sblock180959- Best orthologs

sblock180959	chrX:9219729-9219977 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 9219945-9219965
   star strand at position 9219752-9219772
   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:9219714-9219992 -		1	CAGTCCAGTGAAAA-GCGAAAGGTTAT---GT-CGTCGAC---CCGGGTACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----AATCATACGCA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TGCAG--G-TTCA--GCA--------------------------------ATCC-------------ACTTAGTTTCGTACT-------------------------------------CAGGACCG-CG---ATTA-GAA---CGAACGAAATTTTGCATTT------------GTCACATTCACA--T------------CTCTTC----------GCCTACAGCACCGAAACGCACTGTCCCCG---GGT--------CG--TCAAACACTCCCAGGCGAGAT------------------------------------------------------TTAATGTTTTTT--
droSim1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_68:110181-110457 -	LASTZ	1	CAGTCCAGTGAAAA-GCGAAAGGTTAT---GT-CGTCGAC---CCGGGGACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----ATTCATACGCA----------TTCAGCA------ACCTAAGGTTT----------------------CATTTGAAGTCATTC---TGCAG--A-TTCA--GCA--------------------------------ATCC-------------ACTTATTTTCTTACT-------------------------------------CAGGACCG-CG---ACTA-AAA---CAAACGAAA--TGGCGTTT------------GTCACTTTCACA--T------------CTCTTC----------GCCTACAGCGCCGAAACGCACTGTCCCCA---GGT--------TG--TCATACGCTCCCAGGCGAGAT------------------------------------------------------TTAATGTTTTTT--
droYak2	chrX:17812868-17813118 -	LASTZ	3	CAGTCCAGTGAA---GCGAAAGGTTAT---GT-CGTCG-C---CC-AGTACAGTGCGTTACGAGGCTATA---TGTGCTTGTTGTA--------------------A----------TACAGC-------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TTTGG--G-TTCA--GCA--------------------------------ACCC-------------ACATAGTTTCGTACT-------------------------------------CAGGACCA-TG---ATTA-GAA-------CGAAA--TGGCATTT-------------GCACCATCACA--C------------CGCTGC----------GCCTACAGCTGCGAAACGCACTGTACTCG---GGT--------CG--TCAAACACTCCCAGACGAGAT------------------------------------------------------TTAATGTTTTTT--
droEre2	scaffold_4690:5899758-5900020 +	LASTZ	1	CAGTCCAGTGAA---GCGAAGGGTTAC---GT-CGCCG-C---CC-AGTACAGTGCGTTGCGAGGCTGTA---TGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCC----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---------------A-------------------------------------ACCC-------------ACATAGTTTCGTGCT-------------------------------------CAGGAA-A-TGAC-ATTA-GAA-------CGAAA--TGGCATTT-------------TCACGTTCACA--T------------CTCTTC----------GCCTACAGCCCCGAAACGCACTGTACCCG---GCT--------CG--TCAACTACTCCCAGACGAGAT------------------------------------------------------TTAATGGTTTTTCC
droEug1	scf7180000409032:737185-737440 +	LASTZ	4	CAGACCAGTGAA---GCGAAAGGTTTA---CTTTCTGG-C---CC-AGTATAGTGCGTTTCGTGGCCGTA---TA-G-CTA---TAGTCCTT----ATTCC--TTTA----------TTCAACA------ATCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTCA-------------------------------------AACC-------------ACTTAATTTTTTACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCACT----------GATTACAGCAACGAAACGCACTGTCCTCCGCCGGT--------TA--TTAAACGC-CCCAGATGGGAATTAT-----------------------------------------------------ATG--------
droBia1	scf7180000301760:5192774-5193027 -	LASTZ	4	CAGTCCAGTGAAGT-GCGAAAGGTCAA---AT-CGCGA-C---CCGGGTACGGTGCGTTTCGGGTC-GTA---TG--CCTG---CAATACTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAT--G-TTGA-------------------------------------ACGC-------------ACTTGATTTCTCGCT-------------------------------------CAGGATAT-TA---ATTA-CCA-------GCAAA--CGGCATCC-------------TCACTTTCACC--A------------GTCAC-----------CCTTACGGCCCCGAAACGCACCGTCCCCG-CGGGTG-------CG--TTACACACTCCCAGTAGAGTTTTAT-----------------------------------------------------A-----TAT--
droTak1	scf7180000414672:184361-184564 +	LASTZ	4	CAGTCCAGTGAA---GCGAAAGGTT---------------------GGGACAGTGCGTTTCGTGGCC----------------------CTT----G------TCTA----------TTCAGCC------ACCTAAGGTTT----------------------CATTCAAAGTCATTC---TATTA--G-TTTA-------------------------------------ACGC-------------ACTTACTTTCTTACT-------------------------------------CAGGACAA-TG---ATTA-GCA-------GCAAA--TGGCATTT-------------TCACCTTCACACAA------------ATCA--------------------CCCCGGAACGCACTGTCTCTG------------------------ACTCCCAGTAGAGATTTAT-----------------------------------------------------------TTC--
droEle1	scf7180000491018:31099-31286 +	LASTZ	4	CAGTCCAGTGCA---GCGAAA----------T-CGTAG-CCCCCC-AGTACAGTGCGTTTCGGGAGCGTA-------------------------------------------------GAGCAGTCGAGCCCCAAGGTTT----------------------CATTCGAAGTCATTCTTCTATTA--G-TTCA--GCC--------------------------------ACCC-------------ACTTTATTTCTCACT-------------------------------------CAGGATATTTG---ATTA-ACA-------GA-------------------------------TTAACA--A------------ATCTTC-------CCCCCTTACAGCCCCGAAACGCATTGTCT--------------------------------------------------------------------------------------------------------------
droRho1	scf7180000780067:115346-115596 -	LASTZ	4	CAATCCAGTGAA---GCGAAAGGTTTA---GT-CGTAG-C---CC-AGTACAGTGCGTTTCGGGGCCTTA---------------------------------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAATCATTC---TATAA--G-TTTA-------------------------------------ACTC-------------ACTTAATTTCATACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCTCC---------CCCTTACAGTCCCGAAACGCACTGTCCCTGGGTCGT--------CG--TCACATACTCCCAAAAGAGATTTTT---------------------------------------------TTTT-CTCATATTTGTT--
droFic1	scf7180000454073:2134548-2134826 -	LASTZ	4	CGATCCAGTGAA---GCGAAAGGTTATTCGAT-CGCAG-C---CC-GGTACAGTGCGTTTCGGAGCTGTAGGGTG--TGTG---TATCCCTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTTA-------------------------------------ATTC-------------ACTTACTTTCTTACT-------------------------------------CAGGAGA--TAATGTTTA-GAA-------GGAAA--TAGCATTT-------------GCACTTTCACA--A------------ATCACCTCCT--ACGCTCTTACAGCCCCGAAACGCACTGTCCTCG---GGT--------CG--TCACATACTCCCAAAAGAGATTTGG------------------------------------------TTTAGGT---TTCTTTTTTT--
droKik1	scf7180000302476:268506-268758 -	LASTZ	4	GAGCCCAGTAGCAG-TTCGCTGCTC------T-CGTCGCC---ATCGGGATTTGGTGTCTGGAGGC----------------------CCTG----ACTCAGGCATT----------TCCTGC--------------GACG----------------------CACTTGAATGCATTC---CGCGG--A-ACAG--ATGCTCC----------------------------AGTC-------------ACTCCACGGCGACCA-------------------------GCGGGCCACTGTAAGGGGGG-AG---AGGGGAGA-------GAAAA--AGGCAGTTTAGAAATCAAAAGTCATATTAACA--T------------GATTTA----------GCACACATTCCCGACAGCGGCACTCCCCG---GGT--------CA--TATATCAACCTCAG---------------------------------------------------------------------------
droAna3	scaffold_12916:15308718-15308902 +	LASTZ	0	CCTT-----------------------------------------------------------------------------------------------------------------------------------AAATTT----------------------TAGTCAAATCTATTC---AATATAGACTTCA--AA---------------------------------TATC-------------TCCCAATTTTATGTC-------------------------------------TAAACT---TG---ACCC-ACAAAACAACCAAA----------------------------------------------------------------------------CTTGACAACATTGTCGCCA------------------------AAATCCGATAGCCTTTTACTTCCTCGTCTCCATTACAAACCGGCTCCCACTACGGGGTGCAATTGAATTTCATTTTTTTTT--
droBip1	scf7180000396431:1210000-1210013 -	LASTZ	0	A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTATTGTTTTTT--
dp4	chrXL_group1a:7788225-7788566 +	LASTZ	0	CGACCAACTGATTAGTCGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACCTTTGTGTGT--ACTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATTTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAAGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAG---CC--AACGCGCAGTAGAAACTTCT-------------------------------------------------------CTGTTAT--
droPer1	super_15:138507-138845 +	LASTZ	0	TGACCAACTGATTA-TTGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACATTTGTGTGT--ATTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATGTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAGGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAGCCATAGAAACGCGCAGTAGCAACTT--------------------------------------------------------------CT--
droWil1	scaffold_180698:1644066-1644082 +	LASTZ	0	GAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT------------------------------------------------------GTAATGTTTCTT--
droVir3	scaffold_11422:71-82 -	LASTZ	0	TT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTATTAT--
droMoj3	scaffold_6359:4144759-4144773 -	LASTZ	0	GA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTAGTTCTTTTT--
droGri2	scaffold_15203:2938631-2938653 -	LASTZ	0	CCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGCAAT------------------------------------------------------CCTATATCCAAT--

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	CAGTCCAGTGAAAAGCGAAAGGTTAT---G-TCGTCGAC---CCGGGTACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----AATCATACGCATTCAGCA------ACCTAAGGTTTCATTCGAAGTCATTC---TGCAGGTTCAGCA----ATCCACTTAGTTTCGTACTCAGGACC--GCGATTA---------------------------GAACGAACGAAATTTTGCATTT------------GTCACATTCACA--TCTCTTC------G--CCTACAGCACCGAAACGCACTGTCCCCGG---GT-CGTCAAACACTCCCAGGCGAGATTTAAT-----------------GTTTTTT--
droSec1	CAGTCCAGTGAAAAGCGAAAGGTTAT---G-TCGTCGAC---CCGGGGACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----ATTCATACGCATTCAGCA------ACCTAAGGTTTCATTTGAAGTCATTC---TGCAGATTCAGCA----ATCCACTTATTTTCTTACTCAGGACC--GCGACTA---------------------------AAACAAACGAAA--TGGCGTTT------------GTCACTTTCACA--TCTCTTC------G--CCTACAGCGCCGAAACGCACTGTCCCCAG---GT-TGTCATACGCTCCCAGGCGAGATTTAAT-----------------GTTTTTT--
droYak2	CAGTCCAGTGAA--GCGAAAGGTTAT---G-TCGTCG-C---CC-AGTACAGTGCGTTACGAGGCTATA---TGTGCTTGTTGTA--------------------ATACAGC-------ACCTAAGGTTTCATTCGAAGTCATTC---TTTGGGTTCAGCA----ACCCACATAGTTTCGTACTCAGGACC--ATGATTA---------------------------GAA----CGAAA--TGGCATTT-------------GCACCATCACA--CCGCTGC------G--CCTACAGCTGCGAAACGCACTGTACTCGG---GT-CGTCAAACACTCCCAGACGAGATTTAAT-----------------GTTTTTT--
droEre2	CAGTCCAGTGAA--GCGAAGGGTTAC---G-TCGCCG-C---CC-AGTACAGTGCGTTGCGAGGCTGTA---TGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCCTTCAGCA------ACCTAAGGTTTCATTCGAAGTCATTC------------A-------ACCCACATAGTTTCGTGCTCAGGAAAT-GACATTA---------------------------GAA----CGAAA--TGGCATTT-------------TCACGTTCACA--TCTCTTC------G--CCTACAGCCCCGAAACGCACTGTACCCGG---CT-CGTCAACTACTCCCAGACGAGATTTAAT-----------------GGTTTTTCC
droEug1	CAGACCAGTGAA--GCGAAAGGTTTA---CTTTCTGG-C---CC-AGTATAGTGCGTTTCGTGGCCGTA---TA--GCTA---TAGTCCTT----ATTCC--TTTATTCAACA------ATCTAAGGTTTCATTCGAAGTCATTC---TATAAGTTCA-------AACCACTTAATTTTTTACTCAGGATA--ATGATTA---------------------------GAA----GGAAA--TGGCATTT-------------TCACTTTCACA--AATCACT------G--ATTACAGCAACGAAACGCACTGTCCTCCGCCGGT-TATTAAACGC-CCCAGATGGGAATTA---------TAT-------G--------
droBia1	CAGTCCAGTGAAGTGCGAAAGGTCAA---A-TCGCGA-C---CCGGGTACGGTGCGTTTCGGGTC-GTA---TG--CCTG---CAATACTT----A------TTTATTCAGCA------ACCTAAGGTTTCATTCGAAGTCATTC---TATATGTTGA-------ACGCACTTGATTTCTCGCTCAGGATA--TTAATTA---------------------------CCA----GCAAA--CGGCATCC-------------TCACTTTCACC--AGTCACC---------CTTACGGCCCCGAAACGCACCGTCCCCGC-GGGTGCGTTACACACTCCCAGTAGAGTTTTA---------TA------------TAT--
droTak1	CAGTCCAGTGAA--GCGAAAGGTT---------------------GGGACAGTGCGTTTCGTGGCC----------------------CTT----G------TCTATTCAGCC------ACCTAAGGTTTCATTCAAAGTCATTC---TATTAGTTTA-------ACGCACTTACTTTCTTACTCAGGACA--ATGATTA---------------------------GCA----GCAAA--TGGCATTT-------------TCACCTTCACACAAATCA------------------CCCCGGAACGCACTGTCTCTG---------------ACTCCCAGTAGAGATTTA---------T-------------TTC--
droEle1	CAGTCCAGTGCA--GCGAAA-----------TCGTAG-CCCCCC-AGTACAGTGCGTTTCGGGAGCGTA---------------------------------------GAGCAGTCGAGCCCCAAGGTTTCATTCGAAGTCATTCTTCTATTAGTTCAGCC----ACCCACTTTATTTCTCACTCAGGATAT-TTGATTA---------------------------ACA----GA-------------------------------TTAACA--AATCTTCCC----C-CCTTACAGCCCCGAAACGCATTGTCT----------------------------------------------------------------
droRho1	CAATCCAGTGAA--GCGAAAGGTTTA---G-TCGTAG-C---CC-AGTACAGTGCGTTTCGGGGCCTTA---------------------------------TTTATTCAGCA------ACCTAAGGTTTCATTCGAAATCATTC---TATAAGTTTA-------ACTCACTTAATTTCATACTCAGGATA--ATGATTA---------------------------GAA----GGAAA--TGGCATTT-------------TCACTTTCACA--AATCTCC------C-CCTTACAGTCCCGAAACGCACTGTCCCTGGGTCGT-CGTCACATACTCCCAAAAGAGATTTT---------TTTTTCTCATATTTGTT--
droFic1	CGATCCAGTGAA--GCGAAAGGTTATTCGA-TCGCAG-C---CC-GGTACAGTGCGTTTCGGAGCTGTAGGGTG--TGTG---TATCCCTT----A------TTTATTCAGCA------ACCTAAGGTTTCATTCGAAGTCATTC---TATAAGTTTA-------ATTCACTTACTTTCTTACTCAGGAGATAATGTTTA---------------------------GAA----GGAAA--TAGCATTT-------------GCACTTTCACA--AATCACCTCCTACGCTCTTACAGCCCCGAAACGCACTGTCCTCGG---GT-CGTCACATACTCCCAAAAGAGATTTGGTTTAGGTTTC--------TTTTTTT--
droKik1	GAGCCCAGTAGCAGTTCGCTGC---T---C-TCGTCGCC---ATCGGGATTTGGTGTCTGGAGGC----------------------CCTG----ACTCAGGCATTTCCTGC--------------GACGCACTTGAATGCATTC---CGCGGAACAGATGCTCCAGTCACTCCACGGCGACC----------------AGCGGGCCACTGTAAGGGGGGAGAGGGGAGA----GAAAA--AGGCAGTTTAGAAATCAAAAGTCATATTAACA--TGATTTA------G--CACACATTCCCGACAGCGGCACTCCCCGG---GT-CATATATCAACCTCAG--------------------------------------

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
UNAFold Image		None												None			None	None	None	None

Small RNA-seq read pileup

Species

Alignment

droSim1

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

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

CAGTCCAGTGAAAA-GCGAAAGGTTAT---GT-CGTCGAC---CCGGGGACAGTGCGTTTCGAGGCTGTA---TGTGCTTGTTTTAATCCCC----ATTCATACGCA----------TTCAGCA------ACCTAAGGTTT----------------------CATTTGAAGTCATTC---TGCAG--A-TTCA--GCA--------------------------------ATCC-------------ACTTATTTTCTTACT-------------------------------------CAGGACCG-CG---ACTA-AAA---CAAACGAAA--TGGCGTTT------------GTCACTTTCACA--T------------CTCTTC----------GCCTACAGCGCCGAAACGCACTGTCCCCA---GGT--------TG--TCATACGCTCCCAGGCGAGAT------------------------------------------------------TTAATGTTTTTT--	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................................................................................................ATTTAAGGTTT----------------------CATTTGAAGTC.........................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
.....................................................TGCGTTTCGAGGCTGTA---TGTGC.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00
.................................................ACAGTGCGTTTCGAGGCTGT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00
.......................................C---CCGGGGACAGTGCGTTTCGAGG......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	1.00	0.00	0.00
................................................GACCGTGCGTTTCGAGGCTGT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
......................................................................................................................................................................................................................................................................................................................G---ACTA-AAA---CAAACGAAA--TGGCGTT................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00
.......................................C---CCGGGGACAGTGCGTTTCGAGGC.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00
................................................GATAGTGCGTTTCGxGGCTGT..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................CTACAGCGCCGAAACGCACT..................................................................................................................	20	1	1.00	0.00	1.00	0.00
.........................AT---GT-CGTCGAC---CCGGGGACAGTGCG..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	25	1	1.00	0.00	0.00	1.00

droYak2

CAGTCCAGTGAA---GCGAAAGGTTAT---GT-CGTCG-C---CC-AGTACAGTGCGTTACGAGGCTATA---TGTGCTTGTTGTA--------------------A----------TACAGC-------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TTTGG--G-TTCA--GCA--------------------------------ACCC-------------ACATAGTTTCGTACT-------------------------------------CAGGACCA-TG---ATTA-GAA-------CGAAA--TGGCATTT-------------GCACCATCACA--C------------CGCTGC----------GCCTACAGCTGCGAAACGCACTGTACTCG---GGT--------CG--TCAAACACTCCCAGACGAGAT------------------------------------------------------TTAATGTTTTTT--	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................................................................................................................................................................................................................................................AA-------GGGAA--TGGCATTT-------------G.................................................................................................................................................................................	16	1	2.00	0.00	0.00	0.00	2.00	0.00
................................................................................................................................................................................................................................................................................................................................AA-------AGAAA--CGGCATTT-------------G.................................................................................................................................................................................	16	4	0.25	0.00	0.00	0.00	0.25	0.00
............................................................................................................................................................................................................................................................................................................CAGGACCA-TG---ATTA-GAA-------CGA...........................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................................................................AA-------GGAAA--TGGCATTT-------------GC................................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................A----------TACAGC-------ACCTAAGGTTT----------------------C...................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................................................................................CAGGACCA-TG---ATTA-GAA-------CGG...........................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CAGTCCAGTGAA---GCGAAGGGTTAC---GT-CGCCG-C---CC-AGTACAGTGCGTTGCGAGGCTGTA---TGTGCTTGTTGCAATCCCAGCCTCTTCATGCCCC----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---------------A-------------------------------------ACCC-------------ACATAGTTTCGTGCT-------------------------------------CAGGAA-A-TGAC-ATTA-GAA-------CGAAA--TGGCATTT-------------TCACGTTCACA--T------------CTCTTC----------GCCTACAGCCCCGAAACGCACTGTACCCG---GCT--------CG--TCAACTACTCCCAGACGAGAT------------------------------------------------------TTAATGGTTTTTCC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................................................................................................................................................................................................................................................................................................................................................ACGTTCACA--T------------CACGTC----------GCC.....................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.................................................ACAGTGCGTTGCGAGGCT....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................ATCCCAGCCTCTTCATGCCCC----------TTCAGC............................................................................................................................................................................................................................................................................................................................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00

droEug1

CAGACCAGTGAA---GCGAAAGGTTTA---CTTTCTGG-C---CC-AGTATAGTGCGTTTCGTGGCCGTA---TA-G-CTA---TAGTCCTT----ATTCC--TTTA----------TTCAACA------ATCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTCA-------------------------------------AACC-------------ACTTAATTTTTTACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCACT----------GATTACAGCAACGAAACGCACTGTCCTCCGCCGGT--------TA--TTAAACGC-CCCAGATGGGAATTAT-----------------------------------------------------ATG--------

Size

Hit Count

Total Norm

droBia1

CAGTCCAGTGAAGT-GCGAAAGGTCAA---AT-CGCGA-C---CCGGGTACGGTGCGTTTCGGGTC-GTA---TG--CCTG---CAATACTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAT--G-TTGA-------------------------------------ACGC-------------ACTTGATTTCTCGCT-------------------------------------CAGGATAT-TA---ATTA-CCA-------GCAAA--CGGCATCC-------------TCACTTTCACC--A------------GTCAC-----------CCTTACGGCCCCGAAACGCACCGTCCCCG-CGGGTG-------CG--TTACACACTCCCAGTAGAGTTTTAT-----------------------------------------------------A-----TAT--

Size

Hit Count

Total Norm

droTak1

CAGTCCAGTGAA---GCGAAAGGTT---------------------GGGACAGTGCGTTTCGTGGCC----------------------CTT----G------TCTA----------TTCAGCC------ACCTAAGGTTT----------------------CATTCAAAGTCATTC---TATTA--G-TTTA-------------------------------------ACGC-------------ACTTACTTTCTTACT-------------------------------------CAGGACAA-TG---ATTA-GCA-------GCAAA--TGGCATTT-------------TCACCTTCACACAA------------ATCA--------------------CCCCGGAACGCACTGTCTCTG------------------------ACTCCCAGTAGAGATTTAT-----------------------------------------------------------TTC--

Size

Hit Count

Total Norm

droEle1

CAGTCCAGTGCA---GCGAAA----------T-CGTAG-CCCCCC-AGTACAGTGCGTTTCGGGAGCGTA-------------------------------------------------GAGCAGTCGAGCCCCAAGGTTT----------------------CATTCGAAGTCATTCTTCTATTA--G-TTCA--GCC--------------------------------ACCC-------------ACTTTATTTCTCACT-------------------------------------CAGGATATTTG---ATTA-ACA-------GA-------------------------------TTAACA--A------------ATCTTC-------CCCCCTTACAGCCCCGAAACGCATTGTCT--------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droRho1

CAATCCAGTGAA---GCGAAAGGTTTA---GT-CGTAG-C---CC-AGTACAGTGCGTTTCGGGGCCTTA---------------------------------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAATCATTC---TATAA--G-TTTA-------------------------------------ACTC-------------ACTTAATTTCATACT-------------------------------------CAGGATAA-TG---ATTA-GAA-------GGAAA--TGGCATTT-------------TCACTTTCACA--A------------ATCTCC---------CCCTTACAGTCCCGAAACGCACTGTCCCTGGGTCGT--------CG--TCACATACTCCCAAAAGAGATTTTT---------------------------------------------TTTT-CTCATATTTGTT--

Size

Hit Count

Total Norm

droFic1

CGATCCAGTGAA---GCGAAAGGTTATTCGAT-CGCAG-C---CC-GGTACAGTGCGTTTCGGAGCTGTAGGGTG--TGTG---TATCCCTT----A------TTTA----------TTCAGCA------ACCTAAGGTTT----------------------CATTCGAAGTCATTC---TATAA--G-TTTA-------------------------------------ATTC-------------ACTTACTTTCTTACT-------------------------------------CAGGAGA--TAATGTTTA-GAA-------GGAAA--TAGCATTT-------------GCACTTTCACA--A------------ATCACCTCCT--ACGCTCTTACAGCCCCGAAACGCACTGTCCTCG---GGT--------CG--TCACATACTCCCAAAAGAGATTTGG------------------------------------------TTTAGGT---TTCTTTTTTT--

Size

Hit Count

Total Norm

droKik1

GAGCCCAGTAGCAG-TTCGCTGCTC------T-CGTCGCC---ATCGGGATTTGGTGTCTGGAGGC----------------------CCTG----ACTCAGGCATT----------TCCTGC--------------GACG----------------------CACTTGAATGCATTC---CGCGG--A-ACAG--ATGCTCC----------------------------AGTC-------------ACTCCACGGCGACCA-------------------------GCGGGCCACTGTAAGGGGGG-AG---AGGGGAGA-------GAAAA--AGGCAGTTTAGAAATCAAAAGTCATATTAACA--T------------GATTTA----------GCACACATTCCCGACAGCGGCACTCCCCG---GGT--------CA--TATATCAACCTCAG---------------------------------------------------------------------------

Size

Hit Count

Total Norm

droAna3

CCTT-----------------------------------------------------------------------------------------------------------------------------------AAATTT----------------------TAGTCAAATCTATTC---AATATAGACTTCA--AA---------------------------------TATC-------------TCCCAATTTTATGTC-------------------------------------TAAACT---TG---ACCC-ACAAAACAACCAAA----------------------------------------------------------------------------CTTGACAACATTGTCGCCA------------------------AAATCCGATAGCCTTTTACTTCCTCGTCTCCATTACAAACCGGCTCCCACTACGGGGTGCAATTGAATTTCATTTTTTTTT--	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ACGACTGGGTGCAATTGAA................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................................................................CA-ACAAAACAAACAAA----------------------------------------------------------------------------CTT...........................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................................................................CAACACAACCAAA----------------------------------------------------------------------------TTTGA.........................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................AATTGACTTTCATTGTTTT....	19	1	1.00	0.00	0.00	0.00	1.00

droBip1

A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTATTGTTTTTT--

Size

Hit Count

Total Norm

dp4

CGACCAACTGATTAGTCGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACCTTTGTGTGT--ACTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATTTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAAGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAG---CC--AACGCGCAGTAGAAACTTCT-------------------------------------------------------CTGTTAT--	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................................................................................................................................................................................................................................................................................................................................................................TATGGGGACAG---CC--AACGCGCAGTA.........................................................................	24	1	1.00	1.00	0.00	0.00	0.00
........TGATTAGTCGATTAGTCGA---TT-CGT...................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00

droPer1

TGACCAACTGATTA-TTGATTAGTCGA---TT-CGTTGAT---TCATTTTCA------------------------------TTCAACTTCC----ATTCATACGTAACTTTATTTATTAAA-T------ACTTGATGTTCGATTTTAGAATTGCCTTCAACATTTGTGTGT--ATTT---TATTA--G-TTGTGGTTTCTATGTTTCTAAGTTTTATTTACGGTTCGACAAGGCAACGCCCGACAAAACGCAATCCGATAGCTTTATAGGTATATGTATGGCTTATGGCAATCC----------------ACA------------------------------------------------------CAGAGTTGAAAGGCAATC---T-TTGAGCTTCCCTACAGCCCTGAAACGCACTGTATATG-TTAGTATGGGGACAGCCATAGAAACGCGCAGTAGCAACTT--------------------------------------------------------------CT--	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................................................................................................................................................................................................................................................................................................................................................................AATC---T-TTGAGCTTCCCTACAGCCCTGAA.........................................................................................................................	28	1	2.00	0.00	0.00	0.00	0.00	2.00
...................................................A------------------------------TTTGACTTCC----ATTCATA................................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................................................CTTACAGCCCTGAACCGCAC...................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................ATTA---TATCA--G-TTGTGGTT.................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................................................................................................................................................................................................................................................................................................AAACGGCCAGTAGCAACT...................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................ACA------------------------------------------------------CAGAGTTGAAAGGCAATC---T-T...............................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.GACCAACTGATTA-TTGATTAGTC..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................................................................................................................................................TAGAAACGCGCAGTAGCAACTT--------------------------------------------------------------CT--	24	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................................................ATGTTAGGTTTTAGAATTGC............................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

GAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT------------------------------------------------------GTAATGTTTCTT--	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTCCT--	19	2	0.50	0.00	0.50	0.00	0.00

droVir3

TT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTTATTAT--

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------TTAGTTCTTTTT--

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGCAAT------------------------------------------------------CCTATATCCAAT--

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:15:14 EDT

sblock180959

chrX:9219729-9219977 -

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