logoC.briggsae small RNAs


miR classification

Alignments

other hairpins

novel_lenNOK_shortStem (21 loci)

block91 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.093nono0.67/0.6718/18/0.000.0
0.0
1
0
1
0
4
4
5arm
1
nd
0.17
2
11nana
  readsmiRBase family seed
seed     -----ACCGCCC-----------------------------------------------     1novel
  lencloning frequencies
   AF16
      ----CACCGCCCGGTCGCTAAT-------------------------------------     181
cbriggsae     ccatCACCGCCCGGTCGCTAATtattatgcttccggtatctggtggcccacggagtgga      
      ***********************************************************      
 ---------------------------------------------------------------------NM_026450
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_175692
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001037394
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_104594
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_031795
 ---------------------------------------------------------------------NM_115574
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001124041
cbriggsae     ......((((((((((((((..((((........))))..))))))))...)).)))).     0.800 -19.10

cbriggsaechromosome:chrI:3667431:3667489:-1Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_non-coding|NM_175692|A930034L06Rik ## Opposite_strand|Intronic_coding|NM_115574|NAP57 ## {Repeats: no}


block102 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.147nono0.41/0.4127/27/0.000.0
0.0
1
0
1
0
2
3
5arm
1
nd
0.26
2
11nana
  readsmiRBase family seed
seed     ---CAACGAC------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --GCAACGACGATTGAGAGACCAAATATT-----------------------------------------     271
cbriggsae     aaGCAACGACGATTGAGAGACCAAATATTgcggtcaacgcaaatctggagattttagtttttattccttt      
      **********************************************************************      
 --------------------------------------------------------------------------------NM_026450
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001093227
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001024290
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_175692
 --------------------------------------------------------------------------------NM_001087652
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001071291
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001078787
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001109774
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001114303
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001114304
 --------------------------------------------------------------------------------NM_001089360
 --------------------------------------------------------------------------------NM_059581
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_121223
 --------------------------------------------------------------------------------NM_115574
 --------------------------------------------------------------------------------NM_021399
 --------------------------------------------------------------------------------NM_001079883
 --------------------------------------------------------------------------------NM_001853
 --------------------------------------------------------------------------------NM_000393
cbriggsae     (((.((.((.((((((((..(((.((.(((((.....))))))).)))...)))))))).)).)).))).     1.000 -13.40

cbriggsaechromosome:chrI:4032650:4032719:-1Opposite_strand|Intronic_non-coding|NM_026450|Zfp169 ## Same_strand|Intronic_coding|NM_001093227|MGC80275 ## Same_strand|Intronic_non-coding|NM_001024290|Gal3st3 ## Opposite_strand|Intronic_coding|NM_001087652|col18sv-a ## {Repeats: no}


block167 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.554nono0.39/0.3918/18/0.000.0
0.0
1
0
1
0
2
25
3arm
1
nd
0.22
2
11nana
  readsmiRBase family seed
seed     ---------------------------------------------------------------------------------------------GCUGCUA------------     1novel
  lencloning frequencies
   AF16
      --------------------------------------------------------------------------------------------TGCTGCTAATTTGGTTTC--     181
cbriggsae     ttgaaaaaataaacacggaagacactcgtaaataccaaaaaggttctctgtttcaactcctaattatcatcaagccttttttaatttatcacTGCTGCTAATTTGGTTTCaa      
      ****************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001032899
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001107961
cbriggsae     .(((((...((((...((.((.((...((((((...(((((((((...((.................))...)))))))))..))))))...)))).))..)))).))))).     0.930 -12.53

cbriggsaechromosome:chrI:8686991:8687102:-1Same_strand|Intronic_non-coding|NM_001032899|SLC15A1 ## {Repeats: no}


block561 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.019nono0.40/0.4025/25/0.000.0
0.0
2
0
1
0
1
17
5arm
1
nd
0.24
3
21nana
  readsmiRBase family seed
seed     --AUUACGG------------------------------------------------------------------------------------     2novel
  lencloning frequencies
   AF16
      -GATTACGGATTGCAACCATTTACAC-------------------------------------------------------------------     252
cbriggsae     cGATTACGGATTGCAACCATTTACACtgcaaattttgtagtctttgtagtctttgtagtttttgtagtttttgtagactttgcagtcagaatt      
      *********************************************************************************************      
 -------------------------------------------------------------------------------------------------------NM_012655
 -------------------------------------------------------------------------------------------------------NM_001012534
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_075505
 -------------------------------------------------------------------------------------------------------NM_013672
 <<<<<<<<<<<<<<<<<<<<<<<<...............................................................................NM_074173
cbriggsae     .((((...((((((((...(((((((((((((..(((.((.((....)).))...)))..))))))))....)))))..))))))))..))))     0.970 -22.20

cbriggsaechromosome:chrI_random:2969041:2969133:1Opposite_strand|Intronic_non-coding|NM_012655|Sp1 ## Same_strand|Intronic_non-coding|NM_075505|psa-1 ## Opposite_strand|Boundary_non-coding|NM_074173|F23B12.1 ## {Repeats: no}


block863 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.318nono0.39/0.3918/18/0.000.0
0.0
1
0
1
0
2
21
5arm
7
nd
0.17
1
11nana
  readsmiRBase family seed
seed     ---AAUUGAC---------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --CAATTGACACTGAAGAAC-----------------------------------------------------------------------     181
cbriggsae     tcCAATTGACACTGAAGAACtgagtgactacgtcttcggcgtccactcgcctcttgtagtactgttctgcgtcacgtcttatagctttggg      
      *******************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_030641
 -----------------------------------------------------------------------------------------------------NM_075282
 -----------------------------------------------------------------------------------------------------NM_062337
 -----------------------------------------------------------------------------------------------------NM_011780
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_008746
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001044559
 -----------------------------------------------------------------------------------------------------NM_060557
 -----------------------------------------------------------------------------------------------------NM_008026
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_075282
 -----------------------------------------------------------------------------------------------------NM_067080
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_071121
cbriggsae     .((((.(((.((((((((((..(((.((((((.....((((......))))...))))))))))))))...))).)).))).....)))).     0.500 -22.30

cbriggsaechromosome:chrII:1529359:1529449:1Same_strand|Intronic_non-coding|NM_030641|APOL6 ## Opposite_strand|Intronic_non-coding|NM_075282|wrs-1 ## Opposite_strand|Intronic_coding|NM_067080|Y66D12A.21 ## {Repeats: no}


block1020 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.600nono0.58/0.5819/19/0.000.0
0.0
1
0
1
0
0
24
5arm
1
nd
0.11
2
11nana
  readsmiRBase family seed
seed     -GCCGGGG----------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      TGCCGGGGATGAGCAATTG-----------------------------------------------------------------     191
cbriggsae     TGCCGGGGATGAGCAATTGagcatatcactgactgttggtgaggtgactacatttctgaggcttttgtaatttcattatttggt      
      ************************************************************************************      
 ----------------------------------------------------------------------------------------------NM_001087019
 ----------------------------------------------------------------------------------------------NM_001018915
 ----------------------------------------------------------------------------------------------NM_001854
 ----------------------------------------------------------------------------------------------NM_131292
 ----------------------------------------------------------------------------------------------NM_183186
 ----------------------------------------------------------------------------------------------NM_080629
 ----------------------------------------------------------------------------------------------NM_032085
 ----------------------------------------------------------------------------------------------NM_001113224
 ----------------------------------------------------------------------------------------------NM_080630
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001123511
 ----------------------------------------------------------------------------------------------NM_001001135
cbriggsae     .(((((((((((((((..((((...(((..((.....((((((....)).))))))))).))))))))....))))).))))))     0.640 -17.30

cbriggsaechromosome:chrII:10967253:10967336:1Opposite_strand|Intronic_non-coding|NM_001087019|nr2f2 ## Opposite_strand|Intronic_coding|NM_001018915|exo2 ## Same_strand|Intronic_non-coding|NM_001123511|rab7 ## {Repeats: no}


block1319 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.011nono0.47/0.4719/19/0.000.0
0.0
1
0
1
0
2
5
5arm
1
nd
0.26
3
11nana
  readsmiRBase family seed
seed     ---AUGAAAC-------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --AATGAAACCGAGGGATCTG--------------------------------------     191
cbriggsae     aaAATGAAACCGAGGGATCTGgctcaacactttctgacttggattccaacgtttctttt      
      ***********************************************************      
 ---------------------------------------------------------------------NM_001011629
 ---------------------------------------------------------------------NM_172925
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_065286
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001093260
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_009573
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_130279
cbriggsae     .....(((((...(((((((((.(((........))).)))))))))...)))))....     1.000 -15.20

cbriggsaechromosome:chrIII:2263318:2263376:-1Opposite_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## Same_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}


block1564 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.039nono0.44/0.4425/25/0.000.0
0.0
1
0
1
0
3
6
3arm
1
nd
0.20
2
11nana
  readsmiRBase family seed
seed     --------------------------------------------------UUUUUCU--------------------     1novel
  lencloning frequencies
   AF16
      -------------------------------------------------GTTTTTCTGGCTTTAGCCTTTGAGG---     251
cbriggsae     tggctcacggggttttttggtttcagtaaatagaggaacatttttcttcGTTTTTCTGGCTTTAGCCTTTGAGGcgc      
      *****************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_184109
 ---------------------------------------------------------------------------------------NM_013720
 ---------------------------------------------------------------------------------------NM_001085471
 ---------------------------------------------------------------------------------------NM_204577
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_061965
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_075282
 ---------------------------------------------------------------------------------------NM_005197
 ---------------------------------------------------------------------------------------NM_001107146
 ---------------------------------------------------------------------------------------NM_001022613
 ---------------------------------------------------------------------------------------NM_067668
 ---------------------------------------------------------------------------------------NM_001054815
 ---------------------------------------------------------------------------------------NM_001013538
 ---------------------------------------------------------------------------------------NM_028128
 ---------------------------------------------------------------------------------------NM_067174
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_008425
 ---------------------------------------------------------------------------------------NM_000690
cbriggsae     ((.((((.((((((....(((..(((.(((..((((((.....))))))...)))))))))..)))))))))).)).     1.000 -20.60

cbriggsaechromosome:chrIII:12745900:12745976:-1Same_strand|Intronic_coding|NM_184109|Rtl1 ## Opposite_strand|Intronic_non-coding|NM_013720|Mga ## Same_strand|Intronic_non-coding|NM_061965|F08D12.1 ## Opposite_strand|Intronic_coding|NM_001107146|Rfc5 ## {Repeats: no}


block1839 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.034nono0.57/0.5728/28/0.000.0
0.0
1
0
1
0
3
12
3arm
1
nd
0.25
3
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------CGCAGAU-----------------------     1novel
  lencloning frequencies
   AF16
      ----------------------------------------------------------------------------GCGCAGATGGCGCTGTGGTTAGCGTTTT---     281
cbriggsae     tactaaaattttgaaaaacgttcccatcctctcccccgcgcgattggctactacctcgcactcctagtccccagttGCGCAGATGGCGCTGTGGTTAGCGTTTTagt      
      ***********************************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_013720
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001107146
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001054815
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001013538
 ---------------------------------------------------------------------------------------------------------------------NM_070558
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_028128
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_075459
cbriggsae     .((((((((.((((...(((...(((((.........((((((((((..((((...........))))..)))))))))).)))))...)))..)))).))))))))     0.900 -30.30

cbriggsaechromosome:chrIII:13022240:13022346:1Same_strand|Intronic_non-coding|NM_013720|Mga ## Same_strand|Intronic_coding|NM_001107146|Rfc5 ## Opposite_strand|Intronic_non-coding|NM_070558|rho-1 ## {Repeats: no}


block2060 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.103nono0.48/0.4825/25/0.000.0
0.0
1
0
1
0
0
1
3arm
1
nd
0.25
2
11nana
  readsmiRBase family seed
seed     -------------------------------AACGGAU-----------------     1novel
  lencloning frequencies
   AF16
      ------------------------------GAACGGATGGCTTGAGTCAATGTTG     251
cbriggsae     caactgataggcaccaatgtgtttgtaaacGAACGGATGGCTTGAGTCAATGTTG      
      *******************************************************      
 -----------------------------------------------------------------NM_125682
 -----------------------------------------------------------------NM_112886
 -----------------------------------------------------------------NM_020066
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_016802
cbriggsae     ((((((((((((....((.((((((....)))))).)).))))..))))..))))     0.980 -13.30

cbriggsaechromosome:chrIV:3462273:3462327:-1Opposite_strand|Intronic_coding|NM_125682|ARAC10/ATRAC10/ATROP11 ## Opposite_strand|Intronic_non-coding|NM_112886|ATATM ## Same_strand|Intronic_non-coding|NM_016802|Rhoa ## {Repeats: no}


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