dme-mir-979-as- 12- and 20-way alignments

dme-mir-979-as	chrX:19455870-19455964 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 19455927-19455949
   star strand at position 19455890-19455911
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:19455855-19455979 -	TATACTTTTGTGTATACGGATGCCACAAAATTAGCCTGAGTTCGGGAAGAATTTGTATATACATAAGAATTCCCCCCAAATTCAGTGT--------------------ATT--TGTGACATCCTCACATGTA-------------------------------------------TGTT--------------------------------------------------------------C----CAGTGATTAA
droSim1	chrX_random:5079602-5079664 -	TATACTTTTGTATATACGGCTCCTACAAAATTAGCCTGAATTCGTGAAGAATTTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTAA
droSec1	super_8:1738459-1738521 -	TATACTTTTGTATATACGGTTCCTACAAAAGTAGCCTGAATTCGTGAAGATTTTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTAA
droYak2	chrX:11883257-11883281 +	CTTTTACGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTC--------------------------------------------------------------C----CAGCCATTAA
droEre2	scaffold_4690:9691773-9691847 -	CGTGCTTCAGAATTCC-----------------G----------------------------------------CCCGAATTCAGAGCTAA--------------TCGATTTGTGTGGCA-CCCCATACGTA-------------------------------------------TTTG--------------------------------------------------------------C----CAACGATTAA
droAna3	Unknown	TGAGTTTTGG-TC---------TAACAAATAAAACCCAGACTTGAAACA------------------------------------------------------------TTTTTTAGACG-TTACCTGttTTtTtTTTtTtgttTTTtTttTTGtTTtgTTttTttgTTTTTtttTGtt--------------------------------------------------------------t----CGGTGATTAA
dp4	chrXL_group1e:12509670-12509797 +	TATTGTTTTAACTTCACGAGTATATCAAATCCAGAGCGT--------------------------------------------------------------------------------A-GTTCTTCCTTA-------------------------------------------CTTACTAAGGACTTACTCTTAAATTTACGCGCATAAATATTTTCGATCTTGAAAAATACAAAAATTA----AAATGCTTAA
droPer1	super_14:1990605-1990740 +	TATTGTTTTAGCTTCAAGA-GAATATAAAATCTATATAAATTCGTAGA-----------------------------------------------------------------------A-GTTCTTCCTTA-------------------------------------------CTTACTAAGGACTTACTCTTAATTTAACGCGTTTAAATATTTTCGATCTTGAAAAATATAAAAATTA----AAATGCTTAA
droWil1	scaffold_181096:7961894-7962010 -	TtTtTtTtTtTtTtCTT---------------------------------------------------------TCTAATTTCTTCGATAT----------------------------------------------------------------TGTGTTTTCTTGG------------------TTGATTTATATATAGATGTGTGTGTGTGTGTGTGgGTGTGTTGTGTGTGCTTATTCTAATCATAATCTAA
droVir3	scaffold_13042:902095-902094 +	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6328:2896306-2896380 +	TTTTGTTTtTTATTATT-------ATTATTGTAATCTTAGTTTTGGATT----------------------------------------------------------------------A-TATCGTCATCA-------------------------------------------ATTTCTATAGC------------------------------------------------------------CCTTTCTCAT
droGri2	scaffold_15081:2040291-2040415 +	CTCATTTTAA-TC---------CAATAACCA--GAGAAT--------GA------------------------------CATTTTCAACTTTGTATATACAATTATCAGTTTACATTTAA-GCTCTTCAACT-------------CCTATCACTATTATTATTATTGTCTTCATCTTCA--------------------------------------------------------------T----CTT-AAATTA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:19455855-19455979 -	NA	TATACTTT-TG----TGTATACGGATGCCAC------------AA----A-------------ATTAGC-------CTGAGTTCGGG---------AAGAATTTGTATATA------CAT---------------------------AAGA--------------------------------------------ATTCC-C-----------------------CCCAAATT-------------------------------------------------------------------CA---------------------------------------------------------------------GTGTATTTG--TGACAT------C----------------------------CTCACA--TGTA--T----------------GTTCCAGTGATTAA
droSim1	chr2L:11773332-11773488 +	1	TAAAATGT-AG----TT--------------TA-ATAAGC-----AGAT--A-------------------------------------------------------------TGGATCCT----------------------------------------------AAAAGTATTATATCTTCTT-----------------------------A--------------------------------------------GAAACTATTTTCCTGGATT---------------------TTTAAATGTTGAATTTCTGTAAAATATATCAAAATCTAAATA---------------------------AAATGTGATTT--TAATAG------C----------------------------TAGGGATG--TA--T----------------ATACTTTTGGAAGA
droSec1	super_16:165683-165811 +	1	TAGAAACT-AT----TT--------------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGATTTTTTTGTTGATTTGTTTGATTTTTAAATGTTGAATTTCTGTAAAATATGTCAAAATCTAAATA---------------------------AAATGTGATTT--TAAAAT------C----------------------------TAGGGATG--TATAT----------------ACTTTTGGAAGATA
droYak2	chrX:11883259-11883281 +	1	TTTACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--T----------------TTCCCAGCCATTAA
droEre2	scaffold_4690:9691773-9691868 -	1	GGATGCTA-CAAAAGT-----------------------------GGAT--G--------------CGTG-----------------------------------------------CTT---------------------------CAGA--------------------------------------------ATTCC-G-----------------------CCCGAATT-------------------------------------------------------------------CAGAGCTAATCGATT-------------------------------------------------------------TGTG--TGGCAC------C-----------------------------CCATA--CGTA--T----------------TTGCCAACGATTAA
droEug1	scf7180000409230:876782-876877 +	2	TATATTTT-GT----AT--------------TG-ATT---GATTT----A-A-------------------GTTAAGT-----------------------------------TAA------------------------------------------------------------------------------------GTAGAATATCTACGAAAAATAT--------------------------------------------------------------------------------------------------------------------------------------------------------T-----GC-------------------------------TATAAATATTTTAATTTATTTA--A----------------TTTACGATGATTAA
droBia1	scf7180000302069:1147456-1147673 +	2	TAGAACTT-AG----AG--------------TA-GTA---TTCCT----G-A-------------------ATTCATTTTAGTAGGGTTGGGAGCG---ATGCATTATATA------CGTTATATTTGATAGATTCCAAGGTTTTTG----ATCACATTCCTTTGCAC--TATCGTTTGTTTCTTTTAATTGTACAATTT-TCC----------------------------------------------------------------------TCATTT-------------------------------------------------------------T----------------T-----------ATGTT-----GGTTGGCTTAACTCCGGTTCTAACTATTG--------------CTTTTA--CTAT---T-----TATTGACGCTGTTCCAATGATTAA
droTak1	scf7180000415169:841429-841556 +	3	CATTTCTT-AG----CT--------------TA-AATGGT--TTT----T-A---------------------------------------------------------------------------------------------------GTCAAAGTTTTTTGAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTGGTTCTTATTTTTTCT--------------GTATT--GGCTACTTTAGGACCGCTTCTTATTATTA--------------CTCATA--TCAA----------ATTAAAACTGCTCCACTGATTAG
droEle1	scf7180000491006:819941-820067 +	2	TAATTTGA-ATATGGCA--------------------TTTAAAGTAAACTAAAATATTTTAATATTAAG-------ACATGCTTGAT---------ATGATTTTATATTTAACCATAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCATA--T--------------------------ATT-TATTTGTACT-------T---TTGCACTTTT----------TTTTATCAGTGTAG
droRho1	scf7180000761121:186691-186818 +	2	CCTTACCA-TATAAATA--------------------TTTATCGT----A-------------ATTTAT-------TTATATTAGCAATGAATATGAATT-----TTTTTA------CAT---------------------------TATT--------------------------------------------ATTTA-TACAATATTGACTACAATTACTTATACATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAATGTATCCCAATGATTAA
droFic1	scf7180000454073:1736548-1736631 -	3	TATAACAT-AT----TA--------------AA-ATA---CTTTT----C-AATG-----------------------------------------------------------------------------------------------------------------------------------------------TT-TACAATAGTTTTTACAATGCATTACGCATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAAAATTTCTTCAATGGTTAA
droKik1	scf7180000302621:248346-248471 +	4	TATAATTT-TG----TA--------------TA-TAA----------TT--T--------------TGTATATAAAAT-----------------------------------------------------------------------------------------------------------------------TTCA------------------------TACATTTTCTGTAGAACCAAAACCTTTTCCCTTAAAGGACCACCCTTCTGG-------------------------------------------------------------------------------------------------GTGGTTA--GGGCAT------C----------------------------CGAAAT--TGGT--A----------------AACGGAATGCTTTC
droAna3	scaffold_13417:2459297-2459411 +	2	TATATTTT-TA----TT--------------GAAATATGT-----AAAG--A-------------------------------------------------------------TTGGTATA----------------------------------------------AATATGTACATATTTTCTG-----------------------------AAATAAGACAATTATTT-----------------------------------------TATAGT----------------------------------------------------------------------------------------------TTTATTT--CGAAAT------A----------------------------TTTAAA--TTTA--A----------------TTATAAGTAACTTA
droBip1	scf7180000395874:31563-31685 +	1	TAATCCAT-GT----AC-ATTTCCATATTAT------------TA----C-------------TTTACT-------CTACAAATATG---------AAGTATTTA-----------------------------------------------------------G----------------------AAATAGACATTCA-TATTTTT-----------------TT------------------------------------------------------------------------------------------------------------------T----------------A-----------ATATT-----GGTGTACATAC---A----------------------------TACGTATGTATG--T----------------CTTTTGTTGAATAA
dp4	chrXL_group1e:12509670-12509797 +	2	TATTGTTTTAA----CT--------------TC-ACGAGT-----AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------TCAAATCCAGAGCG-------TAGTTCTTCCTTACTTACTAAGGACT--------TACTCTTAAATTTACGCGCATAA---ATATTTTCGATCTTGAAAAA------------------TACAAAAATTAAAATGCTTAA
droPer1	super_14:1989251-1989367 +	1	AAAATACA-AA----TT--------------TA-AAACCCAAAATGTA--------------------------------------------------------------------------------------------------------------------------------------------------------GCAGATTTTCATGGAAAAA-------------------------------------------------------------------------------------------------------------TTCAACTCAAAATAGAGTTTCCACTCTAATT--------------TTAGTTT--TTACTC------C----------------------------CCAACA--GATG--C----------------GCACGATGACTTAG
droWil1	scaffold_181096:7961895-7962008 -	3	TATATATA-TA----TA-----------------------CTTTC----T-AATTTCTTCGATATTG----------TGTTTTCTTG---------GTTGATTTATATATAGATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------C----------------------------GTGTGTTG--TGTGTGCTTAT------TC---TAATCATAATCTA
droVir3	scaffold_13042:902091-902097 +	2	TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTGA
droMoj3	scaffold_6500:27198225-27198308 +	2	TGCTTTAC-TC----CA--------------GA---GCGC--CGG----A-A-------------------------------------------------------------AGTATGCTACAT----------------------TTGA--------------------------------------------AATC--C-----------------------CTCAAATT-------------------------------------------------------------------CAGACT----------------------------------------------------------------------------------------T----------------------------TCCATA--ACTA--T----------------GTGGAATTCCTTGC
droGri2	scaffold_15081:2040287-2040418 +	2	TGTCCTCA-TTTTAATC--------------CA-ATAACC-----AGAGAATGACATTTTCAACTTTGTATATACAA--------TT---------ATCAGTTTACATTTAAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTCAACT-------------------------------------------------------------CCTA--T--------------------------CAC-TATTATTATT-------A---TTGTCTTCAT------CTTCATCTTAAATTACAA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TATACTTTTGTGTATACGGATGCCACAAAATTAGCCTGAGTTCGGGAAGAATTTGTATATACATAAGAATTCCCCCCAAATTCAGTGT--------------------ATT--TGTGACATCCTCACATGTA-------------------------------------------TGTT--------------------------------------------------------------C----CAGTGATTAA

Size

Hit Count

Total Norm

droSim1

TATACTTTTGTATATACGGCTCCTACAAAATTAGCCTGAATTCGTGAAGAATTTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................AAATTAGxCTGAATTCTTGAA................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00

droSec1

TATACTTTTGTATATACGGTTCCTACAAAAGTAGCCTGAATTCGTGAAGATTTTGT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATTAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................AGCCGGATTTCGTGAAGA..............................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00

droYak2

CTTTTACGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTC--------------------------------------------------------------C----CAGCCATTAA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CGTGCTTCAGAATTCC-----------------G----------------------------------------CCCGAATTCAGAGCTAA--------------TCGATTTGTGTGGCA-CCCCATACGTA-------------------------------------------TTTG--------------------------------------------------------------C----CAACGATTAA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

TGAGTTTTGG-TC---------TAACAAATAAAACCCAGACTTGAAACA------------------------------------------------------------TTTTTTAGACG-TTACCTGttTTtTtTTTtTtgttTTTtTttTTGtTTtgTTttTttgTTTTTtttTGtt--------------------------------------------------------------t----CGGTGATTAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................................................TTATTATGTTTTTTTGTTTTT....................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................TTTTTTTTTTTTTCTTTTT.............................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
............................................................................................................................................................ATGTATTTTTGTTTTTTTTT................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
......................................................................................................................................ATTTTTTGTTTTTTTTTTTTTTT...................................................................................................	23	22	0.05	0.00	0.00	0.00	0.05
................................................................................................................................TTTTTTTTTTTTTTTTTTTTTTTTTCTTTT..................................................................................................	30	16	0.06	0.00	0.00	0.00	0.06
.......................................................................................................................................TTTTTTCTTTTTTTTTTTTTTTT..................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
................................................................................................................................TTTTTTCTTTTTTTTTTTTTTTT.........................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
......................................................................................................................................TTCTTTTGTTTTTTTTTTTTT.....................................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
...............................................................................................................................................................TTCTTTTGTTTTTTTTTTTT--------------------------------------------------------------T----..........	21	33	0.03	0.00	0.00	0.00	0.03
.......................................................................................................................................................TTCTTTTGTTTTTTTTTTTTT....................................................................................	21	33	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................TTTGTGTTTTTTTTTTTTTTTG...............................................................................	22	8	0.13	0.13	0.00	0.00	0.00
.....................................................................................................................................................TTTGGTTTTGTTTTTTTG.........................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
.........................................................................................................................................TTTTGxTTTTTTCTTTGTTTTG.................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................TTTTTTCTTTTTTTTTTTTTTTT........................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00
..................................................................................................................................TTTTTTTATTTCTTTTTTTTT.........................................................................................................	21	25	0.04	0.00	0.00	0.00	0.04
..................................................................................................................................TTTTTTCTTTTTTTTTTTTTTTT.......................................................................................................	23	51	0.02	0.00	0.02	0.00	0.00

dp4

TATTGTTTTAACTTCACGAGTATATCAAATCCAGAGCGT--------------------------------------------------------------------------------A-GTTCTTCCTTA-------------------------------------------CTTACTAAGGACTTACTCTTAAATTTACGCGCATAAATATTTTCGATCTTGAAAAATACAAAAATTA----AAATGCTTAA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TATTGTTTTAGCTTCAAGA-GAATATAAAATCTATATAAATTCGTAGA-----------------------------------------------------------------------A-GTTCTTCCTTA-------------------------------------------CTTACTAAGGACTTACTCTTAATTTAACGCGTTTAAATATTTTCGATCTTGAAAAATATAAAAATTA----AAATGCTTAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................ATTCGTAGA-----------------------------------------------------------------------A-GTTCTTCCT..............................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................AAAAATTA----GAGTGCTTAA	18	2	0.50	0.00	0.00	0.00	0.50	0.00
...................................ATAAATTCGTAGA-----------------------------------------------------------------------A-GTTCTTCCT..............................................................................................................................	23	2	0.50	0.00	0.00	0.00	0.00	0.50

droWil1

TtTtTtTtTtTtTtCTT---------------------------------------------------------TCTAATTTCTTCGATAT----------------------------------------------------------------TGTGTTTTCTTGG------------------TTGATTTATATATAGATGTGTGTGTGTGTGTGTGgGTGTGTTGTGTGTGCTTATTCTAATCATAATCTAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................................................................................................................................TGTGTGCGTCTGTGTGTG....................................	18	16	1.19	0.00	0.94	0.25	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTG..............................	23	16	0.94	0.00	0.19	0.75	0.00
..............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG................................	18	38	0.39	0.00	0.16	0.24	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG....................................	18	38	0.39	0.00	0.16	0.24	0.00
................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG..............................	18	38	0.39	0.00	0.16	0.24	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTG..................................	18	38	0.39	0.00	0.16	0.24	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG..............................	22	20	0.65	0.00	0.10	0.55	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTG................................	22	20	0.65	0.00	0.10	0.55	0.00
..............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTG..............................	20	30	0.37	0.00	0.07	0.30	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGT...............................	21	26	0.42	0.00	0.23	0.19	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTG................................	20	30	0.37	0.00	0.07	0.30	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGT.................................	21	26	0.42	0.00	0.23	0.19	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTG..................................	20	30	0.37	0.00	0.07	0.30	0.00
..............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGT.............................	21	26	0.42	0.00	0.23	0.19	0.00
...............................................................................................................................................................................................................GTGTTTGTGTGTGCGTGT...............................	18	21	0.48	0.10	0.33	0.05	0.00
..........................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTGTG................................	22	24	0.42	0.00	0.00	0.42	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTG..............................	24	12	0.83	0.00	0.00	0.83	0.00
............................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTGTG..............................	22	24	0.42	0.00	0.00	0.42	0.00
.........................................................................................................................................................................................................GTGTGCGTGTGTGTGTGT.....................................	18	43	0.21	0.00	0.19	0.02	0.00
.........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT.....................................	18	41	0.22	0.07	0.07	0.07	0.00
.................................................................................................................................................................................................................GTGTGCGTGTGTGTGTGT.............................	18	43	0.21	0.00	0.19	0.02	0.00
...............................................................................................................................................................................................................GTGTGCGTGTGTGTGTGT...............................	18	43	0.21	0.00	0.19	0.02	0.00
............................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTG................................	20	38	0.24	0.00	0.00	0.24	0.00
..............................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTG..............................	20	38	0.24	0.00	0.00	0.24	0.00
......................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTG......................................	20	38	0.24	0.00	0.00	0.24	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTATGTG..................................	21	13	0.69	0.00	0.62	0.08	0.00
...............................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT...............................	18	41	0.22	0.07	0.07	0.07	0.00
.............................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT.................................	18	41	0.22	0.07	0.07	0.07	0.00
.................................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT.............................	18	41	0.22	0.07	0.07	0.07	0.00
.............................................................................................................................................................................................................GTGTGCGTGTGTGTGTGT.................................	18	43	0.21	0.00	0.19	0.02	0.00
..........................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTG..................................	20	38	0.24	0.00	0.00	0.24	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGT...................................	18	41	0.22	0.07	0.07	0.07	0.00
...........................................................................................................................................................................................................GTGTGCGTGTGTGTGTGT...................................	18	43	0.21	0.00	0.19	0.02	0.00
........................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTG....................................	20	38	0.24	0.00	0.00	0.24	0.00
..........................................................................................................................................................................................................TGTCTGTGTGTGTGTGTGC...................................	19	18	0.44	0.00	0.39	0.06	0.00
............................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTG................................	20	33	0.24	0.00	0.03	0.21	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTGC.............................	25	13	0.62	0.00	0.00	0.62	0.00
..........................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTG..................................	20	33	0.24	0.00	0.03	0.21	0.00
..............................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTG..............................	20	33	0.24	0.00	0.03	0.21	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTGTGC.............................	24	16	0.44	0.00	0.06	0.38	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTG................................	21	25	0.28	0.00	0.04	0.24	0.00
.............................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGTG..............................	21	25	0.28	0.00	0.04	0.24	0.00
.......................................................................................................................................................................................................ATATATGTGTGTGTGTGT.......................................	18	8	0.75	0.00	0.75	0.00	0.00
...................................................................................................................................................................................................ATATATGTGTGTGTGTGT...........................................	18	8	0.75	0.00	0.75	0.00	0.00
............................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTGT...............................	21	29	0.21	0.00	0.07	0.14	0.00
.........................................................................................................................................................................................................ATATATGTGTGTGTGTGT.....................................	18	8	0.75	0.00	0.75	0.00	0.00
.....................................................................................................................................................................................................ATATATGTGTGTGTGTGT.........................................	18	8	0.75	0.00	0.75	0.00	0.00
..............................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTGT.............................	21	29	0.21	0.00	0.07	0.14	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTATATGGGT.................................	20	1	6.00	0.00	6.00	0.00	0.00
..........................................................................................................................................................................................................TGTGTATGTGTGTGTGTGTGT.................................	21	29	0.21	0.00	0.07	0.14	0.00
......................................................................................................................................................................................................TATGTGTGTGTGTGTGTG........................................	18	49	0.10	0.00	0.02	0.08	0.00
...................................................................................................................................................................................................ATATATGTGTGTGTGTGTGTGT.......................................	22	4	1.25	0.00	1.25	0.00	0.00
............................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTGTG..............................	22	26	0.19	0.00	0.04	0.15	0.00
............................................................................................................................................................................................................TATGTGTGTGTGTGTGTG..................................	18	49	0.10	0.00	0.02	0.08	0.00
.....................................................................................................................................................................................................ATATATGTGTGTGTGTGTGTGT.....................................	22	4	1.25	0.00	1.25	0.00	0.00
.............................................................................................................................................................................................................GTGGGTGTGTGGGTGGGTG................................	19	1	5.00	0.00	0.00	5.00	0.00
........................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTGTG..................................	22	26	0.19	0.00	0.04	0.15	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT...................................	19	35	0.14	0.03	0.06	0.06	0.00
..............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT...............................	19	35	0.14	0.03	0.06	0.06	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTGTG....................................	19	15	0.33	0.00	0.13	0.20	0.00
.........................................................................................................................................................................................................AAGTGTGTGTGTGTGTGTGGGTGTG..............................	25	2	2.50	0.00	0.00	2.50	0.00
................................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT.............................	19	35	0.14	0.03	0.06	0.06	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTGT.....................................	18	18	0.28	0.17	0.11	0.00	0.00
......................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTGTG....................................	22	26	0.19	0.00	0.04	0.15	0.00
................................................................................................................................................................................................................TATGTGTGTGTGTGTGTG..............................	18	49	0.10	0.00	0.02	0.08	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTGTGTGC.................................	22	14	0.36	0.00	0.07	0.29	0.00
.........................................................................................................................................................................................................ATATGTGTGTGTGTGTGTG....................................	19	22	0.23	0.14	0.00	0.09	0.00
.......................................................................................................................................................................................................ATATGTGTGTGTGTGTGTG......................................	19	22	0.23	0.14	0.00	0.09	0.00
..........................................................................................................................................................................................................TATGTGTGTGTGTGTGTGTGTG................................	22	26	0.19	0.00	0.04	0.15	0.00
.....................................................................................................................................................................................................ATATGTGTGTGTGTGTGTG........................................	19	22	0.23	0.14	0.00	0.09	0.00
..........................................................................................................................................................................................................TATGTGTGTGTGTGTGTG....................................	18	49	0.10	0.00	0.02	0.08	0.00
........................................................................................................................................................................................................TATGTGTGTGTGTGTGTG......................................	18	49	0.10	0.00	0.02	0.08	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGT.................................	19	35	0.14	0.03	0.06	0.06	0.00
..............................................................................................................................................................................................................TATGTGTGTGTGTGTGTG................................	18	49	0.10	0.00	0.02	0.08	0.00
............................................................................................................................................................................................................TGTATGTGTGTGTGTGTG..................................	18	44	0.09	0.00	0.00	0.09	0.00
............................................................................................................................................................................................................TGTATGTGTGTGTGTGTGTG................................	20	35	0.11	0.00	0.09	0.03	0.00
............................................................................................................................................................................................................TGTGTATGTGTGTGTGTG..................................	18	41	0.10	0.00	0.00	0.10	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGAG................................	22	23	0.17	0.00	0.04	0.13	0.00
..........................................................................................................................................................................................................TGTGTATGTGTGTGTGTG....................................	18	41	0.10	0.00	0.00	0.10	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTGTGTGTGTGC.............................	26	8	0.50	0.00	0.00	0.50	0.00
..............................................................................................................................................................................................................TGTGTATGTGTGTGTGTG................................	18	41	0.10	0.00	0.00	0.10	0.00
................................................................................................................................................................................................................TGTATGTGTGTGTGTGTG..............................	18	44	0.09	0.00	0.00	0.09	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTATATGG...................................	18	3	1.33	0.00	1.33	0.00	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGC...............................	21	31	0.13	0.00	0.03	0.10	0.00
.............................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGT...............................	20	30	0.13	0.10	0.03	0.00	0.00
.....................................................................................................................................................................................................ATATGTGTGTGTGTGTGTGT.......................................	20	20	0.20	0.00	0.15	0.00	0.05
.........................................................................................................................................................................................................ATATGTGTGTGTGTGTGTGT...................................	20	20	0.20	0.00	0.15	0.00	0.05
..............................................................................................................................................................................................................TGTATGTGTGTGTGTGTG................................	18	44	0.09	0.00	0.00	0.09	0.00
.........................................................................................................................................................................................................ATGTGTGTGTGTGTGTGTGTA..................................	21	15	0.27	0.00	0.27	0.00	0.00
........................................................................................................................................................................................................TATGTGTGTTTGTGTGTGTG....................................	20	14	0.29	0.00	0.07	0.21	0.00
......................................................................................................................................................................................................TGTATGTGTGTGTGTGTGTG......................................	20	35	0.11	0.00	0.09	0.03	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGTGTGA.............................	25	12	0.33	0.00	0.08	0.25	0.00
..........................................................................................................................................................................................................TGTATGTGTGTGTGTGTG....................................	18	44	0.09	0.00	0.00	0.09	0.00
..........................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGC.................................	21	31	0.13	0.00	0.03	0.10	0.00
..........................................................................................................................................................................................................TGTATGTGTGTGTGTGTGTG..................................	20	35	0.11	0.00	0.09	0.03	0.00
...............................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGT.............................	20	30	0.13	0.10	0.03	0.00	0.00
......................................................................................................................................................................................................TGTATGTGTGTGTGTGTG........................................	18	44	0.09	0.00	0.00	0.09	0.00
..............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGC.............................	21	31	0.13	0.00	0.03	0.10	0.00
................................................................................................................................................................................................................TGTGTATGTGTGTGTGTG..............................	18	41	0.10	0.00	0.00	0.10	0.00
............................................................................................................................................................................................................TGTGTGTGTGTGTGTGTGTGAG..............................	22	23	0.17	0.00	0.04	0.13	0.00
...........................................................................................................................................................................................................GTGTGTGTGTGTGTGTGTGT.................................	20	30	0.13	0.10	0.03	0.00	0.00

droVir3

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTTTGTTTtTTATTATT-------ATTATTGTAATCTTAGTTTTGGATT----------------------------------------------------------------------A-TATCGTCATCA-------------------------------------------ATTTCTATAGC------------------------------------------------------------CCTTTCTCAT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CTCATTTTAA-TC---------CAATAACCA--GAGAAT--------GA------------------------------CATTTTCAACTTTGTATATACAATTATCAGTTTACATTTAA-GCTCTTCAACT-------------CCTATCACTATTATTATTATTGTCTTCATCTTCA--------------------------------------------------------------T----CTT-AAATTA

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				None						None
UNAFold Image				None						None

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																		None
UNAFold Image				None														None