ID:

dsi_25247

 Coordinate:

3r:24412882-24413031 -

 Confidence:

Candidate

 Type:

Unknown

 [View on UCSC Genome Browser {Cornell Mirror}]
Legend: mature star mismatch in alignment mismatch in read

Predicted structure

-33.7 -33.7 -33.7

Flybase annnotation

intergenic

No Repeatable elements found

mature
  1. 2l:16903887-16903902 +
  2. 2r:2867433-2867448 +
  3. dsi_28947  2r:5101188-5101203 +
  4. 2r:5990010-5990025 +
  5. 2r:7558960-7558975 +
  6. dsi_15720  3l:1310575-1310590 +
  7. 3l:5847387-5847402 +
  8. 3r:6242249-6242264 +
  9. x:663152-663167 +
  10. x:4055017-4055032 +
  11. dsi_12617  x:8443358-8443373 +
  12. x:10410377-10410392 +
  13. dsi_14227  x:15416278-15416293 +
  14. x:15866382-15866397 +
  15. x:16984612-16984627 +
  16. x:19193325-19193340 +
  17. x:19566456-19566471 +
  18. x:20009177-20009192 +
  19. node_89281:735-750 +
  20. node_23929:300-315 +
  21. 2r:12268094-12268109 +
  22. 3l:8941381-8941396 +
  23. 3l:17028600-17028615 +
  24. x:18023511-18023526 +
  25. 2l:940685-940700 -
  26. 2l:20626157-20626172 -
  27. 2r:6006003-6006018 -
  28. 2r:9199711-9199726 -
  29. 2r:14162453-14162468 -
  30. 3l:2471727-2471742 -
  31. 3l:12474803-12474818 -
  32. 3l:23233715-23233730 -
  33. 3l:23831762-23831777 -
  34. x:2164182-2164197 -
  35. x:8222809-8222824 -
  36. x:8404881-8404896 -
  37. x:12409293-12409308 -
  38. x:16347045-16347060 -
  39. x:17803373-17803388 -
  40. x:18975213-18975228 -
  41. node_11282:6065-6080 -
  42. node_118072:64-79 -
  43. node_18214:1945-1960 -
  44. node_66978:151-166 -
  45. 2l:3011452-3011467 -
  46. 2r:7024853-7024868 -
  47. 2r:7024926-7024941 -
  48. 3l:16646094-16646109 -
  49. 3r:4807434-4807449 -
  50. dsi_25247  3r:24412997-24413012 -
  51. x:478663-478678 -
  52. x:3142296-3142311 -
  53. x:7187540-7187555 -
  54. x:11381445-11381460 -
  55. x:12469525-12469540 -
  56. x:17192119-17192134 -
  57. node_44287:90-105 -
  58. dsi_7608  3l:2685273-2685288 -
  59. 2l:19988455-19988470 +
  60. 3r:24366958-24366973 +
star

Sense Strand Reads

AAAAACTTGTTAACGCTTTTACATTAAGTGTTAATGAAAGTGGAAAATAGGTACTGAAAGGGGTGTGGCCCCACGTTGGGCGCCAGAAACATTATCTAACTAACATACGCGTCTATCAAGTGCAGCAAAGTGATAATTAGCTCATAAATATGAATGAGCCAGCGATTAGAGTACCTAACTTCACCCACAATGCCGTATTAATATCAACTAAACGCCAAACAAATGGCTGCAAGTGCGATTGAGTTGTTTG
**************************************************(((((((.(((.(((((((((((...)))).)))......................)))).))).)).))))).(((..(((.......((((((........)))))).........((((.....))))....)))..))).......************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR618934
dsim w501 ovaries
 M053
female body
 M023
head
 SRR553485
Chicharo_3 day-old ovaries
 SRR902009
testis
 M025
embryo
 SRR902008
ovaries
 SRR553488
RT_0-2 hours eggs
 SRR553486
Makindu_3 day-old ovaries
 M024
male body		 SRR553487
NRT_0-2 hours eggs
 GSM343915
embryo
 O002
Head
.....................................................................CCCACGTTGGGCGCCA..................................................................................................................................................................... 16 0 20 4.40 88 84 0 0 0 0 0 0 4 0 0 0 0 0
.................................................................TCGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 20 1 16 2.63 42 33 1 3 1 0 0 0 0 1 2 0 1 0
............................................................GGGTTCGGCCCCACGTTGGGC......................................................................................................................................................................... 21 2 1 2.00 2 0 0 1 0 0 1 0 0 0 0 0 0 0
............................................................GGGTTCGGCCCCACGTTGGG.......................................................................................................................................................................... 20 2 1 2.00 2 0 2 0 0 0 0 0 0 0 0 0 0 0
..................................................................GGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 19 0 20 1.65 33 16 1 13 0 0 1 0 0 0 2 0 0 0
.............................................................GGTTCGGCCCCACGTTGGG.......................................................................................................................................................................... 19 2 3 1.33 4 0 4 0 0 0 0 0 0 0 0 0 0 0
...........................................................TGGGTTCGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 26 3 3 1.33 4 3 1 0 0 0 0 0 0 0 0 0 0 0
............................................................GGGTTCGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 25 2 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0
............................................................TGGGGTCGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 25 3 1 1.00 1 0 1 0 0 0 0 0 0 0 0 0 0 0
.....................................AAGTGGAAAATAGGTACTGT................................................................................................................................................................................................. 20 1 1 1.00 1 0 0 0 0 1 0 0 0 0 0 0 0 0
..........................................................CGGGGTTCGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 27 3 1 1.00 1 0 0 1 0 0 0 0 0 0 0 0 0 0
...............................................................TGGGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 22 1 3 0.67 2 1 0 0 1 0 0 0 0 0 0 0 0 0
...............................................................TGGGGCCCCACGTTGGGCGCC...................................................................................................................................................................... 21 1 3 0.67 2 0 0 0 2 0 0 0 0 0 0 0 0 0
.......................................................................CACGTTGGGCGCCAGAAGC................................................................................................................................................................ 19 1 2 0.50 1 1 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................GTGGGGCCCCACGTTGGGCG........................................................................................................................................................................ 20 1 2 0.50 1 0 0 0 0 1 0 0 0 0 0 0 0 0
..........................................................TGGGGTCGGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 27 3 2 0.50 1 1 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................GTGGGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 23 1 2 0.50 1 0 0 0 0 0 0 1 0 0 0 0 0 0
...........................................................GTCGTGGGGCCCCACGTTGGG.......................................................................................................................................................................... 21 3 2 0.50 1 0 0 0 1 0 0 0 0 0 0 0 0 0
.............................................................CGTGGGGCCCCACGTTGGGC......................................................................................................................................................................... 20 2 2 0.50 1 0 0 1 0 0 0 0 0 0 0 0 0 0
..............................................................TTCTGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 23 2 5 0.40 2 0 0 0 2 0 0 0 0 0 0 0 0 0
.............................................................GGTCGTGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 24 3 15 0.40 6 0 3 0 1 0 0 0 0 2 0 0 0 0
...........................................................TGGGTTCGGCCCCACGTTGGGCGCC...................................................................................................................................................................... 25 3 3 0.33 1 1 0 0 0 0 0 0 0 0 0 0 0 0
...........................................................TGGGTTCGGCCCCACGTTGGGCG........................................................................................................................................................................ 23 3 3 0.33 1 1 0 0 0 0 0 0 0 0 0 0 0 0
............................................................GTGGGGGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 25 3 3 0.33 1 0 0 0 0 0 0 1 0 0 0 0 0 0
...........................................................TGGGTTCGGCCCCACGTTGGG.......................................................................................................................................................................... 21 3 3 0.33 1 1 0 0 0 0 0 0 0 0 0 0 0 0
...............................................................TCTCGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 22 2 3 0.33 1 0 0 0 1 0 0 0 0 0 0 0 0 0
.....................................................................CCCACGTTGGGCGCCAGA................................................................................................................................................................... 18 0 3 0.33 1 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................GGTCGGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 24 2 8 0.25 2 0 1 0 1 0 0 0 0 0 0 0 0 0
...................................................................GCCCCACGTTGGGCGCCA..................................................................................................................................................................... 18 0 20 0.20 4 0 0 0 0 0 4 0 0 0 0 0 0 0
..............................................................GGGTCGCCCCACGTTGGG.......................................................................................................................................................................... 18 2 11 0.18 2 0 2 0 0 0 0 0 0 0 0 0 0 0
........................................................................ACGTTGGGCGCCAGAAG................................................................................................................................................................. 17 1 7 0.14 1 1 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................ACGTTGGGCGCCAGGA.................................................................................................................................................................. 16 1 8 0.13 1 1 0 0 0 0 0 0 0 0 0 0 0 0
........................................................................ACGTTGGGCGCCAGA................................................................................................................................................................... 15 0 8 0.13 1 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................GGTCGGGCCCCACGTTGCGCGCCA..................................................................................................................................................................... 24 3 8 0.13 1 1 0 0 0 0 0 0 0 0 0 0 0 0
.....................................................................CCCACGTTGGGCGCCAGCGTC................................................................................................................................................................ 21 3 10 0.10 1 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................GTTTCGGCCCCACGTTGGGCGCCA..................................................................................................................................................................... 24 3 12 0.08 1 0 1 0 0 0 0 0 0 0 0 0 0 0
.......................................................................CACGTTGGGCGCCAG.................................................................................................................................................................... 15 0 14 0.07 1 1 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................................................................................................................TAGAGTACCTGACTGC.................................................................... 16 2 14 0.07 1 0 0 0 0 0 0 0 1 0 0 0 0 0
.................................................................................................................................................................................................................................GCTGAAAGTGCGATTGTG....... 18 2 14 0.07 1 0 0 0 0 0 1 0 0 0 0 0 0 0
.................................................................TCGCCCCACGTTGGGTGCCA..................................................................................................................................................................... 20 2 17 0.06 1 1 0 0 0 0 0 0 0 0 0 0 0 0
.............................................................................................................................................................................................AGGCCGTACTAATATC............................................. 16 2 17 0.06 1 1 0 0 0 0 0 0 0 0 0 0 0 0
..............................................................GTGGGGCTCCACGTTGGGA......................................................................................................................................................................... 19 3 17 0.06 1 0 0 0 1 0 0 0 0 0 0 0 0 0
............................TGTTTATGTAAGTGGAGAAT.......................................................................................................................................................................................................... 20 3 19 0.05 1 0 0 0 0 0 0 0 0 0 0 0 0 1
......................................................................................................................................................................TAGAGTACCTGACTG..................................................................... 15 2 20 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0
..................................................................GGCCCCACGTTGGGCG........................................................................................................................................................................ 16 0 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................GCCCCCACGTTGGGCGCCA..................................................................................................................................................................... 19 1 20 0.05 1 0 0 0 0 0 0 0 0 1 0 0 0 0
....................................................................CCCCACGTTTGGCGCCA..................................................................................................................................................................... 17 1 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0
....................................................................CCCCACGTTGGGCGCCG..................................................................................................................................................................... 17 1 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0
......................................................................CCACGTTGGGCGCCA..................................................................................................................................................................... 15 0 20 0.05 1 0 0 0 0 0 0 1 0 0 0 0 0 0
..................................................................GGCCCCACGTTGGGCGC....................................................................................................................................................................... 17 0 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0
...................................................................CCCCCACGTTGGGCGCCA..................................................................................................................................................................... 18 1 20 0.05 1 1 0 0 0 0 0 0 0 0 0 0 0 0
..................................................................GGCCCCACGTTGGGC......................................................................................................................................................................... 15 0 20 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0
.....................................................................................................................................................................TTAGAGTACCTGACTG..................................................................... 16 2 20 0.05 1 0 0 0 0 0 0 0 1 0 0 0 0 0
..................................................................GGCCCCACGTTGGGAGCCA..................................................................................................................................................................... 19 1 20 0.05 1 0 0 0 0 0 0 0 1 0 0 0 0 0
.................................................................................................................CATCCAGGGCAGCAAAGTGA..................................................................................................................... 20 3 20 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0
...................................................................GCCTCACGTTGGGCGCCA..................................................................................................................................................................... 18 1 20 0.05 1 0 0 1 0 0 0 0 0 0 0 0 0 0
.....................................................................CTCACGTTGGGCGCCA..................................................................................................................................................................... 16 1 20 0.05 1 0 0 0 0 1 0 0 0 0 0 0 0 0
...................................................................GCCCCACGTTGGGCGCCG..................................................................................................................................................................... 18 1 20 0.05 1 0 0 0 0 0 1 0 0 0 0 0 0 0
....................................................................................................................................ATAATTAGCTCCTAGA...................................................................................................... 16 2 20 0.05 1 0 0 0 0 0 0 0 0 0 0 1 0 0
.....................................................................CCCACGTTGGGCGCC...................................................................................................................................................................... 15 0 20 0.05 1 0 0 0 1 0 0 0 0 0 0 0 0 0

Anti-sense strand reads

TTTTTGAACAATTGCGAAAATGTAATTCACAATTACTTTCACCTTTTATCCATGACTTTCCCCACACCGGGGTGCAACCCGCGGTCTTTGTAATAGATTGATTGTATGCGCAGATAGTTCACGTCGTTTCACTATTAATCGAGTATTTATACTTACTCGGTCGCTAATCTCATGGATTGAAGTGGGTGTTACGGCATAATTATAGTTGATTTGCGGTTTGTTTACCGACGTTCACGCTAACTCAACAAAC
**************************************************(((((((.(((.(((((((((((...)))).)))......................)))).))).)).))))).(((..(((.......((((((........)))))).........((((.....))))....)))..))).......************************************************** 		Read size # Mismatch Hit Count Total Norm Total SRR618934
dsim w501 ovaries
 SRR902009
testis
 GSM343915
embryo
 SRR553488
RT_0-2 hours eggs
..........................................................................................................................................................ACTCGGTGGCGAATCTCAA............................................................................. 19 3 19 1.11 21 19 0 2 0
.......................................................................................................................................................................................GGGTGTTACGGCATAATTA................................................ 19 0 1 1.00 1 0 1 0 0
..........................................................................................................................................................ACTCGGTGGCGAATCTCA.............................................................................. 18 2 2 0.50 1 0 0 1 0
.......................................................................................................................................................CTTACTAGGTGGCGAATCTCA.............................................................................. 21 3 5 0.20 1 1 0 0 0
..................................................................................................................................................................................GAAGTGTGTGGTACGACAT..................................................... 19 3 6 0.17 1 1 0 0 0
........................................................................................................................................................................GTCATGGATGGAAGTGG................................................................. 17 2 6 0.17 1 0 0 0 1
..................................................................................................................................................................GGTAATCTCATGGGTTG....................................................................... 17 2 9 0.11 1 0 0 0 1
.........................................................................................................................................................................TCATTAATTGTAGTGGGTGT............................................................. 20 3 9 0.11 1 0 0 0 1
...........................................................................................................................................................CTAGGTGGCAAATCTCAT............................................................................. 18 3 20 0.05 1 1 0 0 0
..........................................................................................................................................................ACTGGGTGGCGAATCTCA.............................................................................. 18 3 20 0.05 1 1 0 0 0
...................................................................CGGGGTGCAACCCGCGGT..................................................................................................................................................................... 18 0 20 0.05 1 1 0 0 0

Re-alignment of all predicted orthologs

Species Coordinate ID Alignment
droSim2 3r:24412832-24413081 - dsi_25247 AAAAACTTGTTAACGCTT-T---------TAC-------------------ATTAAG--------TGTTAATGAAAGTG-GAAAA-TAGGTACTGAAAG---------GGGTGTGGCCCCACGTTGGGCGC---CAG----------AAACATTATCTAACTAA-CATACGCGTCTATCAAGTGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GC------------C-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AAACGCCAAA---------CAAAT----------------------GGCTGCAAGTGCGATTGAGTTGTTTG
droSec2 scaffold_4:3917147-3917396 - AAAAACTTGTTAACGCTT-T---------TAC-------------------ATTAAG--------TGTTAATGAAAGCG-GAAAA-TAGGTACTGAAAG---------GGGTGTGGCCCCACGTTGGGCGC---CAG----------AAACATTATCTAACTAA-CATACGCGTCTATCAAGTGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GC------------C-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AAACGCCAAA---------CAAAT----------------------GGCTGCAAGTGCGATTGAGTTGTTTG
dm3 chr3R:25054382-25054619 - AGAAACTTGTTAATGAT--T---------TAC-------------------ATTAAG--------TGTCAATGAAAG----------------TGAAAG---------AGGTGTGGCCCCACATTGGGCGC---CAG----------AAACATTATCTAAATAA-TATACGCGTCTATCAAGAGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GCAGTTGTGTGGGCC-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AA-------GTG-----------T----------------------GCCTGCAAGTGCAATTGAGTTGTTTG
droEre2 scaffold_4820:2975869-2976096 + AACATT---CCTACGCTTAT---------TAC-------------------AGTT----------TGTTAATAAA-ATG-GAAAA-TAGGTACTAAAAA---------GGGTGTTGCCCCACGTTGGGCGT---CAG----------AAGCATTATCTAAGTAA-TA-ACGCGGCTATCAAAAGCAGCAGAGTGATAATTAGCCGTGTGCTCACATAATTATGA----------------------------------------CTAACTTCACCCACAATGCC-ATATTAATAGCAAAT----------AAACGTCAT-------------GT----------------------GCTTACAAGTGCAATTGAGTTGTTTG
droYak3 3R:21442680-21442944 + AA---TTTGTTCACGATTGT---------TGC-------------------ATTTAG--------TTTTAATGAAA-TA-TAAAA-CAGATACTAAAAA---------GGGTGTGGCCCCACGATGGGCGC---CAG----------AATCATAATCTAAGTAAATATACGAGTCTATCAATAGCAGCAAAGTGATAATTAGCCGTGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGGCC-AGCGATTAGAGTACCAAACTTCACCCACTATGCCA-TATTAAAATCAACT----------AAACGTCAA-------------GT----------------------GCTTACAAGTGCAATTGAGTTGTTTG
droEug1 scf7180000409787:517251-517455 + TAAAGCATATTT------------------------------------------------------------------G----------GAAAGGCAAA---------AGGTG-----------------------------TTGGCAAAGGTAATTTAAATAT-TATGCTATTCCATAAAG-CCAGCAAAGTGATAATTAGCAGAATACACTCATTAATATGAATAA------GTAGTTGCGTGGAAT-AGCGATTAGAGGGCCTAAATATACTCACAATGACAG------CATGAATTAAAATAAGCTA------------------------------------------------CATAAGTGCAATTGACTTGTTTG
droBia1 scf7180000302136:3082960-3083254 + AAGAACT-GTTACATAC--A---------TGCCTTTAATCCCAACTAATCTATTAAATGTATTTGAGTTGATA----CA-TAGAA-ATG--------GAGTATATGGAGGGAGTGGCCCCACGATGGGCGC---CACAATTGTTGGCAAACACTATTTGAATAT-AATGCTCTTCTATCAAGAGCAGCAAGGTGATAATTAGCCGAGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGGCC-TGCTATTAGGGTACCTAAATTCACTCACAAAGGCAG------CATTAATT----------AAATGCTAAATGTGC----------------------------------TCAAAGTGCAATTGACTTGTTTA
droTak1 scf7180000415310:317128-317367 - TTAACT---------C---------------------------------------------------------AA-TTGGTAGAA-AAGATACTG---A---------GGGCGAGGCCC-TCGTAGGGCGT---CAAATAAGTTGGCAAACATAATTTAAATAT-TATGCTTTTCTATCCAGAGCAGCAAAGTGATAATTAGCAGAGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGTAC-T------CTAATACCTGAATTCACTCACAATGGCAGCATTAATATTAATT----------AAACGCTAAATGTAC----------------------------------TCCAAGTGCAATTGACTTGTTTA
droEle1 scf7180000491280:1243753-1244025 - TAAATA---ATTATAATAATACAGTACCGTAA-------------------AGT----------CTGTTAACGTA-------AATAAGGGCA---TAGA---------GGGCGTGGCTCCACATTGAACATATGCAA----------ATGTATAATTTAAATAT-TATGCACTTCTTCCGAGAGCAGAAAAGTGATAATTAGTAGTGCCCACTCATAAATATGATTGA------GCAACTGCGTGGGCC-TGCGATTAGAGTGCCTAAATTCACCCACAATGGCAG------CATTAATT----------AAACGCTAAATGTGC--TCCAAGT----------------------GCTTACAACTGCAATTGACTTGTTTG
droRho1 scf7180000779659:41336-41595 + AAAAACTTTTTT-----------------------TGACAATGATTATTTTAAAAAATGTAATTCTGTTAGTGTA-------GAAGA------AGAAGA---------AGATA-------------------CAAAG----------ATAAGATATTTAAATAT-TATGCCCTTCTATCAAGAGCAGAAAAGTGATAATTAGCAGTGCGCACTCATAAATATTAATGA------GCAATCGCACGGGCC-TACGATTTGAGTACCTAAATTCACTCACAATGGCAG------TATTAATT----------AAACGCTAAATGTTC--CCCAACT----------------------GCTTAAAAGTGCAATTGACTTGTTTG
droFic1 scf7180000453776:350651-350915 - AGAAATATATGTACAATT-T------------------------------C--------------------TAAAGATG-TAAAA-AAGACA-TAAAAA---------GGGCGCGGTAACAGACTAGACTC---CGC---TGTTGATCAACATAATTTAAATAT-TATGCACTTCTATTATG----GGAAGGTGATAATTAGCTTTGTGCGCTCATAAATATGCATAAAGA--AGCAACGGCGTGGGCC-GGTGATTAGCGTACCCAAATCCACTAACAATAGCAG------TACAAATT----------AAACTCTAAATGTGA--TCCAAGT----------------------GCTTACAAGTGCAATTGACTTGTTTA
droKik1 scf7180000302466:427056-427187 - ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAGCCAAGTGATAATTAGTGGTGCTTACTCATGAGTATGAATGAAAATTAACCATTGCGTGGGCTTCACGACTACAGT----AAACCCACTCCCAAAGGCA-----AACATTAATT----------AAACACCAA-------------------------------------------AAGTGCA-----GTTGTTGA
droAna3 scaffold_13340:14196408-14196576 - ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTGATAATTAGCTCTGCCCACTTATAAATATGAATGA------GCCGTTGCGTGGGCC-CTCGATTAGAGCGCCGAAATTCACTCACAATGCAAA------CATTAATT----------AAATGCTAAGTGCGAGCTTCTTGTGCCCACGCTAGCTGCTAGCTTGGCCCACAACTGCAACCGGCTTGTTTA
droBip1 scf7180000395971:967003-967167 + -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGAGTGATAATTAGCTACGCCCACTTATAAATATGAATCA------GCCATTGCGTGGGCC-CTCGATTAGAGTGCCTAAATCCACTCACAATGGCAA------CATTAATT----------AAAAGCTAAGTGCGAGCTTCTAGTGCCCACGCC-------AGCTTGGCTTACAACTGCAACCGGCTTGTTTA

Re-alignment of all predicted orthologs with sRNA reads

Species Read alignment
droSim2
AAAAACTTGTTAACGCTT-T---------TAC-------------------ATTAAG--------TGTTAATGAAAGTG-GAAAA-TAGGTACTGAAAG---------GGGTGTGGCCCCACGTTGGGCGC---CAG----------AAACATTATCTAACTAA-CATACGCGTCTATCAAGTGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GC------------C-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AAACGCCAAA---------CAAAT----------------------GGCTGCAAGTGCGATTGAGTTGTTTGSizeHit CountTotal NormTotalM023
Head		M024
Male-body		M025
Embryo		M053
Female-body		O001
Testis		O002
Head		SRR553485
Ovary		SRR553486
Ovary		SRR553487
Ovary		SRR553488
Ovary		SRR618934
Ovary		V044
Embryo		SRR902008
Ovary		SRR902009
Testis		SRR1275487
Male larvae		SRR1275485
Male prepupae		SRR1275483
Male prepupae
.....................................................................................................................CCCACGTTGGGCGC---CA......................................................................................................................................................................................................................................................16204.4088000000000484000000
..................................................................................................................GGCCCCACGTTGGGCGC---CA......................................................................................................................................................................................................................................................19201.65331321100000016000000
..........................................................................AAGTG-GAAAA-TAGGTACTGT..............................................................................................................................................................................................................................................................................................2011.00100000000000001000
.....................................................................................................................CCCACGTTGGGCGC---CAG----------A..........................................................................................................................................................................................................................................1830.33100000000001000000
...................................................................................................................GCCCCACGTTGGGCGC---CA......................................................................................................................................................................................................................................................18200.20400400000000000000
........................................................................................................................ACGTTGGGCGC---CAG----------AAG........................................................................................................................................................................................................................................1770.14100000000001000000
........................................................................................................................ACGTTGGGCGC---CAG----------A..........................................................................................................................................................................................................................................1580.13100000000001000000
.......................................................................................................................CACGTTGGGCGC---CAG----------...........................................................................................................................................................................................................................................15140.07100000000001000000
..................................................................................................................GGCCCCACGTTGGGCG............................................................................................................................................................................................................................................................16200.05100000000001000000
....................................................................................................................CCCCACGTTGGGCGC---CG......................................................................................................................................................................................................................................................17200.05100000000001000000
......................................................................................................................CCACGTTGGGCGC---CA......................................................................................................................................................................................................................................................15200.05100000000000010000
..................................................................................................................GGCCCCACGTTGGGCGC---........................................................................................................................................................................................................................................................17200.05100000000001000000
..................................................................................................................GGCCCCACGTTGGGC.............................................................................................................................................................................................................................................................15200.05100000000100000000
...................................................................................................................GCCCCACGTTGGGCGC---CG......................................................................................................................................................................................................................................................18200.05100100000000000000
.....................................................................................................................CCCACGTTGGGCGC---C.......................................................................................................................................................................................................................................................15200.05100000010000000000
droSec2
AAAAACTTGTTAACGCTT-T---------TAC-------------------ATTAAG--------TGTTAATGAAAGCG-GAAAA-TAGGTACTGAAAG---------GGGTGTGGCCCCACGTTGGGCGC---CAG----------AAACATTATCTAACTAA-CATACGCGTCTATCAAGTGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GC------------C-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AAACGCCAAA---------CAAAT----------------------GGCTGCAAGTGCGATTGAGTTGTTTGSizeHit CountTotal NormTotalM054
Female-body		V113
Male-body		V114
Embryo		V115
Head
..................................................................................................................GGCCCCACGTTGGGCGC---CA......................................................................................................................................................................................................................................................19200.751540110
dm3
AGAAACTTGTTAATGAT--T---------TAC-------------------ATTAAG--------TGTCAATGAAAG----------------TGAAAG---------AGGTGTGGCCCCACATTGGGCGC---CAG----------AAACATTATCTAAATAA-TATACGCGTCTATCAAGAGCAGCAAAGTGATAATTAG---------CTCATAAATATGAATGA------GCAGTTGTGTGGGCC-AGCGATTAGAGTACCTAACTTCACCCACAATGCC-GTATTAATATCAACT----------AA-------GTG-----------T----------------------GCCTGCAAGTGCAATTGAGTTGTTTGSizeHit CountTotal NormTotalGSM154618
Ovary		GSM154620
Ovary		GSM154621
Ovary		GSM154622
Ovary		GSM180328
Head		GSM180329
Mixed-body		GSM180330
Embryo		GSM180331
Embryo		GSM180332
Embryo		GSM180333
Embryo		GSM180334
Larvae		GSM180335
Disc		GSM180336
Pupae		GSM180337
S2		GSM231091
Ovary		GSM239041
Head		GSM239050
Head		GSM239051
S2		GSM239052
S2		GSM246084
Head		GSM266765
S2		GSM280082
Ovary		GSM280083
Ovary		GSM280084
Ovary		GSM280085
Testis		GSM280086
Ovary		GSM280087
S2-NP		GSM280088
S2-NP		GSM312995
Head		GSM313160
Head		GSM313161
Head		GSM313162
Head		GSM313163
Head		GSM313164
Head		GSM313165
Head		GSM343287
Embryo		GSM379050
Ovary		GSM379051
Ovary		GSM379052
Ovary		GSM379053
Ovary		GSM379054
Ovary		GSM379055
Ovary		GSM379056
Ovary		GSM379057
Ovary		GSM379058
Ovary		GSM379059
Ovary		GSM379060
Ovary		GSM379061
Ovary		GSM379062
Ovary		GSM379063
Ovary		GSM379064
Ovary		GSM379065
Ovary		GSM379066
Ovary		GSM379067
Ovary		GSM424739
S2		GSM424740
S2		GSM424741
S2		GSM467729
Female-body		GSM467730
Female-body		GSM467731
Female-body		M002
CS		M003
Male-body		M004
Male-body		M005
ML-DmD32		M006
ML-DmD32		M029
OSC		M030
OSC		M031
OSC		M032
S2-R+		M033
S2-R+		M034
S2-R+		M035
S2-R+		M036
S2-R+		M037
S2-R+		M038
S2-R+		M039
S2-R+		M048
S2-R+		OSS2
OSS		OSS6
OSS		OSS7
OSS		OSS8
OSS		S1
Head		S10
Embryo		S11
Embryo		S12
Embryo		S13
Embryo		S14
Embryo		S15
S2-GMR		S16
Kc		S17
Larvae		S18
Larvae		S19
Pupae		S2
Head		S20
Pupae		S21
Disc		S22
Head		S23
Female-body		S24
Male-body		S25
Larvae		S26
Larvae		S27
Pupae		S28
Pupae		S29
Head		S3
Male-body		S30
S2-GMR		S31
S2		S32
S2		S33
Kc		S34
Kc		S35
Kc		S4
Female-body		S5
Disc		S6
Embryo		S7
Embryo		S8
S2		S9
Embryo		SRR001337
Head		SRR001338
Head		SRR001339
Head		SRR001340
Head		SRR001341
Head		SRR001342
Head		SRR001343
Head		SRR001344
Head		SRR001345
Head		SRR001346
Head		SRR001347
Head		SRR001348
Head		SRR001349
Head		SRR001664
Head		SRR010951
Ovary		SRR010952
Ovary		SRR010953
Ovary		SRR010954
Ovary		SRR010955
Ovary		SRR010956
Ovary		SRR010957
Ovary		SRR010958
Ovary		SRR010959
Ovary		SRR010960
Ovary		SRR014268
Embryo		SRR014269
Embryo		SRR014270
Embryo		SRR014271
Embryo		SRR014272
Embryo		SRR014273
Ovary		SRR014274
Ovary		SRR014275
Ovary		SRR014276
Ovary		SRR014277
Ovary		SRR014278
Ovary		SRR014279
Ovary		SRR014280
Ovary		SRR014281
Ovary		SRR014282
Ovary		SRR023197
S2		SRR023399
S2		SRR023400
S2		SRR023402
S2		SRR023407
S2		SRR029028
S2		SRR029029
S2		SRR029030
S2		SRR029031
S2		SRR029032
S2		SRR029033
S2		SRR029608
Head		SRR029633
Head		SRR030145
gb3		SRR031692
Head		SRR031693
Head		SRR031694
Head		SRR031696
Head		SRR031697
Head		SRR031698
Head		SRR031699
Head		SRR031700
Head		SRR031701
Head		SRR031702
Head		SRR031703
Head		SRR031704
Head		SRR032092
S2		SRR032093
S2		SRR032094
S2		SRR032095
S2-NP		SRR032096
S2-NP		SRR032152
Head		SRR060643
Testis		SRR060644
Ovary		SRR060645
Testis		SRR060646
Ovary		SRR060647
Ovary		SRR060648
Ovary		SRR060649
Ovary		SRR060650
Testis		SRR060651
Ovary		SRR060652
Testis		SRR060653
Ovary		SRR065151
Ovary		SRR065152
Ovary		SRR065153
Ovary		SRR065154
Ovary		SRR065155
Ovary		SRR065800
Ovary		SRR065801
Ovary		SRR065802
Ovary		SRR065803
Ovary		SRR065804
Ovary		SRR065805
Ovary		SRR065806
Ovary		SRR065807
Ovary		SRR097865
S2-NP		SRR097866
S2-NP		SRR097867
S2-NP		SRR298536
Ovary		SRR298537
Ovary		SRR298711
Ovary		SRR298712
Ovary		SRR317110
Ovary		SRR317111
Ovary		SRR317112
Ovary		SRR317113
Ovary		SRR317114
Ovary		SRR317115
Ovary		SRR317116
Ovary		SRR317117
Ovary		SRR341115
S2		SRR341116
S2		SRR341117
S2		SRR341118
S2		SRR351332
Mixed-body		SRR351333
Mixed-body		T004
OSC		T005
CME-L1		V001
Embryo		V002
Embryo		V003
S2		V006
Female-body		V007
Head		V008
S2		V009
CME-L1		V010
ML-DmD20-C5		V011
Sg4		V012
Male-body		V013
Head		V014
DTT		V015
DreRFHV		V018
Kc167		V019
GM2		V020
S2-R+		V021
ML-DmD21		V022
ML-DmD32		V023
Head		V024
Kc167		V025
S2-R+		V026
1182-2H		V027
ML-DmD21		V028
CME-W1-Cl.8+		V029
ML-DmD9		V030
ML-DmD8		V031
GM2		V032
S1		V033
CME-W1-Cl.8+		V034
ML-DmD16-C3		V035
ML-DmD32		V036
ML-DmD20-C5		V037
S2		V038
S2		V063
Ovary		V0632
Ovary		V064
Ovary		V0642
Ovary		V065
Ovary		V0652
Ovary		V066
Ovary		V0662
Ovary		V067
S2-NP		V073
mbn2		V074
S3		V075
ML-DmBG1-C1		V076
ML-DmBG3-C2		V077
Head		V078
Head		V079
Head		V080
Head		V081
Embryo		V082
Embryo		V083
Male-body		V084
Female-body		V085
CME-W2		V086
Female-body		V088
Ovary		V0882
Ovary		V089
Ovary		V0892
Ovary		V090
Male-body		V091
fGS/OSS		V092
Male-body		V093
Male-body		V094
S2-R+		V095
S2-R+		V096
Ovary		V097
Ovary		V098
Ovary		V125
ML-DmD9		V126
CME-L1		V127
G2		V128
S3		V129
ML-DmBG1-C1		V130
ML-DmBG3-C2		V131
ML-DmD16-C3		V132
ML-DmD32		V133
Sg4		V134
ML-DmD8		V135
CME-W2		V136
Male-body		V137
Head		V138
Male-body		V139
Female-body		V140
Female-body		V141
Female-body		V142
Female-body		V144
OSC		V145
S2		V146
S1		V147
1182-2H		V148
mbn2		GSM1528798
follicle cells
..................................................................................................................GGCCCCACATTGGGCGC---CA......................................................................................................................................................................................................................................................1916.0060000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000240000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
........................................................................................................................................................................................................................................................................................................................................................................GCAAGTGCAATTGAGTTGC...1911.0010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000
...........................................................................................................................TTGGGCGC---CAG----------AAACATTA...................................................................................................................................................................................................................................1911.0010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000010000000
.......................................................................................................................................................ATTATCTAAATAA-TATACGCG.................................................................................................................................................................................................................2111.0010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
......................................................................................................................................................................................................................................................................................................................................................................CTGCAAGTGCAATTGAGT......1811.0010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000
droEre2
AACATT---CCTACGCTTAT---------TAC-------------------AGTT----------TGTTAATAAA-ATG-GAAAA-TAGGTACTAAAAA---------GGGTGTTGCCCCACGTTGGGCGT---CAG----------AAGCATTATCTAAGTAA-TA-ACGCGGCTATCAAAAGCAGCAGAGTGATAATTAGCCGTGTGCTCACATAATTATGA----------------------------------------CTAACTTCACCCACAATGCC-ATATTAATAGCAAAT----------AAACGTCAT-------------GT----------------------GCTTACAAGTGCAATTGAGTTGTTTGSizeHit CountTotal NormTotalM055
Female-body		M057
Embryo		V060
Head		V040
Embryo		V107
Male-body		V108
Head		GSM1528801
follicle cells
.....................................................................................................................CCCACGTTGGGCGT---CA......................................................................................................................................................................................................................................................1660.3320000002
droYak3
AA---TTTGTTCACGATTGT---------TGC-------------------ATTTAG--------TTTTAATGAAA-TA-TAAAA-CAGATACTAAAAA---------GGGTGTGGCCCCACGATGGGCGC---CAG----------AATCATAATCTAAGTAAATATACGAGTCTATCAATAGCAGCAAAGTGATAATTAGCCGTGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGGCC-AGCGATTAGAGTACCAAACTTCACCCACTATGCCA-TATTAAAATCAACT----------AAACGTCAA-------------GT----------------------GCTTACAAGTGCAATTGAGTTGTTTGSizeHit CountTotal NormTotalM026
Head		M043
Female-body		M056
Embryo		V046
Embryo		V052
Head		V058
Head		V120
Male-body		SRR1275488
Male larvae		SRR1275486
Male prepupae		SRR1275484
Male prepupae		GSM1528802
follicle cells
No Reads
droEug1
TAAAGCATATTT------------------------------------------------------------------G----------GAAAGGCAAA---------AGGTG-----------------------------TTGGCAAAGGTAATTTAAATAT-TATGCTATTCCATAAAG-CCAGCAAAGTGATAATTAGCAGAATACACTCATTAATATGAATAA------GTAGTTGCGTGGAAT-AGCGATTAGAGGGCCTAAATATACTCACAATGACAG------CATGAATTAAAATAAGCTA------------------------------------------------CATAAGTGCAATTGACTTGTTTGSizeHit CountTotal NormTotal
No Reads
droBia1
AAGAACT-GTTACATAC--A---------TGCCTTTAATCCCAACTAATCTATTAAATGTATTTGAGTTGATA----CA-TAGAA-ATG--------GAGTATATGGAGGGAGTGGCCCCACGATGGGCGC---CACAATTGTTGGCAAACACTATTTGAATAT-AATGCTCTTCTATCAAGAGCAGCAAGGTGATAATTAGCCGAGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGGCC-TGCTATTAGGGTACCTAAATTCACTCACAAAGGCAG------CATTAATT----------AAATGCTAAATGTGC----------------------------------TCAAAGTGCAATTGACTTGTTTASizeHit CountTotal NormTotal
No Reads
droTak1
TTAACT---------C---------------------------------------------------------AA-TTGGTAGAA-AAGATACTG---A---------GGGCGAGGCCC-TCGTAGGGCGT---CAAATAAGTTGGCAAACATAATTTAAATAT-TATGCTTTTCTATCCAGAGCAGCAAAGTGATAATTAGCAGAGTGCACTCATAAATATGAATGA------GCAGTTGCGTGGTAC-T------CTAATACCTGAATTCACTCACAATGGCAGCATTAATATTAATT----------AAACGCTAAATGTAC----------------------------------TCCAAGTGCAATTGACTTGTTTASizeHit CountTotal NormTotal
No Reads
droEle1
TAAATA---ATTATAATAATACAGTACCGTAA-------------------AGT----------CTGTTAACGTA-------AATAAGGGCA---TAGA---------GGGCGTGGCTCCACATTGAACATATGCAA----------ATGTATAATTTAAATAT-TATGCACTTCTTCCGAGAGCAGAAAAGTGATAATTAGTAGTGCCCACTCATAAATATGATTGA------GCAACTGCGTGGGCC-TGCGATTAGAGTGCCTAAATTCACCCACAATGGCAG------CATTAATT----------AAACGCTAAATGTGC--TCCAAGT----------------------GCTTACAACTGCAATTGACTTGTTTGSizeHit CountTotal NormTotal
No Reads
droRho1
AAAAACTTTTTT-----------------------TGACAATGATTATTTTAAAAAATGTAATTCTGTTAGTGTA-------GAAGA------AGAAGA---------AGATA-------------------CAAAG----------ATAAGATATTTAAATAT-TATGCCCTTCTATCAAGAGCAGAAAAGTGATAATTAGCAGTGCGCACTCATAAATATTAATGA------GCAATCGCACGGGCC-TACGATTTGAGTACCTAAATTCACTCACAATGGCAG------TATTAATT----------AAACGCTAAATGTTC--CCCAACT----------------------GCTTAAAAGTGCAATTGACTTGTTTGSizeHit CountTotal NormTotal
No Reads
droFic1
AGAAATATATGTACAATT-T------------------------------C--------------------TAAAGATG-TAAAA-AAGACA-TAAAAA---------GGGCGCGGTAACAGACTAGACTC---CGC---TGTTGATCAACATAATTTAAATAT-TATGCACTTCTATTATG----GGAAGGTGATAATTAGCTTTGTGCGCTCATAAATATGCATAAAGA--AGCAACGGCGTGGGCC-GGTGATTAGCGTACCCAAATCCACTAACAATAGCAG------TACAAATT----------AAACTCTAAATGTGA--TCCAAGT----------------------GCTTACAAGTGCAATTGACTTGTTTASizeHit CountTotal NormTotal
No Reads
droKik1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAGCCAAGTGATAATTAGTGGTGCTTACTCATGAGTATGAATGAAAATTAACCATTGCGTGGGCTTCACGACTACAGT----AAACCCACTCCCAAAGGCA-----AACATTAATT----------AAACACCAA-------------------------------------------AAGTGCA-----GTTGTTGASizeHit CountTotal NormTotal
No Reads
droAna3
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTGATAATTAGCTCTGCCCACTTATAAATATGAATGA------GCCGTTGCGTGGGCC-CTCGATTAGAGCGCCGAAATTCACTCACAATGCAAA------CATTAATT----------AAATGCTAAGTGCGAGCTTCTTGTGCCCACGCTAGCTGCTAGCTTGGCCCACAACTGCAACCGGCTTGTTTASizeHit CountTotal NormTotalM044
Female-body		M058
Embryo		V039
Embryo		V055
Head		V105
Male-body		V106
Head
No Reads
droBip1
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGAGTGATAATTAGCTACGCCCACTTATAAATATGAATCA------GCCATTGCGTGGGCC-CTCGATTAGAGTGCCTAAATCCACTCACAATGGCAA------CATTAATT----------AAAAGCTAAGTGCGAGCTTCTAGTGCCCACGCC-------AGCTTGGCTTACAACTGCAACCGGCTTGTTTASizeHit CountTotal NormTotal
No Reads

Generated: 05/18/2015 at 10:35 PM