logoC.elegans small RNAs


miR classification

Alignments

other hairpins

novel_lenNOK_shortStem (17 loci)

block3037 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.015nono0.32/0.3225/25/0.000.0
0.0
1
0
1
0
2
35
3arm
1
nd
0.28
3
11nana
  readsmiRBase family seed
seed     --------------------------------------------------------------------------------------------GAUCCAA-------------------     1novel
  lencloning frequencies
   CE1
      -------------------------------------------------------------------------------------------CGATCCAATGTCTTTAGATTTAATG--     251
celegans     agcacttgatcttcgacttttggattgactcttcgagcaagcattctatattcgaaatacttccattgctttcacattccaagaagttcaaCGATCCAATGTCTTTAGATTTAATGct      
      **********************************************************************************************************************      
 .......................................................................................................<<<<<<<<<<<<<<<<<<<<<<<<<C16A3.8 C16A3.8 thoc-2
celegans     ((((...(((((..(((..((((((((...((((((((((......(((.......)))......))))))...........)))).....)))))))).)))...)))))...))))     0.500 -25.20

celeganschromosome:III:6373825:6373942:-1Opposite_strand|Boundary_non-coding|C16A3.8|C16A3.8 ## C16A3.8|protein_coding|thoc-2|Temporarily Assigned Gene name family member (tag-213) [Source:RefSeq_peptide;Acc:NP_498392] ## {SimpF: WRM0640cG10 -1 fosmid,WRM0636aG04 -1 fosmid,WRM0622dB12 -1 fosmid,WRM0614bD12 -1 fosmid,CEOP3856 -1 Operon,C16A3.8 -1 Expression_profile}


block3195 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.575nono0.31/0.3222/26/0.500.0
2.0
2
0
1
0
0
7
3arm
1
nd
0.27
2
21nana
  readsmiRBase family seed
seed-----------------------------------------------------------UUAGACA------------------2novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------GTTAGACAGAGAAATTACGAAT----221
 ----------------------------------------------------------GTTAGACAGAGAAATTACGAATATTG261
celegansaataatcttaatagctccagttagattagttttcgttaccttagcttacgtgcgaaatGTTAGACAGAGAAATTACGAATATTG 
 ************************************************************************************ 
celegans((((.((.((((..(((..(((.(((....((((((...............)))))).))).))).)))..)))).)).)))).0.940 -12.26

celeganschromosome:III:9748859:9748942:-1intergenic ## {SimpF: WRM0611cA11 -1 fosmid,WRM0614bF09 -1 fosmid,WRM0613bB11 -1 fosmid,WRM0626aE07 -1 fosmid,WRM0611bB05 -1 fosmid,WRM0610bH10 -1 fosmid}


block3217 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.182nono0.50/0.5018/18/0.000.0
0.0
2
0
1
0
4
11
3arm
3
nd
0.22
2
21nana
  readsmiRBase family seed
seed--------------------------------------------------UAGUGAU--------------2novel
  lencloning frequencies
   CE1
 -------------------------------------------------TTAGTGATTCACGAGCCG----182
celegansagccgcgccacgtgcctccctgactctggatccgtttccggctcggaacTTAGTGATTCACGAGCCGgtta 
 *********************************************************************** 
celegans(((((.((..((((..((.((((.(((((..(((....))).)))))..)))).))..)))).))))))).0.920 -23.00

celeganschromosome:III:10050750:10050820:-1intergenic ## {SimpF: WRM0631aC05 -1 fosmid,WRM0639bA05 -1 fosmid,WRM0616bB10 -1 fosmid,WRM0628dH06 -1 fosmid,WRM067aA12 -1 fosmid}


block4205 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.061nono0.33/0.3318/18/0.000.0
0.0
1
0
1
0
0
5
3arm
1
nd
0.24
2
11nana
  readsmiRBase family seed
seed-----------------------------------AAGUUGU----------1novel
  lencloning frequencies
   CE1
 ----------------------------------TAAGTTGTCCAAAGGTTT181
celegansgacttgaaggtacaagtttccgtaaaaaatatgaTAAGTTGTCCAAAGGTTT 
 **************************************************** 
celegans(((((...((.((((.((..((((.....))))..)).))))))..))))).1.000 -10.10

celeganschromosome:IV:5203293:5203344:-1intergenic ## {SimpF: WRM0623dD08 -1 fosmid,WRM0616bF04 -1 fosmid,WRM0632cH10 -1 fosmid,WRM062bD12 -1 fosmid,WRM067dF01 -1 fosmid,WRM069cD11 -1 fosmid}


block4323 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.227nono0.37/0.3719/19/0.000.0
0.0
2
0
1
0
0
3
3arm
1
nd
0.28
2
21nana
  readsmiRBase family seed
seed     -------------------------------------AGUCAUA-----------     2novel
  lencloning frequencies
   CE1
      ------------------------------------TAGTCATAGGGGTATATCT     192
celegans     aggatttattttgaattgaacttcattttaagttgaTAGTCATAGGGGTATATCT      
      *******************************************************      
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++C43G2.2 C43G2.2 C43G2.2
celegans     .((((.((((((....(((...(((........)))...)))..)))))).))))     0.990 -8.40

celeganschromosome:IV:6567474:6567528:-1Same_strand|Intronic_coding|C43G2.2|C43G2.2 ## C43G2.2|protein_coding|C43G2.2|C43G2.2 [Source:RefSeq_peptide;Acc:NP_501001] ## {SimpF: WRM0625dB01 -1 fosmid,WRM0631dD07 -1 fosmid}


block4448 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.094nono0.42/0.4219/19/0.000.0
0.0
1
0
1
0
1
7
3arm
1
nd
0.26
2
11nana
  readsmiRBase family seed
seed----------------------------------------------GCGAAAA------------1novel
  lencloning frequencies
   CE1
 ---------------------------------------------TGCGAAAATATAGTGTGGC-191
celegansgtttcattatattcatttaagaggaacgtggaaatagtcgttcaaTGCGAAAATATAGTGTGGCa 
 ***************************************************************** 
celegans((..(((((((((..(((.....(((((..........))))).....))))))))))))..)).0.910 -13.10

celeganschromosome:IV:9160443:9160507:-1intergenic ## {SimpF: WRM0611cD03 -1 fosmid,WRM0612cA03 -1 fosmid,WRM0618bC10 -1 fosmid,WRM063dB02 -1 fosmid,WRM0610bB03 -1 fosmid,WRM0639dG07 -1 fosmid}


block5025 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.336nono0.21/0.2119/19/0.000.0
0.0
1
0
1
0
1
22
3arm
1
nd
0.11
1
11nana
  readsmiRBase family seed
seed-----------------------------------------------------------------------UAAAUUU------------1novel
  lencloning frequencies
   CE1
 ----------------------------------------------------------------------TTAAATTTATTGATCTCAG-191
celegansatttgagcacaaaatctataaaaattgtttcatggtgttcatttattggaactgttagcatcaacatgaaTTAAATTTATTGATCTCAGa 
 ****************************************************************************************** 
celegans.((((((......(((.(((((..(((.((((((..((((........))))............)))))).))).))))).)))))))))0.640 -12.14

celeganschromosome:IV:15981135:15981224:-1intergenic ## {SimpF: WRM0612dA05 -1 fosmid,WRM065bD04 -1 fosmid,WRM0628dG10 -1 fosmid,WRM0615dA03 -1 fosmid,WRM0636cH06 -1 fosmid}


block5645 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.183nono0.28/0.2818/18/0.000.0
0.0
1
0
1
0
0
12
3arm
1
nd
0.29
3
11nana
  readsmiRBase family seed
seed---------------------------------------------------UUUUGUG----------1novel
  lencloning frequencies
   CE1
 --------------------------------------------------TTTTTGTGTGTCCATTTT181
celegansgagaattgatattggtttttgagagaaaaaaaacgaagttttctttccaaTTTTTGTGTGTCCATTTT 
 ******************************************************************** 
celegans.(((((.(((((.((..((.(((((((((.........))))))))).))..))...))))).)))))0.990 -11.30

celeganschromosome:IV:8945591:8945658:1intergenic ## {SimpF: WRM0626cC12 1 fosmid}


block5841 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.210nono0.33/0.3518/20/0.500.0
1.0
2
0
1
0
1
36
5arm
2
nd
0.15
1
21nana
  readsmiRBase family seed
seed--AUUGGAU---------------------------------------------------------------------------------------------------------------2novel
  lencloning frequencies
   CE1
 -TATTGGATTTAGATCTGG-----------------------------------------------------------------------------------------------------181
 -TATTGGATTTAGATCTGGAG---------------------------------------------------------------------------------------------------201
celeganstTATTGGATTTAGATCTGGAGagaacattgttttgaaataaactgacaacttggatgctaaaatcatctgagaaaattataaattttcgaaaaaaaaattttcaaagtcaaaagttggta 
 ************************************************************************************************************************ 
celegans.((((((.(((.(((.((((((........((((((((...........((..((((.......))))..))............))))))))......))))))..))).))).))))))0.400 -16.44

celeganschromosome:IV:13651721:13651840:1intergenic ## {SimpF: WRM067bD01 1 fosmid,WRM065cG01 1 fosmid,WRM0636aH06 1 fosmid,WRM0634dB07 1 fosmid,WRM0633dA12 1 fosmid}


block5885 [novel_lenNOK_shortStem]

Hairpin parameters
miRNArandfoldRNArepGC min/maxlen min/max/mir_range5'var3'varreadsreads editedlibslibs editedbase distanceloop distancepositionlocationsexon distanceunpairedmax bulgetotal readstotal libsdicerdrosha
no0.634nono0.53/0.5519/20/0.500.0
0.5
2
0
1
0
0
16
3arm
1
nd
0.26
1
21nana
  readsmiRBase family seed
seed     -------------------------------------------------------UGAUAUA------------     2novel
  lencloning frequencies
   CE1
      ------------------------------------------------------CTGATATAATGGCGCCGAC-     191
      ------------------------------------------------------CTGATATAATGGCGCCGACG     201
celegans     gtggttcactgtttcagcatcgtgttatttatgcctttgtattttacgtttcaaCTGATATAATGGCGCCGACG      
      **************************************************************************      
 ------------------------------------------------------------------------------------Y37A1B.10 Y37A1B.10 srw-63
celegans     ((((((((.(((.((((...((((......((((....))))..))))......)))).))).))).))).)).     0.630 -12.00

celeganschromosome:IV:14014808:14014881:1Opposite_strand|Intronic_coding|Y37A1B.10|Y37A1B.10 ## Y37A1B.10|protein_coding|srw-63|Serpentine Receptor, class W family member (srw-63) [Source:RefSeq_peptide;Acc:NP_502686] ## {SimpF: WRM0634bF10 1 fosmid,WRM0631dC06 1 fosmid,WRM0619dE12 1 fosmid,WRM067bC04 1 fosmid}


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