block92371- 12- and 20-way alignments

block92371	chr2L:6973236-6973348 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 6973248-6973268
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:6973221-6973363 -	CGCGCCG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATATTCG-----GCGA-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCCCCATCT-------------CGGATATTACGTGACTTAATGCAAGGCTTTTGGCG-------------------------------------------------------------------------ATTAAAGTCAAGCGGAGAT
droSim1	chr2L:6769566-6769704 -	CCC--CG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCCACATCT-------------CGGATATTACGTGGCTTAATGCCAGGCTTTG-GAG-------------------------------------------------------------------------ATCAAAGTCGAGCGGAGAT
droSec1	super_3:2505870-2506007 -	CCC--CG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCAAGGCTTTG-GAG-------------------------------------------------------------------------ATCAAAGTCGAGCGGAGAT
droYak2	chr2L:5936133-5936278 +	CCC--C-------------AAGAATACTCACTG------------GCGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC--CATCCATCTAT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCCAGGCTTGG--AGAGACGAGGAG-------------------------------------------------------------------GAGTCGAGCAGAGAC
droEre2	scaffold_4929:15889020-15889153 -	CC-----------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATGGCTG------CGG-------TCCA----TC---TTCGA-TC------CATCTGT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCAAGGCTTGG--AG-------------------------------------------------------------------------AGGAAAGTCGAGAGGAGAC
droAna3	scaffold_12916:53086-53238 -	CTC--AC--------------AAATACTCACTGTA----------ATGAGCCTTGCATTGAATCAACGTAATAGCTGTGTCGG--C-------TCTA----TT---TTGGT-CC------GAAATTC--------AG-----TCCC-AATCT-------------GGGATATTACGTGGCTTAATGTAAGGCTTTG--G-----------------------------------------------------------GAGCTGCTTGAAGAAAT--AAATTTAAAAAAGGA
dp4	chr4_group1:3766096-3766258 +	CCC--CA--------------AAATACTCATTGGAGG--------GAGAGCCTTGCATTGAATCAACGTAATTGCTG------TGA-------ACAA----AA----------T------CATCTATCGAATCCGAG-----TCCA-AATGTCAGCCAATTACAGCAGCAATTACGTGGCTTAATGCCAGGCTTTA--AGAGA-GAGA--C----------------------------------------------AGAGCTGCTC---------------GAAACGAAGC
droPer1	super_5:1509795-1509959 -	CCC--CA--------------AAATACTCATTGGAGG--------GAGAGCCTTGCATTGAATCAACGTAATTGCTG------TGA-------ACAA----AA----------T------CATCTATCGAATCCGAG-----TCCA-AATGTCAGCCAATAACAGCAGCAATTACGTGGCTTAATGCCAGGCTTTA--AGAGA-GAGAGAG----------------------------------------------AGAGCTGCTC---------------GAAACGAAGC
droWil1	scaffold_180772:7270850-7270976 +	CAC--AA--------------AAATA---AAAA------------GTTAGCCTAGCATTGAATCGACGTAATAGTTT------GAGTTCATA-----------------AA-TC------CATTG--------------------A-AACTT-------------TGACAATTACGTGACTTAATGCTAAGCTTTG--TAACA-AA-------------------------------------------------------------------ATGAAAATAGAAAAGAAAC
droVir3	scaffold_12963:3413641-3413813 -	CCC--CCAAAAA-------AAAAATACTCATTGAAAGCGT-GTTTGAAAGCTTTGCATTGAATCGCAGTAATCGGCT------GGATTCACA-----------------GAAACCTTAGA----------ACTCTATTATAACTTTTTAAAT----------CAGCTGCAATTACGTGGCTTAATGCAAAGCTTGG--AATGT-GAGGAAA----------------------------------------------AAAGCAGCTTT-----------------ATGAAAA
droMoj3	scaffold_6500:13787238-13787459 -	CCC--CAGGAAGAGAATCATAAAATACTCATTGAGAGCGTTATGCAAAAGCTTTGCATTGAATCGCCGTAATCGC---------AGTCCACACTTTAGATATTTTTTT-GTAACCTTCGA----------A------------------AAT----------CAGCTGCAATTACGCGGCTTAATGCAAAGCTTAT--GATGC-AAGAAAAAAAAGAACGtttTtTTttTGtTttttTttgttTttttttTTttttGAAAGCTGCTTT-----------------ATGAAAA
droGri2	scaffold_15252:2977191-2977338 -	ACA--A-------------TAAAATACTCATTAAAAGCTTCATTTGAAAGCTTTGCATTGAATCGCAGTAATCTC---------GAGCTACA---------T---------ATCCTTAGA----------ACT-------------TTATTG----------CTGTTTTAATTACGTGGCTTAATGCAAAGCTTGA--AATAA-ACG---A----------------------------------------------AAAGCTGCTTT-----------------ATGAAAA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:6973221-6973363 -	NA	CGCGCCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATATTC-GGCGAT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC--CATC--------T---CGGATATTACGTGACTTAATGCAAGGCTTTTGGC---------------------------------------------------------------GATTAAAGTCAAG-----------------------CGGAG-------AT
droSim1	chr2L:6769566-6769705 -	4	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCA--CATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droSec1	super_3:2505870-2506008 -	3	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droYak2	chr2L:5936133-5936280 +	1	CC---CCAAGAATACTCACT------------GG----CGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATCCATCC-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTG-G-AGAGA-CGAG----------------------------------------------GAG----------GAGTCGAG-----------------------CAGAG-----ACGC
droEre2	scaffold_4929:15889020-15889155 -	2	CC----CAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATGGCT--GCGGT-------------CC-ATCTTCG-ATC----C-ATCTGTAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTG-G-A----------------------------------------------------------GAG-----GAAAGTCGAG-----------------------AGGAG-------AC
droEug1	scf7180000409463:94621-94763 -	1	CC----CACAAATACTCACT------------TG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------ACC-GCTTTCG-ATC----C-ATCTACAGTCTCA---ATC--------T---CGGATATCACGTGACTTAATGCAAGGCTCC-A-A----------------------------------------------------------AAGCTGCTTGAAAATGCG---------------------AGTCGAG-------AA
droBia1	scf7180000302422:2439201-2439346 +	2	CC-----AAAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAACT--GCTAC------------ACC-GCTTTCG-ATC----C-AACTTCAGTCCCA---ACCTCCA--TTT---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCA-------AG
droTak1	scf7180000416008:231160-231307 -	1	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC-------TTC--TTC-GCTTTCG-ATC----C-ATCTTCAGTCCCA---ATCTC-------ACGTGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCG-------AG
droEle1	scf7180000490640:333648-333793 +	2	CC-----ACAAATACTCACT------------GG----AGAGCCTTGTATTGAATCAACGTAATAGCT--GCGAT------CGTCTAATC-GTCTTCG-ATC----C-ATCTTCAGTCCCA---ATC--------G---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-A----------------------------------------------------------GAGCTGATTGAAAACGCG-----------------------ATACG-------AT
droRho1	scf7180000779930:68908-69048 -	1	CC-----ACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATAGCC--GCGAC------------ATC-GTTTTCG-ATC----C-ATCTTCAGTCCCA---GTC--------C---CGGATATTACGTGGCTTAATGCAAGGCTTA-G-A----------------------------------------------------------GAGCTGCTTGAA-TCGCG---------------------ATACGAG-------AC
droFic1	scf7180000452011:146-285 -	1	CC-----AAAAATACTCACT------------GG----GGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------CTC-GTTTTCG-ATC----C-ATCTTTAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-G----------------------------------------------------------GAGCCGATTGAAGTCGAG-----------------------ACGAG-------AG
droKik1	scf7180000302468:483720-483875 -	1	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATGGTCTCGCGAC-------------AC-GATTTCG-AAC----C-ATCTTCAGTCCCAAATATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTAC-G-A----------------------------------------------------------GAGCTCCTTCAGAACGCG----AC--------AA-AACGTAACGAG-------AC
droAna3	scaffold_12916:53076-53242 -	1	GGCGCTCACAAATACTCACT------------GTAA--TGAGCCTTGCATTGAATCAACGTAATAGCT--GTGTC-------GGC---TCTATTTTGG-TCC----G-AAATTCAGTCCCA---ATC--------T---GGGATATTACGTGGCTTAATGTAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTTGAAGAAATA--AATTTA------AA-AAA----GGAGAAAGACCTT
droBip1	scf7180000392937:103419-103594 -	1	GGCGCCCACAAATACTCACT------------GAAT--AGAGCCTTGCATTGAATCAACGTAATAGCT--GTGAC-------AGC---TC-TATTCCG-GTC----CAAACTTCAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTCGAAAAAAAATTAAAATAACTTTAAAGAAA--AACGCA--AGACCTT
dp4	chr4_group1:3766092-3766263 +	1	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAG--CCA---ATT--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAG------------------------------------------------ACAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droPer1	super_5:1509790-1509963 -	2	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAGC--CA---ATA--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAGAG----------------------------------------------AGAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droWil1	scaffold_180772:7270846-7270981 +	1	TGAACACAAAAAT---AAAA------------AG----TTAGCCTAGCATTGAATCGACGTAATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------GAA---ACT--------T---TGACAATTACGTGACTTAATGCTAAGCTTT-G-T----------------------------------------------------------AA-CAAAATGAA----------AATA------GA-AAAGAAACAAG-------AT
droVir3	scaffold_12963:3413645-3413810 -	4	CCAAAAAAAAAATACTCATTGAAAGCGT-GTTTG----AAAGCTTTGCATTGAATCGCAGTAATCGGCT-GGATT-CACAGAAA--------CCTTAG-AAC----T-CT--ATTATAACT---TTT---TA-AATCAGCTGCAATTACGTGGCTTAATGCAAAGCTTG-G-AATGTGAGGA----------------------------------------------AAAAAGCAGCTTT---------------------------------AT---------G
droMoj3	scaffold_6500:13787240-13787449 -	3	AGAATCATAAAATACTCATTGAGAGCGTTATGCA----AAAGCTTTGCATTGAATCGCCGTAATCGCA--GT--C------------CAC-ACTTTAG-ATA----T-TTT-TTTGTAACC---TTC---GAAAATCAGCTGCAATTACGCGGCTTAATGCAAAGCTTA-T-GATGCAAGAAAAAAAAGAACGAAATATTAATGATAAAATAACAATAAAAAATTAAAAGAAAGCTGCTTT---------------------------------ATG-------AA
droGri2	scaffold_15252:2977193-2977325 -	5	CA----TTAAAAGCTTCATT------------TG----AAAGCTTTGCATTGAATCGCAGTAATCTCG-AGCTAC------------ATA-TCCTTAG-AAC----T-TT--------------ATT--------GCTGTTTTAATTACGTGGCTTAATGCAAAGCTTG-A-AATAAACGA-------------------------------------------------AAAGCTGCTTT---------------------------------ATG-------AA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CGCGCCG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATATTCG-----GCGA-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCCCCATCT-------------CGGATATTACGTGACTTAATGCAAGGCTTTTGGCG-------------------------------------------------------------------------ATTAAAGTCAAGCGGAGAT

Size

Hit Count

Total Norm

droSim1

CCC--CG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCCACATCT-------------CGGATATTACGTGGCTTAATGCCAGGCTTTG-GAG-------------------------------------------------------------------------ATCAAAGTCGAGCGGAGAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......G------------AAGAATACTCACTG------------GAGAGC.................................................................................................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
............................CACTG------------GAGAGCCTGGCAA..........................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

CCC--CG------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC------CATCTAT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCAAGGCTTTG-GAG-------------------------------------------------------------------------ATCAAAGTCGAGCGGAGAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....CG------------AAGAATACTCACTG------------GAGAGC.................................................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
......................................................................................................................................................................................AATGAAGGGCTTTG-GAG-------------------------------------------------------------------------A..................	18	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................................TG-GAG-------------------------------------------------------------------------ATCAAAGTCGAGCGG....	20	1	1.00	0.00	0.00	1.00
.......................ATACTCACTG------------GAGAGCCTTGC............................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00

droYak2

CCC--C-------------AAGAATACTCACTG------------GCGAGCCTTGCATTGAATCAACGTAATAGCTG------CGG-------TCCA----TC---TACGA-TC--CATCCATCTAT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCCAGGCTTGG--AGAGACGAGGAG-------------------------------------------------------------------GAGTCGAGCAGAGAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................................................................................................................ATGG--AGAxACGAGGAG-------------------------------------------------------------------GAGT...........	19	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................GGACGAGGAG-------------------------------------------------------------------GAGGCGA........	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................GTG--AGxGACGAGGAG-------------------------------------------------------------------GAGT...........	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CC-----------------AAGAATACTCACTG------------GAGAGCCTTGCATTGAATCAACGTAATGGCTG------CGG-------TCCA----TC---TTCGA-TC------CATCTGT--------AG-----TCCC-CATCT-------------CGGATATTACGTGGCTTAATGCAAGGCTTGG--AG-------------------------------------------------------------------------AGGAAAGTCGAGAGGAGAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................................................................................................................TTACGTGGCTTAATGCAAGTCTT..................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00

droAna3

CTC--AC--------------AAATACTCACTGTA----------ATGAGCCTTGCATTGAATCAACGTAATAGCTGTGTCGG--C-------TCTA----TT---TTGGT-CC------GAAATTC--------AG-----TCCC-AATCT-------------GGGATATTACGTGGCTTAATGTAAGGCTTTG--G-----------------------------------------------------------GAGCTGCTTGAAGAAAT--AAATTTAAAAAAGGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................G--C-------TCTA----TT---TTGGT-CC------GAAATTC--------.............................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.......................................................................................................................................................................GATATTACGTGGCTTAATGTA........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................GTGGCTTAATGTAAGGCTTTG--G-----------------------------------------------------------GA................................	24	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................AGAAGT--AAATTAAAAAAA...	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................GCTGCTAGAAGAAAT--AGATT..........	20	1	1.00	0.00	1.00	0.00	0.00
................................................AGCCTTGCATTGAATCAACGTAATA...........................................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00

dp4

CCC--CA--------------AAATACTCATTGGAGG--------GAGAGCCTTGCATTGAATCAACGTAATTGCTG------TGA-------ACAA----AA----------T------CATCTATCGAATCCGAG-----TCCA-AATGTCAGCCAATTACAGCAGCAATTACGTGGCTTAATGCCAGGCTTTA--AGAGA-GAGA--C----------------------------------------------AGAGCTGCTC---------------GAAACGAAGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................................................................................................................................................AGAGA-GAGA--C----------------------------------------------AGAGGAGCTC---------------..........	20	1	5.00	1.00	0.00	0.00	4.00
................................................................................................................................................................................................TGTT--AGAGA-GAGA--C----------------------------------------------AGAGC..............................	19	1	2.00	1.00	0.00	0.00	1.00
.............................................................................................................................................................................................................AGA--C----------------------------------------------AGAGCTGCTC---------------GAAACGAA..	22	1	1.00	1.00	0.00	0.00	0.00

droPer1

CCC--CA--------------AAATACTCATTGGAGG--------GAGAGCCTTGCATTGAATCAACGTAATTGCTG------TGA-------ACAA----AA----------T------CATCTATCGAATCCGAG-----TCCA-AATGTCAGCCAATAACAGCAGCAATTACGTGGCTTAATGCCAGGCTTTA--AGAGA-GAGAGAG----------------------------------------------AGAGCTGCTC---------------GAAACGAAGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................................................................................................GTA--AGAGA-GAGAGAG----------------------------------------------AGAGC..............................	20	1	4.00	0.00	0.00	0.00	0.00	4.00
..................................................................................................................................................................................................AC--AGAGA-GAGAGAG----------------------------------------------AGAGC..............................	19	3	1.33	0.33	0.33	0.00	0.00	0.67
...................................................................................................................................................................................................G--AGAGA-GAGAGAG----------------------------------------------AGAGG..............................	18	14	0.21	0.21	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................................GAGA-GAGAGAG----------------------------------------------AGAGAGG............................	18	14	0.21	0.21	0.00	0.00	0.00	0.00
...................................................................................................................................................................................................T--AGAGA-GAGAGAG----------------------------------------------AGAGA..............................	18	12	0.17	0.08	0.08	0.00	0.00	0.00
.................................................................................................................................................................................................CAA--AGAGA-GAGAGAG----------------------------------------------AGA................................	18	7	0.29	0.29	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................GTG--AGAGA-GAGAGAG----------------------------------------------AGA................................	18	11	0.18	0.18	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................TAG--AGAGA-GAGAGAG----------------------------------------------AGA................................	18	12	0.17	0.08	0.08	0.00	0.00	0.00
...................................................................................................................................................................................................C--AGAGA-GAGAGAG----------------------------------------------AGAGC..............................	18	5	0.40	0.00	0.20	0.00	0.00	0.20
..................................................................................................................................................................................................TG--AGAGA-GAGAGAG----------------------------------------------AGAGA..............................	19	9	0.22	0.11	0.00	0.00	0.11	0.00
......................................................................................................................................................................................................AGAGA-CAGAGAC----------------------------------------------AGAGCT.............................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
......................................................................................................................................................................................................AGAGA-GAGAGAG----------------------------------------------AGAGCT.............................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................GCTGTA--TGAGA-GAGAGAG----------------------------------------------A..................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................AA--AGAGA-GAGAGAG----------------------------------------------CGAGC..............................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................GAGA-GAGAGAG----------------------------------------------AGAGATG............................	18	7	0.14	0.14	0.00	0.00	0.00	0.00
......................................................................................................................................................................................................AGAGA-GGGAGAG----------------------------------------------AGGGCT.............................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................TCG--AGAGA-GAGAGAG----------------------------------------------AGAG...............................	19	7	0.14	0.00	0.00	0.00	0.00	0.14
.................................................................................................................................................................................................CAA--AGAGA-GAGAGAG----------------------------------------------AGAG...............................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................CG--AGAGA-GAGAGAG----------------------------------------------AGAGC..............................	19	6	0.17	0.00	0.00	0.00	0.00	0.17
..................................................................................................................................................................................................AA--AGAGA-GAGAGAG----------------------------------------------AGAC...............................	18	7	0.14	0.00	0.00	0.00	0.00	0.14
......................................................................................................................................................................................................AGAGA-GAGAGAG----------------------------------------------AGAGGT.............................	18	6	0.17	0.00	0.00	0.00	0.00	0.17
...................................................................................TGA-------ACAA----AA----------T------CATCTATCGAATCCGA............................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................CA--ATAGA-GAGAGAG----------------------------------------------AGAG...............................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
................................................................................................................................................................................................TCTG--AGAGA-GAGAGAG----------------------------------------------AGA................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................GTTG--AGAGA-GAGAGAG----------------------------------------------AGAG...............................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................................................AGCGA-GAGAGAG----------------------------------------------AGAGTT.............................	18	3	0.33	0.00	0.00	0.00	0.33	0.00
.......................................................................................................................................................................................................GAGA-GAGAGAG----------------------------------------------AGAGAGGC...........................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................GCTTGT--AGAGA-GAGAGAG----------------------------------------------...................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................GTA--ACAGA-GAGAGAG----------------------------------------------AGA................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
.................................................................................................................................................................................................TTG--AGAGA-GATAGAG----------------------------------------------AGAGC..............................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................A--AGAGA-GAGAGAG----------------------------------------------AGAGA..............................	18	14	0.07	0.00	0.07	0.00	0.00	0.00
..................................................................................................................................................................................................AA--AGAGA-GAGAGAG----------------------------------------------AAAG...............................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...............................................................................................................................................................................................CTTCG--AGAGA-GAGAGAG----------------------------------------------AGA................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................AA--AGAGA-GAGAGAG----------------------------------------------AGAGA..............................	19	10	0.10	0.00	0.00	0.00	0.10	0.00
..................................................................................................................................................................................................TG--AGAGA-GATAGAG----------------------------------------------AGAGC..............................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................................................AGAGA-GAGAGAG----------------------------------------------AGAGATG............................	19	6	0.17	0.17	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................TGT--AGAGA-GAGAGAG----------------------------------------------AGA................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................................................ATG--AGAGA-GAGAGAG----------------------------------------------AGA................................	18	8	0.13	0.13	0.00	0.00	0.00	0.00
......................................................................................................................................................................................................AGAGA-GAGAGAG----------------------------------------------AGAGGG.............................	18	10	0.10	0.00	0.00	0.00	0.10	0.00
..............................................................................................................................................................................................GCTGTG--AGAGA-GAGAGAG----------------------------------------------A..................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................................................................................................................................A--TGAGA-GAGAGAG----------------------------------------------AGAGA..............................	18	8	0.13	0.13	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................ATA--AGCGA-GAGAGAG----------------------------------------------AGAG...............................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................ATA--AGCGA-GAGAGAG----------------------------------------------AGA................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
...................................................................................................................................................................................................A--AGAAA-GAGAGAG----------------------------------------------AGAGA..............................	18	5	0.20	0.20	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................GTC--AGAGA-GAGAGAG----------------------------------------------AGAG...............................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................TGT--AGAGA-GAGAGAG----------------------------------------------AGAG...............................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................TGA--CGAGA-GAGAGAG----------------------------------------------AGA................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
..........................................................................................................................................................................................CCAGGCTTTA--AGAGA-GAGA....................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................CTAA--AGAGA-GAGAGAG----------------------------------------------AG.................................	18	2	0.50	0.00	0.50	0.00	0.00	0.00
.................................................................................................................................................................................................GTA--AGAGA-GxGAGAG----------------------------------------------AGAGC..............................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................A--AGAAA-GAGAGAG----------------------------------------------AGAGATG............................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CAC--AA--------------AAATA---AAAA------------GTTAGCCTAGCATTGAATCGACGTAATAGTTT------GAGTTCATA-----------------AA-TC------CATTG--------------------A-AACTT-------------TGACAATTACGTGACTTAATGCTAAGCTTTG--TAACA-AA-------------------------------------------------------------------ATGAAAATAGAAAAGAAAC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................................................................................................................................................A-AACTT-------------TGACAATTACGTGACT...............................................................................................................	22	1	21.00	0.00	9.00	1.00	11.00
.....................................................................AATAGTTT------GAGTTCATA-----------------AA-TC------CATT........................................................................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................................................................................................A-------------------------------------------------------------------AGGAAAAGAGAAAAGAA..	18	1	1.00	0.00	0.00	1.00	0.00
................................................AGCCTAGCATTGAATCGACGTAATA...........................................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................ATAAAAAAAGAAAAGAAA.	18	3	0.33	0.00	0.33	0.00	0.00
.................................................GCCTAGCATTGAATCGACGT...............................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................CATA-----------------AA-TC------CATTG--------------------A-AACTT-------------T..............................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................A-AACTT-------------TGACAATTATGTGACT...............................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................A-AACTT-------------TGACAATTACGTGAC................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
......................................................................ATAGTTT------GAGTTCATA-----------------AA-TC------CATT........................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................ACGTGACTTAATGCTAAGC....................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................................A-AA-------------------------------------------------------------------AGGAAAAxAGAAAAGA...	18	2	0.50	0.00	0.00	0.50	0.00
......................AATA---AAAA------------GTTAGCCTAGC............................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................TAACA-AA-------------------------------------------------------------------AxGAAAATAAAAA......	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................ATAAAAAGAGAAAAGAAA.	18	2	0.50	0.00	0.50	0.00	0.00

droVir3

CCC--CCAAAAA-------AAAAATACTCATTGAAAGCGT-GTTTGAAAGCTTTGCATTGAATCGCAGTAATCGGCT------GGATTCACA-----------------GAAACCTTAGA----------ACTCTATTATAACTTTTTAAAT----------CAGCTGCAATTACGTGGCTTAATGCAAAGCTTGG--AATGT-GAGGAAA----------------------------------------------AAAGCAGCTTT-----------------ATGAAAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................................................................................................................................TTGG--AATAA-GAGGAAA----------------------------------------------AAA................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................TGG--AATGT-AAAGAAA----------------------------------------------AAAGCA.............................	21	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

CCC--CAGGAAGAGAATCATAAAATACTCATTGAGAGCGTTATGCAAAAGCTTTGCATTGAATCGCCGTAATCGC---------AGTCCACACTTTAGATATTTTTTT-GTAACCTTCGA----------A------------------AAT----------CAGCTGCAATTACGCGGCTTAATGCAAAGCTTAT--GATGC-AAGAAAAAAAAGAACGtttTtTTttTGtTttttTttgttTttttttTTttttGAAAGCTGCTTT-----------------ATGAAAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...................................................................................................................................................................................................................AGAAGAAxGTTTTTTTTTT..............................................................	18	2	4.00	0.00	0.50	1.00	2.50
............................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT....................................	36	24	0.13	0.00	0.00	0.00	0.13
.............................................................................................................................................................................................................................TTTTTTTTTGTTTTTTGTAG...................................................	20	2	0.50	0.00	0.00	0.00	0.50
.........................................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTTTTTT.....................................	22	51	0.02	0.02	0.00	0.00	0.00
............................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTGTTG...................................................	21	14	0.07	0.00	0.00	0.00	0.07
.................................................................................................................................................................................................................................GTTTTGTTTTTTATTGTTTTT..............................................	21	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................................................................................................................................TTTTTTTTTTTTTTCTTTTG...................................	20	12	0.08	0.00	0.00	0.08	0.00
..........................................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTTTTTT....................................	22	51	0.02	0.02	0.00	0.00	0.00
...............................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTGTTG................................................	21	14	0.07	0.00	0.00	0.00	0.07
............................................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTGTTG...................................	21	14	0.07	0.00	0.00	0.00	0.07
.........................................................................................................................................................................................................................................TTTTTTTGTTTTTTGTTTGTT......................................	21	12	0.08	0.08	0.00	0.00	0.00
.......................................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTTTTTT.......................................	22	51	0.02	0.02	0.00	0.00	0.00
.............................................................................................................................................................................................................................TTTTTTTTTTTTTTCTTTTG...................................................	20	12	0.08	0.00	0.00	0.08	0.00
..........................................................................................................................................................................................................................................TTTTTTGTTTTTTTCTTTTGT.....................................	21	6	0.17	0.17	0.00	0.00	0.00
................................................................................................................................................................................................................................TTTCTTGATTTTTTTTGT..................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................TGTTTTGTTTTGTTATTTTT...........................................	20	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................................................................................................TTTTTTTTTTTTTTTTTTTTTT......................................	22	51	0.02	0.02	0.00	0.00	0.00
.....................................................................................................................................................................................................................................TGATTTTTTTTGTTTTTTTTG..........................................	21	1	1.00	0.00	0.00	0.00	1.00
........................................................................................................................................................................................................................................TTGTTTTTGTTGTTTTTTTTT.......................................	21	12	0.08	0.08	0.00	0.00	0.00
....................................................................................................................................................................................................................AAACAACGTTTTTTTTTTTTTTTT........................................................	24	1	1.00	0.00	0.00	0.00	1.00

droGri2

ACA--A-------------TAAAATACTCATTAAAAGCTTCATTTGAAAGCTTTGCATTGAATCGCAGTAATCTC---------GAGCTACA---------T---------ATCCTTAGA----------ACT-------------TTATTG----------CTGTTTTAATTACGTGGCTTAATGCAAAGCTTGA--AATAA-ACG---A----------------------------------------------AAAGCTGCTTT-----------------ATGAAAA

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