dme-mir-4967- Best orthologs

dme-mir-4967	chr2R:5899597-5899704 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5899620-5899641
   star strand at position 5899659-5899680
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:5899582-5899719 -		1	CATAGATAT--GGC-----------------------------------TAAC-TATAGCGTTGTC---TCTTGCGC--A----------------A-------------------------------------AT-T-----------GC-----A-------TTTT--C------T----------CTCTGTT-------AACATGTACACATAATT-CCTGTAACAAAGGGCATTT----G-CAA--TGTGTGAGTCAGCAAA--CCGCATC---CGCTTC---CCG--GCCC--------------CTCCT
droSim1	chr2R:4528976-4529111 -	LASTZ	4	CGAGGAAAT--AGC-----------------------------------TAAC-TATAGCGTTCTC---TCTTGCGC--A----------------A-------------------------------------AT-T-----------GC-----A-------TTTT--C------T----------CTCTGTA-------AACATGTACACATAATT-CCTGTAACAAAGGGCATTT----G-CAA--TGTGTGAGTCAGCAAA--CCGCATA---CGCCCC---CCGC---C---------------CTCCC
droSec1	super_1:3512309-3512447 -	LASTZ	4	CGAGGAAATATCTT-----------------------------------TAAC-TATAGCGTTCTC---TCTTGCGC--A----------------A-------------------------------------AT-T-----------GC-----A-------TTTC--C------T----------CTCTGTA-------AACATGTACACATAATT-CCTGTAACAAAGGGCATTT----G-CAA--TGTGTGAGTCAGCAAA--CCGCATC---CGCCCC---TCT---GC--------------CCTCCT
droYak2	chr2L:18527608-18527740 -	LASTZ	5	CGGGAAACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--A----------------A-------------------------------------AT-T-----------GT-----A-------TTTT--C------T----------CTCTGTT-------AAAATGTACACATAATT-CCTATTTCAAAGGGCTTTG----G-AAA--AGTGTGAGTCAGCAAA--CCGCATC---CGCCCG---ATTT---C---------------TTCCT
droEre2	scaffold_4929:8470755-8470887 +	LASTZ	5	CGGTAAATT--CG--------------------------------------AC-TAAAGCGTTCTC---TCTTGCTT--A----------------A-------------------------------------AT-T-----------GT-----A-------TTTT--C------T----------CTCTGTT-------AACATGTATACATATTT-CCTGTAACAAAGGCCATTG----G-AAA--TGTGTGAGTCAGCAAA--CCGCATC---CGCCCC---CTTT---C---------------TTCCT
droEug1	scf7180000409209:279768-279962 +	LASTZ	0	TAAAATTAT--AAC-----------------------------------TTAT-TATAATATT---------AATAATAATATTTCTCTTTAATATAAACT-TCCTCCTTATTATTCCCCGTGTAAAACTGTAAAA-T-----------AC-----A-------TTTT--T------C----------CTCTGCAAAA----AACATGTACACATAACCCCGTGTAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAAA--CCGCATC---ATCCCCACTTTGCCACCA--------------CTACC
droBia1	scf7180000301506:799111-799301 +	LASTZ	0	CAGTAAAA-------------------------------CTTTTTTTAT-----------TTTA--------TTTAACAAAATCCAGATTTTAAACAAACA-TTTTTACCATTTTTTCCCATTTAAAA------AT-C-----------GG-----ATTT----ATTTTTC------T----------CTGTGCATTGTACATATATGTACGCATAACG-CGCGCAACAAAAGGCATTT----G-AAA--TGAATGAGTCAGCAGA--CCGCATC---CTGCTG---CCGCCTCC--------------TCCCCG
droTak1	scf7180000415870:347835-348002 +	LASTZ	0	CTAGAGCAC------------AAAAATA--------AAATCTGTACAAA-----------ATTGGC------TGGTG--A----------------A-A-----------------------------TTGAGAAATTGAAATTTATTAGAACCGAGAAG----TTTT--C------T----------CTCTGTG-------AATCAGTTCGTATAACG-CGCGTAACAAAAGGCATTT----A-AAA--TGTGTGAGTCAGCAGA--CCGCATC---CTCCCG---CTC---CC--------------TCCCCG
droEle1	scf7180000491107:1192577-1192740 +	LASTZ	0	TATTT---T--GTCTAAGCATATATTTA---------------------TTTA-TGTGAATTTAAGGTGTTTTTAATT-A-----------------AA--TT---------------------AAAAAAGAAGG-------------AATTTAAG---------TTTTTCCCTGTGT----------TTC--CA-------TGCACGTACGTATTACC-CCTGTAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAGA--CCGCATT---GCT-----------------------------GCCCT
droRho1	scf7180000777200:86291-86481 -	LASTZ	0	TATAGATTT--AGT-----TTAT-TTTATGGCAGTAAATATTGTCATGT-----------T--------TTATTCATT-A-----------------AACTTT---------------------AAAATTGAAAA-------------AAGGTCAGAATGTCTTCTTT--T------T----------CTCTGTA-------GACATGTACTTATAACC-CCTGTAACAAAAGGCATTT----A-AAA--TGTGTGAGTCAGCAGA--CCGCAGTACACAT----------CCCCCCATCCTTAGTTACACCCCT
droFic1	scf7180000453948:638218-638352 +	LASTZ	0	AATTTGCTG--TAC-----------C-----------------------TACT-TGTAAGCTTTTA---AATAGTGG--A----------------A----------------------------------------------------AC-----C-------TTTT--T------T----------CTCTGTA-------AACATGTACATGTAACC-CCTGCAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAGA--CCGCATC---ACCGCG---CTT---TC--------------ACCCCT
droKik1	scf7180000302682:1555020-1555157 +	LASTZ	0	AAAATATTT--TAA-----------------------------------TAAA-TTTAAACTTAAT---TTTTTAGC--T----------------AAT-T-TTTTTGATAATAAGCACAGTGTA------------------------------------------------------------------------------------AAATTTATTT-CGTGTAACAAAAGGCATGT----G-AAA--TGCGTGAGTCAGCAGA--CCGCATC---CCTTGG---CTTT--CC--------------TTTCCT
droAna3	scaffold_13266:17255662-17255760 +	LASTZ	0	TGCTATA-TATCTG-----------------------------------TACC-TA-----------------------------------------------------------------------------------------------------------------------------------------TA-------TGTATGTACGGGTG-TT-TATGTAACAAAAGGCATTTTGGTGGAAA--TGCGTGAGTCAGCGGA--CCGCATT---ATG------------CCC--------------TTTGT
droBip1	scf7180000396735:518339-518422 +	LASTZ	0	TCTGTACAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------TATATATACACGTA-TT-TATGTAACAAAAGGCATTT----GGAAA--TGTGTGAGTCAGCGGA--CCGCAGT---ATG------------CCC--------------TTTGT
dp4	chr3:6114287-6114365 -	LASTZ	0	C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCATC-------CATATGTAC---------TTTATAACAAAGGGCATTT----G-GAATATGTGTGAGTCAGCACATGCCGCATC---CGT----------GGCCC--------------CTTCC
droPer1	super_2:6317550-6317666 -	LASTZ	0	TTTTGACA----G---------------------------------------CTTTAAGCGTTCC-------------------------------------------------------------------------------------------A--------TTT--C------CATTCACGAACCTCCATC-------CATATGTAC---------TTTATAACAAAGGGCATTT----G-GAATATGTGTGAGTCAGCACATGCCGCATC---CGT----------GGCCC--------------CTTCC
droWil1	scaffold_180700:5327370-5327375 -	LASTZ	0	CCCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT
droVir3	scaffold_12875:417241-417243 -	LASTZ	0	CCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:5073155-5073192 +	LASTZ	0	GAGACACTT--AAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCGTT---CACCTT---GTGCGACTC--------------CCTAA
droGri2	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	CATAGATATGGC--TAACTATAGCGTTGTCTCTTGCGCAAATTGCATTTTCTCTCTGTTAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCGCTTCCCGGCCCCTCCT
droSim1	CGAGGAAATAGC--TAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTTCTCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATACGCCCC-CCG-CCCTCCC
droSec1	CGAGGAAATATCTTTAACTATAGCGTTCTCTCTTGCGCAAATTGCATTTCCTCTCTGTAAACATGTACACATAATTCCTGTAACAAAGGGCATTTGCAATGTGTGAGTCAGCAAACCGCATCCGCCCCTCTG-CCCTCCT
droYak2	CGGGAAAC-----TCGACTATAGCGTTCTCTCTTGTTTAAATTGTATTTTCTCTCTGTTAAAATGTACACATAATTCCTATTTCAAAGGGCTTTGGAAAAGTGTGAGTCAGCAAACCGCATCCGCCCG-ATT-TCTTCCT
droEre2	CGGTAAAT-----TCGACTAAAGCGTTCTCTCTTGCTTAAATTGTATTTTCTCTCTGTTAACATGTATACATATTTCCTGTAACAAAGGCCATTGGAAATGTGTGAGTCAGCAAACCGCATCCGCCCC-CTT-TCTTCCT

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
UNAFold Image																	None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

CGAGGAAAT--AGC-----------------------------------TAAC-TATAGCGTTCTC---TCTTGCGC--A----------------A-------------------------------------AT-T-----------GC-----A-------TTTT--C------T----------CTCTGTA-------AACATGTACACATAATT-CCTGTAACAAAGGGCATTT----G-CAA--TGTGTGAGTCAGCAAA--CCGCATA---CGCCCC---CCGC---C---------------CTCCC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................................................................................................ATT--C------A----------CTCTGTA-------AACATG...........................................................................................................	18	1	24.00	0.00	23.00	1.00	0.00
.............................................................................................................................................................................................................................................TT----G-CAA--TGTGTGAGTCAGC....................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................TT--C------A----------CTCTGTA-------AACATGAAC........................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................TAGC	26	5	0.20	0.00	0.00	0.20	0.00
........................................................CAGCGTTCAC---TCTTGCGC--............................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................................................................................................GC	26	7	0.14	0.00	0.00	0.00	0.14
......................................................................................................................................................................TT--C------A----------CTCTGTA-------AACATGAA.........................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................TAGC	27	4	0.25	0.00	0.00	0.00	0.25

droSec1

CGAGGAAATATCTT-----------------------------------TAAC-TATAGCGTTCTC---TCTTGCGC--A----------------A-------------------------------------AT-T-----------GC-----A-------TTTC--C------T----------CTCTGTA-------AACATGTACACATAATT-CCTGTAACAAAGGGCATTT----G-CAA--TGTGTGAGTCAGCAAA--CCGCATC---CGCCCC---TCT---GC--------------CCTCCT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........ATGTT-----------------------------------TAAC-TATAGCGTGC...........................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
............TT-----------------------------------TAAC-TATAGxTTTCTC---TC....................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

CGGGAAACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--A----------------A-------------------------------------AT-T-----------GT-----A-------TTTT--C------T----------CTCTGTT-------AAAATGTACACATAATT-CCTATTTCAAAGGGCTTTG----G-AAA--AGTGTGAGTCAGCAAA--CCGCATC---CGCCCG---ATTT---C---------------TTCCT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	24	35	0.46	0.14	0.00	0.17	0.00	0.14
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTT...............................................................................................................................................................................................................................................	25	35	0.34	0.14	0.00	0.20	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	23	37	0.14	0.08	0.03	0.03	0.00	0.00
...........TG--------------------------------------AC-TAxAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	21	41	0.12	0.00	0.02	0.02	0.00	0.07
.......CT--TG--------------------------------------AC-TAxAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	20	40	0.08	0.00	0.00	0.03	0.00	0.05
CGGGGAACT--CG--------------------------------------AC-TATAGCGTTCT..........................................................................................................................................................................................................................................................	24	44	0.07	0.02	0.00	0.02	0.00	0.02
.....AACT--CG--------------------------------------AC-TATAGCGTTCTC---T.....................................................................................................................................................................................................................................................	21	38	0.08	0.00	0.00	0.05	0.00	0.03
......ACT--TG--------------------------------------AC-TAxAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	21	38	0.08	0.00	0.00	0.00	0.00	0.08
.....AACT--TG--------------------------------------AC-TAxAGCGTTCTC---TC....................................................................................................................................................................................................................................................	21	37	0.08	0.00	0.03	0.00	0.05	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGC................................................................................................................................................................................................................................................	24	38	0.08	0.00	0.00	0.00	0.00	0.08
........T--TG--------------------------------------AC-TAxAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	22	39	0.05	0.00	0.00	0.03	0.00	0.03
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGG................................................................................................................................................................................................................................................	24	37	0.05	0.00	0.00	0.00	0.00	0.05
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	26	41	0.05	0.02	0.00	0.02	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGCTCTC---TCTTG.................................................................................................................................................................................................................................................	23	37	0.05	0.05	0.00	0.00	0.00	0.00
CGGGAAACT--CG--------------------------------------AC-TATAGCATTCTC---......................................................................................................................................................................................................................................................	25	36	0.06	0.00	0.00	0.00	0.00	0.06
......ACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	24	35	0.06	0.00	0.00	0.00	0.00	0.06
........T--CG--------------------------------------AC-TATAGCGTTCTC---TCTT..................................................................................................................................................................................................................................................	21	37	0.05	0.00	0.00	0.05	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--A----------------A-------------------------------------GA-T-----------......................................................................................................................................................................	28	3	0.67	0.00	0.00	0.67	0.00	0.00
........T--TG--------------------------------------AC-TAxAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	21	43	0.05	0.00	0.02	0.02	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--T----------------A-------------------------------------AT-C-----------......................................................................................................................................................................	28	15	0.13	0.07	0.00	0.07	0.00	0.00
.....AACC--CG--------------------------------------AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	25	34	0.03	0.00	0.00	0.03	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--A----------------T-------------------------------------A....................................................................................................................................................................................	26	29	0.03	0.00	0.00	0.03	0.00	0.00
.....AACC--CG--------------------------------------AC-TATAGCGTTCTC---T.....................................................................................................................................................................................................................................................	21	38	0.03	0.00	0.00	0.03	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--C----------------A-------------------------------------.....................................................................................................................................................................................	28	36	0.03	0.00	0.00	0.03	0.00	0.00
.....AACT--CG--------------------------------------AT-TATAGCGTTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	28	40	0.03	0.00	0.00	0.03	0.00	0.00
........T--TG--------------------------------------AC-TAxAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	19	45	0.02	0.00	0.00	0.00	0.00	0.02
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTCCT...............................................................................................................................................................................................................................................	25	37	0.03	0.00	0.00	0.00	0.00	0.03
.......CT--CG--------------------------------------AC-TATAGTGTTCTG---TCTTGTTT--............................................................................................................................................................................................................................................	26	57	0.02	0.00	0.00	0.02	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	23	32	0.03	0.00	0.00	0.03	0.00	0.00
.....AGCT--CG--------------------------------------AC-TATAGCGTTCTC---C.....................................................................................................................................................................................................................................................	21	41	0.02	0.00	0.00	0.00	0.00	0.02
.....AACT--CG--------------------------------------AC-TATAGCGTTCT..........................................................................................................................................................................................................................................................	19	38	0.03	0.00	0.00	0.03	0.00	0.00
........T--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	25	44	0.02	0.00	0.00	0.02	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCATTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	26	31	0.03	0.03	0.00	0.00	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	21	40	0.03	0.00	0.00	0.03	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTATT...............................................................................................................................................................................................................................................	25	36	0.03	0.00	0.00	0.00	0.03	0.00
............A--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--A----------------A-------------------------------------TT-..................................................................................................................................................................................	27	7	0.14	0.14	0.00	0.00	0.00	0.00
.....AACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	26	36	0.03	0.00	0.00	0.03	0.00	0.00
.....AACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTCT................................................................................................................................................................................................................................................	26	33	0.03	0.03	0.00	0.00	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTG---TCTTGT................................................................................................................................................................................................................................................	24	35	0.03	0.03	0.00	0.00	0.00	0.00
...........CG--------------------------------------AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	21	37	0.03	0.00	0.00	0.03	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGGTCTC---TCTTGTTT--............................................................................................................................................................................................................................................	26	41	0.02	0.00	0.00	0.00	0.00	0.02
........T--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--T----------------A-------------------------------------.....................................................................................................................................................................................	27	28	0.04	0.00	0.00	0.04	0.00	0.00
.......CT--TG--------------------------------------AC-TAxAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	23	35	0.03	0.00	0.00	0.00	0.03	0.00
.......CA--CG--------------------------------------AC-TATAGCGGTCTC---TCTTGT................................................................................................................................................................................................................................................	24	35	0.03	0.03	0.00	0.00	0.00	0.00
............A--------------------------------------AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	20	51	0.02	0.02	0.00	0.00	0.00	0.00
...GAAACT--CG--------------------------------------GC-TATAGCGC.............................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.00	0.33
...................................................AC-TATAGCGTTCTC---TCTTGTTT--T----------------A-------------------------------------AT-C-----------......................................................................................................................................................................	27	18	0.06	0.00	0.00	0.06	0.00	0.00
......GCT--CG--------------------------------------AC-TATAGCGTTCTC---TC....................................................................................................................................................................................................................................................	21	38	0.03	0.00	0.00	0.00	0.00	0.03
.......CT--CG--------------------------------------CC-TATAGCGTTCTC---TCTTGTT...............................................................................................................................................................................................................................................	25	47	0.02	0.02	0.00	0.00	0.00	0.00
.......CT--GG--------------------------------------AC-TATAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	21	40	0.03	0.00	0.00	0.03	0.00	0.00
......ACT--CG--------------------------------------AC-TATGGCGTTCTC---TCT...................................................................................................................................................................................................................................................	22	36	0.03	0.00	0.00	0.03	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--T----------------A-------------------------------------A....................................................................................................................................................................................	26	19	0.05	0.00	0.00	0.05	0.00	0.00
......ACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTT...............................................................................................................................................................................................................................................	26	34	0.03	0.00	0.00	0.00	0.00	0.03
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTA--............................................................................................................................................................................................................................................	26	38	0.03	0.00	0.00	0.03	0.00	0.00
......ACT--CG--------------------------------------AC-TGTAGCGTTCTC---TC....................................................................................................................................................................................................................................................	21	37	0.03	0.00	0.03	0.00	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTGTC---TCTTGCT...............................................................................................................................................................................................................................................	25	37	0.03	0.00	0.00	0.03	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTCT--C----------------...........................................................................................................................................................................................................................	27	33	0.03	0.03	0.00	0.00	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---CCTTG.................................................................................................................................................................................................................................................	23	60	0.02	0.00	0.00	0.02	0.00	0.00
.....AACT--TG--------------------------------------AC-TAxAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	22	37	0.03	0.00	0.00	0.00	0.00	0.03
......ACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--T----------------...........................................................................................................................................................................................................................	28	35	0.03	0.00	0.00	0.00	0.00	0.03
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTTT--T----------------...........................................................................................................................................................................................................................	27	35	0.03	0.03	0.00	0.00	0.00	0.00
......ACT--CG--------------------------------------AC-CATAGCGTTCTC---......................................................................................................................................................................................................................................................	19	41	0.02	0.00	0.00	0.00	0.00	0.02
...................................................AC-TACAGCGTTCTG---TCTTGTT...............................................................................................................................................................................................................................................	21	43	0.02	0.00	0.00	0.02	0.00	0.00
.....AACT--CG--------------------------------------AC-TATAGCGTTCTC---TCTT..................................................................................................................................................................................................................................................	24	34	0.03	0.00	0.00	0.03	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTTT................................................................................................................................................................................................................................................	24	40	0.03	0.03	0.00	0.00	0.00	0.00
CGGGGAACT--CG--------------------------------------AC-TATAGCGTTCTC---......................................................................................................................................................................................................................................................	25	43	0.02	0.02	0.00	0.00	0.00	0.00
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---T.....................................................................................................................................................................................................................................................	19	41	0.02	0.00	0.02	0.00	0.00	0.00
...................................................AC-TATAGCGTTCTC---TCTTG.................................................................................................................................................................................................................................................	19	48	0.02	0.00	0.02	0.00	0.00	0.00
............G--------------------------------------AC-TATAGCGTTCTC---TCTTT.................................................................................................................................................................................................................................................	20	42	0.02	0.00	0.00	0.02	0.00	0.00
........T--CG--------------------------------------AC-TATAGCGTTCTC---TCTA..................................................................................................................................................................................................................................................	21	38	0.03	0.03	0.00	0.00	0.00	0.00
........T--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGTT...............................................................................................................................................................................................................................................	24	35	0.03	0.03	0.00	0.00	0.00	0.00
.....AACT--CG--------------------------------------AC-TTTAGCATTCTC---TCTTG.................................................................................................................................................................................................................................................	25	37	0.03	0.00	0.00	0.00	0.00	0.03
........T--CG--------------------------------------AC-TATAGCGTCCTC---TCTTG.................................................................................................................................................................................................................................................	22	37	0.03	0.03	0.00	0.00	0.00	0.00
........T--CG--------------------------------------AC-TTTAGCGTTCTC---TCCT..................................................................................................................................................................................................................................................	21	39	0.03	0.00	0.00	0.00	0.00	0.03
.......CT--CG--------------------------------------AC-TATAGCGTTCTC---TCT...................................................................................................................................................................................................................................................	21	38	0.03	0.00	0.00	0.03	0.00	0.00
.......AT--CG--------------------------------------AC-TATAGCGTTCTC---TCTTGT................................................................................................................................................................................................................................................	24	38	0.03	0.00	0.00	0.03	0.00	0.00
.....AACT--TG--------------------------------------AC-TATAGCGTTCTC---T.....................................................................................................................................................................................................................................................	21	40	0.03	0.00	0.00	0.03	0.00	0.00

droEre2

CGGTAAATT--CG--------------------------------------AC-TAAAGCGTTCTC---TCTTGCTT--A----------------A-------------------------------------AT-T-----------GT-----A-------TTTT--C------T----------CTCTGTT-------AACATGTATACATATTT-CCTGTAACAAAGGCCATTG----G-AAA--TGTGTGAGTCAGCAAA--CCGCATC---CGCCCC---CTTT---C---------------TTCCT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................AC-TATAGCGTTCTC---CCTTG.................................................................................................................................................................................................................................................	19	6	0.17	0.00	0.00	0.00	0.17

droEug1

TAAAATTAT--AAC-----------------------------------TTAT-TATAATATT---------AATAATAATATTTCTCTTTAATATAAACT-TCCTCCTTATTATTCCCCGTGTAAAACTGTAAAA-T-----------AC-----A-------TTTT--T------C----------CTCTGCAAAA----AACATGTACACATAACCCCGTGTAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAAA--CCGCATC---ATCCCCACTTTGCCACCA--------------CTACC

Size

Hit Count

Total Norm

droBia1

CAGTAAAA-------------------------------CTTTTTTTAT-----------TTTA--------TTTAACAAAATCCAGATTTTAAACAAACA-TTTTTACCATTTTTTCCCATTTAAAA------AT-C-----------GG-----ATTT----ATTTTTC------T----------CTGTGCATTGTACATATATGTACGCATAACG-CGCGCAACAAAAGGCATTT----G-AAA--TGAATGAGTCAGCAGA--CCGCATC---CTGCTG---CCGCCTCC--------------TCCCCG

Size

Hit Count

Total Norm

droTak1

CTAGAGCAC------------AAAAATA--------AAATCTGTACAAA-----------ATTGGC------TGGTG--A----------------A-A-----------------------------TTGAGAAATTGAAATTTATTAGAACCGAGAAG----TTTT--C------T----------CTCTGTG-------AATCAGTTCGTATAACG-CGCGTAACAAAAGGCATTT----A-AAA--TGTGTGAGTCAGCAGA--CCGCATC---CTCCCG---CTC---CC--------------TCCCCG

Size

Hit Count

Total Norm

droEle1

TATTT---T--GTCTAAGCATATATTTA---------------------TTTA-TGTGAATTTAAGGTGTTTTTAATT-A-----------------AA--TT---------------------AAAAAAGAAGG-------------AATTTAAG---------TTTTTCCCTGTGT----------TTC--CA-------TGCACGTACGTATTACC-CCTGTAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAGA--CCGCATT---GCT-----------------------------GCCCT

Size

Hit Count

Total Norm

droRho1

TATAGATTT--AGT-----TTAT-TTTATGGCAGTAAATATTGTCATGT-----------T--------TTATTCATT-A-----------------AACTTT---------------------AAAATTGAAAA-------------AAGGTCAGAATGTCTTCTTT--T------T----------CTCTGTA-------GACATGTACTTATAACC-CCTGTAACAAAAGGCATTT----A-AAA--TGTGTGAGTCAGCAGA--CCGCAGTACACAT----------CCCCCCATCCTTAGTTACACCCCT

Size

Hit Count

Total Norm

droFic1

AATTTGCTG--TAC-----------C-----------------------TACT-TGTAAGCTTTTA---AATAGTGG--A----------------A----------------------------------------------------AC-----C-------TTTT--T------T----------CTCTGTA-------AACATGTACATGTAACC-CCTGCAACAAAAGGCATTT----G-AAA--TGTGTGAGTCAGCAGA--CCGCATC---ACCGCG---CTT---TC--------------ACCCCT

Size

Hit Count

Total Norm

droKik1

AAAATATTT--TAA-----------------------------------TAAA-TTTAAACTTAAT---TTTTTAGC--T----------------AAT-T-TTTTTGATAATAAGCACAGTGTA------------------------------------------------------------------------------------AAATTTATTT-CGTGTAACAAAAGGCATGT----G-AAA--TGCGTGAGTCAGCAGA--CCGCATC---CCTTGG---CTTT--CC--------------TTTCCT

Size

Hit Count

Total Norm

droAna3

TGCTATA-TATCTG-----------------------------------TACC-TA-----------------------------------------------------------------------------------------------------------------------------------------TA-------TGTATGTACGGGTG-TT-TATGTAACAAAAGGCATTTTGGTGGAAA--TGCGTGAGTCAGCGGA--CCGCATT---ATG------------CCC--------------TTTGT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........CTA-----------------------------------TACC-TT-----------------------------------------------------------------------------------------------------------------------------------------TA-------TGTATGTA.........................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
.................................................AACC-TA-----------------------------------------------------------------------------------------------------------------------------------------TA-------TGGATGTACGG......................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................TACC-TT-----------------------------------------------------------------------------------------------------------------------------------------TA-------TGTATGTACGCG.....................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00

droBip1

TCTGTACAT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------TATATATACACGTA-TT-TATGTAACAAAAGGCATTT----GGAAA--TGTGTGAGTCAGCGGA--CCGCAGT---ATG------------CCC--------------TTTGT

Size

Hit Count

Total Norm

dp4

C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCATC-------CATATGTAC---------TTTATAACAAAGGGCATTT----G-GAATATGTGTGAGTCAGCACATGCCGCATC---CGT----------GGCCC--------------CTTCC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................................................................................................................................................................................ATTT----G-GAATGTGTGTGTGT........................................................	19	1	1.00	1.00	0.00	0.00	0.00

droPer1

TTTTGACA----G---------------------------------------CTTTAAGCGTTCC-------------------------------------------------------------------------------------------A--------TTT--C------CATTCACGAACCTCCATC-------CATATGTAC---------TTTATAACAAAGGGCATTT----G-GAATATGTGTGAGTCAGCACATGCCGCATC---CGT----------GGCCC--------------CTTCC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

CCCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GAGACACTT--AAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCGTT---CACCTT---GTGCGACTC--------------CCTAA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

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

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:54 EDT

dme-mir-4967

chr2R:5899597-5899704 -

Known_mirbase

intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup