dme-mir-276b-as- Best orthologs

dme-mir-276b-as	chr3L:10312885-10312983 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 10312906-10312927
   mutations
   read mismatches

Notes: TODO: This is bizarre. Why does the 12-way have perfect conservation vs. me not finding any with lastz

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3L:10312870-10312998 -		1	TT--------TTAA--CTAT--------A--TGCTGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATATAGGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTT---------------------CG--TTC-GATGGTC
droSim1	chr3L:9702897-9703022 -	LASTZ	5	TT--------TCAA--CTAT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTC----------------------G--GTC-GATGGTC
droSec1	super_0:2526747-2526871 -	LASTZ	5	TT--------TCAA--CTAT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTC----------------------G--TTC--GTGGTC
droYak2	chr3L:10302128-10302256 -	LASTZ	4	TT--------TTAA--CTTT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTG-------------------TTCT--TTC-TGTTGTC
droEre2	scaffold_4784:10306167-10306292 -	LASTZ	0	TT--------TCAA--CTTT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTT----------------------A--TTC-GGTTGTC
droEug1	scf7180000409711:2174289-2174430 -	LASTZ	0	TT--------TAAA--CTTT--------A--CGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----AAATA--GAAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGGCTTCGGTATTTTC------TTTGTTTTTCTTGGCCC--TTC-GATGGAC
droBia1	scf7180000302428:7436352-7436478 +	LASTZ	0	TT--------TCAA--GTTT--------T--GGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTG---------------------TA--TTC-GACGGTC
droTak1	scf7180000415209:361628-361756 -	LASTZ	0	TT--------TCAA--CTTT--------A--TGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACG----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGGCTTCGGTTATTTC------T-------------TCG--TTC-GATGGTC
droEle1	scf7180000490564:1145980-1146108 -	LASTZ	0	TG--------TTAATTCTTT--------A--TGTTGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGATT----AAATG--GGAACGTAGGAACTCTATACCTCGCTGATGGTATAAAGACTTCGGTTTTCTG---------------------CT--TTG-AATGGTC
droRho1	scf7180000780105:56692-56817 +	LASTZ	0	TG--------TAAA--CTTT--------A--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAA-AGACTTCGGATTTTTG---------------------GT--TTC-AATGGTC
droFic1	scf7180000453841:740991-741120 +	LASTZ	0	TT--------TAGT--TTTT--------ATTTGATGGACGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATT--TGAACGTAGGAACTCTATACCTCGCTTATGGTAAAAAGGCTTCGGATTTGGG---------------------GT--TTCTGATGGTC
droKik1	scf7180000302334:94650-94789 +	LASTZ	0	CTCTATAATAAACA--CTTT--------A--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTATTTG---A--GGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAAGGCTTCGTTTGTTTT-----------------TGGCTT--TTC-AGTCTTC
droAna3	scaffold_13337:15233368-15233487 -	LASTZ	0	CT--------T-------TC--------A--TGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTAGTTTAAGT--GGCACGTAGGAACTCTATACCTCGCTGATGGCAAATAGGCTTCGGTTTCTTC----------------------A--------GAAAT
droBip1	scf7180000395933:88091-88219 -	LASTZ	0	GA--------AAGA--CTTT--------C-TCGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTAGTTAAAGT--GGCACGTAGGAACTCTATACCTCGCTGATGGTAAATAGGCTTCGGTTTCTTA--------------------------TA-GAATCTT
dp4	chrXR_group6:8706030-8706135 -	LASTZ	0	--------------------------------GTTGATGGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT-TT-GGATA-CGGCACGTAGGAACTCTATACCTCGCTGATGGTAAAGAGGCTTCGCTTT------------------------------------AGAT
droPer1	super_27:1146105-1146210 -	LASTZ	0	--------------------------------GTTGATGGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT-TT-GGATA-CGGCACGTAGGAACTCTATACCTCGCTGATGGTAAAGAGGCTTCGCTTT------------------------------------AGAT
droWil1	scaffold_181024:290397-290516 +	LASTZ	0	TT-----------------------------TGTTGTTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTTATGGTAAATAGGCTTCGTTTATTTC----------------------A--A---ATTTGTT
droVir3	scaffold_13049:16093198-16093326 -	LASTZ	0	TC--------TTTT--C-----------T--TGCTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTGATGGTATATAGACTTCGGTATCTTT---------------------AA--ATCTTAAGATA
droMoj3	scaffold_6680:20678203-20678343 +	LASTZ	0	TT--------TATT--CGTT--------T--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTGATGGTATATAGACTTCGTTATCTTTACAATCTCTG-----------TT--TCA-CTTGGTC
droGri2	scaffold_15110:12572308-12572448 +	LASTZ	0	AC--------TTAA--TTGTTTTGATCAA--TGCTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTAATGGTAAATAGACTTCGTTATCTTT---------------------CGGTTTT-GAGATTT

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	TTTTAACTATATGCTGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACTGAATATAGGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTT--TTCGTTCGATGGTC
droSim1	TTTCAACTATATGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACTGAA--TAGGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTT---TTCGGTCGATGGTC
droSec1	TTTCAACTATATGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACTGAA--TAGGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTT---TTCGTTCG-TGGTC
droYak2	TTTTAACTTTATGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACTGAA--TAGGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTGTTCTTTCTGTTGTC

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

Small RNA-seq read pileup

Species

Alignment

droSim1

TT--------TCAA--CTAT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTC----------------------G--GTC-GATGGTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................TAGGAACTTCATACCTCG................................................................	18	12	0.17	0.00	0.17	0.00	0.00
......................................................................................................................................GTTTTTC----------------------G--GTC-GATCGTC	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................TAAGAACTCTATACCTAG................................................................	18	8	0.13	0.00	0.13	0.00	0.00

droSec1

TT--------TCAA--CTAT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTC----------------------G--TTC--GTGGTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.31	0.19	0.00	0.13
.....................................................................................................CTCTATACCTCGCTGATGGCA.......................................................	21	8	0.13	0.00	0.00	0.13
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	12	0.08	0.00	0.00	0.08
.....................................................AGCGCGGTATCAAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.13
.....................................................AGCGAGGTATTAAGTTCCT.........................................................................................................	19	12	0.08	0.00	0.00	0.08
.....................................................AGCAAGGTATAAAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.00	0.06
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.00	0.06

droYak2

TT--------TTAA--CTTT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTG-------------------TTCT--TTC-TGTTGTC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.25	0.19	0.00	0.00	0.06	0.00
...............................................................................................TAGGAACTTCATACCTCGCT..............................................................	20	12	0.08	0.00	0.00	0.00	0.08	0.00
...............................................................................................TAGGAACTTCATACCTCG................................................................	18	12	0.08	0.00	0.00	0.00	0.08	0.00
...............................................................................................TAGGAACTTTATACCGCGCT..............................................................	20	16	0.06	0.00	0.00	0.00	0.06	0.00
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	12	0.08	0.08	0.00	0.00	0.00	0.00
.....................................................AGCGCGGTATTAAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.00	0.13	0.00
.....................................................AGCAAGGTATAAAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.00	0.00	0.06	0.00
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.00	0.00	0.06	0.00
...............................................................................................TAGGAACTGTATACCGCGCT..............................................................	20	8	0.13	0.00	0.13	0.00	0.00	0.00

droEre2

TT--------TCAA--CTTT--------A--TGATGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTT----------------------A--TTC-GGTTGTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................TAGGAACTTTATACCTCGCTCA............................................................	22	8	0.13	0.00	0.13	0.00	0.00
.....................................................AGCACGGTATAAAGTTCCTCCG......................................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
.....................................................AGCGCGGTATCAAGTTCCTACG......................................................................................................	22	8	0.13	0.13	0.00	0.00	0.00
...............................................................................................TAGGAACTTCATACCTCGCTG.............................................................	21	8	0.13	0.00	0.13	0.00	0.00

droEug1

TT--------TAAA--CTTT--------A--CGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----AAATA--GAAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGGCTTCGGTATTTTC------TTTGTTTTTCTTGGCCC--TTC-GATGGAC

Size

Hit Count

Total Norm

droBia1

TT--------TCAA--GTTT--------T--GGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGACTTCGGTTTTTTG---------------------TA--TTC-GACGGTC

Size

Hit Count

Total Norm

droTak1

TT--------TCAA--CTTT--------A--TGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACG----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAAAAGGCTTCGGTTATTTC------T-------------TCG--TTC-GATGGTC

Size

Hit Count

Total Norm

droEle1

TG--------TTAATTCTTT--------A--TGTTGGTCGACAGTCCTCCAAGAGCACGGTATTAAGTTCCTACGATT----AAATG--GGAACGTAGGAACTCTATACCTCGCTGATGGTATAAAGACTTCGGTTTTCTG---------------------CT--TTG-AATGGTC

Size

Hit Count

Total Norm

droRho1

TG--------TAAA--CTTT--------A--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATA--GGAACGTAGGAACTCTATACCTCGCTGATGGTAAA-AGACTTCGGATTTTTG---------------------GT--TTC-AATGGTC

Size

Hit Count

Total Norm

droFic1

TT--------TAGT--TTTT--------ATTTGATGGACGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT----GAATT--TGAACGTAGGAACTCTATACCTCGCTTATGGTAAAAAGGCTTCGGATTTGGG---------------------GT--TTCTGATGGTC

Size

Hit Count

Total Norm

droKik1

CTCTATAATAAACA--CTTT--------A--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTATTTG---A--GGAACGTAGGAACTCTATACCTCGCTGATGGCAAAAAGGCTTCGTTTGTTTT-----------------TGGCTT--TTC-AGTCTTC

Size

Hit Count

Total Norm

droAna3

CT--------T-------TC--------A--TGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTAGTTTAAGT--GGCACGTAGGAACTCTATACCTCGCTGATGGCAAATAGGCTTCGGTTTCTTC----------------------A--------GAAAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.25	0.00	0.00	0.25	0.00
..........................................................................................................................ATTAGGCTTCGGTTTGTT.....................................	18	2	1.00	0.00	0.00	1.00	0.00
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	16	0.13	0.00	0.06	0.06	0.00
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	12	0.17	0.08	0.00	0.08	0.00
...............................................................................................TAGGAACTCCATACCTCGCTC.............................................................	21	8	0.13	0.00	0.00	0.13	0.00
..........................................................................................................................ATTAGACTTCGGTTTCTT.....................................	18	2	0.50	0.00	0.00	0.00	0.50
.....................................................AGCACGGTATACAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
.....................................................AGCATGGTATAAAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
.....................................................AGCACGGTATAAAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.13	0.00
...............................................................................................TAGGAACTTAATACCTCGCT..............................................................	20	12	0.08	0.00	0.00	0.08	0.00
...............................................................................................TAGGAACTTTATACCGCGCT..............................................................	20	16	0.06	0.00	0.00	0.06	0.00

droBip1

GA--------AAGA--CTTT--------C-TCGATGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTAGTTAAAGT--GGCACGTAGGAACTCTATACCTCGCTGATGGTAAATAGGCTTCGGTTTCTTA--------------------------TA-GAATCTT

Size

Hit Count

Total Norm

dp4

--------------------------------GTTGATGGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT-TT-GGATA-CGGCACGTAGGAACTCTATACCTCGCTGATGGTAAAGAGGCTTCGCTTT------------------------------------AGAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................................TTGAAACTCTATACCTCGCTGA............................................................	22	8	0.13	0.00	0.13	0.00	0.00

droPer1

--------------------------------GTTGATGGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACT-TT-GGATA-CGGCACGTAGGAACTCTATACCTCGCTGATGGTAAAGAGGCTTCGCTTT------------------------------------AGAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	16	0.19	0.00	0.00	0.00	0.19	0.00
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	12	0.17	0.00	0.00	0.00	0.17	0.00
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.13	0.00	0.00	0.00	0.13	0.00
.....................................................AGCACGGTATAGAGTTCCT.........................................................................................................	19	16	0.06	0.00	0.00	0.00	0.06	0.00
...............................................................................................TAGGAACTATATACCGCGCTG.............................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
...............................................................................................TAGGAACTCCATACCTCGCTC.............................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
...............................................................................................AAGGAGCTCTATACCTCGCTG.............................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
...............................................................................................TAGGAACTTCATACCTCGCT..............................................................	20	12	0.08	0.00	0.00	0.00	0.08	0.00
.....................................................AGCACGGTATAAAGTTCCT.........................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13	0.00
.....................................................AGCACGGTxTTAACTTCCTA........................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25	0.00
...............................................................................................TAGGAACTTTATACCTCGCTC.............................................................	21	8	0.13	0.00	0.00	0.00	0.13	0.00
.....................................................AGCACGGTATCGAGTTCCTACG......................................................................................................	22	8	0.13	0.00	0.00	0.00	0.13	0.00
...............................................................................................TAGGAACTTTAGACCTCGCTGA............................................................	22	8	0.13	0.00	0.00	0.13	0.00	0.00

droWil1

TT-----------------------------TGTTGTTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTTATGGTAAATAGGCTTCGTTTATTTC----------------------A--A---ATTTGTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	12	0.83	0.00	0.08	0.75	0.00
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	12	0.42	0.00	0.00	0.42	0.00
.....................................................AGCAAGGTATAAAGTTCCTACG......................................................................................................	22	12	0.17	0.00	0.00	0.17	0.00
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	10	0.10	0.00	0.00	0.10	0.00
...............................................................................................TAGGAACTTAATACCTCG................................................................	18	10	0.10	0.00	0.00	0.00	0.10

droVir3

TC--------TTTT--C-----------T--TGCTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTGATGGTATATAGACTTCGGTATCTTT---------------------AA--ATCTTAAGATA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.....................................................AGCGCGGTATTGAGTTCCTACG......................................................................................................	22	12	0.17	0.00	0.17	0.00	0.00	0.00
.....................................................AGCACGGTATAGAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.06	0.00	0.00	0.00
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.06	0.00	0.06	0.00	0.00	0.00
...............................................................................................TAGGAACTTTATACCTxGCTGAT...........................................................	22	8	0.13	0.00	0.13	0.00	0.00	0.00

droMoj3

TT--------TATT--CGTT--------T--TGTTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGACTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTGATGGTATATAGACTTCGTTATCTTTACAATCTCTG-----------TT--TCA-CTTGGTC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................AGCGCGGTATAAAGTTCCTACG......................................................................................................	22	16	0.31	0.00	0.19	0.13	0.00
...............................................................................................TAGGAACTTCATACCTCGCT..............................................................	20	12	0.17	0.00	0.17	0.00	0.00
...............................................................................................TAGGAACTCCATACCGCGCTG.............................................................	21	8	0.13	0.00	0.00	0.13	0.00
.....................................................AGCAAGGTATAAAGTTCCT.........................................................................................................	19	16	0.06	0.00	0.06	0.00	0.00
..................TT--------T--TGTTGGACGCCAGCC...................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
.....................................................AGCACGGTTTAAAGTTCCT.........................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13

droGri2

AC--------TTAA--TTGTTTTGATCAA--TGCTGGTCGACAGCCCTCCAAGAGCACGGTATTAAGTTCCTACGATTATTGCAATT--TGCACGTAGGAACTCTATACCTCGCTAATGGTAAATAGACTTCGTTATCTTT---------------------CGGTTTT-GAGATTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:14:15 EDT

dme-mir-276b-as

chr3L:10312885-10312983 -

Candidate

intergenic

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