dme-mir-4956- Best orthologs

dme-mir-4956	chrX:6979769-6979886 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 6979799-6979820
   star strand at position 6979836-6979857
   mutations
   read mismatches

Notes: droWil1 - droGri2 look like tRNAs structures. This is a CDS miRNA so many of the sporadic reads could be degradation product.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:6979754-6979901 -		1	GAGTGCCAACAATTTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	chrX:5492772-5492919 -	LASTZ	1	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	super_24:199934-200081 -	LASTZ	1	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	chrX:14374793-14374940 +	LASTZ	3	GAGTGCCAACAATCTGGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	scaffold_4690:15890244-15890391 -	LASTZ	3	GAGTGCCAATAATCTTGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEug1	scf7180000409095:320865-321012 -	LASTZ	4	TAGTGCCAACAATCTTGGAG---------------------------G---CGGCAACATGTGCCACCTACCGCCAATGGCCAGCAACAATTCGCTAAACAATCTGTGCGGTTTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCAGGGCCAGTAACACCAACCTG
droBia1	scf7180000301760:1606806-1606953 +	LASTZ	4	TAGCGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCCCGGGCGAGCAACACCAACCTG
droTak1	scf7180000415873:625354-625510 -	LASTZ	4	CAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTATGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCAATATGATGATGAACGATCCGCGGGCGAGCAACACCAACCTG
droEle1	scf7180000491023:836960-837107 +	LASTZ	5	AAGTGCCAACAATCTTGGCG---------------------------G---TGGCAACATGTGCCACCTGCCTCCGATGGCCAGCAACAATTCGCTAAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droRho1	scf7180000779514:332128-332275 +	LASTZ	4	GAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droFic1	scf7180000453927:1025569-1025716 +	LASTZ	4	TAGTGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCATCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCGAGCAACACCAACCTG
droKik1	scf7180000302230:43195-43339 +	LASTZ	5	TAGTGCCAACTCCCTTGG---------------------------------CGGCAACATTATCAACCTGCCGCCGATAACCAGCAACAATTCGCTGAACAATCTCTGCGGCCTGTCGTTAGGCAGCGGCGGCAGCGACGATCACC---TA------AACGATCCCAGGGCGAGCAACACCAACCTG
droAna3	scaffold_13117:2326296-2326455 -	LASTZ	3	CAGTGCCAATTCCCTTGGCGGCGGCG------------------GTGG---CGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACA---TGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
droBip1	scf7180000396696:795107-795284 +	LASTZ	4	CAGCGCCAATTCATTGGGCGGCGGCGGCGGTGGAGGCGGTGGCGGCGG---CGGCAATATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGTTGAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGCTG---AACGATCAGCGGGCCAGCAATACCAACCTG
dp4	chrXL_group1a:6391512-6391662 -	LASTZ	3	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	super_25:931278-931428 +	LASTZ	3	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1	scaffold_180777:2984533-2984680 +	LASTZ	5	CAGTGCCAATTCCCTTGGCG---------------------------G---TGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTA---TG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3	scaffold_12928:60655-60799 -	LASTZ	5	CAGCGCCAATTCCCTTGG---------------------------------CGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACA---TG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3	scaffold_6359:1380681-1380818 -	LASTZ	5	C-----C---AATTCCCTCG---------------------------G---CGGCAACATCTGCAACATGC---CAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGA---TG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2	scaffold_14853:6692716-6692854 -	LASTZ	5	CAGCGCCAATTCACTCGGCG---------------------------GACTCTGCAACAT------------GCCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTA---TG------AACGATCCACGCAACAGCAACACCAATTTG

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	GAGTGCCAACAATTTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACCTG
droSim1	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droSec1	GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG
droYak2	GAGTGCCAACAATCTGGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEre2	GAGTGCCAATAATCTTGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG
droEug1	TAGTGCCAACAATCTTGGAG---------------------------G---CGGCAACATGTGCCACCTACCGCCAATGGCCAGCAACAATTCGCTAAACAATCTGTGCGGTTTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCAGGGCCAGTAACACCAACCTG
droBia1	TAGCGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCCCGGGCGAGCAACACCAACCTG
droTak1	CAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTATGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCAATATGATGATGAACGATCCGCGGGCGAGCAACACCAACCTG
droEle1	AAGTGCCAACAATCTTGGCG---------------------------G---TGGCAACATGTGCCACCTGCCTCCGATGGCCAGCAACAATTCGCTAAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droRho1	GAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG
droFic1	TAGTGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCATCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCGAGCAACACCAACCTG
droKik1	TAGTGCCAACTCCCTTGG---------------------------------CGGCAACATTATCAACCTGCCGCCGATAACCAGCAACAATTCGCTGAACAATCTCTGCGGCCTGTCGTTAGGCAGCGGCGGCAGCGACGATCACC---TA------AACGATCCCAGGGCGAGCAACACCAACCTG
droAna3	CAGTGCCAATTCCCTTGGCGGCGGCG------------------GTGG---CGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACA---TGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG
droBip1	CAGCGCCAATTCATTGGGCGGCGGCGGCGGTGGAGGCGGTGGCGGCGG---CGGCAATATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGTTGAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGCTG---AACGATCAGCGGGCCAGCAATACCAACCTG
dp4	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCGAGCAACACCAATCTG
droPer1	CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCCAGCAACACCAATCTG
droWil1	CAGTGCCAATTCCCTTGGCG---------------------------G---TGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTA---TG------AACGATCATCGTCCGAGTAATACCAATTTG
droVir3	CAGCGCCAATTCCCTTGG---------------------------------CGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACA---TG------AACGATCAGCGCAACAGCAACACCAATTTG
droMoj3	C-----C---AATTCCCTCG---------------------------G---CGGCAACATCTGCAACATGC---CAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGA---TG------AACGATCAGCGCACAAGCAACACCAATTTG
droGri2	CAGCGCCAATTCACTCGGCG---------------------------GACTCTGCAACAT------------GCCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTA---TG------AACGATCCACGCAACAGCAACACCAATTTG

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

GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAACCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGTGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................CGATGGCCGGCAACAACTCGCT...........................................................................................	22	1	6.00	0.00	6.00	0.00	0.00
..........................................................................CGATGGCCAGCAACAACTCGCT...........................................................................................	22	1	5.00	0.00	3.00	2.00	0.00
...............................................................................................TGACTAACATCTGCGGAT..........................................................................	18	1	4.00	0.00	0.00	1.00	3.00
...........................................................................................................GCGGATTxTCGCTGGGCGG.............................................................	18	1	3.00	0.00	0.00	0.00	3.00
................................................................................................................................................................CATCCTCGGGCAAGCAACAC.......	20	1	2.00	0.00	0.00	0.00	2.00
..........................................................................................................................GCATCGGTGGTAGTGACGA..............................................	19	1	2.00	0.00	0.00	0.00	2.00
...........................................................................GATGGCCGGCAACAACTCGCTG..........................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
..............................................................................................CTGAATAACCTCTGCGGCTTGTCGCT...................................................................	26	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................G------AACGATCCTCGGGCAAGCAACACC......	25	1	1.00	0.00	0.00	1.00	0.00
................................................................................................GAATAACCTCTGCGGATTGTC......................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................AGTGATGATCTCA---TG------AAC...........................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................AACGATCCTCGGGCAAGCAACACC......	24	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................CCTCGGGCAAGCAACACC......	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................CTGAATAACCTCTGCGGATTGTCGCT...................................................................	26	1	1.00	0.00	0.00	0.00	1.00
.........................................................................ACGATGGACAGCAACAAC................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................CTGAATAACCTCTGCGGAT..........................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................AACGATCCTCGGGCAAGCAAC.........	21	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................CTGAATAACCTCTGCGGATTGTCGCTGGG................................................................	29	1	1.00	0.00	0.00	1.00	0.00
..........................................................................CGATGGCCAGCAACAACTCGCG...........................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................G------AACGATCCTCGGGCAAGCAACAC.......	24	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................AACGATCCTCGGGCAAGC............	18	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................CTGAATATCCTCCGCGGA...........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................AACGATCCTCGGGAAAGCAAC.........	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................ATGGCCATCAAGAACTCGC............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................................................TCTCA---TG------AACGATCCTCGGGCA...............	22	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................CTGAATAACCTCTGCGGATTGTCGCC...................................................................	26	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................CGGATTGTCGCTGGGCAGCG...........................................................	20	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................GATGATCTCA---TG------AACGATCCTCGGGCA...............	27	1	1.00	0.00	0.00	0.00	1.00
..........................................................................CGATGGCCGGCAACAACTCGCC...........................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

GAGTGCCAACAATCTAGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAACTCGCTGAATAATCTCTGCGGATTGTCGCTGGGCAGCGGTGGTAGCGATGATCTCA---TG------AACGATCCTCGGGCAAGCAACACCAACTTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................................................ATTGTCGCTGGGCAGCGGTGG.......................................................	21	1	2.00	1.00	0.00	1.00
..................................................................................................ATAATCTCTGCGGATTGTC......................................................................	19	1	2.00	0.00	2.00	0.00
..............................................................................................................GATTGTCGCTGGGCAGCGGTG........................................................	21	1	1.00	0.00	1.00	0.00
..............................................................................................CTGAATAATCTCTGCGGATT.........................................................................	20	1	1.00	0.00	1.00	0.00
...............................................................................................................ATTGTCGCTGGGCGGCGGTGGT......................................................	22	1	1.00	1.00	0.00	0.00
.............................................................................................................................................................GACGATCCTCGGGCAAGA............	18	1	1.00	1.00	0.00	0.00
.....................................................................................AACAACGCGCTGAATGAT....................................................................................	18	1	1.00	0.00	1.00	0.00
............................................................................................................CGGATTGTCGCTGGGCAGCGGT.........................................................	22	1	1.00	1.00	0.00	0.00
.................................................................................................................................................A---TG------AACGAxxCTCGGGCAAG.............	18	1	1.00	0.00	1.00	0.00
..............................................................................................................GATTGTCGCTGGGCAGCGGTGGT......................................................	23	1	1.00	1.00	0.00	0.00
.......................................................................................CAACTCGCTGAATAATCTCT................................................................................	20	1	1.00	0.00	1.00	0.00
............................................................................................................CGGATTGTCGCTGGGCAGCGGTT........................................................	23	1	1.00	1.00	0.00	0.00
.....................................................................................................................GCTGGGCAGCGGTGGTAGT...................................................	19	1	1.00	0.00	1.00	0.00
......................................................................................................................................................G------AACGATCCTCGGGCAAGC............	19	1	1.00	0.00	1.00	0.00
........................................................................................................TCTGCGGATTATCGGTGG.................................................................	18	1	1.00	0.00	1.00	0.00
............................................................................................................................................ATCTCA---TG------AACGATCCTCGGGC................	22	1	1.00	0.00	1.00	0.00

droYak2

GAGTGCCAACAATCTGGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................................................................................................................................................CCCGGGCxGGCAACACCA.....	17	1	2.00	0.00	0.00	0.00	2.00	0.00
.........................................................................................................CTGCGGACTGTCGCTGGGCAG.............................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................CTGAATAACCTCTGCGGACT.........................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
..............................................................................................CTGAATAACCTCTGCGGACTGTCGCT...................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................................TCTGCGGACTGTCGCTGGGCAGCGGC.........................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................GACGGTCGCxGGGCAGC............................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................ATAACCTCTGCGGACTGTCGCT...................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................TGCGGACTGTCGCTGGGCAGC............................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................CGGACTGTCGCTGGGCAGCGGCT........................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...........ATCTGGGCG---------------------------G---CGGCAC..................................................................................................................................	16	1	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................GATGGCCAGCCACAGTTCGCT...........................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................................................TCTGCGGACTGTCGCTGGGCAGA............................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................................................A---TG------AACGATCCCCGGGCAAG.............	20	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................G------AACGATCCCCGGGCAAGCAACACCA.....	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GAGTGCCAATAATCTTGGGG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAATAACCTCTGCGGACTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCCGGGCAAGCAACACCAACCTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................................................CTGCGGACTGTCGCTGGGCAG.............................................................	21	1	3.00	0.00	1.00	0.00	2.00
...............................................................................................................ACTGTCGCTGGGCAGCGGTT........................................................	20	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................CTCCGGACTGTCGCTGGGCAG.............................................................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................CGGACTGTCGCTGGGCAGCGGC.........................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................GATGATATCA---TG------AACGAAC.......................	19	1	1.00	1.00	0.00	0.00	0.00
............TCTTGGGG---------------------------G---CGGCAACATGTGC...........................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................ACTTTCGCTGGGCAGCGGCG........................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................GATCCCCGGGCAAGCAACACCA.....	22	1	1.00	1.00	0.00	0.00	0.00
...........................................................TGTGCCACCTACCGCCGTTG............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CTGAATAACCTCTGCGGACT.........................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................CTGCGGACTGTCCCTGGGCAG.............................................................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

TAGTGCCAACAATCTTGGAG---------------------------G---CGGCAACATGTGCCACCTACCGCCAATGGCCAGCAACAATTCGCTAAACAATCTGTGCGGTTTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCCAGGGCCAGTAACACCAACCTG

Size

Hit Count

Total Norm

droBia1

TAGCGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCCCGGGCGAGCAACACCAACCTG

Size

Hit Count

Total Norm

droTak1

CAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTATGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCAATATGATGATGAACGATCCGCGGGCGAGCAACACCAACCTG

Size

Hit Count

Total Norm

droEle1

AAGTGCCAACAATCTTGGCG---------------------------G---TGGCAACATGTGCCACCTGCCTCCGATGGCCAGCAACAATTCGCTAAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG

Size

Hit Count

Total Norm

droRho1

GAGTGCCAACAATCTTGGCG---------------------------G---CGGCAACATGTGCCACCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGACGATCTCA---TG------AACGATCCGCGGGCAAGCAACACCAACCTG

Size

Hit Count

Total Norm

droFic1

TAGTGCCAACAACCTTGGCG---------------------------G---CGGCAACATGTGCCATCTGCCGCCGATGGCCAGCAACAATTCGCTGAACAACCTGTGCGGCCTGTCGCTGGGCAGCGGCGGTAGCGATGATCTCA---TG------AACGATCCGCGGGCGAGCAACACCAACCTG

Size

Hit Count

Total Norm

droKik1

TAGTGCCAACTCCCTTGG---------------------------------CGGCAACATTATCAACCTGCCGCCGATAACCAGCAACAATTCGCTGAACAATCTCTGCGGCCTGTCGTTAGGCAGCGGCGGCAGCGACGATCACC---TA------AACGATCCCAGGGCGAGCAACACCAACCTG

Size

Hit Count

Total Norm

droAna3

CAGTGCCAATTCCCTTGGCGGCGGCG------------------GTGG---CGGCAACATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGCTTAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGACGATCACA---TGCTT---AATGACCAGCGGCCGAGCAACACCAACCTG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................GGCGGTGGCA------------------GTGG---CGGC....................................................................................................................................	18	8	0.63	0.00	0.63	0.00	0.00
................GGCGGTGGTG------------------GTGG---CGGC....................................................................................................................................	18	7	0.43	0.00	0.43	0.00	0.00
..................CGGCGGCG------------------AAGG---CGGCAAC.................................................................................................................................	19	1	2.00	1.00	1.00	0.00	0.00
................GGCGGTGGCG------------------GTGG---CGGC....................................................................................................................................	18	10	0.10	0.00	0.10	0.00	0.00
.............GTTGGCGGTGGCG------------------GTGG---C.......................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
.......................................................................................................CTGTGCGGCCTGTCGCTGGGCAGCGGCG........................................................	28	1	1.00	1.00	0.00	0.00	0.00
................GGCGGCGGAG------------------GAGG---CGGC....................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...................GGCGGCG------------------AAGG---CGGCAAC.................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............TGGCGCCGGCG------------------GTAG---CGGC....................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................TAGGCATCGGCGGCAGC...................................................	17	2	0.50	0.00	0.00	0.50	0.00
.....................................................GCAACATGTGCGACCTGCCGCCCATGACC.........................................................................................................	29	1	1.00	0.00	1.00	0.00	0.00
................GGCGGCGGCG------------------GTGG---TGGT....................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
...............AGGCGGCGGCG------------------GTGG---AGGCA...................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.................GCGGCGGCG------------------GTGG---TGGCGA..................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................AGCGGAGGCAGTGACGA..............................................	17	1	1.00	0.00	0.00	1.00	0.00
..................CGGTGGCG------------------ATGG---CGGCAAC.................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................GGTGGCG------------------GAGG---CGGCAA..................................................................................................................................	17	3	0.33	0.00	0.00	0.33	0.00
............................................................................................................................CGCGGAGGCAGCGACGA..............................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GAGGCGGCG------------------GTGG---CGGCAAG.................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.............................................................................................................................GGGGAGGCAGCGACGA..............................................	16	2	0.50	0.00	0.00	0.50	0.00
..............TTGGAGGCGGTG------------------GTGG---CGGC....................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
................GGTGGCGGCG------------------GCGG---CGGC....................................................................................................................................	18	14	0.07	0.00	0.07	0.00	0.00
.....................................................................................................................GCTGGGCAACGGCGGAA.....................................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GCGGCGGCG------------------GTGG---TGGCTA..................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................AATCTGTGCGGCCTGTCGCT...................................................................	20	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................GGGCAGCGGGGGCAACG..................................................	17	1	1.00	0.00	0.00	1.00	0.00
.................GCGGCGGTG------------------GTGG---CGGAAA..................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
..................AGGCGGTG------------------GTGG---CGGCAAC.................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...................GGTGGCG------------------GAGG---CGGCAAC.................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............AATGGCGGCGGCG------------------GTGG---C.......................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droBip1

CAGCGCCAATTCATTGGGCGGCGGCGGCGGTGGAGGCGGTGGCGGCGG---CGGCAATATGTGCAACCTGCCGCCCATGACCAGCAACAATTCGTTGAACAATCTGTGCGGCCTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGCTG---AACGATCAGCGGGCCAGCAATACCAACCTG

Size

Hit Count

Total Norm

dp4

CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCGAGCAACACCAATCTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................AGCAATCTATGCGGACTGTCGCT...................................................................	23	1	3.00	1.00	2.00	0.00	0.00
..........................................................................................................TGCGGACTGTCGCTGGGCAGC............................................................	21	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................GCGGTCTGTCGCTGGGCATC............................................................	20	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................TGCGGACTGTCGCTGGGCAGCG...........................................................	22	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................ATGCACGATxGGCGATCGAG.............	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................GCGGTCTGTCGCTGGGCA..............................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................TTAGCAATCTATGCGGACTGTCGCT...................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................TTAGCAATCTATGCGGACT.........................................................................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TAGCAATCTATGCGGACTGTCG.....................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................GATGAGTACA---TGATGATG..............................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CAGTGCCAATAATCTTGG---------------------------------CGGCAACATGTGCAACCTGCTGCCAATGACCAGCAACAATTCGCTTAGCAATCTATGCGGACTGTCGCTGGGCAGCGGCGGCAGCGATGATCACA---TGATGATGCACGATCAGCGATCCAGCAACACCAATCTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................AGCAATCTATGCGGACTGTCGCT...................................................................	23	1	10.00	0.00	0.00	0.00	0.00	10.00
......................................................................................................TCTATGCGGACTGTCGCT...................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
...............................................................................................TTAGCAATCTATGCGGACT.........................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
....................................................................................................AATCTATGCGGACTGTCGCT...................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
....................................................................................................AATCTACGCGGACTGTCGC....................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................CAACATGTGCAACCTGCTG..................................................................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
...............................................................................................TTAGCAATCTATGCGGACTGTCGCC...................................................................	25	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................ATCTATGCGGACTGTCGCT...................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................GCTGGGCAGCGGCGGCGGC...................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................................AGCAATCTATGCGGACTGTCGCC...................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................ATGCGGACTGTCGCTGGGCAGCG...........................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................AATCTATGCGGACTGTCGC....................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................AATGACCAGCAACAATTCGCTT..........................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

CAGTGCCAATTCCCTTGGCG---------------------------G---TGGCAATATGTGCAATATGCCACCGATGGCCAGTAACAATTCATTGAACAACCTGTGCGGTCTATCATTGGGCAGCGGCGGCAGCGATGATCTTA---TG------AACGATCATCGTCCGAGTAATACCAATTTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................................................................................................GGCAGCGGCGGCGGCGGT................................................	18	33	0.03	0.00	0.03	0.00	0.00
.................................................................................................................................CGGCAGCGATGATCTTA---TG------AAC...........................	22	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................GCAGCGGCGGCAGCGATGAT.............................................	20	1	1.00	1.00	0.00	0.00	0.00

droVir3

CAGCGCCAATTCCCTTGG---------------------------------CGGCAACATCTGCAATATGCCGCCAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATTGGCAGCGGCGGCAGCGATGATCACA---TG------AACGATCAGCGCAACAGCAACACCAATTTG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................................................................ATATGCCGCCAATGGCCAGCA.....................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

C-----C---AATTCCCTCG---------------------------G---CGGCAACATCTGCAACATGC---CAATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATCGGCAGCGGCGGCAGCGATGATCTGA---TG------AACGATCAGCGCACAAGCAACACCAATTTG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................GCCTATCGATCGGCAGCGGCGGCAGCG..................................................	27	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................CTATCGATCGGCAGCGGCGGCAGCGAT................................................	27	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................AGCGATGATCTGA---TG------AACGAT........................	21	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................GA---TG------AACGATCAGCGCACAAGCAACACC......	28	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................ATCGATxGGCAGCTGCGGC......................................................	18	2	0.50	0.00	0.00	0.50	0.00

droGri2

CAGCGCCAATTCACTCGGCG---------------------------GACTCTGCAACAT------------GCCGATGGCCAGCAACAATTCGCTGAACAATCTGTGCGGCCTATCGATAGGCAGCGGGGGCAGCGATGATCTTA---TG------AACGATCCACGCAACAGCAACACCAATTTG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:14 EDT

dme-mir-4956

chrX:6979769-6979886 -

Known_mirbase

CDS

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