGTTTCGGTGAT----------      
cbrenneri     --------CCAGTCTCGTAAAACATGTTGAACTTCGAGTTGGGT-CACGGTGCTTAGTCCTTCCAACAG-----TCGGTAATGACTAGAACCGTGACTCAGCTCGAGGAAGCGGCAGTTTTTCACTGG      
cjaponica     -----------GTC----AAATTTACGCGATTCGCGAGTTGGGCGCACGGCGTTTAGTCCTTTCAACACGTGAAATGGTAATGACTAGAACCGTCGCTCATCCCGCGTCTATGCGGCTATTTGTC---      
                  *                     ****  * *   * **    ******** *            ** ************* *  ***  * ** *     *                     
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_007734
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_001122952
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_001122953
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_059770
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_059769
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_010905
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_000092
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_078262
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_001029071
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_001029072
 +++++        ++++++                 +++++++++++++ ++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++++++             +++++NM_000945
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_079093
 +++++        ++++++                 +++++++++++++ ++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++++++             +++++NM_001089577
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_117764
 +++++        ++++++                 +++++++++++++ ++++++++++++++++++++++++     +++++++++++++++++++++++++++++++++++++++++             +++++NM_153093
 -----        ------                 ------------- ------------------------     -----------------------------------------             -----NM_001085355
cbriggsae             ((((((                 .(((((((.(((( (((((....(((((.(((((....     .))).)).)))))...))))))))).))))))).)))))).                  1.000 -42.10
cremanei     ......((((((..                 ((((((((((((( ((.((..((.((((.(((((....     .))).)).))))))..)).)))))))))))))))..))))))...              1.000 -43.80
celegans                (((           ((((((((((((((((((( .((((..((.((((.((((.....     ..)).)).))))))..)))).))))))))))))))).)))))))               1.000 -50.30
cbrenneri             (((((.....(((((.(((((..((((((((((((( ((((((..((((((.((((.....     ..)).)).)))))).)))))))))))))))))))...))))))))))..)))))     1.000 -55.20
cjaponica                ..(    ((((...((((...((((...((((((.((((..(((((((((((((.....))))).)).....)))))).))))))))))...))))....))))...)))))..        0.994 -36.70

cbriggsaechromosome:chrV:6755274:6755357:-1Opposite_strand|Intronic_coding|NM_007734|Col4a3 ## Opposite_strand|Intronic_non-coding|NM_001122952|Nfia ## Same_strand|Intronic_non-coding|NM_000945|PPP3R1 ## Same_strand|Intronic_coding|NM_001089577|zgc:162132 ## {Repeats: no} ## {MIR: cbr-mir-61}
cremaneichromosome:chrUn:126693023:126693118:-1Opposite_strand|Intronic_coding|NM_073652 ## Same_strand|Intronic_coding|NM_067460
celeganschromosome:chrV:11770038:11770127:-1intergenic ## {MIR: cel-mir-61}
cbrennerichromosome:chrUn:182159919:182160032:1intergenic
cjaponicachromosome:chrUn:133811034:133811143:-1intergenic


cbr-mir-1

Cloning frequencies
absoluteAF16
cbr-mir-1 5arm12
cbr-mir-1 3arm57
normalizedAF16
cbr-mir-1 5arm0.031
cbr-mir-1 3arm0.149
cbr-mir-1 relative cloning frequencies

sblock6 (miRBase cbr-mir-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-10.001nono0.28/0.4318/21/0.990.0
0.0
0.0
0.0
12
56
0
0
1
1
0
0
15
19
5
7
5arm
3arm
1
1
nd
nd
0.14
0.10
2
1
69111
sblock6 hairpin
  readsmiRBase family seed
seed     --------------------------------------------------------------------------------------------GGAAUGU---------------------------------------------------     57miR-1
seed     ----------------------------------------AUACUUC-------------------------------------------------------------------------------------------------------     12novel
  lencloning frequencies
   AF16
      -------------------------------------------------------------------------------------------TGGAATGTAAAGAAGTATGT---------------------------------------     2056
      ---------------------------------------CATACTTCCT-TACATGCCCAT-----------------------------------------------------------------------------------------     2112
      -------------------------------------------------------------------------------------------TGGAATGTAAAGAAGTAT-----------------------------------------     181
cbr-miR-1     -------------------------------------------------------------------------------------------TGGAATGTAAAGAAGTATGTA--------------------------------------     21-
cbriggsae     ------------------------TGCTGTGCCGAGCTGCATACTTCCT-TACATGCCCATACTGTA--------CTG---TGAATGGATATGGAATGTAAAGAAGTATGTAGAACGGA--------ATCTAACGGCG------------      
cremanei     -------------------------GCTGTGCCGAGCTGCATACTTCCT-TACATGCCCATACTATA--------TCA---GTAATGGATATGGAATGTAAAGAAGTATGTAGAACGGT--------TTTGAAAAACGGCTAAATTTTGC      
celegans     ---------CGCTATATTCAAAGTGACCGTACCGAGCTGCATACTTCCT-TACATGCCCATACTATA--------TCA---TAAATGGATATGGAATGTAAAGAAGTATGTAGAACGGG----------GTGGTAGTGTTTTAATGGTG-      
cbrenneri     ------------------TTGAAATGCCGTGCCGAGCTGCATGCTTCTTCTACATGCCCATACTATA--------TCG---TAAATGGATATGGAATGTAAAGAAGTATGTAGAACGGAAAAACACGAAACAAAAACGGCATGAATTCAA      
cjaponica     -----------------------TCGCCGTGCCGAGCTGCATACTTCCT-TGCATACCCATACTTGATCCCCTGGTCG---GACAGAGATATGGAATGTAAAGAAGTATGTAGAGCGGT-------------------------------      
ppacificus     AGAATCTCTCTCTCACTCCTCATTCACCGTTCCG-------TACTTCTT-TGCAGCCCCATACTTGC--------CCGCATGAAGTGGTTATGGAATGTAAAGAAGTATGT--AATGGT------CGAGGCGAGAGCACCACTAGAATCT      
                                * ** ***       * **** * * **  ********                       * **********************  *  **                                      
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_001087279
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_001075644
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_001109726
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_177732
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_007732
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_214466
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_199473
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_073882
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_002069
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_013361
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_012727
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_059914
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_007740
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_152890
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_013256
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_001101755
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_001057654
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_011077
 -----                        ------------------------- -----------------        ---   --------------------------------------        -----------            -----NM_001018587
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_134050
 +++++                        +++++++++++++++++++++++++ +++++++++++++++++        +++   ++++++++++++++++++++++++++++++++++++++        +++++++++++            +++++NM_198749
cbriggsae                             .(((((.(((..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..))).        .....))))).                 1.000 -40.00
cremanei                              (((((((((..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..))))        ........)))))..........     0.989 -40.50
celegans              ((((((..........((((..(((..(((((((((((.( (((((..(((((((((.        ...   ...)))).))))).)))))).)))))))))))..))).          .)))).........))))))      0.990 -44.91
cbrenneri                       .(((((((((((.(((..(((((((((((((.(((((..(((((((((.        ...   ...)))).))))).))))))))))))))))))..))).................)))))))...)))).     0.931 -45.27
cjaponica                            .......((((..(((((((((((.( (((((..((((((((..(((.......)   ))..))).))))).)))))).)))))))))))..))))                                    1.000 -39.20
ppacificus     (((.(((..(((((...((((....((((((.((       (((((((( ((((...(((((.....        ((((.....)))).)))))..)))))))))))))).  ))))))      .)))).))))).......))).)))     0.988 -44.90

cbriggsaechromosome:chrI:7435815:7435908:-1Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Same_strand|Intronic_coding|NM_001075644|ZNF180 ## Opposite_strand|Intronic_coding|NM_001109726|zgc:171740 ## Same_strand|Intronic_non-coding|NM_001057654|Os03g0723800 ## {Repeats: no} ## {MIR: cbr-mir-1}
cremaneichromosome:chrUn:145319807:145319911:1intergenic
celeganschromosome:chrI:6172652:6172769:-1intergenic ## {MIR: cel-mir-1}
cbrennerichromosome:chrUn:167631841:167631961:-1intergenic
cjaponicachromosome:chrUn:124179219:124179310:1intergenic
ppacificuschromosome:chrUn:9699697:9699822:-1intergenic


cbr-mir-70

Cloning frequencies
absoluteAF16
cbr-mir-70 5arm1
cbr-mir-70 3arm34
normalizedAF16
cbr-mir-70 5arm0.003
cbr-mir-70 3arm0.089
cbr-mir-70 relative cloning frequencies

sblock61 (miRBase cbr-mir-70) [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-700.001nono0.37/0.4519/23/0.970.0
0.0
0.0
0.8
1
24
0
0
1
1
0
0
16
13
5
8
5arm
3arm
1
1
nd
nd
0.14
0.17
2
2
35112
sblock61 hairpin
  readsmiRBase family seed
seed     ------------------------------------------------------------------AAUACGU-----------------------------------------------     30miR-70
seed     -------------------------------------------------------------------AUACGUG----------------------------------------------     4novel
seed     --------------------------GGAACAG---------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-70     -----------------------------------------------------------------TAATACGTGA-TTGGTGTTCCCAG-------------------------------     2315
      -----------------------------------------------------------------TAATACGTGA-TTGGTGTTCCC---------------------------------     219
      -----------------------------------------------------------------TAATACGTGA-TTGGTGTTCCCA--------------------------------     224
      ------------------------------------------------------------------AATACGTGA-TTGGTGTTCCCAG-------------------------------     224
      -----------------------------------------------------------------TAATACGTGA-TTGGTGTTCC----------------------------------     201
      -------------------------AGGAACAGCCATCATGTAAGAC-------------------------------------------------------------------------     221
      -----------------------------------------------------------------TAATACGTGA-TTGGTGTTC-----------------------------------     191
cbriggsae     ---------AAACGGATGTATCTCTAGGAACAGCCATCATGTAAGACATTTCTAACTGAAAGATGTAATACGTGA-TTGGTGTTCCCAGAGTTTACCGTTTC------------------      
celegans     TTCAAAATAAAACGATGAAAACTATCGAAATACTATCGACGAATAACACTT---ATGAAGAAATGTAATACGTCG-TTGGTGTTTCCATAGTTTGAATTGTTTATTCCATTATTTTTGAG      
cbrenneri     -------TGGCAGAATTGGAACTTCTGAACCACCACTGACGAATCACATTGAAACTAAAGAGATGTAATACGTCATTTGGTGTTTCCGAAGTTTATACTGTCA-----------------      
                 *       * **   * *  *      * * *  *** *        * * ***********   ******** **  *****    * *                         
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_001011629
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001011629
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_080523
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001046709
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001011563
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_001087279
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_214670
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001079883
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_021399
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001034951
 -----         ------------------------------------------------------------------ --------------------------                  -----NM_001111352
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_001028960
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_182335
 +++++         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++++++++++++++++++                  +++++NM_072288
cbriggsae              ((((((.((...((((.((((((.((((((((((..(((((((.....))..)))))..))))))) ).)))))))).))))..)))))))).                       1.000 -35.40
celegans     .((((((..(((((((..(((((((.(((((((((.(((((.((.(((.((   ......)).))).)).))))) .))))))))).)))))))..)))))))..........)))))).     0.968 -33.10
cbrenneri            .(((((.....(((((((.(((.(((((.(((((.((.(((((...........))))).)).)))))..))))).))).)))))))...))))).                      0.998 -32.90

cbriggsaechromosome:chrV:9902620:9902711:-1Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Opposite_strand|Intronic_coding|NM_080523|clt ## Same_strand|Intronic_coding|NM_001028960|pmp-5 ## {Repeats: no} ## {MIR: cbr-mir-70}
celeganschromosome:chrV:6665504:6665619:-1Same_strand|Intronic_coding|T10H9.5a ## {Repeats: AT_rich 1 29 -1 class=Low_complexity} ## {MIR: cel-mir-70}
cbrennerichromosome:chrUn:187605846:187605941:-1Same_strand|Intronic_coding|NM_072288


cbr-mir-87

Cloning frequencies
absoluteAF16
cbr-mir-87 5arm7
cbr-mir-87 3arm109
normalizedAF16
cbr-mir-87 5arm0.018
cbr-mir-87 3arm0.284
cbr-mir-87 relative cloning frequencies

sblock62 (miRBase cbr-mir-87) [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-870.001nono0.44/0.5318/24/0.950.0
0.0
0.0
0.0
0.0
0.0
2
5
94
0
0
0
1
1
1
0
0
0
17
41
13
6
-13
9
5arm
5arm_loop_3arm
3arm
1
1
1
nd
nd
nd
0.21
0.37
0.14
3
4
1
116123
Families
Member of family miR-233/356/87 (seed UGAGCAA): cbr-mir-233, cbr-mir-87
sblock62 hairpin
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------UGAGCAA------------------------------------------     108miR-233/356/87
seed     -------------------------------------------------------------GCUG--UCA--------------------------------------------------------------     5novel
seed     -------------------------------------GCCUGAU----------------------------------------------------------------------------------------     2novel
seed     ------------------------------------------------------------------------------------GAGCAAA-----------------------------------------     1novel
  lencloning frequencies
   AF16
      ----------------------------------------------------------------------------------GTGAGCAAAGTTTCAGGTGTGC----------------------------     2294
      ----------------------------------------------------------------------------------GTGAGCAAAGTTTCAGGTGTG-----------------------------     2113
      ------------------------------------------------------------CGCTG--TCAGA-ATGTCGTAG--------------------------------------------------     195
      ------------------------------------CGCCTGATACTTTCGTCTCAACCT------------------------------------------------------------------------     242
      ----------------------------------------------------------------------------------GTGAGCAAAGTTTCAGGT--------------------------------     181
      -----------------------------------------------------------------------------------TGAGCAAAGTTTCAGGTGTG-----------------------------     201
cbr-miR-87     ----------------------------------------------------------------------------------GTGAGCAAAGTTTCAGGTGT------------------------------     20-
cbriggsae     -------------------GGTTGTGCCCACCCGGCCGCCTGATACTTTCGTCTCAACCTCGCTG--TCAGA-ATGTCGTAGGTGAGCAAAGTTTCAGGTGTGCCGGAACACACCCA---------------      
cremanei     AAACTTCTTCATCCATACAGGTTGTG-CCTTCCGGCCGCCTGACACTTTCGTCTCAACCTCGCTGTCTGATA-TAGTCGTAGGTGAGCAAAGTTTCAGGTGTGCCGGAACACATCCTCACTTTGCCCAGTTT      
celegans     -------------------GGTTGTGCCAT-CCGGCCGCCTGATACTTTCGTCTCAACCTCGCTG--TCAGATTGGTCGTAGGTGAGCAAAGTTTCAGGTGTGCCGGAACACACCC----------------      
cbrenneri     ----------------------------------GCCGCCTGATACTTTCGTCTCAACCTCGCTTC-TCTCA-TTGTCGTAGGTGAGCAAAGTTTCAGGTGTGC----------------------------      
ppacificus     -----------------GGGGTGACGTCATGCTCGTCGCCTGA-ACTTGTA-CTCAACCTCGTCA--ATAGA-TGAGCGCAGGTGAGCAAAGTTTCAGGTGTGCGAGCTAGCGTCCCCC-------------      
cjaponica     ----------------------------------GCCGCCTGACACTTTCGTCTCAACCTCGCT---TCAGA-TGGCCGTAGGTGAGCAAAGTTTCAGGTGTGC----------------------------      
                                        * ******* ****    **********         *     ** ************************                                  
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_031366
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_007734
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_031362
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_031365
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001122952
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001122953
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_104252
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_059770
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_059769
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001104651
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001104706
 -----                   ----------------------------------------------  ----- --------------------------------------------               -----NM_001087279
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_204902
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_010905
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_000092
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_000091
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_001018032
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_078262
 -----                   ----------------------------------------------  ----- --------------------------------------------               -----NM_203894
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_009655
 +++++                   ++++++++++++++++++++++++++++++++++++++++++++++  +++++ ++++++++++++++++++++++++++++++++++++++++++++               +++++NM_073615
cbriggsae                        ((.((((.....((((((((((((.(((((...(((.((((((.((  (.... ))).)).))))))).))))).))))))).)))))..)))).)).                    1.000 -39.50
cremanei     ..................(((.(((( ..((((((((((((((.(((((...(((.((((((((((.....) ))).)).))))))).))))).))))))).))))))))))).)))...............     0.918 -47.30
celegans                        ((.((((...( ((((((((((((.(((((...(((.(((((((((  ......))).)).))))))).))))).))))))).)))))).)))))).                     0.998 -43.30
cbrenneri                                       (((((((((.(((((...(((.((((((.... ..... ....)).))))))).))))).))))))).))                                 0.999 -23.02
ppacificus                      ((((.(((((...((((((((((((( ((((... (((.(((((((((  ..... ))).)).)))))))..))))).)))))).))))))..)))))))))                  1.000 -50.30
cjaponica                                       (((((((((.(((((...(((.((((((((   ..... .)).)).))))))).))))).))))))).))                                 1.000 -26.20

cbriggsaechromosome:chrV:6389696:6389790:1Same_strand|Intronic_coding|NM_031366|COL4A3 ## Same_strand|Intronic_non-coding|NM_001122952|Nfia ## Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## {Repeats: no} ## {MIR: cbr-mir-87}
cremaneichromosome:chrUn:126942557:126942686:-1Same_strand|Intronic_coding|NM_073615
celeganschromosome:chrV:12038665:12038758:-1Same_strand|Intronic_coding|F10C2.2 ## {MIR: cel-mir-87}
cbrennerichromosome:chrUn:175577610:175577744:-1Same_strand|Intronic_coding|NM_073615
ppacificuschromosome:chrUn:113454284:113454380:-1Same_strand|Intronic_coding|NM_001014737
cjaponicachromosome:chrUn:17231967:17232101:1intergenic


cbr-mir-48

Cloning frequencies
absoluteAF16
cbr-mir-48 5arm39
cbr-mir-48 3arm6
normalizedAF16
cbr-mir-48 5arm0.102
cbr-mir-48 3arm0.016
cbr-mir-48 relative cloning frequencies

sblock64 (miRBase cbr-mir-48) [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-480.001nono0.52/0.5521/23/1.000.0
0.0
0.0
0.0
37
6
0
0
1
1
0
0
17
15
5
6
5arm
3arm
1
1
nd
nd
0.27
0.27
2
2
45112
Families
Member of family miR-241/48/let-7/84 (seed GAGGUAG): cbr-let-7, cbr-mir-48, cbr-mir-241, cbr-mir-84
sblock64 hairpin
  readsmiRBase family seed
seed     ------------------------------------------GAGGUAG--------------------------------------------------------------------------------------------     39miR-241/48/let-7/84
seed     --------------------------------------------------------------------------------------------CAUCGUC------------------------------------------     6novel
  lencloning frequencies
   AF16
      -----------------------------------------TGAGGTAGGCTCAGTAGATGCG------------------------------------------------------------------------------     2237
      -------------------------------------------------------------------------------------------ACATCGTCTGTCCTAACTCGCC----------------------------     226
      -----------------------------------------TGAGGTAGGCTCAGTAGATGC-------------------------------------------------------------------------------     212
cbr-miR-48     -----------------------------------------TGAGGTAGGCTCAGTAGATGCGA-----------------------------------------------------------------------------     23-
cbriggsae     -------------------AGAACCATTCGGG-----ATGTTGAGGTAGGCTCAGTAGATGCGAGGAGA--------TCCACCATTC-CTCACATCGTCTGTCCTAACTCGCCTTCCCTTGTGCTTCA-------------      
cremanei     ------------------------CATACCGG-----ATGTTGAGGTAGGCTCAGTAGATGCGATCAGAGTTGTGCCTCAGGCGTTC-CTCACATCTTCTTGCCTAACTCGCCTTCCTTTATGTTTAACCTTT--------      
celegans     GGTAAGTCAATTAACCAATTGAAACTCCCGGG-----AACTTGAGGTAGGCTCAGTAGATGCGAATTGAACGGTATC------------TCACATCCACCAGCCTAGCTCGCATTCCCAGAGTTTACGGTATTGTTTTATT      
cbrenneri     -----------------------------------------TGAGGTAGGCTCAGTAGATGCGAACGTAAATGAGCCCACATCGGCCTTTCACATCCACTTGCCTTCCTCG------------------------------      
cjaponica     ----------------------GCCGCTGGGGTGTCAAAGTTGAGGTAGGTGCGAGAAATG--ACGAGAAT--CATCCAAATCGCGC--TCATTGCCTCCAATCTGCCTCGACTGGGACGCTC------------------      
ppacificus     -----------------------------------------AGAGGTAGGGGAGAGAG-TGC-AATAGTATTGCATCCTTGCAATACTATTGCAATAGTTCCCCTCTCTCG------------------------------      
                                                ********      *  **  *                         *             **  ****                                    
 -----                   -------------     --------------------------------        ---------- ----------------------------------------             -----NM_074155
 -----                   -------------     --------------------------------        ---------- ----------------------------------------             -----NM_001028773
 -----                   -------------     --------------------------------        ---------- ----------------------------------------             -----NM_001027854
 -----                   -------------     --------------------------------        ---------- ----------------------------------------             -----NM_074150
 +++++                   +++++++++++++     ++++++++++++++++++++++++++++++++        ++++++++++ ++++++++++++++++++++++++++++++++++++++++             +++++NM_001113262
 -----                   -------------     --------------------------------        ---------- ----------------------------------------             -----NM_136816
 +++++                   +++++++++++++     ++++++++++++++++++++++++++++++++        ++++++++++ ++++++++++++++++++++++++++++++++++++++++             +++++NM_001113262
 +++++                   +++++++++++++     ++++++++++++++++++++++++++++++++        ++++++++++ ++++++++++++++++++++++++++++++++++++++++             +++++NM_001113262
cbriggsae                        .(((.(((..(((     (.(.((((.((((..(((..((((.((((((.        .......))) ))).))))..))).)))).)))).).))))..))).))).                  1.000 -37.70
cremanei                             ((((..((     (...((((.(((((..((.(((((......(((..(((((...))))).. ))).))))).)).))))).))))...)))..))))..........             0.975 -28.30
celegans     .(((((.((((..(((.....((((((..(((     ((..((((.((((((..((.((((.((..((.....))..            )).)))).)).)))))).))))..))))).))))))..))))))).))))).     0.968 -39.90
cbrenneri                                              .((((.((((..(((.((((.(((.((..(((......)))..))..))).)))).))).)))).)))).                                   0.950 -24.30
cjaponica                           .......(((((((..((((((((((((((.(((.((((  (((.((..  ........)).)).  )))))..))))).))))))))))))..)))))))                       0.972 -39.90
ppacificus                                              .(((..(((((((.... ((( ((((((((((((....)))))))))))))))....)))))))..))).                                   1.000 -41.40

cbriggsaechromosome:chrV:12275585:12275679:1Opposite_strand|Intronic_non-coding|NM_074155|F47B8.10 ## Opposite_strand|Intronic_coding|NM_001028773|F47B8.14 ## Same_strand|Intronic_coding|NM_001113262|Fib-h ## {Repeats: no} ## {MIR: cbr-mir-48}
cremaneichromosome:chrUn:140422769:140422871:1Opposite_strand|Intronic_coding|NM_182407
celeganschromosome:chrV:14364385:14364508:-1intergenic ## {MIR: cel-mir-48}
cbrennerichromosome:chrUn:191750356:191750490:-1intergenic
cjaponicachromosome:chrUn:25919622:25919716:-1Same_strand|Intronic_coding|NM_001004193
ppacificuschromosome:chrUn:127724478:127724612:-1intergenic


cbr-mir-81

Cloning frequencies
absoluteAF16
cbr-mir-81 5arm3
cbr-mir-81 3arm3064
normalizedAF16
cbr-mir-81 5arm0.008
cbr-mir-81 3arm7.987
cbr-mir-81 relative cloning frequencies

sblock67 (miRBase cbr-mir-81) [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-810.002nono0.39/0.4819/23/0.990.0
0.0
0.0
0.0
3
2924
0
0
1
1
0
0
13
12
4
8
5arm
3arm
1
1
nd
nd
0.14
0.23
2
2
3067112
Families
Member of family miR-80/81/82 (seed GAGAUCA): cel-mir-82, cbr-mir-81, cbr-mir-80, cbr-mir-82
sblock67 hairpin
  readsmiRBase family seed
seed     -------------------------------------------------------------------------------GAGAUCA------------------------------------     3059miR-80/81/82
seed     --------------------------------------------------------------------------------AGAUCAU-----------------------------------     4novel
seed     ---------------------------------GGUUUUC----------------------------------------------------------------------------------     3novel
seed     ----------------------------------------------------------------------------------AUCAUCG---------------------------------     1miR-392
  lencloning frequencies
   AF16
cbr-miR-81     ------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAGT----------------------     222924
      ------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAGTT---------------------     2354
      ------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTAG-----------------------     2150
      ------------------------------------------------------------------------------TGAGATCATCGTGAAAGCT-------------------------     1921
      ------------------------------------------------------------------------------TGAGATCATCGTGAAAGCTA------------------------     2010
      --------------------------------CGGTTTTCACCTTGATCTG-AG--------------------------------------------------------------------     213
      -------------------------------------------------------------------------------GAGATCATCGTGAAAGCTAGT----------------------     212
      -------------------------------------------------------------------------------GAGATCATCGTGAAAGCTAGTT---------------------     222
      ---------------------------------------------------------------------------------GATCATCGTGAAAGCTAGT----------------------     191
cbriggsae     -------------------CGTGATTAACGGTCGGTTTTCACCTTGATCTG-AGAGCAATAACCAGAATGCTT--ATCTGAGATCATCGTGAAAGCTAGTTGTTACTTCACT----------      
cremanei     --------------GCCCTCGTGGCCAGCAGTCGGTTTTCACCTTGATCTG-AGAGC--TAAACATAATGCTT--ATCTGAGATCATCGTGAAAGCTAGTTGCAGGTACACAGGC-------      
celegans     TGCATAAAATCAGTGCCATCGTGCCCAACAGTCGGTTTTCACCGTGATCTG-AGAGCAAT-CCAAAAATGCTT--TTCTGAGATCATCGTGAAAGCTAGTTGTTGGTCTACGGGCTTTTGCG      
cbrenneri     GTGAAATAAAATATGTTCTC----CTAGCAACAGGTTCTCACTGTGATCTGCAGAGT-------ATAAAGCCTACATCTGAGATCATCGTGAAAGCCAGTTGCTTACGAACTAAATTCAT--      
cjaponica     ------------------------------GTCGGTTTTCCCATTGATCTG-AGAGC--TAACTGT-ACGCT---ATCTGAGATCATCGTGAAAGCTAGT----------------------      
ppacificus     ------------------TCACTCCCGGCATGCGGTTTTCACGTTGATCTG-AGAGC--TAATCGATATGTTT----CTGAGATCATAGTGAAAGCTACTTGCCGAAGTGA-----------      
                                       **** ** *  ******* ****           * *       ********** ******** * *                            
 -----                   -------------------------------- ---------------------  -------------------------------------          -----NM_001087279
 -----                   -------------------------------- ---------------------  -------------------------------------          -----NM_178655
 -----                   -------------------------------- ---------------------  -------------------------------------          -----NM_001034168
 +++++                   ++++++++++++++++++++++++++++++++ +++++++++++++++++++++  +++++++++++++++++++++++++++++++++++++          +++++NM_001109816
 -----                   -------------------------------- ---------------------  -------------------------------------          -----NM_065440
 +++++                   ++++++++++++++++++++++++++++++++ +++++++++++++++++++++  +++++++++++++++++++++++++++++++++++++          +++++NM_020367
cbriggsae                        .((((.((((((..(((((((((..((((((. ((((((..........)))..  .))).))))))..)))))))))..))))))..)))).               1.000 -34.60
cremanei                   ..(((.((((((.((((..(((((((((..((((((. (((((  ..........))..  .))).))))))..)))))))))..)))).))).)))))).            1.000 -39.70
celegans     .(((..........(((..((((.(((((((..(((((((((.(((((((. ((((((.. .......)))..  .))).))))))).)))))))))..)))))))..)))))))...))).     0.861 -44.52
cbrenneri     ..............((((..    ..((((((.((((.((((.(((((((.((((((       (.......))).))))))))))).)))).)))).))))))...)))).........       0.968 -36.80
cjaponica                                   ...(((((((....((((((. (((((  ....... ..)).   .))).))))))....)))))))...                           1.000 -17.70
ppacificus                       (((((..(((((...(((((((((..((((((. (((((  ..........))).    )).))))))..)))))))))...))))).)))))                1.000 -36.00

cbriggsaechromosome:chrX:4426667:4426756:-1Opposite_strand|Intronic_non-coding|NM_001087279|fbxl5 ## Same_strand|Intronic_coding|NM_001109816|MHC ## Same_strand|Intronic_non-coding|NM_020367|PARP11 ## {Repeats: no} ## {MIR: cbr-mir-81}
cremaneichromosome:chrUn:34152019:34152114:-1Opposite_strand|Intronic_coding|NM_076043
celeganschromosome:chrX:2431059:2431176:1Opposite_strand|Intronic_coding|T07D1.2.1 ## {MIR: cel-mir-81}
cbrennerichromosome:chrUn:976025:976133:1intergenic
cjaponicachromosome:chrUn:6896855:6896984:1intergenic
ppacificuschromosome:chrUn:128697181:128697266:-1Same_strand|Intronic_coding|NM_022416 ## Opposite_strand|Intronic_coding|NM_001028815 ## {Repeats: GA-rich 1 89 -1 class=Low_complexity}


cbr-mir-34

Cloning frequencies
absoluteAF16
cbr-mir-34 5arm829
cbr-mir-34 3arm1
normalizedAF16
cbr-mir-34 5arm2.161
cbr-mir-34 3arm0.003
cbr-mir-34 relative cloning frequencies

sblock76 (miRBase cbr-mir-34) [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-340.005nono0.50/0.5818/22/0.970.0
0.0
0.0
0.0
696
1
0
0
1
1
0
0
17
19
5
7
5arm
3arm
1
1
nd
nd
0.14
0.16
1
2
830120
Families
Member of family miR-34 (seed GGCAGUG): cbr-mir-34, block869_novel
sblock76 hairpin
  readsmiRBase family seed
seed     -------------------------------------GGCAGUG----------------------------------------------------------------------------------------------     814miR-34
seed     -----------------------------------------GUGUGGU------------------------------------------------------------------------------------------     15novel
seed     ------------------------------------------------------------------------------CGGCU----AC-------------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-34     ------------------------------------AGGCAGTGTGGTTAGCTG-GTTG-------------------------------------------------------------------------------     22696
      ------------------------------------AGGCAGTGTGGTTAGCTG-GTT--------------------------------------------------------------------------------     21106
      ----------------------------------------AGTGTGGTTAGCTG-GTTG-------------------------------------------------------------------------------     1815
      ------------------------------------AGGCAGTGTGGTTAGCTG-G----------------------------------------------------------------------------------     199
      ------------------------------------AGGCAGTGTGGTTAGCTG-GT---------------------------------------------------------------------------------     203
      ---------------------------------------------------------------------------A--CGGCT----ACCTTCACTGCCA--------------------------------------     191
cbriggsae     -------------------AAGCACTCATGGTCGTGAGGCAGTGTGGTTAGCTG-GTTGCATACACAGGTTGACAA--CGGCT----ACCTTCACTGCCACCCCGAACATGTAGTCCTC-------------------      
cremanei     ------------------------------------AGGCAGTGTGGTTAGCTG-GTTGCATATTGA-ATTGACAA--CGGCT----ACCTTCACTGCCA--------------------------------------      
celegans     TACTGACTATTATTCTTATAACGGACAATGCTCGAGAGGCAGTGTGGTTAGCTG-GTTGCATATTTC-CTTGACAA--CGGCT----ACCTTCACTGCCACCCCGAACATGTCGTCCATCTTTGAACACTGGTGAGTG      
cbrenneri     ------------------------------------AGGCAGTGTGGTTAGCTG-GTTGCATACTGACATTGACAA--CGGCT----ACCTTCACTGCCA--------------------------------------      
cjaponica     -----------CTCTCCACAATGGACGGTGCTCGGGAGGCAGTGTGGTTAGCTG-GTTGCATGATGT-TTTGACAA--CGGCT----ACCTTCACTGCCACCCCGATCATGTTGTCCATCTTTGAACATTGGTGAG--      
ppacificus     TAAGCTCCAGACTCTCTCCATTAGCACATG------TGGCAGTGCAATCGGCAGCCTCGCACTGGGG-CTCGCCGATTCGTCTCCACACCTTCTCTGAGA---------------------------------GAATC      
                                           *******   *  ** *  * ***        * * * *  ** **    ****** ***  *                                            
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_076104
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_029999
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_022410
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_031169
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_001027419
 +++++                   +++++++++++++++++++++++++++++++++++ +++++++++++++++++++++  +++++    ++++++++++++++++++++++++++++++++                   +++++NM_181850
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_022416
 -----                   ----------------------------------- ---------------------  -----    --------------------------------                   -----NM_033509
cbriggsae                        .((.(((((((.(((.(.(((((((.(((.((((( .(((((.((....)))).)))  )))))    )))..))))))).)..))).)))).))).)).                        1.000 -34.40
cremanei                                         .(((((((.((.(((((. ((((((...... ..)).)))  )))))    )))..))))))).                                           1.000 -26.50
celegans     ((((.((((...(((.......((((.(((.(((...(((((((.((.(((((. ((((((...... ..)).)))  )))))    )))..)))))))....))).)))...))))......)))...)))).))))     0.880 -42.22
cbrenneri                                         .(((((((.((.(((((. ((((((.........)).)))  )))))    )))..))))))).                                           1.000 -25.70
cjaponica                (((.(((((((((((((((.(((((.(((((((.((.(((((. ((((((...... ..)).)))  )))))    )))..)))))))..))))).)))..)))))))...)).....))).)))       0.965 -48.50
ppacificus     .........((.((((((....((....((      (((.((((.(((((((((((((.....)))) )).))))))))).)))))))....))..))))                                 )).))     0.992 -36.50

cbriggsaechromosome:chrX:3899335:3899427:1Opposite_strand|Intronic_non-coding|NM_076104|Y71H10A.2 ## Same_strand|Intronic_non-coding|NM_181850|Grm3 ## {Repeats: no} ## {MIR: cbr-mir-34}
cremaneichromosome:chrUn:33757012:33757144:1Opposite_strand|Intronic_coding|NM_001107657
celeganschromosome:chrX:2969732:2969861:-1intergenic ## {MIR: cel-mir-34}
cbrennerichromosome:chrUn:541725:541857:1intergenic
cjaponicachromosome:chrUn:18910363:18910479:1Opposite_strand|Intronic_coding|NM_010452
ppacificuschromosome:chrUn:130117543:130117640:1intergenic


cbr-mir-79

Cloning frequencies
absoluteAF16
cbr-mir-79 5arm24
cbr-mir-79 3arm701
normalizedAF16
cbr-mir-79 5arm0.063
cbr-mir-79 3arm1.827
cbr-mir-79 relative cloning frequencies

sblock9 (miRBase cbr-mir-79) [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-790.001nono0.33/0.3820/22/1.000.0
0.0
0.0
0.0
23
686
0
0
1
1
0
0
14
15
5
5
5arm
3arm
1
1
nd
nd
0.18
0.18
2
2
725112
Families
Member of family miR-75/79 (seed UAAAGCU): cbr-mir-75, cbr-mir-79
sblock9 hairpin
  readsmiRBase family seed
seed     -------------------------------------------------------------------------------------UAAAGCU---------------------------------------------     700miR-75/79
seed     --------------------------------UUUGGUG--------------------------------------------------------------------------------------------------     24novel
seed     --------------------------------------------------------------------------------------AAAGCUA--------------------------------------------     1novel
  lencloning frequencies
   AF16
cbr-miR-79     ------------------------------------------------------------------------------------ATAAAGCTAGGTTACCAAAGCT-------------------------------     22686
      -------------------------------CTTTGGTGATTCAGCT-------TAAATG-----------------------------------------------------------------------------     2223
      ------------------------------------------------------------------------------------ATAAAGCTAGGTTACCAAAGC--------------------------------     219
      ------------------------------------------------------------------------------------ATAAAGCTAGGTTACCAAAG---------------------------------     205
      -------------------------------------------------------------------------------------TAAAGCTAGGTTACCAAAGCT-------------------------------     211
      -------------------------------CTTTGGTGATTCAGCT-------TAAAT------------------------------------------------------------------------------     211
cbriggsae     --GAACATTCT---------------CCGATCTTTGGTGATTCAGCT-------TAAATGATAGAA-TTCAGACGT----CTTCATAAAGCTAGGTTACCAAAGCTCGGCGTTCCAGTTCG----------------      
cremanei     -------GTTT---------------CCGATCTTTGGTGATTCAGCT-------TAAATGATAGAC-TCAATATGTTAGACTTCATAAAGCTAGGTTACCAAAGCTCGGCGGC------------------------      
celegans     GTAGACATTCT---------------CCGATCTTTGGTGATTCAGCT-------TCAATGATTGGC---TACAGGTTTC-TTTCATAAAGCTAGGTTACCAAAGCTCGGCGTCTTGATCTAC---------------      
cbrenneri     AGATATGGTT----------------CCGAACTTTGGTGATTCAGTT-------TTAATGATTGACGATTCAACGTTTT-CTTCATAAAGCTAGGTTACCAAAGCTCGGCGCTTCATGTCT----------------      
ppacificus     ---------------------------CG--CTTTGGTTATCTTGCTTTCTGACTAAATGTCCAAG--------------GTTCATAAAGCTAGGTTACCAAAGCT-------------------------------      
cjaponica     GGTAACGTTTTGCGATGAGTGAGCTGCCGACCTTTGGTGATTAAGCT-------TAAATGATCGGC-------CGTGTTGTTTCATAAAGCTAGGTTACCAAAGCTCGGCGGTCGAAACCATACATATTTGTTTACC      
                                 **  ******* **   * *       * ****                     *************************                                     
 +++++  +++++++++               +++++++++++++++++++++       ++++++++++++ +++++++++    +++++++++++++++++++++++++++++++++++++++++                +++++NM_001011629
 +++++  +++++++++               +++++++++++++++++++++       ++++++++++++ +++++++++    +++++++++++++++++++++++++++++++++++++++++                +++++NM_014333
 +++++  +++++++++               +++++++++++++++++++++       ++++++++++++ +++++++++    +++++++++++++++++++++++++++++++++++++++++                +++++NM_001098517
 +++++  +++++++++               +++++++++++++++++++++       ++++++++++++ +++++++++    +++++++++++++++++++++++++++++++++++++++++                +++++NM_061553
 -----  ---------               ---------------------       ------------ ---------    -----------------------------------------                -----NM_067080
cbriggsae       ((((.....               ((((.((((((((((..((((       (..((((.(((. ........)    )))))).)))))..)))))))))).)))).......)))).                     0.990 -31.40
cremanei            ((..               ((((.((((((((((..((((       (..((((..((( .......))).....)))).)))))..)))))))))).))))..))                             0.922 -30.00
celegans     (((((((....               ((((.((((((((((..((((       (..((((..(((   .....))).. ..)))).)))))..)))))))))).)))).....)).)))))                    1.000 -34.50
cbrenneri     (((((((((.                ((((.((((((((((..((((       ((.((((..((((......)))).. ..))))))))))..)))))))))).)))).))..)))))))                     1.000 -39.10
ppacificus                                .(  (((((((.((((.(((((.(((((..........)              )).)).))))).)))).)))))))).                                    1.000 -23.10
cjaponica     (((((((.......(((.((..((((((((.((((((((((..((((       (..((((.((((       ...))))..)))).)))))..)))))))))).))))))))....))))).......)))).)))     0.920 -44.14

cbriggsaechromosome:chrI:1376275:1376366:1Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_coding|NM_061553|C13A10.1 ## Opposite_strand|Intronic_coding|NM_067080|Y66D12A.21 ## {Repeats: no} ## {MIR: cbr-mir-79}
cremaneichromosome:chrUn:105203826:105203908:1intergenic
celeganschromosome:chrI:9332939:9333034:1intergenic ## {MIR: cel-mir-79}
cbrennerichromosome:chrUn:27772761:27772857:-1intergenic
ppacificuschromosome:chrUn:79886586:79886717:1intergenic
cjaponicachromosome:chrUn:79311330:79311452:-1Opposite_strand|Intronic_coding|NM_001027065


miRNAknown_cloningHIGH_randfoldOK (17 loci)

cbr-mir-235

Cloning frequencies
absoluteAF16
cbr-mir-235 3arm83
normalizedAF16
cbr-mir-235 3arm0.216
cbr-mir-235 relative cloning frequencies

block171 (miRBase cbr-mir-235) [miRNAknown_cloningHIGH_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-2350.002nono0.50/0.5319/22/0.860.0
0.0
70
0
1
0
6
10
3arm
1
nd
0.19
2
831nana
Clusters
Located in cluster 1: cbr-mir-235, cel-mir-235
Families
Member of family miR-235 (seed AUUGCAC): cel-mir-235, cbr-mir-235
block171 hairpin
  readsmiRBase family seed
seed     --------------------------------------------------------------AUUGCAC---------------------     83miR-235
  lencloning frequencies
   AF16
      -------------------------------------------------------------TATTGCACTTTCCCTGGCCAG--------     2170
      -------------------------------------------------------------TATTGCACTTTCCCTGGCC----------     1912
      -------------------------------------------------------------TATTGCACTTTCCCTGGCCA---------     201
cbr-miR-235     -------------------------------------------------------------TATTGCACTTTCCCTGGCCAGA-------     22-
cbriggsae     --TCCGATCCGGCCATGGCCAATTGCATATATTGCTTTTACTTTT---TCAAAATGCG-AATATTGCACTTTCCCTGGCCAGATCTGA--      
cremanei     TATCCTACCTTGGAATA-CTAGCCGCC-----GGCACTGGAGCTT---TCGGCGTGCGTAGTATTGCACTTGGC-------GGTCGGATG      
cjaponica     --TCATGTATTGAGAAA---AGCAGTA-ATAGAACTATCAGGTTTGGGTTTGACTTTG-ATTATTGCACTTTCC-------GATGCGGTG      
        **       *  *     *   *         *  *     **   *     *  * * **********  *       * *  *         
 +++++  +++++++++++++++++++++++++++++++++++++++++++   ++++++++++ +++++++++++++++++++++++++++++  +++++NM_001032899
 -----  -------------------------------------------   ---------- -----------------------------  -----NM_199320
 +++++  +++++++++++++++++++++++++++++++++++++++++++   ++++++++++ +++++++++++++++++++++++++++++  +++++NM_005073
cbriggsae       ...((((.(((((.((..((.((((.(((((((((((......   ..)))).)). ))))))))).))..))))))).))))...       1.000 -24.50
cremanei     (((((.(((.((.(((( (((((((((     (((......))..   .))))).)).))))))).))......       ))).)))))     0.930 -27.30
cjaponica       ...(((((((.((((   .(((((( ((.(((...(((((......))))).))). ))))))))..)))))       ))))))...     0.839 -17.80

cbriggsaechromosome:chrI:8823354:8823435:-1Same_strand|Intronic_non-coding|NM_001032899|SLC15A1 ## Opposite_strand|Intronic_non-coding|NM_199320|PHF17 ## {Repeats: no} ## {MIR: cbr-mir-235}
cremaneichromosome:chrUn:138336433:138336554:-1Opposite_strand|Intronic_coding|NM_171077 ## Same_strand|Intronic_coding|NM_001093429
cjaponicachromosome:chrUn:6633772:6633893:1intergenic


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