dme-mir-1005- Best orthologs

dme-mir-1005	chr2L:4343696-4343756 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 4343736-4343756
   star strand at position 4343696-4343718
   mutations
   read mismatches

Notes: "lastz seems to be finding better orthologs than what is reported in multiz (droAna- droGri); however, these are all wrong. droMoj3 ortholog lies in the coding region. droVir3 intron is long and lastz cannot span the large region. "

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:4343681-4343771 +		1	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACGAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droSim1	chr2L:4265544-4265633 +	LASTZ	1	CTACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGTTTTTGG-CC-ACAAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droSec1	super_5:2441095-2441185 +	LASTZ	1	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACAAAT----------------------------------------G---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droYak2	chr2L:4375638-4375728 +	LASTZ	1	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droEre2	scaffold_4929:4420541-4420630 +	LASTZ	1	CCACCATTCTGACCTGTGAGTT--CA-TCGA-TTTCGAGGTTT-GC-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droEug1	scf7180000409554:1722173-1722263 -	LASTZ	4	CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CTCTTAGAA----------------------------------------A---------CAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droBia1	scf7180000302261:2802460-2802551 +	LASTZ	4	CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGGGGTTTTTGGCTGCCTTCA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droTak1	scf7180000414050:34777-34868 -	LASTZ	4	CCACCATTCTGACCTGTGAGTT--GT-GAGA-TTTCATGGTTCCTTTCGGTCATTT----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTCCCCACCGAAATGT
droEle1	scf7180000490458:268801-268894 +	LASTZ	4	CTACCATTCTGACCTGTGAGTT--TA-TGGA-TTTCCAAGTTTTTT-TGA-CATTTTACA------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT
droRho1	scf7180000778291:9908-9998 -	LASTZ	4	CCACCATCCTCACCTGTGAGTT--GA-TCGA-TTTCGAGGTTGTGG-CATCTAACA----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT
droFic1	scf7180000453904:1262363-1262454 -	LASTZ	4	CCACCATCCTGACCTGTGGGTT--GA-TCGA-TTTCGAGGTTGCGGGTTGGCGCTT----------------------------------------C---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAGATGT
droKik1	scf7180000302570:979763-979851 -	LASTZ	5	CAGTGTTGCTGTACTGTGAGTT--GA-AAAT-CCTTGAGGATCTTG-ATACCTTAA----------------------------------------T---------CTAGCAGAATTCT-CT--TTCTTAGTTCCCTCGGAAATCA
droAna3	scaffold_12916:13781299-13781395 -	LASTZ	5	TAACGGTTTTGACTTGTAAGAA--CC-AAAA-CTAC---TTTCTGT--A-TCAAAG---------------------------------CCAGAAACTAATCG---TAAT-TGA-AATT-ATCTTAACCAGTCCCCATTGAGCTGT
droBip1	scf7180000396728:639360-639449 +	LASTZ	5	TAACGATTCTCTCATGTAAGCGGTGT-TAGA-TTCCGAC-TGGTTC-TTC-CGTATAATA------------------------------------A---------CTCTTT---GTAT-CCA--TTTCAGTCCCGCTCGAGATGC
dp4	chr4_group2:339129-339252 +	LASTZ	5	CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT
droPer1	super_8:3550415-3550538 -	LASTZ	5	CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT
droWil1	scaffold_180772:1844874-1844969 -	LASTZ	5	TTACAATTCTATCATGTAAGTT--AAAACGA-TTAAGTAATTTCAC--ACTTACAT------------------------------------ATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC
droVir3	Unknown	MAF	5	CAGTGGTATTGACCTGTAAGTA---------------------------------------------------------------------------------------TGTTGAATTT-TCTTACTGCAGTTCCGCTGGAGATCG
droMoj3	scaffold_6500:22625692-22625724 +	MAF	5	CCTCCATATTGCTCTGCGTGCA--AG-ATGC-GCCCG-------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:16827853-16827948 -	LASTZ	5	CCACCATTCTGACATGTAACC----A-CTGA-TCCTGATCCTT-GA-TT-GCACTG---------------------------------CCCATTTTGAATGCGTTTTC-------TTT-CTGCTTTGCAGTTCCCACGGAAATGG

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	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACGAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droSim1	CTACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGTTTTTGG-CC-ACAAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droSec1	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACAAAT----------------------------------------G---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droYak2	CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droEre2	CCACCATTCTGACCTGTGAGTT--CA-TCGA-TTTCGAGGTTT-GC-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droEug1	CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CTCTTAGAA----------------------------------------A---------CAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droBia1	CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGGGGTTTTTGGCTGCCTTCA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT
droTak1	CCACCATTCTGACCTGTGAGTT--GT-GAGA-TTTCATGGTTCCTTTCGGTCATTT----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTCCCCACCGAAATGT
droEle1	CTACCATTCTGACCTGTGAGTT--TA-TGGA-TTTCCAAGTTTTTT-TGA-CATTTTACA------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT
droRho1	CCACCATCCTCACCTGTGAGTT--GA-TCGA-TTTCGAGGTTGTGG-CATCTAACA----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT
droFic1	CCACCATCCTGACCTGTGGGTT--GA-TCGA-TTTCGAGGTTGCGGGTTGGCGCTT----------------------------------------C---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAGATGT
droKik1	CAGTGTTGCTGTACTGTGAGTT--GA-AAAT-CCTTGAGGATCTTG-ATACCTTAA----------------------------------------T---------CTAGCAGAATTCT-CT--TTCTTAGTTCCCTCGGAAATCA
droAna3	TAACGGTTTTGACTTGTAAGAA--CC-AAAA-CTAC---TTTCTGT--A-TCAAAG---------------------------------CCAGAAACTAATCG---TAAT-TGA-AATT-ATCTTAACCAGTCCCCATTGAGCTGT
droBip1	TAACGATTCTCTCATGTAAGCGGTGT-TAGA-TTCCGAC-TGGTTC-TTC-CGTATAATA------------------------------------A---------CTCTTT---GTAT-CCA--TTTCAGTCCCGCTCGAGATGC
dp4	CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT
droPer1	CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT
droWil1	TTACAATTCTATCATGTAAGTT--AAAACGA-TTAAGTAATTTCAC--ACTTACAT------------------------------------ATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC
droVir3	CAGTGGTATTGACCTGTAAGTA---------------------------------------------------------------------------------------TGTTGAATTT-TCTTACTGCAGTTCCGCTGGAGATCG
droMoj3	CCTCCATATTGCTCTGCGTGCA--AG-ATGC-GCCCG-------------------------------------------------------------------------------------------------------------
droGri2	CCACCATTCTGACATGTAACC----A-CTGA-TCCTGATCCTT-GA-TT-GCACTG---------------------------------CCCATTTTGAATGCGTTTTC-------TTT-CTGCTTTGCAGTTCCCACGGAAATGG

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

CTACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGTTTTTGG-CC-ACAAAT----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................................TCTGGAATCT-TTAATTCGCAG...............	21	1	196.00	5.00	115.00	15.00	61.00
.............................................................................................................TCTGGAATCT-TTAATTCGC.................	19	1	37.00	0.00	37.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGT..............	22	1	13.00	0.00	9.00	0.00	4.00
.............................................................................................................TCTGGAATCT-TTAATTCGCA................	20	1	10.00	0.00	9.00	0.00	1.00
...............GTGAGTT--GA-TCGA-TTTCGAGTT.........................................................................................................	22	1	7.00	1.00	0.00	0.00	6.00
.............................................................................................................TCTGGAATCT-TTAATTCGCT................	20	1	3.00	0.00	3.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGG..............	22	1	3.00	0.00	0.00	0.00	3.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAC...............	21	1	3.00	0.00	2.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGA..............	22	1	2.00	1.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTA.............	23	1	2.00	0.00	1.00	0.00	1.00
.............................................................................................................TCTGGAATTT-TTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAA...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGTAATCT-TTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGGATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCCCA................	20	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCGG...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTT.............	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTCGAATCT-TTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTAGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
..................AGTT--GA-TCGA-TTTCGAGTTTTTGG-C..................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATAT-TTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGA.................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCG..................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGC..............	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CACACAAAT----------------------------------------G---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................................................................TCTGGAATCT-TTAATTCGCAG...............	21	1	309.00	25.00	161.00	123.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGT..............	22	1	45.00	8.00	26.00	11.00
...............GTGAGTT--GA-TCGA-TTTCGAGGTT........................................................................................................	23	1	43.00	1.00	38.00	4.00
.............................................................................................................TCTGGAATCT-TTAATTCGCA................	20	1	28.00	2.00	13.00	13.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGA..............	22	1	19.00	1.00	7.00	11.00
.............................................................................................................TCTGGAATCT-TTAATTCGC.................	19	1	12.00	0.00	0.00	12.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTT.............	23	1	9.00	5.00	1.00	3.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTA.............	23	1	6.00	1.00	1.00	4.00
...............GTGAGTT--GA-TCGA-TTTCGAGGT.........................................................................................................	22	1	4.00	0.00	4.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCG..................	18	1	3.00	0.00	0.00	3.00
.............................................................................................................TCTAGAATCT-TTAATTCGCAG...............	21	1	2.00	0.00	2.00	0.00
.............................................................................................................TTTGGAATCT-TTAATTCGCAGT..............	22	1	2.00	0.00	2.00	0.00
.............................................................................................................CCTGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTTGCAG...............	21	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCCCA................	20	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTGATTCGC.................	19	1	1.00	0.00	0.00	1.00
.................GAGTT--GA-TCGA-TTTCGAGGT.........................................................................................................	20	1	1.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATCCGCAG...............	21	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCCCAG...............	21	1	1.00	0.00	0.00	1.00
..............................................................................................................CTGGAATCT-TTAATTCGCAGT..............	21	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGCAATCT-TTAATTCGCAGT..............	22	1	1.00	1.00	0.00	0.00
............................................................................................................CTCTGGAATCT-TTAATTCGCAGT..............	23	1	1.00	0.00	0.00	1.00
...............GTGAGTT--GA-TCGA-TTTCGAGG..........................................................................................................	21	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGC..............	22	1	1.00	0.00	1.00	0.00
...............GTGAGTT--GA-TCGA-TTTCGAGATT........................................................................................................	23	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-ATAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00
.............................................................................................................TCCGGAATCT-TTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00
.............................................................................................................TCTGCAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCTCAGA..............	22	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-CTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00
...............GTGAGTT--GA-TTGA-TTTCGAGGTT........................................................................................................	23	1	1.00	0.00	1.00	0.00
...............GTGAGTT--GA-CCGA-TTTCGAGGTTT.......................................................................................................	24	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTTGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.............................................................................................................TCTGTAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
...............GTGAGTT--GA-TCGA-TTTCGAG...........................................................................................................	20	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTACTTCGCAG...............	21	1	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCC-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00

droYak2

CCACCATTCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.............................................................................................................TCTGGAATCT-TTAATTCGCAG...............	21	1	579.00	18.00	79.00	9.00	234.00	239.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGT..............	22	1	135.00	7.00	25.00	24.00	55.00	24.00
.............................................................................................................TCTGGAATCT-TTAATTCGC.................	19	1	73.00	0.00	12.00	0.00	25.00	36.00
.............................................................................................................TCTGGAATCT-TTAATTCGCA................	20	1	73.00	0.00	4.00	8.00	41.00	20.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTT.............	23	1	42.00	5.00	5.00	7.00	19.00	6.00
...............GTGAGTT--GA-TCGA-TTTCGAGGTT........................................................................................................	23	1	13.00	5.00	0.00	1.00	1.00	6.00
.............................................................................................................TCTGGAATCT-TTAATTCGCCG...............	21	1	12.00	1.00	1.00	0.00	7.00	3.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGA..............	22	1	11.00	0.00	1.00	2.00	6.00	2.00
.............................................................................................................TCTGGGATCT-TTAATTCGCAG...............	21	1	6.00	1.00	2.00	0.00	3.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCG..................	18	1	5.00	0.00	0.00	0.00	0.00	5.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAC...............	21	1	5.00	0.00	0.00	0.00	0.00	5.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGC..............	22	1	3.00	0.00	0.00	0.00	1.00	2.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTA.............	23	1	3.00	1.00	1.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAT...............	21	1	3.00	0.00	2.00	0.00	1.00	0.00
.............................................................................................................CCTGGAATCT-TTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCTCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
...............GTGAGTT--GA-TCGA-TTTCGAGG..........................................................................................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGAATCT-TTAATTCACAG...............	21	1	2.00	1.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAA...............	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGTATAT-TTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................TCTGGAGTCT-TTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.............................................................................................................TCCGGAATCT-TTAATTCGCAG...............	21	1	2.00	1.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCGG...............	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGAATTT-TTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	1.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGG..............	22	1	2.00	0.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGCATCT-TTAATTCGCAG...............	21	1	2.00	0.00	1.00	0.00	1.00	0.00
.............................................................................................................TATGGAATCT-GTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTT--GA-TCGA-TTTCGAGGTTT.......................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TCACTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTGATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATCCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTGGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TGAATTCGAAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGGATCT-TTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................CTGGACTCT-TTAATTCGCGGT..............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................................CTGGAATCT-TTAATTCGCA................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCGGGGATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TGAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TATGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGTAG...............	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGCATCT-TGAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GTGAGTT--GA-TCGA-TTTCGAGGT.........................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCTCAGTT.............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................GCTGGAATCT-TTAATGCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAACCT-TTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-CTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTCGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTCATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTGATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TTTGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCGGGAATCT-TTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGACTCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCC................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTCATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTCATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCT................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTT--GA-TCGA-TTTCGAGGC.........................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TATGGAATCT-GTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCATGT.............	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCG................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TCAATTCGCAT...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TGTGGGATCT-TTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTT--GA-CCGA-TTTCGAGAT.........................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................CTGGAATCT-TTAATTCGCAGT..............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCTC.................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAAGCT-TTAAGTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATAT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCGGGAATCT-TGAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCGGGCATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGCATCT-TTAATTCGCCG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TATTGAATCT-TTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTT--CA-TCCA-TTTCGAGGTT........................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGCATCT-TTATTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGAAATCT-TTAATTCTCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TCAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTC.............	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................ACTGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGGATCT-TTAATTCGCTGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATACGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAACTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-GTAATTCGCT................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TTTGTAATCT-TTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTAGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCTCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTG.............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-GTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGACG...............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATGCGTAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATAT-TTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGCCTTT.............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCTCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................TCGGGAATCT-GTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CCACCATTCTGACCTGTGAGTT--CA-TCGA-TTTCGAGGTTT-GC-CAGCCAAAA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................................TCTGGAATCT-TTAATTCGCAG...............	21	1	132.00	4.00	19.00	0.00	109.00
...............GTGAGTT--CA-TCGA-TTTCGAGGTT........................................................................................................	23	1	14.00	6.00	0.00	0.00	8.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGT..............	22	1	13.00	0.00	3.00	0.00	10.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGA..............	22	1	10.00	0.00	2.00	0.00	8.00
.............................................................................................................TCTGGAATCT-TTAATTCGCA................	20	1	7.00	0.00	4.00	0.00	3.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAGTT.............	23	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGAATCT-TTAATTCGC.................	19	1	2.00	0.00	0.00	0.00	2.00
.............................................................................................................TCTGGCATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCCGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAGTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTT--AA-TCGA-TTTCGAGGTT........................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCGCAT...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TATGGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATAT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTT--CA-TCGA-TTTCGA............................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGCAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCTCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAATTCGAAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCT-TTAATTCACAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTGGAATCC-TTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCTTGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TCCTGAATCT-TTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................TTTGGGATCT-TTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................................TCTGGAATCT-TTAAxTCGC.................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGAGGTTTTGG-CTCTTAGAA----------------------------------------A---------CAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT

Size

Hit Count

Total Norm

droBia1

CCACCATCCTGACCTGTGAGTT--GA-TCGA-TTTCGGGGTTTTTGGCTGCCTTCA----------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACCGAAATGT

Size

Hit Count

Total Norm

droTak1

CCACCATTCTGACCTGTGAGTT--GT-GAGA-TTTCATGGTTCCTTTCGGTCATTT----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTCCCCACCGAAATGT

Size

Hit Count

Total Norm

droEle1

CTACCATTCTGACCTGTGAGTT--TA-TGGA-TTTCCAAGTTTTTT-TGA-CATTTTACA------------------------------------A---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

droRho1

CCACCATCCTCACCTGTGAGTT--GA-TCGA-TTTCGAGGTTGTGG-CATCTAACA----------------------------------------T---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

droFic1

CCACCATCCTGACCTGTGGGTT--GA-TCGA-TTTCGAGGTTGCGGGTTGGCGCTT----------------------------------------C---------TAATCTGGAATCT-TTAATTCGCAGTTCCCACTGAGATGT

Size

Hit Count

Total Norm

droKik1

CAGTGTTGCTGTACTGTGAGTT--GA-AAAT-CCTTGAGGATCTTG-ATACCTTAA----------------------------------------T---------CTAGCAGAATTCT-CT--TTCTTAGTTCCCTCGGAAATCA

Size

Hit Count

Total Norm

droAna3

TAACGGTTTTGACTTGTAAGAA--CC-AAAA-CTAC---TTTCTGT--A-TCAAAG---------------------------------CCAGAAACTAATCG---TAAT-TGA-AATT-ATCTTAACCAGTCCCCATTGAGCTGT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

TAACGATTCTCTCATGTAAGCGGTGT-TAGA-TTCCGAC-TGGTTC-TTC-CGTATAATA------------------------------------A---------CTCTTT---GTAT-CCA--TTTCAGTCCCGCTCGAGATGC

Size

Hit Count

Total Norm

dp4

CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CCACCATTTTGACATGTAAGTG--TC-CATATCCTCGAGGCTCCTG-CAA-TGCACTGCAATGCACTGCAATGACCGCAATGCTGACGT-------A---------TTATTTATGTTCT-CCGATCCCCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TTACAATTCTATCATGTAAGTT--AAAACGA-TTAAGTAATTTCAC--ACTTACAT------------------------------------ATATT---------TATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CAGTGGTATTGACCTGTAAGTA---------------------------------------------------------------------------------------TGTTGAATTT-TCTTACTGCAGTTCCGCTGGAGATCG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CCTCCATATTGCTCTGCGTGCA--AG-ATGC-GCCCG-------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CCACCATTCTGACATGTAACC----A-CTGA-TCCTGATCCTT-GA-TT-GCACTG---------------------------------CCCATTTTGAATGCGTTTTC-------TTT-CTGCTTTGCAGTTCCCACGGAAATGG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:22:12 EDT

dme-mir-1005

chr2L:4343696-4343756 +

Known_mirbase

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