sblock21449- 12- and 20-way alignments

sblock21449	chr2L:5745968-5746114 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5746064-5746085
   star strand at position 5746002-5746023
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:5745953-5746129 +	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CACGATCGTCTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGTC---------GGAGCGGATGGAGTTGCGAGGAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC
droSim1	chr2L:5542462-5542638 +	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CGCGATCGTCTGTGGCT-----------------------------------TGTTGTTGCCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGAC---------TGAGCGGATGGAGTTGCGAGAAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC
droSec1	super_5:3824688-3824864 +	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CGCGATCGTCTGTGGCT-----------------------------------TGTTGTTGCCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGAC---------GAAGCAGTTGGAGTTGCGAGAAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC
droYak2	chr2L:13445718-13445903 -	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCTTCCCCATCCTC---------TGCGATCGTGTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGACGAGGCGGACGGAGCGAACGGAGTTGCGAGGAGGGGACTCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC
droEre2	scaffold_4929:5836074-5836241 +	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATC----------------CCGTCTCCATCCTC---------TGCGATCGTGTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---TGC-----CAGCCGAC------------------GGAGTTGCGAGGAGGGGATTCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC
droAna3	scaffold_12916:11185040-11185180 +	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGT----------------CCGCCTCGTGTCCC---------CGC-----------CCC-----------------------------------AGCTGATGCCTTTAATGGAAAGAACCGCC--AGCTGAGAGTCAAAGCC--------------------------------------------------GGACCCACCGTTCGTAT--------------ACG--T-TATTTTTTGGC
dp4	chr4_group1:654984-655116 -	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTCTGTGTACCC------------------CTCTGTACCCCTC--------------CCCTCTCTCTTTGTCTGAGTGAAGTTTTTCG-----------------------------------------------------------------------------------------------------AGTGGAGTCTGTTTCCATGT--------------TCAGAAACAATTTATGCG
droPer1	super_1:651227-651364 -	TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTCTGtgtaccc------------------ctc---------tgtacccctctgtacccctctCTCTTTGTCTGAGTGAAGTTTTTCG-----------------------------------------------------------------------------------------------------AGTGGAGTCTGTTTCCATGT--------------TCAGAAACAATTTATGCG
droWil1	scaffold_180708:8432993-8433167 -	TCGGTCAACGCTTTTAAGTCAAGTTCTGAgttgt-tg----------------------ttgttgccattgtt--gatgcttt-------ttttttgtt-------tttat-----------------------ttttgGTGACTATAATGGAA-GAAATGAGTTGC-TC-GAG-TTAAA---AGT-----GAGTGAG----------TGAACGAC-TGAGTTG----------AG---TCTTATG--TTCATTAAGTTTGTT------TTTTTTTGGGGC
droVir3	scaffold_12963:3798442-3798596 +	TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGC-----------------------------------------------------------CGGCTCTCgttgttgttgttgttgttgttgtctgttgGCTGTTGCTTTTAATGGAAGG-AACGAGT-GC--------TTGAG---TACTCGTTACGAGCT----------CAAACA---------------------------ATGCGAAT--------------TTA--TATTGTTTGA-GT
droMoj3	scaffold_6500:14252169-14252319 +	TCGGTCAACGCATTCGAGTCAAGTTCTGTAGT----GGCA-----------GCTCTAAACTATGCCGGGT----------------------T----GT-----------------------------------TGTTGCTGTTTTTAATGGAAGGAATTGAGT-GC--------TCAAG---TGCTCAATGAGCGCT----------CAAACAG--AGAGCTG--AAACAGCA-----------ATGT--------------TTA--TATTGTACGAGA-
droGri2	scaffold_15252:3298030-3298174 +	TCGGTCAACGCATTCAAGTCAAGTTCTGTGTA-----------------GCC------------------TAG---------TGAGCCGGCATGCGATT-----------------------------------TGTTTTTGCCTTTAATGGAA-GAAATGAGT-GC--------TTGAGGAGTACTCGTT-----------------------------GTT-CGAGATGTTGTT---GTCTGAGTT-----------CGCTTCA--TTTTGTTTGAGG-

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:5745953-5746129 +	NA	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCACGATCGTCTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGTC---------GGAGCGGAT----G--GAGTTGCGAGGAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSim1	chr2L:5542462-5542638 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------TGAGCGGAT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSec1	super_5:3824688-3824864 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------GAAGCAGTT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droYak2	chr2L:13445718-13445903 -	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------TTC-----------------CCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGACGAGGCGGACGGAGCGAAC----G--GAGTTGCGAGGAGGGGACTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEre2	scaffold_4929:5836074-5836241 +	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATCCC--------GTC-----------------TCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGTGCCAGCCG------------------AC----G--GAGTTGCGAGGAGGGGATTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEug1	scf7180000409004:248542-248715 -	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCATATCCC--------GTCCGC-CTC----------CCCGACCTCTGCGATCGTCTGCTGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTCG------TT---------AAC----A--GAGCCGCGA---GGGGATCCGGCC------------------------------TGCGAAT-----------TCATATA----G---------T------------TTA---AGGC
droBia1	scf7180000302422:3953216-3953389 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCTCCCCGCCTATCCC--------GTCCCC-AGC----------CCCATCCCCGGCGCTGGTGTACGACT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGCGA---GGGGATCCGGCC------------------------------TGTGGAT-----------TCACATG----G---------T------------TTG---TGGC
droTak1	scf7180000415871:528958-529118 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCC----------C--------TTC-----------------CCTGTCCCCTGCGATCGTGTGAGGCCTGT--------TGTTGCTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGTGC---GGGGATCCGGCC------------------------------TGTGGAT-----------TCATGTA----C---------T------------TTG---TGGC
droEle1	scf7180000491024:383572-383755 -	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTCCCC-GTCCCCTCC----CTCATCCTCTGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATGTG------TG---------AGC----A--GAGCTGCGA---GGGGATCCGGCC------------------------------TGTGAGT-----------TCGTATACATAG---------T------------TTG---TGGC
droRho1	scf7180000764260:8287-8454 +	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTC-----------------CCCGTCCTCAGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATTTG------CG---------AGC----A--GAGTTGTGA---GGGGATCCGGCC------------------------------TGTGAAT-----------TTATAAA----G---------T------------TTG---TGGC
droFic1	scf7180000448889:28174-28341 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC-C--------GTCTC---------------TCCTTCCTCTGCGGTCGCATGGGTCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAATT---TG---AGAGCGAGTTG------CG---------AGC----G--GAGTTTCGA---GGGGATCC-GCC------------------------------TGCGGAG-----------TCGCACA----G---------A------------TTG---AGGC
droKik1	scf7180000300796:309227-309401 -	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCAGC------------------------------------------------AACGATCGCGTGTGG-TTGT--------TGTTTCTGGCTTTAATGGAAAGAAATGAGTT---GG---AGTGCGAGTTG------TG---------AGCCGTTGTCGGGCTATGA---GTGAATCCGGCCCATAATTGCTC-----------------------GAGGCAAAAGCAGTTCATATATGGTG---------T------------TTG---TGAC
droAna3	scaffold_12916:11185040-11185180 +	1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCTCGTGTCCCC-----------GCC-----------------CC-----------AGCTGATGCCTTTAATGGAAAGAACCGC-CA-GCTG---AGAGTCA-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGT-TA----T---------T------------TTT---TGGC
droBip1	scf7180000396572:843756-843896 +	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCCCTTGTCCCC-----------GCC-----------------CC-----------AGCCGGTGCGTTTAATGGAAAGAACCG-CCA-GCTG---TGGATCC-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGTA------A--------TT------------TTT---GGGC
dp4	chr4_group1:654984-655116 -	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTC-----CCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droPer1	super_1:651227-651364 -	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTCTGTACCCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droWil1	scaffold_180708:8432983-8433167 -	2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGTTGT-TG------TT--------GTT-----------------GCCATTGTTGATGCTTTTTTTTTGTT-TT-----TATTTTTGGTGACTATAATGGAA-GAAATGAGTTGCTCG---AGTTAAAAGTG-----------------AGT--------------------------------------GAGTGAACGACTGAGTTGAGTCTTAT--GT-----------TCATTAA----GTTTGTTTTTTTTTGGGGCTTGTTCA---T-AG
droVir3	scaffold_12963:3798442-3798596 +	3	TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGCCGG-----------------------------------CTCTCGTTGTTGTTGTTGTTGTTGTTGTCTGTTGGCTGTTGCTTTTAATGGAAGG-AACGAGTG-CTTG---AGTACTCGTTA------CG---------AGC----T---------------------CA---------------AACAA-------------TGCGAAT-----------TTATATT----G---------T------------TTG---A-GT
droMoj3	scaffold_6500:14252169-14252332 +	2	TCGGTCAACGCATTCGAGTCAAGTTCTGTAGTGG----C----------------A-----------------GCTCTAAACTATGCC-------GGGTTGT--------TGTTGCTGTTTTTAATGGAAGGAATTGAGTG-CTCA---AGTGCTCAATG-----------------AGC--------------------------------------GCTCAAACAG-AGAGCTGAAACAGCAATGT-----------TTATATT----G---------TACGAGATTCCATTTA---TAGC
droGri2	scaffold_15252:3298030-3298190 +	4	TCGGTCAACGCATTCAAGTCAAGTTCTGTGTAGC------------------CTAG--------------------------TGAGCCGGCATGCGATT-----------TGTTTTTGCCTTTAATGGAA-GAAATGAGTG-CTTGAGGAGTACTCGTTGTT----CG---------AGAT---G--TTGTTGTC-----TGAGTTC--------------------------------------GCT-----------TCATTTT----G---------TTTGAGGTTCCATTCAAACTAGC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CACGATCGTCTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGTC---------GGAGCGGATGGAGTTGCGAGGAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC

Size

Hit Count

Total Norm

droSim1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CGCGATCGTCTGTGGCT-----------------------------------TGTTGTTGCCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGAC---------TGAGCGGATGGAGTTGCGAGAAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..................................................................................................T-----------------------------------TGTTGTTGCTTATAATG..................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................T-----------------------------------TGTAGTTGGCTTTAATG..................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................TGAG---AGC-----AAGCGGAC---------GGA......................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCGTCCCCATCCTC---------CGCGATCGTCTGTGGCT-----------------------------------TGTTGTTGCCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGAC---------GAAGCAGTTGGAGTTGCGAGAAGGGGATCCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................................ATCGTTTGTGGxT-----------------------------------TGTTGTTG...........................................................................................................................................	20	1	1.00	0.00	0.00	1.00
.....................................................................................................................................................................................................................ACCTGGAGTTGCGAGAAG..................................................	18	1	1.00	0.00	0.00	1.00
...GTCAACTCTTTTATGTCA....................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................GAAAGAGATGAGT-----------TTGAG---G.................................................................................................	19	1	1.00	0.00	1.00	0.00
...GTCAACTCTTTTATGTCAA...................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
........................................................................................................................................................AACGAAAGGAGT-----------TTGAG---A.................................................................................................	18	1	1.00	0.00	1.00	0.00
...................................................................ATCCTC---------GGCGAGCGTCTG...........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC----------------CCTTCCCCATCCTC---------TGCGATCGTGTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---AGC-----CAGCGGACGAGGCGGACGGAGCGAACGGAGTTGCGAGGAGGGGACTCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.............................................................................................................................................................................................................................TTGCGGGGAGGGGAATCG..........................................	18	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................................................................................................................................TTGCGGGGAGGGGAAT............................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................TGCGGGGAGGGGATTC...........................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................TTGCGGGGAGGGGAATC...........................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................TCAAGTACTGAGGCCCGTCCCA.................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................AGAAATGAGT-----------TTGAG---AGC-----CAGCGGAC..................................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATC----------------CCGTCTCCATCCTC---------TGCGATCGTGTGTGGCT-----------------------------------TGTTGTTGGCTTTAATGGAAAGAAATGAGT-----------TTGAG---TGC-----CAGCCGAC------------------GGAGTTGCGAGGAGGGGATTCGGCCTGTGAAT--------------TCA--TATAGTTTGTGGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................CCTC---------TGCGATCGTxTGTGTC.......................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00

droAna3

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGT----------------CCGCCTCGTGTCCC---------CGC-----------CCC-----------------------------------AGCTGATGCCTTTAATGGAAAGAACCGCC--AGCTGAGAGTCAAAGCC--------------------------------------------------GGACCCACCGTTCGTAT--------------ACG--T-TATTTTTTGGC

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTCTGTGTACCC------------------CTCTGTACCCCTC--------------CCCTCTCTCTTTGTCTGAGTGAAGTTTTTCG-----------------------------------------------------------------------------------------------------AGTGGAGTCTGTTTCCATGT--------------TCAGAAACAATTTATGCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................GTCAAGTTCTGAGCC-AGTCCC..................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droPer1

TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTCTGtgtaccc------------------ctc---------tgtacccctctgtacccctctCTCTTTGTCTGAGTGAAGTTTTTCG-----------------------------------------------------------------------------------------------------AGTGGAGTCTGTTTCCATGT--------------TCAGAAACAATTTATGCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................TC---------TGTATGCCTCTGTACC.......................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00

droWil1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAgttgt-tg----------------------ttgttgccattgtt--gatgcttt-------ttttttgtt-------tttat-----------------------ttttgGTGACTATAATGGAA-GAAATGAGTTGC-TC-GAG-TTAAA---AGT-----GAGTGAG----------TGAACGAC-TGAGTTG----------AG---TCTTATG--TTCATTAAGTTTGTT------TTTTTTTGGGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................TTGTTTGTT-------TGTAT-----------------------TTTTGGT............................................................................................................................................	21	1	15.00	1.00	13.00	0.00	1.00
............................................................................................GTTTGTT-------TGTAT-----------------------TTTTGGT............................................................................................................................................	19	1	13.00	0.00	13.00	0.00	0.00
...............................TGT-TG----------------------TTGCTGCCATTGTT--G.............................................................................................................................................................................................................	20	1	10.00	0.00	10.00	0.00	0.00
...............................TGT-TG----------------------TTGCTGCAATTGTT--G.............................................................................................................................................................................................................	20	1	9.00	0.00	9.00	0.00	0.00
...........................................................................................TGTTTGTT-------TGTAT-----------------------TTTTGGT............................................................................................................................................	20	1	5.00	0.00	5.00	0.00	0.00
............................TGTTGT-TG----------------------TTGCTGCCATTGT.................................................................................................................................................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
..........................................................................................TTGTTTGTT-------TGTAT-----------------------TTTTGGTG...........................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
............................TGTTGT-TG----------------------TTGCTGCCATTGTT--G.............................................................................................................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
...........................................................................................TGTTTGTT-------TGTAT-----------------------TTTTGGTGA..........................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
...............................................................TGCCATTGTT--GCTGCTGT-------T..............................................................................................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
.................................T-TG----------------------TTGTTGCCGTTGTA--G.............................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	2.00
........................TCTGCTTTGT-TG----------------------TTGTTG........................................................................................................................................................................................................................	18	2	1.00	0.00	0.50	0.50	0.00
................................................................................................................................................................................TAAA---AGT-----GAGTGAG----------TGAAAGA..................................................................	21	1	2.00	0.00	0.00	2.00	0.00
..........................................................................................TTGTTTGTT-------TGTAT-----------------------TTTTGG.............................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
...............................TGT-TG----------------------TTGCTGCCATTGTT--GC............................................................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
.................................................................................................................................................................................................................................................................TTTTTT------TTTTTTTTGGGC	18	3	0.33	0.00	0.00	0.00	0.33
...............................TGT-TG----------------------TTGCTGCCATTGTT--..............................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................TTGT-TG----------------------TTGCTGCCATTGGT--..............................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................AGT-----GAATGAx----------TGAACGAC-T...............................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................CTATAATGGGA-AAAATGA.......................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................TTTTGTT-------TATGT-----------------------TTTTGGT............................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...............................TGT-TG----------------------TTGTTGCTGTTGTT--G.............................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................TTT-------TTTTTTGTT-------TTTGT-----------------------TTTT...............................................................................................................................................	21	8	0.13	0.00	0.13	0.00	0.00
..............................TTGT-TG----------------------TTGTGTCCATTGT.................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................TTTTTAGTTGT-TG----------------------TTGTTG........................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................GGT-----GAGTGAG----------TGAATGAC-TGA.............................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................GTTTGTT-------TGTAT-----------------------TTTTGGTG...........................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................TTTAGAGTTGT-TG----------------------TTGTTG........................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TTGTT-------TGTAT-----------------------TTTTGGTGG..........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................TTTTGTT-------TGTAT-----------------------TTTTGGTG...........................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
......................GTTTTGAxTTGT-TG----------------------TTGTTG........................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................TTG-------TTTTTTGTT-------TTTGT-----------------------TTT................................................................................................................................................	20	15	0.07	0.00	0.07	0.00	0.00
..................................................................................T-------GTTTTTGTT-------TTTTT-----------------------TTTTG..............................................................................................................................................	20	12	0.08	0.00	0.00	0.00	0.08
.............................GTTGT-TG----------------------TTGCTGCCATTGT.................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................T-------TTTTTTGTT-------TTTAA-----------------------TTTCGGT............................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................................................TT--GTTGCTTG-------TTTTTTGT.......................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................................................................................................................................TATTAAGTTTGTT------TTTTT.......	18	1	1.00	0.00	1.00	0.00	0.00
.............................GTTGT-TG----------------------TTGTTGCTGTTG..................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...................................TG----------------------TTGCTGCCATTGTT--GCTGC.........................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.............................GTTGT-TG----------------------TTGCTGCTATTGTT--G.............................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................TGTGATTTGT-TG----------------------TTGTTG........................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................TTTTGTT-------TTTTC-----------------------TTTTGGT............................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
................................................................................TTT-------TTTTTTGTT-------TTTGT-----------------------TTT................................................................................................................................................	20	8	0.13	0.00	0.13	0.00	0.00
............................................................................................TTTTGGT-------TTTAA-----------------------TTTTGGT............................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................TGT-TG----------------------GTGTTGGCATTGTT--GA............................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..................................................................................A-------TTTTTTGTT-------TGTAT-----------------------TTTTGGT............................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................................TGATGCCACTGTT--GATGCTT.......................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................GTT-------TTTAT-----------------------TTTGGGTGAA.........................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................GTTGT-TG----------------------TTGTTGCTGTT...................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
......................................................................GTT--GTTGATTT-------TTTTTTGT.......................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................TGTTTGTT-------TGTAT-----------------------TTTTGGTG...........................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................T-TG----------------------TTGTTGCTGTTGTT--G.............................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TTTGTT-------TGTAT-----------------------TTTTGGT............................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................ATAATGAAT-GAAATGAGTT....................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................TGT-TG----------------------TTGCTGCCATTGTT--GT............................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TTTTTT-------TCTAT-----------------------TTTTGGT............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................TGTT-------TGTAT-----------------------TTTTGGTGAA.........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................................................................ATTGTG--GATGATTT-------TTTT...........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................TGTTGCCATTATT--GATGT.........................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TTGTT-------TGTAT-----------------------TTTTGGTG...........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.....................AGTTxTCAGTTGT-TG----------------------TTGTT.........................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................TTTTTGTT-------TTTCT-----------------------TTTTGGT............................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00

droVir3

TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGC-----------------------------------------------------------CGGCTCTCgttgttgttgttgttgttgttgtctgttgGCTGTTGCTTTTAATGGAAGG-AACGAGT-GC--------TTGAG---TACTCGTTACGAGCT----------CAAACA---------------------------ATGCGAAT--------------TTA--TATTGTTTGA-GT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................................................TTGTTGTTGTTGTTGTTGTTG.........................................................................................................................................................	21	4	2.00	1.50	0.25	0.00	0.00	0.25
........................................................................................................TTGTTGTTGTTGTTGTTGTTG............................................................................................................................................................	21	4	2.00	1.50	0.25	0.00	0.00	0.25
........................................................................................................TTGTTGTTGTTGTTGTTGTTGT...........................................................................................................................................................	22	3	2.33	2.00	0.00	0.00	0.33	0.00
...........................................................................................................TTGTTGTTGTTGTTGTTGTTGT........................................................................................................................................................	22	3	2.33	2.00	0.00	0.00	0.33	0.00
............................................................................................................TGTTGTTGTTGTTxTTGTTTTC.......................................................................................................................................................	21	1	5.00	4.00	1.00	0.00	0.00	0.00
............................................................................................................TGTTGTTGCTGTTGTTGCTGT........................................................................................................................................................	21	1	4.00	4.00	0.00	0.00	0.00	0.00
............................................................................................................TGTTGTTGCTGTTGTTGCT..........................................................................................................................................................	19	5	0.60	0.00	0.00	0.00	0.60	0.00
...........................................................................................................TTGTTGTTGTTGTTGTTGCTG.........................................................................................................................................................	21	7	0.43	0.43	0.00	0.00	0.00	0.00
........................................................................................................TTGTTGTTGTTGTTGTTGCTG............................................................................................................................................................	21	7	0.43	0.43	0.00	0.00	0.00	0.00

droMoj3

TCGGTCAACGCATTCGAGTCAAGTTCTGTAGT----GGCA-----------GCTCTAAACTATGCCGGGT----------------------T----GT-----------------------------------TGTTGCTGTTTTTAATGGAAGGAATTGAGT-GC--------TCAAG---TGCTCAATGAGCGCT----------CAAACAG--AGAGCTG--AAACAGCA-----------ATGT--------------TTA--TATTGTACGAGA-	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................................................TTTTTTATTGAAGGAATTG........................................................................................................................	19	1	6.00	4.00	2.00	0.00	0.00
................................................................................................................................................TTTTATTGAAGGAATTGA.......................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
....................................................................GT----------------------T----GT-----------------------------------TGTTGTTGTTGTT......................................................................................................................................	18	7	0.29	0.29	0.00	0.00	0.00
...............................................................................................................................................TTTTTATTGAAGGAATTGA.......................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................GT----------------------T----GT-----------------------------------TGTTGCTGTTTTTTC....................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................GT----------------------T----GC-----------------------------------TGTTGCTGTTGTT......................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................TTTTTTATTGAAGGAATTGA.......................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................GT----------------------T----GT-----------------------------------TGTTGCTGTTTTTTCTG..................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droGri2

TCGGTCAACGCATTCAAGTCAAGTTCTGTGTA-----------------GCC------------------TAG---------TGAGCCGGCATGCGATT-----------------------------------TGTTTTTGCCTTTAATGGAA-GAAATGAGT-GC--------TTGAGGAGTACTCGTT-----------------------------GTT-CGAGATGTTGTT---GTCTGAGTT-----------CGCTTCA--TTTTGTTTGAGG-

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