dme-mir-4946- Best orthologs

dme-mir-4946	chr2L:18867045-18867161 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 18867114-18867134
   star strand at position 18867072-18867094
   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	chr2L:18867030-18867176 -		1	TAAAAATAAAAAAATGCTCGA------------------------------TTG---------CTGCAACTAA-------------------------GAAACAA-----------------------------------------------ATATTTTCAGTTGTTCATTGCAAATTAA-------TT--------TATGTACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCTAGGCTTATCA-----GCTGCAATGCCTCTATGAAGGG
droSim1	chr2L:18557325-18557471 -	LASTZ	4	TAAAAATAACAAAACGCTCAT------------------------------TTG---------CTGCAAATAA-------------------------GAAACAA-----------------------------------------------ATATTTTCAGTTGTTCATTGCAAGTTAA-------TT--------TATAAACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCCAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG
droSec1	super_7:2494148-2494294 -	LASTZ	5	TAAAAATAACAAAACGTTCAT------------------------------TTG---------CTGATAATAA-------------------------GAAACAA-----------------------------------------------ATATCTTAAGATGTTCATTGCAAATTAA-------TT--------TATGTACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCTAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG
droYak2	chr2R:5382904-5383074 -	LASTZ	0	TAAAAATAACAAAGCATAT--------------------------TAGCATATG---------CTGCAAACAA-------------------------TAAATAA-----------------------------------------------ATATTTTCAGCTGTGCATTGCAAATTAA-------TG--------TATTTACATAGCTATGAAAGCAATTGAAACG---------------------------------------ACAA------------------------------------------------------------------------------TTGCAGGTCATTTTTATTGCACACA---------------------------------TCCTAGGCTTATCA-----GTGGCAATGCCCCTACGAAGAG
droEre2	scaffold_4845:5409251-5409398 +	LASTZ	0	TACAAGTAACAAAGTGCTAAT------------------------------TCG---------CTGCAAATAG-------------------------GAAATAA-----------------------------------------------ATATTTTCAT---------------TA---------T--------TA-TCACATTGCCA-GAAACCAATTGAAAAG---------------------------------------ATAA------------------------------------------------------------------------------TTGTAGGCCACTTTTGTTGCACGCA---------------------------------TCCTAGGCTTATCA-----GCTGATATGCCCCCACGAAGGG
droEug1	scf7180000409478:17863-18010 +	LASTZ	0	TAGCAAAATTAATATTTTAAA------------------------------ATT---------GTGTAAAAAA-------------------------GTAACGG-----------------------------------------------GTATCTTA---TAGTCGTGGCA--CTCG-------AC--------TATAGCGTTTCCTCTTGTTTTGATTAGAAAT---------------------------------------GTGC------CTTGTATACCAAGGGGGCTTATCCG----------------------------------------------------------------------------------------------------------------------------CCATAGCCGGATACCGCAACGG
droBia1	scf7180000301754:1283245-1283392 -	LASTZ	0	TTACAATATTTAATTTAGT--------------------------------TTT---------TTATATTTAAAATTCAAACTGTTTGCCCACAGTAG-------------TATATTGAACAAAA---------------------------ATATT------------------------------------------TCTGTCTC-------AAAATACTGTTAAA-------------ATTAT---------------------TACT------------------------------------------------------------------------------TGAT--------------------A---------------------------------TTCATAGAGTATGT-----AAAAAAATATTTTTATGACTAC
droTak1	scf7180000415653:126845-126987 +	LASTZ	0	TTTTTATAAAAATGTTTTCAACTTAAGAGA--------------------G-CCTTTTTTATTTTTTATTTATCATTGAAACTGA-------------GAGGGGAACATATTTTTGA----------------------------------------------------GGTGAAATTCA-------GT-----------------------------AATTGA-----------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------TTTAGAGGC-CTAAATATAACTAAAATACCTCTAGAAAGGG
droEle1	scf7180000490094:78887-79034 -	LASTZ	0	TAAAATCGAACAAATTATAGC----------------------------TGCCA---------TAGTAACTAT-------------------------CGAATAA--------------------------------------------T--TAATCTTCAAATCATCATAGCT--TCAA-------TG--------TTTTTAAACATATACGCAAGTAAATCATAAT---------------------------------------ATTA------------------------------------------------------------------------------ATGT--------------------T--------------TTCAAGAA---TATTTAATT------------------TTTGCAATAG---CTGCAAGGG
droRho1	scf7180000767530:65055-65201 +	LASTZ	0	TAAGAAGCTGATTAAATTCTA------------------------------TTG---------AAGCACATAC-------------------------AGAGAAA-----------------------------------------------ATATTTCTTAAAATTCACTGTCCCTTAA-------TAATCAACAAAATTTAGATTGATATGGTTAGATTTGTATTT---------------------------------------ATAT------------------------------------------------------------------------------T-------------------------------------------------------------AAAATAACAT-----TCTTCAAGAGCACAATTAATGT
droFic1	scf7180000453829:52830-52979 -	LASTZ	0	TTAATATGAAAAA-TGAATGC-----------------------------------------------------------------------------------------------------------------------------------TGAATGGAACC------------------------------------------------------------------------------------------------------------------------------------TTAACAAAAAAAGCCCAATACCATAATAAAGTTAATAATAAAAATAAATTAAATACGT--------------------TATAAAATGTTTAATGCAAAGAA---CGCTTGTTCCTTGGATTTATTA-----A------TAAAACTATTAATGT
droKik1	scf7180000302469:216489-216636 -	LASTZ	0	TAAAATAATTAAAAAATTA--------------------------------TTA---------AAATAATTAA-------------------------AACATT------------------------------------------------ACTTATTATTTTATAAAATGTATTTAAA-------TT--------TTTTTTCATCTTCGTATA---------AATTGTATTATTTAAAT--------------------------AAAT------------------------------------------------------------------------------TTAA--------------------A---------------------------------TCTGATAAATGCCA-----ACCTAAATATATATTTAAATGA
droAna3	scaffold_13334:1096999-1097137 -	LASTZ	0	TAAATATTTTTAAGTAATTAA---------------------------TTG-GG---------CTACTGGCTT-------------------------TAAAAAA------------------TA---------------------------ATATTTTCAAATGTTATTGGTAATTTAA-------TT--------TTTTTATAATTTT-TAAAT---------------------------------------------------ACAT------------------------------------------------------------------------------TTTT--------------------T---------------TAAACTAAAATCCTTGTTTTCTG--------------------CTTCC--TTTTCAGCT
droBip1	scf7180000395356:37886-38031 -	LASTZ	0	AAAGGGTACATAGGATTAA--------------------------AAGCACTCG---------TTTAGACCAA-------------------------AGAATAA-------------ATGA------------------------------TAA---ATGGTGGTTTGTCTAAAA---------------------------CTTAATTAAGGAAAAGTATGAAAAA---------------------------------------TAAAATATACCT---------------------------------------------------------------------------------------------------------------TAGGTA---TACT-------TAGTATTCTCA-----CTTGTAACCTCTTTT----CGA
dp4	chrXR_group6:8932576-8932713 +	LASTZ	0	TTAAAATAAAAACATTTCATATTTAAATTA------------------CAA-GG---------TTTTATATTT-------------------------TAAATAA-----------------------------------------------ATATA------------TTT------------------------------CCC-------ACAAATTAAAGATAAT-------------ATATTTATTTTAAAGTAATTTATAATTAAA------------------------------------------------------------------------------TTGA--------------------A---------------------------------TATGGGCCC-----------------TACTACAAAGACTTT
droPer1	super_1:5889084-5889218 +	LASTZ	0	GATAGGTTTTTG----------------------------------------CA---------ACACAAAAAA-------------------------TAAACAA-----------------------------------------------AGATTAGTTTCCAGTTATTAAATATTAA-------TA--------TATATATTTGAAGCAGAAATATGTATATTTT---------------------------------------AGAA------------------------------------------------------------------------------TCGT--------------------T---------------------------------TCTGTGGGGTTTTC-----ATTGCAATACCT--TTTATGAA
droWil1	scaffold_180698:8557325-8557469 -	LASTZ	0	ACCAAAGAGAAATATCTCAAACTCAAACTCACAAACAAGACACATCAGCG----------------------------------------------------------------------------------------------------------CGCAAGAGCAACAACGCAAAGAA--------CA--------ATTAAACAATTCTATTAAATTGATCGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------ACAT--------------------T---------------------------------TCA-CAGCATAACA-----ACAACAA-----AAGAAAAGGA
droVir3	scaffold_12855:7203873-7204022 +	LASTZ	0	TGAAAATGAATAAATATAT--------------------------------ATG---------CTCCAATTAAAATTGAAACTACTATCCGATCGAAG-------------GTCTTT----------------------------------------------------GTTCAAATTCA-------TT----------TGAGGGGTTTTTCGCACTTTTTGGAAAAT---------------------------------------CCAT------------------------------------------------------------------------------CACT--------------------C---------------------------------CCCGATGGAAATGG-----GCTTCAATGACTTAGTGGGTGG
droMoj3	scaffold_6500:29247639-29247782 -	LASTZ	0	GGCCAATTAACAAACGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------AACAGCA-----------------------------------------------TCGTGTGCACACATACATTCAAACTTCTTCTGGAACA--------T-----TCTTTTAATCACATCAGCTGTTAGT------------T----------TGGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGCT-----G------CAGCACTGAATCTAT
droGri2	scaffold_14853:9426729-9426870 +	LASTZ	0	TCCACAAAGATAT---------------------------------------------------------------------------------------------------------------CAAAATCTCAGATACTGCTTGAAAGTTGACATT--TCC---CTCATAGAATA-TCC-------TT--------TATGTACAGTAATATGAGT--GTTTGTATTT-----------------------GAA-------------GTCT------------------------------------------------------------------------------TCTT--------------------T---------------------------------TTCATCGTCATTTA-----TCTCCATCCTCTCTTTGACTGC

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	TAAAAATAAAAAAATGCTCGATTGCTGCAACTAAGAAACAAATATTTTCAGTTGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATGCCTCTATGAAGGG
droSim1	TAAAAATAACAAAACGCTCATTTGCTGCAAATAAGAAACAAATATTTTCAGTTGTTCATTGCAAGTTAATTTATAAACATTGCTATGAAATCAATTGAAAATATAATTGTATCCCAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG
droSec1	TAAAAATAACAAAACGTTCATTTGCTGATAATAAGAAACAAATATCTTAAGATGTTCATTGCAAATTAATTTATGTACATTGCTATGAAATCAATTGAAAATATAATTGTATCCTAGGCTTATCAGCTGCAATCCCCCCAAGAAGGG

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

TAAAAATAACAAAACGCTCAT------------------------------TTG---------CTGCAAATAA-------------------------GAAACAA-----------------------------------------------ATATTTTCAGTTGTTCATTGCAAGTTAA-------TT--------TATAAACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCCAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TAAAAATAACAAAACGTTCAT------------------------------TTG---------CTGATAATAA-------------------------GAAACAA-----------------------------------------------ATATCTTAAGATGTTCATTGCAAATTAA-------TT--------TATGTACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCTAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................................................................................................................G--------TATGTAGATTGCTATGA..........................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TAAAAATAACAAAGCATAT--------------------------TAGCATATG---------CTGCAAACAA-------------------------TAAATAA-----------------------------------------------ATATTTTCAGCTGTGCATTGCAAATTAA-------TG--------TATTTACATAGCTATGAAAGCAATTGAAACG---------------------------------------ACAA------------------------------------------------------------------------------TTGCAGGTCATTTTTATTGCACACA---------------------------------TCCTAGGCTTATCA-----GTGGCAATGCCCCTACGAAGAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................................................................................................................................................AACG---------------------------------------ACAA------------------------------------------------------------------------------TTGxATGTCAT........................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................ATGAAAGCAATCGAATCG---------------------------------------A....................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TACAAGTAACAAAGTGCTAAT------------------------------TCG---------CTGCAAATAG-------------------------GAAATAA-----------------------------------------------ATATTTTCAT---------------TA---------T--------TA-TCACATTGCCA-GAAACCAATTGAAAAG---------------------------------------ATAA------------------------------------------------------------------------------TTGTAGGCCACTTTTGTTGCACGCA---------------------------------TCCTAGGCTTATCA-----GCTGATATGCCCCCACGAAGGG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................TAG-----------------------------------------------ATATCTTCAT---------------TA---------T--------TA-T.......................................................................................................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00
...............................................................................................................................................................CCT---------------TA---------T--------TA-TCACxTTGCCA-............................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................TGCAAATAG-------------------------GAAATCA-----------------------------------------------AC......................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......AACAAAGTACxAAT------------------------------TCG---------CTG..............................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

TAGCAAAATTAATATTTTAAA------------------------------ATT---------GTGTAAAAAA-------------------------GTAACGG-----------------------------------------------GTATCTTA---TAGTCGTGGCA--CTCG-------AC--------TATAGCGTTTCCTCTTGTTTTGATTAGAAAT---------------------------------------GTGC------CTTGTATACCAAGGGGGCTTATCCG----------------------------------------------------------------------------------------------------------------------------CCATAGCCGGATACCGCAACGG

Size

Hit Count

Total Norm

droBia1

TTACAATATTTAATTTAGT--------------------------------TTT---------TTATATTTAAAATTCAAACTGTTTGCCCACAGTAG-------------TATATTGAACAAAA---------------------------ATATT------------------------------------------TCTGTCTC-------AAAATACTGTTAAA-------------ATTAT---------------------TACT------------------------------------------------------------------------------TGAT--------------------A---------------------------------TTCATAGAGTATGT-----AAAAAAATATTTTTATGACTAC

Size

Hit Count

Total Norm

droTak1

TTTTTATAAAAATGTTTTCAACTTAAGAGA--------------------G-CCTTTTTTATTTTTTATTTATCATTGAAACTGA-------------GAGGGGAACATATTTTTGA----------------------------------------------------GGTGAAATTCA-------GT-----------------------------AATTGA-----------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------TTTAGAGGC-CTAAATATAACTAAAATACCTCTAGAAAGGG

Size

Hit Count

Total Norm

droEle1

TAAAATCGAACAAATTATAGC----------------------------TGCCA---------TAGTAACTAT-------------------------CGAATAA--------------------------------------------T--TAATCTTCAAATCATCATAGCT--TCAA-------TG--------TTTTTAAACATATACGCAAGTAAATCATAAT---------------------------------------ATTA------------------------------------------------------------------------------ATGT--------------------T--------------TTCAAGAA---TATTTAATT------------------TTTGCAATAG---CTGCAAGGG

Size

Hit Count

Total Norm

droRho1

TAAGAAGCTGATTAAATTCTA------------------------------TTG---------AAGCACATAC-------------------------AGAGAAA-----------------------------------------------ATATTTCTTAAAATTCACTGTCCCTTAA-------TAATCAACAAAATTTAGATTGATATGGTTAGATTTGTATTT---------------------------------------ATAT------------------------------------------------------------------------------T-------------------------------------------------------------AAAATAACAT-----TCTTCAAGAGCACAATTAATGT

Size

Hit Count

Total Norm

droFic1

TTAATATGAAAAA-TGAATGC-----------------------------------------------------------------------------------------------------------------------------------TGAATGGAACC------------------------------------------------------------------------------------------------------------------------------------TTAACAAAAAAAGCCCAATACCATAATAAAGTTAATAATAAAAATAAATTAAATACGT--------------------TATAAAATGTTTAATGCAAAGAA---CGCTTGTTCCTTGGATTTATTA-----A------TAAAACTATTAATGT

Size

Hit Count

Total Norm

droKik1

TAAAATAATTAAAAAATTA--------------------------------TTA---------AAATAATTAA-------------------------AACATT------------------------------------------------ACTTATTATTTTATAAAATGTATTTAAA-------TT--------TTTTTTCATCTTCGTATA---------AATTGTATTATTTAAAT--------------------------AAAT------------------------------------------------------------------------------TTAA--------------------A---------------------------------TCTGATAAATGCCA-----ACCTAAATATATATTTAAATGA

Size

Hit Count

Total Norm

droAna3

TAAATATTTTTAAGTAATTAA---------------------------TTG-GG---------CTACTGGCTT-------------------------TAAAAAA------------------TA---------------------------ATATTTTCAAATGTTATTGGTAATTTAA-------TT--------TTTTTATAATTTT-TAAAT---------------------------------------------------ACAT------------------------------------------------------------------------------TTTT--------------------T---------------TAAACTAAAATCCTTGTTTTCTG--------------------CTTCC--TTTTCAGCT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................AA------------------AA---------------------------ATGTTTTCAAATGT..........................................................................................................................................................................................................................................................................................	18	2	1.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................................................TATAATTTT-TAACT---------------------------------------------------ACAG------------------------------------------------------------------------------...................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................ATAATTTG-TAAAT---------------------------------------------------TCAT------------------------------------------------------------------------------TT.................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droBip1

AAAGGGTACATAGGATTAA--------------------------AAGCACTCG---------TTTAGACCAA-------------------------AGAATAA-------------ATGA------------------------------TAA---ATGGTGGTTTGTCTAAAA---------------------------CTTAATTAAGGAAAAGTATGAAAAA---------------------------------------TAAAATATACCT---------------------------------------------------------------------------------------------------------------TAGGTA---TACT-------TAGTATTCTCA-----CTTGTAACCTCTTTT----CGA

Size

Hit Count

Total Norm

dp4

TTAAAATAAAAACATTTCATATTTAAATTA------------------CAA-GG---------TTTTATATTT-------------------------TAAATAA-----------------------------------------------ATATA------------TTT------------------------------CCC-------ACAAATTAAAGATAAT-------------ATATTTATTTTAAAGTAATTTATAATTAAA------------------------------------------------------------------------------TTGA--------------------A---------------------------------TATGGGCCC-----------------TACTACAAAGACTTT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GATAGGTTTTTG----------------------------------------CA---------ACACAAAAAA-------------------------TAAACAA-----------------------------------------------AGATTAGTTTCCAGTTATTAAATATTAA-------TA--------TATATATTTGAAGCAGAAATATGTATATTTT---------------------------------------AGAA------------------------------------------------------------------------------TCGT--------------------T---------------------------------TCTGTGGGGTTTTC-----ATTGCAATACCT--TTTATGAA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ACCAAAGAGAAATATCTCAAACTCAAACTCACAAACAAGACACATCAGCG----------------------------------------------------------------------------------------------------------CGCAAGAGCAACAACGCAAAGAA--------CA--------ATTAAACAATTCTATTAAATTGATCGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------ACAT--------------------T---------------------------------TCA-CAGCATAACA-----ACAACAA-----AAGAAAAGGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................................................................................................................................................................................................................................................................................................................................................G-----ACAAGAA-----AAGAAAAGGA	18	3	0.67	0.00	0.67	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................................................................AAAA-----AAGAAAAGGA	20	20	0.05	0.00	0.05	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................................................................................................ACAAAAA-----AAGAAAAAGA	19	41	0.02	0.00	0.02	0.00	0.00
.....................................................................................................................................................................AACxACTCAAAGAA--------CA--------ATT........................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................A-----ACAAAAA-----AAGAAAAGCA	18	11	0.09	0.00	0.09	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----GCAAAAA-----AAGAAAA...	18	10	0.10	0.00	0.10	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................A-----ACAACAA-----AAGAAAAGAG	19	5	0.20	0.00	0.20	0.00	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................TAA-AAGCATAACA-----ACAACAA-----AAGAAA....	26	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................................A------------------------------------------------------------------------------ACAT--------------------T---------------------------------TAA-AAGCATAAC............................	18	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----ACAACAA-----AAGAAAAGGA	21	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----AAAACAA-----AAGAACA...	18	26	0.04	0.00	0.04	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................................................................AAAA-----AAGAAAAGGA	18	39	0.03	0.00	0.03	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................................................................................ATAA-----AACAAAAGGA	19	7	0.14	0.00	0.14	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----ACAACAG-----AAGAAGA...	18	6	0.17	0.00	0.17	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................................................................................AAA-----AAGAAAAGGA	18	39	0.03	0.00	0.03	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................................................................................................AACAA-----AAGAAGAGAA	19	6	0.17	0.00	0.17	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----AAAACAA-----AAGAAAG...	18	34	0.03	0.00	0.03	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................AACA-----ACAAxAG-----AAGAAAAGGA	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

TGAAAATGAATAAATATAT--------------------------------ATG---------CTCCAATTAAAATTGAAACTACTATCCGATCGAAG-------------GTCTTT----------------------------------------------------GTTCAAATTCA-------TT----------TGAGGGGTTTTTCGCACTTTTTGGAAAAT---------------------------------------CCAT------------------------------------------------------------------------------CACT--------------------C---------------------------------CCCGATGGAAATGG-----GCTTCAATGACTTAGTGGGTGG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................TTT----------------------------------------------------GTTCAAATTTA-------TT----------TGAGGGGTGT...............................................................................................................................................................................................................................................	26	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................................................................ATTCA-------TT----------TGAGGTGTGTTTCGC..........................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................GTTCAAATTCA-------TT----------TGAGGGGT.................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................TTT----------------------------------------------------GTTCAAATTCA-------TG----------TGAGGGGT.................................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................TTT----------------------------------------------------GTTCAAATTCA-------TT----------TGATGTGTTT...............................................................................................................................................................................................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................TGG-----GCTTCAATGAGTTTGTG.....	20	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................................TGAGGGGTGTTTCGCACTT......................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................AATTCA-------TT----------TGAGGGGTGTTTCG...........................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
...................................................................................................................TT----------------------------------------------------GTTCAAATTCA-------TT----------TGAGGGGTGT...............................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

GGCCAATTAACAAACGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------AACAGCA-----------------------------------------------TCGTGTGCACACATACATTCAAACTTCTTCTGGAACA--------T-----TCTTTTAATCACATCAGCTGTTAGT------------T----------TGGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGCT-----G------CAGCACTGAATCTAT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......TAACAAACGCAC--------------------------------GTG---------TAGCAGCTAC-------------------------A.............................................................................................................................................................................................................................................................................................................................................................	26	7	1.71	1.57	0.00	0.00	0.14
...........................................................................................................................................................................................................................................................TGGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGC............................	24	8	0.75	0.00	0.00	0.00	0.75
...........................................................................................................................................................................................................TCTTTGAATCACATCAGCTGTTAGG------------................................................................................................................................................................................................................	25	7	0.71	0.29	0.00	0.00	0.43
...........................................................................................................................................................................................................................................................TCGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGC..............................	22	8	0.50	0.00	0.00	0.00	0.50
.......TAACAAACGCAC--------------------------------GTG---------CAGCAGCT.........................................................................................................................................................................................................................................................................................................................................................................................	23	8	0.50	0.38	0.13	0.00	0.00
..............CGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------AACAGCA-----------------------------------------------........................................................................................................................................................................................................................................................................................................	25	5	0.60	0.20	0.00	0.00	0.40
...................................................................................................................................................................................................................TCACATCAGCTGTTAGT------------T----------TCGTTTAG.............................................................................................................................................................................................	26	8	0.38	0.25	0.00	0.00	0.13
.......TAACAAACGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------AA............................................................................................................................................................................................................................................................................................................................................................	27	7	0.43	0.29	0.00	0.00	0.14
..............................................................................................................................................................................................................................................................TTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGCT-----G------...............	23	8	0.38	0.25	0.00	0.00	0.13
.......TAACAAACGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------A.............................................................................................................................................................................................................................................................................................................................................................	26	7	0.43	0.43	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................TCGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGC............................	24	7	0.43	0.00	0.14	0.00	0.29
................................................................................................................................................................................................................................TAGT------------T----------TCGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGG...............................	26	8	0.38	0.38	0.00	0.00	0.00

droGri2

TCCACAAAGATAT---------------------------------------------------------------------------------------------------------------CAAAATCTCAGATACTGCTTGAAAGTTGACATT--TCC---CTCATAGAATA-TCC-------TT--------TATGTACAGTAATATGAGT--GTTTGTATTT-----------------------GAA-------------GTCT------------------------------------------------------------------------------TCTT--------------------T---------------------------------TTCATCGTCATTTA-----TCTCCATCCTCTCTTTGACTGC

Size

Hit Count

Total Norm

V109
Male body

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

dme-mir-4946

chr2L:18867045-18867161 -

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup