dme-mir-983-1- Best orthologs

dme-mir-983-1	chrX:4262342-4262432 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 4262394-4262415
   star strand at position 4262358-4262379
   mutations
   read mismatches

Notes: This is in a cluster with 983-2. droYak2 is confidently loss.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:4262327-4262447 -		1	ATATGCATATGCTATT--ATA-------------------------------------------TTGCAATAATTAAATAATAC-GT----------TTCGAACTA----------ATG-ATTTTCAGT---TCATTCATTAGGTAGTTACG---------------------------------------CATTATCTAGTTGTTGTAAACATTCAACTCGCTGGC-GTA
droSim1	chrX:3277334-3277447 -	LASTZ	1	TGCA---TA---TGAT--ATC-------------------------------------------TTGCAGTAATTTAGTAATAC-CT----------TTCGAACAC----------ATG-ATTTTCAG----TCATTCATGAGTTCGTCAGG---------------------------------------TATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA
droSec1	super_4:2462215-2462328 +	LASTZ	1	TGCA---TA---TGAT--ATG-------------------------------------------TTGCAGTAATTTAGTAATAC-CT----------TTCGAACAT----------ATG-ATTTTCAG----TCATTCATGAGTTCGTTAGG---------------------------------------TATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA
droYak2	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:1633112-1633231 -	LASTZ	1	GGAATTGTGTGATATT--ATG-------------------------------------------TTACAGTGATTTAATAATTC-GA----------TTCGAAGTT----------ATG-TGCTTTAA----TCATTCATAAATGCGAAACG---------------------------------------GATTATTAAGTTATTGTTAACATTCAACTCGTTGGC-GTG
droEug1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301703:495454-495597 +	LASTZ	0	TTATA-------AAAG--GTTTTTCATTATTAAATTAAGGGTACATATTGCCATCTTAAATTGTGTGT--------AGT------GT----------TTCAAACGC----------A----TTTCCAA----TCATTAGAAAGTTCGTTACGTACTATTTGCTCGGTTTAAAAA-CAAATAGTACGTG----------------------------------TCGGA-TTT
droTak1	scf7180000415394:1160785-1160886 +	LASTZ	0	AAAGG----------A--AAT-------------------------------------------TTCCAATCATTTAATAGTCC-GA----------TTCGTTCTT----------A-----------------------------------------GTGCTTATTTTGAAAATGCAGTAGTGCGTTTCGGATTATTCAATTATTGTTAACAAACATC------------
droEle1	scf7180000491011:2112374-2112507 +	LASTZ	0	CGACATACATACATAC--ATA-------------------------------------------TTACAAAAAATATATAATAA-AG----------TGAATAGATATAAAAACAAGTGAATTTTCAAGTTCTCTTTTAACATTTTGTTGAC---TATGCACTCCTTTTTAAAATCAACTTGTTCGCA----------------------------------TT----GTC
droRho1	scf7180000779334:415671-415796 +	LASTZ	0	ATCTGC------TTAAAAGTT-------------------------------------------GTGTAGTTGTATAGTAACAT-ATCATAAGTTGCTCCTAAAAT----------ATT-AGTTTTAG----ATATCTATTACCTAATCAAT---------------------------------------ATTAAAATAGTTCGAATTAATAAATAGCACACTGCT-TAG
droFic1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:31109889-31110001 -	LASTZ	0	AACAACGTATGTTACT--ATA-------------------------------------------TTAAAATAACTAAATAATTAAAA----------CCAAAACCT----------ATC-AATTTAA-----TCAAT----AAA-CGAAATT---------------------------------------TGTTATCTAGCT---TTAAGTACTTGAAAAGCTCATGATA
droGri2	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	ATATGCATATGCTATTATATTGCAATAATTAAATAATACGTTTCGAACTAATGATTTTCAGTTCATTCATTAGGTAGTTACGCATTATCTAGTTGTTGTAAACATTCAACTCGCTGGCGTA
droSim1	---TGCATATGA---TATCTTGCAGTAATTTAGTAATACCTTTCGAACACATGATTTTCAG-TCATTCATGAGTTCGTCAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGCGGA
droSec1	---TGCATATGA---TATGTTGCAGTAATTTAGTAATACCTTTCGAACATATGATTTTCAG-TCATTCATGAGTTCGTTAGGTATTATCTAGTTATTGTAAACATTCAACTCGCTGGCGGA
droEre2	GGAATTGTGTGATATTATGTTACAGTGATTTAATAATTCGATTCGAAGTTATGTGCTTTAA-TCATTCATAAATGCGAAACGGATTATTAAGTTATTGTTAACATTCAACTCGTTGGCGTG

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image				None		None					None	None	None	None	None	None	None	None		None
UNAFold Image				None		None					None	None	None	None	None	None	None	None		None

Small RNA-seq read pileup

Species

Alignment

droSim1

TGCA---TA---TGAT--ATC-------------------------------------------TTGCAGTAATTTAGTAATAC-CT----------TTCGAACAC----------ATG-ATTTTCAG----TCATTCATGAGTTCGTCAGG---------------------------------------TATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCT................................	22	4	430.75	0.00	25.00	307.25	98.50
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATC.................................	21	4	110.50	0.25	6.25	88.25	15.75
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCT................................	21	4	106.50	0.50	6.75	85.00	14.25
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTA...............................	22	4	51.50	0.25	1.25	33.00	17.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCC................................	22	4	20.50	0.00	1.75	13.75	5.00
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-A..............................................................................................................	23	3	20.33	1.67	0.67	9.33	8.67
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-...............................................................................................................	22	3	18.67	2.67	0.67	14.33	1.00
............................................................................AGTAATAC-CT----------TTCGAACAC----------AT.................................................................................................................	21	3	14.00	0.00	3.00	9.00	2.00
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATC.................................	20	4	10.25	0.25	1.00	7.75	1.25
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTAA..............................	23	4	7.75	0.00	0.00	4.00	3.75
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------GATTATCT................................	22	4	7.75	0.00	0.25	6.75	0.75
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCG................................	22	4	6.00	0.00	0.50	4.00	1.50
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCC................................	21	4	4.75	0.00	0.75	2.75	1.25
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-AAA............................................................................................................	25	3	5.67	0.33	0.00	3.33	2.00
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-G..............................................................................................................	23	3	5.33	0.00	0.00	4.00	1.33
............................................................................AGTAATAC-CT----------TTCGAACAC----------A..................................................................................................................	20	3	4.67	0.00	0.67	4.00	0.00
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTAT..............................	23	4	3.25	0.25	0.25	2.25	0.50
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCTT...............................	23	4	3.00	0.00	0.00	3.00	0.00
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-T..............................................................................................................	23	3	3.67	0.00	0.00	3.33	0.33
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCTA...............................	23	4	2.50	0.00	0.00	2.25	0.25
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-AT.............................................................................................................	24	3	2.67	0.00	0.67	2.00	0.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------AATTATCT................................	22	4	1.75	0.00	0.00	1.75	0.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------GATTATC.................................	21	4	1.75	0.00	0.00	1.75	0.00
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTAAA.............................	24	4	1.25	0.00	0.00	1.00	0.25
............................................................................AGTAATAC-CT----------TTCGAACAC----------ATG-AA.............................................................................................................	24	3	1.67	0.00	0.00	1.00	0.67
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCA................................	22	4	1.25	0.00	0.00	1.25	0.00
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCG................................	21	4	1.25	0.00	0.00	0.75	0.50
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------GATTATCT................................	21	4	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTAT..................................	20	4	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................TGATTTCGTCAGG---------------------------------------TATTATCT................................	21	4	1.00	0.00	0.00	0.25	0.75
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATCTTT..............................	24	4	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATT....................................	18	4	1.00	0.00	0.00	0.75	0.25
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------AATTATC.................................	21	4	1.00	0.00	0.00	1.00	0.00
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTAC..............................	23	4	1.00	0.00	0.00	0.75	0.25
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTTT..............................	23	4	0.75	0.00	0.00	0.75	0.00
..........................................................................................................................................ATGATTTCGTCAGG---------------------------------------TATTATCT................................	22	4	0.75	0.00	0.00	0.50	0.25
...........................................................................................................................................TGAGTTCGTCAGG---------------------------------------TATTATCTG...............................	22	4	0.75	0.00	0.00	0.25	0.50
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTA...................................	19	4	0.75	0.00	0.00	0.75	0.00
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------CATTATCT................................	22	4	0.75	0.00	0.00	0.75	0.00
..........................................................................................................................................ATGAGTTCGTCAxG---------------------------------------TATTATC.................................	20	4	0.75	0.00	0.00	0.00	0.75

droSec1

TGCA---TA---TGAT--ATG-------------------------------------------TTGCAGTAATTTAGTAATAC-CT----------TTCGAACAT----------ATG-ATTTTCAG----TCATTCATGAGTTCGTTAGG---------------------------------------TATTATCTAGTTATTGTAAACATTCAACTCGCTGGC-GGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCT................................	21	4	69.50	56.25	5.75	7.50
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTA...............................	22	4	40.25	33.50	2.50	4.25
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAA..............................	23	4	17.50	14.25	2.00	1.25
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAT..............................	23	4	16.25	16.00	0.25	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTATCT................................	22	4	13.75	12.75	0.50	0.50
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATC.................................	20	4	7.75	6.50	0.25	1.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAG..............................	23	4	5.75	5.50	0.00	0.25
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAAA.............................	24	4	5.25	4.50	0.75	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAC..............................	23	4	3.25	3.00	0.25	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTATC.................................	21	4	2.75	2.00	0.25	0.50
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAGT.............................	24	4	2.50	1.25	0.00	1.25
............................................................................AGTAATAC-CT----------TTCGAACAT----------ATG-...............................................................................................................	22	3	2.33	2.00	0.33	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTACCT................................	21	4	1.25	1.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTATA.............................	24	4	1.25	1.25	0.00	0.00
............................................................................AGTAATAC-CT----------TTCGAACAT----------AT.................................................................................................................	21	3	1.67	1.33	0.00	0.33
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTAT..................................	20	4	1.00	1.00	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTACT.............................	24	4	0.75	0.50	0.00	0.25
.............................................................................................................................................AGTTCGTTAGG---------------------------------------TATTATCTAG..............................	21	4	0.75	0.75	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTACCTA...............................	22	4	0.75	0.75	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAT..................................	19	4	0.75	0.50	0.25	0.00
...........................................................................................................................................TGAGATCGTTAGG---------------------------------------TATTATCT................................	21	4	0.50	0.50	0.00	0.00
...........................................................................................................................................TGATTTCGTTAGG---------------------------------------TATTATCTA...............................	22	4	0.50	0.50	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAGCTA...............................	22	4	0.50	0.50	0.00	0.00
...........................................................................................................................................TGAGTTTGTTAGG---------------------------------------TATTATCTAA..............................	23	4	0.50	0.00	0.50	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTACCTAT..............................	23	4	0.50	0.50	0.00	0.00
............................................................................AGTAATAC-CT----------TTCGAACAT----------ATG-T..............................................................................................................	23	3	0.67	0.67	0.00	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTATCTAA..............................	24	4	0.50	0.50	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAGCT................................	21	4	0.50	0.50	0.00	0.00
.............................................................................................................................................AGTTCGTTAGG---------------------------------------TATTATCTAGT.............................	22	4	0.50	0.50	0.00	0.00
............................................................................................................................................GAGTTCGTTAGG---------------------------------------TATTATCTATT.............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCATTAGG---------------------------------------TATTATCTA...............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TACTATC.................................	20	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTATAT............................	25	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAACTA...............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCTTTAGG---------------------------------------TATTATCTA...............................	22	4	0.25	0.00	0.00	0.25
............................................................................................................................................GAGTTCGTTAGG---------------------------------------TATTATAT................................	20	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TCAGTTCGTTAGG---------------------------------------TATTATCTA...............................	22	4	0.25	0.25	0.00	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTA...................................	19	4	0.25	0.00	0.00	0.25
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAAT.............................	24	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAACTAA..............................	23	4	0.25	0.25	0.00	0.00
............................................................................................................................................GAGTTCGTTAGG---------------------------------------TATTATCTAT..............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGCTAGG---------------------------------------TATTATCTA...............................	22	4	0.25	0.25	0.00	0.00
..........................................................................TTAGTAATAC-CT----------TTCGAACAT----------A..................................................................................................................	22	3	0.33	0.33	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAA..................................	19	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TACTATCTAA..............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTAACT................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TCTTATCT................................	21	4	0.25	0.00	0.00	0.25
...........................................................................................................................................TGAGTTCGTTATG---------------------------------------TATTATCT................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCTTTAGG---------------------------------------TATTATCT................................	21	4	0.25	0.00	0.00	0.25
...........................................................................................................................................TGAGATCGTTAGG---------------------------------------TATTATCTAT..............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TGTTATCT................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCCAT..............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAGTA............................	25	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTCGG---------------------------------------TATTATCTCG..............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------AATTATCTA...............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAGTAA...........................	26	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTATC.............................	24	4	0.25	0.25	0.00	0.00
...........................................................................................................................................AGAGTTCGTTAGG---------------------------------------TATTATCTA...............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------CATTATCTAA..............................	23	4	0.25	0.25	0.00	0.00
..........................................................................TTAGTAATAC-CT----------TTCGAACAT----------...................................................................................................................	21	3	0.33	0.00	0.00	0.33
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TTTTATCT................................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGC---------------------------------------TATTATC.................................	20	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGACTTCGTTAGG---------------------------------------TATTATCT................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------AATTATCTAA..............................	23	4	0.25	0.25	0.00	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTATCTT...............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGC---------------------------------------TATTATCT................................	21	4	0.25	0.25	0.00	0.00
.....................................................................................................AACAT----------ATG-ATTTGCAT----TCA................................................................................................	19	4	0.25	0.00	0.00	0.25
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAGTT............................	25	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTACCTT...............................	22	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGT---------------------------------------TATTATCTAA..............................	23	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAAG---------------------------------------TATTATCTAT..............................	23	4	0.25	0.25	0.00	0.00
..........................................................................................................................................ATGAGTTCGTTAGG---------------------------------------TATTTTC.................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTGT..............................	23	4	0.25	0.25	0.00	0.00
.............................................................................................................................................TCTTCGTTAGG---------------------------------------TATTATCTA...............................	20	4	0.25	0.00	0.00	0.25
..........................................................................................................................................ATGAGTTCGTCAGG---------------------------------------TATTATC.................................	21	4	0.25	0.25	0.00	0.00
...........................................................................................................................................TGAGTTCGTTAGG---------------------------------------TATTATCTAGA.............................	24	4	0.25	0.25	0.00	0.00
............................................................................................................................................GAGTTCGTTAGG---------------------------------------TATTATCTAG..............................	22	4	0.25	0.25	0.00	0.00

droYak2

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

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GGAATTGTGTGATATT--ATG-------------------------------------------TTACAGTGATTTAATAATTC-GA----------TTCGAAGTT----------ATG-TGCTTTAA----TCATTCATAAATGCGAAACG---------------------------------------GATTATTAAGTTATTGTTAACATTCAACTCGTTGGC-GTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAG..............................	21	3	107.33	0.67	4.33	0.00	102.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGT.............................	22	3	97.33	4.33	2.67	0.00	90.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAA...............................	20	3	9.67	0.00	0.67	0.00	9.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTT............................	23	3	3.67	0.00	0.00	0.00	3.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAA..............................	21	3	3.33	0.00	0.00	0.00	3.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGA.............................	22	3	3.33	0.00	0.00	0.00	3.33
...........................................................................................................................................TAAATGCGAAACG---------------------------------------GATTATTAA...............................	22	3	2.67	0.00	0.00	0.00	2.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTA............................	23	3	2.33	0.00	0.33	0.00	2.00
............................................................................................................................................AAATGCGAAACG---------------------------------------GATTATTAAG..............................	22	3	2.00	0.33	0.00	0.00	1.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATT.................................	18	3	2.00	0.00	0.00	0.00	2.00
...........................................................................................................................................TAAATGCGAAACG---------------------------------------GATTATTAAG..............................	23	3	2.00	0.00	0.33	0.00	1.67
...........................................................................................................................................TAAATGCGAAACG---------------------------------------GATTATTAAA..............................	23	3	2.00	0.00	0.00	0.00	2.00
.............................................................................................................................................AATTCGAAACG---------------------------------------GATTATTAAG..............................	21	3	1.67	0.00	0.00	0.00	1.67
.............................................................................................................................................AATGCGAAACT---------------------------------------GATTATTAAG..............................	21	3	1.67	0.00	0.00	0.00	1.67
.............................................................................................................................................AATGCGAAACT---------------------------------------GATTATTAAGT.............................	22	3	1.67	0.00	0.00	0.00	1.67
............................................................................................................................................CAATGCGAAACG---------------------------------------GATTATTAAG..............................	22	3	1.67	0.00	0.00	0.00	1.67
.............................................................................................................................................AATGCTAAACG---------------------------------------GATTATTAAGT.............................	22	3	1.33	0.00	0.00	0.00	1.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTAA...........................	24	3	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................AATGCGAAACG---------------------------------------TATTATTAAG..............................	21	3	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTTT...........................	24	3	1.00	0.00	0.33	0.00	0.67
..............................................................................................................................................ATGCGAAACG---------------------------------------GATTATTAAG..............................	20	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATTCGAAACG---------------------------------------GATTATTAAGT.............................	22	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTGTTAAGT.............................	22	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAATT.............................	22	3	0.67	0.00	0.33	0.00	0.33
..........................................................................TTAATAATTC-GA----------TTCGAAGTT----------A..................................................................................................................	22	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAT..............................	21	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCTAAACG---------------------------------------GATTATTAAG..............................	21	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTT................................	19	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATACGAAACG---------------------------------------GATTATTAAGT.............................	22	3	0.67	0.00	0.00	0.00	0.67
.............................................................................................................................................AATGCGAAGCG---------------------------------------GATTGTTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
...........................................................................................................................................TAAATGCGAAACT---------------------------------------GATTATTAAG..............................	23	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AACGCGAAACG---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAT...............................	20	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGAGAAACG---------------------------------------GATTATTAAG..............................	21	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................AAATGCGAAGCG---------------------------------------GATTATTAAG..............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTAAA..........................	25	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAGACG---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCxAAACG---------------------------------------GATTATTAAG..............................	20	3	0.33	0.00	0.00	0.00	0.33
...........................................................................................................................................TAAATGCGAAACG---------------------------------------GATTATT.................................	20	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................AAATGCGAAACG---------------------------------------GATTATTAA...............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACT---------------------------------------GATTATTAAGTT............................	23	3	0.33	0.00	0.00	0.00	0.33
...........................................................................................................................................TAAATGCGAAACG---------------------------------------GATTATTAAAA.............................	24	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------TATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAGGCG---------------------------------------GATTATTAA...............................	20	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATTCGAAACG---------------------------------------GATTATTAA...............................	20	3	0.33	0.00	0.00	0.00	0.33
..............................................................................................................................................ATGCGAAACT---------------------------------------GATTATTAAGT.............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTGAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTCTTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGxAACG---------------------------------------GATTATTAAG..............................	20	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTAATAAA..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAACCG---------------------------------------GCTTATTAAGT.............................	22	3	0.33	0.00	0.33	0.00	0.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGAA............................	23	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AGTGCGAAACG---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTTA...........................	24	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................AAATGCGAAACG---------------------------------------GATTATTAAGT.............................	23	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTACGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAGCG---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................ACTGCGAAACG---------------------------------------GATTATTAAG..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGC.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAGGCG---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTACG..............................	21	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................AAATGCGAACCG---------------------------------------GATTATTAAG..............................	22	3	0.33	0.33	0.00	0.00	0.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTTTTAAGT.............................	22	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACA---------------------------------------GATTATTAAGT.............................	22	3	0.33	0.33	0.00	0.00	0.00
.............................................................................................................................................AATGCGAAACA---------------------------------------GATTATTAAG..............................	21	3	0.33	0.00	0.33	0.00	0.00
.............................................................................................................................................GATGCGAAACG---------------------------------------GATTATTAAG..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTC............................	23	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACA---------------------------------------GATTATTACG..............................	21	3	0.33	0.00	0.33	0.00	0.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAC..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGCAACG---------------------------------------GATTATTAAG..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTA................................	19	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................AAATGCGAAACG---------------------------------------GATTATTA................................	20	3	0.33	0.00	0.33	0.00	0.00
.............................................................................................................................................AATGCGAAACG---------------------------------------GATTATTAAGTG............................	23	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GGTTATTAAG..............................	21	3	0.33	0.00	0.00	0.00	0.33
.............................................................................................................................................AATGCGAAACG---------------------------------------GACTATTAA...............................	20	3	0.33	0.00	0.00	0.00	0.33

droEug1

Size

Hit Count

Total Norm

droBia1

TTATA-------AAAG--GTTTTTCATTATTAAATTAAGGGTACATATTGCCATCTTAAATTGTGTGT--------AGT------GT----------TTCAAACGC----------A----TTTCCAA----TCATTAGAAAGTTCGTTACGTACTATTTGCTCGGTTTAAAAA-CAAATAGTACGTG----------------------------------TCGGA-TTT

Size

Hit Count

Total Norm

droTak1

AAAGG----------A--AAT-------------------------------------------TTCCAATCATTTAATAGTCC-GA----------TTCGTTCTT----------A-----------------------------------------GTGCTTATTTTGAAAATGCAGTAGTGCGTTTCGGATTATTCAATTATTGTTAACAAACATC------------

Size

Hit Count

Total Norm

droEle1

CGACATACATACATAC--ATA-------------------------------------------TTACAAAAAATATATAATAA-AG----------TGAATAGATATAAAAACAAGTGAATTTTCAAGTTCTCTTTTAACATTTTGTTGAC---TATGCACTCCTTTTTAAAATCAACTTGTTCGCA----------------------------------TT----GTC

Size

Hit Count

Total Norm

droRho1

ATCTGC------TTAAAAGTT-------------------------------------------GTGTAGTTGTATAGTAACAT-ATCATAAGTTGCTCCTAAAAT----------ATT-AGTTTTAG----ATATCTATTACCTAATCAAT---------------------------------------ATTAAAATAGTTCGAATTAATAAATAGCACACTGCT-TAG

Size

Hit Count

Total Norm

droFic1

Size

Hit Count

Total Norm

droKik1

Size

Hit Count

Total Norm

droAna3

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AACAACGTATGTTACT--ATA-------------------------------------------TTAAAATAACTAAATAATTAAAA----------CCAAAACCT----------ATC-AATTTAA-----TCAAT----AAA-CGAAATT---------------------------------------TGTTATCTAGCT---TTAAGTACTTGAAAAGCTCATGATA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................................................................................................TT---------------------------------------TGTTATCTAGCT---GTATG....................	19	3	0.33	0.00	0.33	0.00	0.00

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:14:34 EDT

dme-mir-983-1

chrX:4262342-4262432 -

Known_mirbase

antisense_to_intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup