dme-mir-2498- Best orthologs

dme-mir-2498	chr2R:16472214-16472325 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 16472241-16472261
   star strand at position 16472276-16472297
   mutations
   read mismatches

Notes: droSim1 - droEre2 have several paralogs of 2498. This miRNA is near the 310-313 cluster.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:16472199-16472340 -		1	ATGTGAT-ATTTTTTTCACATT---------------------------------------------------------------------------------------TGCCATAATCTCCTTAAAA---------------------------------------------------------TAGTAA--AGGCTG----TTATGCTTAT------------------------------------TTTTGTGTTTTTTACAAAACTGGCA-TTCC-CGTCT--TACT-TA---TTTTCAGAAAA---------------------------CTTACACCAA-AGTGCACAGA-------------------------------------------------TTGAAAAAA
droSim1	chr2R:15133840-15133990 -	LASTZ	1	AAAAAGA-CAATAA-TGTGAATT-TC----------------------------------------------------------------------------ATCAAATTGCCATAATCTC---AAAA---------------------------------------------------------TAGTAAAAAGTCTG----TTATGCCTTT------------------------------------TTTTGTGTGTTTTACAAAAC-CGTA-TAAC-CGACTTTTACT-TA---TTTTTAGAAAA---------------------------CTAACACCGA-CGTGTACAGA-------------------------------------------------ACGAAAAAA
droSec1	super_1:14027148-14027283 -	LASTZ	1	AATTGTG-AATTTC----------------------------------------------------------------------------------------ATCAAATTGGCATAATCTC---AAAA---------------------------------------------------------T----A--AGCCTG----TTATGCTTTT------------------------------------TTTTGTGTGTTTTACAAAATTTGCA-TATT-CGACTTTTACT-TA---TTTTCAGAAAA---------------------------CTGACCACGA-TGTGCACAGA-------------------------------------------------TTGAAGAAA
droYak2	chr2R:12723862-12724011 +	LASTZ	1	TTTGATT-CTGCAT-TAGAAATCGCC----------------------------------------------------------------------------ACCCAACTTTGATTT--TTCTAGAAA---------------------------------------------------------TATTTA--AGTCTG----TTCTGCTTAG------------------------------------ATTTGTGAATTTGACAAAATCTGCA-CAGC-CGGCT--TAATGTA---TTTTTAGAAAC---------------------------TTAGCACCTTTTGTGTAAAGA----------------------------------------------------AAAAAC
droEre2	scaffold_4845:10617439-10617588 -	LASTZ	1	TTTGATT-CTGCTT-CTTAAATCGCC----------------------------------------------------------------------------ACCCAACTTATAGTA--TTCCAAAAA---------------------------------------------------------TATTTA--AGTCTG----TTATGCATAC------------------------------------TTTTGTGAGTTTGACAAAATGTGCA-CAAC-CGGCT--TACTGTA---TTTTTAGAAAA---------------------------CAAACACCTTAGTTGTAAAGA-------------------------------------------------A---TAAAC
droEug1	scf7180000409474:1489373-1489512 +	LASTZ	0	CTTGAGTAAAGCGT-TA------------AAAAA------------------------------------------------------------------------GTCGGTCCTAACCTA---AATA---------------------------------------------------------A----A--AATTCG----TTGAAT-----------T-AATTTCTTTAAA-------------------------------------GCT-TTTTGGCAATT-------A---CA--TATAAAGGTAAAATAAAGTGCCTTTCTTAAAAATCAAGTGCTTA--------ATA-------------------------------------------------TTGAAAGTA
droBia1	scf7180000302291:2815544-2815703 +	LASTZ	0	ACTAGTA-CAGTTA---------------AAAAG------------------------------------------------------------------------AATAAGCCCAACCTC---AAAGAGTTGTAACCTAA---------------------------------------------AGTTA--CATATATATTCCGCTTATTAATAACT-TAATTGCATTTAAAAACTTCGATTTATCTTTCTAGATTACTTA----AA--GTA-CTTTCACAG---------------------------------------------------CTTAGACTGA--------GTT-------------------------------------------------TTCTAGAAT
droTak1	scf7180000415401:100661-100805 -	LASTZ	0	ATGGTTA-AAGCTA---------------AAAAAGTGCGTGTTTAAGTTCCTATCG---------------------------------------------------------------------------------------------------------------------------------G-----------------------------------------AATCA-GTACTTTTATTTGCTTTTCTGGATTATTTAACAAAG--GTA-TTTTGGAAGCCTAAGT-TAAGTTTTCCAGAAAA---------------------------GTAATAT-AA-AGTTAATTCA-------------------------------------------------TCAAAAATA
droEle1	scf7180000491201:736729-736843 -	LASTZ	0	ATTTAAT-TTTTTTATAACTTG--TGCTATAAAGAAACACGTAGATAACAATTAA--------------------------------------------------------------------------------------------------------------------------------A-G-----------------------------------------AAAAA-ATGTTTTTATATTCAAATCCGGACTTTTTAATGGTGTAGTA-ATCC-C---------------------------------------------------------GCATCCT----------------------------------------------------------------T--AT
droRho1	scf7180000780104:82947-83087 -	LASTZ	0	GTACAAG-CT---T----------------------------------------------------------------------------------------GTGAAAGGGACATAACCTC---AAAA--T-------TGA------------------------------------------AGTAATAA--GATATA----TTATTTATTTGTTAGTAT-ATTTTATTTACAGCGTCCC-------------------------------------------T-------TT---TATCCAGATAA---------------------------AAAATAATT------------TGGTTTGTCAAAGGGT----------------------------AATAAACTTCAAGA
droFic1	scf7180000454039:1776722-1776852 -	LASTZ	0	AACTACA-ATTCGT-TCTA----------AAAAAGAGTTCGC------------------------------------------------------------------------------------------------------------------------------------------------------------------TATAATCTT------------------------------------ACATGAAAGTTTTAGG------TCTACT--------------------TTCCAAGAAAA---------------------------ATG------------------GAAA--TCAATAACAAACTGTTATTGTACTGTAAGGTAAAATGTCCAAATTCCTATTA
droKik1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13266:4132040-4132139 +	LASTZ	0	AATAAAT-AAACAA---------------------AATTCTC----------------------------AAATATTTAACGTA------------------------------------------AA---------------------------------------------------------AACTTA--ATTTTG----T--------------------------------------------------CGCGATATACAAATT---------------------------------------------------------------------------------------TGGC--GCCAAAACGTATTTTCATAAAAT--------------------TTTAAGCTA
droBip1	scf7180000396427:2574583-2574750 +	LASTZ	0	ATTGTGG-ATTTTT-TTTAGGTTCTT--------------------------TGCGGACTCATGTTTTTAAGATCTTAGCTCTTGATATTCATTTTTATCGAATTAAAGGGCTATGGTCTT---AAAA--A-------TGTTATTCCGTCAATACATCATAGTAACTTGTGAATTTCATGTTCA------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAA-AATGTGAAAA-------------------------------------------------GTGAAATAA
dp4	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend

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

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	AT------------GTGATATTTTTTTCACATTTGCCA-----------TAATCTCCTTAAAATAGTA--AAGGCTGTTATGCTTATTTTTGTGTTTTTTACAAAACTGGCATTCCCGTCT--TACT-TATTTTCAGAAAACTTACACCAA-AGTGCACAGATTGAAAAAA
droSim1	AAAAAGACAATAATGTGA--ATTTCATCAAA-TTGCCA-----------TAATCTC---AAAATAGTAAAAAGTCTGTTATGCCTTTTTTTGTGTGTTTTACAAAAC-CGTATAACCGACTTTTACT-TATTTTTAGAAAACTAACACCGA-CGTGTACAGAACGAAAAAA
droSec1	AAT----------TGTGA--ATTTCATCAAA-TTGGCA-----------TAATCTC---AAAAT------AAGCCTGTTATGCTTTTTTTTGTGTGTTTTACAAAATTTGCATATTCGACTTTTACT-TATTTTCAGAAAACTGACCACGA-TGTGCACAGATTGAAGAAA
droYak2	TTTG-------------ATTCTGCATTAGAAATCGCCACCCAACTTTGATT--TTTCTAGAAATATTT--AAGTCTGTTCTGCTTAGATTTGTGAATTTGACAAAATCTGCACAGCCGGCT--TAATGTATTTTTAGAAACTTAGCACCTTTTGTGTAAAGA---AAAAAC
droEre2	TTTG-------------ATTCTGCTTCTTAAATCGCCACCCAACTTATAGT--ATTCCAAAAATATTT--AAGTCTGTTATGCATACTTTTGTGAGTTTGACAAAATGTGCACAACCGGCT--TACTGTATTTTTAGAAAACAAACACCTTAGTTGTAAAGAA---TAAAC

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AAAAAGA-CAATAA-TGTGAATT-TC----------------------------------------------------------------------------ATCAAATTGCCATAATCTC---AAAA---------------------------------------------------------TAGTAAAAAGTCTG----TTATGCCTTT------------------------------------TTTTGTGTGTTTTACAAAAC-CGTA-TAAC-CGACTTTTACT-TA---TTTTTAGAAAA---------------------------CTAACACCGA-CGTGTACAGA-------------------------------------------------ACGAAAAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAC-CGACTTTTACT-..........................................................................................................................	22	1	86.00	1.00	2.00	66.00	17.00
.........................................................................................................................................................................................................................................................................AAAC-CGTA-TAAC-CGACTTTTACT-..........................................................................................................................	23	1	7.00	0.00	0.00	4.00	3.00
............................................................................................................................................................................................TAAAAAGTCTG----TTATGCCTTT------------------------------------T....................................................................................................................................................................	22	1	5.00	0.00	0.00	2.00	3.00
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAC-CGACTTTTACC-..........................................................................................................................	22	1	4.00	0.00	0.00	3.00	1.00
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAC-CGACTTTTACT-T.........................................................................................................................	23	1	3.00	0.00	0.00	2.00	1.00
...........................................................................................................................................................................................................................................................................AC-CGTA-TAAC-CGACTTTTACT-T.........................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAC-CGACTTTTAC............................................................................................................................	21	1	2.00	0.00	0.00	2.00	0.00
...........................................................................................................................................................................................................................................................................AC-CGTA-TAAC-CGACTTTTACT-..........................................................................................................................	21	1	2.00	0.00	0.00	2.00	0.00
.............................................................................................................................................................................................AAAAAGTCTG----TTATGCCTTT------------------------------------T....................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................TAAAAAGTCTG----TTATGCCT...........................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAC-CGACTTTTACT-G.........................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................AAC-CGTA-TAAA-CGACTTTTACT-..........................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................................................................................................................................................AC-CGTA-TAAC-CGACTTTTACT-C.........................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................GAC-CGTA-TAAC-CGACTTTTACT-..........................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................TAAAAAGTCTG----TTATGCCTT..........................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00

droSec1

AATTGTG-AATTTC----------------------------------------------------------------------------------------ATCAAATTGGCATAATCTC---AAAA---------------------------------------------------------T----A--AGCCTG----TTATGCTTTT------------------------------------TTTTGTGTGTTTTACAAAATTTGCA-TATT-CGACTTTTACT-TA---TTTTCAGAAAA---------------------------CTGACCACGA-TGTGCACAGA-------------------------------------------------TTGAAGAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................................................................................................................................................................................................................................................................................TCTGCACAGA-------------------------------------------------TTGAAGATA	19	2	0.50	0.00	0.50	0.00
...................................................................................................................................................................................................................................................................................................................................................CGACGA-TGTGCAxAGA-------------------------------------------------TTG......	18	2	0.50	0.00	0.50	0.00
...........................................................................................................................................................................................................TTTTGTTTTT------------------------------------TTTTGTGTGT...........................................................................................................................................................	20	3	0.33	0.33	0.00	0.00
.............................................................................................................................................................................................................................................................................................TTTACT-Tx---TTTTTAGAAAA---------------------------...............................................................................	18	4	0.25	0.00	0.25	0.00
.................................................................................................................................................................................................................................................................................................................AAA---------------------------CTGACCACCA-TGGGCACA............................................................	21	2	0.50	0.00	0.50	0.00

droYak2

TTTGATT-CTGCAT-TAGAAATCGCC----------------------------------------------------------------------------ACCCAACTTTGATTT--TTCTAGAAA---------------------------------------------------------TATTTA--AGTCTG----TTCTGCTTAG------------------------------------ATTTGTGAATTTGACAAAATCTGCA-CAGC-CGGCT--TAATGTA---TTTTTAGAAAC---------------------------TTAGCACCTTTTGTGTAAAGA----------------------------------------------------AAAAAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------ATT..................................................................................................................................................................	22	1	56.00	0.00	0.00	3.00	0.00	53.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TAAT...........................................................................................................................	21	1	18.00	1.00	0.00	16.00	1.00	0.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TAATG..........................................................................................................................	22	1	14.00	0.00	0.00	8.00	0.00	6.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------A....................................................................................................................................................................	20	1	11.00	0.00	0.00	3.00	0.00	8.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TAATGT.........................................................................................................................	23	1	9.00	1.00	0.00	7.00	1.00	0.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAATGT.........................................................................................................................	22	1	9.00	0.00	0.00	9.00	0.00	0.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------AT...................................................................................................................................................................	21	1	5.00	0.00	0.00	2.00	0.00	3.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAATG..........................................................................................................................	21	1	4.00	1.00	0.00	1.00	0.00	2.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------ATA..................................................................................................................................................................	22	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAAT...........................................................................................................................	20	1	2.00	0.00	0.00	1.00	0.00	1.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------ATC..................................................................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------ATTT.................................................................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................................................................................................................................................................................................................................ACAATCTGCA-CCGC-CGGC..................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................TTA--AGCCTG----TTCTGCTTAG------------------------------------A....................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................................................................................................................................................................................................CAG	21	10	0.10	0.00	0.00	0.10	0.00	0.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAATT..........................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................................AAA---------------------------------------------------------TxTTTA--AGTCTG----TTCA...............................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................AATCTTCA-CAGC-CGGCT--TAATG..........................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................TCTGCA-CAGC-CGGCT--TAATG..........................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------AA...................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................TTA--AGTCTG----TTCTGCTTAG------------------------------------G....................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TAATGTT---.....................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TA.............................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAAA...........................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................................................AATCTGCA-CAGC-CGGCT--TAAA...........................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................TGAGATTGACAAAATCTG..............................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................................................ATCTGCA-CAGC-CGGCT--TAT............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TTTGATT-CTGCTT-CTTAAATCGCC----------------------------------------------------------------------------ACCCAACTTATAGTA--TTCCAAAAA---------------------------------------------------------TATTTA--AGTCTG----TTATGCATAC------------------------------------TTTTGTGAGTTTGACAAAATGTGCA-CAAC-CGGCT--TACTGTA---TTTTTAGAAAA---------------------------CAAACACCTTAGTTGTAAAGA-------------------------------------------------A---TAAAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCT--TACT...........................................................................................................................	21	1	10.00	4.00	0.00	0.00	6.00
.............................................................................................................................AAA---------------------------------------------------------TxTTTA--AGTCTG----TTAA...............................................................................................................................................................................................................	18	2	4.50	0.00	0.00	0.00	4.50
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCT--TACTGT.........................................................................................................................	23	1	9.00	1.00	0.00	0.00	8.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAG------------------------------------TT...................................................................................................................................................................	21	2	3.50	0.00	1.00	0.00	2.50
.............................................................................................................................................................................................................................................................GGGTGxTTGACAAAATGTG..............................................................................................................................................	18	1	6.00	0.00	0.00	0.00	6.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAG------------------------------------TTT..................................................................................................................................................................	22	2	2.50	0.00	0.00	0.00	2.50
..........................................................................................................................................................................................................................................................................AATCTGCA-CAAC-CGGCT--TA.............................................................................................................................	19	2	2.50	0.00	0.00	0.00	2.50
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCT--TACTG..........................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAG------------------------------------TTTT.................................................................................................................................................................	23	2	2.00	0.00	1.00	0.00	1.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAG------------------------------------TTTTG................................................................................................................................................................	24	2	1.50	0.00	0.00	0.00	1.50
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAC------------------------------------T....................................................................................................................................................................	20	2	1.50	0.00	0.00	0.00	1.50
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCT--TACTGTT---.....................................................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CTGCT--TACT...........................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATA..........................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................................................AATCTGCA-CAAC-CGGCT--TAT............................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................................................AATGTGAA-CAAC-CGGCT--TACTC..........................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAG------------------------------------T....................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................................................................................................................................................................AAATGTGCA-CAAC-CCGAT--TACT...........................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCC--TACTGT.........................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....ACT-CxGCTT-CTTAAATCGCC----------------------------------------------------------------------------A.......................................................................................................................................................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
............................................................................................................................................................................................TTA--AGTCTG----TTATGCATAC------------------------------------TTT..................................................................................................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
.............................................................................................................................................................................................TA--AGTCTG----TTATGCATAG------------------------------------TTTTGTGA.............................................................................................................................................................	26	2	0.50	0.00	0.00	0.00	0.50
............................................................................................................................................................................................TTA--AGTCTG----TTATGGATAG------------------------------------T....................................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CGGCT--TA.............................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.............................................................................................................................................................................................TA--AGTCTG----TTATGCATAG------------------------------------TTTTGA...............................................................................................................................................................	24	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................................................AATGTGCA-CAAC-CTGCT--TACTGTT---.....................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................CAAA---------------------------------------------------------TxTTTA--AGTCTG----TTA................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50

droEug1

CTTGAGTAAAGCGT-TA------------AAAAA------------------------------------------------------------------------GTCGGTCCTAACCTA---AATA---------------------------------------------------------A----A--AATTCG----TTGAAT-----------T-AATTTCTTTAAA-------------------------------------GCT-TTTTGGCAATT-------A---CA--TATAAAGGTAAAATAAAGTGCCTTTCTTAAAAATCAAGTGCTTA--------ATA-------------------------------------------------TTGAAAGTA

Size

Hit Count

Total Norm

droBia1

ACTAGTA-CAGTTA---------------AAAAG------------------------------------------------------------------------AATAAGCCCAACCTC---AAAGAGTTGTAACCTAA---------------------------------------------AGTTA--CATATATATTCCGCTTATTAATAACT-TAATTGCATTTAAAAACTTCGATTTATCTTTCTAGATTACTTA----AA--GTA-CTTTCACAG---------------------------------------------------CTTAGACTGA--------GTT-------------------------------------------------TTCTAGAAT

Size

Hit Count

Total Norm

droTak1

ATGGTTA-AAGCTA---------------AAAAAGTGCGTGTTTAAGTTCCTATCG---------------------------------------------------------------------------------------------------------------------------------G-----------------------------------------AATCA-GTACTTTTATTTGCTTTTCTGGATTATTTAACAAAG--GTA-TTTTGGAAGCCTAAGT-TAAGTTTTCCAGAAAA---------------------------GTAATAT-AA-AGTTAATTCA-------------------------------------------------TCAAAAATA

Size

Hit Count

Total Norm

droEle1

ATTTAAT-TTTTTTATAACTTG--TGCTATAAAGAAACACGTAGATAACAATTAA--------------------------------------------------------------------------------------------------------------------------------A-G-----------------------------------------AAAAA-ATGTTTTTATATTCAAATCCGGACTTTTTAATGGTGTAGTA-ATCC-C---------------------------------------------------------GCATCCT----------------------------------------------------------------T--AT

Size

Hit Count

Total Norm

droRho1

GTACAAG-CT---T----------------------------------------------------------------------------------------GTGAAAGGGACATAACCTC---AAAA--T-------TGA------------------------------------------AGTAATAA--GATATA----TTATTTATTTGTTAGTAT-ATTTTATTTACAGCGTCCC-------------------------------------------T-------TT---TATCCAGATAA---------------------------AAAATAATT------------TGGTTTGTCAAAGGGT----------------------------AATAAACTTCAAGA

Size

Hit Count

Total Norm

droFic1

AACTACA-ATTCGT-TCTA----------AAAAAGAGTTCGC------------------------------------------------------------------------------------------------------------------------------------------------------------------TATAATCTT------------------------------------ACATGAAAGTTTTAGG------TCTACT--------------------TTCCAAGAAAA---------------------------ATG------------------GAAA--TCAATAACAAACTGTTATTGTACTGTAAGGTAAAATGTCCAAATTCCTATTA

Size

Hit Count

Total Norm

droKik1

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

Size

Hit Count

Total Norm

droAna3

AATAAAT-AAACAA---------------------AATTCTC----------------------------AAATATTTAACGTA------------------------------------------AA---------------------------------------------------------AACTTA--ATTTTG----T--------------------------------------------------CGCGATATACAAATT---------------------------------------------------------------------------------------TGGC--GCCAAAACGTATTTTCATAAAAT--------------------TTTAAGCTA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

ATTGTGG-ATTTTT-TTTAGGTTCTT--------------------------TGCGGACTCATGTTTTTAAGATCTTAGCTCTTGATATTCATTTTTATCGAATTAAAGGGCTATGGTCTT---AAAA--A-------TGTTATTCCGTCAATACATCATAGTAACTTGTGAATTTCATGTTCA------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAA-AATGTGAAAA-------------------------------------------------GTGAAATAA

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:27:31 EDT

dme-mir-2498

chr2R:16472214-16472325 -

Known_mirbase

intergenic

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup