dme-mir-2281- 12- and 20-way alignments

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
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr3R:10222106-10222238 -	TC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACACGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGCTGCTTTATTCATATCCATGAGACGCGTCGCG
droSim1	chr3R:11233896-11234028 +	GC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACCCGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCG
droSec1	super_0:11818438-11818570 +	GC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGTTGCTTTATTCGTATCCATGTGACGCGTCGCG
droYak2	chr3R:16218838-16218961 +	TC------------------------------------------------------------------CAGTGCATCCTACGGATGCCGAGCTGC------GTTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATCTGTATCTT--TCAG-------------TAT-TGCAATGTTGCAGTATCTTTGCTTTATTCGTATCCGTGTGACGCGTCGCG
droEre2	scaffold_4770:9756449-9756546 -	TC------------------------------------------------------------------CAGTGCATCCTACGGATGCCGAGCATC------GTTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGT------------ATCTG-------------TATCTGCAGTACGGCT-----------------GTATCCGTGTGACGCGGCGCG
droAna3	scaffold_13340:401762-401872 -	G----------------------------------------------------------------------TGCATCCTACGGATTCG---------------TATCTG--------------------------------------------------------------------------------------------------------------AGGCCCCGCATGCAGCTGTATCTGTGGCTGTGTCTGTGAATGTGAAATGTATCTGCA---TCGCAGTATCA--GCTT----C-----G--GCTACGCGTCGCG
dp4	chr2:16274089-16274236 -	GTAGGGGATCAGGCATGGCCAGAGGCAGGGACAGCGGCAACGGCAGGGGCTGGGGCAGCTTTTCCAGGCTGTGCATCCTACGGATGGCAGGCTGTA---------------------------------------------------------------------------------------------------------------------------------------CAACCGTATCGGCAGCCGTATCGG-------------TATCGG--------------------------TGTATCTGTGTGACGCGTCGCG
droPer1	super_0:4124990-4125137 +	GTAGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCTGTGCATCCTACGGATGGCAGGCTGTA---------------------------------------------------------------------------------------------------------------------------------------CAACCGTATCGGCAGCCGTATCGG-------------TATCGG--------------------------TGTATCTGTGTGACGCGTCGCG
droWil1	Unknown	CC------------------------------------------------------------------TGGTAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGCGACGCAATGCGACGCG
droVir3	scaffold_13047:14699724-14699849 +	G----------------------------------------------------------------------TGCATCCTACGGAACTGCAACAGTTCGTATCTC-----ACGGCATCGCC--------AGCCTGCCAGCCAGCCAGCCGCT-------------------------------------------------GCCTGCCTG------------CCTGTAGCTGTAAATGTATCTGCATCTGTATCTG-------------TAAC----------------------------------A-----GTGCGGCGCG
droMoj3	scaffold_6540:18156181-18156336 +	G----------------------------------------------------------------------TACATCCTACGGAACTGCAACAGTTCGTATCTC-----ACGGCATC---------------------------AATGggTGggtGggtGggtGggttGgtGTgttggtGGgtGgTtGTTGGgTtGggTGGCCTGCCTG------------CCTGTAGCTGTAAATGTATCTGCATTTGTATCTG-------------TAAC----------------------------------A-----GTGCGAGGCG
droGri2	scaffold_14830:5268153-5268296 -	G----------------------------------------------------------------------TGCATCCTACGGAACTGCCACAGTTCGTATCTC-----ACGGCATCGCCTGCCACTCAGCTAGGCAGCTAGCCA---------------------------------------------------GCTAGCCTGACTCCCTGTTGCCGTAGCCGTAGCTGTAAATGTATCTGCATCTGTATCTG-------------TAAC----------------------------------A-----GTGCGACGCG

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:10222106-10222238 -	NA	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACACG-------TAT---TATCTGCAGCTGCAGATGCAAATGTATA------TG--TATCTGTATCT-----------GTATC-------------TGCAGTATT--GCAG--------TATCGCTGCTTT-AT--------TCATAT-------CC---ATGAGACGCGTCGCG
droSim1	chr3R:11233896-11234028 +	1	GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACCCG-------TAT---TATCTGCAGCTGCAGATGCAAATGTATA------TG--TATCTGTATCT-----------GTATC-------------TGCAGTATT--GCAG--------TATCGCTGCTTT-AT--------TCGTAT-------CC---ATGTGACGCGTCGCG
droSec1	super_0:11818438-11818570 +	1	GC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGTACTCG-------TAT---TATCTGCAGCTGCAGATGCAAATGTATA------TG--TATCTGTATCT-----------GTATC-------------TGCAGTATT--GCAG--------TATCGTTGCTTT-AT--------TCGTAT-------CC---ATGTGACGCGTCGCG
droYak2	chr3R:16218838-16218961 +	2	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCTGC-----G--------T---TATCTGCAGCTGCAGATGCAAATGTATC------TG--TATCTTT--CA-----------GTAT--------------TGCAATGTT--GCAG--------TATCTTTGCTTT-AT--------TCGTAT-------CC---GTGTGACGCGTCGCG
droEre2	scaffold_4770:9756449-9756546 -	3	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGCCGA---GCATC-----G--------T---TATCTGCAGCTGCAGATGCAAATGTATC------TG--TATCT------------------------------------GCAGTA--CGGC----------------------------------TGTAT-------CC---GTGTGACGCGGCGCG
droEug1	scf7180000409584:290211-290321 +	1	TC-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTTGACGGGCCGT-----A--------T---TATCTGCAGCTGCAGATGCAAATGTATC------TG--TATCT------------------------------------GCAGTA--TCGC----------------TGTTTTAAT--------TCGTAT-------CT---GTGTGACGCGTCGCG
droBia1	scf7180000302075:5567085-5567191 -	2	CG-------CAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT-----G--------C---TATCTGCAGCTGCAGATGCGAATGTATC------TG--TATCT------------------------------------GCAGTA--TCGC----------------CGCTTT-AT--------TCGTAT-------CT---GTGCGACGCGTCGCG
droTak1	scf7180000415396:184472-184588 -	3	TCAGGCACCCAGTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT-----A--------C---TATCTGCAGCTGCAGATGCAAATGTATC------TG--TATCT------------------------------------GCAGTA--TCGC-------------CGCTGCTTT-AT--------TCGTAT-------CT---GTGCGACGCGTCGCG
droEle1	scf7180000491011:1825266-1825390 +	2	TA-------TACTG-------------------------------------------------------------------------CATAG---AGATGAAGA---TACAGATACG-------------TATCTGTAAATGTATCTGTAAATGTATC------TG--TATCTGTGTCT-----------GTGTC-------------TGTGGCTGG-TGCAT--------TCTGAATGCACC-AT--------TAA----------TG---ATCAGACGGGCGGCG
droRho1	scf7180000762751:7752-7858 -	2	A-----------TG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGC-----A--------T---TATCTGCAGCTGCAGATGCAAATGTATC------TG--TATCT------------------------------------GCTGTA--TCGCCG-------------CTTCATT-AT--------TTGTGT-------CT---GTGTGACGCGTCGCG
droFic1	scf7180000453912:712927-713041 -	6	GC---------GTG-------------------------------------------------------------------------CATCCTACGGATGTCGA---GCAGT-----G--------C---TATCTGCAGCTGCAGATGCAAATGTATC------TGGGTATCCGT---------------GTATC-------------TGCGCTA--TCGCAG----------------TTTC-AT--------TTGTAT-------CT---GTGTGACGCGTCGCG
droKik1	scf7180000302610:1086546-1086678 -	6	TC-------T--TT-------------------------------------------------------------------------CCTTCCGCCGCTGTGTA---GCTGTATCTG-------TATCTGTATCTGTATCTGTAGCTGAAAATGTATC------TG--TATCTGTAGCT-----------GTATC-------------TTTTGCTAA--GCCAGCCGAGGG-GCCTCTGTTTT-TT---------TAAAC-----------------CCAATTCTCG
droAna3	scaffold_13117:2846333-2846460 -	1	GT-------ATCTC-------------------------------------------------------------------------GAGAT---GCATCTG------TAAG-----A--------G---TATCTGCATCTGCAAATGTATCTGTATC------TG--TATCTGTATCT-----------GTATC-------------TGTATCTGT--GCAAGACTTGCC-ACCTCTCCTTT-TC--------TCCTTT-------TCCTGA--GCAAATGTCGC-
droBip1	scf7180000394085:572453-572558 +	1	G-----------TG-------------------------------------------------------------------------CATCCTACGGATTC-------------------------G---TATCCGAGGCCTCAGATGCAGCTGTATC------TG--TATCTGTGA-----------------ATGTGAAATGTATCTG---CATC--GCAG--------TATC--AGCTT-------------CG-----------------GCTACGCGTCGCG
dp4	chrXR_group8:8158458-8158593 +	1	GC-------TAGTG-------------------------------------------------------------------------CCCACTACTGCCTTTGG---CATGTATCTG-TATCTGTACCCGTATCCGTATCCGTATCCGTTACTGTATC------TG--TATCTGTATCT-----------GTAGC-------------TGCTCTGA--------------------ATGCAGT-ATATATTTCATCAAAT-------TT---TTGT-A---CTCGCA
droPer1	super_0:4124990-4125137 +	1	GT-------AGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCT-------GTGCATCCTACGGATGGCAG---GCTGT-----ACAACC---G---TATCGG--------------------------------CAGCCGTATCG-----------GTATC-------------GG---------------------------------------------TGTAT-------CT---GTGTGACGCGTCGCG
droWil1	scaffold_181089:10073219-10073346 +	1	CC-------TGGTAGA----------------------GAACG-TTGGGG--GAGGGGGGGGTTAGTTTTCCAGGCTCGCTGCAAAACATCCTACGATGTGAAA---A-------------------------------------TTGTGAAGGCTAC------TG--AAAGC------------------------------------GGTGCAAT--GCGA-------------------------------GGAGAG-------CG---ACGCAATGCGACGCG
droVir3	scaffold_12928:2113057-2113188 +	4	GT-------ATCTA-------------------------------------------------------------------------TATCT---GTATATGTA---TCTGTATCTG-------------TATCTGTATCTGTATCTGTATCTGTATCTGTATCTG--TATCTGTATCT-----------GTATC-------------TGTATC-------TA----------TATTTGCTTC-T---------TTAAATCCGCCTCTT---TCGAGACATTTATCC
droMoj3	scaffold_6654:2537235-2537365 +	19	TT-------CAGTG-------------------------------------------------------------------------AATCT---GTATCTGTA---TCTGTATCTG-TATCT---G---TATCTGTATCTGTATCTGTATCTGTATC------TG--TATCTGTATCTGTATCTGTATCGTATC-------------TG---TA--T--C-------------TGTATCTGT-AT--------CTGTAT-------CT---G---TATTTGTATCT
droGri2	scaffold_14830:2155779-2155908 -	8	GC-------GA-TG-------------------------------------------------------------------------TATCT--CGTATCTCGG---CGAGT-----A--------C---GTCGCGCATCCGTATCTGCAAATGTATC------TC--TATCTATAGCT-----------GTATCTGAGCAATGTA--TG---TAGT--ATAG--------TATC--TGTTGT-TG--------GGGTTT-------TC---ATATTGCTTGTGCTG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACACGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGCTGCTTTATTCATATCCATGAGACGCGTCGCG

Size

Hit Count

Total Norm

droSim1

GC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACCCGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGCTGCTTTATTCGTATCCATGTGACGCGTCGCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................................................................................................................................................................................ATGTATCTGTATCTG-------------AACC..................................................	19	1	4.00	0.00	0.00	4.00	0.00
...........................................................................................................................................................................................................................................TGTATCTGTATCTGTATCTC-------------T.....................................................	21	2	1.50	0.50	1.00	0.00	0.00
..............................................................................................................................................................................................................................................ATCCGTATCTGTATCTG-------------TATC..................................................	21	1	3.00	0.00	3.00	0.00	0.00
.................................................................................................................................................................................................................................................TGTATCTGTATCTG-------------TATCTCT...............................................	21	2	1.50	0.50	1.00	0.00	0.00
..........................................................................................................................................................................................................................................CTGTATCTGTATCTGTATCT....................................................................	20	2	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................TATCTGAATCTG-------------TATCTGA...............................................	19	1	2.00	0.00	2.00	0.00	0.00
.......................................................................................................................................................................................................................................................TGTATCTG-------------TATCTGCATC............................................	18	3	0.67	0.00	0.00	0.00	0.67
..............................................................................................................................................................................................................................................CTGTGTATCTGTATCTG-------------TATC..................................................	21	1	2.00	0.00	0.00	0.00	2.00
..................................................................................................................................................................................................................................................GTATCTGCATCGG-------------TATCTGC...............................................	20	1	2.00	0.00	0.00	2.00	0.00
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------T.....................................................	18	2	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................ATGTATCTGTATCTG-------------AAC...................................................	18	1	2.00	0.00	0.00	2.00	0.00
................................................................................................................................................................................................................................................CTGTATCTGTATCTG-------------TATCT.................................................	20	2	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................ATCTGTATCTG-------------TATCTGT...............................................	18	2	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................TGTATCTGTATCTGCATC.....................................................................	18	3	0.67	0.00	0.00	0.00	0.67
.................................................................................................................................................................................................................................................TGTATCTGTATCTG-------------CATC..................................................	18	3	0.67	0.00	0.00	0.00	0.67
....................................................................................................................................................................................................................................................ATCTGTATCTG-------------TGTCTGTA..............................................	19	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................................ATCTGTATCTGTGTCTG-------------TA....................................................	19	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................................................................................................................GTATCTGTATCTG-------------TATCC.................................................	18	2	0.50	0.00	0.00	0.00	0.50
................................................................................................................................................................................................................................................CTGTATCTGTATCTG-------------TAC...................................................	18	2	0.50	0.00	0.00	0.00	0.50
...............................................................................................................................................................................................................................................AACGTATCTGTATCTG-------------TA....................................................	18	2	0.50	0.00	0.00	0.00	0.50
....................................................................................................................................................................................................................................................ATTTGTATCTG-------------CATCTGC...............................................	18	2	0.50	0.00	0.00	0.00	0.50
............................................................................................................................................................................................................................................GTATCTGTATCTGTATCTG-------------TA....................................................	21	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................................................................................................................................................TGTATCTGTATCTGTATC.....................................................................	18	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................................................................................................................GTATCTGTATCTG-------------TATCTGTA..............................................	21	2	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................................................................................................................ATCTGTATCTG-------------TATCTGTA..............................................	19	2	0.50	0.00	0.00	0.00	0.50
.....................................................................................................................................................................................................................................................TCTGAATCTG-------------TATCTGCC..............................................	18	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGTATCTG-------------TATCT.................................................	24	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................CTGTATCTGTATCTG-------------CAT...................................................	18	2	0.50	0.00	0.00	0.00	0.50
..........................................................................................................................................................................................................................................GTxTTTATGTATCTGTATCTG-------------......................................................	20	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................CAAATGTATCTGTATCTGA........................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................TGTATCTGTATCTG-------------TATC..................................................	18	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................TGTATCTTTATCTG-------------TATCTG................................................	20	2	0.50	0.00	0.00	0.50	0.00
...............................................................................................................................................................................................................................................TATCTATCTGTATCTG-------------AATC..................................................	20	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................AACGTATCTGTATCTGTA.......................................................................	18	2	0.50	0.00	0.00	0.00	0.50
...........................................................................................................................................................................................................................................TGTATCTTTATCTGTATCTG-------------......................................................	20	2	0.50	0.00	0.00	0.50	0.00
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------TATCTG................................................	23	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................TATCTGTATCTGTATCTG-------------TATT..................................................	22	2	0.50	0.00	0.00	0.00	0.50
......................................................................................................................................................................................................................................................CTGTATCTG-------------TATCTGTAC.............................................	18	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................................ATTTGTATCTGTATCTG-------------TATC..................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGTATCC....................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------TATCC.................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................TGCATTTGTATCTG-------------TATCTGC...............................................	21	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................TCAGTATCTGTATCTG-------------TATCT.................................................	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................................................................................CTGTATCTGTATCTGTATCTG-------------TATC..................................................	25	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................TGTATCTGTATCTG-------------TATCTCC...............................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................TCTTTATCTGTATCTG-------------TATCT.................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................................TATCTGTATCTG-------------TATCTGTATT............................................	22	2	0.50	0.00	0.00	0.00	0.50
......................................................................................................................................................................................................................................................CTGTATCTG-------------TATCTGCAT.............................................	18	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------TA....................................................	19	2	0.50	0.00	0.00	0.00	0.50
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------AATCT.................................................	22	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................GTATCTTTATCTG-------------TAGCT.................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

GC------------------------------------------------------------------CAGTGCATCCTACGGATGTCGAGCAGTACTCGTATTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATATGTATCTGTATCTG-------------TATCTGCAGTATTGCAGTATCGTTGCTTTATTCGTATCCATGTGACGCGTCGCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................................................................................................................................................................................................................GTATCTGCATCGG-------------TATCTGC...............................................	20	1	1.00	0.00	1.00	0.00
...........................................................................................................................................................................................................................CAGCTGCAGATGCAAATGTATATGT..............................................................................	25	1	1.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................ATATGTATCTGTGTGTG-------------T.....................................................	18	1	1.00	0.00	1.00	0.00
................................................................................................................................................................................................................................................ATGCATCTGCATCTG-------------TATCT.................................................	20	1	1.00	0.00	1.00	0.00
............................................................................................................................................................................................................................................GTATxTGTATCTGTATCTG-------------......................................................	18	2	0.50	0.00	0.00	0.50
............................................................................................................................................................................................................................................ATATATGTATCTTTATCTG-------------T.....................................................	20	1	1.00	0.00	0.00	1.00
................................................................................................................................................................................................................................GCAGATCCAAGTGTATATG...............................................................................	19	1	1.00	0.00	0.00	1.00
..............................................................................................................................................................................................................................................ATATGTATCTTTATCTG-------------TA....................................................	19	1	1.00	0.00	0.00	1.00
...........................................................................................................................................................................................................................................TATATATGTATCTTTATCTG-------------T.....................................................	21	1	1.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................GTATxTGTATCTG-------------TATCTG................................................	18	2	0.50	0.00	0.00	0.50
..............................................................................................................................................................................................................................................ACAAGTATCTGTATCTG-------------TATCT.................................................	22	1	1.00	1.00	0.00	0.00

droYak2

TC------------------------------------------------------------------CAGTGCATCCTACGGATGCCGAGCTGC------GTTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGTATCTGTATCTT--TCAG-------------TAT-TGCAATGTTGCAGTATCTTTGCTTTATTCGTATCCGTGTGACGCGTCGCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................................................................................................................GTATCTGTATCTT--TCCT-------------TAT-..................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TC------------------------------------------------------------------CAGTGCATCCTACGGATGCCGAGCATC------GTTATCTG--------------------------------------------------------------------------------------------------------------CAGCTGCAGATGCAAATGT------------ATCTG-------------TATCTGCAGTACGGCT-----------------GTATCCGTGTGACGCGGCGCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................................................................................................................................GT------------ATCTG-------------TATCTGCAGCT...........................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

G----------------------------------------------------------------------TGCATCCTACGGATTCG---------------TATCTG--------------------------------------------------------------------------------------------------------------AGGCCCCGCATGCAGCTGTATCTGTGGCTGTGTCTGTGAATGTGAAATGTATCTGCA---TCGCAGTATCA--GCTT----C-----G--GCTACGCGTCGCG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................................................................................................................................................................................................................................GGCCGTGTGTGTGAATGTG...........................................................	19	1	5.00	1.00	4.00	0.00	0.00
.....................................................................................................................................................................................................................................................GCCGTGTGTGTGAATGTG...........................................................	18	1	3.00	2.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................TCTGTGGCTGTGTCCGTGTAT..............................................................	21	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................................TGTGGCCGTGTGTGTGAATGTG...........................................................	22	1	1.00	0.00	1.00	0.00	0.00

dp4

GTAGGGGATCAGGCATGGCCAGAGGCAGGGACAGCGGCAACGGCAGGGGCTGGGGCAGCTTTTCCAGGCTGTGCATCCTACGGATGGCAGGCTGTA---------------------------------------------------------------------------------------------------------------------------------------CAACCGTATCGGCAGCCGTATCGG-------------TATCGG--------------------------TGTATCTGTGTGACGCGTCGCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................................................................................................................................................................................................................................................................TG	24	17	1.47	0.24	0.00	1.24	0.00
.................................................................................................................................................................................................................................................................................................................................G	25	15	0.53	0.07	0.00	0.47	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	25	15	0.53	0.07	0.00	0.47	0.00
................................................................................................................................................................................................................................................................................................................................TG	25	13	0.46	0.08	0.00	0.38	0.00
.................................................................................................................................................................................................................................................................................................................................G	23	20	0.30	0.00	0.00	0.30	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	23	20	0.30	0.00	0.00	0.30	0.00
.................................................................................................................................................................................................................................................................................................................................G	18	29	0.17	0.00	0.17	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	26	11	0.45	0.00	0.00	0.45	0.00
.................................................................................................................................................................................................................................................................................................................................G	19	26	0.19	0.08	0.08	0.04	0.00
................................................................................................................................................................................................................................................................................................................................TG	22	21	0.19	0.00	0.00	0.19	0.00
................................................................................................................................................................................................................................................................................................................................TT	18	37	0.08	0.03	0.03	0.03	0.00
................................................................................................................................................................................................................................................................................................................................TG	19	27	0.11	0.04	0.00	0.07	0.00
................................................................................................................................................................................................................................................................................................................................TG	26	14	0.21	0.00	0.00	0.21	0.00
.................................................................................................................................................................................................................................................................................................................................G	26	13	0.23	0.15	0.00	0.08	0.00

droPer1

GTAGGGGATCAGGCATGGCCAGGGGCAGCGGCAACGGCAGGGGCAGGGGCAGGGGCAGCTTTTCCAGGCTGTGCATCCTACGGATGGCAGGCTGTA---------------------------------------------------------------------------------------------------------------------------------------CAACCGTATCGGCAGCCGTATCGG-------------TATCGG--------------------------TGTATCTGTGTGACGCGTCGCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................................................................................................................................................................................................................................G	20	32	0.47	0.47	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	20	32	0.47	0.47	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	20	26	0.46	0.12	0.35	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	18	41	0.22	0.17	0.05	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	18	41	0.22	0.17	0.05	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	21	29	0.31	0.31	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	21	29	0.31	0.31	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	18	26	0.31	0.04	0.27	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	19	42	0.19	0.10	0.10	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	19	42	0.19	0.10	0.10	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................GTGCG	19	42	0.19	0.10	0.10	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	21	29	0.24	0.17	0.07	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	18	39	0.18	0.08	0.00	0.08	0.03	0.00
................................................................................................................................................................................................................................................................................................................................TG	20	32	0.22	0.19	0.00	0.03	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	19	36	0.14	0.14	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	21	23	0.22	0.17	0.04	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	24	20	0.25	0.15	0.00	0.05	0.05	0.00
.................................................................................................................................................................................................................................................................................................................................G	22	35	0.11	0.11	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	22	26	0.15	0.15	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	18	27	0.11	0.04	0.00	0.00	0.00	0.07
.................................................................................................................................................................................................................................................................................................................................G	20	32	0.09	0.09	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................CGTG	20	29	0.10	0.10	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	21	20	0.15	0.15	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................CG	20	29	0.10	0.10	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................CG	19	4	0.75	0.75	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................GG	19	24	0.13	0.13	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	22	30	0.10	0.10	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	19	27	0.11	0.11	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	21	20	0.15	0.15	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................TG	26	15	0.20	0.20	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	18	28	0.11	0.11	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................CG	21	4	0.75	0.75	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	20	32	0.09	0.09	0.00	0.00	0.00	0.00
...............................................................................................................................................................................................................................................................................................................................GTG	22	30	0.10	0.10	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................CGAG	19	4	0.75	0.75	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................G	20	22	0.14	0.14	0.00	0.00	0.00	0.00

droWil1

CC------------------------------------------------------------------TGGTAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGCGACGCAATGCGACGCG

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

G----------------------------------------------------------------------TGCATCCTACGGAACTGCAACAGTTCGTATCTC-----ACGGCATCGCC--------AGCCTGCCAGCCAGCCAGCCGCT-------------------------------------------------GCCTGCCTG------------CCTGTAGCTGTAAATGTATCTGCATCTGTATCTG-------------TAAC----------------------------------A-----GTGCGGCGCG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................TGCAAGAGTTCGAATCTC-----.....................................................................................................................................................................................................................	18	1	8.00	4.00	0.00	0.00	3.00	1.00
.....................................................................................ATGCAAGAGTTCGTATCTC-----.....................................................................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................GTATCTGTACCTGTATCTG-------------TA....................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................................TATATGTATCTGTATCTGTATCTG-------------......................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................TATCTGTAACTGTATCTGCATCTGT........................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................TAACTGTATCTGCATCTGTATCTG-------------......................................................	24	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGTATCTG-------------TA....................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................ATCTGTATCTG-------------TGAC----------------------------------T-----GTG.......	19	1	1.00	0.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGTATCT....................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................ATCTGTATCTGTATCTG-------------TATC----------------------------------................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGTAGCTG-------------TA....................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................................................................................GTATATGTATCTGTATCTGTATC.....................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................................................................CTGGATCTGTATCTG-------------TATC----------------------------------................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................TC-----AAGGCATCGCC--------AGACT.............................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................................................................................................................................................................................................................TCTGTAACTGTATCTGCATCTGTAT......................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................................................GTATCTGTATCTGCATCTG-------------T.....................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................................................................................................................................................................................................................GTATCTGTATCTGCATCTGT........................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00

droMoj3

G----------------------------------------------------------------------TACATCCTACGGAACTGCAACAGTTCGTATCTC-----ACGGCATC---------------------------AATGggTGggtGggtGggtGggttGgtGTgttggtGGgtGgTtGTTGGgTtGggTGGCCTGCCTG------------CCTGTAGCTGTAAATGTATCTGCATTTGTATCTG-------------TAAC----------------------------------A-----GTGCGAGGCG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................................................................................................................GTGGGTGGGTGGGTGGTA...........................................................................................................................................................	18	1	105.00	105.00	0.00	0.00	0.00
.....................................................................................................................................................GCGGGTGGTTGGGTGGGT...........................................................................................................................................................	18	1	83.00	73.00	5.00	5.00	0.00
.................................................................................................................................................GTGGGTGGGTGGGTGGCT...............................................................................................................................................................	18	3	11.00	11.00	0.00	0.00	0.00
.........................................................................................................................................................GTGGGTGGGTGGGTGGCT.......................................................................................................................................................	18	3	11.00	11.00	0.00	0.00	0.00
.....................................................................................................................................................GTGGGTGGGTGGGTGGCT...........................................................................................................................................................	18	3	11.00	11.00	0.00	0.00	0.00
.............................................................................................................................................................................GTGGGTGGGTGGTTGGTGGG.................................................................................................................................	20	1	22.00	19.00	3.00	0.00	0.00
.....................................................................................................................................................GTGGGTGGGTGGGTGGTT...........................................................................................................................................................	18	4	5.00	5.00	0.00	0.00	0.00
.................................................................................................................................................GTGGGTGGGTGGGTGGTT...............................................................................................................................................................	18	4	5.00	5.00	0.00	0.00	0.00
.........................................................................................................................................................................GTGGGTGGGTGGGTGGTT.......................................................................................................................................	18	4	5.00	5.00	0.00	0.00	0.00
.........................................................................................................................................................GTGGGTGGGTGGGTGGTT.......................................................................................................................................................	18	4	5.00	5.00	0.00	0.00	0.00
.....................................................................................................................................................GTGGGTGGTTGGGTGGTTTG.........................................................................................................................................................	20	1	17.00	5.00	7.00	4.00	1.00
.....................................................................................................................................................GTGGGTGGTTGGGTGGATTG.........................................................................................................................................................	20	1	16.00	12.00	1.00	0.00	3.00
.....................................................................................................................................................GTGGGTGGCTGGGTGGGTTG.........................................................................................................................................................	20	1	12.00	6.00	3.00	3.00	0.00
.....................................................................................................................................................GTGGGTGGATGGGTGGTTT..........................................................................................................................................................	19	1	11.00	3.00	3.00	5.00	0.00
.....................................................................................................................................................GTGGGCGGTTGGGTGGGT...........................................................................................................................................................	18	1	10.00	7.00	1.00	1.00	1.00
.....................................................................................................................................................GTGGGTGGGTGGGTxGTTTGG........................................................................................................................................................	20	1	8.00	8.00	0.00	0.00	0.00
.....................................................................................................................................................GTGGGTGGCTGGGTGGGTTT.........................................................................................................................................................	20	1	8.00	2.00	4.00	2.00	0.00
....................................................................................................................................................TGxGGGTGGTTGGGTGGGT...........................................................................................................................................................	18	2	4.00	1.50	2.00	0.50	0.00
.............................................................................................................................................................................GTGGGTGGGTGGTTGGTGGGT................................................................................................................................	21	1	7.00	7.00	0.00	0.00	0.00
......................................................................................................................................................TGGGTGGGTGGGTGGCTGG.........................................................................................................................................................	19	2	3.50	0.00	2.50	1.00	0.00
..................................................................................................................................................TGGGTGGGTGGGTGGCTGG.............................................................................................................................................................	19	2	3.50	0.00	2.50	1.00	0.00
......................................................................................................................................................TGGGTGGGTGGGTGGATGG.........................................................................................................................................................	19	2	3.00	0.50	2.00	0.50	0.00
.....................................................................................................................................................ATGGGTGGGTGGTTGGG............................................................................................................................................................	17	2	3.00	0.00	3.00	0.00	0.00
..........................................................................................................................................................TGGGTGGGTGGGTGGCT.......................................................................................................................................................	17	4	1.50	0.00	1.50	0.00	0.00
.........................................................................................................................................................GTGGGTGGGTGGGTGGAT.......................................................................................................................................................	18	3	2.00	2.00	0.00	0.00	0.00
..................................................................................................................................................TGGGTGGGTGGGTGGATGG.............................................................................................................................................................	19	2	3.00	0.50	2.00	0.50	0.00
.....................................................................................................................................................GTGGGTGGGTGGGTTGGTTG.........................................................................................................................................................	20	2	3.00	2.50	0.50	0.00	0.00
.....................................................................................................................................................GTGGGTGGGTGGGTGGAT...........................................................................................................................................................	18	3	2.00	2.00	0.00	0.00	0.00
......................................................................................................................................................TGGGTGGGTGGGTGGCT...........................................................................................................................................................	17	4	1.50	0.00	1.50	0.00	0.00
.................................................................................................................................................ATGGGTGGGTGGTTGGG................................................................................................................................................................	17	2	3.00	0.00	3.00	0.00	0.00
..................................................................................................................................................TGGGTGGGTGGGTGGCT...............................................................................................................................................................	17	4	1.50	0.00	1.50	0.00	0.00
.................................................................................................................................................GTGGGTGGGTGGGTGGAT...............................................................................................................................................................	18	3	2.00	2.00	0.00	0.00	0.00
.........................................................................................................................................................GTGGGTGGGTGGGTTGGTTG.....................................................................................................................................................	20	2	3.00	2.50	0.50	0.00	0.00
.....................................................................................................................................................GTGGGTGGGTGGCTGGGTTT.........................................................................................................................................................	20	1	5.00	1.00	1.00	3.00	0.00
......................................................................................................................................................TGGGTGGCTGGGTGGGTTG.........................................................................................................................................................	19	2	2.50	0.00	0.00	2.50	0.00
..................................................................................................................................................TGGGTGGCTGGGTGGGTTG.............................................................................................................................................................	19	2	2.50	0.00	0.00	2.50	0.00
.....................................................................................................................................................GTGGGTGGCTGGGTGGGTTGC........................................................................................................................................................	21	1	5.00	0.00	1.00	0.00	4.00
.........................................................................................................................................................GTGGGTGGGTGGCTGGGTGT.....................................................................................................................................................	20	1	5.00	1.00	3.00	1.00	0.00
.....................................................................................................................................................GCGGGTGGTTGGGTGGGTT..........................................................................................................................................................	19	1	4.00	2.00	1.00	1.00	0.00
.............................................................................................................................................................................GTGGGTGGGTGGTTGGTGGGTT...............................................................................................................................	22	1	4.00	1.00	2.00	1.00	0.00
..........................................................................................................................................................TGGGTGGGTGGGTTGGTTG.....................................................................................................................................................	19	3	1.33	0.33	0.67	0.33	0.00
.................................................................................................................................................ATGGGCGGGTGGGTGGCT...............................................................................................................................................................	18	1	4.00	1.00	2.00	1.00	0.00
....................................................................................................................................................GGTGGGTGGTTGGGTGGATTG.........................................................................................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
..................................................................................................................................................TGGGTGGCTGGGTGGCTGGG............................................................................................................................................................	20	1	4.00	3.00	1.00	0.00	0.00
..................................................................................................................................................TGGGTGGGTGGGTTGGTTG.............................................................................................................................................................	19	3	1.33	0.33	0.67	0.33	0.00
......................................................................................................................................................TGGGTGGGTGGGTTGGTTG.........................................................................................................................................................	19	3	1.33	0.33	0.67	0.33	0.00
.............................................................................................................................................................................GTGGGTGGGTGGTTGGTGG..................................................................................................................................	19	1	4.00	4.00	0.00	0.00	0.00
.....................................................................................................................................................GTGGTTGGGTGGGTGGGTC..........................................................................................................................................................	19	1	3.00	3.00	0.00	0.00	0.00
.................................................................................................................................................ATGGGTGGGTGGGTGTGA...............................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
..................................................................................................................................................TGGGTGGATGGGTGGATGGG............................................................................................................................................................	20	1	3.00	1.00	1.00	1.00	0.00
......................................................................................................................................................TGGGTGGCTGGGTGGGTTA.........................................................................................................................................................	19	1	3.00	0.00	1.00	2.00	0.00
......................................................................................................................................................TGGGTGGGTGGTTGGGTTT.........................................................................................................................................................	19	1	3.00	0.00	3.00	0.00	0.00
.....................................................................................................................................................GTGGGTGAGGGGGTGGGT...........................................................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
.................................................................................................................................................CTGGGTGGGTGGTTGGGTGG.............................................................................................................................................................	20	1	3.00	1.00	0.00	2.00	0.00
.............................................................................................................................................................................GTGGGTGGGTGGTTGGTGGGTTG..............................................................................................................................	23	1	3.00	2.00	1.00	0.00	0.00

droGri2

G----------------------------------------------------------------------TGCATCCTACGGAACTGCCACAGTTCGTATCTC-----ACGGCATCGCCTGCCACTCAGCTAGGCAGCTAGCCA---------------------------------------------------GCTAGCCTGACTCCCTGTTGCCGTAGCCGTAGCTGTAAATGTATCTGCATCTGTATCTG-------------TAAC----------------------------------A-----GTGCGACGCG

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image									None

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