sblock180959- 12- and 20-way alignments

sblock180959	chrX:9219729-9219977 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 9219945-9219965
   star strand at position 9219752-9219772
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:9219714-9219992 -	CAGTCCAGTGAAAAG-CGAAAGGTTATGTCGTCGACCCGGGTACAGTGCGTTTCGAGGCTGTATGTGCTTGTTTTAATCCCCA----ATCATACGCATT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTCGAAGTCATTC-----TGCAGG---------------------TTCAGCAATCCACTTAGTTTCGTACTCAGGACCGCG--ATTAGAACGAACGAAATTTTGCA-TTTGTCACATTCACATCTCTTCGCCTACAGCACCGAAACGCACTGTCCCC--------------------------GGGTCGTCAAACACTC--------------CCAGGCGAGATTTAAT--GTTTTTT
droSim1	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_68:110181-110457 -	CAGTCCAGTGAAAAG-CGAAAGGTTATGTCGTCGACCCGGGGACAGTGCGTTTCGAGGCTGTATGTGCTTGTTTTAATCCCCA----TTCATACGCATT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTTGAAGTCATTC-----TGCAGA---------------------TTCAGCAATCCACTTATTTTCTTACTCAGGACCGCG--ACTAAAACAAACGAAA--TGGCG-TTTGTCACTTTCACATCTCTTCGCCTACAGCGCCGAAACGCACTGTCCCC--------------------------AGGTTGTCATACGCTC--------------CCAGGCGAGATTTAAT--GTTTTTT
droYak2	chrX:17812868-17813118 -	CAGTCCAGTGA--AG-CGAAAGGTTATGTCGTCGCCC--AGTACAGTGCGTTACGAGGCTATATGTGCTTGTTGTAAT--------------------A------------------------------------------------------------------------------------------------------CAGC-ACCTAAGGTTTCATTCGAAGTCATTC-----TTTGGG---------------------TTCAGCAACCCACATAGTTTCGTACTCAGGACCATG--ATTAGAA----CGAAA--TGGCA-TTTG-CACCATCACACCGCTGCGCCTACAGCTGCGAAACGCACTGTACTC--------------------------GGGTCGTCAAACACTC--------------CCAGACGAGATTTAAT--GTTTTTT
droEre2	scaffold_4690:5899758-5900018 +	CAGTCCAGTGA--AG-CGAAGGGTTACGTCGCCGCCC--AGTACAGTGCGTTGCGAGGCTGTATGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCCTT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTCGAAGTCATTC--------------------------------------AACCCACATAGTTTCGTGCTCAGGAA-ATGACATTAGAA----CGAAA--TGGCA-TTT-TCACGTTCACATCTCTTCGCCTACAGCCCCGAAACGCACTGTACCC--------------------------GGCTCGTCAACTACTC--------------CCAGACGAGATTTAAT--GGTTTTT
droAna3	scaffold_13334:330256-330279 +	C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAAGTCAAGTTCAAT--GTTTTTT
dp4	chrXL_group1a:7788225-7788568 +	CGACCAACTGATTAGTCGATTAGTCGATTCGTTGATTCATTTTCA---------------------------TTCAACTTCCA----TTCATACGTAACTTTATTTATTAAATACTTGATGTTCGATTTTAGAATTGCCTTCAACCTTTGTGTGTACTTTATTAGTTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGA-----CAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATTTATGGCTTATGGCAATCCACAC-------------------------A-GAG---TTGAAA---AGCAATCT-TTG---------A-GCTTCCCTACAGCCCTGAAACGCACTGTATATGTTAGTATGGGGACAGCC-----AACG--------------CGCAGTAGAAACTTCTCTGTT---------------ATAA
droPer1	super_15:138507-138854 +	TGACCAACTGATTAT-TGATTAGTCGATTCGTTGATTCATTTTCA---------------------------TTCAACTTCCA----TTCATACGTAACTTTATTTATTAAATACTTGATGTTCGATTTTAGAATTGCCTTCAACATTTGTGTGTATTTTATTAGTTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGA-----CAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATGTATGGCTTATGGCAATCCACAC-------------------------A-GAG---TTGAAA---GGCAATCT-TTG---------A-GCTTCCCTACAGCCCTGAAACGCACTGTATATGTTAGTATGGGGACAGCCATAGAAACG--------------CGCAGTAGCAACTTCTCTGTT---------------ATAA
droWil1	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:15804337-15804344 +	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--GTTTTTT
droGri2	scaffold_14853:9454202-9454220 +	GGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTATTTCGTTTTTT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:9219714-9219992 -	NA	CAGTCCAGTGAAAA-GCGAAAGGTTAT---GT-CGTCGAC---CCGGGTACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----AATCATACGCA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TGCAG--G-TTCA--GCA--------------------------------ATCC-------------ACTTAGTTTCGTACT-------------------------------------CAGGACCG-CG---ATTA-GAA---CGAACGAAATTTTGCATTT------------GTCACATTCACA--T------------CTCTTC----------GCCTACAGCACCGAAACGCACTGTCCCCG---GGT--------CG--TCAAACACTCCCAGGCGAGAT------------------------------------------------------TTAATGTTTTTT--
droSim1	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_68:110181-110457 -	1	CAGTCCAGTGAAAA-GCGAAAGGTTAT---GT-CGTCGAC---CCGGGGACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----ATTCATACGCA----------TTCAGCA------ACCTAAGGTTT----------------------CATTTGAAGTCATTC---TGCAG--A-TTCA--GCA--------------------------------ATCC-------------ACTTATTTTCTTACT-------------------------------------CAGGACCG-CG---ACTA-AAA---CAAACGAAA--TGGCGTTT------------GTCACTTTCACA--T------------CTCTTC----------GCCTACAGCGCCGAAACGCACTGTCCCCA---GGT--------TG--TCATACGCTCCCAGGCGAGAT------------------------------------------------------TTAATGTTTTTT--
droYak2	chrX:17812868-17813118 -	10	CAGTCCAGTGAA---GCGAAAGGTTAT---GT-CGTCG-C---CC-AGTACAGTGCGTTACGAGGCTATA---TGTGCTTGTTGTA--------------------A----------TACAGC-------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TTTGG--G-TTCA--GCA--------------------------------ACCC-------------ACATAGTTTCGTACT-------------------------------------CAGGACCA-TG---ATTA-GAA-------CGAAA--TGGCATTT-------------GCACCATCACA--C------------CGCTGC----------GCCTACAGCTGCGAAACGCACTGTACTCG---GGT--------CG--TCAAACACTCCCAGACGAGAT------------------------------------------------------TTAATGTTTTTT--
droEre2	scaffold_4690:5899758-5900020 +	1	CAGTCCAGTGAA---GCGAAGGGTTAC---GT-CGCCG-C---CC-AGTACAGTGCGTTGCGAGGCTGTA---TGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCC----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---------------A-------------------------------------ACCC-------------ACATAGTTTCGTGCT-------------------------------------CAGGAA-A-TGAC-ATTA-GAA-------CGAAA--TGGCATTT-------------TCACGTTCACA--T------------CTCTTC----------GCCTACAGCCCCGAAACGCACTGTACCCG---GCT--------CG--TCAACTACTCCCAGACGAGAT------------------------------------------------------TTAATGGTTTTTCC
droEug1	scf7180000409032:737185-737440 +	59	CAGACCAGTGAA---GCGAAAGGTTTA---CTTTCTGG-C---CC-AGTATAGTGCGTTTCGTGGCCGTA---TA-G-CTA---TAGTCCTT----ATTCC--TTTA----------TTCAACA------ATCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTCA-------------------------------------AACC-------------ACTTAATTTTTTACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCACT----------GATTACAGCAACGAAACGCACTGTCCTCCGCCGGT--------TA--TTAAACGC-CCCAGATGGGAATTAT-----------------------------------------------------ATG--------
droBia1	scf7180000301760:5192774-5193027 -	1	CAGTCCAGTGAAGT-GCGAAAGGTCAA---AT-CGCGA-C---CCGGGTACGGTGCGTTTCGGGTC-GTA---TG--CCTG---CAATACTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAT--G-TTGA-------------------------------------ACGC-------------ACTTGATTTCTCGCT-------------------------------------CAGGATAT-TA---ATTA-CCA-------GCAAA--CGGCATCC-------------TCACTTTCACC--A------------GTCAC-----------CCTTACGGCCCCGAAACGCACCGTCCCCG-CGGGTG-------CG--TTACACACTCCCAGTAGAGTTTTAT-----------------------------------------------------A-----TAT--
droTak1	scf7180000414672:184361-184564 +	33	CAGTCCAGTGAA---GCGAAAGGTT---------------------GGGACAGTGCGTTTCGTGGCC----------------------CTT----G------TCTA----------TTCAGCC------ACCTAAGGTTT----------------------CATTCAAAGTCATTC---TATTA--G-TTTA-------------------------------------ACGC-------------ACTTACTTTCTTACT-------------------------------------CAGGACAA-TG---ATTA-GCA-------GCAAA--TGGCATTT-------------TCACCTTCACACAA------------ATCA--------------------CCCCGGAACGCACTGTCTCTG------------------------ACTCCCAGTAGAGATTTAT-----------------------------------------------------------TTC--
droEle1	scf7180000491018:31099-31286 +	2	CAGTCCAGTGCA---GCGAAA----------T-CGTAG-CCCCCC-AGTACAGTGCGTTTCGGGAGCGTA-------------------------------------------------GAGCAGTCGAGCCCCAAGGTTT----------------------CATTCGAAGTCATTCTTCTATTA--G-TTCA--GCC--------------------------------ACCC-------------ACTTTATTTCTCACT-------------------------------------CAGGATATTTG---ATTA-ACA-------GA-------------------------------TTAACA--A------------ATCTTC-------CCCCCTTACAGCCCCGAAACGCATTGTCT--------------------------------------------------------------------------------------------------------------
droRho1	scf7180000780067:115346-115596 -	31	CAATCCAGTGAA---GCGAAAGGTTTA---GT-CGTAG-C---CC-AGTACAGTGCGTTTCGGGGCCTTA---------------------------------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAATCATTC---TATAA--G-TTTA-------------------------------------ACTC-------------ACTTAATTTCATACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCTCC---------CCCTTACAGTCCCGAAACGCACTGTCCCTGGGTCGT--------CG--TCACATACTCCCAAAAGAGATTTTT---------------------------------------------TTTT-CTCATATTTGTT--
droFic1	scf7180000454073:2134548-2134826 -	263	CGATCCAGTGAA---GCGAAAGGTTATTCGAT-CGCAG-C---CC-GGTACAGTGCGTTTCGGAGCTGTAGGGTG--TGTG---TATCCCTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTTA-------------------------------------ATTC-------------ACTTACTTTCTTACT-------------------------------------CAGGAGA--TAATGTTTA-GAA-------GGAAA--TAGCATTT-------------GCACTTTCACA--A------------ATCACCTCCT--ACGCTCTTACAGCCCCGAAACGCACTGTCCTCG---GGT--------CG--TCACATACTCCCAAAAGAGATTTGG------------------------------------------TTTAGGT---TTCTTTTTTT--
droKik1	scf7180000302476:268506-268758 -	378	GAGCCCAGTAGCAG-TTCGCTGCTC------T-CGTCGCC---ATCGGGATTTGGTGTCTGGAGGC----------------------CCTG----ACTCAGGCATT----------TCCTGC--------------GACG----------------------CACTTGAATGCATTC---CGCGG--A-ACAG--ATGCTCC----------------------------AGTC-------------ACTCCACGGCGACCA-------------------------GCGGGCCACTGTAAGGGGGG-AG---AGGGGAGA-------GAAAA--AGGCAGTTTAGAAATCAAAAGTCATATTAACA--T------------GATTTA----------GCACACATTCCCGACAGCGGCACTCCCCG---GGT--------CA--TATATCAACCTCAG---------------------------------------------------------------------------
droAna3	scaffold_12916:15308718-15308902 +	14	CCTT-----------------------------------------------------------------------------------------------------------------------------------AAATTT----------------------TAGTCAAATCTATTC---AATATAGACTTCA--AA---------------------------------TATC-------------TCCCAATTTTATGTC-------------------------------------TAAACT---TG---ACCC-ACAAAACAACCAAA----------------------------------------------------------------------------CTTGACAACATTGTCGCCA------------------------AAATCCGATAGCCTTTTACTTCCTCGTCTCCATTACAAACCGGCTCCCACTACGGGGTGCAATTGAATTTCATTTTTTTTT--
droBip1	scf7180000396431:1210000-1210013 -	62	A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTATTGTTTTTT--
dp4	chrXL_group1a:7788225-7788566 +	9	CGACCAACTGATTAGTCGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACCTTTGTGTGT--ACTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATTTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAAGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAG---CC--AACGCGCAGTAGAAACTTCT-------------------------------------------------------CTGTTAT--
droPer1	super_15:138507-138845 +	2	TGACCAACTGATTA-TTGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACATTTGTGTGT--ATTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATGTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAGGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAGCCATAGAAACGCGCAGTAGCAACTT--------------------------------------------------------------CT--
droWil1	scaffold_180698:1644066-1644082 +	3	GAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT------------------------------------------------------GTAATGTTTCTT--
droVir3	scaffold_11422:71-82 -	464	TT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTATTAT--
droMoj3	scaffold_6359:4144759-4144773 -	19	GA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTAGTTCTTTTT--
droGri2	scaffold_15203:2938631-2938653 -	50	CCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGCAAT------------------------------------------------------CCTATATCCAAT--

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CAGTCCAGTGAAAAG-CGAAAGGTTATGTCGTCGACCCGGGTACAGTGCGTTTCGAGGCTGTATGTGCTTGTTTTAATCCCCA----ATCATACGCATT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTCGAAGTCATTC-----TGCAGG---------------------TTCAGCAATCCACTTAGTTTCGTACTCAGGACCGCG--ATTAGAACGAACGAAATTTTGCA-TTTGTCACATTCACATCTCTTCGCCTACAGCACCGAAACGCACTGTCCCC--------------------------GGGTCGTCAAACACTC--------------CCAGGCGAGATTTAAT--GTTTTTT

Size

Hit Count

Total Norm

droSim1

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

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

CAGTCCAGTGAAAAG-CGAAAGGTTATGTCGTCGACCCGGGGACAGTGCGTTTCGAGGCTGTATGTGCTTGTTTTAATCCCCA----TTCATACGCATT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTTGAAGTCATTC-----TGCAGA---------------------TTCAGCAATCCACTTATTTTCTTACTCAGGACCGCG--ACTAAAACAAACGAAA--TGGCG-TTTGTCACTTTCACATCTCTTCGCCTACAGCGCCGAAACGCACTGTCCCC--------------------------AGGTTGTCATACGCTC--------------CCAGGCGAGATTTAAT--GTTTTTT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................ATTTAAGGTTTCATTTGAAGTC.....................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
..............................................TGCGTTTCGAGGCTGTATGTGC.....................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
..........................................ACAGTGCGTTTCGAGGCTGT...........................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
...................................CCCGGGGACAGTGCGTTTCGAGG...............................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00
.........................................GACCGTGCGTTTCGAGGCTGT...........................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................................................................................G--ACTAAAACAAACGAAA--TGGCG-TT.................................................................................................................................	24	1	1.00	0.00	1.00	0.00
...................................CCCGGGGACAGTGCGTTTCGAGGC..............................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00
.........................................GATAGTGCGTTTCGxGGCTGT...........................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................CTACAGCGCCGAAACGCACT.......................................................................................	20	1	1.00	0.00	1.00	0.00
.........................ATGTCGTCGACCCGGGGACAGTGCG.......................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00

droYak2

CAGTCCAGTGA--AG-CGAAAGGTTATGTCGTCGCCC--AGTACAGTGCGTTACGAGGCTATATGTGCTTGTTGTAAT--------------------A------------------------------------------------------------------------------------------------------CAGC-ACCTAAGGTTTCATTCGAAGTCATTC-----TTTGGG---------------------TTCAGCAACCCACATAGTTTCGTACTCAGGACCATG--ATTAGAA----CGAAA--TGGCA-TTTG-CACCATCACACCGCTGCGCCTACAGCTGCGAAACGCACTGTACTC--------------------------GGGTCGTCAAACACTC--------------CCAGACGAGATTTAAT--GTTTTTT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................................................................................................................................................................AA----GGGAA--TGGCA-TTTG-..............................................................................................................................	16	1	2.00	0.00	0.00	0.00	2.00	0.00
...................................................................................................................................................................................................................................................................................................................AA----AGAAA--CGGCA-TTTG-..............................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................CAGGACCATG--ATTAGAA----CGA.............................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................................................AA----GGAAA--TGGCA-TTTG-C.............................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................AT--------------------A------------------------------------------------------------------------------------------------------CAGC-ACCTAAGGTTTC...............................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................CAGGACCATG--ATTAGAA----CGG.............................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CAGTCCAGTGA--AG-CGAAGGGTTACGTCGCCGCCC--AGTACAGTGCGTTGCGAGGCTGTATGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCCTT------------------------------------------------------------------------------------------------------CAGCAACCTAAGGTTTCATTCGAAGTCATTC--------------------------------------AACCCACATAGTTTCGTGCTCAGGAA-ATGACATTAGAA----CGAAA--TGGCA-TTT-TCACGTTCACATCTCTTCGCCTACAGCCCCGAAACGCACTGTACCC--------------------------GGCTCGTCAACTACTC--------------CCAGACGAGATTTAAT--GGTTTTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................................................................................................................................................................................................................................ACGTTCACATCACGTCGCC..........................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..........................................ACAGTGCGTTGCGAGGCT.............................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................ATCCCAGCCTCTTCATGCCCCTT------------------------------------------------------------------------------------------------------CAGC............................................................................................................................................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00

droAna3

C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAAGTCAAGTTCAAT--GTTTTTT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CGACCAACTGATTAGTCGATTAGTCGATTCGTTGATTCATTTTCA---------------------------TTCAACTTCCA----TTCATACGTAACTTTATTTATTAAATACTTGATGTTCGATTTTAGAATTGCCTTCAACCTTTGTGTGTACTTTATTAGTTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGA-----CAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATTTATGGCTTATGGCAATCCACAC-------------------------A-GAG---TTGAAA---AGCAATCT-TTG---------A-GCTTCCCTACAGCCCTGAAACGCACTGTATATGTTAGTATGGGGACAGCC-----AACG--------------CGCAGTAGAAACTTCTCTGTT---------------ATAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................................................................................................................................................................................................................TATGGGGACAGCC-----AACG--------------CGCAGTA.................................	24	1	1.00	1.00	0.00	0.00	0.00
........TGATTAGTCGATTAGTCGATTCGT.........................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00

droPer1

TGACCAACTGATTAT-TGATTAGTCGATTCGTTGATTCATTTTCA---------------------------TTCAACTTCCA----TTCATACGTAACTTTATTTATTAAATACTTGATGTTCGATTTTAGAATTGCCTTCAACATTTGTGTGTATTTTATTAGTTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGA-----CAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATGTATGGCTTATGGCAATCCACAC-------------------------A-GAG---TTGAAA---GGCAATCT-TTG---------A-GCTTCCCTACAGCCCTGAAACGCACTGTATATGTTAGTATGGGGACAGCCATAGAAACG--------------CGCAGTAGCAACTTCTCTGTT---------------ATAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................................................................................................................................................................................................................................................................................AATCT-TTG---------A-GCTTCCCTACAGCCCTGAA..............................................................................................	28	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................A---------------------------TTTGACTTCCA----TTCATA............................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................CTTACAGCCCTGAACCGCAC........................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................ATTATATCAGTTGTGGTT............................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................................................................................................................................................................................AAACG--------------GCCAGTAGCAACT...........................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................................................ACAC-------------------------A-GAG---TTGAAA---GGCAATCT-T..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.GACCAACTGATTAT-TGATTAGTC................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................................................................TAGAAACG--------------CGCAGTAGCAACTTCT........................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................ATGTTAGGTTTTAGAATTGC...............................................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTATTTCGTTTTTT

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	None	None	None
UNAFold Image		None				None			None	None	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												None			None	None	None
UNAFold Image		None												None			None	None	None	None