dme-mir-2494- 12- and 20-way alignments

dme-mir-2494	chr3R:12444488-12444604 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 12444559-12444581
   star strand at position 12444510-12444530
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:12444473-12444619 +	G--GCAACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATTG--------GGAATAACCTT------------CA-----------AAAGCTGCAACTTAA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droSim1	chr3R:9022585-9022731 -	G--GCAACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATTG--------GGAATAACCTT------------CA-----------AAAGCTGCAACTTAA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droSec1	super_12:1702814-1702963 -	G--GCATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATAGTA-----AATGGAATAACCTT------------CA-----------AAATCTGCAACTTAA-ATATTCCCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC
droYak2	chr3R:11948210-11948356 -	G--GCGACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACCAGATTG--------GGATTAACCTT------------CA-----------AAAGCTGCAGCTTAA-CTATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC
droEre2	scaffold_4770:9192977-9193123 -	G--GCAACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAACAGATTG--------GGAGTAACCGT------------CA-----------AAAGCTACAACTTCA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC
droAna3	scaffold_13340:7435217-7435360 -	G--GCAGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTATATACGT--------CCTGCTGTCTT------------AT-----------AAAATTGTTATTT----TTTTTCTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC
dp4	chr2:5294042-5294203 -	G--GCGACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCT----TAGATGAT-GCAAGGCCTTGGATGGAACTGAAA-----------CATTGTGTAACATGA-CTCTCCACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC
droPer1	super_19:1006170-1006331 -	G--GCGACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCT----TAGATGAT-GCAAGGCCTTGGATGGAACTGAAA-----------CATTGTGTAACATGA-CTCTCCACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC
droWil1	scaffold_181108:4575766-4575914 -	G--GCAATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCAAAATTC-------------AACTTG------TAACTATA-----------GCTGTTAAATTTTCTCCTTATTATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC
droVir3	scaffold_13047:18500357-18500519 -	ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCCCGCTA-----ACT-GGTTGGGCTTGACAAGTAACCATA-----------TTTATTTTTTTTTTT-GTTCGCCCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC
droMoj3	scaffold_6496:22335084-22335230 -	G--CCGGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTC----GAAGTATAAA--------TCTAATT------------GAGAAGGCCCTAACTGACTGCTATT----------ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC
droGri2	scaffold_15074:333824-333973 -	GCAGCGGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTCGAATCA--------TTAAGATCAGT------------AAGAAGATGTTCTCAG-------TCT----CCATTTCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:12444473-12444619 +	NA	GGCAACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCA-C----CAG----ATTGGGAAT---AACCT----TCAAAAGCTG-CAACT---------TAAA--------------TATTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC-
droSim1	chr3R:9022585-9022731 -	21	GGCAACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCA-C----CAG----ATTGGGAAT---AACCT----TCAAAAGCTG-CAACT---------TAAA--------------TATTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC-
droSec1	super_12:1702814-1702963 -	28	GGCATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCA-C----CATAGTAAA-TGGAAT---AACCT----TCAAAATCTG-CAACT---------TAAA--------------TATTC---CCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAACCTATTCGGACC-
droYak2	chr3R:11948210-11948356 -	27	GGCGACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCA-C----CAG----ATTGGGATT---AACCT----TCAAAAGCTG-CAGCT---------TAAC--------------TATTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAACCTATTCGGACC-
droEre2	scaffold_4770:9192977-9193123 -	20	GGCAACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCA-A----CAG----ATTGGGAGT---AACCG----TCAAAAGCTA-CAACT---------TCAA--------------TATTC---CCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAACCTATTCGGACC-
droEug1	scf7180000409557:86539-86685 -	21	GGCAACCTGCCCGTGAGCATCTTTCGACCAGCGATCAGTAAGTCCA-C----CAG----ATTGGGATT---AATCT----TCAAAAGTTG-CAACT---------TAAA--------------TATTC---CCAGTAATGTCCACCTACAAGGAGCCTCTGAATGGGTGGGTGGACAATCTATTTGGACC-
droBia1	scf7180000299102:379899-380045 +	4	GGCAACCTGCCCCTGTGTGTCTACCGGCCGGCGATCAGTAAGTGCA-T----CAG----ATTGGAGTT---AATCT----TGAACAGCTG-CAACT---------TAAA--------------TATTC---CCAGTTATGTCCACCTACAAGGAGCCCGTAAGCGGGTGGGTGGACAATCTGTTTGGACC-
droTak1	scf7180000415580:230298-230451 -	35	GGCAACCTGCCCCTGTCCATCTTCCGGCCGGCGATCAGTAAGTGCT-TTACCCCG----CATGGGATT---AACCT----TCAAAAGCTG-CAACT---------TGAA--------------TATTCCATCCAGTAATGTCCACCTACAAGGAGCCACTGAATGGGTGGGTGGACAATCTGTACGGACC-
droEle1	scf7180000490967:720355-720501 +	10	GACGCCCTGCCCTTGTGCATCTTCCGACCGGCGATCAGTAAGTGCT-C----CCG----ATTGGAATT---GACAT----TCA-AAGCTA-CAACC--------ACAAA--------------TATTC---CCAGTAATGTCCACCTACAAGGAGCCACTGCGTGGGTGGGTGGACAACCTATTCGGACC-
droRho1	scf7180000778413:42160-42305 -	19	GGCAACCTGCCCTTGTGCATCTTCCGACCGGCAATCAGTAAGTGCA-C----CAG----ATTGGGGTG---GACCT----T-AAACGCTG-CAACT---------TAAA--------------TATTC---ACAGTAATGTCCACCTACAAGGAGCCTTTCGACGGGTGGGTGGACAACATGTTCGGACC-
droFic1	scf7180000453796:140197-140344 -	19	GGCGACCTGCCGCTCTGCATCTTCCGACCGGCGATCAGTAAGTGCA-C----CAA----ACTTATATT---GTCTC--T-TCAAAGGCTG-CCACT---------TGAA--------------TCTTT---ACAGTAATGTCCACCTACAAGGAACCCCTGCATGGCTGGGTGGACAACCTGTTTGGACC-
droKik1	scf7180000302475:105618-105766 -	19	GGTGACCTGCCCCTGTGCGTCTTCCGACCGGCGATCAGTAAGTT-A-A----TAA----ATTAGGATACCCCAGAA----TCTGGCGCTG-CAACT---------AACT--------------TATCC---TTAGTTATGCCTACCTACAAGGACCCCGTCGTTGGATGGACGGAGAATTTATATGGACC-
droAna3	scaffold_13340:7435217-7435360 -	18	GGCAGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACT-A----TAT----ACGTCCTGC---TGTCT----TATAAAATTG-TTATT---------T-----------------TTTTT---CTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAACCTTTATGGACC-
droBip1	scf7180000396708:1418496-1418640 +	11	GGTAGCCTACCGGTCAGCATTTATCGACCTGCCATAAGTAAGTGCT-G----TA------TTAATATTTC-TGTGT----TCTGAAACTG-TTATT---------G-----------------TTTCT---CTAGTAATTGGCACTTACAAGGAGCCATTAGTTGGGTGGATAGATAACCTCTATGGACCG
dp4	chr2:5291706-5291847 -	7	GGCGACTTGCCGCTGTCCATCTTTCGTCCAGCAGTTAGTAAGTGAT-T----TGC----GTGCAGAAT---AACT---------GAATTT-CATGA---------TCAA--------------TAATT---GCAGTCATGGCAAGCCACAAGGAGCCCGTCGCAGGCTGGATCGATAACCTCTATGGACC-
droPer1	super_19:1003844-1003985 -	17	GGCGACTTGCCGCTGTCCATCTTTCGTCCAGCAGTTAGTAAGTGAT-T----TGC----GTGCAGAAT---AACT---------GAATTT-CATGA---------TCAA--------------TAATT---GCAGTCATGGCAAGCCACAAGGAGCCCGTCGCAGGCTGGATCGATAACCTCTATGGACC-
droWil1	scaffold_181108:4575766-4575914 -	17	GGCAATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCT-C----AAA----ATTCAACT--------T----G-TAACTATA-GCTGTTAAATTTT-CTCC--------------TTATT---ATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAATTTATATGGACC-
droVir3	scaffold_12875:12811190-12811339 -	15	GGTGATTTGCCCGTCTGCATCTTTCGTCCGGGTTCCAGTGGGTAGCAC----TAG----CTAAACCAT---TTGATTCATTTGTAAATAG-T-------------CCAT------------TAATCAT---TCAGTTGTGGCGACCAGCAAGGAGCCCGTTGCCGGCTGGATAGACAACATCTACGGACC-
droMoj3	scaffold_6540:10933524-10933670 +	8	GCTGGTCTGCCCATATGCATCGTTCGGCCAAGCATTAGTAAGTGGA--------------------------ATGA----TCAAATGATC-TAGGT---------TAAATATATATCAAATCATTTGC---TCAGTTATTGGCAGCTATAAGGAGCCCGTCTCTGGCTGGGTTGACAATCTGTATGGTCC-
droGri2	scaffold_15074:333824-333971 -	17	AGCGGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCG-T----CGA----ATCATTAAG---ATCAG----TAAGAAGATGTTCTCA---------GTCT--------------CCATT---TCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAATCTATATGGTCC-

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

G--GCAACCTGCCACTGTCCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATTG--------GGAATAACCTT------------CA-----------AAAGCTGCAACTTAA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC

Size

Hit Count

Total Norm

droSim1

G--GCAACCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCAGATTG--------GGAATAACCTT------------CA-----------AAAGCTGCAACTTAA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................GTAAGTGCACCAGATTGGGAC.................................................................................................................................................	21	1	2.00	1.00	0.00	1.00	0.00
.................GTAAGTGCACCAGATTGGGAAT................................................................................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
...................AAGTGCAACTGATTGGGA..................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................AAGTGCAACTGATTGGGAA.................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................GTAAGTGCACCAGATTGGGAA.................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.................GTAAGTGCACCAGATTGGG...................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................AAAGCTGCA--------ACTTAAATG..............................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................GTAAGTGCACCAGATTGGGAAA................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

G--GCATCCTGCCATTGTGCATCTTCCGACCGGCGATCAGTAAGTGCACCATAGTA-----AATGGAATAACCTT------------CA-----------AAATCTGCAACTTAA-ATATTCCCAGTAATGTCCGCTTACAAGGAGCCCCTGGTTGGATGGGTGGACAA--CCTATTCGGACC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

G--GCGACCTGCCACTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCACCAGATTG--------GGATTAACCTT------------CA-----------AAAGCTGCAGCTTAA-CTATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGATGGCTGGGTGGACAA--CCTATTCGGACC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................GTAAGTGCACCAGATTGGGATT................................................................................................................................................	22	1	18.00	0.00	0.00	18.00	0.00	0.00
.................GTAAGTGCACCAGATTGGGAT.................................................................................................................................................	21	1	4.00	0.00	0.00	4.00	0.00	0.00
.................GTAAGTGCACCAGATTGGGA..................................................................................................................................................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
..........................................................................T------------CC-----------CAGTAATGTCCACTT-ACA................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................TT------------CC-----------CAGTAATGTCCACTT-ACA................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.................GTAACTGCACCAGATTGGGATT................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

G--GCAACCTGCCCCTGTGCATCTTCCGCCCGGCGATCAGTAAGTGCAACAGATTG--------GGAGTAACCGT------------CA-----------AAAGCTACAACTTCA-ATATTCCCAGTAATGTCCACTTACAAGGAGCCCCTGGTTGGCTGGATAGACAA--CCTATTCGGACC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................TTGGGAGTAACCGTAAAGAGC...................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.................GTAAGTGCAACAGATTGGGAGT................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droAna3

G--GCAGCCTGCCAGTCAGCATTTATCGGCCTTCCATAAGTAAGTACTATATACGT--------CCTGCTGTCTT------------AT-----------AAAATTGTTATTT----TTTTTCTAGTAATTGCCACATATAAGGAGCCATTAGTTGGATGGGTGGATAA--CCTTTATGGACC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................AATGTG--------ATTTTTTTTCT------------A...............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........TTCCATAAGCGAGTACTA............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

dp4

G--GCGACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCT----TAGATGAT-GCAAGGCCTTGGATGGAACTGAAA-----------CATTGTGTAACATGA-CTCTCCACAGTCGTGCCCACCTACCAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

G--GCGACCTGCCCGTGTGCATTTTTCGGCCGGCCATTAGTAAGTTTTTCCT----TAGATGAT-GCAAGGCCTTGGATGGAACTGAAA-----------CATTGTGTAACATGA-CTCTCCACAGTCGTGCCCACCTACAAGGAGCCCGTCGTTGGTTGGACTGACAA--TCTGTACGGGCC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

G--GCAATCTACCAATCTGTATTTTTCGCCCTGGTGTCAGTAAGTCCTCAAAATTC-------------AACTTG------TAACTATA-----------GCTGTTAAATTTTCTCCTTATTATAGTTATTGCCACCGCCAAGGAGCCAGTTTCGGGTTGGATTGACAA--TTTATATGGACC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............CAGTAAGTGCTCxAAATTC.....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

ACAAAAAGCTGCCCATTATCGTCACAAGGCCTTCCATCGGTATGTAGGTCCCGCTA-----ACT-GGTTGGGCTTGACAAGTAACCATA-----------TTTATTTTTTTTTTT-GTTCGCCCAGTGACGGCGGCCATACACGAGCCCATGCCCGGATGGATTGAGGG--CGTGAACGGACC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................A-TATGTGTGTGTGTGTGTGT................................................	20	9	0.89	0.89	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTGT................................................	18	11	0.18	0.00	0.00	0.18	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTGTGT..............................................	20	21	0.10	0.10	0.00	0.00	0.00	0.00
....................................................................................................................CATATGTGTGTGTGTGTGT................................................	19	3	0.67	0.67	0.00	0.00	0.00	0.00
....................................................................................................................TATGTGTGTGTGTGTGTGT................................................	19	24	0.08	0.04	0.04	0.00	0.00	0.00
....................................................................................................................CATGTATGTGTGTGTGTGT................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGCGT................................................	18	14	0.07	0.00	0.07	0.00	0.00	0.00
..................................................................................................................G-CATGTGTGTGTGTGTGTGT................................................	20	9	0.11	0.00	0.00	0.11	0.00	0.00
..................................................................................................................G-CATGTGTGTGTGTGTGTG.................................................	19	11	0.09	0.09	0.00	0.00	0.00	0.00
....................................................................................................................CGTGTGTGTGTGTGTGTGT................................................	19	25	0.04	0.04	0.00	0.00	0.00	0.00
.....................................................................................................................GTGTGTGTGTGTCTGTGTGTG.............................................	21	18	0.06	0.06	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTTT................................................	18	12	0.08	0.00	0.00	0.08	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTGTG...............................................	19	26	0.04	0.04	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTATGTGTGT................................................	18	11	0.09	0.09	0.00	0.00	0.00	0.00
..................................................................................................................A-CATATGTGTGTGTGTGTGT................................................	20	2	0.50	0.50	0.00	0.00	0.00	0.00
..................................................................................................................A-CATATGTGTGTGTGTGT..................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
.....................................................................................................................GTGTCTGTGTGTCTGTGT................................................	18	10	0.10	0.00	0.10	0.00	0.00	0.00
.....................................................................................................................ATGTGTATGTGTATGTGT................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
.....................................................AAC-----ATG-TTTATTTTTTTT..........................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................TTTTTTTTTTTGTTGGCTC...............................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................ATGCGTGTGTGTGTGTGT................................................	18	12	0.08	0.00	0.00	0.08	0.00	0.00
.....................................................................................................................ATGTGTGTGTGCGTGTGT................................................	18	14	0.07	0.07	0.00	0.00	0.00	0.00
....................................................................................................................TATGTGTGTGTGTGTGTGTCT..............................................	21	7	0.14	0.14	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTGTC...............................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
..................................................................................................................A-AATGTGTGTGTGTGTGTGT................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
....................................................................................................................CATGTGTGTTTGTGTGTGT................................................	19	3	0.33	0.33	0.00	0.00	0.00	0.00
.....................................................................................................................ATGTGTGTGTGTGTGTGTGTG.............................................	21	19	0.05	0.05	0.00	0.00	0.00	0.00
.................................................................................................................TG-CATGTGTGTGTGTGTG...................................................	18	12	0.08	0.08	0.00	0.00	0.00	0.00
...................................................................AATTTTTTTTTTTGGTCG..................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................ATGTGTGTGTGTGTGTGTGTGT............................................	22	16	0.06	0.06	0.00	0.00	0.00	0.00
.....................................................................................................................ATGCGTGTGTGTGTGTG.................................................	17	15	0.07	0.00	0.07	0.00	0.00	0.00
................................................................................................................ATG-CATGTGTGTGTGTGTG...................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
..................................................GTAAxC-----ATT-TTTATTTTTT............................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

G--CCGGTCTGCCGGCAGCCATAGTTAGGCCATCCATAGGTGAGTC----GAAGTATAAA--------TCTAATT------------GAGAAGGCCCTAACTGACTGCTATT----------ACAGTATACGGTACACTGGAGCACCCCATGAAGGGCTGGGTGGGCAATGCCAACTCGGGTC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GCAGCGGTTTGCCCATAAGCATCTTTCGCCCGGGTGTCAGTAAGTTCGTCGAATCA--------TTAAGATCAGT------------AAGAAGATGTTCTCAG-------TCT----CCATTTCAGTTATTGGCAGCTACAAGGACCCCCTCCCGGGCTGGGTTGACAA--TCTATATGGTCC

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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

20-way Secondary Structure

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