logoC.briggsae small RNAs


miR classification

Alignments

other hairpins

novel (77 loci)

block2209 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.051nono0.43/0.4321/21/1.000.0
0.0
1
0
1
0
8
14
5arm
1
nd
0.19
1
11nana
  readsmiRBase family seed
seed     ---------UGGUGGA----------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --------TTGGTGGATTTAGGTCAGGTT---------------------------------------------------------------------------     211
cbriggsae     ttgcttggTTGGTGGATTTAGGTCAGGTTtattcaaacgaatagaaaaaatatcgaaatatatcgtttgatcaacttttatcaaaaatttcactgttctagcaa      
      ********************************************************************************************************      
 ------------------------------------------------------------------------------------------------------------------NM_057270
 ------------------------------------------------------------------------------------------------------------------NM_164773
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001082682
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001001344
cbriggsae     .((((.((..(((((((((.(((.(((((...(((((((((((...............))).))))))))..)))))..))).)))..))))))..)).)))).     0.980 -21.66

cbriggsaechromosome:chrIV:9125090:9125193:-1Opposite_strand|Intronic_coding|NM_057270|LanB1 ## Same_strand|Intronic_non-coding|NM_001082682|4F2LC-5 ## Same_strand|Intronic_coding|NM_001001344|ATP2B3 ## {Repeats: no}


block2294 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.165nono0.40/0.4020/20/1.000.0
0.0
2
0
1
0
6
26
3arm
1
nd
0.15
1
21nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------------------------------------UCCAAAU------------------     2novel
  lencloning frequencies
   AF16
      ----------------------------------------------------------------------------------------------TTCCAAATTACTCAATGCCG------     202
cbriggsae     ttgaaaatcgtcaaatttgaataaattgggagcaaaattttaaaattactgtttcaaactctattgtcagattgtgttaggtgattctgaacaaTTCCAAATTACTCAATGCCGattcaa      
      ************************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001026518
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_067755
 ----------------------------------------------------------------------------------------------------------------------------------NM_001047596
 ----------------------------------------------------------------------------------------------------------------------------------NM_075282
cbriggsae     .(((..((((.((...((((.(((.((((((.......((((.(((((((....((...(((......)))...))...))))))).))))...)))))).))).)))))).))))))).     0.780 -20.80

cbriggsaechromosome:chrIV:12838098:12838217:-1Same_strand|Intronic_coding|NM_001026518|Y105E8A.29 ## Same_strand|Intronic_non-coding|NM_067755|xpc-1 ## Opposite_strand|Intronic_non-coding|NM_001047596|tag-349 ## {Repeats: no}


block2356 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.216nono0.48/0.4821/21/1.000.0
0.0
1
0
1
0
13
12
5arm
1
nd
0.29
3
11nana
  readsmiRBase family seed
seed     --------------UGAAGUG--------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      -------------TTGAAGTGGGCTCAGATCTTG-------------------------------------------------------     211
cbriggsae     tttcaagtttcagTTGAAGTGGGCTCAGATCTTGtatcattttcggcattttgaagaatttcgtatttgatatttcgattttttgaaat      
      *****************************************************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_123965
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_024349
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_019034
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001016369
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001032772
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001040602
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001093711
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001095157
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_199692
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001033835
 ---------------------------------------------------------------------------------------------------NM_001047948
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_175092
 ---------------------------------------------------------------------------------------------------NM_065286
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001123190
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001126828
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001010953
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001127285
cbriggsae     (((((((....((((((((((...((((((..((.....(((((((....)))))))....)).)))))))))))))))).))))))).     0.560 -15.60

cbriggsaechromosome:chrIV:613287:613375:1Same_strand|Intronic_coding|NM_123965|ARAC2 ## Same_strand|Intronic_non-coding|NM_024349|Ak1 ## Opposite_strand|Intronic_coding|NM_001047948|LOC499584 ## Opposite_strand|Intronic_non-coding|NM_065286|Y53G8AR.6 ## {Repeats: no}


block2377 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.339nono0.45/0.4520/20/1.000.0
0.0
2
0
1
0
20
2
3arm
1
nd
0.25
3
21nana
  readsmiRBase family seed
seed     ---------------------------------------------------------UUGACAU--------------------------------     2novel
  lencloning frequencies
   AF16
      --------------------------------------------------------TTTGACATTGGCAGGAATCG--------------------     202
cbriggsae     aatgtttttgatgtttcaatttctagagttaaccagtagttgtgtttcaaaatcaaTTTGACATTGGCAGGAATCGaaattgatttctagaccatt      
      ************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_070458
 ----------------------------------------------------------------------------------------------------------NM_182297
cbriggsae     ((((.(((.((....((((((((..((.((..(((((.((((.(((........))).)))))))))...)).))))))))))..)).))).))))     0.650 -14.70

cbriggsaechromosome:chrIV:1118135:1118230:1Same_strand|Intronic_non-coding|NM_070458|Y73F8A.24 ## Opposite_strand|Intronic_non-coding|NM_182297|B0546.4 ## {Repeats: no}


block2520 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.053nono0.48/0.4821/21/1.000.0
0.0
1
0
1
0
18
8
3arm
1
nd
0.29
2
11nana
  readsmiRBase family seed
seed     --------------------------------------------------------------------GCAUAGU-------------------------------     1novel
  lencloning frequencies
   AF16
      -------------------------------------------------------------------TGCATAGTTCGGTGTCGAATG------------------     211
cbriggsae     tgagttgtaaaaacattttggtttcagatttgtgacaaagaaatatgggaaaatttataattttcagTGCATAGTTCGGTGTCGAATGaaaaaaaattgcacttca      
      **********************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------NM_001105717
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_198022
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_020066
cbriggsae     .(((.((((.....(((((..(((((......(((((..(((.((((.((((((.....))))))....)))).)))..)))))..))))).))))))))).))).     0.890 -21.40

cbriggsaechromosome:chrIV:3297743:3297848:1Opposite_strand|Intronic_non-coding|NM_001105717|Dpysl2 ## Same_strand|Intronic_non-coding|NM_198022|Tnrc6c ## Same_strand|Intronic_coding|NM_020066|FMN2 ## {Repeats: no}


block2658 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.527nono0.40/0.4020/20/1.000.0
0.0
2
0
1
0
6
30
3arm
1
nd
0.25
2
21nana
  readsmiRBase family seed
seed     --------------------------------------------------------------------------------------------CAUUUAA------------------     2novel
  lencloning frequencies
   AF16
      -------------------------------------------------------------------------------------------TCATTTAAGGCTGTATGTGC------     202
cbriggsae     aagataatatccacttaaaatgtttttcaaatcttcaaaatttcccggtttcaccaaacactgaaaaatacaatatttttggattatgtgaTCATTTAAGGCTGTATGTGCatttta      
      *********************************************************************************************************************      
 -------------------------------------------------------------------------------------------------------------------------------NM_066961
cbriggsae     (((((.((((.(((((.(((((....(((....(((((((........(((((........)))))..........))))))).....))).))))).))).)).))))..))))).     0.790 -14.37

cbriggsaechromosome:chrIV:8523222:8523338:1Opposite_strand|Intronic_non-coding|NM_066961|W09D10.4 ## {Repeats: no}


block2660 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.402nono0.43/0.4321/21/1.000.0
0.0
1
0
1
0
20
14
5arm
1
nd
0.24
3
11nana
  readsmiRBase family seed
seed     ---------------------UCUUCGU-------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --------------------TTCTTCGTCCATATACAGCGT------------------------------------------------------------------------     211
cbriggsae     gaattttacaaaatgttcatTTCTTCGTCCATATACAGCGTgcggcaaaagtatggtaacacaagtttcgcgcaagctggtgggcgcaggcgtacttttagtgtcctgaattc      
      *****************************************************************************************************************      
 ---------------------------------------------------------------------------------------------------------------------------NM_066961
cbriggsae     ((((((.(((........((.(((.(((((((...((((.(((.(((((....((....))....))).))))).))))))))))).))).))........)))...))))))     0.640 -26.29

cbriggsaechromosome:chrIV:8556915:8557027:1Opposite_strand|Intronic_non-coding|NM_066961|W09D10.4 ## {Repeats: no}


block2667 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.949nono0.45/0.4520/20/1.000.0
0.0
1
0
1
0
8
13
5arm
1
nd
0.30
3
11nana
  readsmiRBase family seed
seed     ---------GUCAAGC------------------------------------------------------------------------------     1novel
  lencloning frequencies
   AF16
      --------TGTCAAGCAGTTGGAATTGG------------------------------------------------------------------     201
cbriggsae     gcgattatTGTCAAGCAGTTGGAATTGGatgttcgaattctatgattctcggaattgaaccaaattttttgtactcatttgaatgaaatatacg      
      **********************************************************************************************      
 --------------------------------------------------------------------------------------------------------NM_066961
 --------------------------------------------------------------------------------------------------------NM_064619
 --------------------------------------------------------------------------------------------------------NM_001057621
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_068392
cbriggsae     .((..((((.(((((.(((.((((((....((((.((((((.........))))))))))..))))))....)))..)))))....))))..))     0.560 -11.90

cbriggsaechromosome:chrIV:8751142:8751235:1Opposite_strand|Intronic_non-coding|NM_066961|W09D10.4 ## Same_strand|Intronic_coding|NM_068392|elo-5 ## {Repeats: no}


block2682 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.520nono0.45/0.4520/20/1.000.0
0.0
1
0
1
0
15
7
3arm
1
nd
0.20
2
11nana
  readsmiRBase family seed
seed     ------------------------------------------------------------------------------UCGUGAA---------------------------     1novel
  lencloning frequencies
   AF16
      -----------------------------------------------------------------------------TTCGTGAACAGTGTTGGAAC---------------     201
cbriggsae     ttgtattggaaactgactttttgataaaatgctgtttcaaaaatctacaataacagataataagataaaatgtccgaTTCGTGAACAGTGTTGGAACattttctggtgtaat      
      ****************************************************************************************************************      
 --------------------------------------------------------------------------------------------------------------------------NM_001090075
 --------------------------------------------------------------------------------------------------------------------------NM_001082682
 --------------------------------------------------------------------------------------------------------------------------NM_001001344
cbriggsae     ((((((..((((.((...(((..((.....((((.((((..((((.(((.....................)))..))))..))))))))))..))))).))))..)))))).     0.510 -17.10

cbriggsaechromosome:chrIV:9159636:9159747:1Opposite_strand|Intronic_coding|NM_001090075|MGC69046 ## Opposite_strand|Intronic_non-coding|NM_001082682|4F2LC-5 ## {Repeats: no}


block2704 [novel]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.111nono0.43/0.4323/23/1.000.0
0.0
1
0
1
0
5
19
3arm
1
nd
0.09
1
11nana
  readsmiRBase family seed
seed     ---------------------------------------------------------------------------------CAUGCGA--------------------     1novel
  lencloning frequencies
   AF16
      --------------------------------------------------------------------------------GCATGCGAAATGATACCAGTCTT-----     231
cbriggsae     ttgcttgggccaacaagtggtgtgcatgtatcgcaatgccaatgttcgtagatgtggtactcccattgttcaagactagtGCATGCGAAATGATACCAGTCTTggcaa      
      ************************************************************************************************************      
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001069271
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_214466
 ----------------------------------------------------------------------------------------------------------------------NM_182461
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_033380
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_021760
 ----------------------------------------------------------------------------------------------------------------------NM_001022613
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_214466
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_007740
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_134452
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001858
 ----------------------------------------------------------------------------------------------------------------------NM_011448
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001011629
 ----------------------------------------------------------------------------------------------------------------------NM_001105289
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001033832
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_214509
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001033832
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_001011005
 ----------------------------------------------------------------------------------------------------------------------NM_000393
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_007737
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_152888
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_033381
 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++NM_000495
 ----------------------------------------------------------------------------------------------------------------------NM_000090
 ----------------------------------------------------------------------------------------------------------------------NM_001004090
cbriggsae     .((((.((((.......((((((.(((...((((.((((....(((....((((.((....))))))......)))....)))))))).))))))))))))).)))).     0.690 -30.61

cbriggsaechromosome:chrIV:9883982:9884089:1Same_strand|Intronic_coding|NM_001069271|Os09g0271100 ## Opposite_strand|Intronic_coding|NM_182461|set-33 ## Opposite_strand|Intronic_non-coding|NM_011448|Sox9 ## Same_strand|Intronic_non-coding|NM_001011629|Mblk-1 ## {Repeats: no}


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