dme-mir-2281- Best orthologs

dme-mir-2281	chr3R:10222121-10222223 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 10222146-10222165
   star strand at position 10222183-10222203
   mutations
   read mismatches

Notes: "There is a small insertion which happened on the ancestor dm3-droSec1 which is where the structure looks most confident. The hairpin structure and reads exist in several species, but these reads don't align to the mature/star regions."

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr3R:10222106-10222238 -		1	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACACGTATTAT-----CT------------GCAGCTGCAGATGCAAATGTATATGT------ATCTGTATCTGTATCT-------------------GCAGT-ATTGC--------AGTATCGCTGCT---TT-ATTCATATCCATGAGACG------------------------------------------CGTC---GCG
droSim1	chr3R:11233896-11234028 +	LASTZ	4	GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACCCGTATTAT-----CT------------GCAGCTGCAGATGCAAATGTATATGT------ATCTGTATCTGTATCT-------------------GCAGT-ATTGC--------AGTATCGCTGCT---TT-ATTCGTATCCATGTGACG------------------------------------------CGTC---GCG
droSec1	super_0:11818438-11818570 +	LASTZ	4	GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACTCGTATTAT-----CT------------GCAGCTGCAGATGCAAATGTATATGT------ATCTGTATCTGTATCT-------------------GCAGT-ATTGC--------AGTATCGTTGCT---TT-ATTCGTATCCATGTGACG------------------------------------------CGTC---GCG
droYak2	chr3R:16218838-16218961 +	LASTZ	5	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCTGC------GTTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCTTTCAGTA----TT------GCAAT-GTTGCAGTATCTT--------TGCT---TT-ATTCGTATCCGTGTGACG------------------------------------------CGTC---GCG
droEre2	scaffold_4770:9756449-9756546 -	LASTZ	5	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCATC------GTTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTACGGC---------------------TGTATCCGTGTGACG------------------------------------------CGGC---GCG
droEug1	scf7180000409584:290211-290321 +	LASTZ	5	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTTGACGGGCCGT------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC--------TGTT---TTAATTCGTATCTGTGTGACG------------------------------------------CGTC---GCG
droBia1	scf7180000302075:5567085-5567191 -	LASTZ	5	CG-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------GCTAT-----CT------------GCAGCTGCAGATGCGAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC--------CGCT---TT-ATTCGTATCTGTGCGACG------------------------------------------CGTC---GCG
droTak1	scf7180000415396:184472-184588 -	LASTZ	5	TCAGGCACCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------ACTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC-----CGCTGCT---TT-ATTCGTATCTGTGCGACG------------------------------------------CGTC---GCG
droEle1	scf7180000491047:916740-916846 +	LASTZ	5	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCGGTATCGC--------CGCT---TT-ACCAGTGTCTGTGTGACG------------------------------------------CGTC---GCG
droRho1	scf7180000762751:7752-7858 -	LASTZ	5	A-----------TG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGC------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCTGTATCGC--------CGCTTCATT-ATTTGTGTCTGTGTGACG------------------------------------------CGTC---GCG
droFic1	scf7180000453912:712927-713041 -	LASTZ	5	GC---------GTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------GCTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGGGT----ATCCG----TGTATCT----------------------------GCGCTATCGC--------AGTT---TC-ATTTGTATCTGTGTGACG------------------------------------------CGTC---GCG
droKik1	scf7180000302610:1086546-1086678 -	LASTZ	0	TC-------T--TT-------------------------------------------------------------------------CCTTCCGCCGCTGTGTA---GCTGT------AT--------CTGTATCTGTATCTGTATCTGTAGCTGAAAATGTATCTGT------ATCTGTAGCTGTATCT-------------------TTTG-----------------------------------------CTAAGCCAGCCGAGGGGCCTCTGTTTTTTTAAACC---------------CAATTC---TCG
droAna3	scaffold_13117:2846333-2846460 -	LASTZ	0	GT-------ATCTC-------------------------------------------------------------------------GAGAT---GCATCTG------TAAG------AGTAT-----CT------------GCATCTGCAAATGTATCTGTATCTGT------ATCTGTATCTGT------------------------------------------------------------ATCTGTATCTGTGCAAGACTTGCCACCTCTCCTTTTCT-------CCTTTTCCTGAGCAAATGT---CGC
droBip1	scf7180000394085:572453-572558 +	LASTZ	0	G-----------TG-------------------------------------------------------------------------CATCCTACGGATTCG------------------TAT-----CC------------GAGGCCTCAGATGCAGCTGTATCTGT------ATCTGTGAAT------------GTGAAATGTATCTGC----ATCGC--------AGTATCA--GCT---T-----CG-------GCTACG------------------------------------------CGTC---GCG
dp4	chrXR_group8:8158458-8158593 +	LASTZ	0	GC-------TAGTGCCCACTACTGCCTTTG-------------------------------------------------------------------GCATGTA---TCTGT------AT--------CTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGT------ATCTGTATCTGTAGCT-------------------GCTCTGAATGC--------AGTATAT-----------------------------------------ATTTCATCAAATT---------------TTTGTACTCGCA
droPer1	super_0:4124990-4125137 +	LASTZ	0	GT-------AGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCT-------GTGCATCCTACGGATGGCAG---GCTGT------ACAACCGTATCG------------GCAGC------------CGTATCGGT------A------------TCG----------------------------------------------------------GTGTATCTGTGTGACG------------------------------------------CGTC---GCG
droWil1	scaffold_181089:10073219-10073346 +	LASTZ	0	CC-------TGGTAGAGAACGTTGGGGGAG-------------------------GGGGGGGTTAGTTTTCCAGGCTCGCTGCAAAACATCCTACGATGTGAAA---AT--------------------------------------------TGTGAAGGCTACTGA------A------------AGC-------------------GGT------GC---AATGC------------------GAGGAGAGCGACGCAATG------------------------------------------CGAC---GCG
droVir3	scaffold_12928:2113057-2113188 +	LASTZ	0	GT-------ATCTA-------------------------------------------------------------------------TATCT---GTATATGTA---TCTGT---------AT-----CTGTATCT------GTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCT------------------------------------------------------------GTATCTATAT---T-----------TGCTTCTTTAAATCCGCCTC-TTTCGAGACATTTA---TCC
droMoj3	scaffold_6654:2537235-2537365 +	LASTZ	0	TT-------CAGTG-------------------------------------------------------------------------AATCT---GTATCTGTA---TCTGTATCTGTAT--------CT------GTATCTGTATCTGTATCTGTATCTGTATCTGT------ATCTGTATCTGTATCT-------------------GTATC-GTATCTGTATCT-------GTATCT---GT-ATCTGTATCTG---TATT------------------------------------------TGTA---TCT
droGri2	scaffold_14830:2155779-2155908 -	LASTZ	0	GC-------GA-TG-------------------------------------------------------------------------TATCT--CGTATCTCGG---CGAGT------ACGTC-----GC------------GCATCCGTATCTGCAAATGTATCTCT------ATCTATAGCTGTATCT------GAGCAATGTAT--G---T-AGTAT--------AGTATCT--GTT---GT-TGGGGTTTTCATATTGCT------------------------------------------TGTG---CTG

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	TC-------CAGTGCATCCTACGGATGTCGA---GCAGTACACGTATTATCTGCAGCTGCAGATGCAAATGTATAT----------GTATCTGTATCTGTATCTGCAGTATTGCAGTATCGC---TGCT---TT-ATTCATATCCATGAGACGCGTCGCG
droSim1	GC-------CAGTGCATCCTACGGATGTCGA---GCAGTACCCGTATTATCTGCAGCTGCAGATGCAAATGTATAT----------GTATCTGTATCTGTATCTGCAGTATTGCAGTATCGC---TGCT---TT-ATTCGTATCCATGTGACGCGTCGCG
droSec1	GC-------CAGTGCATCCTACGGATGTCGA---GCAGTACTCGTATTATCTGCAGCTGCAGATGCAAATGTATAT----------GTATCTGTATCTGTATCTGCAGTATTGCAGTATCGT---TGCT---TT-ATTCGTATCCATGTGACGCGTCGCG
droYak2	TC-------CAGTGCATCCTACGGATGCCGA---GCT------GCGTTATCTGCAGCTGCAGATGCAAATGTATCT----------GTATCTT--TCAGTAT-TGCAATGTTGCAGTATCTT---TGCT---TT-ATTCGTATCCGTGTGACGCGTCGCG
droEre2	TC-------CAGTGCATCCTACGGATGCCGA---GCA------TCGTTATCTGCAGCTGCAGATGCAAATGTATCT----------GTAT------------CT--------GCAGTACGGC----------------TGTATCCGTGTGACGCGGCGCG
droEug1	TC-------CAGTGCATCCTACGGATGTTGACGGGCC------GTATTATCTGCAGCTGCAGATGCAAATGTATCT----------GTAT------------CT--------GCAGTATCGC---TGTT---TTAATTCGTATCTGTGTGACGCGTCGCG
droBia1	CG-------CAGTGCATCCTACGGATGTCGA---GCA------GTGCTATCTGCAGCTGCAGATGCGAATGTATCT----------GTAT------------CT--------GCAGTATCGC---CGCT---TT-ATTCGTATCTGTGCGACGCGTCGCG
droTak1	TCAGGCACCCAGTGCATCCTACGGATGTCGA---GCA------GTACTATCTGCAGCTGCAGATGCAAATGTATCT----------GTAT------------CT--------GCAGTATCGCCGCTGCT---TT-ATTCGTATCTGTGCGACGCGTCGCG
droEle1	TC-------CAGTGCATCCTACGGATGTCGA---GCA------GTATTATCTGCAGCTGCAGATGCAAATGTATCT----------GTAT------------CT--------GCGGTATCGC---CGCT---TT-ACCAGTGTCTGTGTGACGCGTCGCG
droRho1	-----------ATGCATCCTACGGATGTCGA---GCA------GCATTATCTGCAGCTGCAGATGCAAATGTATCT----------GTAT------------CT--------GCTGTATCGC---CGCTTCATT-ATTTGTGTCTGTGTGACGCGTCGCG
droFic1	GC---------GTGCATCCTACGGATGTCGA---GCA------GTGCTATCTGCAGCTGCAGATGCAAATGTATCTGGGTATCCGTGTAT------------CT--------GCGCTATCGC---AGTT---TC-ATTTGTATCTGTGTGACGCGTCGCG

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

GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACCCGTATTAT-----CT------------GCAGCTGCAGATGCAAATGTATATGT------ATCTGTATCTGTATCT-------------------GCAGT-ATTGC--------AGTATCGCTGCT---TT-ATTCGTATCCATGTGACG------------------------------------------CGTC---GCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................................ATGT------ATCTGTATCTGAACC...............................................................................................................................	19	2	2.00	0.00	0.00	2.00	0.00
...............................................................................................................................................................TGTATCTGT------ATCTGTATCTCT..................................................................................................................................	21	6	0.50	0.17	0.33	0.00	0.00
..................................................................................................................................................................ATCCGT------ATCTGTATCTGTATC...............................................................................................................................	21	3	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................TGT------ATCTGTATCTGTATCT-------------------CT.........................................................................................................	21	6	0.50	0.17	0.33	0.00	0.00
..............................................................................................................................................................CTGTATCTGT------ATCTGTATCT....................................................................................................................................	20	6	0.33	0.00	0.00	0.00	0.33
.......................................................................................................................................................................T------ATCTGAATCTGTATCT-------------------GA.........................................................................................................	19	2	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................TGTATCTGTATCT-------------------GCATC-.....................................................................................................	18	9	0.22	0.00	0.00	0.00	0.22
..................................................................................................................................................................CTGTGT------ATCTGTATCTGTATC...............................................................................................................................	21	2	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................GT------ATCTGCATCGGTATCT-------------------GC.........................................................................................................	20	2	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................ATCTGT------ATCTGTATCTGT..................................................................................................................................	18	8	0.25	0.00	0.00	0.00	0.25
....................................................................................................................................................................ATGT------ATCTGTATCTGAAC................................................................................................................................	18	3	0.67	0.00	0.00	0.67	0.00
....................................................................................................................................................................CTGT------ATCTGTATCTGTATCT-------------------...........................................................................................................	20	6	0.33	0.00	0.00	0.00	0.33
..............................................................................................................................................................................ATCTGTATCTGTATCT-------------------GT.........................................................................................................	18	8	0.25	0.00	0.00	0.00	0.25
...............................................................................................................................................................TGTATCTGT------ATCTGCATC.....................................................................................................................................	18	9	0.22	0.00	0.00	0.00	0.22
.....................................................................................................................................................................TGT------ATCTGTATCTGCATC...............................................................................................................................	18	9	0.22	0.00	0.00	0.00	0.22
......................................................................................................................................................................GT------ATCTGTATCTGTATCC-------------------...........................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
....................................................................................................................................................................CTGT------ATCTGTATCTGTAC................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
...................................................................................................................................................................AACGT------ATCTGTATCTGTA.................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
..............................................................................................................................................................................ATTTGTATCTGCATCT-------------------GC.........................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25
................................................................................................................................................................GTATCTGT------ATCTGTATCTGTA.................................................................................................................................	21	6	0.17	0.00	0.17	0.00	0.00
...............................................................................................................................................................TGTATCTGT------ATCTGTATC.....................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
......................................................................................................................................................................GT------ATCTGTATCTGTATCT-------------------GTA........................................................................................................	21	6	0.17	0.00	0.17	0.00	0.00
..............................................................................................................................................................................ATCTGTATCTGTATCT-------------------GTA........................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13
...............................................................................................................................................................................TCTGAATCTGTATCT-------------------GCC........................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................................................GTATCTGT------ATCTGTATCTGTATCT-------------------...........................................................................................................	24	3	0.33	0.00	0.00	0.00	0.33
....................................................................................................................................................................CTGT------ATCTGTATCTGCAT................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
..............................................................................................................................................................GTxTTTATGT------ATCTGTATCTG...................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
...........................................................................................................................................................CAAATGTATCTGT------ATCTGA........................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.....................................................................................................................................................................TGT------ATCTGTATCTGTATC...............................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
.....................................................................................................................................................................TGT------ATCTTTATCTGTATCT-------------------G..........................................................................................................	20	5	0.20	0.00	0.00	0.20	0.00
...................................................................................................................................................................TATCT------ATCTGTATCTGAATC...............................................................................................................................	20	2	0.50	0.00	0.00	0.50	0.00
.............................................................................................................................................................AACGTATCTGT------ATCTGTA.......................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
...............................................................................................................................................................TGTATCTTT------ATCTGTATCTG...................................................................................................................................	20	5	0.20	0.00	0.00	0.20	0.00
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTATCT-------------------G..........................................................................................................	23	3	0.33	0.00	0.00	0.33	0.00
.................................................................................................................................................................TATCTGT------ATCTGTATCTGTATT...............................................................................................................................	22	5	0.20	0.00	0.00	0.00	0.20
................................................................................................................................................................................CTGTATCTGTATCT-------------------GTAC.......................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
..................................................................................................................................................................ATTTGT------ATCTGTATCTGTATC...............................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
................................................................................................................................................................GTATCTGT------ATCTGTATCC....................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTATCC-------------------...........................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
.....................................................................................................................................................................TGC------ATTTGTATCTGTATCT-------------------GC.........................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
...................................................................................................................................................................TCAGT------ATCTGTATCTGTATCT-------------------...........................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
..............................................................................................................................................................CTGTATCTGT------ATCTGTATCTGTATC...............................................................................................................................	25	3	0.33	0.00	0.00	0.00	0.33
.....................................................................................................................................................................TGT------ATCTGTATCTGTATCT-------------------CC.........................................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................................................................................TCTTT------ATCTGTATCTGTATCT-------------------...........................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
.......................................................................................................................................................................T------ATCTGTATCTGTATCT-------------------GTATT-.....................................................................................................	22	5	0.20	0.00	0.00	0.00	0.20
................................................................................................................................................................................CTGTATCTGTATCT-------------------GCAT.......................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTA.................................................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13
..................................................................................................................................................................ATCTGT------ATCTGTATCTGAATCT-------------------...........................................................................................................	22	3	0.33	0.33	0.00	0.00	0.00
......................................................................................................................................................................GT------ATCTTTATCTGTAGCT-------------------...........................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACTCGTATTAT-----CT------------GCAGCTGCAGATGCAAATGTATATGT------ATCTGTATCTGTATCT-------------------GCAGT-ATTGC--------AGTATCGTTGCT---TT-ATTCGTATCCATGTGACG------------------------------------------CGTC---GCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................................................................................................................................ATATGT------ATCTGTGTGTGT..................................................................................................................................	18	4	0.25	0.00	0.25	0.00
...............................................................................................................................................CAGCTGCAGATGCAAATGTATATGT------..............................................................................................................................................	25	3	0.33	0.00	0.00	0.33
................................................................................................................................................................GTATxTGT------ATCTGTATCTG...................................................................................................................................	18	8	0.13	0.00	0.00	0.13
...............................................................................................................................................................TATATATGT------ATCTTTATCTGT..................................................................................................................................	21	3	0.33	0.33	0.00	0.00
....................................................................................................................................................GCAGATCCAAGTGTATATG.....................................................................................................................................................	19	3	0.33	0.00	0.00	0.33
......................................................................................................................................................................GT------ATxTGTATCTGTATCT-------------------G..........................................................................................................	18	8	0.13	0.00	0.00	0.13
..................................................................................................................................................................ACAAGT------ATCTGTATCTGTATCT-------------------...........................................................................................................	22	3	0.33	0.33	0.00	0.00
...............................................................................................................................................................................................................................................................CATGTGACG------------------------------------------CGTC---GAG	18	2	0.50	0.00	0.00	0.50
......................................................................................................................................................................GT------ATCTGCATCGGTATCT-------------------GC.........................................................................................................	20	3	0.33	0.00	0.33	0.00
....................................................................................................................................................................ATGC------ATCTGCATCTGTATCT-------------------...........................................................................................................	20	3	0.33	0.00	0.33	0.00
................................................................................................................................................................ATATATGT------ATCTTTATCTGT..................................................................................................................................	20	3	0.33	0.00	0.00	0.33
..................................................................................................................................................................ATATGT------ATCTTTATCTGTA.................................................................................................................................	19	3	0.33	0.00	0.00	0.33

droYak2

TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCTGC------GTTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCTTTCAGTA----TT------GCAAT-GTTGCAGTATCTT--------TGCT---TT-ATTCGTATCCGTGTGACG------------------------------------------CGTC---GCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................................................................................GTATCTGT------A------------TCTTTCCTTA----T..................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................G	24	32	0.03	0.00	0.00	0.03	0.00	0.00

droEre2

TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCATC------GTTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTACGGC---------------------TGTATCCGTGTGACG------------------------------------------CGGC---GCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................................................................................................................GTATCTGT------A------------TCT----------------------------GCAGCT............................................................................................	18	7	0.14	0.00	0.00	0.00	0.14

droEug1

TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTTGACGGGCCGT------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC--------TGTT---TTAATTCGTATCTGTGTGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droBia1

CG-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------GCTAT-----CT------------GCAGCTGCAGATGCGAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC--------CGCT---TT-ATTCGTATCTGTGCGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droTak1

TCAGGCACCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------ACTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCAGTATCGC-----CGCTGCT---TT-ATTCGTATCTGTGCGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droEle1

TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCGGTATCGC--------CGCT---TT-ACCAGTGTCTGTGTGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droRho1

A-----------TG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGC------ATTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGT------A------------TCT----------------------------GCTGTATCGC--------CGCTTCATT-ATTTGTGTCTGTGTGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droFic1

GC---------GTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT------GCTAT-----CT------------GCAGCTGCAGATGCAAATGTATCTGGGT----ATCCG----TGTATCT----------------------------GCGCTATCGC--------AGTT---TC-ATTTGTATCTGTGTGACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

droKik1

TC-------T--TT-------------------------------------------------------------------------CCTTCCGCCGCTGTGTA---GCTGT------AT--------CTGTATCTGTATCTGTATCTGTAGCTGAAAATGTATCTGT------ATCTGTAGCTGTATCT-------------------TTTG-----------------------------------------CTAAGCCAGCCGAGGGGCCTCTGTTTTTTTAAACC---------------CAATTC---TCG

Size

Hit Count

Total Norm

droAna3

GT-------ATCTC-------------------------------------------------------------------------GAGAT---GCATCTG------TAAG------AGTAT-----CT------------GCATCTGCAAATGTATCTGTATCTGT------ATCTGTATCTGT------------------------------------------------------------ATCTGTATCTGTGCAAGACTTGCCACCTCTCCTTTTCT-------CCTTTTCCTGAGCAAATGT---CGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................................................................................................................CTGGATCTGG------------------------------------------------------------ATCTGTATC.............................................................	19	3	0.67	0.00	0.67	0.00	0.00
....................................................................................................................................................................CTGG------ATCTGGATCTGT------------------------------------------------------------ATC...................................................................	19	3	0.67	0.00	0.67	0.00	0.00
..............................................................................................................................................................CTGGATCTGG------ATCTGTATC.....................................................................................................................................	19	3	0.67	0.00	0.67	0.00	0.00
......................................................................................................................................................................GT------ATCTGTATCTGT------------------------------------------------------------GTGT..................................................................	18	5	0.20	0.00	0.00	0.00	0.20
............................................................................................................................................................ATCTGTATCTGT------ATCTGTGTG.....................................................................................................................................	21	5	0.20	0.00	0.20	0.00	0.00
..............................................................................................................................................................CTGTTTCTGT------TTCTGTATC.....................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
......................................................................................................................................................................GT------ATCTGTATCTGT------------------------------------------------------------GTGTGT................................................................	20	4	0.25	0.25	0.00	0.00	0.00
..........................................................................................................................................................GTATCTGTATCTGT------GTGT..........................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
...................................................................................................................................................TGCxACTGTATCTGTATCTGT------..............................................................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
..................................................................................................................................................................................GTATCTGT------------------------------------------------------------ATCTGTGTGT............................................................	18	5	0.20	0.00	0.00	0.00	0.20
..............................................................................................................................................................................ATCTGTATCTGT------------------------------------------------------------ATCTGTGTG.............................................................	21	5	0.20	0.00	0.20	0.00	0.00
....................................................................................................................................................................CTGT------TTCTGTTTCTGT------------------------------------------------------------ATC...................................................................	19	3	0.33	0.00	0.00	0.00	0.33
................................................................................................................................................................................CTGTTTCTGT------------------------------------------------------------TTCTGTATC.............................................................	19	3	0.33	0.00	0.00	0.00	0.33
..................................................................................................................................................................ATCTGT------ATCTGTATCTGT------------------------------------------------------------GTG...................................................................	21	5	0.20	0.00	0.20	0.00	0.00
................................................................................................................................................................GTATCTGT------ATCTGTGTGT....................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
....................................................................................................................................................................................ATCTGT------------------------------------------------------------ATCTGTATCTGTGTG.......................................................	21	5	0.20	0.00	0.20	0.00	0.00
...................................................................................................................................................................................CATCTGT------------------------------------------------------------ATCTGTATCTGTCCAA......................................................	23	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................GTATCTGTATCTGT------GTGTGT........................................................................................................................................	20	4	0.25	0.25	0.00	0.00	0.00
.....................................................................................................................................................................TGC------AxCTGTATCTGT------------------------------------------------------------ATCTGT................................................................	20	5	0.20	0.00	0.20	0.00	0.00
..................................................................................................................................................................................GTATCTGT------------------------------------------------------------ATCTGTGTGTGT..........................................................	20	4	0.25	0.25	0.00	0.00	0.00
...............................................................................................................................................................TGCAxCTGT------ATCTGTATCTGT------------------------------------------------------------......................................................................	20	5	0.20	0.00	0.20	0.00	0.00
.........................................................................................................................................................TGCAxCTGTATCTGT------ATCTGT........................................................................................................................................	20	5	0.20	0.00	0.20	0.00	0.00
.................................................................................................................................................................................TGCAxCTGT------------------------------------------------------------ATCTGTATCTGT..........................................................	20	5	0.20	0.00	0.20	0.00	0.00
................................................................................................................................................................GTATCTGT------ATCTGTGTGTGT------------------------------------------------------------......................................................................	20	4	0.25	0.25	0.00	0.00	0.00

droBip1

G-----------TG-------------------------------------------------------------------------CATCCTACGGATTCG------------------TAT-----CC------------GAGGCCTCAGATGCAGCTGTATCTGT------ATCTGTGAAT------------GTGAAATGTATCTGC----ATCGC--------AGTATCA--GCT---T-----CG-------GCTACG------------------------------------------CGTC---GCG

Size

Hit Count

Total Norm

dp4

GC-------TAGTGCCCACTACTGCCTTTG-------------------------------------------------------------------GCATGTA---TCTGT------AT--------CTGTACCCGTATCCGTATCCGTATCCGTTACTGTATCTGT------ATCTGTATCTGTAGCT-------------------GCTCTGAATGC--------AGTATAT-----------------------------------------ATTTCATCAAATT---------------TTTGTACTCGCA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................................................................................................................................ATGT------ATCTGTATCTGTAGC...............................................................................................................................	19	9	0.11	0.00	0.11	0.00	0.00
......................................................................................................................................................................GT------ATCTGTATCTGTATCT-------------------GC.........................................................................................................	20	8	0.13	0.00	0.13	0.00	0.00
....................................................................................................................................................................CTGT------ATCTGTATCTGTATCT-------------------...........................................................................................................	20	10	0.10	0.00	0.00	0.00	0.10
...............................................................................................................................................................TTTATCTGT------ATCTGTATCTGA..................................................................................................................................	21	8	0.13	0.00	0.13	0.00	0.00
......................................................................................................TA---TCTGT------AT--------CTGTATCTGTATCC..............................................................................................................................................................................	23	8	0.13	0.00	0.00	0.00	0.13
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTGTC...............................................................................................................................	21	8	0.13	0.13	0.00	0.00	0.00
..........................................................................................................................................ATCCGTATCCGTGTCCGTT...............................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................ATATATGT------ATCTGTATCTGTA.................................................................................................................................	21	7	0.14	0.00	0.14	0.00	0.00
..................................................................................................................................................................ATCTGT------ATCTGTATCTGT..................................................................................................................................	18	12	0.08	0.00	0.00	0.08	0.00
..............................................................................................................................................................CTGTATCTGA------ATCTGTATA.....................................................................................................................................	19	9	0.11	0.00	0.00	0.11	0.00
................................................................................................................................................................ATATATGT------ATCTGTATCTGTAGCT-------------------...........................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................CGCATxCGTATCCGTATCCGT................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTA.................................................................................................................................	19	11	0.09	0.00	0.00	0.09	0.00
..................................................................................................................................................................ATCCGT------ATCTGTATCTGT..................................................................................................................................	18	7	0.14	0.00	0.14	0.00	0.00
...................................................................................................ATGTA---TCTGT------AT--------CTGTAGC.....................................................................................................................................................................................	19	9	0.11	0.00	0.11	0.00	0.00
...................................................................................................................................................................TGTGT------ATATGTATCTGTAGCT-------------------...........................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................TATCTGT------ATCTGTATCTGTATCC-------------------...........................................................................................................	23	8	0.13	0.00	0.00	0.00	0.13
................................................................................................................................................................GTATCTGT------ATCTGTATCTGC..................................................................................................................................	20	8	0.13	0.00	0.13	0.00	0.00
..................................................................................................................................................................ATCTGT------ATCTGTATCTGTGGAT-------------------...........................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................CTGTATCTGT------ATCTGTATCT....................................................................................................................................	20	10	0.10	0.00	0.00	0.00	0.10
..............................................................................................................................................................ATGTATCTGT------ATCTGTAGC.....................................................................................................................................	19	9	0.11	0.00	0.11	0.00	0.00
.................................................................................................................................................................TATCTGT------ATCTGTATCTGTA.................................................................................................................................	20	10	0.10	0.00	0.00	0.10	0.00

droPer1

GT-------AGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCT-------GTGCATCCTACGGATGGCAG---GCTGT------ACAACCGTATCG------------GCAGC------------CGTATCGGT------A------------TCG----------------------------------------------------------GTGTATCTGTGTGACG------------------------------------------CGTC---GCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................................GGGCAGGAGCAGGGGCAGTT.........................................................................................................................................................................................................................................................	20	1	2.00	2.00	0.00	0.00	0.00	0.00
...........................................GCAGGGGCAGGGGCAGCGGA.............................................................................................................................................................................................................................................................	20	4	0.25	0.00	0.00	0.00	0.25	0.00
.......................GGCCAGGGGCTGxGGCAAC..................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................CCGGCAGGGGCAGGGGCAGGGGC.............................................................................................................................................................................................................................................................	23	2	0.50	0.50	0.00	0.00	0.00	0.00
.................................................GCAGGGGCAAGGGCAGCA.........................................................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................AGGGGCAGGGACGGGGGC.............................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...........................................GCAGTGGCAGTGGCAGGGGCA............................................................................................................................................................................................................................................................	21	18	0.06	0.06	0.00	0.00	0.00	0.00
.............................................AGGGGTAGGGGCAGGGGCAGG..........................................................................................................................................................................................................................................................	21	7	0.14	0.00	0.00	0.14	0.00	0.00
.............................................AGGGGCTGGGGCTGGGGC.............................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
...........................................GCAGAGGCAGGGGCATGGG..............................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00
...........................................GCAGGGGCAGGGGCAGGAGC.............................................................................................................................................................................................................................................................	20	10	0.10	0.10	0.00	0.00	0.00	0.00
...........................AATGGCAGCGGCAACGGCA..............................................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00	0.00

droWil1

CC-------TGGTAGAGAACGTTGGGGGAG-------------------------GGGGGGGTTAGTTTTCCAGGCTCGCTGCAAAACATCCTACGATGTGAAA---AT--------------------------------------------TGTGAAGGCTACTGA------A------------AGC-------------------GGT------GC---AATGC------------------GAGGAGAGCGACGCAATG------------------------------------------CGAC---GCG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................................................................................................................................................GAAGGCTGCTGA------A------------AGC-------------------GAT------..................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................GAAGGCTGCTGA------A------------AGC-------------------GAT------G.................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................A---AT--------------------------------------------TGGGAAGGCTGCTGA------..............................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droVir3

GT-------ATCTA-------------------------------------------------------------------------TATCT---GTATATGTA---TCTGT---------AT-----CTGTATCT------GTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCTGTATCT------------------------------------------------------------GTATCTATAT---T-----------TGCTTCTTTAAATCCGCCTC-TTTCGAGACATTTA---TCC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............A-------------------------------------------------------------------------TATCT---GTATATATA---TCTT.............................................................................................................................................................................................................	19	14	0.07	0.00	0.00	0.07	0.00	0.00
...............................................................................................GTATATGTA---TCTGT---------AT-----CTGTATC.....................................................................................................................................................................................	23	148	0.01	0.00	0.00	0.00	0.01	0.00
...................................................................................................................................................................................TATCTGTATCT------------------------------------------------------------GCAGCTA...........................................................	18	13	0.08	0.00	0.00	0.00	0.00	0.08
.........................................................................................................................................................................TCTGTATCTGTAGCTGTAGCT------------------------------------------------------------GTATCTA...........................................................	28	8	0.13	0.00	0.00	0.00	0.13	0.00
........................................................................................ATCT---GTATATGTG---GCTGT---------...................................................................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00	0.00
.............................................................................................................................................................TCTGTATCTGTATCTGGGTCT..........................................................................................................................................	21	150	0.01	0.01	0.00	0.00	0.00	0.00
................................................................................................TATATGTA---TCTGT---------AT-----CTGTATCT------G.............................................................................................................................................................................	24	146	0.01	0.01	0.00	0.00	0.00	0.00
................................................................................................................................................................................CTGTATCTGTATCT------------------------------------------------------------GTAACCA...........................................................	21	6	0.17	0.17	0.00	0.00	0.00	0.00

droMoj3

TT-------CAGTG-------------------------------------------------------------------------AATCT---GTATCTGTA---TCTGTATCTGTAT--------CT------GTATCTGTATCTGTATCTGTATCTGTATCTGT------ATCTGTATCTGTATCT-------------------GTATC-GTATCTGTATCT-------GTATCT---GT-ATCTGTATCTG---TATT------------------------------------------TGTA---TCT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................................................................................................................................................................................................ATCTGTATATG---TATT------------------------------------------TGT.......	18	511	0.00	0.00	0.00	0.00	0.00

droGri2

GC-------GA-TG-------------------------------------------------------------------------TATCT--CGTATCTCGG---CGAGT------ACGTC-----GC------------GCATCCGTATCTGCAAATGTATCTCT------ATCTATAGCTGTATCT------GAGCAATGTAT--G---T-AGTAT--------AGTATCT--GTT---GT-TGGGGTTTTCATATTGCT------------------------------------------TGTG---CTG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:31:07 EDT

dme-mir-2281

chr3R:10222121-10222223 -

Known_mirbase

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