logoC.elegans small RNAs


miR classification

Alignments

other hairpins

novel_lenNOK (42 loci)

block56 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.133nono0.32/0.3228/28/0.000.0
0.0
1
0
1
0
20
2
3arm
1
nd
0.11
2
11nana
  readsmiRBase family seed
seed-----------------------------------------------------------------------UUUGAAC----------------------------------------1novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------------------TTTTGAACGTGAATAAGCTAGGAATTGT--------------------281
celegansttttatgttttccgagtttttaaatggcaatttttagactttttggtgaataatttagatttatatgagaTTTTGAACGTGAATAAGCTAGGAATTGTtaaatttggaggttttaggg 
 ********************************************************************************************************************** 
celegans.((((...((((((((((......(((((((((((((.(((.((..((.....((((((.((......)).))))))))..)).))))))))))))))))))))))))))...)))).0.920 -21.20

celeganschromosome:I:1030507:1030624:-1intergenic ## {SimpF: WRM0614aH12 1 fosmid,Y34D9A_151.B -1 Expression_profile}


block72 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.545nono0.50/0.5018/18/0.000.0
0.0
1
0
1
0
11
12
5arm
2
nd
0.28
2
11nana
  readsmiRBase family seed
seed------------GUCUCGC----------------------------------------------------------------1novel
  lencloning frequencies
   CE1
 -----------GGTCTCGCAGCGATTTTT------------------------------------------------------181
celegansgaatactggtgGGTCTCGCAGCGATTTTTgaattttttaaataatttttttttttgaaaaattgtcgatttttatgaaattcc 
 *********************************************************************************** 
celegans((((....(((((..(((..(((((((((.((......(((....))).....)).))))))))))))..)))))...)))).0.410 -10.00

celeganschromosome:I:1621125:1621207:-1intergenic ## {Repeats: dust 46431 46435 0 class=dust}


block84 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.208nono0.37/0.3719/19/0.000.0
0.0
1
0
1
0
23
8
3arm
1
nd
0.21
2
11nana
  readsmiRBase family seed
seed------------------------------------------------------------------GGUUUUU----------------------------------1novel
  lencloning frequencies
   CE1
 -----------------------------------------------------------------TGGTTTTTCGCTAGGTTTT-----------------------191
celeganstcagattttgggagacacactcactgaatttttgcgaatattttaggatttctttttgttctcaaTGGTTTTTCGCTAGGTTTTaatgaaaaaagtgtgtgatctgg 
 *********************************************************************************************************** 
celegans.((((((.......(((((((((.((((.(((.(((((.(((..(((((........)))))....)))..))))).))).)))).))).....)))))))))))).0.920 -21.51

celeganschromosome:I:2070767:2070873:-1intergenic


block426 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.024nono0.38/0.3826/26/0.000.0
0.0
1
0
1
0
6
12
3arm
2
nd
0.19
2
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------CUCUUUA------------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------------------------------GCTCTTTATTGAGTGTTCAAATCAGG------     261
celegans     caattccaatgatatcttgaacgtccattgatagcgtcgatagtcgcaaacttgcagttgacaaGCTCTTTATTGAGTGTTCAAATCAGGaaatga      
      ************************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.............................................K07A1.5 K07A1.5 K07A1.5
celegans     ((.((((..((((...(((((((..((.(((.(((((((((....(((....))).))))))..)))..))).))..))))))))))))))).)).     0.980 -24.70

celeganschromosome:I:9590546:9590641:-1intergenic ## {SimpF: WRM0629cA06 -1 fosmid,WRM0634aA12 -1 fosmid,WRM0639cA02 -1 fosmid,WRM065bH01 -1 fosmid,K07A1.5 -1 Expression_profile,WRM0623cA08 -1 fosmid}


block1077 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.024nono0.38/0.3826/26/0.000.0
0.0
1
0
1
0
6
12
3arm
2
nd
0.19
2
11nana
  readsmiRBase family seed
seed     -----------------------------------------------------------------CUCUUUA------------------------     1novel
  lencloning frequencies
   CE1
      ----------------------------------------------------------------GCTCTTTATTGAGTGTTCAAATCAGG------     261
celegans     caattccaatgatatcttgaacgtccattgatagcgtcgatagtcgcaaacttgcagttgacaaGCTCTTTATTGAGTGTTCAAATCAGGaaatga      
      ************************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<.........................................................................C04F12.6 C04F12.6 C04F12.6
celegans     ((.((((..((((...(((((((..((.(((.(((((((((....(((....))).))))))..)))..))).))..))))))))))))))).)).     0.980 -24.70

celeganschromosome:I:9693744:9693839:1intergenic ## {SimpF: WRM0630dC04 1 fosmid,WRM0612dG10 1 fosmid,WRM0637bB03 1 fosmid,WRM064dE10 1 fosmid,WRM0619bF10 1 fosmid}


block1261 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.165nono0.42/0.4219/19/0.000.0
0.0
1
0
1
0
9
6
3arm
1
nd
0.11
1
11nana
  readsmiRBase family seed
seed-----------------------------------------------------------CUUGCAG--------------------1novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------GCTTGCAGTCGAAAAATTG---------191
celegansctgtacttttagtagttttcaagctgcaaaaacttaaaattataactcacatttttacGCTTGCAGTCGAAAAATTGaaaaatagt 
 ************************************************************************************** 
celegans((((..(((((((..(((((..(((((((.....(((((.............)))))...))))))).)))))))))))).)))).0.950 -12.42

celeganschromosome:I:14220490:14220575:1intergenic ## {SimpF: WRM0628dF11 1 fosmid}


block1672 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.166nono0.36/0.3625/25/0.000.0
0.0
2
0
1
0
8
16
5arm
1
nd
0.16
2
21nana
  readsmiRBase family seed
seed     ---------UCAAUCU---------------------------------------------------------------------------------------------------     2novel
  lencloning frequencies
   CE1
      --------GTCAATCTTGAATTGCCAAGTAGTT----------------------------------------------------------------------------------     252
celegans     ggaatatcGTCAATCTTGAATTGCCAAGTAGTTaagtaatgattgaaattgtctttttccgttctgtttcaatatttattgattatttttcatgttttagattcacgtgtaaacc      
      *******************************************************************************************************************      
 <<<<<<<<<<<<<<<<<<<<<<<<.....................................................................................................F09C12.8 F09C12.8 F09C12.8
celegans     ((..((((((.(((((.((((((..((((((((((......((((((((................)))))))).....))))))))))..)).)))).))))).))).)))..))     1.000 -20.49

celeganschromosome:II:5112646:5112760:-1Opposite_strand|Boundary_non-coding|F09C12.8|F09C12.8 ## F09C12.8|protein_coding|F09C12.8|F09C12.8 encodes an ortholog, predicted to be catalytically inactive, of Bombyx mori ecdysteroid phosphate phosphatase (EPP), human STS1 (OMIM:609201) and human UBASH3A (OMIM:605736). F09C12.8 is also paralogous to C. elegans C52E4.7, F53B6.7, F55A11.11, and T07F12.1. [Source: WormBase] ## {SimpF: WRM0613dB07 -1 fosmid,WRM0639aD02 -1 fosmid,WRM0621bD01 -1 fosmid,WRM062cF07 -1 fosmid,WRM0619cA05 -1 fosmid,WRM0623bH01 -1 fosmid,WRM068aD06 -1 fosmid,WRM0616dA04 -1 fosmid,WRM0620bB06 -1 fosmid,WRM0627aE10 -1 fosmid,WRM0619dB08 -1 fosmid,WRM0624aH11 -1 fosmid}


block2022 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.012nono0.40/0.4719/20/0.500.0
0.0
0.0
0.0
1
1
0
0
1
1
0
0
1
8
40
34
5arm
5arm
1
1
nd
nd
0.55
0.21
7
3
21nana
  readsmiRBase family seed
seed     ---------AGGAGUG--------------------------------------------------------------------------------------------------------     1novel
seed     --UGGUAAU---------------------------------------------------------------------------------------------------------------     1novel
  lencloning frequencies
   CE1
      --------TAGGAGTGATGGTACGAAG---------------------------------------------------------------------------------------------     191
      -ATGGTAATAGGAGTGATGGT---------------------------------------------------------------------------------------------------     201
celegans     gATGGTAATAGGAGTGATGGTACGAAGagatggtattggaactgatggtaggaggtatttatgtttgacgtcctcctctgttggaagtggttctcttcgacatgattcttccttttttca      
      ************************************************************************************************************************      
 ...............................................................<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<----F15D4.5 F15D4.5 F15D4.5
celegans     ((.......((((((.(((...((((((((...((((....(((((((.((((((...(((....)))...))))))))))))).))))..)))))))).))).)))))).......)).     1.000 -35.34

celeganschromosome:II:13247491:13247610:-1intergenic ## {Repeats: trf 1 11 0 class=trf} ## {SimpF: WRM0636aG07 -1 fosmid,WRM0637cD09 -1 fosmid}


block2035 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.710nono0.22/0.2218/18/0.000.0
0.0
2
0
1
0
17
9
5arm
1
nd
0.22
3
21nana
  readsmiRBase family seed
seed     ------------------UUGAUUG------------------------------------------------------------------     2novel
  lencloning frequencies
   CE1
      -----------------TTTGATTGAGTTTTTTTG--------------------------------------------------------     182
celegans     ctgaaatagcagggaatTTTGATTGAGTTTTTTTGggaattggaaggttttgaattatgagaaggcatattaatatgtatgggttttgagg      
      *******************************************************************************************      
 <<<<<------------------------------------------------------------------------------------------------ZK131.11b ZK131.11 ZK131.11
celegans     ((.(((...((....((.(((((...(((((((((..((((.((.....)).)))).)))))))))..))))).))...))...))).)).     0.640 -10.20

celeganschromosome:II:13801858:13801948:-1Opposite_strand|Boundary_non-coding|ZK131.11a|ZK131.11 ## Opposite_strand|Intronic_coding|ZK131.11b|ZK131.11 ## ZK131.11|protein_coding|ZK131.11|ZK131.11b [Source:RefSeq_peptide;Acc:NP_872046] ## {SimpF: WRM0617cG02 -1 fosmid,WRM0638dF08 -1 fosmid,WRM068bD11 -1 fosmid}


block2125 [novel_lenNOK]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.723nono0.36/0.3719/22/0.670.0
1.0
3
0
1
0
8
8
5arm
1
nd
0.26
3
31nana
  readsmiRBase family seed
seed     ---------UUCCAAG----------------------------------------------------------------------------------     3novel
  lencloning frequencies
   CE1
      --------GTTCCAAGATGTTGATTTGATG--------------------------------------------------------------------     222
      --------GTTCCAAGATGTTGATTTG-----------------------------------------------------------------------     191
celegans     gtctcattGTTCCAAGATGTTGATTTGATGaagactgattatttactcttttctatctctatttatatcaaaatttgcccttatctttgccccagatc      
      **************************************************************************************************      
 <<<<<<<<<<<<................................................................................................F46F5.9 F46F5.9 F46F5.9
celegans     ((((....((...(((((((((((..((((.(((..((.............))..))).))))...)))))..........)))))).))...)))).     0.530 -9.02

celeganschromosome:II:822830:822927:1intergenic ## {SimpF: WRM0622dC12 1 fosmid,WRM0626dE09 1 fosmid,WRM0627cG11 1 fosmid,F46F5.9 1 Expression_profile,WRM0638dH08 1 fosmid,WRM067dE12 1 fosmid,WRM0626dF08 1 fosmid,WRM0618cG04 1 fosmid,WRM063cA07 1 fosmid,WRM069bC02 1 fosmid}


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