dme-mir-979- Best orthologs

dme-mir-979	chrX:19455870-19455964 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_3pUTR

Legend:

   mature strand at position 19455928-19455950
   star strand at position 19455892-19455914
   mutations
   read mismatches

Notes: Newly evolved in dm3 only

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	TTAATCAC---TGGAA-----------------------------CATACATGT--GAGGATGT-------------------------------CACAA--------ATACACTGAAT----------------------------TTGGGGGGAATTCT-------------------------------------------------------T--ATGTATATACAAATTCTTCCCGAACTCAGGCTAATTTTGTGGCATC------------------------------------------CG---------------------------------------------TATAC----------------------------AC-----------------------------------------------------------------------AAAAGT-----------------------ATA
droSim1	chrX_random:5079602-5079664 +	MAF	0	TTAATATA---CAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTTCACGAATTCAGGCTAATTTTGTAGGAGC------------------------------------------CG---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAAGT-----------------------ATA
droSec1	super_8:1738459-1738521 +	MAF	0	TTAATATA---CAAAA-----------------------------TC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACGAATTCAGGCTACTTTTGTAGGAAC------------------------------------------CG---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAAGT-----------------------ATA
droYak2	chrX:11883259-11883281 -	LASTZ	0	TTAATGGC---TGGGA-----------------------------AATACGTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A
droEre2	scaffold_4690:9691773-9691867 +	LASTZ	0	TTAATCGT---TGGCA-----------------------------AATACGTAT--GG-GGTGCCACACAAATCGATTAG-------------------------------CTCTGAAT----------------------------TCGGGCGGAATTCTGAAG------------------------------C-----------------ACGCAT------------------------------CCACTTTTGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCA-----------------------TCC
droEug1	scf7180000409230:876782-876877 -	LASTZ	0	TTAATCAT---CGTAA-----------------------------ATTAAATAAATTAAAATAT----------------------------------------------------------------------------------TTATAGCAAT-----------------------------ATTTTTCGTAGATATTCTACTTAACTTA------AC------TTAAA-------------------------------TC------------------------------------------AA---------------------------------------------TCAAT----------------------------A------------------------------------------------------------------------CAAAAT-----------------------ATA
droBia1	scf7180000302069:1147456-1147673 -	LASTZ	0	TTAATCAT---TGGAACAGCGTCAATAAATAGTAAAAGCAATAGT--------------------------------TAGAACCGGAGTTAAGCCAACCA--------ACATA------------------------------------AAAATGAGGAAA---------------------------------------------A------------TTG-----------------------------------------------------------------------------------------------------------TACAATTAAAAGAAACAAACGA---TAGTGCAAAGGAATGTGATCAAAAACCTTGGAATCTATCAAATATAACGTATATAATGCATCGCTCCCAACCCTACTAAAATGAATTCAGGAA--TACTACT---CTAAGTT-----------------------CTA
droTak1	scf7180000415169:841429-841556 -	LASTZ	0	CTAATCAG---TGGAGCAGTTTTAATT--TGATATGAGTAATAAT--------------------------------AAGAAGCGGTCCTAAAGTAGCCA--------ATACAGAAAA-AATAAGAACCAAA--------------------------------------------------------------------------------------------------------------TTTCAAAAAACTTTGA------------------------------------------------------------------------------------------------------------------CTAAAAACCATTTAAGC-----------------------------------------------------------------------TAAGAA-----------------------ATG
droEle1	scf7180000491006:819941-820067 -	LASTZ	0	CTACACTG-ATAAAAA-----------------------------AAAGTGCAA-----AAGTACAAATAAATATATGGTT------------------------------------------------------------------------------------------------------------------------------------ATATGG--TTAAATATAAAATCATATCAAGCATGTCTTAATATTAAAATATT------------------------------------------TT---------------------------------------------AGTTT---------------------------------------------------------A--------------CTTTAAATGCCA-------------TAT-T-CAAA-----------------------TTA
droRho1	scf7180000761121:186691-186818 -	LASTZ	0	TTAATCAT---TGGGATACATTAAAA-----------------------------------------------------------------------------------------------------------------------------------------AAAATGTATAAGTAATTGTAGTC---------AATATTGTATAAATAATA------ATG------TAAA-------------------------------AA------------------------------------------AA-----------------------------------TTC---------------------------------------------------------------------ATATTCATTGCTAATATAAATAAATTACGAT-------------AAATAT-------------TTATATGGTAAGG
droFic1	scf7180000454073:1736548-1736631 +	LASTZ	0	TTAACCAT---TGAAGAAATTTTAAT-----------------------------------------------------------------------------------------------------------------------------------------GAAATGCGTAATGCATTGTAAAA---------AC--------------------------------------------------------TATTGTAAACA---------------TTG--------------------------A---------------------------------------------AAAGT-------------------------------------------------------------------------------------------ATTTTA---ATATGTT-----------------------ATA
droKik1	scf7180000302621:248346-248471 -	LASTZ	0	GAAAGCAT---TCCGT-----------------------------TTACCAATT--TCGGATGC-------------------------------CCTAA--------CCACCCAGAAGGGTGGT----CCTTTAAGGGAAAAGGTTTT-GG---TTCTACAGAAAATGTATGAAATTTTATAT-----------------------------ACAAAA-----------------------------------------------------------------------------------------T---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAATT-----------------------ATA
droAna3	scaffold_13417:2459297-2459411 -	LASTZ	0	TAAGTTAC---TTATA-----------------------------ATTAAATTT--AAATATTT-------------------------------CGAAA--------TAAAACTATA-----------------AAAT--------AATTGTCTTATTTCAGAA------------------------------A-----------------ATA-------------------TGTACATATTTATACCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCTTTACATATTTCAAT-------------AAAAAT-----------------------ATA
droBip1	scf7180000395874:31563-31685 -	LASTZ	0	TTATTCAA---CAAAA-----------------------------GACATACATACGTATGTAT----------------------------GTACACCA--------ATATT------------------------------------AAAAAAAATATG---------------------------------------------A------------ATG-----------------------------------------------------------------------------------------------------------TCTATTTCTAAATACTTCATATTTGTAGAGTA----------------------------------------------------------------------------------------------------AAGTAATAATATGGAAATGTACATGGA-TTA
dp4	chrXL_group1e:12509670-12509797 -	LASTZ	0	TTAAGCAT---TTTAA-----------------------------TTTTTGTATTTTTCAAGATCGAAAATATTTATGCGCGTAAATTTAAGAGTAAGTCCTTAGTAAGTAAGGAAGA-AC--------------------------------------------------------------------------------------------------------------------------TACGCTCTGGATTTGATATACT------------------------------------------CG---------------------------------------------TGAAG----------------------------TT-----------------------------------------------------------------------AAAACA-----------------------ATA
droPer1	super_14:1989251-1989367 -	LASTZ	0	CTAAGTCA---TCGTG-----------------------------C---------------------------------GCATCTGTTGGGGAGTAAAAA--------CTAAAATTAG-AGTGGAAACTCTA---T----------TTTGAGTTGA-----------------------------AT---------------------------------------------TTTTCCATGAAAATCTGCTACATTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGGGTTTTA-------------AAT-TTGTAT-----------------------TTT
droWil1	scaffold_181096:7961895-7962008 +	LASTZ	0	TAGATTATGATTAGAA-----------------------------TAAGCACACA----CAACACACGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTATATATAAATCAACCAAGAAAACA---CAATATCGAAGAAA---------------TTA--------------------------G---------------------------------------------AAAGT----------------------------AT-----------------------------------------------------------------------ATATAT-----------------------ATA
droVir3	scaffold_13042:902091-902097 -	LASTZ	0	TCAATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6328:2896306-2896380 -	MAF	0	ATGAGAAA---GGG-------------------------------------------------CTATAGAAATTGATGAC-------------------------------------------------------------------------------------------------------------------GATATA----------------------------------ATCCAAAACTAAGATTACAATAATAATAAT------------------------------------------aa-------------------------------------------------------------------------------------------------------------------------------------------------------taaaca-----------------------aaa
droGri2	scaffold_15081:2040284-2040418 -	LASTZ	0	TTGTAATT---TAAGA-----------------------------TG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGATGAAGACA----------ATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAGTTGAAAATGTC-------------------------------------------------------------------------------------A------------TTCTCTGGTTATTGGATTAA-------AATGAGGACA-----------------------CTT

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	TTAATCACTGGAACATACATGTGAGGATGTCACAAATACACTGAATTTGGGGGGAATTCTTATGTATATACAAATTCTTCCCGAACTCAGGCTAATTTTGTGGCATCCGTATACACAAAAGTATA

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

TTAATATA---CAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTTCACGAATTCAGGCTAATTTTGTAGGAGC------------------------------------------CG---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAAGT-----------------------ATA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................................................................................................................................................................AATTTTGTAGGAGC------------------------------------------TG---------------------------------------------CA........................................................................................................................................	18	2	1.50	0.50	0.00	1.00	0.00
.................................................................................................................................................................................................................................................................GTAGGAGC------------------------------------------CG---------------------------------------------TAGAT----------------------------AC-----------------------------------------------------------------------C...............................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

TTAATATA---CAAAA-----------------------------TC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACGAATTCAGGCTACTTTTGTAGGAAC------------------------------------------CG---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAAGT-----------------------ATA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................................................................................................................................................................................................AC------------------------------------------CG---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAGAT-----------------------A..	18	2	0.50	0.00	0.50	0.00

droYak2

TTAATGGC---TGGGA-----------------------------AATACGTAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTAATCGT---TGGCA-----------------------------AATACGTAT--GG-GGTGCCACACAAATCGATTAG-------------------------------CTCTGAAT----------------------------TCGGGCGGAATTCTGAAG------------------------------C-----------------ACGCAT------------------------------CCACTTTTGTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCA-----------------------TCC

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

TTAATCAT---CGTAA-----------------------------ATTAAATAAATTAAAATAT----------------------------------------------------------------------------------TTATAGCAAT-----------------------------ATTTTTCGTAGATATTCTACTTAACTTA------AC------TTAAA-------------------------------TC------------------------------------------AA---------------------------------------------TCAAT----------------------------A------------------------------------------------------------------------CAAAAT-----------------------ATA

Size

Hit Count

Total Norm

droBia1

TTAATCAT---TGGAACAGCGTCAATAAATAGTAAAAGCAATAGT--------------------------------TAGAACCGGAGTTAAGCCAACCA--------ACATA------------------------------------AAAATGAGGAAA---------------------------------------------A------------TTG-----------------------------------------------------------------------------------------------------------TACAATTAAAAGAAACAAACGA---TAGTGCAAAGGAATGTGATCAAAAACCTTGGAATCTATCAAATATAACGTATATAATGCATCGCTCCCAACCCTACTAAAATGAATTCAGGAA--TACTACT---CTAAGTT-----------------------CTA

Size

Hit Count

Total Norm

droTak1

CTAATCAG---TGGAGCAGTTTTAATT--TGATATGAGTAATAAT--------------------------------AAGAAGCGGTCCTAAAGTAGCCA--------ATACAGAAAA-AATAAGAACCAAA--------------------------------------------------------------------------------------------------------------TTTCAAAAAACTTTGA------------------------------------------------------------------------------------------------------------------CTAAAAACCATTTAAGC-----------------------------------------------------------------------TAAGAA-----------------------ATG

Size

Hit Count

Total Norm

droEle1

CTACACTG-ATAAAAA-----------------------------AAAGTGCAA-----AAGTACAAATAAATATATGGTT------------------------------------------------------------------------------------------------------------------------------------ATATGG--TTAAATATAAAATCATATCAAGCATGTCTTAATATTAAAATATT------------------------------------------TT---------------------------------------------AGTTT---------------------------------------------------------A--------------CTTTAAATGCCA-------------TAT-T-CAAA-----------------------TTA

Size

Hit Count

Total Norm

droRho1

TTAATCAT---TGGGATACATTAAAA-----------------------------------------------------------------------------------------------------------------------------------------AAAATGTATAAGTAATTGTAGTC---------AATATTGTATAAATAATA------ATG------TAAA-------------------------------AA------------------------------------------AA-----------------------------------TTC---------------------------------------------------------------------ATATTCATTGCTAATATAAATAAATTACGAT-------------AAATAT-------------TTATATGGTAAGG

Size

Hit Count

Total Norm

droFic1

TTAACCAT---TGAAGAAATTTTAAT-----------------------------------------------------------------------------------------------------------------------------------------GAAATGCGTAATGCATTGTAAAA---------AC--------------------------------------------------------TATTGTAAACA---------------TTG--------------------------A---------------------------------------------AAAGT-------------------------------------------------------------------------------------------ATTTTA---ATATGTT-----------------------ATA

Size

Hit Count

Total Norm

droKik1

GAAAGCAT---TCCGT-----------------------------TTACCAATT--TCGGATGC-------------------------------CCTAA--------CCACCCAGAAGGGTGGT----CCTTTAAGGGAAAAGGTTTT-GG---TTCTACAGAAAATGTATGAAATTTTATAT-----------------------------ACAAAA-----------------------------------------------------------------------------------------T---------------------------------------------TATAT----------------------------AC-----------------------------------------------------------------------AAAATT-----------------------ATA

Size

Hit Count

Total Norm

droAna3

TAAGTTAC---TTATA-----------------------------ATTAAATTT--AAATATTT-------------------------------CGAAA--------TAAAACTATA-----------------AAAT--------AATTGTCTTATTTCAGAA------------------------------A-----------------ATA-------------------TGTACATATTTATACCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCTTTACATATTTCAAT-------------AAAAAT-----------------------ATA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TTATTCAA---CAAAA-----------------------------GACATACATACGTATGTAT----------------------------GTACACCA--------ATATT------------------------------------AAAAAAAATATG---------------------------------------------A------------ATG-----------------------------------------------------------------------------------------------------------TCTATTTCTAAATACTTCATATTTGTAGAGTA----------------------------------------------------------------------------------------------------AAGTAATAATATGGAAATGTACATGGA-TTA

Size

Hit Count

Total Norm

dp4

TTAAGCAT---TTTAA-----------------------------TTTTTGTATTTTTCAAGATCGAAAATATTTATGCGCGTAAATTTAAGAGTAAGTCCTTAGTAAGTAAGGAAGA-AC--------------------------------------------------------------------------------------------------------------------------TACGCTCTGGATTTGATATACT------------------------------------------CG---------------------------------------------TGAAG----------------------------TT-----------------------------------------------------------------------AAAACA-----------------------ATA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................................................AATTTATGAGTAAATCCT......................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droPer1

CTAAGTCA---TCGTG-----------------------------C---------------------------------GCATCTGTTGGGGAGTAAAAA--------CTAAAATTAG-AGTGGAAACTCTA---T----------TTTGAGTTGA-----------------------------AT---------------------------------------------TTTTCCATGAAAATCTGCTACATTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGGGTTTTA-------------AAT-TTGTAT-----------------------TTT

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TAGATTATGATTAGAA-----------------------------TAAGCACACA----CAACACACGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTATATATAAATCAACCAAGAAAACA---CAATATCGAAGAAA---------------TTA--------------------------G---------------------------------------------AAAGT----------------------------AT-----------------------------------------------------------------------ATATAT-----------------------ATA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........ATTAGAA-----------------------------TAAGCACAxA----CAAC.............................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	1.50	0.00	1.50	0.00	0.00
.........ATTAGAA-----------------------------TAAGCACAxA----CAACC............................................................................................................................................................................................................................................................................................................................................................................................................................................	21	2	1.00	0.00	1.00	0.00	0.00
..............................................................CACTTGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACA....................................................................................................................................................................................................................................................................................	22	5	0.40	0.00	0.00	0.20	0.20
........................................................................CACACACAA------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTGT...........................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
...TTTGTxATTAGAA-----------------------------TAAGCAC........................................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...............................................................ACACGCGCACACCCACAC------------------------------------------------------------------------------------------------------------------------------------AC.....................................................................................................................................................................................................................................................................................	20	5	0.20	0.20	0.00	0.00	0.00
....................................................ATA----CAACACACACACACACACACAC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	26	3	0.33	0.00	0.33	0.00	0.00
......................................................................CACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAA--CTG............................................................................................................................................................................................................................................................................	20	9	0.11	0.00	0.00	0.00	0.11
..............................................................AACGCGCACACACACACA............................................................................................................................................................................................................................................................................................................................................................................................................................	18	21	0.05	0.00	0.05	0.00	0.00
..........................................................................CACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTATACACA......................................................................................................................................................................................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
.................................................CTCACA----CAACACACACACAC...................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.................................................................ATGCACGCACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACA..................................................................................................................................................................................................................................................................................	21	15	0.07	0.00	0.07	0.00	0.00
...........................................................CAATACACACACACACACA..............................................................................................................................................................................................................................................................................................................................................................................................................................	19	42	0.02	0.00	0.02	0.00	0.00
....................................................................CACACACGCACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTG............................................................................................................................................................................................................................................................................	22	3	0.33	0.00	0.00	0.00	0.33
...............................................................ACATGCACACACACGCAC------------------------------------------------------------------------------------------------------------------------------------ACA....................................................................................................................................................................................................................................................................................	21	5	0.20	0.00	0.00	0.20	0.00
.......................................................................ACACACACAA------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTGT...........................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
....................................................................CACACACACACAC------------------------------------------------------------------------------------------------------------------------------------AGAGAT--...............................................................................................................................................................................................................................................................................	19	43	0.02	0.00	0.02	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AT-----------------------ATA	20	43	0.02	0.00	0.02	0.00	0.00
....................................................................CACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--CTG............................................................................................................................................................................................................................................................................	22	7	0.14	0.00	0.00	0.00	0.14
..........TTAGAA-----------------------------TAAGCACAxA----CAACC............................................................................................................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00
..............................................................CACACGCAAATACACACAC------------------------------------------------------------------------------------------------------------------------------------ACA....................................................................................................................................................................................................................................................................................	22	7	0.14	0.00	0.14	0.00	0.00
................................................................TATGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACA..................................................................................................................................................................................................................................................................................	22	26	0.04	0.00	0.00	0.04	0.00
...............................................................ACACGCACACACACACGC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	19	88	0.01	0.00	0.01	0.00	0.00
.....................................................................ACACAGACGCAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--...............................................................................................................................................................................................................................................................................	18	22	0.05	0.00	0.05	0.00	0.00
................................................................CACGCACACACACACAG------------------------------------------------------------------------------------------------------------------------------------TCACAT--...............................................................................................................................................................................................................................................................................	23	3	0.33	0.00	0.33	0.00	0.00
..............................................................CTCACGCACACACACACGC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	20	5	0.20	0.00	0.00	0.20	0.00
.............................................................ACACGCGCACACCCACACAC------------------------------------------------------------------------------------------------------------------------------------.......................................................................................................................................................................................................................................................................................	20	5	0.20	0.20	0.00	0.00	0.00
.....................................................................ACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--GT.............................................................................................................................................................................................................................................................................	20	37	0.03	0.00	0.03	0.00	0.00
.......................................................................................................................................................................................................................................................................A---------------TGA--------------------------G---------------------------------------------AAAGT----------------------------AT-----------------------------------------------------------------------ATATAT-----------------------TT.	20	2	0.50	0.00	0.50	0.00	0.00
.....................................................CA----CAGTACACGCACACACACA..............................................................................................................................................................................................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
.....................................................CA----CAACACACACACACACACA..............................................................................................................................................................................................................................................................................................................................................................................................................................	21	15	0.07	0.00	0.07	0.00	0.00
...........TAGAA-----------------------------TAAGCACAxA----CAACC............................................................................................................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.............................................................ATGCACGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	21	15	0.07	0.00	0.07	0.00	0.00
..................................................................CTCACACACACACAA------------------------------------------------------------------------------------------------------------------------------------ACACAT--...............................................................................................................................................................................................................................................................................	21	10	0.10	0.00	0.10	0.00	0.00
......................................................A----CAACACACACACACACACA..............................................................................................................................................................................................................................................................................................................................................................................................................................	20	40	0.03	0.00	0.03	0.00	0.00
.......................................................................ACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--TTGT...........................................................................................................................................................................................................................................................................	20	13	0.08	0.00	0.08	0.00	0.00
......................................................................CATACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAA--CT.............................................................................................................................................................................................................................................................................	19	8	0.13	0.00	0.13	0.00	0.00
...............................................................ACAAGCACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACA..................................................................................................................................................................................................................................................................................	23	51	0.02	0.00	0.00	0.02	0.00
..GATTATGATGAGAA-----------------------------TATG...........................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
.....................................................TA----CAACACACGGACACAC.................................................................................................................................................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..............................................................CACACGCATACAAACACAC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	20	10	0.10	0.00	0.10	0.00	0.00
...............................................................................................................................................................................................................................ATATATAAATCAAGCAAGCAAAC......................................................................................................................................................................................................................................................	23	2	0.50	0.00	0.50	0.00	0.00
..................................................................CGCACACACACAAAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--G..............................................................................................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.25	0.00
.................................................................ACACACACACACACAC------------------------------------------------------------------------------------------------------------------------------------ACACAT--C..............................................................................................................................................................................................................................................................................	23	60	0.02	0.00	0.02	0.00	0.00
................................................................AACGCGCACACACACAC------------------------------------------------------------------------------------------------------------------------------------A......................................................................................................................................................................................................................................................................................	18	21	0.05	0.00	0.05	0.00	0.00

droVir3

TCAATCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ATGAGAAA---GGG-------------------------------------------------CTATAGAAATTGATGAC-------------------------------------------------------------------------------------------------------------------GATATA----------------------------------ATCCAAAACTAAGATTACAATAATAATAAT------------------------------------------aa-------------------------------------------------------------------------------------------------------------------------------------------------------taaaca-----------------------aaa

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTGTAATT---TAAGA-----------------------------TG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGATGAAGACA----------ATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAGTTGAAAATGTC-------------------------------------------------------------------------------------A------------TTCTCTGGTTATTGGATTAA-------AATGAGGACA-----------------------CTT	Size	Hit Count	Total Norm	V109 Male body
.......................................................................................................................................................................................................................................................................................................................................................................................................................................................ATTGGATTAC-------GATGAGGA............................	18	2	0.50	0.50

Generated: 04/20/2012 at 05:22:28 EDT

dme-mir-979

chrX:19455870-19455964 +

Known_mirbase

antisense_to_3pUTR

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