dme-mir-4940- 12- and 20-way alignments

dme-mir-4940	chr3L:9137692-9137797 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 9137715-9137736
   star strand at position 9137754-9137775
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr3L:9137677-9137812 +	CCAG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAACTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CAT-------------------TGGTTATCCCTTAATTAAA-----------------GCAA--AC-----------AAGATTTGTTTCGGCCGC-CCGATTTT---ACATACAACGACACGAATAGCAGG-----------------------------------------ATATAG
droSim1	chr3L:8545595-8545743 +	CCTG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAGCTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CATAGCAAGC--CCTATCGAATTGGTTATACCT--ATTAAA-----------------GC-A--AC-----------TAGGTTTGTTTCGGCCGC-CCGATTTT---ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG
droSec1	super_0:1396669-1396817 +	CCTG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAGCTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CATAGCAACC--CCTATCGAATCGGTTATACCT--ATTAAT-----------------GC-A--AC-----------TAGGTTTGTTTCGGCCGC-CCGATTTA---ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG
droYak2	chr3L:2783249-2783373 -	CCAG------------------------------------------------------------------------------------ACTCAGACGGACT-------AGCAACTTCGCGATCGGGTGGCGGCTGTAGAT------------------------------------------------------------------------TGT--------------------------CCTTGTATCAAA-----------------GGAA--AA-----------GAGATTTCTTTTGGCCAC-CCGATTCA---AAATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG
droEre2	scaffold_4784:4908876-4909031 -	CCTG------------------------------------------------------------------------------------ACTCAGACGGACT-------AGCAACTTATCGATCGGGTGGCGGATATACCC--------------------------------------------------------------GTGCACAGATTGTAGCACAC--CCTATCGAATTGGAATTCCCC--ATTAAA-----------------ACTG--AG-----------TGGGCTTATATCGGCCGC-CCGATTC----ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG
droAna3	scaffold_13337:19535970-19536137 +	TGTTTCAAGG-------------------ATTC-TTTTGCGAGCCCACCTCAAGGATGTCAAACTCTAGAGATGTCTCTTTTAAACCGACTCAGACGGACTC-------------TACAAATCAGGAAGGGAATAAAAAT-------------------------------------------------------------------------------------------------------------------------------------------------------AGTTTATTTTGACTGC-CCGACTAATATGCATACAACGACAC-AATAGCAGG------------------------------------ACTATCTATAG
dp4	chrXR_group5:393324-393505 -	---G------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTAGCAGTTTAACGATCGGGAAACGGGAATAAAC------------------------------------------------------------------------CAAAGTCGGCAGCCTAT----------------CCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGCTGGTTTATTTACGTTTC-TCGAGCC----ACATACAACGACAC-AACAGCAGGTCTTCAGATAAC-T--------------------------CATATGA
droPer1	super_58:12641-12822 +	---G------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTAGCAGTTTAACGATCGGGAAACGGGAATAAAC------------------------------------------------------------------------CAAAGTCGGCAGCCTAT----------------CCATCAAAATTCCAATAGAATCACAACAGAAACCCAATTTGTTGCTGGTTTATTTACGTTTC-TCGAGCC----ACATACAACGACAC-AACAGCAGGTCTTCAGATAAC-T--------------------------CATATGA
droWil1	Unknown	GACACATATTCAATT--------------ACA---CTTACAGATC---------------------------------------------------------------CACACAATATCTCTAGATATACATATATAGTAAATTGGTTTATATATTCCTTGACTCAGACGGACAAAGCAAATAATAATTATTTGCAGTCTCT----------GGC--------------------------ACTTATAGCATA-----------------TG-----------------------------------------------------AAAGatat-attaatata------------------------------------tatatatataG
droVir3	scaffold_13049:712504-712640 +	CCAGATCGGA---AGGCCATATAGTAAAAGTTCTTGGTATAACCCCTTCTCTATCGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGGT---------CGTTGTAGTTC-TCT---------------CAGTCTC-TGAAACGGATCTTCGAATATCAGCTTATAATCGAGCAATAatatatatatatatat
droMoj3	scaffold_6680:522955-523081 -	ACAG------------------------------------------------------------------------------------ACCCATATATATGC----A--------TACTAACTGAATAATATACATATAT--------------------------------------------------------------GAATGTATATTGTT----------------------------------------------------------------ATGCTGGTGTTGTAGTTTTCTCAGTCTCTGAATTGG---ATATTCGA-----------------------ATATCAGCTTATTGTCGAG---------------CAatat
droGri2	scaffold_15110:1946056-1946101 +	GGATACAATG-------------------CAAT-C--------------------AAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT--------------------------------AATTACAACGATGC-CATTTCTG-----------------------------------------------T

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:9137677-9137812 +	NA	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAACTTATC----GATCGGGTGGCGGATAT----------AGATCAT-----------------T---------G------------GTTA----TCCC-TT---A-------------------------------------------------------------------AT--------T-----AAA----GC--------AAACAAG------ATTTGTTTCGGCCGC---CCGATT-T---------------TACATACAACGACACGAATA----------------------------G---CAGGATATAG
droSim1	chr3L:8545595-8545743 +	6	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAAGCCCTATCGAATT---------G------------GTTA----TACC-TATTAA-----A------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------TACATACAACGACACAATAG--------------------------------CAGGATATAG
droSec1	super_0:1396669-1396817 +	1	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------TATCGCAGCTTATC----GATCGGGTGGCGGATAT----------AGATCATAGCAACCCCTATCGAATC---------G------------GTTA----TACC-TATTAA-----T------------------------------------------------------------------------------------GC--------AA-CTAG------GTTTGTTTCGGCCGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG
droYak2	chr3L:2783249-2783373 -	20	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTCGC----GATCGGGTGGCGGCTGT----------AGATTGT-------------------------------------------------CCT-TG---T-------------------------------------------------------------------AT--------C-----AAA----GG--------AAAAGAG------ATTTCTTTTGGCCAC---CCGATT-C---------------AAAATACAACGACACAATAG--------------------------------CAGGATATAG
droEre2	scaffold_4784:4908876-4909031 -	23	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGATATACCCGTGCACAGATTGTAGCACACCCTATCGAATT---------G------------GAAT----TCCC-CATTAA----AA------------------------------------------------------------------------------------CT--------GA-GTGG------GCTTATATCGGCCGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droEug1	scf7180000409467:339436-339588 +	17	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTGGCGGAAAT----------AGATTGTAGGAAGTTTTACT-AATT---------G------------GACTTT--TCCC-TATATA-----A------------------------------------------------------------------------------------GT--------AA-ATAGAAAATAGTTTATTTTGGCTGC---CCGATT-T---------------AACATACAACGACACAATAG--------------------------------CAGGATATAG
droBia1	scf7180000300910:2070791-2070920 -	17	CCGG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT------------------ATC----GATCGGGTGGCGGAAAT----------AGATTGTAGCC----------ATTT---------G------------GATT----TCCC-C--A-TAGAGAA------------------------------------------------------------------------------------GT--------GA-AT-------AGTTTATTTTGGCTGC---CCGATTCT---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG
droTak1	scf7180000415356:50643-50795 -	11	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GTCACTTATCGATCGATCGGGTGGCGGAAAT----------AGATTGTAGAAAGCTCTATT-AATT---------GAAAAT-----------CCAATCCC-CATATA-----A------------------------------------------------------------------------------------GT--------AA-AT-------AGTTTATTTTGGCTGC---CCGATT-C---------------CACATACAACGACACAATAG--------------------------------CAGGATATAG
droEle1	scf7180000491193:3377542-3377694 +	39	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACACAGACGGACA-------A---GCAACTTATC----GATCGGGTGGCGGCAAT----------AGATTGTAGTAAGCTCTGTT-AATT---------G------------GATATTG--CCCCT--ATA-----A------------------------------------------------------------------------------------GTACAT----AAA-TA--TGATAGTTTATTTTGGCTGC---CCGATT-T----------------TAATACAACGACACAATAG--------------------------------CAGAATATAG
droRho1	scf7180000777034:211800-211946 +	3	CCTG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCAGACGGACT-------A---GCAACTTATC----GATCGGGTAGCGGAATT----------AGATTGTAGTAAGCTCTATT-GATT---------G------------GATATTG--TCG-C--ATA-----A------------------------------------------------------------------------------------GTACGT----AA-AT-------AGTTCATTTTGGCTGC---CCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droFic1	scf7180000454065:2533611-2533748 -	19	CCAG--------------------------------------------------------------------------------------------------------------------------------------------------ACTCGGACGGACT-------G---GGAACTTATC----GATCTTATCG-----AT----------AACTTAT-----------------CGGTTAACT-TCGTTT-----------TCA--GCC-C--A-A-----A------------------------------------------------------------------------------------GT--------AAA-TA--TAGTAGTTTATTTTGGCTACCACCCGATT-C----------------ACATACAACGACACAATAG--------------------------------CAGGATATAG
droKik1	scf7180000302373:173620-173654 -	38	ATTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---------------AAAAAATATATAAGGCATAG--------------------------------TATGGTATAG
droAna3	scaffold_13337:19535893-19536018 +	7	CACT-----GCGATCTCGAGTACTTTGATCTC-------------------------------------------------------------------------------------------------------------------------------------------------TCTTCTC----A--GGGCCCCAAAAAGT----------ATGCTATGAAATATTTCGTT-TGCT---------A------------------------------------------------------------------------------------------------------------------AAG----TG--------TTTCAAG------GATTCTTTTGCGAGC---C----------------------------CACCTCAAGGATGT--------------------------------CAAACTCTAG
droBip1	scf7180000396360:730594-730829 +	17	AAAAACACTGCGATCTCGAGTACTTTGATCTCTCTTCTCAGGGCCCCAAAAAGTATGCTATGAAATGTTTCATTGCCAAAGTGTTTCAGAGGATCCTTTTGAGAGCCCAACTCACGGACGTCAAACTCTAGAGATGTCTCTTTTAAACCGACTCAGACGGACTTTGGTCT--TTGCAGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--AGG----CAGATCAGGCAGG---ACTATA-T----------------ACATACAACGACACAATAGCAGGACTAT---------------------------CTATAG
dp4	chrXR_group5:393309-393508 -	56	C-AG--------------------------------------------------------------------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTA---GCAGTTTAAC----GATCGGGAAACGGGAAT----------AAACCAAAGTCGGC---------------------------------------------------------------------AGCCTATCCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGC-----------------------------------T-------GGTTTATTTACGTTTC---TCGAGC-C----------------ACATACAACGACACAACAGCAGGTCTTCAGATAACTCATATGAAATAT---ACTTATGCGG
droPer1	super_9:3484001-3484112 -	41	GCAT--------------------------------------------------------------------------------------------------------------------------------------------------ACATAGGCATCGC-------A---TCCA------------TCGGG--------------------------------------------------------------------GTC----ACCC-G--G-TGGAGGA---------------------------------------------------TAAATTTTGCGG--TGGTAACCCCGCAACACAAGCACTC------------------------------------------A---------------CACACACAGCGACCCAAACA----------------------------C---GTGCAATAAC
droWil1	scaffold_181096:6035694-6035827 -	107	TCAG--------------------------------------------------------------------------------------------------------------------------------------------------GCCTAAAATTAGT-------TGCCATAACT-CTC----ATTTATATAGTAGATTT----------GATGCTTTTTTG-----------------------------------------------------------------TTTT----------------------------------------------------TT--------T-----AAT----AT--------AT-TAAA------ATTTTTATTA-ATGC--------------ATTTCAGTGTAAAAATTAAAATGACACATTTT----------------------------T---CCTTACGTAA
droVir3	scaffold_13246:101577-101715 -	373	CAGG-----------------------------------------------------------------------------------------------------------------------------------------------------CAGACGAAA--------------GTATCTCC----GACCCCATGAAGTGTAT----------ATATTCT-----------------TGATCAGCATCAATAGCTGAGTCGAT-------------GTA-----GCCATGTCCGTCT------------------------------------------------------------------------------------------------GCCTGTCCGTCCGT---CCGTCC-GTATGTA--------------TGAACGCAAGGATCT--------------------------------CAGAACCTTT
droMoj3	scaffold_6540:2381798-2381917 -	402	GTAG--------------------------------------------------------------------------------------------------------------------------------------------------ATTCAGTTGTACT-------TTATAGAA--TTTC----GATTTA------------------------------------------TGT----------TAAAAT-----------TCA--TCC-C--T-T-------------------------------------------------------------------AC--------C-----AAT----AT--------AT-ATG-------TGTTTTTTCAAATGC-ATGCATT--T---------------TAATGGTATCAACACAATTT----------------------------G---AAAGTCTCAT
droGri2	scaffold_15074:3698733-3698860 +	83	CTGA--------------------------------------------------------------------------------------------------------------------------------------------------ACATAACTGAATA-------A---ATT-----------------------------------------------------------------------------------------------------------------------------------------------------CACAACAT--ATTTAGTCAGTTACTTATGTATATACTTGATACAATTGTGCAAACATGCAAA------ATTCCAATTAAATGT--------------------------------------CACAATAT------------------ATAAAAACTGATGCGAGAAGATTG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CCAG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAACTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CAT-------------------TGGTTATCCCTTAATTAAA-----------------GCAA--AC-----------AAGATTTGTTTCGGCCGC-CCGATTTT---ACATACAACGACACGAATAGCAGG-----------------------------------------ATATAG

Size

Hit Count

Total Norm

droSim1

CCTG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAGCTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CATAGCAAGC--CCTATCGAATTGGTTATACCT--ATTAAA-----------------GC-A--AC-----------TAGGTTTGTTTCGGCCGC-CCGATTTT---ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................................................................................................................AC-----------TAGTTTTGTTTCGGCT.....................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..............................................................................................................................TGGCGGATATAGAT------------------------------------------------------------------------CATAGCAAGC--......................................................................................................................................................................	24	1	2.00	0.00	2.00	0.00	0.00
................................................................................................GGACTT----ATCGCAGCTTATCGATC...........................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................................TGGCGGATATAGAT------------------------------------------------------------------------CATAGC............................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................................C-A--AC-----------TAGGTTTGTTTCGGCCGC-C.................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................T-A--AC-----------TAGTTTTGTTTCGGCC.....................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................TAGCAAGC--CCTATCGAATTG..........................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droSec1

CCTG------------------------------------------------------------------------------------ACTCAGACGGACTT----ATCGCAGCTTATCGATCGGGTGGCGGATATAGAT------------------------------------------------------------------------CATAGCAACC--CCTATCGAATCGGTTATACCT--ATTAAT-----------------GC-A--AC-----------TAGGTTTGTTTCGGCCGC-CCGATTTA---ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................................................................................................................................................CC--CCTATCGAATCGGTTATACCT--...............................................................................................................................................	23	1	1.00	0.00	0.00	1.00

droYak2

CCAG------------------------------------------------------------------------------------ACTCAGACGGACT-------AGCAACTTCGCGATCGGGTGGCGGCTGTAGAT------------------------------------------------------------------------TGT--------------------------CCTTGTATCAAA-----------------GGAA--AA-----------GAGATTTCTTTTGGCCAC-CCGATTCA---AAATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................CTCGCGATCGGGTGGT....................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................CTACxCGATCGGGTGGC....................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................................CAGACGGACT-------AGCAACTTCGCGATC...........................................................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................CTACGxGATCGGGTGGCGG..................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................................................................................................AGGGATCGGGTGGCGG..................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................................AGTGATCGGGTGGCGG..................................................................................................................................................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CCTG------------------------------------------------------------------------------------ACTCAGACGGACT-------AGCAACTTATCGATCGGGTGGCGGATATACCC--------------------------------------------------------------GTGCACAGATTGTAGCACAC--CCTATCGAATTGGAATTCCCC--ATTAAA-----------------ACTG--AG-----------TGGGCTTATATCGGCCGC-CCGATTC----ACATACAACGACAC-AATAGCAGG-----------------------------------------ATATAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................................T-------AGCAACTTATCGATCGGGTGGC....................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................TATCGATCGGGTGGCGGAT................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................................................................................TTGGAATTxCCC--ATTAAA-----------------AGTG--..................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................AACTTATCGATCGGGTGGCG...................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00

droAna3

TGTTTCAAGG-------------------ATTC-TTTTGCGAGCCCACCTCAAGGATGTCAAACTCTAGAGATGTCTCTTTTAAACCGACTCAGACGGACTC-------------TACAAATCAGGAAGGGAATAAAAAT-------------------------------------------------------------------------------------------------------------------------------------------------------AGTTTATTTTGACTGC-CCGACTAATATGCATACAACGACAC-AATAGCAGG------------------------------------ACTATCTATAG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
............................................................................................................................GGACGGGAATAAAGAT-------------------------------------------------------------------------------------------------------------------------------------------------------AGT................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................AGGAAGGGAAAAAAAAT-------------------------------------------------------------------------------------------------------------------------------------------------------A..................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................TCAGGAAGGGAATAAAAAT-------------------------------------------------------------------------------------------------------------------------------------------------------AGTTT..............................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................GTCAGGAAGGGAGTAAAAA...........................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................GACTC-------------TACAAATCAGGAAGGGA..................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00

dp4

---G------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTAGCAGTTTAACGATCGGGAAACGGGAATAAAC------------------------------------------------------------------------CAAAGTCGGCAGCCTAT----------------CCATCAAAATTCCAATATAATCACAACAGAAATCCAATTTGTTGCTGGTTTATTTACGTTTC-TCGAGCC----ACATACAACGACAC-AACAGCAGGTCTTCAGATAAC-T--------------------------CATATGA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................................................................AACGGGTAACGGGAATAA............................................................................................................................................................................................................................................................	18	1	16.00	16.00	0.00	0.00	0.00
.......................................................................................................AATCTAGCAGTTTAACGCTCGGGG.......................................................................................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00

droPer1

---G------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTAGCAGTTTAACGATCGGGAAACGGGAATAAAC------------------------------------------------------------------------CAAAGTCGGCAGCCTAT----------------CCATCAAAATTCCAATAGAATCACAACAGAAACCCAATTTGTTGCTGGTTTATTTACGTTTC-TCGAGCC----ACATACAACGACAC-AACAGCAGGTCTTCAGATAAC-T--------------------------CATATGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................................................................AACGGGTAACGGGAATAA............................................................................................................................................................................................................................................................	18	1	4.00	4.00	0.00	0.00	0.00	0.00
.....................................................................................................................................................................................................................AAAGTCGGCAGCCTAT----------------CC...............................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................................................................................................................................................................................................................................................................ATCCAATTTGTTGCTGTT................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
...G------------------------------------------------------------------------------------ACTTAGACGGACTTCAATCTAGCAGT....................................................................................................................................................................................................................................................................................	27	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................................................................................AAC------------------------------------------------------------------------CAAAGTCGGCAGCCTAT----------------.................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................AACAGCAGGTCTTCAGATAAC-T--------------------------C......	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................AATCTGGCAGTGTAACGA.............................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................................................................................................TGAAAATTCCAATTGAAT............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................AATCTAGCAGTGTAAGGA.............................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GACACATATTCAATT--------------ACA---CTTACAGATC---------------------------------------------------------------CACACAATATCTCTAGATATACATATATAGTAAATTGGTTTATATATTCCTTGACTCAGACGGACAAAGCAAATAATAATTATTTGCAGTCTCT----------GGC--------------------------ACTTATAGCATA-----------------TG-----------------------------------------------------AAAGatat-attaatata------------------------------------tatatatataG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................................................................................................................................................................................................................................................................................ATTAATATA------------------------------------AAGATATATA.	19	1	4.00	0.00	4.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TTT-ATTAATATA------------------------------------TATATA.....	18	2	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................GAATAATTATTTGCAGTCT..............................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................TATACATATATAGxGAATTGGTTTATAT.............................................................................................................................................................................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................AT-ATCAATATA------------------------------------TATATATGT..	20	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................A-ATTAATATA------------------------------------TATATATAT..	19	4	0.25	0.00	0.25	0.00	0.00
..............................................................................................................................................................................AAGCAAAAAGTAATTATTT.....................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TAT-ATACATATA------------------------------------TATATATATA.	22	5	0.20	0.00	0.20	0.00	0.00
............................................................................................................................................AATTGGTTTATATATTTTTT......................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................ATCT-ATTTATATA------------------------------------TATATAT....	20	1	1.00	0.00	1.00	0.00	0.00
...........AATT--------------ACA---CTTAAAGAAC---------------------------------------------------------------C.........................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................................................................................T-ATTTATATA------------------------------------TGTATATAT..	19	4	0.25	0.00	0.25	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TAT-ATAGATATA------------------------------------TATATATAT..	21	4	0.25	0.00	0.00	0.25	0.00
................................................................................................................................................................GACTCAGACGGACAAAGCAAATGGTA............................................................................................................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................GACTCAGACGGACAAAGCA...................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droVir3

CCAGATCGGA---AGGCCATATAGTAAAAGTTCTTGGTATAACCCCTTCTCTATCGAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGGT---------CGTTGTAGTTC-TCT---------------CAGTCTC-TGAAACGGATCTTCGAATATCAGCTTATAATCGAGCAATAatatatatatatatat

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ACAG------------------------------------------------------------------------------------ACCCATATATATGC----A--------TACTAACTGAATAATATACATATAT--------------------------------------------------------------GAATGTATATTGTT----------------------------------------------------------------ATGCTGGTGTTGTAGTTTTCTCAGTCTCTGAATTGG---ATATTCGA-----------------------ATATCAGCTTATTGTCGAG---------------CAatat	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................................................................................................................................................................................T----------------------------------------------------------------ATGCTGCTGATGTAGTT.............................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................TT----------------------------------------------------------------ATGCTGGTGTTGTCGC..............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................TGAAxAATATACATATAT--------------------------------------------------------------GT..........................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................................GTTGTT----------------------------------------------------------------ATGCTCGTGTTGT.................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................TGCTGTTGTAGTTTTCTCCGTCTC..................................................................................	24	1	1.00	0.00	0.00	0.00	1.00

droGri2

GGATACAATG-------------------CAAT-C--------------------AAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGAT--------------------------------AATTACAACGATGC-CATTTCTG-----------------------------------------------T

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image