dme-mir-4971- Best orthologs

dme-mir-4971	chr2L:3463289-3463400 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 3463361-3463381
   star strand at position 3463306-3463328
   mutations
   read mismatches

Notes: droSim1 ortholog may lie in a gap at position chr2L:3417964-3420113

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:3463274-3463415 -		1	GGAAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droSim1	chr3R:4556078-4556201 -	LASTZ	4	GCCAACTGGCAAGTCC---TCGCCAGT--------GGATGTC----ACCAGC-AACCAGTTGCCCAGC------CAG---GAGCC-----------------------GGTC-ATGTTGACCAC-T--GTGCCACAGCCC----------------------ACGCCGCCCAGGAGCAGCGCCTTCAG-G--------CCTGTGATA
droSec1	super_129:25371-25512 -	LASTZ	3	GGAAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------AGTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droYak2	chrU:14964015-14964156 +	LASTZ	4	GGAAGG-GCCAACTTC---TCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droEre2	scaffold_4929:3498112-3498253 -	LASTZ	3	GGAAGG-GCCAACTTC---ACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droEug1	scf7180000409554:2625850-2625991 +	LASTZ	4	GGAAGG-GCCAATTTC---TCGGCCCT--------CGACACAGTAGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAATTCTGCCGCT---GGCGATA--GATT------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCT-G--------GCTCGGATG
droBia1	scf7180000302261:1009341-1009482 -	LASTZ	4	GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAACTCTGCCGCT---GGCGACA--GACT------CTCAGCCA--CTGACAACGCCC----------------------ACCTGCTGTTCGAGGAGATCATGTCC-G--------GCTCGGACG
droTak1	scf7180000415438:449917-450058 +	LASTZ	4	GGAAGG-GCCAACTTC---TCGGCTTT--------GGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------GTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAGATAATGTCC-G--------GTTCGGATG
droEle1	scf7180000490728:125384-125525 -	LASTZ	4	GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCC---GGCGACA--GATT------GTCAGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG
droRho1	scf7180000779523:136149-136290 -	LASTZ	4	GGAATG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCC---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTTGAGGAGATCATGTCC-G--------GCTCGGATG
droFic1	scf7180000453924:1447325-1447466 -	LASTZ	4	GGCAGG-CCGAACTAC---TCGGCCCT--------CGACACGGTGGACGAACTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCT---GGCGACA--GACT------GTCCGCCA--CTGACAACGCCC----------------------ACTCGTTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG
droKik1	scf7180000302472:1777222-1777363 +	LASTZ	4	GGAATG-GCCAACTTC---TCGGCCCT--------CGACACAGTGGACGAGCTTGTCAGTGGCGGATC------AAC---GAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG
droAna3	scaffold_12943:2497935-2498076 +	LASTZ	4	GGCAGA-GCCAACTTC---GGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CAT---AAAGAATCCTGCCGCT---GGCGACA--GACA------GTCGGCCA--CTGACAACGCGC----------------------ACTCGCTGTTCGAGGAAATAATGTCT-G--------GCTCCGACG
droBip1	scf7180000396728:833305-833449 -	LASTZ	4	GGCAGA-GCCAACTTT---GGAGCCCT--------CGAAACAGTCGACGAGCTTGTCAGTGGCGGATC------GAT---TAAGAACCCTGCCGCC---GGCGACA--GGCTCCT---CTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAAATCATGTCT-G--------GCTCGGACG
dp4	chr4_group3:936699-936854 -	LASTZ	5	GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG
droPer1	super_1:2415168-2415323 -	LASTZ	5	GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG
droWil1	scaffold_189765:461-602 -	LASTZ	0	GTAACG-ATAGACGGA---GATACCTT--------CGAGGTGGTGGACGAGTTCGTCTACCTCGGATC------CTT---GTTGATGGCTGACAAC---AA----------T------GTTAGTCG--GGAAATACGAAG----------------------GCGCATTATCAGCGGAAGTCGTGCCT-ACTATTGGCTCCAGAAGA
droVir3	scaffold_12963:15952027-15952160 -	LASTZ	0	ATTAGATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT------------------CAATGCTGCCGCT---GGCGACA--GCC--------TCGG-CG--CTGACAAGGAGC----------------------ATGCCATGTTTGAGTATTTCCTCAAC-G--------AAGATGACG
droMoj3	scaffold_6473:12510219-12510341 +	LASTZ	0	GGTTTG-----------------------------------------TGTGTGTGTGTGTGGTGGAAC------TTCAATGCGAACCTCTTGC--CACAATCGAGTGCAATT------AACTGCCA--TGATATATGGCCAATCCC----------------ATA---TGCAGACGGCGACCGAGTCGAA--------GTTCGGCTG
droGri2	scaffold_14853:4216060-4216150 -	LASTZ	0	---------------------------------------------------------------------------------------TCGACCGCT---GGCCACA--AATG------GCCGGACAGACAGACA-------GACAGACAGACAGACAGACAGACTCACTGACATAATTGATCATATC-----------GCTTATACG

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	GGAA-GGGCCAACTTCTCGGCCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGAT---CATCGGCCACT--GACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droSim1	GCCAACTGGCAAGTCCTCGCCAGT--------GGATGTC----ACCAGC-AACCAGTTGCCCAGC------CAGGAGCC------------------GGT-CATGTTGACCACTGTGCCACAGCCCACGCCGCCCAGGAGCAGCGCCTTCAGGCCTGTGATA
droSec1	GGAA-GGGCCAACTTCTCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGAT---CATCGGCCACT--GACAATGCCCAGTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droYak2	GGAA-GGGCCAACTTCTCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGAT---CATCGGCCACT--GACAATGCCCACTCACTGTTCGAGGAGATCATGTCGGGCTCGGATG
droEre2	GGAA-GGGCCAACTTCACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAGGAGCAATTCTGCCGCTGGCGACAGAT---CATCGGCCACT--GACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG
droEug1	GGAA-GGGCCAATTTCTCGGCCCT--------CGACACAGTAGACGAGCTTGTCAGTGGCGGATC------CAGGAGTAATTCTGCCGCTGGCGATAGAT---TATCGGCCACT--GACAATGCCCACTCACTGTTCGAGGAGATCATGTCTGGCTCGGATG
droBia1	GGCA-GGGCCAACTTCTCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAGGAGTAACTCTGCCGCTGGCGACAGAC---TCTCAGCCACT--GACAACGCCCACCTGCTGTTCGAGGAGATCATGTCCGGCTCGGACG
droTak1	GGAA-GGGCCAACTTCTCGGCTTT--------GGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAGGAGCAATTCTGCCGCTGGCGACAGAT---CGTCGGTCACT--GACAACGCCCACTCGCTGTTCGAGGAGATAATGTCCGGTTCGGATG
droEle1	GGCA-GGGCCAACTTCTCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAGGAGCAACTCTGCCGCCGGCGACAGAT---TGTCAGCCACT--GACAATGCCCACTCACTGTTCGAGGAGATCATGTCCGGCTCGGATG
droRho1	GGAA-TGGCCAACTTCTCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAGGAGCAATTCTGCCGCCGGCGACAGAT---TGTCGGCCACT--GACAATGCCCACTCACTGTTTGAGGAGATCATGTCCGGCTCGGATG
droFic1	GGCA-GGCCGAACTACTCGGCCCT--------CGACACGGTGGACGAACTTGTCAGTGGCGGATC------GAGGAGCAACTCTGCCGCTGGCGACAGAC---TGTCCGCCACT--GACAACGCCCACTCGTTGTTCGAGGAGATCATGTCCGGCTCGGATG
droKik1	GGAA-TGGCCAACTTCTCGGCCCT--------CGACACAGTGGACGAGCTTGTCAGTGGCGGATC------AACGAGCAATTCTGCCGCTGGCGACAGAT---TGTCGGCCACT--GACAATGCCCACTCGCTGTTCGAGGAGATCATGTCGGGCTCGGATG
droAna3	GGCA-GAGCCAACTTCGGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CATAAAGAATCCTGCCGCTGGCGACAGAC---AGTCGGCCACT--GACAACGCGCACTCGCTGTTCGAGGAAATAATGTCTGGCTCCGACG
droBip1	GGCA-GAGCCAACTTTGGAGCCCT--------CGAAACAGTCGACGAGCTTGTCAGTGGCGGATC------GATTAAGAACCCTGCCGCCGGCGACAGGCTCCTCTCGGTCACT--GACAACGCCCACTCGCTGTTCGAGGAAATCATGTCTGGCTCGGACG
dp4	GGAG-TGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGAT---TGTCGGCCACT--GACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG
droPer1	GGAG-TGCTCGTCTACGTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCATTAGCAATTCTGCCGCTGGCGACAGAT---TGTCGGCCACT--GACAATGCCCATTCACTGTTCGAGGAGATCATGTCGGGCTCTGATG

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

GCCAACTGGCAAGTCC---TCGCCAGT--------GGATGTC----ACCAGC-AACCAGTTGCCCAGC------CAG---GAGCC-----------------------GGTC-ATGTTGACCAC-T--GTGCCACAGCCC----------------------ACGCCGCCCAGGAGCAGCGCCTTCAG-G--------CCTGTGATA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GGAAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTTGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------AGTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................................................................................................TGTTCGAGGAGATCATGTCG-G--------GCTCGGA..	28	1	1.00	1.00	0.00	0.00
......................................................................................................................................................................TCTGTCCGAGGAGATCAT.......................	18	1	1.00	0.00	1.00	0.00
....................................GACACGGTTGATGAGATTG........................................................................................................................................................	19	1	1.00	0.00	0.00	1.00
........................CTG--------CGACACGGTTGATGAG............................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
..........................G--------CGACACGGTTGATGAGA...........................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
...........................................TTGATGAxCTGGTCAGTGG.................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
......................................CACGGTTGATGAGATTGA.......................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
..................................................................................................................................................................................GATCATGTCG-G--------GCTCGGAT.	19	1	1.00	0.00	1.00	0.00
.....................................ACACGGTTGATGAGATTG........................................................................................................................................................	18	2	0.50	0.00	0.00	0.50
.....................................ACACGGTTGATGAGCTTGTCAGTGGC................................................................................................................................................	26	1	1.00	1.00	0.00	0.00
...................................CGACACGGTTGATGAGATTGA.......................................................................................................................................................	21	1	1.00	0.00	0.00	1.00
........................................................CTGTGGCGGATC------CGG---GAGC...........................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

GGAAGG-GCCAACTTC---TCGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................................................................................GATCATGTCG-G--------GCTCGGAT.	19	2	0.50	0.00	0.00	0.50	0.00	0.00
.........................................GGTGGATGAGCTTGTCAGTGG.................................................................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
....................................GACACGGTGGATGAGCTTGTCAGTGGC................................................................................................................................................	27	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

GGAAGG-GCCAACTTC---ACGGGCCT--------CGACACGGTGGATGAGCTTGTCAGTGGTGGATC------CAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------ATCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................................................ATGCCC----------------------ACTCGCTGTTCGAGGAG............................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................GATGAGCTTGTCAGTGGTGGAAA------.....................................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.............................................GATGAGCTTGTCAGTGGTGGA.............................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
..............................................ATGAGCTTGTCAGTGGTGGA.............................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
..............................................ATGAGCTTGTCAGTGGTGGATC------.....................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..............................................ATGAGCTTGTCATTGGTGGAT............................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
........................CCT--------GGACACGGTGGAGGA.............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................ATGAGCTTGTCAGTGGTGG..............................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

droEug1

GGAAGG-GCCAATTTC---TCGGCCCT--------CGACACAGTAGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAATTCTGCCGCT---GGCGATA--GATT------ATCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCT-G--------GCTCGGATG

Size

Hit Count

Total Norm

droBia1

GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGTAACTCTGCCGCT---GGCGACA--GACT------CTCAGCCA--CTGACAACGCCC----------------------ACCTGCTGTTCGAGGAGATCATGTCC-G--------GCTCGGACG

Size

Hit Count

Total Norm

droTak1

GGAAGG-GCCAACTTC---TCGGCTTT--------GGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAATTCTGCCGCT---GGCGACA--GATC------GTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAGATAATGTCC-G--------GTTCGGATG

Size

Hit Count

Total Norm

droEle1

GGCAGG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCC---GGCGACA--GATT------GTCAGCCA--CTGACAATGCCC----------------------ACTCACTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG

Size

Hit Count

Total Norm

droRho1

GGAATG-GCCAACTTC---TCGGCCCT--------CGACACGGTGGACGAGCTTGTCAGTGGCGGATC------CAG---GAGCAATTCTGCCGCC---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCACTGTTTGAGGAGATCATGTCC-G--------GCTCGGATG

Size

Hit Count

Total Norm

droFic1

GGCAGG-CCGAACTAC---TCGGCCCT--------CGACACGGTGGACGAACTTGTCAGTGGCGGATC------GAG---GAGCAACTCTGCCGCT---GGCGACA--GACT------GTCCGCCA--CTGACAACGCCC----------------------ACTCGTTGTTCGAGGAGATCATGTCC-G--------GCTCGGATG

Size

Hit Count

Total Norm

droKik1

GGAATG-GCCAACTTC---TCGGCCCT--------CGACACAGTGGACGAGCTTGTCAGTGGCGGATC------AAC---GAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ACTCGCTGTTCGAGGAGATCATGTCG-G--------GCTCGGATG

Size

Hit Count

Total Norm

droAna3

GGCAGA-GCCAACTTC---GGAGCCCT--------TGAAACGGTCGACGAGCTTGTCAGTGGCGGCTC------CAT---AAAGAATCCTGCCGCT---GGCGACA--GACA------GTCGGCCA--CTGACAACGCGC----------------------ACTCGCTGTTCGAGGAAATAATGTCT-G--------GCTCCGACG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................GAGCCCT--------TGAAACGGTCGACGAGCT..........................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
....................GAGCCCG--------TGGAACGGTCG.................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................AATGGTTGACGAGCTT.........................................................................................................................................................	16	2	0.50	0.00	0.00	0.50	0.00

droBip1

GGCAGA-GCCAACTTT---GGAGCCCT--------CGAAACAGTCGACGAGCTTGTCAGTGGCGGATC------GAT---TAAGAACCCTGCCGCC---GGCGACA--GGCTCCT---CTCGGTCA--CTGACAACGCCC----------------------ACTCGCTGTTCGAGGAAATCATGTCT-G--------GCTCGGACG

Size

Hit Count

Total Norm

dp4

GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................ATGAGCTGGTTAGGGGTG...............................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................CA--GATT------GTCGGCCA--CTGAC..........................................................................	19	2	0.50	0.00	0.50	0.00	0.00

droPer1

GGAGTG-CTCGTCTAC---GTGGTTTTGCCCCACGCAATACCATTGATGAGCTGGTCAGTGGTGGCTCCTCCGCCAT---TAGCAATTCTGCCGCT---GGCGACA--GATT------GTCGGCCA--CTGACAATGCCC----------------------ATTCACTGTTCGAGGAGATCATGTCG-G--------GCTCTGATG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
................................................................................................................................................................................GAAATCATGTxG-G--------GCTCTG...	18	1	2.00	2.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................G	18	8	0.25	0.25	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................TA	21	7	0.14	0.14	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................G	25	7	0.14	0.14	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................TA	18	8	0.13	0.00	0.13	0.00	0.00	0.00
.............................................................................................................................................................................................................TA	22	7	0.14	0.14	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................AA	21	7	0.14	0.14	0.00	0.00	0.00	0.00
............................................................................................................................................................................................................AAG	21	8	0.13	0.13	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................................TA	20	8	0.13	0.13	0.00	0.00	0.00	0.00

droWil1

GTAACG-ATAGACGGA---GATACCTT--------CGAGGTGGTGGACGAGTTCGTCTACCTCGGATC------CTT---GTTGATGGCTGACAAC---AA----------T------GTTAGTCG--GGAAATACGAAG----------------------GCGCATTATCAGCGGAAGTCGTGCCT-ACTATTGGCTCCAGAAGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........................................GGTGGTGGAGTTCGTCTA....................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...................................CGAGGTGGTGGACGAGCA..........................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
......................................GTTGGTGGATGAGTTCGT.......................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droVir3

ATTAGATGCCGATTGCGGTTCGTCCAT--------CAAGTCTGCGGCTGAGCTTGTCAGCGCCGT------------------CAATGCTGCCGCT---GGCGACA--GCC--------TCGG-CG--CTGACAAGGAGC----------------------ATGCCATGTTTGAGTATTTCCTCAAC-G--------AAGATGACG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.......................................................................................................................................GGGGC----------------------ATGCCxTGTTTGAG...............................	18	1	5.00	1.00	3.00	0.00	1.00	0.00
.........CGATTCCGGTTCGTCCAC--------C...........................................................................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
......................................................................................................GACA--TCC--------TCGG-CG--CTGTC..........................................................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.............................................................................................................CC--------TCGG-CG--CTGACAAGGAGC----------------------A............................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................GACAAGGAGC----------------------ATGACATCT....................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................................................................................................................................GGGGC----------------------ATGCCxTGTTTGAGT..............................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................AGGAGC----------------------ATGCCxTGTTTGAGTG.............................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................T------------------CCATGCTGCTGCT---GG..........................................................................................................	16	11	0.09	0.00	0.09	0.00	0.00	0.00
........................CAT--------CAAGTCTGCTGTTGA.............................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

GGTTTG-----------------------------------------TGTGTGTGTGTGTGGTGGAAC------TTCAATGCGAACCTCTTGC--CACAATCGAGTGCAATT------AACTGCCA--TGATATATGGCCAATCCC----------------ATA---TGCAGACGGCGACCGAGTCGAA--------GTTCGGCTG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.GTTTG-----------------------------------------TGTGTGTGTGTGTG..................................................................................................................................................	19	165	0.01	0.01	0.00	0.00	0.00
.GTTTG-----------------------------------------TGTGCGTGTCTGT...................................................................................................................................................	18	8	0.13	0.00	0.00	0.00	0.13
.....A-----------------------------------------TGTGTGTGTGTGTGCTG...............................................................................................................................................	18	31	0.03	0.00	0.03	0.00	0.00
..TTTG-----------------------------------------TGTGTGTGTGTGCAG.................................................................................................................................................	19	20	0.05	0.00	0.00	0.05	0.00
..TTTG-----------------------------------------TATGTGTGTGTGTGCT................................................................................................................................................	20	10	0.10	0.10	0.00	0.00	0.00
...TTG-----------------------------------------TGTTTGTGTGTGTGGCG...............................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
....TG-----------------------------------------TGTGTGTGTGCGTTGTGGA.............................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...............................................TGTGTGTGTGTGTGTTGG..............................................................................................................................................	18	19	0.05	0.00	0.00	0.00	0.05
.GTTTG-----------------------------------------TGTGTGTxTGTTTGGT................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...TTG-----------------------------------------TATGTGTGTGTGTGCT................................................................................................................................................	19	13	0.08	0.08	0.00	0.00	0.00
...............................................TGTGTTTGTGAGTGGTGG..............................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

---------------------------------------------------------------------------------------TCGACCGCT---GGCCACA--AATG------GCCGGACAGACAGACA-------GACAGACAGACAGACAGACAGACTCACTGACATAATTGATCATATC-----------GCTTATACG	Size	Hit Count	Total Norm	V109 Male body
...........................................................................................................................ACAGACAGACA-------GACAGACAGACC......................................................	23	10	0.10	0.10
................................................................................................................................CAGACA-------GACAGACCGACAGACA..................................................	22	16	0.06	0.06
..................................................................................................................................GACA-------GACAGACAGACAGCTA..................................................	20	10	0.10	0.10
..............................................................................................................................GACAGACA-------GATAGACAGACA......................................................	20	20	0.05	0.05
..................................................................................................................................GACA-------GACAGATAGACAGACA..................................................	20	20	0.05	0.05
.................................................................................................................................................GACAGACAGATAGACAGACA..........................................	20	20	0.05	0.05
...........................................................................................................................ACTGACAGATA-------GACAGACA..........................................................	19	12	0.08	0.08
..............................................................................................................................................ACAGACAGACAGACAGACAGACC..........................................	23	10	0.10	0.10
............................................................................................................................CAGACAGACA-------GACCGACAGACA......................................................	22	16	0.06	0.06
...............................................................................................................................ACTGACA-------GATAGACAGACA......................................................	19	12	0.08	0.08
...................................................................................................................................ACA-------GACAGACAGACAGACAGACC..............................................	23	10	0.10	0.10
........................................................................................................................CAGACAGACAGACC-------GACAGACA..........................................................	22	16	0.06	0.06
...................................................................................................................................ACT-------GACAGATAGACAGACA..................................................	19	12	0.08	0.08
..........................................................................................................................GACAGACAGATA-------GACAGACA..........................................................	20	20	0.05	0.05
....................................................................................................................................CA-------GACAGACAGACCGACAGACA..............................................	22	16	0.06	0.06
.............................................................................................................................................GACAGACAGATAGACAGACA..............................................	20	20	0.05	0.05
..........................................................................................................................GACAGACAGACA-------GACAGCTA..........................................................	20	10	0.10	0.10
..............................................................................................................................................ACTGACAGATAGACAGACA..............................................	19	12	0.08	0.08
...............................................................................................................................................CAGACAGACAGACCGACAGACA..........................................	22	16	0.06	0.06
.............................................................................................................................................GACAGACAGACAGACAGCTA..............................................	20	10	0.10	0.10
..............................................................................................................................GACAGACA-------GACAGACAGCTA......................................................	20	10	0.10	0.10
...............................................................................................................................ACAGACA-------GACAGACAGACAGACC..................................................	23	10	0.10	0.10

Generated: 04/20/2012 at 05:32:38 EDT

dme-mir-4971

chr2L:3463289-3463400 -

Known_mirbase

CDS

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup