dme-mir-2279-as- Best orthologs

dme-mir-2279-as	chr2RHet:1322833-1322945 +	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 1322860-1322881
   star strand at position 1322896-1322917
   mutations
   read mismatches

Notes: MAF reports no orthologs in any of the 12 fly species. Many paralogs exists in almost all species. droGri2 sequence looks suspicious.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2RHet:1322818-1322960 +		1	ATGTATG-TTGG---CACC-------------------------------------------------------CC-------------------------------GGTTATT--ATAGGGACAAATGTAAA-------------------------AATAAATATCTTCGCGTGAAATTAAT----------------------------------------------------CTTTTAA-ATAAT------TTCAC-A----------------------------------------------------C-------------------------------------------------------ACAGATATTTAATTTCAAATTGTCT-TTCATAATCCTCTCCCGCCATGGGT-CATCGGA
droSim1	chr2R:265657-265783 -	LASTZ	0	TTTA-TGT-CGG---CATA-------------------------------------------------------CT-------------------------------GGTTATT--CTAGGGAA-AATTTA----------------------AACAAAATAAATATCTTTACGTGAAACTAAACCTTTGA----A---------------------------CTCATT-------GTTTTTA-ATAAT------TCCAC-A----------------------------------------------------C-------------------------------------------------------ACAGATATTTAATTGAAAAT--------------TGC--------------------CT
droSec1	super_55:122657-122780 -	LASTZ	0	TTTA-TG-TTGG---CCCC-------------------------------------------------------CC-------------------------------GGTTATT--CTATGGACAAATGTAAA-------------------------AATAAATACTTTCGCGTGAAACTAAACTTTCGA----A---------------------------CTTACC-------GTTTA---TTAAT------TTCAC-A----------------------------------------------------C-------------------------------------------------------ACATATTTATAATTT-------------TAAGTTTAC--------------------TT
droYak2	chr2h_random:1837226-1837349 +	LASTZ	0	TTTA-TG-TTGG---GACC-------------------------------------------------------TC-------------------------------GGTTATT--CTAGGGACAAATGCAGA-------------------------AATAAATAACTTTACACGAAACTAAATTTTCGA----A---------------------------CTCACT-------GTTTC---TTAAT------TTCCC-A----------------------------------------------------C-------------------------------------------------------ACAGATATAAAAATTTAAG-------------TTGTC--------------------TT
droEre2	scaffold_4845:21278391-21278511 -	LASTZ	0	TACA-AAAA--------------------------------------------------------------------------------------------------------------------AATGTA----------------------AAAAAAATAAATTTTTAAAT--------------TTGA----A---------------------------TGCAGT-------TTTTTAG-ATAAT------TGCACCACAAACATTTAGAGGTATGC----------------------------------------------------CACTTCAAAATCCGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG
droEug1	scf7180000409142:16534-16652 +	LASTZ	0	TTTT-TATAG-G-------------------------------------------------------------------------------------------------------------AAATAACGCAAA-------------------------TTTAAATATATTAATTTATTATTGAT--------------------------------------------T-------TTTTTTAATATATCTGGCAATTCATAAAAAGGTTTACATGAAT------------------------------------------TTA-----------------------------------------------------------TGAAAAT-TTTC-TTTCTTCTTTT--------------------TC
droBia1	scf7180000302069:1281651-1281776 +	LASTZ	0	ATGT-CTTTATG---AAAC-TGGGC---------------------ACTATAAGAT--GCACC---------------CC--------------------------------------------------AGAAACTACTGCATAGAAGTTTGAA---AAAAAA------------------------------------------------------------------------AACTTAA-ATAAT------ATCGT-A----------------------------------------------------C-------------------------------------------------------ATAGATATGTTTTGCATATTTGCACTTCAATTTCTTC--------------------CC
droTak1	scf7180000414441:15526-15661 +	LASTZ	0	AAGCATG-TAAG---AATT-------------------------------------------------------GT-------------------------------ACTCGTT--ATAGGGTT-----------------------------------------------------------------------------------------------------------------TCCTTAAATTAC------ACTTATAGAAATATTTACAGGGATCGCAAGTAAGAGTTACTTTTTTAAAAAAATTGACAA-------------------------------------------------------ATAAGTCTTATTTTTCAAT-------TTGTATTATAA--------------------AA
droEle1	scf7180000486807:9902-10004 -	LASTZ	0	TGTC-AGAAG----------------------------------------------AAATATC---------------TT-TT-----------------------GATGAATTTAAT----------------------------------------------------AAT--------------ATTG----ATTGGATTTCCATAAAATT----------------------------------------------------------------TTC----------------------------------------------------CGCTTTCAAGTCAGTTTCTTAT-------------------------------AAA-------T----------TTACCGATATGGAT------CA
droRho1	scf7180000767875:903-1047 -	LASTZ	0	TGAG-AGACATG---ACTG---CTAAAATA--------------------------------------------CCTCTTATTACAAAGAACTTATGATATCTCTTA---------------------AGA---------------------------AATTCAGAACTCTC------------------C----AAACACTTAA---------------------------------------------------------------TTTAAAAGTGTAC----------------------------------------------------CCTTTCTTAATACAAAAC-------------------AAGA-GAGAACGCTAT-AG-------TCG-------------------GGT-GCTCCGA
droFic1	Unknown		0	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000298698:14727-14830 +	LASTZ	0	TTAT-TATAG-C---GCCC-------------------------------------------------------AA-------------------------------A-----------------CGTGTT----------------------GGCCAAATCAAAGTTTTGTT--------------TTGA----A---------------------------TTTAAT-------GTTTAAA-ATGAT------GTCAC-A----------------------------------------------------CACATGTTTTTTTTAGTTTTGCT-----------------------------------------------------------TC----GTTTT--------------------TC
droAna3	scaffold_13334:5190-5293 -	LASTZ	0	TCTT-AAAAAGA---CT-AATATTTAACTACCAATTGCCATATAAA----------AAATATC---------------TT-TT-----------------------A---------------------------------------------------------------------------------------------------------------------------------------A-AAAAT------CCCAC-C----------------------------------------------------A------------------------------------------TATTT-------------TTTTTTATTTATTATTTTTT-TTACTAATTTT--------------------TT
droBip1	scf7180000395238:27783-27922 -	LASTZ	0	ATTG-TAGG----------------------------------------------------------------------------------------------------------------GGCACATGTAAA-------------------------AGCTCCACGATTTGCGTGAAGTCTAAAA-CTGTAATAATTGAATGTAAAAAA--TTTTATATATTT--TTT-------TTATCGA-AAAGT------TGTATTATACATA--------------------------------------------------------------------------------------------------------------------------------CC----ATCGTCTGCCGTTATATGGCCATGACG
dp4	Unknown_group_37:8363-8450 -	LASTZ	0	AAAA-TA-TACA---ACCC---------------------------GCAGTAAAAT--GTATC---------------CT-TTGCGTAGGTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAATAC----AAAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCCTC-CTACCTCATTG--------------------CC
droPer1	super_5473:1216-1318 -	LASTZ	0	ATGT-TAAAGCT---TAAA----------------------------------------CC-------------TC--AG-CT-----------------------TAGGAATGCAATA------GGTACA----------------------GGCGAATCGACTTTCTTCATGTGAAATCATT----------------------------------------------------CCCCTGC-ATAGT------TCCAC-T----------------------------------------------------T-------------------------------------------------------ACAC----------------------------ACGTA--------------------TA
droWil1	scaffold_180772:5217896-5218034 -	LASTZ	0	GGTC-GAAATCTAGACA-AATATTAAA----------------AAA----------AAATTCATTGCAACAAGTCC----------------------------------------------------------------------------------------TCTTTCAAT--------------TTTA----ATTGAATTTTCAGGA--A----------CATACT-------ATCCA---GCTAA------CTCTG-A----------------------------------------------------C----------------------------------------AAGAATATGTGCACT--T-TGGCGCCGCC------------AC-------------------TGGT-CAACGGC
droVir3	scaffold_291:1622-1745 +	LASTZ	0	ATATATA-TAAA---TATT-------------------------------------------------------TA-------------------------------ATATATT--ATATAATTAACAATTTA-------------------------AATAAAAAATTTCGCAATCCAAA-----------------------------------------------------------------------------------AATCATTACAAATATGGTAAA-----------------------------A------------------------------------------AAAAA-------------TCTATATTTTAAAGATTTAT-CTAATGATTCT--------------------TT
droMoj3	scaffold_6473:7010400-7010528 -	LASTZ	0	ATGT-ATGTGCA---TACA-------------------------------------------------------TA-------------------------------TATATAT--TTATGTACATATGTAAA-------------------------TATAGAAATCTACGTATGATTTGTTGGCATTGC----A---------------------------CTCTTTACACACTTTTGTTTGTTTAT------TTTTT------------------------------------------------------------------------------------------------------------------TTATTTTATT------------TTTTTTTGTCT--------------------TT
droGri2	scaffold_14906:12727535-12727642 -	LASTZ	0	ATAC-AAATATA---AATT-TATTCAAATTCAAATT------------------------ATC---------------TT-----------------------------------------------------------------------------------------------------------TCAA----A-TAAAAGGACAAGA--T-------------AAG-------ATAAA---TTAAA------TAATA-T----------------------------------------------------A--------A--------------------------C----AAAATTG-----------------TATTCT-------------CGTTTTCCCTTCTCGG-------------CA

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	ATGTATGTTGGCACCCCGGTTATTATAGGGACAAATGTAAAAATAAATATCTTCGCGTGAAATTAATCTTTTAAATAATTTCACACACAGATATTTAATTTCAAATTGTCTTTCATAATCCTCTCCCGCCATGGGTCATCGGA

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

TTTA-TGT-CGG---CATA-------------------------------------------------------CT-------------------------------GGTTATT--CTAGGGAA-AATTTA----------------------AACAAAATAAATATCTTTACGTGAAACTAAACCTTTGA----A---------------------------CTCATT-------GTTTTTA-ATAAT------TCCAC-A----------------------------------------------------C-------------------------------------------------------ACAGATATTTAATTGAAAAT--------------TGC--------------------CT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TTTA-TG-TTGG---CCCC-------------------------------------------------------CC-------------------------------GGTTATT--CTATGGACAAATGTAAA-------------------------AATAAATACTTTCGCGTGAAACTAAACTTTCGA----A---------------------------CTTACC-------GTTTA---TTAAT------TTCAC-A----------------------------------------------------C-------------------------------------------------------ACATATTTATAATTT-------------TAAGTTTAC--------------------TT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................................................................................................AAA-------------------------AATAAATATTTGCGCGT..............................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00

droYak2

TTTA-TG-TTGG---GACC-------------------------------------------------------TC-------------------------------GGTTATT--CTAGGGACAAATGCAGA-------------------------AATAAATAACTTTACACGAAACTAAATTTTCGA----A---------------------------CTCACT-------GTTTC---TTAAT------TTCCC-A----------------------------------------------------C-------------------------------------------------------ACAGATATAAAAATTTAAG-------------TTGTC--------------------TT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....TG-TTGG---GACC-------------------------------------------------------AC-------------------------------GGTTATT--CTAGGG...................................................................................................................................................................................................................................................................................................................	25	9	0.22	0.22	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................TCCC-A----------------------------------------------------C-------------------------------------------------------ACAGATATATAAATTTAAG-------------T..........................	26	14	0.07	0.07	0.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................CT------TTCCC-A----------------------------------------------------C-------------------------------------------------------ACAGATATATAAATT............................................	24	14	0.07	0.07	0.00	0.00	0.00	0.00

droEre2

TACA-AAAA--------------------------------------------------------------------------------------------------------------------AATGTA----------------------AAAAAAATAAATTTTTAAAT--------------TTGA----A---------------------------TGCAGT-------TTTTTAG-ATAAT------TGCACCACAAACATTTAGAGGTATGC----------------------------------------------------CACTTCAAAATCCGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................................................................................................................................................................................................................................................................................................................GAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	18	28	0.36	0.07	0.00	0.00	0.29
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAG-------TTG-------------------AGT-.......	18	29	0.10	0.03	0.00	0.00	0.07
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	24	25	0.12	0.00	0.00	0.00	0.12
...........................................................................................................................................................................................................................................................................................................................................................ATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATG...	21	27	0.07	0.00	0.00	0.00	0.07
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	20	26	0.08	0.00	0.04	0.00	0.04
......................................................................................................................................................................................................................................................................................................................................................ATCCGAATAAGAT-------------------------------AAG-------TTG-------------------AGT-T......	23	21	0.10	0.00	0.00	0.00	0.10
.........................................................................................................................................................AACATAATAAATTTTTAA..................................................................................................................................................................................................................................................................	18	5	0.40	0.40	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TAT....	21	27	0.07	0.00	0.04	0.00	0.04
...........................................................................................................................................................................................................................................................................ATTTAGAGGTATGC----------------------------------------------------CACTT...........................................................................................	19	40	0.03	0.00	0.00	0.00	0.03
............................................................................................................................................................................................TGA----A---------------------------TGCAGT-------GTTTTAG-A........................................................................................................................................................................................	18	38	0.03	0.00	0.00	0.00	0.03
......................................................................................................................................................................................................................................................................................................................................................ATCCGATTAAGAT-------------------------------AAG-------CTG-------------------AGT-TATG...	26	19	0.05	0.05	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------TAG-------TTG-------------------AGT-TATGGAC	21	25	0.04	0.00	0.00	0.00	0.04
..................................................................................................................................................................................................................................................................TCCACAAACATTTAGAGGTATGC----------------------------------------------------................................................................................................	23	12	0.08	0.00	0.00	0.00	0.08
................................................................................................................................................................................................................................................................GCGCCATAAACATTTAGAG..........................................................................................................................................................	19	25	0.04	0.00	0.00	0.00	0.04
.................................................................................................................................................................................................................................................................................................................................................................AT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	19	31	0.03	0.03	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................ATTAAGAT-------------------------------AAG-------CTG-------------------AGT-TATGGCG	24	6	0.17	0.00	0.00	0.00	0.17
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAC-------TTG-------------------AGT-TATGGAG	26	15	0.07	0.00	0.00	0.00	0.07
......................................................................................................................................................................................................................................................................................................................................................ATCCGATTAAGAG-------------------------------AAG-------TTG-------------------AGT-TATGG..	27	18	0.06	0.00	0.00	0.00	0.06
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------GAG-------TTG-------------------AGT-TTTGGA.	20	16	0.06	0.00	0.00	0.00	0.06
..........................................................................................................................................................................................................................................................................................................................................................GATTAATAT-------------------------------AGG-------TTG-------------------AGT-TATG...	22	19	0.05	0.05	0.00	0.00	0.00
................................................................................................................................................................................................................................................................GCACCAGAAACATTTAGAGGT........................................................................................................................................................	21	30	0.03	0.00	0.00	0.00	0.03
.........................................................................................................................................................................................................................................................................................................................................................CGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	25	23	0.04	0.00	0.00	0.00	0.04
.........................................................................................................................................................................CAAT--------------TTGA----A---------------------------TGCAGT-------TTTTCA...........................................................................................................................................................................................	21	40	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................................................................................................................................ATTTAGAGGTATGC----------------------------------------------------CACTTCAAA.......................................................................................	23	36	0.03	0.00	0.00	0.00	0.03
....................................................................................................................................................................ATTTTAAAT--------------TTGA----A---------------------------TGCAGT-------TTCTTA...........................................................................................................................................................................................	26	10	0.10	0.00	0.00	0.00	0.10
...........................................................................................................................................................................................................................................................................................................................................................ATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGC.	23	26	0.04	0.00	0.04	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................TAAGAT-------------------------------AAG-------TTG-------------------AGT-TAT....	18	27	0.04	0.00	0.04	0.00	0.00
.......................................................................................................................................................................................................................................................................................GC----------------------------------------------------CACTTCAAAATCCGATCAAGAT-------------------------------AAG-------T................................	28	10	0.10	0.00	0.00	0.00	0.10
..................................................................................................................................................................................................................................................................................................................................................CCAAATCCGATTAAGAT-------------------------------AAA-------TTG-------------------A..........	24	10	0.10	0.00	0.00	0.00	0.10
..........................................................................................................................................................................................................................................................................CATTTAGAGGTATGC----------------------------------------------------CACGTC..........................................................................................	21	37	0.03	0.00	0.00	0.00	0.03
.......................................................................................................................................................................................................................................................AT------GGCACCAGAAACATTTAGAGGTA.......................................................................................................................................................	25	18	0.06	0.00	0.00	0.00	0.06
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	19	27	0.04	0.00	0.00	0.00	0.04
................................................................................................................................................................................................................................................................................................................................................................GAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	20	20	0.05	0.00	0.00	0.00	0.05
.......................................................................................................................................................................CTAAAT--------------TTGA----A---------------------------TGCAGT-------TTTTTGG-.........................................................................................................................................................................................	24	49	0.02	0.00	0.00	0.00	0.02
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------TAG-------TTG-------------------CGT-TATGGA.	24	18	0.06	0.06	0.00	0.00	0.00
................................................................................................................................................................................................................................................................GCACCAGAAAAATTTAGAGGT........................................................................................................................................................	21	18	0.06	0.00	0.00	0.00	0.06
....................................................................................................................................................................................................................................................................CAGAAACATTTAGAGGTATG.....................................................................................................................................................	20	32	0.03	0.00	0.00	0.00	0.03
....................................................................................................................................................................................................................................................................CAGAAACATTTAGAGGTATGC----------------------------------------------------CACTT...........................................................................................	26	31	0.03	0.00	0.00	0.00	0.03
.....................................................................................................................................................................................................................................................................................ATGA----------------------------------------------------CACTTCAAAATCCGAT................................................................................	20	33	0.03	0.00	0.00	0.00	0.03
............................................................................................................................................................................................................................................................................................................................................................TTAAGAT-------------------------------AAG-------TTG-------------------AGA-TA.....	18	29	0.03	0.00	0.00	0.00	0.03
...............................................................................................................................................................................................................................................................................................................................................................AGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	21	18	0.06	0.00	0.00	0.00	0.06
............................................................................................................................................................................................................................................................................................................................................................TTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	21	26	0.04	0.00	0.00	0.00	0.04
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATTGA.	24	25	0.04	0.00	0.00	0.00	0.04
................................................................................................................................................................................................................................................................................................................................................................GAT-------------------------------AAG-------TTG-------------------AGA-TATGGA.	18	29	0.03	0.00	0.00	0.00	0.03
........................................................................................................................................................................................................................................................................................C----------------------------------------------------CACTTCAAAATCCGATTAA.............................................................................	20	28	0.04	0.00	0.00	0.00	0.04
.................................................................................................................................................................................................................................................................................................................................................................AT-------------------------------AAG-------TTG-------------------AGT-TATGGAC	18	24	0.04	0.04	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................................................................................................................ATTAAGGT-------------------------------AAG-------TTG-------------------AGA-TATGGA.	23	10	0.10	0.00	0.00	0.00	0.10
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAC-------TTG-------------------AGT-TATGGA.	24	25	0.04	0.00	0.00	0.00	0.04
.....................................................................................................................................................................................................................................................................................................................................................ATTCCGATTAAGAT-------------------------------TAG-------TTG-------------------AGT-.......	23	21	0.05	0.00	0.00	0.00	0.05
.............................................................................................................................................................................................................................................................................TAAGAGGTATGC----------------------------------------------------CACTTCAAA.......................................................................................	21	36	0.03	0.00	0.00	0.00	0.03
............................................................................................................................................................................................................................................................................................................................................................TAAAGAT-------------------------------TAG-------TTG-------------------AGT-TATGG..	21	22	0.05	0.00	0.00	0.00	0.05
...........................................................................................................................................................................................................................................................................................................................................................ATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	22	26	0.04	0.00	0.00	0.00	0.04
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	22	18	0.06	0.00	0.00	0.00	0.06
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAG-------------------------------AAG-------TTG-------------------AGG-TATGGAG	25	6	0.17	0.17	0.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................ATCCGATCAAGAT-------------------------------AAG-------TTG-------------------AGT-TATG...	26	22	0.05	0.00	0.00	0.00	0.05
............................................................................................................................................................................................................................................................................................................................................................TTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	22	25	0.04	0.00	0.00	0.00	0.04
..............................................................................................................................................................................................A----A---------------------------TGCAGA-------TTTTAAG-ATAAT------T.............................................................................................................................................................................	21	20	0.05	0.00	0.00	0.00	0.05
................................................................................................................................................................................................................................................................................................................................................................GAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	19	25	0.04	0.04	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................TAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	23	15	0.07	0.00	0.00	0.00	0.07
...............................................................................................................................................................................................................................................................................................................................................................AGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAC	20	16	0.06	0.00	0.00	0.00	0.06
.............................................................................................................................................................................................................................................................................................................................................................TAAGAT-------------------------------AAG-------CTG-------------------AGT-TATG...	19	27	0.04	0.04	0.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................ATCCGATTAAGAT-------------------------------TAG-------TTG-------------------CGT-T......	23	16	0.06	0.00	0.00	0.00	0.06
..........................................................................................................................................................................................................................................................................................................................................................GATAAAGAT-------------------------------AAG-------TTG-------------------AGT-TATG...	22	16	0.06	0.00	0.00	0.00	0.06
..............................................................................................................................................................................................................................................................................................................................................................AAAAT-------------------------------AAG-------GTG-------------------AGT-TATGGAG	21	14	0.07	0.00	0.00	0.00	0.07
...........................................................................................................................................................................................................................................................................................................................................................ATGAAGAT-------------------------------AAG-------TTG-------------------AGT-TAT....	20	28	0.04	0.00	0.00	0.00	0.04
.................................................................................................................................................................................................................................................................................................................................................................AT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	18	30	0.03	0.00	0.00	0.00	0.03
..............................................................................................................................................................................................................................................................................................................................................................AAGAT-------------------------------AAG-------TGG-------------------AGT-TATGGAG	21	23	0.04	0.00	0.00	0.00	0.04
........................................................................................................................................................................................................................................................................................................................................................CCGATTCAGAT-------------------------------AAG-------TTG-------------------AGT-.......	20	25	0.04	0.04	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................GGTATGC----------------------------------------------------CACTTCAAAATCGGATT...............................................................................	24	21	0.05	0.05	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................T-------------------------------AAG-------TTG-------------------AGT-TATGGAG	18	27	0.04	0.00	0.00	0.00	0.04
...A-CAAG--------------------------------------------------------------------------------------------------------------------AATGTA----------------------AAAAAAA.............................................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.00	0.20
.............................................................................................................................................................................................................................................................................................................................................................CAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	21	26	0.04	0.00	0.04	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................AATCCGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-.......	23	20	0.05	0.00	0.00	0.00	0.05
.......................................................................................................................................................................................................................................................AT------TCCACCAGAAACATTTAGAG..........................................................................................................................................................	22	21	0.05	0.00	0.00	0.00	0.05
.............................................................................................................................................................................................................................................................................................................................................................TAAGAG-------------------------------AAG-------TTG-------------------AGT-TATGGA.	21	26	0.04	0.04	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................TAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	20	26	0.04	0.00	0.00	0.00	0.04
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG	25	20	0.05	0.00	0.00	0.00	0.05
..............................................................................................................................................................................................................................................TTTAG-AxAAT------AGCACCACAA....................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50
.........................................................................................................................................................................................................................................................................................................................................................CGATTAAAAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	24	14	0.07	0.00	0.00	0.00	0.07
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAG-------------------------------AAG-------TTG-------------------AGT-TATGGAG	26	15	0.07	0.00	0.00	0.00	0.07
........................................................................................................................................................................................................................................................................................................................................................CCGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGG..	25	21	0.05	0.00	0.00	0.00	0.05
...............................................................................................................................................................................................................................................................................................................................................................ATAT-------------------------------AAG-------TTG-------------------AGT-TATGGA.	19	20	0.05	0.00	0.00	0.00	0.05
...................................................................................................................................................................................................................................................................CCAGAAACATTTAGAGGTATG.....................................................................................................................................................	21	30	0.03	0.00	0.00	0.00	0.03
..............................................................................................................................................................................................................................................................................................................................................................AAGAG-------------------------------AAG-------TTG-------------------AGT-TATGGA.	20	27	0.04	0.04	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................CATTCAGAGATATGC----------------------------------------------------CACTTCAAA.......................................................................................	24	21	0.05	0.05	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................CACATCTAAATCCGATTAAGA...........................................................................	21	13	0.08	0.00	0.00	0.00	0.08
.............................................................................................................................................................................................................................................................................................................................................................TAAGAT-------------------------------AAG-------TGG-------------------AGT-TATGGA.	21	25	0.04	0.00	0.00	0.00	0.04
.....................................................................................................................................................................................................................................................................AGAAACATTTAGAGGTATGC----------------------------------------------------................................................................................................	20	35	0.03	0.00	0.00	0.00	0.03
..........................................................................................................................................................................................................................................................................................................................................................GATTAAGAG-------------------------------AAG-------TGG-------------------AGT-.......	18	15	0.07	0.07	0.00	0.00	0.00
.......................................................................................................................................................................................................................................................................AAAAATTTAGAGGTAAGC----------------------------------------------------C...............................................................................................	19	31	0.03	0.00	0.00	0.00	0.03
................................................................................................................................................................................................................................................................................................................................................................GAT-------------------------------AAG-------TGG-------------------AGT-TATGGAG	19	25	0.04	0.00	0.00	0.00	0.04

droEug1

TTTT-TATAG-G-------------------------------------------------------------------------------------------------------------AAATAACGCAAA-------------------------TTTAAATATATTAATTTATTATTGAT--------------------------------------------T-------TTTTTTAATATATCTGGCAATTCATAAAAAGGTTTACATGAAT------------------------------------------TTA-----------------------------------------------------------TGAAAAT-TTTC-TTTCTTCTTTT--------------------TC

Size

Hit Count

Total Norm

droBia1

ATGT-CTTTATG---AAAC-TGGGC---------------------ACTATAAGAT--GCACC---------------CC--------------------------------------------------AGAAACTACTGCATAGAAGTTTGAA---AAAAAA------------------------------------------------------------------------AACTTAA-ATAAT------ATCGT-A----------------------------------------------------C-------------------------------------------------------ATAGATATGTTTTGCATATTTGCACTTCAATTTCTTC--------------------CC

Size

Hit Count

Total Norm

droTak1

AAGCATG-TAAG---AATT-------------------------------------------------------GT-------------------------------ACTCGTT--ATAGGGTT-----------------------------------------------------------------------------------------------------------------TCCTTAAATTAC------ACTTATAGAAATATTTACAGGGATCGCAAGTAAGAGTTACTTTTTTAAAAAAATTGACAA-------------------------------------------------------ATAAGTCTTATTTTTCAAT-------TTGTATTATAA--------------------AA

Size

Hit Count

Total Norm

droEle1

TGTC-AGAAG----------------------------------------------AAATATC---------------TT-TT-----------------------GATGAATTTAAT----------------------------------------------------AAT--------------ATTG----ATTGGATTTCCATAAAATT----------------------------------------------------------------TTC----------------------------------------------------CGCTTTCAAGTCAGTTTCTTAT-------------------------------AAA-------T----------TTACCGATATGGAT------CA

Size

Hit Count

Total Norm

droRho1

TGAG-AGACATG---ACTG---CTAAAATA--------------------------------------------CCTCTTATTACAAAGAACTTATGATATCTCTTA---------------------AGA---------------------------AATTCAGAACTCTC------------------C----AAACACTTAA---------------------------------------------------------------TTTAAAAGTGTAC----------------------------------------------------CCTTTCTTAATACAAAAC-------------------AAGA-GAGAACGCTAT-AG-------TCG-------------------GGT-GCTCCGA

Size

Hit Count

Total Norm

droFic1

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

Size

Hit Count

Total Norm

droKik1

TTAT-TATAG-C---GCCC-------------------------------------------------------AA-------------------------------A-----------------CGTGTT----------------------GGCCAAATCAAAGTTTTGTT--------------TTGA----A---------------------------TTTAAT-------GTTTAAA-ATGAT------GTCAC-A----------------------------------------------------CACATGTTTTTTTTAGTTTTGCT-----------------------------------------------------------TC----GTTTT--------------------TC

Size

Hit Count

Total Norm

droAna3

TCTT-AAAAAGA---CT-AATATTTAACTACCAATTGCCATATAAA----------AAATATC---------------TT-TT-----------------------A---------------------------------------------------------------------------------------------------------------------------------------A-AAAAT------CCCAC-C----------------------------------------------------A------------------------------------------TATTT-------------TTTTTTATTTATTATTTTTT-TTACTAATTTT--------------------TT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................................................................................................................................................................................................................................................................ATT-------------TTTTTTATTTTTTATT......................................	19	27	0.04	0.00	0.00	0.00	0.04
.........................................................................................................................................................................................................................................................................................................................................................................T-------------TTTTTTATTTCTTTTTTTTT-.................................	21	18	0.06	0.00	0.00	0.00	0.06
...............................AAATTGCCATAGAAA----------AAA..................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33

droBip1

ATTG-TAGG----------------------------------------------------------------------------------------------------------------GGCACATGTAAA-------------------------AGCTCCACGATTTGCGTGAAGTCTAAAA-CTGTAATAATTGAATGTAAAAAA--TTTTATATATTT--TTT-------TTATCGA-AAAGT------TGTATTATACATA--------------------------------------------------------------------------------------------------------------------------------CC----ATCGTCTGCCGTTATATGGCCATGACG

Size

Hit Count

Total Norm

dp4

AAAA-TA-TACA---ACCC---------------------------GCAGTAAAAT--GTATC---------------CT-TTGCGTAGGTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAATAC----AAAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCCTC-CTACCTCATTG--------------------CC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................................................................TGCGTAGGTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAC....................................................................................................................................................................................................................................	27	2	1.00	1.00	0.00	0.00	0.00
............................................................................................TAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAATAC----AAAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.........................................	26	2	0.50	0.00	0.50	0.00	0.00
......................................................GT--GTATC---------------CT-CTGCGTAGGTC.................................................................................................................................................................................................................................................................................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
..................................................................................TGCGTAGTTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAA....................................................................................................................................................................................................................................	27	2	0.50	0.50	0.00	0.00	0.00
..................................................TAAAAA--TTATC---------------CT-TTGCGT......................................................................................................................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00
.................................................................................CTGCGTAGGTCTAAC-----------GATA--------------AT..............................................................................................................................................................................................................................................................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...............................................................................T-CTGCGTAGGTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------A.........................................................................................................................................................................................................................................	24	2	0.50	0.50	0.00	0.00	0.00

droPer1

ATGT-TAAAGCT---TAAA----------------------------------------CC-------------TC--AG-CT-----------------------TAGGAATGCAATA------GGTACA----------------------GGCGAATCGACTTTCTTCATGTGAAATCATT----------------------------------------------------CCCCTGC-ATAGT------TCCAC-T----------------------------------------------------T-------------------------------------------------------ACAC----------------------------ACGTA--------------------TA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

GGTC-GAAATCTAGACA-AATATTAAA----------------AAA----------AAATTCATTGCAACAAGTCC----------------------------------------------------------------------------------------TCTTTCAAT--------------TTTA----ATTGAATTTTCAGGA--A----------CATACT-------ATCCA---GCTAA------CTCTG-A----------------------------------------------------C----------------------------------------AAGAATATGTGCACT--T-TGGCGCCGCC------------AC-------------------TGGT-CAACGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................................................................................................................................................................................................................................................................................AGCGCCGCC------------AC-------------------TGGC-CAACG..	20	7	0.14	0.00	0.14	0.00	0.00
..............................................................................................................................................................................................A----ATTGAATTTTTAGGA--A----------C.............................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..TC-GAAATCTAGACA-AATACC.....................................................................................................................................................................................................................................................................................................................................................................................................................	20	4	0.25	0.00	0.25	0.00	0.00
...C-GAAATCTAGACA-AATACCAA...................................................................................................................................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
..TC-GAAATCTAGACA-AATACCA....................................................................................................................................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00
........................................................................................................................................................................................................................................................................................................................................................................TACGTGCACT--T-TGACGCC................................................	18	2	0.50	0.00	0.00	0.00	0.50
GGTC-GAAATCTAGACA-AATACC.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25

droVir3

ATATATA-TAAA---TATT-------------------------------------------------------TA-------------------------------ATATATT--ATATAATTAACAATTTA-------------------------AATAAAAAATTTCGCAATCCAAA-----------------------------------------------------------------------------------AATCATTACAAATATGGTAAA-----------------------------A------------------------------------------AAAAA-------------TCTATATTTTAAAGATTTAT-CTAATGATTCT--------------------TT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................................................................................................................................................................................................................................................................................AAGTATGGTGAA-----------------------------A------------------------------------------AAAAA-------------......................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00

droMoj3

ATGT-ATGTGCA---TACA-------------------------------------------------------TA-------------------------------TATATAT--TTATGTACATATGTAAA-------------------------TATAGAAATCTACGTATGATTTGTTGGCATTGC----A---------------------------CTCTTTACACACTTTTGTTTGTTTAT------TTTTT------------------------------------------------------------------------------------------------------------------TTATTTTATT------------TTTTTTTGTCT--------------------TT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................................................................................................................................................................................................................AT------TTTTT------------------------------------------------------------------------------------------------------------------TTCTTTTAAT------------TTTTT............................	22	7	0.29	0.00	0.00	0.00	0.29
.....................................................................................................................TATGTACATATGTAAG-------------------------TGT............................................................................................................................................................................................................................................................................	19	11	0.09	0.00	0.09	0.00	0.00
..................................................................................................................................................................................................................................................................TT------------------------------------------------------------------------------------------------------------------TTATTTTATT------------TTTGTGTGT........................	21	3	0.33	0.00	0.33	0.00	0.00

droGri2

ATAC-AAATATA---AATT-TATTCAAATTCAAATT------------------------ATC---------------TT-----------------------------------------------------------------------------------------------------------TCAA----A-TAAAAGGACAAGA--T-------------AAG-------ATAAA---TTAAA------TAATA-T----------------------------------------------------A--------A--------------------------C----AAAATTG-----------------TATTCT-------------CGTTTTCCCTTCTCGG-------------CA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:07 EDT

dme-mir-2279-as

chr2RHet:1322833-1322945 +

Novel

antisense_to_intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup