dme-mir-979-as- Best orthologs

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

Legend:

   mature strand at position 19455927-19455949
   star strand at position 19455890-19455911
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:19455855-19455979 -		1	TATACTTT-TG----TGTATACGGATGCCAC------------AA----A-------------ATTAGC-------CTGAGTTCGGG---------AAGAATTTGTATATA------CAT---------------------------AAGA--------------------------------------------ATTCC-C-----------------------CCCAAATT-------------------------------------------------------------------CA---------------------------------------------------------------------GTGTATTTG--TGACAT------C----------------------------CTCACA--TGTA--T----------------GTTCCAGTGATTAA
droSim1	chr2L:11773332-11773488 +	LASTZ	0	TAAAATGT-AG----TT--------------TA-ATAAGC-----AGAT--A-------------------------------------------------------------TGGATCCT----------------------------------------------AAAAGTATTATATCTTCTT-----------------------------A--------------------------------------------GAAACTATTTTCCTGGATT---------------------TTTAAATGTTGAATTTCTGTAAAATATATCAAAATCTAAATA---------------------------AAATGTGATTT--TAATAG------C----------------------------TAGGGATG--TA--T----------------ATACTTTTGGAAGA
droSec1	super_16:165683-165811 +	LASTZ	0	TAGAAACT-AT----TT--------------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGATTTTTTTGTTGATTTGTTTGATTTTTAAATGTTGAATTTCTGTAAAATATGTCAAAATCTAAATA---------------------------AAATGTGATTT--TAAAAT------C----------------------------TAGGGATG--TATAT----------------ACTTTTGGAAGATA
droYak2	chrX:11883259-11883281 +	LASTZ	0	TTTACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--T----------------TTCCCAGCCATTAA
droEre2	scaffold_4690:9691773-9691868 -	LASTZ	0	GGATGCTA-CAAAAGT-----------------------------GGAT--G--------------CGTG-----------------------------------------------CTT---------------------------CAGA--------------------------------------------ATTCC-G-----------------------CCCGAATT-------------------------------------------------------------------CAGAGCTAATCGATT-------------------------------------------------------------TGTG--TGGCAC------C-----------------------------CCATA--CGTA--T----------------TTGCCAACGATTAA
droEug1	scf7180000409230:876782-876877 +	LASTZ	0	TATATTTT-GT----AT--------------TG-ATT---GATTT----A-A-------------------GTTAAGT-----------------------------------TAA------------------------------------------------------------------------------------GTAGAATATCTACGAAAAATAT--------------------------------------------------------------------------------------------------------------------------------------------------------T-----GC-------------------------------TATAAATATTTTAATTTATTTA--A----------------TTTACGATGATTAA
droBia1	scf7180000302069:1147456-1147673 +	LASTZ	0	TAGAACTT-AG----AG--------------TA-GTA---TTCCT----G-A-------------------ATTCATTTTAGTAGGGTTGGGAGCG---ATGCATTATATA------CGTTATATTTGATAGATTCCAAGGTTTTTG----ATCACATTCCTTTGCAC--TATCGTTTGTTTCTTTTAATTGTACAATTT-TCC----------------------------------------------------------------------TCATTT-------------------------------------------------------------T----------------T-----------ATGTT-----GGTTGGCTTAACTCCGGTTCTAACTATTG--------------CTTTTA--CTAT---T-----TATTGACGCTGTTCCAATGATTAA
droTak1	scf7180000415169:841429-841556 +	LASTZ	0	CATTTCTT-AG----CT--------------TA-AATGGT--TTT----T-A---------------------------------------------------------------------------------------------------GTCAAAGTTTTTTGAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTGGTTCTTATTTTTTCT--------------GTATT--GGCTACTTTAGGACCGCTTCTTATTATTA--------------CTCATA--TCAA----------ATTAAAACTGCTCCACTGATTAG
droEle1	scf7180000491006:819941-820067 +	LASTZ	0	TAATTTGA-ATATGGCA--------------------TTTAAAGTAAACTAAAATATTTTAATATTAAG-------ACATGCTTGAT---------ATGATTTTATATTTAACCATAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCATA--T--------------------------ATT-TATTTGTACT-------T---TTGCACTTTT----------TTTTATCAGTGTAG
droRho1	scf7180000761121:186691-186818 +	LASTZ	0	CCTTACCA-TATAAATA--------------------TTTATCGT----A-------------ATTTAT-------TTATATTAGCAATGAATATGAATT-----TTTTTA------CAT---------------------------TATT--------------------------------------------ATTTA-TACAATATTGACTACAATTACTTATACATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAATGTATCCCAATGATTAA
droFic1	scf7180000454073:1736548-1736631 -	LASTZ	0	TATAACAT-AT----TA--------------AA-ATA---CTTTT----C-AATG-----------------------------------------------------------------------------------------------------------------------------------------------TT-TACAATAGTTTTTACAATGCATTACGCATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAAAATTTCTTCAATGGTTAA
droKik1	scf7180000302621:248346-248471 +	LASTZ	0	TATAATTT-TG----TA--------------TA-TAA----------TT--T--------------TGTATATAAAAT-----------------------------------------------------------------------------------------------------------------------TTCA------------------------TACATTTTCTGTAGAACCAAAACCTTTTCCCTTAAAGGACCACCCTTCTGG-------------------------------------------------------------------------------------------------GTGGTTA--GGGCAT------C----------------------------CGAAAT--TGGT--A----------------AACGGAATGCTTTC
droAna3	scaffold_13417:2459297-2459411 +	LASTZ	0	TATATTTT-TA----TT--------------GAAATATGT-----AAAG--A-------------------------------------------------------------TTGGTATA----------------------------------------------AATATGTACATATTTTCTG-----------------------------AAATAAGACAATTATTT-----------------------------------------TATAGT----------------------------------------------------------------------------------------------TTTATTT--CGAAAT------A----------------------------TTTAAA--TTTA--A----------------TTATAAGTAACTTA
droBip1	scf7180000395874:31563-31685 +	LASTZ	0	TAATCCAT-GT----AC-ATTTCCATATTAT------------TA----C-------------TTTACT-------CTACAAATATG---------AAGTATTTA-----------------------------------------------------------G----------------------AAATAGACATTCA-TATTTTT-----------------TT------------------------------------------------------------------------------------------------------------------T----------------A-----------ATATT-----GGTGTACATAC---A----------------------------TACGTATGTATG--T----------------CTTTTGTTGAATAA
dp4	chrXL_group1e:12509670-12509797 +	LASTZ	0	TATTGTTTTAA----CT--------------TC-ACGAGT-----AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------TCAAATCCAGAGCG-------TAGTTCTTCCTTACTTACTAAGGACT--------TACTCTTAAATTTACGCGCATAA---ATATTTTCGATCTTGAAAAA------------------TACAAAAATTAAAATGCTTAA
droPer1	super_14:1989251-1989367 +	LASTZ	0	AAAATACA-AA----TT--------------TA-AAACCCAAAATGTA--------------------------------------------------------------------------------------------------------------------------------------------------------GCAGATTTTCATGGAAAAA-------------------------------------------------------------------------------------------------------------TTCAACTCAAAATAGAGTTTCCACTCTAATT--------------TTAGTTT--TTACTC------C----------------------------CCAACA--GATG--C----------------GCACGATGACTTAG
droWil1	scaffold_181096:7961895-7962008 -	LASTZ	0	TATATATA-TA----TA-----------------------CTTTC----T-AATTTCTTCGATATTG----------TGTTTTCTTG---------GTTGATTTATATATAGATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------C----------------------------GTGTGTTG--TGTGTGCTTAT------TC---TAATCATAATCTA
droVir3	scaffold_13042:902091-902097 +	LASTZ	0	TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTGA
droMoj3	scaffold_6500:27198225-27198308 +	LASTZ	0	TGCTTTAC-TC----CA--------------GA---GCGC--CGG----A-A-------------------------------------------------------------AGTATGCTACAT----------------------TTGA--------------------------------------------AATC--C-----------------------CTCAAATT-------------------------------------------------------------------CAGACT----------------------------------------------------------------------------------------T----------------------------TCCATA--ACTA--T----------------GTGGAATTCCTTGC
droGri2	scaffold_15081:2040287-2040418 +	LASTZ	0	TGTCCTCA-TTTTAATC--------------CA-ATAACC-----AGAGAATGACATTTTCAACTTTGTATATACAA--------TT---------ATCAGTTTACATTTAAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTCAACT-------------------------------------------------------------CCTA--T--------------------------CAC-TATTATTATT-------A---TTGTCTTCAT------CTTCATCTTAAATTACAA

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	TATACTTTTGTGTATACGGATGCCACAAAATTAGCCTGAGTTCGGGAAGAATTTGTATATACATAAGAATTCCCCCCAAATTCAGTGTATTTGTGACATCCTCACATGTATGTTCCAGTGATTAA

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image																		None
UNAFold Image				None														None

Small RNA-seq read pileup

Species

Alignment

droSim1

TAAAATGT-AG----TT--------------TA-ATAAGC-----AGAT--A-------------------------------------------------------------TGGATCCT----------------------------------------------AAAAGTATTATATCTTCTT-----------------------------A--------------------------------------------GAAACTATTTTCCTGGATT---------------------TTTAAATGTTGAATTTCTGTAAAATATATCAAAATCTAAATA---------------------------AAATGTGATTT--TAATAG------C----------------------------TAGGGATG--TA--T----------------ATACTTTTGGAAGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................................................................................................................................................................TTGxATATCTGTAAAATAT.............................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droSec1

TAGAAACT-AT----TT--------------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGATTTTTTTGTTGATTTGTTTGATTTTTAAATGTTGAATTTCTGTAAAATATGTCAAAATCTAAATA---------------------------AAATGTGATTT--TAAAAT------C----------------------------TAGGGATG--TATAT----------------ACTTTTGGAAGATA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................................................................................................................................................TTTTTGTTGxTTTGTTTGTT.........................................................................................................................................................................	19	3	0.67	0.00	0.67	0.00
................T--------------T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGGTTGTTTTGTTG....................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00
...............................T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGGTTGTTTTGTTG....................................................................................................................................................................................	18	2	0.50	0.50	0.00	0.00
.....................................................................................................................................................................................................................................................................................................TTTGATTATTAGATGTTGA............................................................................................................................................................	19	3	0.33	0.00	0.33	0.00
.........................................................................................................................................................................................................................................................................................TTTGTTGATTAGTTTGAT.........................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00
........................................................................................................................................................................................................................................................................................TTTTGGTGTTTTGTTTGATTT.......................................................................................................................................................................	21	2	0.50	0.00	0.00	0.50
........................................................................................................................................................................................................................................................................................TTTTGTTGCTATGTTTGATT........................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00
.......................................................................................................................................................................................................................................................................................TTTTTGTTGxTTTGTTTGTTT........................................................................................................................................................................	20	3	0.33	0.00	0.33	0.00

droYak2

TTTACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA--T----------------TTCCCAGCCATTAA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GGATGCTA-CAAAAGT-----------------------------GGAT--G--------------CGTG-----------------------------------------------CTT---------------------------CAGA--------------------------------------------ATTCC-G-----------------------CCCGAATT-------------------------------------------------------------------CAGAGCTAATCGATT-------------------------------------------------------------TGTG--TGGCAC------C-----------------------------CCATA--CGTA--T----------------TTGCCAACGATTAA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TATATTTT-GT----AT--------------TG-ATT---GATTT----A-A-------------------GTTAAGT-----------------------------------TAA------------------------------------------------------------------------------------GTAGAATATCTACGAAAAATAT--------------------------------------------------------------------------------------------------------------------------------------------------------T-----GC-------------------------------TATAAATATTTTAATTTATTTA--A----------------TTTACGATGATTAA

Size

Hit Count

Total Norm

droBia1

TAGAACTT-AG----AG--------------TA-GTA---TTCCT----G-A-------------------ATTCATTTTAGTAGGGTTGGGAGCG---ATGCATTATATA------CGTTATATTTGATAGATTCCAAGGTTTTTG----ATCACATTCCTTTGCAC--TATCGTTTGTTTCTTTTAATTGTACAATTT-TCC----------------------------------------------------------------------TCATTT-------------------------------------------------------------T----------------T-----------ATGTT-----GGTTGGCTTAACTCCGGTTCTAACTATTG--------------CTTTTA--CTAT---T-----TATTGACGCTGTTCCAATGATTAA

Size

Hit Count

Total Norm

droTak1

CATTTCTT-AG----CT--------------TA-AATGGT--TTT----T-A---------------------------------------------------------------------------------------------------GTCAAAGTTTTTTGAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTGGTTCTTATTTTTTCT--------------GTATT--GGCTACTTTAGGACCGCTTCTTATTATTA--------------CTCATA--TCAA----------ATTAAAACTGCTCCACTGATTAG

Size

Hit Count

Total Norm

droEle1

TAATTTGA-ATATGGCA--------------------TTTAAAGTAAACTAAAATATTTTAATATTAAG-------ACATGCTTGAT---------ATGATTTTATATTTAACCATAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCATA--T--------------------------ATT-TATTTGTACT-------T---TTGCACTTTT----------TTTTATCAGTGTAG

Size

Hit Count

Total Norm

droRho1

CCTTACCA-TATAAATA--------------------TTTATCGT----A-------------ATTTAT-------TTATATTAGCAATGAATATGAATT-----TTTTTA------CAT---------------------------TATT--------------------------------------------ATTTA-TACAATATTGACTACAATTACTTATACATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTAATGTATCCCAATGATTAA

Size

Hit Count

Total Norm

droFic1

TATAACAT-AT----TA--------------AA-ATA---CTTTT----C-AATG-----------------------------------------------------------------------------------------------------------------------------------------------TT-TACAATAGTTTTTACAATGCATTACGCATTT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAAAATTTCTTCAATGGTTAA

Size

Hit Count

Total Norm

droKik1

TATAATTT-TG----TA--------------TA-TAA----------TT--T--------------TGTATATAAAAT-----------------------------------------------------------------------------------------------------------------------TTCA------------------------TACATTTTCTGTAGAACCAAAACCTTTTCCCTTAAAGGACCACCCTTCTGG-------------------------------------------------------------------------------------------------GTGGTTA--GGGCAT------C----------------------------CGAAAT--TGGT--A----------------AACGGAATGCTTTC

Size

Hit Count

Total Norm

droAna3

TATATTTT-TA----TT--------------GAAATATGT-----AAAG--A-------------------------------------------------------------TTGGTATA----------------------------------------------AATATGTACATATTTTCTG-----------------------------AAATAAGACAATTATTT-----------------------------------------TATAGT----------------------------------------------------------------------------------------------TTTATTT--CGAAAT------A----------------------------TTTAAA--TTTA--A----------------TTATAAGTAACTTA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................................................A----------------------------------------------AATATGTACTTAGTTTCT...........................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00

droBip1

TAATCCAT-GT----AC-ATTTCCATATTAT------------TA----C-------------TTTACT-------CTACAAATATG---------AAGTATTTA-----------------------------------------------------------G----------------------AAATAGACATTCA-TATTTTT-----------------TT------------------------------------------------------------------------------------------------------------------T----------------A-----------ATATT-----GGTGTACATAC---A----------------------------TACGTATGTATG--T----------------CTTTTGTTGAATAA

Size

Hit Count

Total Norm

dp4

TATTGTTTTAA----CT--------------TC-ACGAGT-----AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------TCAAATCCAGAGCG-------TAGTTCTTCCTTACTTACTAAGGACT--------TACTCTTAAATTTACGCGCATAA---ATATTTTCGATCTTGAAAAA------------------TACAAAAATTAAAATGCTTAA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AAAATACA-AA----TT--------------TA-AAACCCAAAATGTA--------------------------------------------------------------------------------------------------------------------------------------------------------GCAGATTTTCATGGAAAAA-------------------------------------------------------------------------------------------------------------TTCAACTCAAAATAGAGTTTCCACTCTAATT--------------TTAGTTT--TTACTC------C----------------------------CCAACA--GATG--C----------------GCACGATGACTTAG

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TATATATA-TA----TA-----------------------CTTTC----T-AATTTCTTCGATATTG----------TGTTTTCTTG---------GTTGATTTATATATAGATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------C----------------------------GTGTGTTG--TGTGTGCTTAT------TC---TAATCATAATCTA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................................................................................................................................................................................................................................................................................................................GTGTTTG--TGTGTG------C----------------------------GTGT.........................................	18	100	0.07	0.00	0.07	0.00	0.00
...................................................................................................................TGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTx--TGTGTG------C----------------------------ATGTG........................................	21	2	3.50	0.00	3.50	0.00	0.00
............................................................................................................ATATATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--T.....................................................................................	18	16	0.38	0.00	0.38	0.00	0.00
............................................................................................................ATATATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGT.................................................................................	22	5	1.00	0.00	1.00	0.00	0.00
................................................................................................................AAGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------G----------------------------GTGTG........................................	25	9	0.56	0.00	0.00	0.56	0.00
................................................................................................................ATATGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------..........................................................................	19	26	0.19	0.12	0.00	0.08	0.00
..............................................................................................................ATATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTG..................................................................................	19	26	0.19	0.12	0.00	0.08	0.00
..............................................................................................................ATATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGT.................................................................................	20	21	0.19	0.00	0.14	0.00	0.05
................................................................................................................ATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------T----------------------------GTGTGC.......................................	26	38	0.11	0.00	0.00	0.11	0.00
............................................................................................................ATCGATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--T.....................................................................................	18	10	0.30	0.10	0.20	0.00	0.00
.............................................................................................................TATATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGT...................................................................................	19	25	0.12	0.04	0.00	0.08	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................GTGTGTG--TGTTTG------C----------------------------CTGTGT.......................................	20	6	0.50	0.00	0.50	0.00	0.00
.................................................................................................................TGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTATGTG--TGTGTG------C----------------------------A............................................	20	26	0.12	0.00	0.12	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................GTGTTTG--TGTGTG------C----------------------------GTGTT........................................	19	8	0.38	0.13	0.25	0.00	0.00
...........................................................................................................AACAGATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--......................................................................................	18	4	0.75	0.00	0.00	0.75	0.00
................................................................................................................ATGTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------T----------------------------GTGTG........................................	25	36	0.08	0.06	0.00	0.03	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................GAG------T----------------------------GTGTGTTG--TGTGTG.............................	18	2	1.50	0.00	0.50	1.00	0.00
.................................................................................................................TATGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGGGTG------C----------------------------G............................................	20	9	0.33	0.11	0.00	0.22	0.00
...................................................................................................................TGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGTG--TGTGTG------C----------------------------A............................................	18	24	0.13	0.00	0.04	0.08	0.00

droVir3

TG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTGA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TGCTTTAC-TC----CA--------------GA---GCGC--CGG----A-A-------------------------------------------------------------AGTATGCTACAT----------------------TTGA--------------------------------------------AATC--C-----------------------CTCAAATT-------------------------------------------------------------------CAGACT----------------------------------------------------------------------------------------T----------------------------TCCATA--ACTA--T----------------GTGGAATTCCTTGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...............................................................................................................................................................................................................................................................................................................ACT----------------------------------------------------------------------------------------T----------------------------TCCATA--CCTx--T----------------GTGGA.........	19	2	1.50	0.50	0.00	1.00	0.00

droGri2

TGTCCTCA-TTTTAATC--------------CA-ATAACC-----AGAGAATGACATTTTCAACTTTGTATATACAA--------TT---------ATCAGTTTACATTTAAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTCAACT-------------------------------------------------------------CCTA--T--------------------------CAC-TATTATTATT-------A---TTGTCTTCAT------CTTCATCTTAAATTACAA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:21:55 EDT

dme-mir-979-as

chrX:19455870-19455964 -

Novel

three_prime_UTR

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