logoC.briggsae small RNAs

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noncloned miRBase miRNAs

miRNAknown_randfoldOK_bulgeHIGH (1 loci)

miRNAknown_shortStem_randfoldOK (1 loci)

cbr-lsy-6

block3748 (miRBase cbr-lsy-6) [miRNAknown_shortStem_randfoldOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
miRBase cbr-lsy-60.001nono0.43/0.4321/21/1.00nd
nd
0
0
0
0
4
6
3arm
1
nd
0.14
2
00nana
block3748 hairpin
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------UUUGUAU-------------------------------------     0lsy-6
  lencloning frequencies
   
cbr-lsy-6     -----------------------------------------------------------------------------TTTTGTATGAGACGCA-TTCCG-----------------------     21
cbriggsae     ---------------------CCACAGAATGCGTCCAGTATCAAAATCACATC------AAAGAGAATAC-GGTGGATTTTGTATGAGACGCA-TTCCGTGGC-------------------      
cremanei     TCGAATTTT----GATTTCCGCCACCGACTGCTTCGAATACCAAAATCATGGG----TAATCTACAGTAT-GCCAGATTTTGTATGAGACGCA-TTCAGTGGCGGGAAGACAAGAAAGA---      
celegans     ------TTTCTGAAAAATAAGCCATCAAATGCGTCTAGTATCAAAATCATGT-------AAAAACTGTAA-AACAGATTTTGTATGAGACGCATTTCGATGACGGGCACAACAGAGA-----      
cbrenneri     TATTGCTGTTCAAAAAACTTGCCACAGAATGCGTCGAATATCAAAATCATGTC----------AAAATATGGATAGATTTTGTATGAGACGCATTTCCGTGGCTGCAATGAACGTGGCGGTG      
cjaponica     ------------GATTAATTGCCACTGGATGCGTCGAATAACAAAATCGAGTGTTCTTACTTTGAAGTAT-AACTGATTTTGTATGAGACGCATTCCAGTGGCATTCTGATC----------      
                           ***     *** ** * ** *******                   **      ****************** * *  ** *                         
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_073462
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_070877
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_031362
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_000091
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_001083844
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_008331
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_026030
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_072417
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_031365
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_001100591
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_007729
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_001087789
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_203889
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_001087352
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_204577
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_001038742
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_080338
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_167026
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_167027
 -----                     --------------------------------      ----------- ---------------------- ---------                   -----NM_141224
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_031366
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_007737
 +++++                     ++++++++++++++++++++++++++++++++      +++++++++++ ++++++++++++++++++++++ +++++++++                   +++++NM_001029897
cbriggsae                          ((((.(((((((((..(((.(((((((.((((      ........... ))))))))))))))..)))))) ))).)))).                        1.000 -32.40
cremanei     .....((((    (.((((((((((.((.(((.((..(((.(((((((...((    ((..........) ))).))))))))))..)).))) .)).))))))))))..)))))....        0.999 -39.30
celegans           ((((((..........((((((((((((((.(((.(((((((.(((       ........... .))))))))))))).)))))))))).))))..........))))))          0.991 -30.25
cbrenneri     ((((((((((((........(((((.(((((((((..(((.(((((((.((((          ........))))))))))))))..)))))))))..))))).....)))))..)))))))     0.995 -41.62
cjaponica                 (((((..((((((((((((((((..((.((((((((.(((.....((((....)))). .)))))))))))))..))))))).)))))))))...)))))               0.998 -44.30

cbriggsaechromosome:chrV:7813065:7813138:-1Same_strand|Intronic_coding|NM_073462|clec-223 ## Opposite_strand|Intronic_coding|NM_070877|ugt-42 ## Same_strand|Intronic_non-coding|NM_008331|Ifit1 ## Opposite_strand|Intronic_non-coding|NM_001100591|Rc3h2 ## {Repeats: no} ## {MIR: cbr-lsy-6}
cremaneichromosome:chrUn:57701742:57701850:1Same_strand|Intronic_coding|NM_001114256
celeganschromosome:chrV:10647191:10647293:1intergenic ## {MIR: cel-lsy-6}
cbrennerichromosome:chrUn:66936444:66936555:1intergenic
cjaponicachromosome:chrUn:8397009:8397107:1Opposite_strand|Intronic_coding|NM_022073


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