logoC.briggsae small RNAs

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cbr-mir-232

cbr-mir-232

Cloning frequencies
absoluteAF16
cbr-mir-232 3arm15
normalizedAF16
cbr-mir-232 3arm0.039
cbr-mir-232 relative cloning frequencies

block2588 (miRBase cbr-mir-232-2) [miRNAknown_cloningOK_randfoldOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-232-20.001nono0.39/0.4122/23/1.000.0
0.0
14
0
1
0
17
5
3arm
2
nd
0.32
4
151nana
Families
Member of family miR-232 (seed AAAUGCA): cbr-mir-232, cbr-mir-232
block2588 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------------------------AAAUGCA-------------------------------------------------     14miR-232
seed     ---------------------------------------------------------------------------------UAAAUGC--------------------------------------------------     1novel
  lencloning frequencies
   AF16
      ---------------------------------------------------------------------------------TAAATGCAT-CTTAACTGCGGTG----------------------------------     2214
      --------------------------------------------------------------------------------ATAAATGCAT-CTTAACTGCGGTG----------------------------------     231
cbr-miR-232     ---------------------------------------------------------------------------------TAAATGCAT-CTTAACTGCGGTGA---------------------------------     23-
cbriggsae     -------------TTCAAGATTT---------CGGATCTCCGTAGTTTTGACCATTTTATCCAAC----CTAATAATGTGATAAATGCAT-CTTAACTGCGGTGATCTG-GATTTTGTGAAC----------------      
cremanei     GAGGTAAGTTGAAGTCTGATTGT---------CGGATCTCCGTAGTTTCGATCATTTTATCCTATCT--CCAACAAAGCGATAAATGCAT-CTTAACTGCGGTGATCTG-AATTCTTGGACACTTTTTTCTTTATTTC      
celegans     TTTGAAAAATAAGTTC-AATTTT---------TGGATCCCTGCAGTTTCGATGATTTTATCCTTAATT-CTGAAGATGTGATAAATGCAT-CTTAACTGCGGTGATCTA-GATCATGAACACTTTTTTAAA-------      
cbrenneri     -------------------------------------CCCCGTAGTTTCGATCATTTTATCCTGCCCAACTCAAAAAGTGATAAATGCAT-CTTAACTGCGGTG----------------------------------      
cjaponica     ------GGTAAGTTTCTGGGTCCTCACGAGCGTGGATCTCCGTAGTTTCGATCGTTTTATCCAGCGCCACAAACCGTGCGATAAATGCAT-CTTAACTGCGGTGATCTGCAATTCTGGGACACGCTTTTTTC------      
ppacificus     --------------------------------------CCTGCAATT--GAGCATGCAATTTAAC--------AAATAACATAAATGCATGCTTCCATTCGGA-----------------------------------      
                                             * * * **  **   *   **                    ********** ***   * ***                                          
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001106790
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001128722
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069625
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069625
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001273
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001083844
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069822
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069822
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171311
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_011416
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_025685
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_122970
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_005402
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001033832
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_214509
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001090075
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001011629
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_135592
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001087352
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_078712
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001011005
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_003070
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_003269
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_139045
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171312
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_000692
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001081235
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171903
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001087789
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001034039
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_007742
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_072974
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_067302
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_000493
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001127025
cbriggsae                  (((((((.((         ((((((.((((((((..((....((((((((..    .......)).))))))....) )..)))))))).)))))) )).))).)))).                     1.000 -31.30
cremanei     ((((((((..(((((((((...(         ((((((.((((((((..(((((.((((((((....  .......)).)))))))).)) )..)))))))).)))))) )....))))))....)))..))))))))     1.000 -37.80
celegans     .((((((((...(((( (...((         ((((((.((((((((..((((..((((((......( (....))...))))))..))) )..)))))))).)))))) ))...)))))..)))))))).            0.989 -37.90
cbrenneri                                          ..((((((((..(((((.((((((((.............)).)))))))).)) )..))))))))..                                       1.000 -18.42
cjaponica           .............((((.((.((..(((((((.((((((((..(((((.((((((..((((........)))))))))))).)) )..)))))))).)))))))..)).))))))...........           0.951 -40.90
ppacificus                                           .(((.(((.  ((((((((.(((((..        ........)))))))))))))..)))))).                                        0.967 -13.60

cbriggsaechromosome:chrIV:5589891:5589984:1Same_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-232-2}
cremaneichromosome:chrUn:56798774:56798898:-1Opposite_strand|Intronic_coding|NM_069625
celeganschromosome:chrIV:10994129:10994246:-1intergenic ## {MIR: cel-mir-232}
cbrennerichromosome:chrUn:102760940:102761073:1intergenic
cjaponicachromosome:chrUn:41745063:41745187:-1Opposite_strand|Intronic_coding|NM_172827
ppacificuschromosome:chrUn:170249641:170249774:1Same_strand|Intronic_coding|NM_000209 ## Opposite_strand|Intronic_coding|NM_016248


block2597 (miRBase cbr-mir-232-1) [miRNAknown_cloningOK_randfoldOK_nonpairedHIGH_bulgeHIGH]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-mir-232-10.001nono0.39/0.4122/23/1.000.0
0.0
14
0
1
0
17
5
3arm
2
nd
0.32
4
151nana
Families
Member of family miR-232 (seed AAAUGCA): cbr-mir-232, cbr-mir-232
block2597 hairpin
  readsmiRBase family seed
seed     ----------------------------------------------------------------------------------AAAUGCA-------------------------------------------------     14miR-232
seed     ---------------------------------------------------------------------------------UAAAUGC--------------------------------------------------     1novel
  lencloning frequencies
   AF16
      ---------------------------------------------------------------------------------TAAATGCAT-CTTAACTGCGGTG----------------------------------     2214
      --------------------------------------------------------------------------------ATAAATGCAT-CTTAACTGCGGTG----------------------------------     231
cbr-miR-232     ---------------------------------------------------------------------------------TAAATGCAT-CTTAACTGCGGTGA---------------------------------     23-
cbriggsae     -------------TTCAAGATTT---------CGGATCTCCGTAGTTTTGACCATTTTATCCAAC----CTAATAATGTGATAAATGCAT-CTTAACTGCGGTGATCTG-GATTTTGTGAAC----------------      
cremanei     GAGGTAAGTTGAAGTCTGATTGT---------CGGATCTCCGTAGTTTCGATCATTTTATCCTATCT--CCAACAAAGCGATAAATGCAT-CTTAACTGCGGTGATCTG-AATTCTTGGACACTTTTTTCTTTATTTC      
celegans     TTTGAAAAATAAGTTC-AATTTT---------TGGATCCCTGCAGTTTCGATGATTTTATCCTTAATT-CTGAAGATGTGATAAATGCAT-CTTAACTGCGGTGATCTA-GATCATGAACACTTTTTTAAA-------      
cbrenneri     -------------------------------------CCCCGTAGTTTCGATCATTTTATCCTGCCCAACTCAAAAAGTGATAAATGCAT-CTTAACTGCGGTG----------------------------------      
cjaponica     ------GGTAAGTTTCTGGGTCCTCACGAGCGTGGATCTCCGTAGTTTCGATCGTTTTATCCAGCGCCACAAACCGTGCGATAAATGCAT-CTTAACTGCGGTGATCTGCAATTCTGGGACACGCTTTTTTC------      
ppacificus     --------------------------------------CCTGCAATT--GAGCATGCAATTTAAC--------AAATAACATAAATGCATGCTTCCATTCGGA-----------------------------------      
                                             * * * **  **   *   **                    ********** ***   * ***                                          
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001106790
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_001128722
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069625
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069625
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069822
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_069822
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171311
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171311
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_025685
 +++++             ++++++++++         +++++++++++++++++++++++++++++++++    +++++++++++++++++++++ ++++++++++++++++++ ++++++++++++                +++++NM_001011629
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_135592
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_205170
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_204577
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171312
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171312
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171903
 -----             ----------         ---------------------------------    --------------------- ------------------ ------------                -----NM_171903
cbriggsae                  (((((((.((         ((((((.((((((((..((....((((((((..    .......)).))))))....) )..)))))))).)))))) )).))).)))).                     1.000 -31.30
cremanei     ((((((((..(((((((((...(         ((((((.((((((((..(((((.((((((((....  .......)).)))))))).)) )..)))))))).)))))) )....))))))....)))..))))))))     1.000 -37.80
celegans     .((((((((...(((( (...((         ((((((.((((((((..((((..((((((......( (....))...))))))..))) )..)))))))).)))))) ))...)))))..)))))))).            0.989 -37.90
cbrenneri                                          ..((((((((..(((((.((((((((.............)).)))))))).)) )..))))))))..                                       1.000 -18.42
cjaponica           .............((((.((.((..(((((((.((((((((..(((((.((((((..((((........)))))))))))).)) )..)))))))).)))))))..)).))))))...........           0.951 -40.90
ppacificus                                           .(((.(((.  ((((((((.(((((..        ........)))))))))))))..)))))).                                        0.967 -13.60

cbriggsaechromosome:chrIV:5768761:5768854:1Same_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-232-1}
cremaneichromosome:chrUn:56798774:56798898:-1Opposite_strand|Intronic_coding|NM_069625
celeganschromosome:chrIV:10994129:10994246:-1intergenic ## {MIR: cel-mir-232}
cbrennerichromosome:chrUn:102760940:102761073:1intergenic
cjaponicachromosome:chrUn:41745063:41745187:-1Opposite_strand|Intronic_coding|NM_172827
ppacificuschromosome:chrUn:170249641:170249774:1Same_strand|Intronic_coding|NM_000209 ## Opposite_strand|Intronic_coding|NM_016248


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