dme-mir-4943- Best orthologs

dme-mir-4943	chr2L:16528374-16528491 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 16528403-16528425
   star strand at position 16528441-16528462
   mutations
   read mismatches

Notes: Othologs look confident due to the conservation of the flanking 3p end.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:16528359-16528506 -		1	ATTTTAA------ACAACTAT-----------------------------T-T--------------------CGGATCGTTTGAATG-AC------------------------------------------------------------------CAATTTTGTC---------------------------------------------------------------TTTT-A--TTTTCTC---------------------------------------T-----GTGTTT-------------TCAGTTAA-TG-AAAGAT-AG-TGAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droSim1	chr2L_random:601476-601603 -	LASTZ	5	ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGGC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----GTCGTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droSec1	super_7:174891-175018 -	LASTZ	5	ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGTC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----TTCTTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droYak2	chr2R:4574442-4574584 +	LASTZ	5	ATTTTAT------AAAACTAT-----------------------------G-G--------------------GGGATAC-TTAGATA-AT------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTGTTCTT---------------------------------------T-----GTC-TT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEre2	scaffold_4845:19592406-19592554 -	LASTZ	5	ATTTTAT------GCAACTATTGTGTGTATCT-------------------------------------------------TTAAATG-AC------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTCTTCTC---------------------------------------T--GTTTTTTTT-------------TCAGTTAA-TG-AATAGT-AG-CAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEug1	scf7180000408961:97346-97507 -	LASTZ	5	ATATCTA------AAAA---------------------------------------------------------------------TG-ACTAA--GATT------------CTCT----TC----AAC--------------------------------------------------------------------AACATGAC----------AAATT--AACTTATA-----A--TCTTCTC--T-------------------------TTGCTTG-TT-T-----TTCTTT-------------TTAGTAAA-TG-AAAAAT-AG-TAAACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droBia1	scf7180000301468:656432-656584 -	LASTZ	5	TGTGAAA------GTAGTTAG-----------------------------------------------------------------------------TTATAGTTTAAAATATGG----AG---------------------------------------------------------------------------------------------ATATTAAATGAAATCCCTT----ACTTTCT---------------------------------------T-----ATCGTT-------------TCAGTTGA-TG-AAAAGT-AG-TGAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droTak1	scf7180000415914:214815-214954 -	LASTZ	5	ACTCTAC------CTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAAAGTGTC----------AAATT--GACTAATCGTCTTG-TTCTTTCT---------------------------------------T-----ATCATT-------------TTAGTAAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droEle1	scf7180000490579:831701-831934 +	LASTZ	5	ATGTTGCTTCTATAAAACTAT-----------------------------TAA--------------------AAAATAA-TTA------------------------AAATCTG-AAGTTCCCGAAAA---GTGTTTATTAACACTTTTATATTAATTA-GTTAAA------TACAAACTAAGTTTAT-TTCATGAAAGGTG------------ACAATTTTTCAAATCTCCAT-----TTTCC---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TAGACAAAGAGCTAAATGATAGAGAATGAGACCCAGTCAACAGGACC---------CAAAAAGACAATGTTGATTG
droRho1	scf7180000780143:38260-38494 -	LASTZ	5	ATTTTCC------AAAACAAA-GTTCGT--TTTTAAATCTTAAAAATTATTATAAGATATCTTTTAAAATTTTCAAATCAAATAAACG-A---------------------TCTG-ATGGCTC---------------------------------------------------------------------CATAAAAGGTGCAAAATTGAAAAATATTTTTTCTAATCCCCTGT-TTTCTGTT---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TTCACCAAGTGCTAAATGATAGAGAATGAGACCCAGTCGACAGGACC---------CAAAAAGACAATGTTGATTG
droFic1	scf7180000454078:456928-457118 -	LASTZ	5	AATATAA------TAAA-----------------------------------T--------------------GTGACCATTAAAAAGTAC------------------------------------------------------------------CACTTATGTCTTTAAATT-----GATA-----T---------------------------------------T----AAA----TA-TTTTTGACAAAACTATAACTACAATATACTATCTCGTTTAT-----CTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TATACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------TAAGAAGACGATGTTGATTG
droKik1	scf7180000302382:320881-321046 -	LASTZ	5	CTTCTTG------ATAATTGC-----------------------------TGG--------------------GAAATTT-TTA------------------------AATTTTGT----TT----AAC----------------------------TAAATTTAT------------------------T------------------------A--------CTTATTCCTT-----------------------------------------AATTT-TT-TTCTTATTTTTT-------------ACAGTAAA-TG-AAAAGT-AG-TACACGCAGTGCTCAATGAATGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG
droAna3	scaffold_12916:16031637-16031788 +	LASTZ	5	ATGTTTA------AA-----------------------------------------------------------------------TG-ATTAAAAAATT------------ATGT----TC----AACTAATTAT---------------------TA----------------------------------------------------------------------------AT----TT-ATAT-------------------------TTTATTG-TC-T----TCCCATT-------------ACAGTTAA-TGAAAAAGT-AATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG
droBip1	scf7180000396717:268070-268207 +	LASTZ	5	ATTTTAA------AATA------------------------------------------------------------------------------------------------TTT----TT----AAT--------------------------------------------TT-----AAAA-----T---------------------------------------T----AAT----TA-TTTT-------------------------TTTATCA-TT-T----TCTCATT-------------ACAGTTGA-TG-AAAAGT-AG-TTATAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG
dp4	chr4_group3:8251613-8251715 -	LASTZ	5	TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTT-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG
droPer1	super_1:9700572-9700674 -	LASTZ	5	TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTC-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG
droWil1	scaffold_180772:4810613-4810759 -	LASTZ	0	AAGTTTA------CCAATTAA-----------------------------TAG--------------------CAAATTG-TTG------------------------GTATTT------CC-------------------------------------ATTTTAAA-----ATT-----GCT-------A------------------------ACATTTA--------CCTTAAT----TT-CTCT-------------------------TCTT-------T-----TC---------------------TTTT-TC-AATTCC-AG-CTTACGTTGCTATAAATGAGAAAGGATCAAGAT------------CA---------AACGAAAAGGATGTTGATTG
droVir3	scaffold_13052:1601321-1601473 -	LASTZ	0	ATATTGC------GCAACCAT-----------------------------T-C--------------------TGG----------------------TC-------------CG-AATTTCATTGAGT-------------------------CAGTCATTTTGGG------TAACTCTTGAGT--------------------------------------------------------TT-ATTT-------------------------CTTA-------A--TT-GTC-TTTCGCTGAAATTGTGCAATAAA-TA-----AC-AA-TT---------------------TTACCATCAGCATTAGCCAGCACA---------CACACGCACGCTATCGGTTT
droMoj3	scaffold_6500:21042727-21042874 -	LASTZ	0	AATTATA------ATT---G---AACACTTG-------------------A-T--------------------GCGATT----------GC------------------------------------------------------------------CAAATTTTTG--------------------------------------------------------------------A-TTTTTGGT---------------------------------------T--C-TATTTTT-------------AGAGTTAC-AG-CTAA----A-TGAAAACTATACCAATTATAAAATCAAAAGGGCTACACAAGAACATTTATGATTTCAAAGAAAAGTGTTTCATTTG
droGri2	scaffold_14822:853797-853916 -	LASTZ	0	GCATGAT------GA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTGGTCTCT-ATTCTATA---------------------------------------T-----GCTGGT-------------TGAGTTTG-TG-AATGGTCAG-TTGCCGTGGCGAAAGATAAAAGACAA--GGAACAGGTTGGATTGACC---------AAAGAGAAATATGATCATAG

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	ATTTT------AAACAACTATTTC--GGATCGTTTGAATG-AC----------------------CA--------------AT----------------------TT------------------------------------------------------------------------------------------------------------------------TGTCTT----------TT----ATT----------------T-----TC------TC-------------TGTGTTTTCAGTTAA-TG-AAAGATAGT-GAACACAGTGCTAAATGAAAGATAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droSim1	ATTT------------------------ATTT-TTGAATG-AC----------------------CA--------------AT----------------------TT------------------------------------------------------------------------------------------------------------------------TGGCTT----------------T-C----------------T-----TC------TC-------------TGTCGTTTCAGTTAA-TG-AAAAGTAGT-AAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droSec1	ATTT------------------------ATTT-TTGAATG-AC----------------------CA--------------AT----------------------TT------------------------------------------------------------------------------------------------------------------------TGTCTT----------------T-C----------------T-----TC------TC-------------TTTCTTTTCAGTTAA-TG-AAAAGTAGT-AAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droYak2	ATTTT------ATAAAACTATGGG--GGATAC-TTAGATA-AT----------------------TA--------------AT----------------------TT------------------------------------------------------------------------------------------------------------------------TGTCAT----------------T-G----------------T-----TC------TT-------------TGTC-TTTCAGTTAA-TG-AAAAGTAGT-AAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droEre2	ATTTT------ATGCAACTATTGTGTGTATCT-TTAAATG-AC----------------------TA--------------AT----------------------TT------------------------------------------------------------------------------------------------------------------------TGTCAT----------------T-C----------------T-----TC------TCT---G--T-----TTTTTTTTCAGTTAA-TG-AATAGTAGC-AAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droEug1	ATATC------TAAA---------------------AATG-AC----------------------TA--------------AG----------------------ATT------------CTC---T---------------------------------------------TCAAC----------------AACATGACAAA----------TTAACT--TA-------------------TAA---T-C----------------T-----TCTCTTTG---CTTG--TT----TTTCTTTTTAGTAAA-TG-AAAAATAGT-AAACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droBia1	TGTG---------AA---------------------AGTA-GT----------------------TAG--------------------------------------TTATAGTTTAAAATATG---G---------------------------------------------AG-------------------------------------ATATTAAATGAAATCC---CTT----------------A-C----------------T-----TT------CT-------------TATCGTTTCAGTTGA-TG-AAAAGTAGT-GAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droTak1	ACTCT------AC-----------------CT-------------------------------------------------------------------------------------------------------------------------------------------------------------ATAAAAAGTGTCAAA------------TTGACTAATCGTCTTGT----------------T-C----------------T-----TT------CT-------------TATCATTTTAGTAAA-TG-AAAAGTAGT-AAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droEle1	ATGTTGCTTCTATAAAACTAT--------------------------------------------TAAAA---AATAATTAAA--------------------AT---------------CTGAAGTTCCCGAAAAGTGTTTATTAACACTTTTATATTAATTAGTTAAATACAAACTAAGTTTATTTCATGAAAGGTGACAA------------TTTTTCAAATCTCCATT------------------------------------------TT------CC-------------TTTCTTTTTAGTAAA-TG-AAAAGTAAT-AGACAAAGAGCTAAATGATAGAGAATGAGACCCAGTCAACAGGACCCAAAAAGACAATGTTGATTG
droRho1	ATTTT------CCAAAACAAA------------------GTTCGTTTTTAAATCTTAAAAATTATTATAAGATATCTTTTAAAATTTTCAAATCAAATAAACGAT---------------CTGATGGCTC----------------------------------------------------------CATAAAAGGTGCAAAATTGAAAAATATTTTTTCTAATCCCCTGT------------------------------------------TT------TCT---G--TT----TTTCTTTTTAGTAAA-TG-AAAAGTAAT-TCACCAAGTGCTAAATGATAGAGAATGAGACCCAGTCGACAGGACCCAAAAAGACAATGTTGATTG
droFic1	AATAT------AATA----AATG---TGACCATTAAAAAGTAC----------------------CA--------------CT----------------------TA------------------------------------------------------------------------------------------------------------------------TGTCTTTAAATTGATATTAAATATTTTTGACAAAACTATAACTACAATATACTAT---CTCGTTTA----TCTCTTTTTAGTAAA-TG-AAAAGTAAT-ATACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACCTAAGAAGACGATGTTGATTG
droKik1	CTTCT------TGATAATTGC--------------------------------------------TGGGA---AATTTTTAAA--------------------TT---------------TTG---T---------------------------------------------TTAACTAAAT-------------------------------------T-------TA--------------TTACTTA-------------------------TTCCTTA---ATTT-TTTTCTTATTTTTTACAGTAAA-TG-AAAAGTAGT-ACACGCAGTGCTCAATGAATGAGAATGAGACCCAGTCGACAGGACCCAAGAAGACGATGTTGATTG
droAna3	ATGTT------TA-----------------------AATG-AT----------------------TA--------------AA--------------------AAATT------------ATG---T---------------------------------------------TCAACTAA---------------------------------------T---------------------TATTAATTT-------------------------ATATTTT---ATTG-TCT----TCCCATTACAGTTAA-TGAAAAAGTAATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCCCAAGAAGACCATGTTGATTG
droBip1	ATTTT------AAAA---T-----------------------------------------------------------------------------------------------------ATT---T---------------------------------------------TTAATTTA---------------------------------------A---------------------AATTAATTA-------------------------TTTTTTT---ATC-ATTT----TCTCATTACAGTTGA-TG-AAAAGTAGT-TATAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCCCAAGAAGACCATGTTGATTG
dp4	TTTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTC-CTTT----TCTCTTTACAGTTATTTG-CCAAGCAG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAACAGAAGACGATGTTGATTG
droPer1	TTTG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTC-CTTT----TCTCTTCACAGTTATTTG-CCAAGCAG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGAACAGAAGACGATGTTGATTG

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

ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGGC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----GTCGTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................................................................................................................................................................................AAATGAAAGATAATGAGACC...........................................	20	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................................................................................................................................................................................................GAGACCCAGTCGACAGGACC---------CAAG................	24	1	1.00	0.00	0.00	0.00	1.00
ATTTAT------------------------TT-------------------------------------------------TTTATTG-AC------------------------------------------------------------------CA........................................................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................TGAGACCCAGTCGACAGGACC---------C...................	22	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................GAGACCCAGTCGACAGGACC---------....................	20	1	1.00	0.00	0.00	0.00	1.00

droSec1

ATTTAT------------------------TT-------------------------------------------------TTGAATG-AC------------------------------------------------------------------CAATTTTGTC--------------------------------------------------------------------T-TTCTTCTC---------------------------------------T-----TTCTTT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................................................................................................................................................................................................................................................................................................GACAGGACC---------CAAGAAGACGATGTTGA...	26	1	1.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................ACGAAGACGATGTTGATGG	19	1	1.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................GAxC---------TAAGAAGACGATGTT.....	18	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................AGT-AG-TAAACACAGTGCTAAATGAAAG......................................................	27	1	1.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................CGTTAA-TG-AAAAGT-AG-TAAACACAGT..................................................................	26	1	1.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................TGAGACCCAGTCGACAGGA...............................	19	1	1.00	0.00	1.00	0.00

droYak2

ATTTTAT------AAAACTAT-----------------------------G-G--------------------GGGATAC-TTAGATA-AT------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTGTTCTT---------------------------------------T-----GTC-TT-------------TCAGTTAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................................................................................................................................................................................................................................................................................................................................................................ACC---------CAAGAAGACGATGTTG....	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................................................................................................................................................TA-TT-------------TGAGTTAA-TG-AAAAG.................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................GGACC---------CAAGAAGACGATGT......	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................GACAGGACC---------CAAGAAGACGATGTTGA...	26	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................................................CGACAGGACC---------CAAGAAGACGATGTTG....	26	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................GAGACGCAGTCGACAGGACC---------....................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................TGAGACGCAGTCGACAGGACC---------C...................	22	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ATTTTAT------GCAACTATTGTGTGTATCT-------------------------------------------------TTAAATG-AC------------------------------------------------------------------TAATTTTGTC--------------------------------------------------------------------A-TTCTTCTC---------------------------------------T--GTTTTTTTT-------------TCAGTTAA-TG-AATAGT-AG-CAAACACAGTGCTAAATGAAAGAGAATGAGACGCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................................................................................................................................................................................................................................ATAGT-AG-CAAACACAGTGCT...............................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................T-------------------------------------------------TTAAATG-AC------------------------------------------------------------------xAACTTTGT.................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................................................................................................................................................................................................................................GAxC---------TAAGAAGACGATGTT.....	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................................................................................................................................................................................................................ACC---------CAAGAAGACGATGTTT....	19	1	1.00	1.00	0.00	0.00	0.00

droEug1

ATATCTA------AAAA---------------------------------------------------------------------TG-ACTAA--GATT------------CTCT----TC----AAC--------------------------------------------------------------------AACATGAC----------AAATT--AACTTATA-----A--TCTTCTC--T-------------------------TTGCTTG-TT-T-----TTCTTT-------------TTAGTAAA-TG-AAAAAT-AG-TAAACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droBia1

TGTGAAA------GTAGTTAG-----------------------------------------------------------------------------TTATAGTTTAAAATATGG----AG---------------------------------------------------------------------------------------------ATATTAAATGAAATCCCTT----ACTTTCT---------------------------------------T-----ATCGTT-------------TCAGTTGA-TG-AAAAGT-AG-TGAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droTak1

ACTCTAC------CTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAAAGTGTC----------AAATT--GACTAATCGTCTTG-TTCTTTCT---------------------------------------T-----ATCATT-------------TTAGTAAA-TG-AAAAGT-AG-TAAACACAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droEle1

ATGTTGCTTCTATAAAACTAT-----------------------------TAA--------------------AAAATAA-TTA------------------------AAATCTG-AAGTTCCCGAAAA---GTGTTTATTAACACTTTTATATTAATTA-GTTAAA------TACAAACTAAGTTTAT-TTCATGAAAGGTG------------ACAATTTTTCAAATCTCCAT-----TTTCC---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TAGACAAAGAGCTAAATGATAGAGAATGAGACCCAGTCAACAGGACC---------CAAAAAGACAATGTTGATTG

Size

Hit Count

Total Norm

droRho1

ATTTTCC------AAAACAAA-GTTCGT--TTTTAAATCTTAAAAATTATTATAAGATATCTTTTAAAATTTTCAAATCAAATAAACG-A---------------------TCTG-ATGGCTC---------------------------------------------------------------------CATAAAAGGTGCAAAATTGAAAAATATTTTTTCTAATCCCCTGT-TTTCTGTT---------------------------------------T-----TTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TTCACCAAGTGCTAAATGATAGAGAATGAGACCCAGTCGACAGGACC---------CAAAAAGACAATGTTGATTG

Size

Hit Count

Total Norm

droFic1

AATATAA------TAAA-----------------------------------T--------------------GTGACCATTAAAAAGTAC------------------------------------------------------------------CACTTATGTCTTTAAATT-----GATA-----T---------------------------------------T----AAA----TA-TTTTTGACAAAACTATAACTACAATATACTATCTCGTTTAT-----CTCTTT-------------TTAGTAAA-TG-AAAAGT-AA-TATACAAAGTGCTAAATGAAAGAGAATGAGACCCAGTCGACAGGACC---------TAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droKik1

CTTCTTG------ATAATTGC-----------------------------TGG--------------------GAAATTT-TTA------------------------AATTTTGT----TT----AAC----------------------------TAAATTTAT------------------------T------------------------A--------CTTATTCCTT-----------------------------------------AATTT-TT-TTCTTATTTTTT-------------ACAGTAAA-TG-AAAAGT-AG-TACACGCAGTGCTCAATGAATGAGAATGAGACCCAGTCGACAGGACC---------CAAGAAGACGATGTTGATTG

Size

Hit Count

Total Norm

droAna3

ATGTTTA------AA-----------------------------------------------------------------------TG-ATTAAAAAATT------------ATGT----TC----AACTAATTAT---------------------TA----------------------------------------------------------------------------AT----TT-ATAT-------------------------TTTATTG-TC-T----TCCCATT-------------ACAGTTAA-TGAAAAAGT-AATTTAAAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................................................................................................................................................................................................................................................TAAAAGAAAGAGAAAGAGA.............................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................................ATGCAAGAGAATGTGAC............................................	17	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................AGAATGAGACCCAGTCGACATT................................	22	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................AT-------------------------TTTATTG-TC-T----TTACAT................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
...............................................................................................................................................................................................................................................................................................................................................AAAATxGCTAAAAGAAAGA.....................................................	18	2	0.50	0.00	0.00	0.00	0.50
.................................................................................................................................................................................................................................................................................................................................................................................GACATTTCC---------CAAGAAGACC..........	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................................................................................................................................................................................................................GAGAATGAGACCCAGTCGAC...................................	20	1	1.00	1.00	0.00	0.00	0.00

droBip1

ATTTTAA------AATA------------------------------------------------------------------------------------------------TTT----TT----AAT--------------------------------------------TT-----AAAA-----T---------------------------------------T----AAT----TA-TTTT-------------------------TTTATCA-TT-T----TCTCATT-------------ACAGTTGA-TG-AAAAGT-AG-TTATAAAATCGCTAAATGAAAGAGAATGAGACCCAGTCGACATTTCC---------CAAGAAGACCATGTTGATTG

Size

Hit Count

Total Norm

dp4

TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTT-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................................................................................................................................................................................................................................................................................................................CGACAGACGA---------ACAGAAGACGAT........	22	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................................GACGACxGACGA---------ACAGAAGA............	19	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................GAGACACAGTCGACAGAC...............................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

TTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------------------CC-TT-T----TCTCTTC-------------ACAGTTATTTG-CCAAGC-AG--AAGAAAAGTGCTAAATGAAAGAGAATGAGACACAGTCGACAGACGA---------ACAGAAGACGATGTTGATTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................................................................................................................................................................................................................................................GAGACACAGTCGACAGACGA---------....................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
...................................................................................................................................................................................................................................................................................................................................................................................................ACAGAAGATGATGTTGAGT.	19	1	2.00	2.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................AAAGTGCTAAATGAAAGAGAAT.................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................CAGATGGCGATGTTGATT.	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AAGTTTA------CCAATTAA-----------------------------TAG--------------------CAAATTG-TTG------------------------GTATTT------CC-------------------------------------ATTTTAAA-----ATT-----GCT-------A------------------------ACATTTA--------CCTTAAT----TT-CTCT-------------------------TCTT-------T-----TC---------------------TTTT-TC-AATTCC-AG-CTTACGTTGCTATAAATGAGAAAGGATCAAGAT------------CA---------AACGAAAAGGATGTTGATTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................................................................................................................................................................................................................................................................ATTTAAATGAGAAAGGAT.................................................	18	1	2.00	0.00	2.00	0.00	0.00
.........................................................................................................................C-------------------------------------TTTTTAAA-----ATT-----GCA-------A------------------------AC..............................................................................................................................................................................................	18	2	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................................TTTTAAA-----ATT-----GCA-------A------------------------ACAAT...........................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................................................................................................................................................................................................................GTTGCTATAAATGAGAAAGGATCAAGAT------------...............................	28	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................................................................................................................................................................................TCAAGxT------------CA---------AACGAAAAGA..........	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................AATGAGAAAGGATCAAGAT------------...............................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................................A---------AACGAAAAGGATGTTGATTG	21	1	1.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................ATAAATGAGAAAGGATCAA..............................................	19	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................GGTTCAAGAT------------CA---------AAAGAAA.............	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

ATATTGC------GCAACCAT-----------------------------T-C--------------------TGG----------------------TC-------------CG-AATTTCATTGAGT-------------------------CAGTCATTTTGGG------TAACTCTTGAGT--------------------------------------------------------TT-ATTT-------------------------CTTA-------A--TT-GTC-TTTCGCTGAAATTGTGCAATAAA-TA-----AC-AA-TT---------------------TTACCATCAGCATTAGCCAGCACA---------CACACGCACGCTATCGGTTT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................................................................................................................................................................................................................................ATTT-------------------------CCTA-------A--TT-GxC-TTTCGCTG.........................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................................................................................................................................................................................................................................................................................................................TTACCATCAGCATTGGGC...................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................................................................................................................................................CAGCATTAGCCxCCACA---------CACA................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................................................................................................................................................................................................................................................CACA---------CACACGCACGCACTCGG...	21	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

AATTATA------ATT---G---AACACTTG-------------------A-T--------------------GCGATT----------GC------------------------------------------------------------------CAAATTTTTG--------------------------------------------------------------------A-TTTTTGGT---------------------------------------T--C-TATTTTT-------------AGAGTTAC-AG-CTAA----A-TGAAAACTATACCAATTATAAAATCAAAAGGGCTACACAAGAACATTTATGATTTCAAAGAAAAGTGTTTCATTTG	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.................................................................................................................................................................................................................................................................................................................................................................................................TCAAAGAAAAGCGTCTCAT...	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

GCATGAT------GA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTGGTCTCT-ATTCTATA---------------------------------------T-----GCTGGT-------------TGAGTTTG-TG-AATGGTCAG-TTGCCGTGGCGAAAGATAAAAGACAA--GGAACAGGTTGGATTGACC---------AAAGAGAAATATGATCATAG

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:21:28 EDT

dme-mir-4943

chr2L:16528374-16528491 -

Known_mirbase

intron

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup