candidate miRBase miRNAs
miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK (11 loci)
cel-mir-45
| absolute | CE1 |
| cel-mir-45 5arm | 6 |
| cel-mir-45 3arm | 454 |
| normalized | CE1 |
| cel-mir-45 5arm | 0.004 |
| cel-mir-45 3arm | 0.317 |
sblock14 (miRBase cel-mir-45) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-45 | 0.001 | no | no | 0.39/0.53 | 18/22/0.99 | 0.0 0.0 | 0.0 0.0 | 5 749 | 0 0 | 1 1 | 0 0 | 14 15 | 10 7 | 5arm 3arm | 1 2 | nd nd | 0.11 0.10 | 2 1 | 914 | 1 | -1 | 2 |
| Member of family miR-44/45/61 (seed GACUAGA): cel-mir-61, cel-mir-44, cel-mir-45 |
| reads | miRBase family seed | ||
| seed | ------------------------------------------------------------------------------GACUAGA------------------------------------------------- | 902 | miR-44/45/61 |
| seed | ------------------------------UGGAUGU------------------------------------------------------------------------------------------------- | 6 | novel |
| seed | -------------------------------------------------------------------------------ACUAGAG------------------------------------------------ | 5 | novel |
| seed | ---------------------------------------------------------------------------------UAGAGAC---------------------------------------------- | 1 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| cel-miR-44 | -----------------------------------------------------------------------------TGACTAGAGACACATTCAGCT------------------------------------ | 21 | 749 |
| -----------------------------------------------------------------------------TGACTAGAGACACATTCAGC------------------------------------- | 20 | 122 | |
| -----------------------------------------------------------------------------TGACTAGAGACACATTCAGCTT----------------------------------- | 22 | 27 | |
| -----------------------------CTGGATGTGC--TCGTTAGTC------------------------------------------------------------------------------------ | 19 | 5 | |
| ------------------------------------------------------------------------------GACTAGAGACACATTCAGCT------------------------------------ | 20 | 4 | |
| -----------------------------------------------------------------------------TGACTAGAGACACATTCA--------------------------------------- | 18 | 3 | |
| --------------------------------------------------------------------------------CTAGAGACACATTCAGCT------------------------------------ | 18 | 1 | |
| -----------------------------------------------------------------------------TGACTAGAGACACATTCAG-------------------------------------- | 19 | 1 | |
| -----------------------------CTGGATGTGC--TCGTTAGTCAT---------------------------------------------------------------------------------- | 21 | 1 | |
| ------------------------------------------------------------------------------GACTAGAGACACATTCAGC------------------------------------- | 19 | 1 | |
| celegans | ---------------CACCATGTGCCACGCTGGATGTGC--TCGTTAGTCATAATATCCTCCACAAAGCAAGGACTATGACTAGAGACACATTCAGCTTGGCGC--------------CGAATGCAT------- | ||
| cbriggsae | ---------TTCTGCTAAACAGTGCCACGCTGGATGTGT--TCGTTAGTCATAGTAACCT-CATCAATTCAGGCTTATGACTAGAGACACATTCAGCTTGGCGC--------------CAAAC-TATGCAGAA- | ||
| cjaponica | GTTCCGAGCTGCTCTGAAATCTTGCCACGCTGAATGTGC--TCGTTAGTCATAACCACCCATATCGTCAAGGGCATATGACTAGAGACACATTCAGCTTGGCTCACATTTTCAGTCTTTAAAC----------- | ||
| cbrenneri | -------------TCGGGAAACTGCCACGCTGGATGTGC--TCGTTAGTCATAGTAGCCT--ATCCTGAACGGCCTATGACTAGAGACACATTCAGCTTGGCTC--------------CGA------------- | ||
| ppacificus | -------------GAGTCGCAGCCCCGCTCTGGATGTGTGATC-TTGGTCGTATCCGCGC-AAATGCTCAATGATTATGACTAGAGACACATTCAGCTTGGGGC--------------CGGCTC---------- | ||
| cremanei | --------ACTGTACCAAAACGTGCCACGCTGGATGTGC--TCGTTAGTCATAATAACCT-CATTTAGTAAGGCTTATGACTAGAGACACATTCAGCTTGGCGC--------------CGAAC-TATAAACAGT | ||
| ** * *** ***** ** ** *** ** * * * ************************** * | |||
| celegans | ......((((((.((((((((((( ((..((((((((...((((..........)))).))))))))))).)))))))))).)))))) ......... | 1.000 -41.00 | |
| cbriggsae | .(((((......((((((.((((((((((( (..((((((((((...((( .........))).)))))))))).)))))))))))).)))))) ..... ...))))). | 1.000 -46.64 | |
| cjaponica | (((..(((.....((((((....((((.((((((((((( ((..((((((((....(((..........)))..))))))))))).)))))))))).))))......)))))).)))..))) | 0.913 -43.80 | |
| cbrenneri | (((((.....((((.((((((((((( ((..(((((((((..(((. .........))))))))))))))).)))))))))).)))))) ))) | 0.965 -44.40 | |
| ppacificus | ((((((..((((((..((((((((((..(( .((((((((..((.(( ....))....))..)))))))))).))))))))))..)))))) )))))) | 0.999 -44.40 | |
| cremanei | (((((........((((((.((((((((((( ((..(((((((((...((( .........))).)))))))))))).)))))))))).)))))) ..... .....))))) | 0.994 -42.77 |
| celegans | chromosome:II:11880860:11880955:-1 | intergenic ## {SimpF: WRM0618bC04 -1 fosmid,WRM061cG08 -1 fosmid,WRM064dE11 -1 fosmid,WRM0615cF06 -1 fosmid,WRM0623bB10 -1 fosmid} ## {MIR: cel-mir-45} |
| cbriggsae | chromosome:chrII:8061347:8061452:1 | Opposite_strand|Intronic_coding|NM_001047975 ## Same_strand|Intronic_coding|NM_133464 ## {MIR: cbr-mir-45-2} |
| cjaponica | chromosome:chrUn:98930653:98930773:1 | intergenic |
| cbrenneri | chromosome:chrUn:101670648:101670737:-1 | Same_strand|Intronic_coding|NM_007742 ## Opposite_strand|Intronic_coding|NM_138591 |
| ppacificus | chromosome:chrUn:21366498:21366592:-1 | Opposite_strand|Intronic_coding|NM_001032504 ## Same_strand|Intronic_coding|NM_066966 ## {Repeats: G-rich 6 78 -1 class=Low_complexity} |
| cremanei | chromosome:chrUn:8356876:8356983:-1 | intergenic |
cel-mir-244
| absolute | CE1 |
| cel-mir-244 5arm | 12 |
| cel-mir-244 3arm | 18 |
| normalized | CE1 |
| cel-mir-244 5arm | 0.008 |
| cel-mir-244 3arm | 0.013 |
sblock2 (miRBase cel-mir-244) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-244 | 0.001 | no | no | 0.33/0.40 | 20/24/1.00 | 0.0 0.0 | 1.4 0.0 | 11 17 | 0 0 | 1 1 | 0 0 | 15 22 | 3 6 | 5arm 3arm | 1 1 | nd nd | 0.21 0.25 | 3 2 | 30 | 1 | 2 | 0 |
| reads | miRBase family seed | ||
| seed | -----------------------------------------------------------------------------------ACUGCUU----------------------------------------- | 18 | novel |
| seed | ------------------------------------CUUUGGU---------------------------------------------------------------------------------------- | 12 | miR-244 |
| len | cloning frequencies | ||
| CE1 | |||
| ----------------------------------------------------------------------------------TACTGCTT----TTCAGCTAAAGG------------------------- | 20 | 17 | |
| cel-miR-244 | -----------------------------------TCTTTGGTTGTACA-AAGTGGTATG----------------------------------------------------------------------- | 24 | 6 |
| -----------------------------------TCTTTGGTTGTACA-AAGTGGT-------------------------------------------------------------------------- | 21 | 5 | |
| ----------------------------------------------------------------------------------TACTGCTT----TTCAGCTAAAGGAATT--------------------- | 24 | 1 | |
| -----------------------------------TCTTTGGTTGTACA-AAGTGG--------------------------------------------------------------------------- | 20 | 1 | |
| celegans | ---------------CTCCATATCTCAATC-----TCTTTGGTTGTACA-AAGTGGTATG----GCTCATCGAATAAGCACATACTGCTT----TTCAGCTAAAGGAATTGAGATTTTGTAGGCTTTT--- | ||
| cremanei | -----------------------------------TCTTTGGTGCTAGAAAAGTAATAAC------------TTCATGTGAAGAATTCCT----TCTCACCAAAGG------------------------- | ||
| cbriggsae | --------------CCCAAATTTCTCGATT-----TCTTTGGTTGTACA-AAGTGGTATGGCTCTCTT---------GCTCATACCGCTT----TACAGCTAAAGGAATCGATTGATTTTGG--------- | ||
| cjaponica | ----------------GCCGATTCTCGATC-----TCTTTGGTTGTACA-AAGTGGTATGAGTACTATAAGAGGCA-ATGCATACCGCTT----TTCAACTGAAGGAATCGAGTGTTTGGC---------- | ||
| cbrenneri | ATTCTGATTTTTCCGCCCCATTTCTCGATC-----TCTTTGGTTGTACA-AAGTGGTATGGCAATTTCATTAAAAATGCTCATACCGCTT----TTCAGCTGAAGGAATCGTGTTTGTGGGTAATTAGAAT | ||
| ppacificus | -------------------GATCTTTGACCTTTAATCTTTGGTTTTTGATCTTTGGTGTCTGATTTGTCTGGAATACGATCGTGATGCCGAAGATTGAACCGGAG-------------------------- | ||
| ******** * * * * * * * ** | |||
| celegans | ((.((.((((((((. .(((((((((...( (((..((((( (((.........))).)))))..))) ).)))))))))..))))))))..)).))...... | 1.000 -38.20 | |
| cremanei | .((((((((..(((..((.(((..( (((....)))).))).)) ))))))))))). | 0.705 -13.80 | |
| cbriggsae | ((.(((((..(((((( ((((((((((((.. ((((((((((((...... )).)))))))))) ))))))))))))))))))..))))).)) | 1.000 -45.10 | |
| cjaponica | (((((..((((((. .(((..((((...( ((((((((((....((.....))... ...)))))))))) ).))))..)))..))))))...))))) | 1.000 -41.90 | |
| cbrenneri | (((((((((.....((((((.....((((. .(((..((((...( (((((((((((((.(((.....))).))).)))))))))) ).))))..)))..))))....)).))))))))))))) | 1.000 -47.30 | |
| ppacificus | .................(((((((((..((((((((((((((((.((((.......))))))).)))))))))))))))))))))) | 0.961 -27.50 |
| celegans | chromosome:I:4684317:4684415:-1 | intergenic ## {SimpF: WRM0635aD01 -1 fosmid,WRM065dB07 -1 fosmid} ## {MIR: cel-mir-244} |
| cremanei | chromosome:chrUn:54114870:54115008:-1 | Same_strand|Intronic_coding|NM_071346 ## Opposite_strand|Intronic_coding|NM_070932 |
| cbriggsae | chromosome:chrI:2688433:2688521:1 | Opposite_strand|Intronic_coding|NM_080376 ## Same_strand|Intronic_coding|NM_131292 ## {MIR: cbr-mir-244} |
| cjaponica | chromosome:chrUn:44620221:44620314:-1 | Same_strand|Intronic_coding|NM_143141 |
| cbrenneri | chromosome:chrUn:31651738:31651858:1 | Same_strand|Intronic_coding|NM_203889 |
| ppacificus | chromosome:chrUn:141119355:141119440:-1 | Same_strand|Intronic_coding|NM_001065677 |
cel-mir-43
| absolute | CE1 |
| cel-mir-43 5arm | 1 |
| cel-mir-43 3arm | 26 |
| normalized | CE1 |
| cel-mir-43 5arm | 0.001 |
| cel-mir-43 3arm | 0.018 |
sblock24 (miRBase cel-mir-43) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-43 | 0.001 | no | no | 0.33/0.43 | 19/23/0.96 | 0.0 0.0 | 0.0 0.0 | 1 25 | 0 0 | 1 1 | 0 0 | 20 15 | 5 5 | 5arm 3arm | 1 1 | nd nd | 0.14 0.09 | 1 1 | 27 | 1 | 0 | 2 |
| Located in cluster 2: cel-mir-42, cel-mir-43, cel-mir-44 |
| Member of family miR-43 (seed AUCACAG): cel-mir-2, cel-mir-797, cel-mir-43 |
| reads | miRBase family seed | ||
| seed | ---------------------------------------------------------------------------------------AUCACAG------------------------------------------------------ | 26 | miR-43 |
| seed | ------------------------------------ACAUCAA--------------------------------------------------------------------------------------------------------- | 1 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| cel-miR-43 | --------------------------------------------------------------------------------------TATCACAGTT-----TACTTGCTGTCGC---------------------------------- | 23 | 25 |
| --------------------------------------------------------------------------------------TATCACAGTT-----TACTTGCTG-------------------------------------- | 19 | 1 | |
| -----------------------------------GACATCAAGAAACTAGTGATT-------------------------------------------------------------------------------------------- | 21 | 1 | |
| celegans | ---------------TATTGGCACTAGTCGCCCGTGACATCAAGAAACTAGTGATT-ATGC---CAAACC-------ACAGGGACATATCACAGTT-----TACTTGCTGTCGCGGGCGG---------------TGCTGAGTT---- | ||
| cbriggsae | CATAAGAAAAGAGGCGATT--------CTGCCCGTGACATCAAGATGCTTGTGATT-ATGC---GAAAAT-------GTTGGGACATATCACAGTT-----TACTTGCTGTCGCAGGCGGATTATTGCTATTGCTCATTTTGTG---- | ||
| cjaponica | ----------------------------------GGACCGCAAGAAACTCGTGTTATATGC---CAAATC-------AGTGGGTCATATCACAGTT-----TACTTGCTGTCC----------------------------------- | ||
| cbrenneri | GAGCAGAATGAAAAGTGGTGTCA----CTGCCCGTGATATCAAGGAACTTGTGATTTATGC---CATAACTAACATAACCTCGACATATCACAGTT-----TACTTGCTGTCGCAGGCAGGTGTTACTGAAAAGTCTCGGGTTGATTC | ||
| ppacificus | -----------------------------------GAAAAGGAGATATCAGAGCTTGAT-----CAGGTCT----CTTTCTTAATTTATCACAGTTATTGATATCTTCT--------------------------------------- | ||
| cremanei | ---------------GATT--------CTGCCCGTGACAACAAGAAACTTGTGATT-ATGCCTAGAGAATG----AAGAAGGGACATATCACAGTT-----TACTTGCTGTCGCAGGCGG--------------------TGTC---- | ||
| ** ** * * * ** * ********** ** * ** | |||
| celegans | ..(..((((....(((((((((((.(((((((((.(((((. (((( (..... ....)).)))))))))))) ).)))).)))))))))))) )))..)... | 1.000 -47.00 | |
| cbriggsae | (((((((..((.((((((( (((((.((((((.((((..((.(((((.( (((. ...... .......))))))))))). ..)))).)))))).))))))..))))))....))..))))))) | 0.997 -39.84 | |
| cjaponica | ((((.((((((((((.(((..(((((( (..... ....)).)))))))))))) ).))))).)))) | 1.000 -23.50 | |
| cbrenneri | ((((((..(((....(((((.(( (((((.((((((.((((((((.(((((((((((. .........))))).........))))))))) ).)))).)))))).))))).)).))))).......)))..))).))) | 0.830 -35.60 | |
| ppacificus | ....(((((((((((((((((((( .((((.. ........)))))))).)))).)))))))))))) | 0.928 -16.90 | |
| cremanei | (((. (((((.((((((.((((((((.(((((.( ((((((........ .....))).)))))))))))) ).)))).)))))).))))) .))) | 1.000 -37.32 |
| celegans | chromosome:II:11889826:11889923:1 | intergenic ## {SimpF: WRM0618bC04 1 fosmid,WRM0615cF06 1 fosmid,WRM061cG08 1 fosmid,WRM0623bB10 1 fosmid,WRM064dE11 1 fosmid} ## {MIR: cel-mir-43} |
| cbriggsae | chromosome:chrII:8049403:8049522:-1 | Same_strand|Intronic_coding|NM_001047975 ## Opposite_strand|Intronic_coding|NM_133464 ## {MIR: cbr-mir-43} |
| cjaponica | chromosome:chrUn:98919132:98919269:-1 | intergenic |
| cbrenneri | chromosome:chrUn:101676581:101676716:1 | Opposite_strand|Intronic_coding|NM_007742 ## Same_strand|Intronic_coding|NM_138591 |
| ppacificus | chromosome:chrUn:65292805:65292869:-1 | Same_strand|Intronic_coding|NM_001065794 ## Opposite_strand|Intronic_coding|NM_001087971 |
| cremanei | chromosome:chrUn:8362216:8362306:1 | intergenic |
cel-mir-231
| absolute | CE1 |
| cel-mir-231 5arm | 2 |
| cel-mir-231 3arm | 24 |
| normalized | CE1 |
| cel-mir-231 5arm | 0.001 |
| cel-mir-231 3arm | 0.017 |
sblock27 (miRBase cel-mir-231) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-231 | 0.001 | no | no | 0.38/0.50 | 20/24/1.00 | 0.0 0.0 | 0.5 0.8 | 2 24 | 0 0 | 1 1 | 0 0 | 17 17 | 5 9 | 5arm 3arm | 1 1 | nd nd | 0.14 0.23 | 2 2 | 26 | 1 | 1 | 0 |
| Member of family miR-231/787 (seed AAGCUCG): cel-mir-231, cel-mir-787 |
| reads | miRBase family seed | ||
| seed | ----------------------------------------------------------------------AAGCUCG----------------------------------------------- | 24 | miR-231/787 |
| seed | ---------------------------UGACUGU------------------------------------------------------------------------------------------ | 2 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| ---------------------------------------------------------------------TAAGCTCGTGATCAACAGGCAG--------------------------------- | 22 | 15 | |
| ---------------------------------------------------------------------TAAGCTCGTGATCAACAGGC----------------------------------- | 20 | 9 | |
| --------------------------CTGACTGTTTCAAAAGCTTG------------------------------------------------------------------------------ | 20 | 1 | |
| --------------------------CTGACTGTTTCAAAAGCTTGT----------------------------------------------------------------------------- | 21 | 1 | |
| cel-miR-231 | ---------------------------------------------------------------------TAAGCTCGTGATCAACAGGCAGAA------------------------------- | 24 | - |
| celegans | --------TAGCACCAC-AGGTTGTTCTGACTGTTTCAAAAGCTTGTAGTATCTTAATAAATAAACATATAAGCTCGTGATCAACAGGCAGAACAACTCGGTTTTGTG---------------- | ||
| cbriggsae | TTTGCTACTAGCACCTCAATGTTGTTCTGTCTGTTTCCATAGCTTATATTGT-------AAGGTACTTATAAGCTCGTGAACAACAGGCAGGACAACTGGAAGTGGTGTTTTTTTTCAGGCAGG | ||
| cjaponica | ---------CGCACCCC-TTGTGGTTCTGACTGTTTCAGTAGCTTATAGC---------CGTGGGCGTATAAGCTCGTGATCAACAGGCAGGACCACTTGGAAGTGTG---------------- | ||
| cbrenneri | --------------------------CTGACTGTTTCAAAAGCTTATATTGTTCGTTCAAAGTTACTTATAAGCTCGTGATCAACAGGCAG--------------------------------- | ||
| cremanei | -----ATCGAGCACCCCGATGTTGTTCTGACTGTTTCCATAGCTTATATTGTCTC----AAAATGCATATAAGCTCGTGAACAACAGGCAGGACAACTGGTCTTTTTGGTGTGCATTTTGAT-- | ||
| *** ******* ***** ** * ************* ********** | |||
| celegans | ..(((..(( .((((((((((.((((((((..((((((((.(((........)))....))))))))..)))..))))).))))))))))..))..))). | 1.000 -32.60 | |
| cbriggsae | .(((((...((((((((...(((((((((((((((..(((((((((((..(( (...))).)))))))).)))...)))))))))))))))..))...))))))........))))). | 0.995 -42.70 | |
| cjaponica | (((((.(( ..(((((((((.((((((((..(((((((((( (...))).))))))))..)))..))))).)))))))))..))..))))) | 1.000 -43.10 | |
| cbrenneri | (((.((((((((..((((((((..((............)).))))))))..)))..))))).))) | 0.999 -17.20 | |
| cremanei | (((((((((.((((.(((((((((.(((((..(((((((((((.(((... .....))))))))))).)))...))))).)))))))))........)))).))))...))))) | 0.996 -38.00 |
| celegans | chromosome:III:7544981:7545079:-1 | intergenic ## {SimpF: WRM0636cE06 -1 fosmid,WRM0622cC06 -1 fosmid,WRM0630bD02 -1 fosmid,WRM0616aE11 -1 fosmid,WRM0627cC08 -1 fosmid,WRM0612cA07 -1 fosmid,WRM068bF09 -1 fosmid} ## {MIR: cel-mir-231} |
| cbriggsae | chromosome:chrIII:9825061:9825177:1 | Opposite_strand|Intronic_coding|NM_001022613 ## Same_strand|Intronic_coding|NM_065267 ## {MIR: cbr-mir-231} |
| cjaponica | chromosome:chrUn:140689401:140689489:-1 | intergenic |
| cbrenneri | chromosome:chrUn:17428268:17428406:1 | Same_strand|Intronic_coding|NM_209426 |
| cremanei | chromosome:chrUn:5285616:5285728:1 | intergenic |
cel-mir-65
| absolute | CE1 |
| cel-mir-65 5arm | 1732 |
| cel-mir-65 3arm | 16 |
| normalized | CE1 |
| cel-mir-65 5arm | 1.210 |
| cel-mir-65 3arm | 0.011 |
sblock30 (miRBase cel-mir-65) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-65 | 0.001 | no | no | 0.39/0.64 | 18/23/0.99 | 0.0 0.0 | 0.0 0.0 | 1687 16 | 0 0 | 1 1 | 0 0 | 17 21 | 7 7 | 5arm 3arm | 1 1 | nd nd | 0.24 0.23 | 2 1 | 1748 | 1 | 0 | 2 |
| Located in cluster 3: cel-mir-229, cel-mir-64, cel-mir-65, cel-mir-66 |
| Member of family miR-64 (seed AUGACAC): cel-mir-64, cel-mir-229, cel-mir-65, cel-mir-66, cel-mir-63 |
| reads | miRBase family seed | ||
| seed | --------------------------------------AUGACAC------------------------------------------------------------------------------------------------------- | 1715 | miR-64 |
| seed | ---------------------------------------------------------------------------------------UGCUACG------------------------------------------------------ | 16 | novel |
| seed | ------------------------------------------CACUGAA--------------------------------------------------------------------------------------------------- | 9 | novel |
| seed | ---------------------------------------UGACACU------------------------------------------------------------------------------------------------------ | 8 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| -------------------------------------TATGACACTGAAGCGTAA-CCG----------------------------------------------------------------------------------------- | 21 | 1687 | |
| --------------------------------------------------------------------------------------CTGCTACGCGCAGTGCCATGCT---------------------------------------- | 22 | 16 | |
| -------------------------------------TATGACACTGAAGCGTAA-CC------------------------------------------------------------------------------------------ | 20 | 9 | |
| -----------------------------------------ACACTGAAGCGTAA-CCGAA--------------------------------------------------------------------------------------- | 19 | 9 | |
| cel-miR-65 | -------------------------------------TATGACACTGAAGCGTAA-CCGAA--------------------------------------------------------------------------------------- | 23 | 9 |
| --------------------------------------ATGACACTGAAGCGTAA-CCGA---------------------------------------------------------------------------------------- | 21 | 8 | |
| -------------------------------------TATGACACTGAAGCGTAA-CCGA---------------------------------------------------------------------------------------- | 22 | 4 | |
| -------------------------------------TATGACACTGAAGCGTAA--------------------------------------------------------------------------------------------- | 18 | 4 | |
| -------------------------------------TATGACACTGAAGCGTAA-C------------------------------------------------------------------------------------------- | 19 | 2 | |
| celegans | --------------------ATGGAGCCTTCGCCGATTATGACACTGAAGCGTAA-CCGAAC--------ACCATATTTTGAGATTCTGCTACGCGCAGTGCCATGCTCGGCGCGTTGGCTCC-------ATTAAA------------ | ||
| cbriggsae | TAAGGTCC------------TAAAGACCCTCACCAATCATGACACTGAAGCGGGA-ATGGA---AGCGTAGTCAGATTGC-AATTCCTACCGGGTTCAGTGTCATACTTGGTGCG---------------GATGAGTCT--------- | ||
| cbrenneri | --------------------CTGGG--CCTCGCCGATTATGACACTTAAGCATAG-GTGGACCATTCAAGACCATA-----GGATCCAGCTACGCTAAGTGGAATAGTCGGCGAG-TGCCTGG-------AGCA-------------- | ||
| cremanei | CGAGTGCCCCCATACATTAACCAGAGGCCTCGCCGAATATGACACTGACGCTTAATATGGACCGATCTCCCCC--------GGATCCATAAAAGCTCAGTGTCAAACTCGGCGAG-TGCCCCGCCCCCTAATTGTATTCCGCCGTTCG | ||
| * ** ** * ******** * ** * * * * * * **** * * ** * * | |||
| celegans | ((((((((..((((((.((((.(((((..(((((. (.(((. ..((.....))...))).).))))).))))).)))).))))))....)))))) )).... | 1.000 -43.80 | |
| cbriggsae | ........ ...((((((.((((((..(((((((((((.(((.. ..((( (..(((((...))))) ..))))..)))..)))))))))))..)))))).) )....)))) | 0.844 -40.20 | |
| cbrenneri | ((((( (((((((((((((..(((((.(((.((( .((((((............. )).)))).))).))))))))..)))))))))))) .)))))) .... | 1.000 -52.72 | |
| cremanei | ((((((.....(((((.........(((((((((((...(((((((((.((((..(((((((((........) )).)))))).)))))))))))))...)))))))) .)))............))))).....)))))) | 0.983 -54.00 |
| celegans | chromosome:III:2172990:2173089:1 | intergenic ## {MIR: cel-mir-65} |
| cbriggsae | chromosome:chrIII:218507:218613:-1 | Same_strand|Intronic_coding|NM_001102902 ## Opposite_strand|Intronic_coding|NM_001077612 |
| cbrenneri | chromosome:chrUn:131005919:131006016:-1 | intergenic ## {SimpF: trf,trf} |
| cremanei | chromosome:chrUn:10328993:10329131:1 | intergenic |
cel-mir-66
| absolute | CE1 |
| cel-mir-66 5arm | 3140 |
| cel-mir-66 3arm | 4 |
| normalized | CE1 |
| cel-mir-66 5arm | 2.194 |
| cel-mir-66 3arm | 0.003 |
sblock31 (miRBase cel-mir-66) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-66 | 0.001 | no | no | 0.38/0.45 | 18/24/0.98 | 0.0 0.8 | 0.0 3.0 | 2870 4 | 0 0 | 1 1 | 0 0 | 16 19 | 2 2 | 5arm 3arm | 1 1 | nd nd | 0.14 0.06 | 1 1 | 3144 | 1 | 0 | 1 |
| Located in cluster 3: cel-mir-229, cel-mir-64, cel-mir-65, cel-mir-66 |
| Member of family miR-64 (seed AUGACAC): cel-mir-64, cel-mir-229, cel-mir-65, cel-mir-66, cel-mir-63 |
| reads | miRBase family seed | ||
| seed | ----------------------------------AUGACAC-------------------------------------------------------------------------------------------- | 3057 | miR-64 |
| seed | -----------------------------------UGACACU------------------------------------------------------------------------------------------- | 39 | novel |
| seed | --------------------------------------CACUGAU---------------------------------------------------------------------------------------- | 38 | novel |
| seed | ------------------------------------GACACUG------------------------------------------------------------------------------------------ | 4 | novel |
| seed | ---------------------------------CAUGACA--------------------------------------------------------------------------------------------- | 2 | novel |
| seed | ----------------------------------------------------------------------------------AAAUUCC-------------------------------------------- | 2 | novel |
| seed | -----------------------------------------------------------------------------------AAUUCCU------------------------------------------- | 1 | novel |
| seed | ------------------------------------------------------------------------------------AUUCCUA------------------------------------------ | 1 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| ---------------------------------CATGACACTGATTAG--GGATGTG---------------------------------------------------------------------------- | 22 | 2870 | |
| ---------------------------------CATGACACTGATTAG--GGATGTGA----T---------------------------------------------------------------------- | 24 | 117 | |
| -------------------------------------ACACTGATTAG--GGATGTGA--------------------------------------------------------------------------- | 19 | 35 | |
| ---------------------------------CATGACACTGATTAG--GGAT------------------------------------------------------------------------------- | 19 | 27 | |
| ----------------------------------ATGACACTGATTAG--GGATGTGA--------------------------------------------------------------------------- | 22 | 26 | |
| ---------------------------------CATGACACTGATTAG--GGATGT----------------------------------------------------------------------------- | 21 | 15 | |
| ---------------------------------CATGACACTGATTAG--GGATG------------------------------------------------------------------------------ | 20 | 12 | |
| ----------------------------------ATGACACTGATTAG--GGATGTG---------------------------------------------------------------------------- | 21 | 12 | |
| cel-miR-66 | ---------------------------------CATGACACTGATTAG--GGATGTGA--------------------------------------------------------------------------- | 23 | 9 |
| ---------------------------------CATGACACTGATTAG--GGA-------------------------------------------------------------------------------- | 18 | 7 | |
| -----------------------------------TGACACTGATTAG--GGATGTG---------------------------------------------------------------------------- | 20 | 4 | |
| -------------------------------------ACACTGATTAG--GGATGTG---------------------------------------------------------------------------- | 18 | 2 | |
| ---------------------------------------------------------------------------------CAAATTCCTAACGGTGTCAAAC------------------------------ | 22 | 1 | |
| -------------------------------------ACACTGATTAG--GGATGTGA----T---------------------------------------------------------------------- | 20 | 1 | |
| -----------------------------------------------------------------------------------AATTCCTAACGGTGTCAAAC------------------------------ | 20 | 1 | |
| ----------------------------------------------------------------------------------AAATTCCTAACGGTGTCAAAC------------------------------ | 21 | 1 | |
| --------------------------------ACATGACACTGATTAG--GG--------------------------------------------------------------------------------- | 18 | 1 | |
| ----------------------------------ATGACACTGATTAG--GGATGT----------------------------------------------------------------------------- | 20 | 1 | |
| ---------------------------------------------------------------------------------CAAATTCCTAACGGTGTC---------------------------------- | 18 | 1 | |
| --------------------------------ACATGACACTGATTAG--GGATGTG---------------------------------------------------------------------------- | 23 | 1 | |
| celegans | --------------CCACAAAA---ATGCCATACATGACACTGATTAG--GGATGTGA----TGAATGTTAAGATCCCGATCAAATTCCTAACGGTGTCAAACATGGC---GTATGTGGTTGTAG-------- | ||
| cremanei | ---------------------------------CATGACACACTCTCA--AAGTTGAACAATTTTAACTGAAAAC---GTTCAACCTTTTGAC-CTGTACTGTACAAT------------------------- | ||
| cbrenneri | GGGACCTAGGCCGCCGACAGAACAGGTGCCAACCATGACACTGATAAA--TAGTTTGA----CGCGACAGGAAAT---GATCAAATATTTCTCGGTGTCAAGACTGGCTAGTTCTCTTGGTGTGAGCCGTCCC | ||
| cjaponica | ---------------------------------AATGACACTTTTGCGTCTTGTTTGA----TTTACAACAAAAT-----GCGATGAGTCGTCGTT------------------------------------- | ||
| ppacificus | ----------------TCAGTCCGCTGCCCTTTTATGACACTGACCCCTCAATGCGGATG--TATAACTGGAGAT----ACCGCATTGTGGGCAGTGTCATCCAAGGG-------CTGAGAATGA-------- | ||
| ******* * * * * * * | |||
| celegans | (((((... (((((((...((((((((.(((( ((((.((( (................)))).))))))))))))))))...))))) )).)))))...... | 1.000 -37.49 | |
| cremanei | ..(((((.((..((( (((((((((..((((....)))).. )))))))..))))). ..))..))).)).. | 0.954 -11.10 | |
| cbrenneri | (((((...(((((((((.(((((....((((....(((((((((.((( (.(((((( ((..........) ).)))))))))).)))))))))....))))..))))).))))))...)))))))) | 0.967 -46.50 | |
| cjaponica | ((((((((((((((((.(((((... .....))))).)) )))).)))).)))))) | 1.000 -16.30 | |
| ppacificus | (((.((....((((((..(((((((((.(((..((((((((.(( (..........)) ))))))))).))))))))))))..))))) )...)).))) | 0.997 -44.70 |
| celegans | chromosome:III:2173096:2173194:1 | intergenic ## {MIR: cel-mir-66} |
| cremanei | chromosome:chrUn:140364416:140364554:-1 | Same_strand|Intronic_coding|NM_182407 |
| cbrenneri | chromosome:chrUn:123881332:123881455:1 | intergenic |
| cjaponica | chromosome:chrUn:7639001:7639139:-1 | Opposite_strand|Intronic_coding|NM_001071380 |
| ppacificus | chromosome:chrUn:95556299:95556394:1 | Same_strand|Intronic_coding|NM_175692 |
cel-mir-83
| absolute | CE1 |
| cel-mir-83 5arm | 2 |
| cel-mir-83 3arm | 88 |
| normalized | CE1 |
| cel-mir-83 5arm | 0.001 |
| cel-mir-83 3arm | 0.061 |
sblock46 (miRBase cel-mir-83) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-83 | 0.008 | no | no | 0.27/0.32 | 19/22/0.95 | 0.0 0.0 | 0.0 0.0 | 2 81 | 0 0 | 1 1 | 0 0 | 16 18 | 5 9 | 5arm 3arm | 1 1 | nd nd | 0.14 0.10 | 1 1 | 90 | 1 | 1 | 0 |
| Member of family miR-49/83 (seed AGCACCA): cel-mir-49, cel-mir-83 |
| reads | miRBase family seed | ||
| seed | --------------------------------------------------------------AGCACCA------------------------------- | 88 | miR-49/83 |
| seed | -----------------CUGAAUU---------------------------------------------------------------------------- | 2 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| -------------------------------------------------------------TAGCACCAT-ATAAATTCAGT------------------ | 20 | 81 | |
| -------------------------------------------------------------TAGCACCAT-ATAAATTCAG------------------- | 19 | 5 | |
| ----------------ACTGAATTTATGTGTGTACTT-G------------------------------------------------------------- | 22 | 2 | |
| cel-miR-83 | -------------------------------------------------------------TAGCACCAT-ATAAATTCAGTAA---------------- | 22 | 1 |
| -------------------------------------------------------------TAGCACCAT-ATAAATTCAGTA----------------- | 21 | 1 | |
| celegans | AGCACCACTCGGAACCACTGAATTTATGTGTGTACTT-GACGGCCAACAAGAGCATCGATCTAGCACCAT-ATAAATTCAGTAATTTCGCGTCGAGAGCT | ||
| cbriggsae | ----------------ACTGAGTTTATGTGTGTACTT-GACGGCG-ATCAGAGCAACGATCTAGCACCAT-ATAAATTCAGT------------------ | ||
| cjaponica | ----------------ACTGAGTTTACGTGTGTGCTT-GACGGCCTTCTCGAGCAACGATCTAGCACCAT-ATAAATTCAGT------------------ | ||
| cbrenneri | ---------CGGAAAAACTGAGTTTATTTGAGTACTTAGACGGCC-ATTAGAGCAACGATCTAGCACCAT-ATAAATTCAGTATTTTCGTGGATGA---- | ||
| ppacificus | --------ACGGTACCATTG---CTCTCTGTGCTTTGGGAC--------AGATCAA------AGCACCATAATGATTACGGT------------------ | ||
| cremanei | ---------CGGAAAAACTGAGTTTATGTGTGTACTT-GACGGCC-ACTCGAGCAACGATCTAGCACCAT-ATAAATTCAGTATTTTCGTGGAGAGAG-- | ||
| * ** * ** * * *** ** ** ******** ** * * * ** | |||
| celegans | (((.((((.(((((..((((((((((((((.((.((. ((((((........))..)).)).)).))))) )))))))))))..))))).)).).).))) | 1.000 -28.50 | |
| cbriggsae | ((((((((((((((.((.((. ((((((. ......))..)).)).)).))))) ))))))))))) | 0.975 -20.70 | |
| cjaponica | ((((((((((..((.(((((. ((((..(((...)))...)).)).))))))). .)))))))))) | 1.000 -22.80 | |
| cbrenneri | ((((((.(((((((((((.((.((.((.(((((((. ......))..)).))))).)))). ))))))))))).))))))....... | 0.995 -22.70 | |
| ppacificus | ((.(((.((((( ......(((((((((... ...)))) )))))..)))))..))).)) | 0.983 -14.40 | |
| cremanei | ((((((.((((((((((((((.((.((. ((((((. ......))..)).)).)).))))) ))))))))))).))))))......... | 0.985 -25.90 |
| celegans | chromosome:IV:7841614:7841711:1 | intergenic ## {SimpF: WRM0633aF09 1 fosmid,WRM0620aE05 1 fosmid,WRM0616bH10 1 fosmid,WRM0621cH03 1 fosmid,WRM061bD09 1 fosmid,WRM0635cG10 1 fosmid} ## {MIR: cel-mir-83} |
| cbriggsae | chromosome:chrIV:10882730:10882867:-1 | Opposite_strand|Intronic_coding|NM_001014737 ## Same_strand|Intronic_coding|NM_001030400 ## {MIR: cbr-mir-83} |
| cjaponica | chromosome:chrUn:113084146:113084283:-1 | intergenic ## {SimpF: trf} |
| cbrenneri | chromosome:chrUn:82234152:82234236:-1 | Same_strand|Intronic_coding|NM_001083844 |
| ppacificus | chromosome:chrUn:173961248:173961385:1 | Opposite_strand|Intronic_coding|NM_067212 |
| cremanei | chromosome:chrUn:43807341:43807426:-1 | intergenic |
cel-mir-34
| absolute | CE1 |
| cel-mir-34 5arm | 341 |
| cel-mir-34 3arm | 2 |
| normalized | CE1 |
| cel-mir-34 5arm | 0.238 |
| cel-mir-34 3arm | 0.001 |
sblock61 (miRBase cel-mir-34) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-34 | 0.004 | no | no | 0.50/0.61 | 18/22/0.99 | 0.0 0.0 | 0.0 0.0 | 307 2 | 0 0 | 1 1 | 0 0 | 15 27 | 2 5 | 5arm 3arm | 1 1 | nd nd | 0.14 0.17 | 1 2 | 343 | 1 | 2 | -1 |
| reads | miRBase family seed | ||
| seed | --------------------------GGCAGUG--------------------------------------------------------------------------------------------- | 340 | miR-34 |
| seed | ----------------------------------------------------------------CGGCUAC------------------------------------------------------- | 2 | novel |
| seed | ------------------------------GUGUGGU----------------------------------------------------------------------------------------- | 1 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| cel-miR-34 | -------------------------AGGCAGTGTGGTTAGCTGGTTG------------------------------------------------------------------------------- | 22 | 307 |
| -------------------------AGGCAGTGTGGTTAGCTGGTT-------------------------------------------------------------------------------- | 21 | 29 | |
| ---------------------------------------------------------------ACGGCTAC--------CTTCACTGCC------------------------------------- | 18 | 2 | |
| -------------------------AGGCAGTGTGGTTAGCTGGT--------------------------------------------------------------------------------- | 20 | 2 | |
| -------------------------AGGCAGTGTGGTTAGCTG----------------------------------------------------------------------------------- | 18 | 1 | |
| -----------------------------AGTGTGGTTAGCTGGTTG------------------------------------------------------------------------------- | 18 | 1 | |
| -------------------------AGGCAGTGTGGTTAGCTGG---------------------------------------------------------------------------------- | 19 | 1 | |
| celegans | ----------CGGACAATGCTCGAGAGGCAGTGTGGTTAGCTGGTTGCATATTTC-CTTGACAACGGCTAC--------CTTCACTGCCACCCCGAACATGTCGTCCATCTTTGAA---------- | ||
| cbriggsae | -------------------------AGGCAGTGTGGTTAGCTGGTTGCATACACAGGTTGACAACGGCTAC--------CTTCACTGCCA------------------------------------ | ||
| cjaponica | CTCTCCACAATGGACGGTGCTCGGGAGGCAGTGTGGTTAGCTGGTTGCATGATGT-TTTGACAACGGCTAC--------CTTCACTGCCACCCCGATCATGTTGTCCATCTTTGAACATTGGTGAG | ||
| cbrenneri | -------------------------AGGCAGTGTGGTTAGCTGGTTGCATACTGACATTGACAACGGCTAC--------CTTCACTGCCA------------------------------------ | ||
| ppacificus | -------------------------GGGCAGTGTGTTTG--TGATGCCATCTATTTCAGCACAATGGCAACATCGAGGACTTCATTGC-------------TCATTTTTTTTGGCA---------- | ||
| cremanei | -----------GGACGGTGCTCGAGAGGCAGTGTGGTTAGCTGGTTGCATATTGA-ATTGACAACGGCTAC--------CTTCACTGCCACCCCGAACATGTAGTCC------------------- | ||
| ********* ** ** * *** **** *** ** ***** *** | |||
| celegans | .((((.(((.(((.(.(((((((.(((.(((((.(((((...... ..)).)))))))))) )..))))))).)..))).)))...))))......... | 1.000 -37.00 | |
| cbriggsae | .(((((((.((.(((((.((((((.((....)))).)))))))))) )..))))))). | 1.000 -26.10 | |
| cjaponica | (((.(((((((((((((((.(((((.(((((((.((.(((((.((((((...... ..)).)))))))))) )..)))))))..))))).)))..)))))))...)).....))).))) | 0.965 -48.50 | |
| cbrenneri | .(((((((.((.(((((.((((((.........)).)))))))))) )..))))))). | 1.000 -25.70 | |
| ppacificus | ((((((((.(((.. (((((((((.............))))))...)))..)))..)))))) ))............. | 0.995 -21.72 | |
| cremanei | ((((.(((.(((...(((((((.((.(((((.((((((...... ..)).)))))))))) )..)))))))....))).)))...)))) | 1.000 -34.70 |
| celegans | chromosome:X:2969744:2969840:-1 | intergenic ## {SimpF: WRM0618bF01 -1 fosmid,WRM0614aG02 -1 fosmid} ## {MIR: cel-mir-34} |
| cbriggsae | chromosome:chrX:3899317:3899453:1 | Opposite_strand|Intronic_coding|NM_076104 ## Same_strand|Intronic_coding|NM_181850 ## {MIR: cbr-mir-34} |
| cjaponica | chromosome:chrUn:18910363:18910479:1 | Opposite_strand|Intronic_coding|NM_010452 |
| cbrenneri | chromosome:chrUn:541727:541863:1 | intergenic |
| ppacificus | chromosome:chrUn:134082778:134082853:1 | intergenic |
| cremanei | chromosome:chrUn:33757035:33757121:1 | Opposite_strand|Intronic_coding|NM_001107657 |
cel-mir-56
| absolute | CE1 |
| cel-mir-56 3arm | 798 |
| normalized | CE1 |
| cel-mir-56 3arm | 0.557 |
sblock62 (miRBase cel-mir-56) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-56 | 0.001 | no | no | 0.46/0.53 | 18/24/0.99 | nd 0.0 | nd 0.9 | 0 781 | 0 0 | 0 1 | 0 0 | 17 15 | 5 6 | 5arm 3arm | 1 1 | nd nd | 0.30 0.23 | 3 2 | 798 | 1 | 0 | 2 |
| Located in cluster 7: cel-mir-56, cel-mir-55, cel-mir-54 |
| Member of family miR-51/52/55 (seed ACCCGUA): cel-mir-53, cel-mir-51, cel-mir-55, cel-mir-54, cel-mir-56, cel-mir-52 |
| reads | miRBase family seed | ||
| seed | -----------------------------------------------------------------------------------ACCCGUA------------------------------------------------- | 789 | miR-51/52/55 |
| seed | ------------------------------------------------------------------------------------CCCGUAA------------------------------------------------ | 8 | novel |
| seed | --------------------------------------------------------------------------------------CGUAAUG---------------------------------------------- | 1 | novel |
| seed | --------------------------------------GGCGGAU---------------------------------------------------------------------------------------------- | 0 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| cel-miR-56 | ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGCTGAG----------------------------------- | 22 | 416 |
| ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGCTG------------------------------------- | 20 | 365 | |
| ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGCTGAGAA--------------------------------- | 24 | 3 | |
| -----------------------------------------------------------------------------------ACCCGTAATGTTTCCGCTGAGA---------------------------------- | 22 | 2 | |
| -----------------------------------------------------------------------------------ACCCGTAATGTTTCCGCTGA------------------------------------ | 20 | 2 | |
| ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGCTGAGA---------------------------------- | 23 | 2 | |
| -----------------------------------------------------------------------------------ACCCGTAATGTTTCCGCTGAG----------------------------------- | 21 | 2 | |
| -----------------------------------------------------------------------------------ACCCGTAATGTTTCCGCTG------------------------------------- | 19 | 2 | |
| ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGC--------------------------------------- | 18 | 2 | |
| ----------------------------------------------------------------------------------TACCCGTAATGTTTCCGCTGA------------------------------------ | 21 | 1 | |
| -------------------------------------------------------------------------------------CCGTAATGTTTCCGCTGA------------------------------------ | 18 | 1 | |
| cel-miR-56* | -------------------------------------TGGCGGATCCATTTTGGGTTGTA------------------------------------------------------------------------------- | 23 | - |
| celegans | -------------------GAGCCAGTG-TCTGTTCTTGGCGGATCCATTTTGGGTTGTACCTCATCCTAAATTT--GACGGTACCCGTAATGTTTCCGCTGAGAACCGACTGTGCAC---------C----------- | ||
| cbriggsae | --------------------------------GTTCTCAGGGGATCCAGTTCCGGTTGTGCCTCATCTCAATACCCAGATGGCACCCGTATTGCTTCCTCTGAGAATCGACTGCGTAC---------CG---------- | ||
| cjaponica | -------------GGAATGGATGCGGTACTCTGTTCTTGGCAGATCCATTTTAG---GTACCTCATC----ATTT--GACGGTACCCGTAATGCTTCTGCTGAGAGCCGACCGTGAGC---------CATTTTCC---- | ||
| cbrenneri | CCATGGTAGGTTGGAACAGGAGACAGTT-TCTGTTCTCGGCCGATACATTTCTGGT-GTACCTCA-----AAACT--GATGGTACCCGTAATGTTTCCGCCGAGAACCGACTGCGCTCATTTTTAGGCCCCTTCTATGG | ||
| cremanei | -TGAGGTGAGTTGGAACGGAATTCAGTT-TCTGTTCTTGGCGAATCCATTCCGGGT-GTACCTCACAGCAATCCT--GACGGTACCCGTAATGCTTCCGCTGAGAACCGACTGTTACCACCAT--GGCTTCTTCG---- | ||
| ***** * ** ** * * ** ***** ** ** ******* ** *** * **** **** * * * | |||
| celegans | ..((((..( ((.(((((..(((((..((((.(((((...((((((.........) )).)))))))).))))..)))))..))))).))))).)).. . | 1.000 -42.00 | |
| cbriggsae | ((((((((((((..((((..(((..(((((..((((........)))))))))))).))))..))))))))))))........... .. | 0.875 -33.80 | |
| cjaponica | (((((((..(((((.....(((((..(((((..((((...( ((((((((.. ...) )).))))))...))))..)))))..)))))..)))))...) )))))).. | 1.000 -47.00 | |
| cbrenneri | ((((((..(((..(((...(((.((((( ...(((((((((.((.(((((..(((. (((((((( ....) )).)))))))).))))).)).))))))))).)))))..)))...)))..)))....)))))) | 0.999 -53.80 | |
| cremanei | .((((.(((((((...((....((((( ...(((((..(((....((((.((((( ..(((...(((.....)) )..)))))))).))))....)))..))))).)))))...)).))). .)))))))). | 0.903 -42.40 |
| celegans | chromosome:X:13144612:13144708:-1 | intergenic ## {SimpF: WRM0612dE03 -1 fosmid,WRM0611bA10 -1 fosmid,WRM061aC12 -1 fosmid,WRM0634cE07 -1 fosmid,WRM0610aG08 -1 fosmid,WRM0628bB11 -1 fosmid,oe = 1.31 0 CpG,WRM066dC07 -1 fosmid,WRM063aF02 -1 fosmid,WRM061aD10 -1 fosmid} ## {MIR: cel-mir-56} |
| cbriggsae | chromosome:chrX:16836844:16836931:-1 | Opposite_strand|Intronic_coding|NM_026450 ## Same_strand|Intronic_coding|NM_064155 |
| cjaponica | chromosome:chrUn:66592629:66592732:-1 | Same_strand|Intronic_coding|NM_001027065 |
| cbrenneri | chromosome:chrUn:8944084:8944213:1 | intergenic |
| cremanei | chromosome:chrUn:90883024:90883151:1 | intergenic |
cel-mir-63
| absolute | CE1 |
| cel-mir-63 5arm | 17 |
| cel-mir-63 3arm | 155 |
| normalized | CE1 |
| cel-mir-63 5arm | 0.012 |
| cel-mir-63 3arm | 0.108 |
sblock70 (miRBase cel-mir-63) [miRNAknown_cloningHIGH_multiarm_DicerNOK_randfoldOK]
| miRNA | randfold | RNA | rep | GC min/max | len min/max/mir_range | 5'var | 3'var | reads | reads edited | libs | libs edited | base distance | loop distance | position | locations | exon distance | unpaired | max bulge | total reads | total libs | dicer | drosha |
| miRBase cel-mir-63 | 0.001 | no | no | 0.42/0.50 | 18/24/0.98 | 0.0 0.0 | 0.0 0.0 | 15 142 | 0 0 | 1 1 | 0 0 | 16 18 | 3 7 | 5arm 3arm | 1 1 | nd nd | 0.09 0.10 | 1 2 | 172 | 1 | 2 | -1 |
| Member of family miR-64 (seed AUGACAC): cel-mir-64, cel-mir-229, cel-mir-65, cel-mir-66, cel-mir-63 |
| reads | miRBase family seed | ||
| seed | ------------------------------------------------------------------------------------AUGACAC-------------------------------------------------- | 152 | miR-64 |
| seed | --------------------------------------CUAACUC------------------------------------------------------------------------------------------------ | 16 | novel |
| seed | ----------------------------------------------------------------------------------------CACUGAA---------------------------------------------- | 2 | novel |
| seed | ---------------------------------------UAACUCG----------------------------------------------------------------------------------------------- | 1 | novel |
| seed | -------------------------------------------------------------------------------------UGACACU------------------------------------------------- | 1 | novel |
| len | cloning frequencies | ||
| CE1 | |||
| -----------------------------------------------------------------------------------TATGACACTGAAGCGAGTT------------------GG------------------- | 21 | 142 | |
| -------------------------------------TCTAACTCGTCGGTAGTCATCGT--------------------------------------------------------------------------------- | 23 | 15 | |
| -----------------------------------------------------------------------------------TATGACACTGAAGCGAGT---------------------------------------- | 18 | 4 | |
| cel-miR-63 | -----------------------------------------------------------------------------------TATGACACTGAAGCGAGTT------------------GGAAA---------------- | 24 | 3 |
| -----------------------------------------------------------------------------------TATGACACTGAAGCGAGTT------------------G-------------------- | 20 | 3 | |
| ---------------------------------------------------------------------------------------ACACTGAAGCGAGTT------------------GGAAA---------------- | 20 | 2 | |
| --------------------------------------CTAACTCGTCGGTAGTCATCGT--------------------------------------------------------------------------------- | 22 | 1 | |
| ------------------------------------------------------------------------------------ATGACACTGAAGCGAGTT------------------GGA------------------ | 21 | 1 | |
| -------------------------------------TCTAACTCGTCGGTAGTCATCG---------------------------------------------------------------------------------- | 22 | 1 | |
| celegans | --------------------ACAAGCAGACA-CAATTTCTAACTCGTCGGTAGTCATCGTTC-----TAGCTGAAAAGGACACTATGACACTGAAGCGAGTT------------------GGAAATAGTGGTTCTACTTG- | ||
| cbrenneri | --------------------TCTCTGGGACA-CCGTTTTCAACTCGTCGGTAGTCATTGTTC----GGACCAGGAAATGAAACTATGACACTGAAGCGAGTT------------------GGAAATGGTGGTTCTGTGAGA | ||
| ppacificus | CTCTCTCTCCCCTCTAATCCCCCCTTAGCCGTCCCTTCTCGGCT--TTGGTTGTCATTGTCT------ACTTGAAGA--GAACTATGACACTGAAGCGAGATGGTACGGCGAGGGGAGGAGGAAGAGGGAGGGCAGAGAG- | ||
| cremanei | ----------------------CAGAAAACATCCACTTCTAACTCGTCGGTAGTCATTGTTTCCATAAACCAGGAAGTGAAACTATGACACTGAAGCGAGTT------------------AGAAATGGTGATTCTG----- | ||
| * * * ** * *** ***** ** * * * ******************* * *** * * | |||
| celegans | .((((.((((( (.(((((((((((((((((.(((((.(((( (........)))))...)))))))))..))))))) )))))).)))..))).)))) | 1.000 -36.90 | |
| cbrenneri | ((((((((((( (((((((((((((((((((.(((((..((( (..........))))...)))))))))..))))))) )))))))))).))))).)))) | 1.000 -43.00 | |
| ppacificus | (((((((((((((((..(((((((((.(((((.((.((((.((( (..((.(((((..((( ........) ))...)))))))..)))))))).)).))))))))))).)))...)))))).))).)))))) | 1.000 -73.20 | |
| cremanei | (((((..((.(((.(((((((((((((((.(((((.(((((...............))))).)))))))))..))))))) )))).))))).))))) | 0.999 -35.36 |
| celegans | chromosome:X:17598683:17598778:-1 | intergenic ## {SimpF: WRM0624aB04 -1 fosmid,WRM0624aH07 -1 fosmid,WRM0610bF09 -1 fosmid,WRM0624cG03 -1 fosmid,WRM0627bD03 -1 fosmid} ## {MIR: cel-mir-63} |
| cbrenneri | chromosome:chrUn:21294851:21294948:1 | intergenic |
| ppacificus | chromosome:chrUn:95313911:95314040:-1 | Same_strand|Intronic_coding|NM_117511 ## Opposite_strand|Intronic_coding|NM_175692 |
| cremanei | chromosome:chrUn:15081192:15081287:1 | Opposite_strand|Intronic_coding|NM_057976 |
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