dme-mir-3642- Best orthologs

dme-mir-3642	chr3L:11622605-11622680 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	tailed_mirtron

Legend:

   mature strand at position 11622605-11622626
   star strand at position 11622648-11622669
   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	chr3L:11622590-11622695 +		1	ATGGATGACGTCAAGGTGAGTGGGTCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCATGGCTGACGAA---------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	chr3L:10995092-10995212 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGAG-CG--------------CA------CGG-GGGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	super_0:3809862-3809984 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	chr3L:11651195-11651318 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CA------CGAACCGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGACGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	scaffold_4784:11607138-11607238 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGACCGC-------------CA--TTTC-------------------------GAATT-------------CCCCTGTC--------------------------TGACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEug1	scf7180000409711:3494930-3495053 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGGACCGC-------------CA--CTTG-------------------------GAATT-------------CCCATGGCTATCAAAACGCT--AA-AGAACTTCATAACGCTCACTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droBia1	scf7180000302334:58069-58192 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGC-------------CA--TTCG-------------------------GAATT-------------CCCATGGCTATCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droTak1	scf7180000414445:587576-587697 -	LASTZ	5	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGG--CGT-------------CA--CTCG-------------------------GAATT-------------CCCCTGGCTAGCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTGCAGGACATAATCAGTAAA
droEle1	scf7180000490993:2183328-2183453 -	LASTZ	5	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGGGCGT-------------CA--TTCG-------------------------GAATT-------------CCCGTGGCAATCGAAACGCTATAA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droRho1	scf7180000777142:12217-12340 +	LASTZ	5	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGT-------------CA--TTTG-------------------------GAACT-------------CCCCTGTCAAACGAAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCGATTACAGGACATAATCAGTAAA
droFic1	scf7180000454113:3086558-3086682 -	LASTZ	5	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CT------TGGAGCGC------------CAT--TATC-------------------------GGATT-------------CCATTGGCAATCAAAGCGCT--AA-AGAACTTCATAACGCTCGCTCTGCTCTTTTCGATTTCAGGACATAATCAGTAAA
droKik1	scf7180000302391:1217462-1217584 -	LASTZ	5	ATGGATGACGTCAAGGTGAGTTCGGCT----------------------TGAACTGG-----A------AT---TCTA-------------------------GAATT-------------GACCTGACAATGGCAACGCT--AA-AGAACTTCATTACGCTCTGTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droAna3	scaffold_13337:5894397-5894534 +	LASTZ	5	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTT------GCAGCAAA------------GT---GCTG-------------------------GAACT-------------TAATAAGCTAATGAAACGCT--AA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droBip1	scf7180000396371:1230115-1230235 +	LASTZ	5	ATGGACGACGTCAAGGTGAGTTAGAAGAG------------GT------GCTGGTGCACCAAA------GC---TCTG-------------------------GAACT-------------TACTCA-----------GCT--AA-TGAACTTCATTACACTCTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	chrXR_group6:10064193-10064317 -	LASTZ	5	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGC------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	super_61:344655-344779 -	LASTZ	5	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGT------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	scaffold_180698:2114822-2114981 +	LASTZ	5	ATGGACGACGTAAAGGTGAGTGTAACA----------------------GCAC--TA----GTGTGTGTACG--CCTGTGCGTGTGTGTGTGTGTGTGTGCGTATATTTTCATG-------TAATTATCCAACG-ACCGCT--AATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	scaffold_13049:23825799-23825928 +	LASTZ	5	ATGAATGATGTCAAGGTGAGTGCGCGG--------------CG------CGGCGGCT-------------GCTTCTTA-------------------------ATAAT-TGAT--------GAATTGACAATCTTATCGTT--AA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	scaffold_6680:18448682-18448807 +	LASTZ	5	ATGAACGACGTGAAGGTGAGTGAGCGG------------AATG------CTGAACTG-------------AA--TTTA-------------------------TTGAT-------------GAATTGACAATCTTATCGTT--AA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	scaffold_15110:13832957-13833097 -	LASTZ	5	ATGAGCGATGTAAAGGTGAGTTCGGAGCGT---------TATTCTAGTTGATTGTGT------------TTA---------------------------------ATTTTTATATATTTGGCAATTGTTAATCAATTCGTT--AA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

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	ATGGATGACGTCAAGGTGAGTGGGTCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCATGGCTGACGAA---------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	ATGGATGACGTCAAGGTGAGTGAG-CG--------------CA------CGG-GGGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CA------CGAACCGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGACGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGACCGC-------------CA--TTTC-------------------------GAATT-------------CCCCTGTC--------------------------TGACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEug1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGGACCGC-------------CA--CTTG-------------------------GAATT-------------CCCATGGCTATCAAAACGCT--AA-AGAACTTCATAACGCTCACTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droBia1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGC-------------CA--TTCG-------------------------GAATT-------------CCCATGGCTATCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droTak1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGG--CGT-------------CA--CTCG-------------------------GAATT-------------CCCCTGGCTAGCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTGCAGGACATAATCAGTAAA
droEle1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGGGCGT-------------CA--TTCG-------------------------GAATT-------------CCCGTGGCAATCGAAACGCTATAA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droRho1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGT-------------CA--TTTG-------------------------GAACT-------------CCCCTGTCAAACGAAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCGATTACAGGACATAATCAGTAAA
droFic1	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CT------TGGAGCGC------------CAT--TATC-------------------------GGATT-------------CCATTGGCAATCAAAGCGCT--AA-AGAACTTCATAACGCTCGCTCTGCTCTTTTCGATTTCAGGACATAATCAGTAAA
droKik1	ATGGATGACGTCAAGGTGAGTTCGGCT----------------------TGAACTGG-----A------AT---TCTA-------------------------GAATT-------------GACCTGACAATGGCAACGCT--AA-AGAACTTCATTACGCTCTGTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droAna3	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTT------GCAGCAAA------------GT---GCTG-------------------------GAACT-------------TAATAAGCTAATGAAACGCT--AA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droBip1	ATGGACGACGTCAAGGTGAGTTAGAAGAG------------GT------GCTGGTGCACCAAA------GC---TCTG-------------------------GAACT-------------TACTCA-----------GCT--AA-TGAACTTCATTACACTCTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGC------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGT------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	ATGGACGACGTAAAGGTGAGTGTAACA----------------------GCAC--TA----GTGTGTGTACG--CCTGTGCGTGTGTGTGTGTGTGTGTGCGTATATTTTCATG-------TAATTATCCAACG-ACCGCT--AATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	ATGAATGATGTCAAGGTGAGTGCGCGG--------------CG------CGGCGGCT-------------GCTTCTTA-------------------------ATAAT-TGAT--------GAATTGACAATCTTATCGTT--AA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	ATGAACGACGTGAAGGTGAGTGAGCGG------------AATG------CTGAACTG-------------AA--TTTA-------------------------TTGAT-------------GAATTGACAATCTTATCGTT--AA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	ATGAGCGATGTAAAGGTGAGTTCGGAGCGT---------TATTCTAGTTGATTGTGT------------TTA---------------------------------ATTTTTATATATTTGGCAATTGTTAATCAATTCGTT--AA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

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

ATGGATGACGTCAAGGTGAGTGAG-CG--------------CA------CGG-GGGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................................................................................................................CTGGCTGAGCAACCGCT--A--......................................................	18	1	2.00	0.00	2.00	0.00	0.00
........................................................................................................................................ACGCT--A--AGAACTTCATTACG........................................	20	1	2.00	0.00	2.00	0.00	0.00

droSec1

ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......GACAGCAAGGTGAGTGAGGC..............................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00
...............GTGAGTGAGGCG--------------CA------CGGAGCGT-------------..................................................................................................................................	22	1	1.00	1.00	0.00	0.00
.TGGATGACGTCAAGGACA.....................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........AGCAAGGTGAGTGAGGCG--------------...............................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

ATGGATGACGTCAAGGTGAGTGCGGCG--------------CA------CGAACCGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGACGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....ATGACGTAAAGGTGAATGC.................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGACCGC-------------CA--TTTC-------------------------GAATT-------------CCCCTGTC--------------------------TGACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................................................AATCACAGGACATCATCA.....	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................CACGCTGCTCTTTCCAAT....................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................................ATTACxGGAAATAATCAGT...	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGGACCGC-------------CA--CTTG-------------------------GAATT-------------CCCATGGCTATCAAAACGCT--AA-AGAACTTCATAACGCTCACTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droBia1

ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGC-------------CA--TTCG-------------------------GAATT-------------CCCATGGCTATCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droTak1

ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGG--CGT-------------CA--CTCG-------------------------GAATT-------------CCCCTGGCTAGCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTGCAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droEle1

ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGGGCGT-------------CA--TTCG-------------------------GAATT-------------CCCGTGGCAATCGAAACGCTATAA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droRho1

ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGT-------------CA--TTTG-------------------------GAACT-------------CCCCTGTCAAACGAAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCGATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droFic1

ATGGATGACGTCAAGGTGAGTGCGGCG--------------CT------TGGAGCGC------------CAT--TATC-------------------------GGATT-------------CCATTGGCAATCAAAGCGCT--AA-AGAACTTCATAACGCTCGCTCTGCTCTTTTCGATTTCAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droKik1

ATGGATGACGTCAAGGTGAGTTCGGCT----------------------TGAACTGG-----A------AT---TCTA-------------------------GAATT-------------GACCTGACAATGGCAACGCT--AA-AGAACTTCATTACGCTCTGTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

droAna3

ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTT------GCAGCAAA------------GT---GCTG-------------------------GAACT-------------TAATAAGCTAATGAAACGCT--AA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................ATGAAGTGGAGGAGGGG..................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..........................GCGGTGGxGGGGGTGTT------GC.....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......ACGTAAAGGTGAxTAAGAA..............................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................GGGGTGGAGGGGGGGT..............................................................................................................................................................	16	1	1.00	0.00	0.00	1.00	0.00

droBip1

ATGGACGACGTCAAGGTGAGTTAGAAGAG------------GT------GCTGGTGCACCAAA------GC---TCTG-------------------------GAACT-------------TACTCA-----------GCT--AA-TGAACTTCATTACACTCTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

dp4

ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGC------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........GAAGGTGAGTTGGGTG--------------CT------.......................................................................................................................................................	18	1	3.00	1.00	0.00	0.00	2.00
...........GAAGGTGAGTTGGGTG--------------CT------G......................................................................................................................................................	19	1	3.00	3.00	0.00	0.00	0.00
.............AGGTGAGTTGGGTG--------------CT------GC.....................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CT------GC.....................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
............AAGGTGAGTTGGGTG--------------CT------GC.....................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................G--------------CT------GCACGTGC------------CCG--CTTG-------------------------AGACT-------------...............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
ATGGACGACGTGAAGGAC......................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
............AAGGTGAGTTGGGTG--------------CT------G......................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...........GAGGGTGAGTTGGGCG--------------CT------.......................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGT------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........GAAGGTGAGTTGGGTG--------------CT------.......................................................................................................................................................	18	1	9.00	9.00	0.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CT------GC.....................................................................................................................................................	20	1	2.00	2.00	0.00	0.00	0.00	0.00
...........GAGGGTGAGTTGGGCG--------------CT------.......................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CT------G......................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
...............................................................................................................................................GA-AGAACTTCAATACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..........TGAAGGTGAGTTGGGTG--------------CT------G......................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................................................................................................GA-AGAACTTCATTACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........GAAGGTGAGTTGGGCG--------------CT------GC.....................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................................................................GA-AGAACTTCACTACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
............AAGGGGAGTGGGGGG--------------CT------G......................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATGGACGACGTAAAGGTGAGTGTAACA----------------------GCAC--TA----GTGTGTGTACG--CCTGTGCGTGTGTGTGTGTGTGTGTGCGTATATTTTCATG-------TAATTATCCAACG-ACCGCT--AATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................................................GTGTGCGTCTGTGTGTGTGTGT.......................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
............................................................................TGTGCGTATATGTGTGTGTGT.......................................................................................................	21	7	1.57	0.29	1.29	0.00	0.00
............................................................................TGTGTGTGTGTGTGTGTGTGTGTGC...................................................................................................	25	33	0.24	0.00	0.00	0.24	0.00
.............................................................................GTGTGTGTGTGTGTGTGTGTGTGC...................................................................................................	24	35	0.20	0.00	0.03	0.17	0.00
............................................................................TGTGCGTATATGTGTGTGTG........................................................................................................	20	9	0.78	0.00	0.78	0.00	0.00
............................................................................TGTGTGTGTGTGTGTGTGTGTGTGCG..................................................................................................	26	24	0.29	0.00	0.00	0.29	0.00
............................................................................TGTGCGTATATGTGTGTGTGTG......................................................................................................	22	6	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................CATCG-ACCGCT--AATGGAA..................................................	18	1	5.00	0.00	5.00	0.00	0.00
..............................................................................TGCGTATATGTGTGTGTGTG......................................................................................................	20	12	0.42	0.00	0.42	0.00	0.00
.............................................................................GTGCGTGTGTGTGTGTGT.........................................................................................................	18	89	0.06	0.00	0.06	0.00	0.00
...........................................................................TTGTGTGTGTGTGTGTGTGTGTGTGC...................................................................................................	26	39	0.10	0.00	0.00	0.10	0.00
...........................................................................ATGTGTGTGTGTGTGTGTGTGTGTGC...................................................................................................	26	38	0.11	0.00	0.00	0.11	0.00
...............................................................................GCCAGTGTGTGTGTGTGTG......................................................................................................	19	16	0.19	0.00	0.13	0.06	0.00
..................................................................................TATGTGTGTGTGTGGGTGCG..................................................................................................	20	9	0.33	0.11	0.00	0.22	0.00
..............................................................................TGCGTATATGTGTGTGTGTGT.....................................................................................................	21	12	0.25	0.00	0.25	0.00	0.00
..............................................................................TGTGTGTGTGTGTGTGTGTGTGC...................................................................................................	23	44	0.07	0.00	0.02	0.05	0.00
...........................................................................GTGTGCGTGTGTGTGTGTGTGTGCGC...................................................................................................	26	4	0.75	0.00	0.75	0.00	0.00
....................................................................................TGTGTGTGTGTGTGTGCA..................................................................................................	18	24	0.13	0.00	0.04	0.08	0.00
.............................................................................GTGCGTGTGCCTGTGTGT.........................................................................................................	18	5	0.60	0.00	0.60	0.00	0.00
...........................................................................GTGTGCGTGTGTGTGTCTGTGTG......................................................................................................	23	36	0.08	0.00	0.08	0.00	0.00
.............................................................................GTGCGTATGCGTGTGTGTGTG......................................................................................................	21	6	0.50	0.00	0.00	0.50	0.00
.............................................................................GTGTGTGTGTGTGTGTGTGTGTGCG..................................................................................................	25	26	0.12	0.00	0.00	0.12	0.00
...............................................................................GTGTGTGTGTGTGTGTGTGTGC...................................................................................................	22	49	0.06	0.00	0.04	0.02	0.00
...........................................................................CTGTGCATGTGTTTGTGTGT.........................................................................................................	20	2	1.50	0.50	1.00	0.00	0.00
..................................................................................TGTGTGTATGTGTGTGTGCA..................................................................................................	20	26	0.12	0.00	0.12	0.00	0.00
.......................................................................G--CCAGTGTGTGTGTGTGTG............................................................................................................	19	16	0.19	0.00	0.13	0.06	0.00
..............................................................................TGCCTGTGTTTGTGTGTGTGTG....................................................................................................	22	6	0.50	0.00	0.17	0.33	0.00

droVir3

ATGAATGATGTCAAGGTGAGTGCGCGG--------------CG------CGGCGGCT-------------GCTTCTTA-------------------------ATAAT-TGAT--------GAATTGACAATCTTATCGTT--AA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................................................................AT-TGAT--------GAATTGACAAACTG.................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

ATGAACGACGTGAAGGTGAGTGAGCGG------------AATG------CTGAACTG-------------AA--TTTA-------------------------TTGAT-------------GAATTGACAATCTTATCGTT--AA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ATGAGCGATGTAAAGGTGAGTTCGGAGCGT---------TATTCTAGTTGATTGTGT------------TTA---------------------------------ATTTTTATATATTTGGCAATTGTTAATCAATTCGTT--AA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:33 EDT

dme-mir-3642

chr3L:11622605-11622680 +

Known_mirbase

tailed_mirtron

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