sblock177975- Best orthologs

sblock177975	chrX:5963712-5963792 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 5963727-5963746
   star strand at position 5963761-5963786
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:5963697-5963807 -		1	CGGAGACAAG--TCG-------A--------------AAC----AAAA----TTGAACTGGCAGCAAAAT-----G-----ACAAA------TTCGCACTGGGCA------------------------CAGTGTGA---ACATGTCATATTGCTGCCGGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droSim1	chrX:4687883-4687994 -	LASTZ	4	CGAAGACAAGAGTC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----ACAGA------TTCGCACTGGGCG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--TAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droSec1	super_4:802740-802849 +	LASTZ	1	CGAAGACAAG--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----GCAGA------TTCGCACTGGACG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droYak2	chrX:1971149-1971223 -	LASTZ	5	CGAAGACATA--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAG----------------------------------------------------------------------------------TTGCTACCGGTGTTAAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----TAT----------ATGTAGTTAGC-----
droEre2	scaffold_4690:14942392-14942483 -	LASTZ	3	CGAAGACATA--TC----------------------GAAC----AAAA----TTAAACTGGCAGCCAGAT-----G-----AC----------------------------------------------CAGTGTGA---ACGTGGCATAAGGCTGCCGGT----AACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----
droEug1	scf7180000409033:286585-286701 -	LASTZ	5	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG--GCGTTAAGAC-----C-----A---A---------TCACTATATG------------------------GAGTGTGAAAAGAATGGGTTAATGCTCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAA----------A----TATTTGCAAAGTTATTTAGTTAGC-----
droBia1	scf7180000302421:723293-723411 -	LASTZ	4	CGAAGACATA--TC----------------------GAAC----AAAA----TTCAGGGG--ACTGGGAT-----G-----ACACG------TTCGCACTGAAGG------------------------CAGTGTGG---ACAGGGCTC-ATGTCCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------G----TATTTACAAAGACGTTTAGTTAGC-----
droTak1	scf7180000415769:469591-469710 +	LASTZ	4	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAGAGGG--CTAAGAT-----G-----GTGTG------TTCGCACTGAAGG------------------------CAGTGCGA---ACAGGGCATTAAGCTCCAAGTG--ACCAA--------------------------------------------------------------------------------------------------------ATCAC----------A----CATTTACCAAGATGATTAGTTAGC-----
droEle1	scf7180000490141:671400-671527 -	LASTZ	4	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAGGAT-----G-----ACGTG------TCCACATCAACGG------------------------CAGTGTGA---ACAGGGCATAATGTTCCCAGTG--TT-----------------------------------------------------------------------------------------CCCA------------CAATCAC----------ATACATATATACAGAGATGTTTAGTTAGC-----
droRho1	scf7180000778072:152382-152502 -	LASTZ	4	CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAAAAT-----G-----TCGTG------TTTACATTAAAGA------------------------CAGTGTGA---ACAGGGCATAATGTACCCAATG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----GATATACAGAGATGTTTAGTTAGC-----
droFic1	scf7180000454072:1399768-1399881 +	LASTZ	4	CGAAAACATA--TC----------------------GAAC----AAAT----CTAAAG-GG---CTAGAC-----G-----ATGTG------TTCGCACTGTGGG------------------------CAGTGTGA---ACGGGACATACGGCTCCCAGTA--AAACA--------------------------------------------------------------------------------------------------------AACGC----------A----C----ACAGAGATGTTAAGTTAAC-----
droKik1	scf7180000302610:1501511-1501678 +	LASTZ	4	CAAAAACATA--AC----------------------GAAA----AAGAAAAATTCAAT--G---CGAACA-----G-----GTCAA------CTTACACTGAAAGACAGTGAGAAGAGGACATTATGCTCAGTGTAA---ACGCCGCATAATGCTTTCCGTT--AA---------------------------------T-----GTTA---TTCAGTGTGCAGAGGGCATTTTT-------------------------------------GTTCTCAAA-AAATATG----------------TATTTAGTTAGC-----
droAna3	scaffold_13417:548659-548772 -	LASTZ	5	CGAAAAAAAA--GA---AAACAAAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAATGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----
droBip1	scf7180000396362:585451-585558 +	LASTZ	5	CGAAAAAAAA--A---------AAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAGTGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----
dp4	chrXL_group1e:5411646-5411745 +	LASTZ	5	GGAGAAAAGC--GT----------------------ATTC----GAAG----TTCATTAG--------------------------------G----------TT------------------------TCATTAGAAGGACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----
droPer1	super_21:323762-323858 +	LASTZ	5	AGAAAACCGT--------------------------ATTCGAAGTTCA----TTAGG----------------------------------------------TT------------------------TCGTCAGAAGTACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----
droWil1	scaffold_181150:1838778-1838880 +	LASTZ	5	AGGAGAAAAA--AGA-------AAAAAAAACATATCTAAA---AAACA----TATA-------------C-----GAAAACTTAGGTCAGCTTCAAAACCGAACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------CTATTAGTTAGT-----
droVir3	scaffold_12928:603918-604086 +	LASTZ	0	AAATGCTAAG--GC----------------------GAAA----AAAT----ATCTGA-AG---CGAGGC-----GAAAAAGCAAG----------------------------------------------------------------CTGAGCCCAAAG--CTGAGTTCACACAAGTTTAGTATTTTTTCTGTTGCTTGTCTCTTTTCCAGCAGTATTTAGT-GGTATTTTTTTTGTGAAGTCAGCTTTGCGAG------------CCT-CTAAT---------------------------CTATTAGTTAGC-----
droMoj3	scaffold_6328:1569195-1569320 +	LASTZ	0	TGATGCATCA--TCCAAA-------------------AGC----CCAG----CTGAGCTCGCCGTTCGTC-----T-----A---A------TTAG----------------------------------------------------------------------------------------------------TATTTCTCTCTT------------------------------ATTCAGTATTCACTGTAAGCGACGGTGCGTGCTT-CAGCT-CTATTCACTG----T------------ATCCAACTAGCTTTCT
droGri2	scaffold_14853:7866730-7866831 -	LASTZ	0	CAAATAATAC--TC----------------------GTAA----CATA----TCTGAAAG----AAAGAA-----GGAAAAACAAG------AAAACA-----TT------------------------TATCAAGAAGCCCAA-----AAAGCTG-----------AATTCACAA-------------------------------------------------------------------------------------------------CGCCT----------G----------------TTTTTAGTATTT-----

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	CGGAGACAAG-----TCGA--------------AACAA----AATTGAACTGGCAGCAAAA--------TGACAA--------------------ATTCGCACTG------------------------GGCACAGTGTGA---ACATGTCATATTGCTGCCGGTG---AA--------------------------ACAATCA---------CAT------------ATTTAGTTAGC
droSim1	CGAAGACAAG---AGTCG---------------AACAA----AATTGAACTGGCAGCAAGA--------TGACAG--------------------ATTCGCACTG------------------------GGCGCAGTGTGA---ACATGGCATAATGCTGCCGGTG---TA--------------------------ACAATCA---------CAT------------ATTTAGTTAGC
droSec1	CGAAGACAAG-----TCG---------------AACAA----AATTGAACTGGCAGCAAGA--------TGGCAG--------------------ATTCGCACTG------------------------GACGCAGTGTGA---ACATGGCATAATGCTGCCGGTG---AA--------------------------ACAATCA---------CAT------------ATTTAGTTAGC
droYak2	CGAAGACATA-----TCG---------------AACAA----AATTGAACTGGCAGCAAG----------------------------------------------------------------------------------------------TTGCTACCGGTGTT-AA--------------------------ACAATCA---------CATAT----------ATGTAGTTAGC
droEre2	CGAAGACATA-----TCG---------------AACAA----AATTAAACTGGCAGCCAGA--------TGAC------------------------------------------------------------CAGTGTGA---ACGTGGCATAAGGCTGCCGGT-----A--------------------------ACAATCA---------CAT------------ATTTAGTTAGC
droEug1	CGAAGACATA-----TCG---------------AACAA----AATTTAAG--GCGTTAAGA--------CCA-----------------------A---TCACTA------------------------TATGGAGTGTGAAAAGAATGGGTTAATGCTCCCAGTG---AA--------------------------ACAATCA---------AATATTTGCAAAGTTATTTAGTTAGC
droBia1	CGAAGACATA-----TCG---------------AACAA----AATTCAGGG-G-ACTGGGA--------TGACAC--------------------GTTCGCACTG------------------------AAGGCAGTGTGG---ACAGGGCTC-ATGTCCCCAGTG---AA--------------------------ACAATCA---------CGTATTTACAAAGACGTTTAGTTAGC
droTak1	CGAAGACATA-----TCG---------------AACAA----AATTTAGAG-G-GCTAAGA--------TGGTGT--------------------GTTCGCACTG------------------------AAGGCAGTGCGA---ACAGGGCATTAAGCTCCAAGTG---AC--------------------------CAAATCA---------CACATTTACCAAGATGATTAGTTAGC
droEle1	CGAAGACATA-----TCG---------------AACAA----AATTTAAG-GGCGCTAGGA--------TGACGT--------------------GTCCACATCA------------------------ACGGCAGTGTGA---ACAGGGCATAATGTTCCCAGTGTTCCC--------------------------ACAATCACATA-----CATATATACAGAGATGTTTAGTTAGC
droRho1	CGAAGACATA-----TCG---------------AACAA----AATTTAAG-GGCGCTAAAA--------TGTCGT--------------------GTTTACATTA------------------------AAGACAGTGTGA---ACAGGGCATAATGTACCCAATG---AA--------------------------ACAATCA---------CAGATATACAGAGATGTTTAGTTAGC
droFic1	CGAAAACATA-----TCG---------------AACAA----ATCTAAAG--G-G-CTAGA--------CGATGT--------------------GTTCGCACTG------------------------TGGGCAGTGTGA---ACGGGACATACGGCTCCCAGTA---AA--------------------------ACAAACG---------CAC----ACAGAGATGTTAAGTTAAC
droKik1	CAAAAACATA-----ACG---------------AAAAAGAAAAATTCAAT-GC-GA---AC--------AGGTCA--------------------ACTTACACTGAAAGACAGTGAGAAGAGGACATTATGCTCAGTGTAA---ACGCCGCATAATGCTTTCCGTT---AATGTTATTCAGTGTGCAGAGGGCATTTTTGTTCTCAAAAAATATG------------TATTTAGTTAGC
droAna3	CGAAAAAAAAGAAA-ACAAAACAAAACATATCGAACA------------------ACAAAATTGTTTGGAGGC--TTTCTTGGGCAATCT------------------------------------------CCAATGTGA---A-------------------------C--------------------------ACACTCACAAA--------AAATACAGTGTTGTTTAGGTAGC
droBip1	CGAAAAAAAA-------AAAACAAAACATATCGAACA------------------ACAAAATTGTTTGGAGGC--TTTCTTGGGCAATCT------------------------------------------CCAGTGTGA---A-------------------------C--------------------------ACACTCACAAA--------AAATACAGTGTTGTTTAGGTAGC
dp4	GGAGAAAAGC-----GTA---------------TTCGA----AGTTCATTA--------------------------------------------GGTTTCATT----------------------------------AGAAGGACGTGGCGTAGATCCTCGACAG---AA--------------------------ACACTCA---------CACATATCGAAACCGGTTTAGTTAGT
droPer1	AGAAAACCGT-------A---------------TTCGA----AGTTCATT------------------------------------------------------A------------------------GGTTTCGTCAGAAGTACGTGGCGTAGATCCTCGACAG---AA--------------------------ACACTCA---------CACATATCGAAACCGGTTTAGTTAGT
droWil1	AGGAGAAAAA-----AGAAAAAAAAACATATCTAAAAA----ACATA-----------------TACGAAAAC--TT---AGGTCAGCTTCAAAA-------CCG------------------------AACGGAAGCTGA---ACAAAGGCT--------------------------------------------------A---------AA------------CTATTAGTTAGT

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

CGAAGACAAGAGTC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----ACAGA------TTCGCACTGGGCG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--TAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................TGTGA---ACATGGCATAATGCTG......................................................................................................................................................................	21	1	2.00	0.00	2.00	0.00	0.00
......................................................................................................................................TGA---ACATGGCATAATGCTGCCT...................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................AATGCTGCCGATG--TAACT--------------------------------------------------------------------------------------------------------.................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................GAAC----AAAA----TTGAAATGCC....................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

CGAAGACAAG--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAGAT-----G-----GCAGA------TTCGCACTGGACG------------------------CAGTGTGA---ACATGGCATAATGCTGCCGGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................GCTAGAT-----G-----GCCGA------TTCGC.................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
....................................................TTGAAxAGGCAGCAAGAT-----G-----.................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
...........................................................................G-----GCAGA------GTCGCACTGGAAG------------------------C................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
.......................................C----AAAA----TTGATCTGGGAGC.................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CGAAGACATA--TC----------------------GAAC----AAAA----TTGAACTGGCAGCAAG----------------------------------------------------------------------------------TTGCTACCGGTGTTAAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----TAT----------ATGTAGTTAGC-----	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............TC----------------------GAAC----AAAA----TTGAACTGGCA...................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CGAAGACATA--TC----------------------GAAC----AAAA----TTAAACTGGCAGCCAGAT-----G-----AC----------------------------------------------CAGTGTGA---ACGTGGCATAAGGCTGCCGGT----AACA--------------------------------------------------------------------------------------------------------ATCAC----------A----T------------ATTTAGTTAGC-----	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................................................................TGTGA---ACGTGCAATAAGGC........................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................TAAGGCTGCCGGT----AACA--------------------------------------------------------------------------------------------------------ATC..............................................	20	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................TGA---ACGTGGCATAAGGCTGCC....................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................GCAGCCAGAC-----G-----AG----------------------------------------------CAGTGT...........................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG--GCGTTAAGAC-----C-----A---A---------TCACTATATG------------------------GAGTGTGAAAAGAATGGGTTAATGCTCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAA----------A----TATTTGCAAAGTTATTTAGTTAGC-----

Size

Hit Count

Total Norm

droBia1

CGAAGACATA--TC----------------------GAAC----AAAA----TTCAGGGG--ACTGGGAT-----G-----ACACG------TTCGCACTGAAGG------------------------CAGTGTGG---ACAGGGCTC-ATGTCCCCAGTG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------G----TATTTACAAAGACGTTTAGTTAGC-----

Size

Hit Count

Total Norm

droTak1

CGAAGACATA--TC----------------------GAAC----AAAA----TTTAGAGGG--CTAAGAT-----G-----GTGTG------TTCGCACTGAAGG------------------------CAGTGCGA---ACAGGGCATTAAGCTCCAAGTG--ACCAA--------------------------------------------------------------------------------------------------------ATCAC----------A----CATTTACCAAGATGATTAGTTAGC-----

Size

Hit Count

Total Norm

droEle1

CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAGGAT-----G-----ACGTG------TCCACATCAACGG------------------------CAGTGTGA---ACAGGGCATAATGTTCCCAGTG--TT-----------------------------------------------------------------------------------------CCCA------------CAATCAC----------ATACATATATACAGAGATGTTTAGTTAGC-----

Size

Hit Count

Total Norm

droRho1

CGAAGACATA--TC----------------------GAAC----AAAA----TTTAAG-GGCGCTAAAAT-----G-----TCGTG------TTTACATTAAAGA------------------------CAGTGTGA---ACAGGGCATAATGTACCCAATG--AAACA--------------------------------------------------------------------------------------------------------ATCAC----------A----GATATACAGAGATGTTTAGTTAGC-----

Size

Hit Count

Total Norm

droFic1

CGAAAACATA--TC----------------------GAAC----AAAT----CTAAAG-GG---CTAGAC-----G-----ATGTG------TTCGCACTGTGGG------------------------CAGTGTGA---ACGGGACATACGGCTCCCAGTA--AAACA--------------------------------------------------------------------------------------------------------AACGC----------A----C----ACAGAGATGTTAAGTTAAC-----

Size

Hit Count

Total Norm

droKik1

CAAAAACATA--AC----------------------GAAA----AAGAAAAATTCAAT--G---CGAACA-----G-----GTCAA------CTTACACTGAAAGACAGTGAGAAGAGGACATTATGCTCAGTGTAA---ACGCCGCATAATGCTTTCCGTT--AA---------------------------------T-----GTTA---TTCAGTGTGCAGAGGGCATTTTT-------------------------------------GTTCTCAAA-AAATATG----------------TATTTAGTTAGC-----

Size

Hit Count

Total Norm

droAna3

CGAAAAAAAA--GA---AAACAAAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAATGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..AAAAAAAA--GA---AAAAAAAA.........................................................................................................................................................................................................................................................................................................	18	23	0.09	0.00	0.00	0.00	0.09
.......AAA--GA---AAACAAAAAAAAA....................................................................................................................................................................................................................................................................................................	18	46	0.04	0.00	0.00	0.00	0.04
..........................................................................................................................................................................................................................................................ATGTCAACA------------CATTCACAAA-------------AAA.........................	22	1	1.00	0.00	0.00	0.00	1.00
.GAAAAAAAA--GA---ACACCAA..........................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..AAAAAAAA--GA---CCACAAAACAA......................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....AAAAGA--Gx---AAACAAAAGAAAA....................................................................................................................................................................................................................................................................................................	20	4	0.25	0.25	0.00	0.00	0.00
..AAAAAAGA--AA---AAACAAAA.........................................................................................................................................................................................................................................................................................................	18	44	0.02	0.00	0.00	0.00	0.02
......AAAA--GA---AAACAAAACCAAA....................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.......AGA--GA---AAACAGAACAAAA....................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......AAAA--GA---AAGCAAACCAAAA....................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.GAAAAAACA--GA---AGACAAA..........................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.......AAA--GA---AAACxAACCAAAACA..................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..AAAAAGAG--GA---AAACAAAA.........................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..AAAAAACA--GA---ACACAAAA.........................................................................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
.GAAAAAAAA--CA---AAACAAAC.........................................................................................................................................................................................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
...AAAAAAA--AA---AAACAAAAAAAAA....................................................................................................................................................................................................................................................................................................	22	41	0.02	0.00	0.00	0.00	0.02
.......AGA--xA---AAACACAACAAAACA..................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.GAAAAAAAA--GA---AAAAAAGA.........................................................................................................................................................................................................................................................................................................	19	6	0.17	0.00	0.00	0.00	0.17
..AAAAAAAA--GA---AAAGAAAAAAA......................................................................................................................................................................................................................................................................................................	21	18	0.06	0.00	0.00	0.00	0.06
..AAAACAGA--Gx---AAACAAAACA.......................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....AAAAA--GA---AAAGAAAAAAAAA....................................................................................................................................................................................................................................................................................................	20	20	0.05	0.00	0.00	0.00	0.05
.........A--GA---AAACAGAACAAAAGA..................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....AAAAAA--GA---AAGAAAAACAA......................................................................................................................................................................................................................................................................................................	19	11	0.09	0.00	0.00	0.00	0.09
..AAAAAAAA--GA---AAGAAAAA.........................................................................................................................................................................................................................................................................................................	18	48	0.02	0.00	0.00	0.00	0.02
.....................................................................................................................................................................................................................................................CTCCAACGTGAAGA------------CACTC..............................................	19	1	1.00	0.00	0.00	0.00	1.00
....AAAGAA--GA---AAACAAAACT.......................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
...AAAAAAA--GA---CAACAAAACA.......................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.....AAAAA--GA---CAACAAAAAAAA.....................................................................................................................................................................................................................................................................................................	19	9	0.11	0.00	0.00	0.00	0.11
...AAAACAA--GA---AAAGAAAACA.......................................................................................................................................................................................................................................................................................................	19	10	0.10	0.00	0.00	0.00	0.10
...AAAAACA--GA---AAAGAAAACA.......................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
..AAAAAGGA--xA---AAACAAAACAAAA....................................................................................................................................................................................................................................................................................................	22	3	0.33	0.33	0.00	0.00	0.00
...AAAAAAA--GA---AAAGAAAAGA.......................................................................................................................................................................................................................................................................................................	19	10	0.10	0.00	0.00	0.00	0.10
..AAAAAAAA--AG---AAACAAAACA.......................................................................................................................................................................................................................................................................................................	20	12	0.08	0.00	0.00	0.00	0.08
...AAAAAAA--GA---AAAGAAAACCAA.....................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
..AAAAAAAA--GA---AAAAAAAAGAAA.....................................................................................................................................................................................................................................................................................................	22	14	0.07	0.00	0.00	0.00	0.07
..AAAAAAAG--GA---AAACATAA.........................................................................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
....AAAAAA--GA---AAACACAAAAAAA....................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
......AAAA--CA---AAACAGAACAAAA....................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
....AAAAAA--AA---AACCAAAACA.......................................................................................................................................................................................................................................................................................................	18	21	0.05	0.00	0.00	0.00	0.05
.....AAAAA--GA---AAAAACAACAAAA....................................................................................................................................................................................................................................................................................................	20	10	0.10	0.00	0.00	0.00	0.10
.CGAAAAAAA--GA---AAACAAA..........................................................................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
.....AAAAA--GA---AAACGAGACAAA.....................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....AAAAA--GA---AAACAAACAAA......................................................................................................................................................................................................................................................................................................	18	13	0.08	0.00	0.00	0.00	0.08
.....AAAAA--GA---AAACAAAACCCA.....................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.GAAAAAAAA--GA---AAAAAAAAA........................................................................................................................................................................................................................................................................................................	20	22	0.05	0.00	0.05	0.00	0.00
......AAAA--GA---AAACAGAAxAAAACA..................................................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
.GAAAAAAAA--GC---AAAxAAAACA.......................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.GAAAAACAA--GG---AAACAAA..........................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
......AAAA--GA---AAACAAAACGCAAC...................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
AGGAAAAAAA--GA---AAACAAA..........................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00
.......AAA--GA---AAACAAAACAAAGGA..................................................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
..AAAAAAAA--GA---AAAGAAAAAA.......................................................................................................................................................................................................................................................................................................	20	35	0.03	0.00	0.00	0.00	0.03
..AAAAAAAA--GA---GAAAAAAA.........................................................................................................................................................................................................................................................................................................	18	47	0.02	0.00	0.02	0.00	0.00
..AAAAAAAA--AA---AAAAAAAACAAAA....................................................................................................................................................................................................................................................................................................	23	37	0.03	0.00	0.00	0.00	0.03
....AAACAA--GA---AAACAAAACAGA.....................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
......AAAA--GA---AAACAAGAAAAA.....................................................................................................................................................................................................................................................................................................	18	10	0.10	0.00	0.00	0.00	0.10
.....AAAAA--GA---GAACAAAAAAAA.....................................................................................................................................................................................................................................................................................................	19	7	0.14	0.00	0.00	0.00	0.14

droBip1

CGAAAAAAAA--A---------AAACAAAACATATCGAAC----A------------------ACAAAATTGTTTGGAGGCT-------------------------------------------------------------------------------------------------------------------------TTCTT------------------------------GGGCAATCTCCAGTGTGAACA------------CACTCACAAA-------------AAATACAGTGTTGTTTAGGTAGC-----

Size

Hit Count

Total Norm

dp4

GGAGAAAAGC--GT----------------------ATTC----GAAG----TTCATTAG--------------------------------G----------TT------------------------TCATTAGAAGGACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.....................................................................................................................................TAGAAGGACGTGGCGAAGATCCTCTAC..................................................................................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00

droPer1

AGAAAACCGT--------------------------ATTCGAAGTTCA----TTAGG----------------------------------------------TT------------------------TCGTCAGAAGTACGTGGCGTAGATCCTCGACAG--AAACA--------------------------------------------------------------------------------------------------------CTCAC----------A----CATATCGAAACCGGTTTAGTTAGT-----	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................................................................................................................GTCAGAAGTACGGGGTGT.............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AGGAGAAAAA--AGA-------AAAAAAAACATATCTAAA---AAACA----TATA-------------C-----GAAAACTTAGGTCAGCTTCAAAACCGAACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------CTATTAGTTAGT-----	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................................................................................TCAAAACCGAACG------------------------GAAGCTGA---AC....................................................................................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
...............................................................................ACTTAGGTCAGCTTCAAAAC...............................................................................................................................................................................................................................	20	1	4.00	0.00	0.00	0.00	4.00
......................................................................................................ACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------C................	24	1	3.00	0.00	0.00	0.00	3.00
AGGAGAAGAA--CGA-------AAAAAA......................................................................................................................................................................................................................................................................................................	19	1	3.00	2.00	1.00	0.00	0.00
....................................................................................................GAACG------------------------GAAGCTGA---ACAAAG................................................................................................................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
....................................................................................................GAACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------C................	26	1	2.00	0.00	0.00	0.00	2.00
.GGAGAAGAA--CGA-------AAAAAA......................................................................................................................................................................................................................................................................................................	18	2	1.00	0.00	1.00	0.00	0.00
.............................................................................................CAAAACCGAACG------------------------GAAGCTGA---ACA...................................................................................................................................................................................	23	1	2.00	0.00	0.00	0.00	2.00
...AGTAAAA--GGA-------AAAAAAAAC...................................................................................................................................................................................................................................................................................................	19	3	0.67	0.00	0.67	0.00	0.00
...........................................................................................TTCAAAACCGAACG------------------------GAAGCTGA---AC....................................................................................................................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
AGGAGAAGAA--CGA-------AAAAAAA.....................................................................................................................................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
AGGGGAAAAA--AAA-------AAAAAA......................................................................................................................................................................................................................................................................................................	19	9	0.11	0.00	0.11	0.00	0.00
................................................................................................AACCGAACG------------------------GAAGCTGA---ACA...................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.........A--AAA-------AAAAAAAACAGATC..............................................................................................................................................................................................................................................................................................	18	24	0.04	0.00	0.04	0.00	0.00
.....................................................................................................AACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------AA----------A----------------C................	25	1	1.00	0.00	0.00	0.00	1.00
......AAAA--AGA-------AAAAAGAACAAA................................................................................................................................................................................................................................................................................................	19	21	0.05	0.00	0.05	0.00	0.00
AGGAGAAAAA--AGA-------GAGAAA......................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
......................................................................................................ACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------..............................................	20	1	1.00	0.00	0.00	0.00	1.00
.....AAAAA--GGA-------AAAAAAAACC..................................................................................................................................................................................................................................................................................................	18	11	0.09	0.00	0.09	0.00	0.00
.............................................................................................CAAAACCGAACG------------------------GAAGCTGA---AC....................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
......AAAA--AGA-------AAAAAACAAATA................................................................................................................................................................................................................................................................................................	19	33	0.03	0.00	0.03	0.00	0.00
............................................................................................TCAAAACCGAACG------------------------GAAGCTGA---A.....................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................TTCxxAACCGAACG------------------------GAAGCTGA---AC....................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...AGAAAAA--AGG-------AAAAAAGA....................................................................................................................................................................................................................................................................................................	18	8	0.13	0.00	0.13	0.00	0.00
...AGGAAAA--ACA-------AAAAAAAA....................................................................................................................................................................................................................................................................................................	18	51	0.02	0.00	0.02	0.00	0.00
....GAAAAA--AGA-------ATAGAAAAC...................................................................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
................................................................................CTTAGGTCAGCTTCAAAACC..............................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
AGGAGGAAGA--AGA-------AAAAAA......................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.....AAGAA--AGA-------AAGAAAAACA..................................................................................................................................................................................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
....GAAAAA--AGA-------AAACAAAAT...................................................................................................................................................................................................................................................................................................	18	15	0.07	0.00	0.07	0.00	0.00
...AGAAAAA--AGA-------AAAAAAAA....................................................................................................................................................................................................................................................................................................	18	15	0.07	0.00	0.07	0.00	0.00
.....AAAAA--GGA-------AAAACAAACA..................................................................................................................................................................................................................................................................................................	18	24	0.04	0.00	0.04	0.00	0.00
.....AAAAG--AGA-------AAAAAAAAGA..................................................................................................................................................................................................................................................................................................	18	44	0.02	0.00	0.02	0.00	0.00
...........................................................................GGAAACTTAGGTCAGCTTCAAAACC..............................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00
AGGAGAAGGA--AGA-------AAAAA.......................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.....AAAAA--AGA-------ACAAAAAACAA.................................................................................................................................................................................................................................................................................................	19	34	0.03	0.00	0.03	0.00	0.00
......AAAA--AGA-------AAAAAAAAGAGA................................................................................................................................................................................................................................................................................................	19	45	0.02	0.00	0.02	0.00	0.00
...AGGAAAA--AGA-------AAAAAGAA....................................................................................................................................................................................................................................................................................................	18	13	0.08	0.00	0.00	0.08	0.00
AGGAGAAAAA--AGA-------AAAGA.......................................................................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.25	0.00
.................................................................................................ACCGAACG------------------------GAAGCTGA---AA....................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
AGGAGAAAAG--AGA-------AAAAAAA.....................................................................................................................................................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
...AGAAAAA--ATA-------AAAAAAAAG...................................................................................................................................................................................................................................................................................................	19	19	0.05	0.00	0.05	0.00	0.00
...................................................................................................................................................................................................................................................................................................................ATTAATTAGT-----	18	3	0.33	0.00	0.33	0.00	0.00
.....AAAAA--AGA-------AGAAAAAAGA..................................................................................................................................................................................................................................................................................................	18	36	0.03	0.00	0.03	0.00	0.00
.....AAAAA--AGA-------AAAAAAAACAAA................................................................................................................................................................................................................................................................................................	20	103	0.01	0.00	0.01	0.00	0.00
....................................................................................................GAACG------------------------GAAGCTGA---ACAAAGGCT-------------------------------------------------------------------------------------------------------------------------------..............................................	22	1	1.00	0.00	0.00	1.00	0.00
.GGAGAAGAA--CGA-------AAAAAAA.....................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.AGAGAAAAA--AGA-------AAAAAA......................................................................................................................................................................................................................................................................................................	18	31	0.03	0.00	0.03	0.00	0.00
AGGAGTAAAA--AAA-------AAAAAAAA....................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
...AGAAAAG--AGA-------AAAAAAGA....................................................................................................................................................................................................................................................................................................	18	12	0.08	0.00	0.00	0.08	0.00
.......AAG--AGA-------AAAAAAAACAAAT...............................................................................................................................................................................................................................................................................................	19	8	0.13	0.00	0.13	0.00	0.00
AGGAAAAAGA--AGA-------AAAAAA......................................................................................................................................................................................................................................................................................................	19	7	0.14	0.00	0.14	0.00	0.00
..GAAGAAAA--AGA-------AAAAAAA.....................................................................................................................................................................................................................................................................................................	18	35	0.03	0.00	0.03	0.00	0.00
....GAAAAA--AGA-------AAAAGAAAAA..................................................................................................................................................................................................................................................................................................	19	22	0.05	0.00	0.05	0.00	0.00
......................................................TA-------------C-----GAAAACTTAGGTCAGCTTC....................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....AAAAC--AGA-------AAAGAAAACA..................................................................................................................................................................................................................................................................................................	18	11	0.09	0.00	0.09	0.00	0.00

droVir3

AAATGCTAAG--GC----------------------GAAA----AAAT----ATCTGA-AG---CGAGGC-----GAAAAAGCAAG----------------------------------------------------------------CTGAGCCCAAAG--CTGAGTTCACACAAGTTTAGTATTTTTTCTGTTGCTTGTCTCTTTTCCAGCAGTATTTAGT-GGTATTTTTTTTGTGAAGTCAGCTTTGCGAG------------CCT-CTAAT---------------------------CTATTAGTTAGC-----

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TGATGCATCA--TCCAAA-------------------AGC----CCAG----CTGAGCTCGCCGTTCGTC-----T-----A---A------TTAG----------------------------------------------------------------------------------------------------TATTTCTCTCTT------------------------------ATTCAGTATTCACTGTAAGCGACGGTGCGTGCTT-CAGCT-CTATTCACTG----T------------ATCCAACTAGCTTTCT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CAAATAATAC--TC----------------------GTAA----CATA----TCTGAAAG----AAAGAA-----GGAAAAACAAG------AAAACA-----TT------------------------TATCAAGAAGCCCAA-----AAAGCTG-----------AATTCACAA-------------------------------------------------------------------------------------------------CGCCT----------G----------------TTTTTAGTATTT-----

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:16:50 EDT

sblock177975

chrX:5963712-5963792 -

Candidate

three_prime_UTR

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup