dme-mir-275-as- Best orthologs

dme-mir-275-as	chr2L:7425795-7425892 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 7425812-7425834
   star strand at position 7425851-7425873
   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:7425780-7425907 -		1	ATGG--TGAA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TA----------CAGTCGGG--GGAACA--T--CA
droSim1	chr2L:7217350-7217477 -	LASTZ	1	ATGG--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droSec1	super_3:2941240-2941367 -	LASTZ	1	ATGA--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droYak2	chr2L:5473766-5473897 +	LASTZ	4	ATATCGTGGA------------------GTTGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTC-TG-------T-TCAGTCGGG--GGAACA--T--CA
droEre2	scaffold_4929:16344506-16344633 -	LASTZ	4	ATGG--TGGA------------------GATGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droEug1	scf7180000409463:614687-614823 -	LASTZ	4	GCGA--TGAAG--------------ACATATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATGT--A-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCAAGGTAGAAGACAT-TTAAGCCTTT-TCA---GGG--AGAACA--T--CA
droBia1	scf7180000302422:9125514-9125641 -	LASTZ	4	GCGG--TGGA------------------TGTGG-AG----ATG--TCTGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAC--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTTT----------AAGCCGGG--GGAACA--T--CA
droTak1	scf7180000415604:142420-142542 +	LASTZ	4	ATGG------------------------GTTGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCCGGG--GGAACA--T--CG
droEle1	scf7180000491028:1624837-1624954 +	LASTZ	4	AAA--------------------------ATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--G-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTTGG---GGAACA-------
droRho1	scf7180000766421:7648-7769 +	LASTZ	4	------TGGA------------------AATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATATGAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCTGG---GGAACA-------
droFic1	scf7180000454115:155668-155793 -	LASTZ	4	GTGC--TGGA------------------TATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGCAGTAGACTT-TT-------TTCCAGC-TGG--GGAACA-------
droKik1	scf7180000302384:54817-54950 +	LASTZ	4	GAGT--TGTT------------------G---GC-GATG-ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAAGAGACTTTTT----------CAGCTGGGAAGGAACACATCCCG
droAna3	scaffold_12916:15333988-15334092 -	LASTZ	4	ATGG--CG---------------------------G----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG-GA----------GAGT-------------------
droBip1	scf7180000396572:1689389-1689508 +	LASTZ	4	ATGT--CGGA------------------TATGGCGG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TG----------GAG---------TACA--T--GG
dp4	chr4_group1:4175727-4175841 -	LASTZ	4	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droPer1	super_5:1086448-1086562 +	LASTZ	4	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droWil1	scaffold_180772:5257564-5257692 +	LASTZ	4	GTGT--CGTCGTTGTCGCCGTCGTC--GT---GC-GATGAATC--TTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGTATTG-AATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC--------------------------------------
droVir3	scaffold_12963:15419953-15420066 +	LASTZ	4	AAGC--TTAA-------------------------GATG-A-A--TACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAACCAAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG-CG----------CAG--------------------
droMoj3	scaffold_6500:18399385-18399491 +	LASTZ	4	GCAG------------------------A---GC-GTTG-A-A--TGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGA---GATAATCGAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC--------------------------------------
droGri2	scaffold_15126:5008401-5008495 -	LASTZ	4	ATG--------------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAATCAAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC--------------------------------------

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	ATGG--TGAA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TA----------CAGTCGGG--GGAACA--T--CA
droSim1	ATGG--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droSec1	ATGA--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droYak2	ATATCGTGGA------------------GTTGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTC-TG-------T-TCAGTCGGG--GGAACA--T--CA
droEre2	ATGG--TGGA------------------GATGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA
droEug1	GCGA--TGAAG--------------ACATATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATGT--A-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCAAGGTAGAAGACAT-TTAAGCCTTT-TCA---GGG--AGAACA--T--CA
droBia1	GCGG--TGGA------------------TGTGG-AG----ATG--TCTGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAC--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTTT----------AAGCCGGG--GGAACA--T--CA
droTak1	ATGG------------------------GTTGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCCGGG--GGAACA--T--CG
droEle1	AAA--------------------------ATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--G-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTTGG---GGAACA-------
droRho1	------TGGA------------------AATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATATGAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCTGG---GGAACA-------
droFic1	GTGC--TGGA------------------TATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGCAGTAGACTT-TT-------TTCCAGC-TGG--GGAACA-------
droKik1	GAGT--TGTT------------------G---GC-GATG-ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAAGAGACTTTTT----------CAGCTGGGAAGGAACACATCCCG
droAna3	ATGG--CG---------------------------G----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG-GA----------GAGT-------------------
droBip1	ATGT--CGGA------------------TATGGCGG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TG----------GAG---------TACA--T--GG
dp4	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droPer1	ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G
droWil1	GTGT--CGTCGTTGTCGCCGTCGTC--GT---GC-GATGAATC--TTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGTATTG-AATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC--------------------------------------
droVir3	AAGC--TTAA-------------------------GATG-A-A--TACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAACCAAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG-CG----------CAG--------------------
droMoj3	GCAG------------------------A---GC-GTTG-A-A--TGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGA---GATAATCGAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC--------------------------------------
droGri2	ATG--------------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAATCAAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC--------------------------------------

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

ATGG--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................CCCCGGTCACTGATTAGCGCGC..................................................	22	2	3.50	0.00	2.00	0.00	1.50
...........................................................................................................CCCCGGTCACTGATTAGCGCGCA.................................................	23	2	3.50	0.00	1.00	1.50	1.00
...............................................................................CTGACTGxATAT-AA-----AAAAG...........................................................................	18	2	1.00	0.00	1.00	0.00	0.00
.............................................................................................................CCGGTCACTGATTAGCGCGCA.................................................	21	2	0.50	0.00	0.50	0.00	0.00
............................................................................................................CCCGGTCACTGATTAGCGCG...................................................	20	2	0.50	0.00	0.00	0.50	0.00
...........................................................................................................CCCCGGTCACTGATTAGCGC....................................................	20	2	0.50	0.00	0.50	0.00	0.00
..............................................................CGCGCTACTTCAGGTACCTGACT..............................................................................................	23	2	0.50	0.00	0.50	0.00	0.00
...............................................................................CTGACTGTCTAx-AA-----AAAAC...........................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

ATGA--CGGA------------------GATGG-AG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACAAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................................................CCCCGGTCACTGATTAGCGCGC..................................................	22	2	0.50	0.00	0.00	0.50
...........................................................................................................CCCCGGTCACTGATTAGCGCG...................................................	21	2	0.50	0.00	0.00	0.50

droYak2

ATATCGTGGA------------------GTTGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTC-TG-------T-TCAGTCGGG--GGAACA--T--CA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................TCTGG-GCCCACGCGCGCTA..............................................................................................................	19	2	0.50	0.00	0.00	0.00	0.00	0.50

droEre2

ATGG--TGGA------------------GATGG-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT-AA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTCGGG--GGAACA--T--CA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................T----------CAGTCGGT--TGAACA--T--CA	18	2	0.50	0.50	0.00	0.00	0.00

droEug1

GCGA--TGAAG--------------ACATATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATGT--A-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCAAGGTAGAAGACAT-TTAAGCCTTT-TCA---GGG--AGAACA--T--CA

Size

Hit Count

Total Norm

droBia1

GCGG--TGGA------------------TGTGG-AG----ATG--TCTGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAC--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTCTTT----------AAGCCGGG--GGAACA--T--CA

Size

Hit Count

Total Norm

droTak1

ATGG------------------------GTTGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCCGGG--GGAACA--T--CG

Size

Hit Count

Total Norm

droEle1

AAA--------------------------ATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--G-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGTTGG---GGAACA-------

Size

Hit Count

Total Norm

droRho1

------TGGA------------------AATGA-AG----ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATATGAA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TT----------CAGCTGG---GGAACA-------

Size

Hit Count

Total Norm

droFic1

GTGC--TGGA------------------TATGG-AG----ATG--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGCAGTAGACTT-TT-------TTCCAGC-TGG--GGAACA-------

Size

Hit Count

Total Norm

droKik1

GAGT--TGTT------------------G---GC-GATG-ATA--TATGTCTGG-CACCACGCGCGCTACTTCAGGTACCTGACTGTATAT--A-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAAGAGACTTTTT----------CAGCTGGGAAGGAACACATCCCG

Size

Hit Count

Total Norm

droAna3

ATGG--CG---------------------------G----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTG-GA----------GAGT-------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................CTGACTGx-TG--CA-----AAGACCA.........................................................................	18	2	0.50	0.00	0.00	0.00	0.50
...........................................................................GTACCxGACTGT-TG--GA-----AAAA............................................................................	19	2	0.50	0.00	0.00	0.00	0.50

droBip1

ATGT--CGGA------------------TATGGCGG----ATA--TATGTCTGC-CACCACGCGCGCTACTTCAGGTACCTGACTGT-TG--CA-----AAAACCAGCCCCGGTCACTGATTAGCGCGCAAGGTAGGAGACTT-TG----------GAG---------TACA--T--GG

Size

Hit Count

Total Norm

dp4

ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

ACAC------------------------------AG----ATGTTCGTGTCTAG-CACCACGCGCGCTACTTCAGGTACCTGACTGCAGTG-AA-----AAAACCAGCCCCGGTCTCTGATTAGCGCGCATGGTAGGAGACTT-TC----------AAGAAGGT--G-----------G	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................................CTAG-CTGCACGCGCGCTA..............................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.AAC------------------------------AG----CTGTTCGTGTCTA..............................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00

droWil1

GTGT--CGTCGTTGTCGCCGTCGTC--GT---GC-GATGAATC--TTGGTCTAA-AACCACGCGCGCTACTTCAGGTACCTGACTGTATTG-AATAAAATTACTCAGCCCTGGTCACTGATTAGCGCGCAAGGTAAGAGAC--------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
GTGT--CGTAGTCGTCGCCGTC.............................................................................................................................................................	20	2	1.50	1.00	0.50	0.00	0.00
..CT--CGTCGTTGTCGTCGTC.............................................................................................................................................................	18	17	0.18	0.00	0.00	0.00	0.18
.......GTCGTTGTCGTCGTCGTC--........................................................................................................................................................	18	43	0.05	0.00	0.00	0.00	0.05
.TGG--CGTCGTTGTCGTCGTC.............................................................................................................................................................	19	5	0.20	0.00	0.20	0.00	0.00
..........GTCGTCGCCGTCGTC--GT---C..................................................................................................................................................	18	31	0.03	0.00	0.00	0.00	0.03
..GT--AGTCGTTGTCGCTGTC.............................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
.......GTCGTTGTCGTCGTCGTC--GT---C..................................................................................................................................................	21	20	0.05	0.00	0.05	0.00	0.00
.........CGTCGTCGCCGTCGTC--GT---C..................................................................................................................................................	19	26	0.04	0.00	0.00	0.00	0.04
.........................................................................................................................TAGCGCGCAAGTTAAGAGT.......................................	19	2	0.50	0.50	0.00	0.00	0.00
..GT--CGTCGTTGTCGTCGTC.............................................................................................................................................................	18	35	0.03	0.00	0.00	0.00	0.03
..GT--CGTCGTCGTCGCCGTC.............................................................................................................................................................	18	37	0.03	0.00	0.00	0.00	0.03
......AGTCGCTGTCGCCGTCGT...........................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.ATT--CGTCGTTGTCGCCGTC.............................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.......GTCGCCGTCGCCGTCGTC--........................................................................................................................................................	18	18	0.06	0.06	0.00	0.00	0.00

droVir3

AAGC--TTAA-------------------------GATG-A-A--TACGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAACCAAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGACGG-CG----------CAG--------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................ATG-G-A--TGCGTCTGGCCACCAC......................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50	0.00
.................................................TCTGGGCxCCACGCGCGCT...............................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00

droMoj3

GCAG------------------------A---GC-GTTG-A-A--TGCGTCTAGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGA---GATAATCGAAACCAGCCCCGGTCACTGATTAGCGCGCACGGTAAAAGAC--------------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...............................................................................CTGACTGTGA---GCTAAACGAA.............................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droGri2

ATG--------------------------------------------CGTCTGGCCACCACGCGCGCTACTTCAGGTACCTGACTGTGG---GATAATCAAAACCAGCCCCGGTCACTGATTAGCGCGCGCGGTAAACGAC--------------------------------------	Size	Hit Count	Total Norm	V109 Male body
..................................................CTGGGCAGCACGCGCGCTA..............................................................................................................	19	2	1.00	1.00
..................................................CTGGGCTCCACGCGCGCT...............................................................................................................	18	2	1.00	1.00
..................................................CTGGGCAGCACGCGCGCTAC.............................................................................................................	20	2	0.50	0.50
..................................................CTGGCCTGCACGCGCGCTAC.............................................................................................................	20	2	0.50	0.50

Generated: 04/20/2012 at 05:29:35 EDT

dme-mir-275-as

chr2L:7425795-7425892 -

Novel

intergenic

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup