sblock21449- Best orthologs

sblock21449	chr2L:5745968-5746114 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 5746064-5746085
   star strand at position 5746002-5746023
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:5745953-5746129 +		1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCACGATCGTCTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGTC---------GGAGCGGAT----G--GAGTTGCGAGGAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSim1	chr2L:5542462-5542638 +	LASTZ	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------TGAGCGGAT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSec1	super_5:3824688-3824864 +	LASTZ	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------GAAGCAGTT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droYak2	chr2L:13445718-13445903 -	LASTZ	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------TTC-----------------CCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGACGAGGCGGACGGAGCGAAC----G--GAGTTGCGAGGAGGGGACTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEre2	scaffold_4929:5836074-5836241 +	LASTZ	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATCCC--------GTC-----------------TCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGTGCCAGCCG------------------AC----G--GAGTTGCGAGGAGGGGATTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEug1	scf7180000409004:248542-248715 -	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCATATCCC--------GTCCGC-CTC----------CCCGACCTCTGCGATCGTCTGCTGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTCG------TT---------AAC----A--GAGCCGCGA---GGGGATCCGGCC------------------------------TGCGAAT-----------TCATATA----G---------T------------TTA---AGGC
droBia1	scf7180000302422:3953216-3953389 +	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCTCCCCGCCTATCCC--------GTCCCC-AGC----------CCCATCCCCGGCGCTGGTGTACGACT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGCGA---GGGGATCCGGCC------------------------------TGTGGAT-----------TCACATG----G---------T------------TTG---TGGC
droTak1	scf7180000415871:528958-529118 +	LASTZ	5	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCC----------C--------TTC-----------------CCTGTCCCCTGCGATCGTGTGAGGCCTGT--------TGTTGCTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGTGC---GGGGATCCGGCC------------------------------TGTGGAT-----------TCATGTA----C---------T------------TTG---TGGC
droEle1	scf7180000491024:383572-383755 -	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTCCCC-GTCCCCTCC----CTCATCCTCTGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATGTG------TG---------AGC----A--GAGCTGCGA---GGGGATCCGGCC------------------------------TGTGAGT-----------TCGTATACATAG---------T------------TTG---TGGC
droRho1	scf7180000764260:8287-8454 +	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTC-----------------CCCGTCCTCAGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATTTG------CG---------AGC----A--GAGTTGTGA---GGGGATCCGGCC------------------------------TGTGAAT-----------TTATAAA----G---------T------------TTG---TGGC
droFic1	scf7180000448889:28174-28341 +	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC-C--------GTCTC---------------TCCTTCCTCTGCGGTCGCATGGGTCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAATT---TG---AGAGCGAGTTG------CG---------AGC----G--GAGTTTCGA---GGGGATCC-GCC------------------------------TGCGGAG-----------TCGCACA----G---------A------------TTG---AGGC
droKik1	scf7180000300796:309227-309401 -	LASTZ	5	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCAGC------------------------------------------------AACGATCGCGTGTGG-TTGT--------TGTTTCTGGCTTTAATGGAAAGAAATGAGTT---GG---AGTGCGAGTTG------TG---------AGCCGTTGTCGGGCTATGA---GTGAATCCGGCCCATAATTGCTC-----------------------GAGGCAAAAGCAGTTCATATATGGTG---------T------------TTG---TGAC
droAna3	scaffold_12916:11185040-11185180 +	LASTZ	5	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCTCGTGTCCCC-----------GCC-----------------CC-----------AGCTGATGCCTTTAATGGAAAGAACCGC-CA-GCTG---AGAGTCA-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGT-TA----T---------T------------TTT---TGGC
droBip1	scf7180000396572:843756-843896 +	LASTZ	4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCCCTTGTCCCC-----------GCC-----------------CC-----------AGCCGGTGCGTTTAATGGAAAGAACCG-CCA-GCTG---TGGATCC-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGTA------A--------TT------------TTT---GGGC
dp4	chr4_group1:654984-655116 -	LASTZ	5	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTC-----CCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droPer1	super_1:651227-651364 -	LASTZ	5	TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTCTGTACCCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droWil1	scaffold_180708:8432983-8433167 -	LASTZ	3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGTTGT-TG------TT--------GTT-----------------GCCATTGTTGATGCTTTTTTTTTGTT-TT-----TATTTTTGGTGACTATAATGGAA-GAAATGAGTTGCTCG---AGTTAAAAGTG-----------------AGT--------------------------------------GAGTGAACGACTGAGTTGAGTCTTAT--GT-----------TCATTAA----GTTTGTTTTTTTTTGGGGCTTGTTCA---T-AG
droVir3	scaffold_12963:3798442-3798596 +	LASTZ	4	TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGCCGG-----------------------------------CTCTCGTTGTTGTTGTTGTTGTTGTTGTCTGTTGGCTGTTGCTTTTAATGGAAGG-AACGAGTG-CTTG---AGTACTCGTTA------CG---------AGC----T---------------------CA---------------AACAA-------------TGCGAAT-----------TTATATT----G---------T------------TTG---A-GT
droMoj3	scaffold_6500:14252169-14252332 +	LASTZ	5	TCGGTCAACGCATTCGAGTCAAGTTCTGTAGTGG----C----------------A-----------------GCTCTAAACTATGCC-------GGGTTGT--------TGTTGCTGTTTTTAATGGAAGGAATTGAGTG-CTCA---AGTGCTCAATG-----------------AGC--------------------------------------GCTCAAACAG-AGAGCTGAAACAGCAATGT-----------TTATATT----G---------TACGAGATTCCATTTA---TAGC
droGri2	scaffold_15252:3298030-3298190 +	LASTZ	4	TCGGTCAACGCATTCAAGTCAAGTTCTGTGTAGC------------------CTAG--------------------------TGAGCCGGCATGCGATT-----------TGTTTTTGCCTTTAATGGAA-GAAATGAGTG-CTTGAGGAGTACTCGTTGTT----CG---------AGAT---G--TTGTTGTC-----TGAGTTC--------------------------------------GCT-----------TCATTTT----G---------TTTGAGGTTCCATTCAAACTAGC

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	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCACGATCGTCTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGTC---------GGAGCGGAT----G--GAGTTGCGAGGAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSim1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------TGAGCGGAT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droSec1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------GAAGCAGTT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droYak2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------TTC-----------------CCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGACGAGGCGGACGGAGCGAAC----G--GAGTTGCGAGGAGGGGACTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEre2	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATCCC--------GTC-----------------TCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGTGCCAGCCG------------------AC----G--GAGTTGCGAGGAGGGGATTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC
droEug1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCATATCCC--------GTCCGC-CTC----------CCCGACCTCTGCGATCGTCTGCTGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTCG------TT---------AAC----A--GAGCCGCGA---GGGGATCCGGCC------------------------------TGCGAAT-----------TCATATA----G---------T------------TTA---AGGC
droBia1	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCTCCCCGCCTATCCC--------GTCCCC-AGC----------CCCATCCCCGGCGCTGGTGTACGACT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGCGA---GGGGATCCGGCC------------------------------TGTGGAT-----------TCACATG----G---------T------------TTG---TGGC
droTak1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCC----------C--------TTC-----------------CCTGTCCCCTGCGATCGTGTGAGGCCTGT--------TGTTGCTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGTGC---GGGGATCCGGCC------------------------------TGTGGAT-----------TCATGTA----C---------T------------TTG---TGGC
droEle1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTCCCC-GTCCCCTCC----CTCATCCTCTGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATGTG------TG---------AGC----A--GAGCTGCGA---GGGGATCCGGCC------------------------------TGTGAGT-----------TCGTATACATAG---------T------------TTG---TGGC
droRho1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTC-----------------CCCGTCCTCAGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATTTG------CG---------AGC----A--GAGTTGTGA---GGGGATCCGGCC------------------------------TGTGAAT-----------TTATAAA----G---------T------------TTG---TGGC
droFic1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC-C--------GTCTC---------------TCCTTCCTCTGCGGTCGCATGGGTCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAATT---TG---AGAGCGAGTTG------CG---------AGC----G--GAGTTTCGA---GGGGATCC-GCC------------------------------TGCGGAG-----------TCGCACA----G---------A------------TTG---AGGC
droKik1	TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCAGC------------------------------------------------AACGATCGCGTGTGG-TTGT--------TGTTTCTGGCTTTAATGGAAAGAAATGAGTT---GG---AGTGCGAGTTG------TG---------AGCCGTTGTCGGGCTATGA---GTGAATCCGGCCCATAATTGCTC-----------------------GAGGCAAAAGCAGTTCATATATGGTG---------T------------TTG---TGAC
droAna3	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCTCGTGTCCCC-----------GCC-----------------CC-----------AGCTGATGCCTTTAATGGAAAGAACCGC-CA-GCTG---AGAGTCA-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGT-TA----T---------T------------TTT---TGGC
droBip1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCCCTTGTCCCC-----------GCC-----------------CC-----------AGCCGGTGCGTTTAATGGAAAGAACCG-CCA-GCTG---TGGATCC-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGTA------A--------TT------------TTT---GGGC
dp4	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTC-----CCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droPer1	TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTCTGTACCCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG
droWil1	TCGGTCAACGCTTTTAAGTCAAGTTCTGAGTTGT-TG------TT--------GTT-----------------GCCATTGTTGATGCTTTTTTTTTGTT-TT-----TATTTTTGGTGACTATAATGGAA-GAAATGAGTTGCTCG---AGTTAAAAGTG-----------------AGT--------------------------------------GAGTGAACGACTGAGTTGAGTCTTAT--GT-----------TCATTAA----GTTTGTTTTTTTTTGGGGCTTGTTCA---T-AG
droVir3	TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGCCGG-----------------------------------CTCTCGTTGTTGTTGTTGTTGTTGTTGTCTGTTGGCTGTTGCTTTTAATGGAAGG-AACGAGTG-CTTG---AGTACTCGTTA------CG---------AGC----T---------------------CA---------------AACAA-------------TGCGAAT-----------TTATATT----G---------T------------TTG---A-GT
droMoj3	TCGGTCAACGCATTCGAGTCAAGTTCTGTAGTGG----C----------------A-----------------GCTCTAAACTATGCC-------GGGTTGT--------TGTTGCTGTTTTTAATGGAAGGAATTGAGTG-CTCA---AGTGCTCAATG-----------------AGC--------------------------------------GCTCAAACAG-AGAGCTGAAACAGCAATGT-----------TTATATT----G---------TACGAGATTCCATTTA---TAGC
droGri2	TCGGTCAACGCATTCAAGTCAAGTTCTGTGTAGC------------------CTAG--------------------------TGAGCCGGCATGCGATT-----------TGTTTTTGCCTTTAATGGAA-GAAATGAGTG-CTTGAGGAGTACTCGTTGTT----CG---------AGAT---G--TTGTTGTC-----TGAGTTC--------------------------------------GCT-----------TCATTTT----G---------TTTGAGGTTCCATTCAAACTAGC

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

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------TGAGCGGAT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..................................................................................................T-----------TGTTGTTGCTTATAATG................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................T-----------TGTAGTTGGCTTTAATG................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................TG---AGAGCAAGCGGAC---------GGA.................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------GTC-----------------CCCATCCTCCGCGATCGTCTGTGGCT-----------TGTTGTTGCCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGAC---------GAAGCAGTT----G--GAGTTGCGAGAAGGGGATCCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................................................................ATCGTTTGTGGxT-----------TGTTGTTG.........................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................ACCT----G--GAGTTGCGAGAAG.......................................................................................................	18	1	1.00	0.00	0.00	1.00
...GTCAACTCTTTTATGTCA..........................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
...............................................................................................................................GAAAGAGATGAGTT---TG---AGG.......................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
...GTCAACTCTTTTATGTCAA.........................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
................................................................................................................................AACGAAAGGAGTT---TG---AGA.......................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
............................................................................ATCCTCGGCGAGCGTCTG.................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATCCC--------TTC-----------------CCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGCGGACGAGGCGGACGGAGCGAAC----G--GAGTTGCGAGGAGGGGACTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..............................................................................................................................................................................................TTGCGGGGAGGGGAATCG...............................................................................................	18	1	2.00	0.00	0.00	0.00	2.00	0.00
..............................................................................................................................................................................................TTGCGGGGAGGGGAAT.................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................TGCGGGGAGGGGATTC................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................TTGCGGGGAGGGGAATC................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................TCAAGTACTGAGGCCCGTCCCA.......................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................AGAAATGAGTT---TG---AGAGCCAGCGGAC.............................................................................................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCGCAATCCC--------GTC-----------------TCCATCCTCTGCGATCGTGTGTGGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGTGCCAGCCG------------------AC----G--GAGTTGCGAGGAGGGGATTCGGCC------------------------------TGTGAAT-----------TCATATA----G---------T------------TTG---TGGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................................................................CCTCTGCGATCGTxTGTGTC.............................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00

droEug1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCATATCCC--------GTCCGC-CTC----------CCCGACCTCTGCGATCGTCTGCTGCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTCG------TT---------AAC----A--GAGCCGCGA---GGGGATCCGGCC------------------------------TGCGAAT-----------TCATATA----G---------T------------TTA---AGGC

Size

Hit Count

Total Norm

droBia1

TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCTCCCCGCCTATCCC--------GTCCCC-AGC----------CCCATCCCCGGCGCTGGTGTACGACT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGCGA---GGGGATCCGGCC------------------------------TGTGGAT-----------TCACATG----G---------T------------TTG---TGGC

Size

Hit Count

Total Norm

droTak1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCC----------C--------TTC-----------------CCTGTCCCCTGCGATCGTGTGAGGCCTGT--------TGTTGCTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCCAGTTG------CG---------AAC----A--GAGTTGTGC---GGGGATCCGGCC------------------------------TGTGGAT-----------TCATGTA----C---------T------------TTG---TGGC

Size

Hit Count

Total Norm

droEle1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTCCCC-GTCCCCTCC----CTCATCCTCTGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATGTG------TG---------AGC----A--GAGCTGCGA---GGGGATCCGGCC------------------------------TGTGAGT-----------TCGTATACATAG---------T------------TTG---TGGC

Size

Hit Count

Total Norm

droRho1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTATCCC--------GTC-----------------CCCGTCCTCAGCGATCGTGTGTGGTT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAGTT---TG---AGAGCGATTTG------CG---------AGC----A--GAGTTGTGA---GGGGATCCGGCC------------------------------TGTGAAT-----------TTATAAA----G---------T------------TTG---TGGC

Size

Hit Count

Total Norm

droFic1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCCCCGTCCCAATC-C--------GTCTC---------------TCCTTCCTCTGCGGTCGCATGGGTCT-----------TGTTGTTGGCTTTAATGGAAAGAAATGAATT---TG---AGAGCGAGTTG------CG---------AGC----G--GAGTTTCGA---GGGGATCC-GCC------------------------------TGCGGAG-----------TCGCACA----G---------A------------TTG---AGGC

Size

Hit Count

Total Norm

droKik1

TCGGTCAACGCTTTTAAGTCAAGTTCTGGGCAGC------------------------------------------------AACGATCGCGTGTGG-TTGT--------TGTTTCTGGCTTTAATGGAAAGAAATGAGTT---GG---AGTGCGAGTTG------TG---------AGCCGTTGTCGGGCTATGA---GTGAATCCGGCCCATAATTGCTC-----------------------GAGGCAAAAGCAGTTCATATATGGTG---------T------------TTG---TGAC

Size

Hit Count

Total Norm

droAna3

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCTCGTGTCCCC-----------GCC-----------------CC-----------AGCTGATGCCTTTAATGGAAAGAACCGC-CA-GCTG---AGAGTCA-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGT-TA----T---------T------------TTT---TGGC

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCTCTGTCCCTAGTCC--------GCCCCTTGTCCCC-----------GCC-----------------CC-----------AGCCGGTGCGTTTAATGGAAAGAACCG-CCA-GCTG---TGGATCC-------------------------------AAG---------CCGGACCCACCG------------------------------TTCGTAT-----------ACGTA------A--------TT------------TTT---GGGC

Size

Hit Count

Total Norm

dp4

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTC-----CCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................GTCAAGTTCTGAGCC-AGTCCC........................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droPer1

TCGGTCAACGCTTTTAAGTCAAGTTCTGATCC-AGTCCCGCTC-TGTGTACCCCTC--TGTACCCCTCTGTACCCCTCTCTCTTTGTCTGAGTGAAGTT-------------------------------------------------------------------------------------------TTTCGA---GTGGAGTCTGTT------------------------------TCCATGTTCAG---------AAACA----A---------T------------TTA---TGCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................TC--TGTATGCCTCTGTACC.....................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00

droWil1

TCGGTCAACGCTTTTAAGTCAAGTTCTGAGTTGT-TG------TT--------GTT-----------------GCCATTGTTGATGCTTTTTTTTTGTT-TT-----TATTTTTGGTGACTATAATGGAA-GAAATGAGTTGCTCG---AGTTAAAAGTG-----------------AGT--------------------------------------GAGTGAACGACTGAGTTGAGTCTTAT--GT-----------TCATTAA----GTTTGTTTTTTTTTGGGGCTTGTTCA---T-AG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................TTGTTTGTT-TG-----TATTTTTGGT..........................................................................................................................................................................................	21	1	15.00	1.00	13.00	0.00	1.00
............................................................................................GTTTGTT-TG-----TATTTTTGGT..........................................................................................................................................................................................	19	1	13.00	0.00	13.00	0.00	0.00
...............................TGT-TG------TT--------GCT-----------------GCCATTGTTG............................................................................................................................................................................................................................	20	48	0.21	0.00	0.21	0.00	0.00
...........................................................................................TGTTTGTT-TG-----TATTTTTGGT..........................................................................................................................................................................................	20	1	5.00	0.00	5.00	0.00	0.00
..........................................................................................TTGTTTGTT-TG-----TATTTTTGGTG.........................................................................................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TGTTTGTT-TG-----TATTTTTGGTGA........................................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
........................................................................................................................................................TAAAAGTG-----------------AGT--------------------------------------GAGTGAAAGA...........................................................................	21	1	2.00	0.00	0.00	2.00	0.00
..........................................................................................TTGTTTGTT-TG-----TATTTTTGG...........................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..............................TTGT-TG------TT--------GCT-----------------GCCATTGGT.............................................................................................................................................................................................................................	20	38	0.03	0.00	0.03	0.00	0.00
.......................................................................................................................CTATAATGGGA-AAAATGA.....................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................AGTG-----------------AAT--------------------------------------GAxTGAACGACT.........................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................................................................TTTTGTT-TA-----TGTTTTTGGT..........................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.......................................................................................TTTTTTTTTGTT-TT-----TGTTTTT.............................................................................................................................................................................................	21	8	0.13	0.00	0.13	0.00	0.00
..............................TTGT-TG------TT--------GTG-----------------TCCATTGT..............................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
............................................................................................................................................................GGTG-----------------AGT--------------------------------------GAGTGAATGACTGA.......................................................................	21	2	0.50	0.00	0.50	0.00	0.00
............................................................................................GTTTGTT-TG-----TATTTTTGGTG.........................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................TTGTT-TG-----TATTTTTGGTGG........................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................TTTTGTT-TG-----TATTTTTGGTG.........................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................TTGTTTTTTGTT-TT-----TGTTTT..............................................................................................................................................................................................	20	40	0.03	0.00	0.03	0.00	0.00
.............................GTTGT-TG------TT--------GCT-----------------GCCATTGT..............................................................................................................................................................................................................................	20	32	0.03	0.00	0.03	0.00	0.00
................................................................................................................................................................................................................................................................................TTTTTTTTTGTTGGGGCT.............	18	4	0.25	0.00	0.00	0.00	0.25
.........................................................................................TTTTTTTGTT-TT-----TAATTTCGGT..........................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
................................................................................TTGTTGCTTGTTTTTTGT.............................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................ATTTTGTT-TT-----TAGTTTTG............................................................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
....................................................................................................................................................................................................................................................................TATTAA----GTTTGTTTTTTT.....................	18	6	0.17	0.00	0.17	0.00	0.00
........................TGTGATTTGT-TG------TT--------GTT-----------------G.....................................................................................................................................................................................................................................	18	9	0.11	0.00	0.11	0.00	0.00
............................................................................................TTTTGGT-TT-----TAATTTTGGT..........................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................TGT-TG------GT--------GTT-----------------GGCATTGTTGA...........................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................ATTTTTTGTT-TG-----TATTTTTGGT..........................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
............................................T--------GAT-----------------GCCACTGTTGATGCTT......................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................GTT-TT-----TATTTTGGGTGAA.......................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................GTTGTTGATTTTTTTTTGT.............................................................................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
...........................................................................................TGTTTGTT-TG-----TATTTTTGGTG.........................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................TTTGTT-TG-----TATTTTTGGT..........................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.........................................................................................................................ATAATGAAT-GAAATGAGTT..................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................TCTGCTTTGT-TG------TT--------GTT-----------------G.....................................................................................................................................................................................................................................	18	10	0.10	0.00	0.00	0.10	0.00
.............................................................................................TTTTTT-TC-----TATTTTTGGT..........................................................................................................................................................................................	18	10	0.10	0.00	0.10	0.00	0.00
...............................................................................................TGTT-TG-----TATTTTTGGTGAA.......................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................ATTGTGGATGATTTTTTT.................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
............................................T--------GTT-----------------GCCATTATTGATGT........................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................TTGTT-TG-----TATTTTTGGTG.........................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................TTTTTGTT-TT-----TCTTTTTGGT..........................................................................................................................................................................................	20	13	0.08	0.00	0.08	0.00	0.00

droVir3

TCGGTCAACGCATTCAAGTCAAGTTCTGTAGCCTACTGCCGG-----------------------------------CTCTCGTTGTTGTTGTTGTTGTTGTTGTCTGTTGGCTGTTGCTTTTAATGGAAGG-AACGAGTG-CTTG---AGTACTCGTTA------CG---------AGC----T---------------------CA---------------AACAA-------------TGCGAAT-----------TTATATT----G---------T------------TTG---A-GT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................................................................................TCTTTGTAGTTGTTGTTGTTG..........................................................................................................................................................................................................	21	14	0.07	0.07	0.00	0.00	0.00	0.00
.......................................................................................TGTCGTTGTTGGTGTTGTC.....................................................................................................................................................................................................	19	17	0.06	0.06	0.00	0.00	0.00	0.00
.........................................................................................TTGTTGTTGTTGTTGTCT....................................................................................................................................................................................................	18	26	0.04	0.00	0.00	0.00	0.00	0.04
.........................................................................................................CTGTTGGCTGTTGGTTTTG...................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
................................................................................TCGTTGTACTTGTTGTTGTTG..........................................................................................................................................................................................................	21	9	0.11	0.11	0.00	0.00	0.00	0.00
..........................................................................................CGTTGCTGTTGTTGTCTG...................................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.00	0.17
........................................................................................GTTGTTGTTGTTGTTGAC.....................................................................................................................................................................................................	18	39	0.03	0.00	0.00	0.00	0.03	0.00
...................................................................................................TGTTGTCTGTxxGCTGTTGCTT......................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................GATGTGTGTTGGCTGTTG.........................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................GTTCTTGTTGTTCTTGTCT....................................................................................................................................................................................................	19	5	0.20	0.00	0.00	0.20	0.00	0.00
.................................................................................CGTTGTCGTTGTTGTTGTA...........................................................................................................................................................................................................	19	30	0.03	0.03	0.00	0.00	0.00	0.00
......................................................................................TTGTTTTTGTTATTGTTGTCTG...................................................................................................................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00	0.00
.........................................................................................TTGTTGTTGTTGTTGTGCGTT.................................................................................................................................................................................................	21	10	0.10	0.00	0.10	0.00	0.00	0.00
...............................................................................CTCCTTGTTGTTGTTGTTG.............................................................................................................................................................................................................	19	38	0.03	0.00	0.03	0.00	0.00	0.00
.........................................................................................TTGTTGTTGTTGTTGTCTG...................................................................................................................................................................................................	19	8	0.13	0.13	0.00	0.00	0.00	0.00
.................................................................................CGTTGATGTTGTTGTTGTC...........................................................................................................................................................................................................	19	37	0.03	0.03	0.00	0.00	0.00	0.00
......................................CCGG-----------------------------------CCCTCGTTGTTGTT....................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.......................................................................................CGTTGATGTTGTTGTTGTC.....................................................................................................................................................................................................	19	37	0.03	0.03	0.00	0.00	0.00	0.00
........................................................................................................TCTGTTGGCTGTTGGTGTT....................................................................................................................................................................................	19	4	0.25	0.25	0.00	0.00	0.00	0.00
.......................................................................................TGTTGTTCTTGTTGATGTC.....................................................................................................................................................................................................	19	22	0.05	0.00	0.00	0.05	0.00	0.00
...............................................................................CTCGCTGTGGTTGTTGTTG.............................................................................................................................................................................................................	19	9	0.11	0.11	0.00	0.00	0.00	0.00

droMoj3

TCGGTCAACGCATTCGAGTCAAGTTCTGTAGTGG----C----------------A-----------------GCTCTAAACTATGCC-------GGGTTGT--------TGTTGCTGTTTTTAATGGAAGGAATTGAGTG-CTCA---AGTGCTCAATG-----------------AGC--------------------------------------GCTCAAACAG-AGAGCTGAAACAGCAATGT-----------TTATATT----G---------TACGAGATTCCATTTA---TAGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................................................................TTTTTTATTGAAGGAATTG......................................................................................................................................................................	19	1	6.00	4.00	2.00	0.00	0.00
........................................................................................................................TTTTATTGAAGGAATTGA.....................................................................................................................................................................	18	1	2.00	0.00	0.00	2.00	0.00
.......................................................................................................................TTTTTATTGAAGGAATTGA.....................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................GTTGT--------TGTTGCTGTTTTTTC..................................................................................................................................................................................	20	42	0.02	0.00	0.02	0.00	0.00
......................................................................................................................TTTTTTATTGAAGGAATTGA.....................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................GTTGT--------TGTTGCTGTTTTTTCTG................................................................................................................................................................................	22	30	0.03	0.00	0.00	0.00	0.03

droGri2

TCGGTCAACGCATTCAAGTCAAGTTCTGTGTAGC------------------CTAG--------------------------TGAGCCGGCATGCGATT-----------TGTTTTTGCCTTTAATGGAA-GAAATGAGTG-CTTGAGGAGTACTCGTTGTT----CG---------AGAT---G--TTGTTGTC-----TGAGTTC--------------------------------------GCT-----------TCATTTT----G---------TTTGAGGTTCCATTCAAACTAGC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:29 EDT

sblock21449

chr2L:5745968-5746114 +

Candidate

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup