Secondary structure and small RNA-seq evidence for dme-mir-4908

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr3R:26332536-26332624 + TTCAAGA--------TGAACTTG-GTAGGATTT--------TA-AGCA-TTAAGCATGTAT-ATAGTT-------------------TTTGCTGTGCTCATAAAGTTCTATAGGTTCTCGAT------------------------ACTTGG
droSim1 chr3R:25978440-25978522 + TCCAAGA--------TAACCTAG-GTAGGATTT--------TA-AGCA-TTA-G-----CT-ATAGTT-------------------TTTGCTGTGACCATAAAGTTCTACAGGCCTTCGAT------------------------TTTTAG
droSec1 super_4:5152157-5152239 + TCCAAGA--------TAACCTAG-GTAGGATTT--------TA-AGCA-TTA-G-----CT-ATAGTT-------------------TTTGCTGTGACCATAAAGTTCTACAGGCCTTCGAT------------------------TTTTGG
droYak2 chr3R:27249454-27249531 + TCCATGA--------TGAACTAG-GTAGGACTA--------TG-AGCA-T------------ATTGGA-------------------TGTACCATACTCATAAGGTTCCACAGGTACTAGGT------------------------ATTTGG
droEre2 scaffold_4820:1676549-1676626 - TCCTCGA--------TGAACTAG-GTAGGATAA--------TG-AGTA-CAA------------GGCA-------------------TTGGCCGTTCTTATAGAGCTACACAGGTACTCGAT------------------------TTTTGG
droAna3 scaffold_12911:4648843-4648934 + CTAAAGTTTT-----GGGACTTA-TTAGGATAA--------AACGGCG-TGA-G-----TAAAAGAGT-------------------TTAAACCAACTAAGAAAACT-CATTATTATTTAAA-------------------CATGTAGTCGA
dp4 chr3:12022571-12022657 + AACCTTT--------TGAACATGAGTAAGGAAT--------CG-GGAT-CGA-C-----GT-GTAGATCCATCCGTCCACTGACAACGT----------------CTTTGCAGACAAGAAGG------------------------AGCTCG
droPer1 super_20:1381640-1381720 + TACGCGG--------TGAGTGTT-GAAGGGAAG--------CA-AGCT-TTGAG-----CC-AAAGAT-------------------CT--GCAGGTTTTCAT---TTGACAGGCCTTGGTT---------------------T-GTCGGAT
droWil1 scaffold_181130:9833040-9833125 - TCCAACAC-------TGAATCAG-GTGGG-TAA--------TA-AGAAATTG-G-----C---------------------------------CTACAGGCTAA---------ATACTGAAATTCTGGAGAAAGATCCAAATCACGAAACGG
droVir3 scaffold_13049:21775409-21775494 + TTTGCCAGAGCGCGTCTATTGCAAGGTAGGTGG--------TG-GAAC-GCA-T-----CT-ATT-------------------------GATATGCCCGTACCTGATCAACTGTTGGCTAG------------------------GTATGC
droMoj3 scaffold_6540:13565415-13565500 - TGTAAGAAT------TAAGTTCA-AAACGATCGACTAACGCTT-AAAC-GCA-T-----AT-ACA----------TATATAAATATATTCCCTGTGTATACAA----------------TGT------------------------GCCTTG
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr3R:26332536-26332624 + TTCAAGATGAACTTGGTAGGATTTTAAGCATTAAGCATGTATATAGTTTTTGCTGTGCTCATAAAGTTCTATAGGTTCTCGATACTTGG

Small RNA-sequencing read pileup

Species Read pileup
droSim1
TCCAAGATAACCTAG-GTAGGATTTTAAGCATTAG----C--TATAGTTTT--TGCTGTGACCATAAAGTT-CTACAGGCCTTCGATTTTTAGSizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
AACCTTTTGAACATGAGTAAGGAATCGGGATCGAC----G--TGTAGATCCATCCGTCCACTGACAACGTCTTTGCAGACAAGAAGGAGCTCGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-16.4,  p-value=0.009901

droSim1

dG=-14.3,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-13.3,  p-value=0.009901

droSec1

dG=-14.3,  p-value=0.009901 dG=-13.3,  p-value=0.009901 dG=-13.3,  p-value=0.009901

droYak2

dG=-9.9,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-9.3,  p-value=0.009901 dG=-9.2,  p-value=0.009901 dG=-9.2,  p-value=0.009901

droEre2

dG=-10.9,  p-value=0.009901 dG=-10.8,  p-value=0.009901

droAna3

dG=-6.5,  p-value=0.009901 dG=-5.6,  p-value=0.009901

dp4

dG=-13.1,  p-value=0.009901 dG=-13.0,  p-value=0.009901 dG=-12.2,  p-value=0.009901 dG=-11.1,  p-value=0.009901

droPer1

dG=-7.4,  p-value=0.009901 dG=-7.1,  p-value=0.009901 dG=-6.7,  p-value=0.009901 dG=-6.6,  p-value=0.009901 dG=-6.5,  p-value=0.009901

droWil1

dG=-6.2,  p-value=0.009901 dG=-6.2,  p-value=0.009901 dG=-6.1,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-5.9,  p-value=0.009901

droVir3

dG=-9.4,  p-value=0.009901 dG=-9.0,  p-value=0.009901 dG=-8.9,  p-value=0.009901 dG=-8.9,  p-value=0.009901 dG=-8.9,  p-value=0.009901

droMoj3

dG=-4.6,  p-value=0.009901 dG=-4.1,  p-value=0.009901 dG=-3.7,  p-value=0.009901

droGri2

No secondary structure predictions returned

Generated: 03/07/2013 at 05:29 PM