dme-mir-4939- 12- and 20-way alignments

dme-mir-4939	chr2R:18872733-18872842 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 18872760-18872780
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:18872718-18872857 -	ATGCACATTTATTTGGCATCATGCTTC---TGCGATCT-------------------------------------CTACCAATTT----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAAC-----------------GACTGCAACCGGACGACTCTTGGT
droSim1	chr2R:17459524-17459663 -	ATCCACATTTATTTGGCATCATGCTTC---TGCGAGCT-------------------------------------CTACCACTTC----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGCGACACTGATGCTGGTGAAGATTCGGAGGAGGACGACAGCGAA-----------------GACTGCAACAGGACGACTCTTGGT
droSec1	super_9:2164747-2164886 -	ATCCACATTTATTTGGCATCATGCTTC---TGCGAGCT-------------------------------------CTACCACTTC----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGCGACACTGATGCAGGTGAAGATTCAGAGGAGGACGACAGCGAA-----------------GACTGCAACAGGACGACTCTTGGT
droYak2	chr2R:18832811-18832950 -	AACCGCGTTTATTTGCCAAAATGCTGC---TCCGAGCT-------------------------------------CTACCACTTC----------------------TGCTCACACTCTGTGTGTTGGTCCTCTCC-------AACGACGACACGGATGCAGATGAAGAAGAGGAAGAGGACGAC-----------------------GACTGCAACAAGGCGACTCTTGGT
droEre2	scaffold_4845:20234099-20234238 -	AACCACGTTTATTTGCCATAATGCTGC---TCCGAACT-------------------------------------CTGCTC----------------------------CTTACGCTCTTCGTGTTTGTCCTTGCC-------AAAAACGATACGATTGCAGAAGTAGAGGAAGAGTCGGACGAGGACGAA-----------------GGATGCAACAAGGCGACTCTTGGT
droAna3	scaffold_13266:15205113-15205273 -	GTCCAATCCAGTTACTCACCATGTCTC---CTCGTCTG-------------------------CTGATCTTGGTGCTGCAGCTCC----------------------TGCTCCTGCCCTCCATTTTGGC----GCAAGAACGTAAAAAGGGAAAGGAGAAGAATAAAGAGCCCTCGCAGGACGTCAAGATG-----------------GAGTGCGACAATGCTACCATTGGC
dp4	chr3:14089101-14089284 -	AAGCAA-TTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTT------TAGTAAC-----------------------------------------TCCCAGAACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCT
droPer1	super_4:1228949-1229132 +	AAGCAA-TTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTT------TAGTAGC-----------------------------------------TCCCAGAACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCT
droWil1	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:5728482-5728538 -	ACCCATTTTATTTTACTG-------------------------------------------------------------------------------ATAATCCATTTAGATTCATGTT------TGGTCATTTGA-------AGAAGT-----------------------------------------------------------------------------------
droMoj3	scaffold_6496:24343095-24343103 -	AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC
droGri2	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:18872718-18872857 -	NA	ATGCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------TCTCTA------------------CCAATTTTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGTGAC--------------------ACGGGTGCAGGTGAAGA---TTCGGAA------GAG----GACGACGA-AAAC-GACTGCA-A---CCGGACGACTCTTGGT
droSim1	chr2R:17459524-17459663 -	7	ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCTGGTGAAGA---TTCGGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT
droSec1	super_9:2164747-2164886 -	10	ATCCACATTTA--TTTGGCATCATGCTTCTGC-----------GA------------------GCTCTA------------------CCACTTCTCCT------------------TGCACTCTTTG------TCCTTTCCAAAAGCGAC--------------------ACTGATGCAGGTGAAGA---TTCAGAG------GAG----GACGACAG-CGAA-GACTGCA-A---CAGGACGACTCTTGGT
droYak2	chr2R:18832811-18832950 -	13	AACCGCGTTTA--TTTGCCAAAATGCTGCTCC-----------GA------------------GCTCTA------------------CCACTTCTGCT------------------CACACTCTGTGTGTTGGTCCTCTCCAACGACGAC--------------------ACGGATGCAGATGAAGA---AGAGGAA------GAG----G---A----CGAC-GACTGCA-A---CAAGGCGACTCTTGGT
droEre2	scaffold_4845:20234099-20234238 -	7	AACCACGTTTA--TTTGCCATAATGCTGCTCC-----------GA------------------ACTCTG------------------CTCCT------------------------TACGCTCTTCGTGTTTGTCCTTGCCAAAAACGAT--------------------ACGATTGCAGAAGTAGA---GGAAGAGTCGGACGAG----G---A----CGAA-GGATGCA-A---CAAGGCGACTCTTGGT
droEug1	scf7180000409672:6848444-6848567 -	10	ACCA-ATATCG--TTTGCCACAATGATACTAC-----------CA------------------GTTCTG------------------CCACTCCTTCT------------------AGGACTTTTTGTATCTGTCCAGT------GTGGC--------------------AAGTTCCCACCATCG-------------------------GAATA----CGAA-GAGTGCA-G---CAATGCAACTATTGGC
droBia1	scf7180000301754:4157293-4157441 -	12	AACCAATGTCA--TTCGCAATAATGATGCCAA-----------AA------------------GCTGTG------------------CCCCTCCTTCT------------------GGGGCTCCTCGTGCTCGTTCTCTCCGATCCCTAT--------------CCCGGTCGTGCGGATTACACGGA---TCCAGAG------GAG----GAGGA----GGCT-AAGTGCA-A---CAATAAGACTATTGGT
droTak1	scf7180000415411:112699-112853 +	13	AACCAGTTTTA--ATCGAGACCGTGATGCTAA-----------GA------------------GCTCTA------------------CCACTCTTTCT------------------AGGGCTATTCCTGATCGTTCATTCCGATCCCTTC--------CCAGATCCCTTTCCCGCTACCTATACGGA---TCCGGAG------GAG----GAGGA----AGCT-AAGTGCA-A---TTCTAAAACAATCGGT
droEle1	scf7180000491283:40306-40430 +	8	AGCCAATTTCA--TTTGCGATAATGATTCTAC-----------CA------------------GCTCTA------------------CAACTCTTCCT------------------AGGATTGTTGGTGCTCGTATATTCCGAGGACGAC--------------------GAGGAAAT---------------------------A----GAAGC----GGAC-AAGTGCA-G---AAACGCCACTATGGGA
droRho1	scf7180000767166:1286-1419 -	18	AATCAATTCTA--TTTGCGATAATGATTCTAC-----------CAGTG---------------GCGCTA------------------CCACTCTTTCT------------------AGGGCTGTGTGTGCTCGTCCTTTCCGAGGACT--------------------------------CGGAGGA---CTCGGAA------ATG----GAAGT----CGAC-AAGTGCG-A---CAACACCACTATTGGC
droFic1	scf7180000454066:2882629-2882771 -	12	AGCCAATTCCA--TTTGCGATCATGATTCTGT-----------CG------------------ACTCTG------------------CTACTCATCCT------------------GGGGATGACTGTATTTGTTCTTTCCGATGAAACT--------------------ACAACCACAACCAAGAAACCTTCGGAG------GAT----A---A----CGAT-AGCTGCA-A---CAAGACGACCATTGGC
droKik1	scf7180000302408:508066-508140 -	4	TTGAAAGTTTAAACTCAATTCCATGATTCTGC------GGC--CAAAA---------------AGCTTA------------------TTACTTCCTCT------------------AGCATTCTCTA------TTCCTCC----------------------------------------------------------------------------------------------------------------
droAna3	scaffold_13266:15204126-15204261 -	4	ATTTAAGAGCT--TTTCCCTTCAAAGCCTAAACAGTTGACACAAAATGTGGC---------------TA------------------CC----------------------------------------------CTTCTTGCTAGTGGC--------------------ACTGCCTTGGGGGACTG---TG-G----------TGGGGGGAGGTCCTCTGAC-ATTGGCCAATCTTAGCCGAATCATTGGA
droBip1	scf7180000396385:367904-368012 -	5	AAGCAGTT-GA--CTCAGAATG--------------------------TGGC---------------TA------------------CCTATCTTTCT------------------A----------------------------GTGGC--------------------ACTGCCAT-GGTGGACA---GTTGCGG------AGG----GACGTCCC-CAGTCGTTGTCCAATCTTACCCGAATTGTTGGA
dp4	chr3:14089101-14089284 -	5	AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAAC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT
droPer1	super_4:1228949-1229132 +	1	AAGCAATT-AG--TTTGCCATT--------------------------TGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATT----CAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTTTAGTAGC----------------TCCCAGAACAACA---AA-A----------TGAACAAAGCTCGATCCGC-GTTCGCC-G---CCGCCCTTCTTTTGCT
droWil1	Unknown	NA	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	NA	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:24343095-24343103 -	1	AT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC
droGri2	scaffold_15112:3934700-3934745 -	3	ATATTCAATA-----TGC------------------------------------------------TGA------------------GCACATCTTCT------------------GAAAGCATTTCAGACTTTC---------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATGCACATTTATTTGGCATCATGCTTC---TGCGATCT-------------------------------------CTACCAATTT----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGTGACACGGGTGCAGGTGAAGATTCGGAAGAGGACGACGAAAAC-----------------GACTGCAACCGGACGACTCTTGGT

Size

Hit Count

Total Norm

droSim1

ATCCACATTTATTTGGCATCATGCTTC---TGCGAGCT-------------------------------------CTACCACTTC----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGCGACACTGATGCTGGTGAAGATTCGGAGGAGGACGACAGCGAA-----------------GACTGCAACAGGACGACTCTTGGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................C---TACGAGCT-------------------------------------CTACCACTC....................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................GATTTGGACGAGGACGAC...............................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................GGTGAAGATTCGGAGGAGGAC..................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................GAGGATTCGGAGGAGGTC..................................................	18	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................AGAACGACAGCGxA-----------------GACTG...................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................AGCGAA-----------------GACTGCAACAGGACGACT......	24	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................GAGGATTCGGATGAGGAC..................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

ATCCACATTTATTTGGCATCATGCTTC---TGCGAGCT-------------------------------------CTACCACTTC----------------------TCCTTGCACTCT------TTGTCCTTTCC-------AAAAGCGACACTGATGCAGGTGAAGATTCAGAGGAGGACGACAGCGAA-----------------GACTGCAACAGGACGACTCTTGGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................................................................................GCTGAAGATTCCGAGGAG.....................................................	18	1	1.00	0.00	1.00	0.00
...............................................................................................................................................................................GGAGAACGACAGCGAA-----------------GAG.....................	19	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................................GAATCAGAGGAGGAGGAC...............................................	18	1	1.00	0.00	1.00	0.00
...........TTTGGCATCCTGGTTC---TG........................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.......................................................................................................................................................................GATTCAGAGGCGGAGGACA..............................................	19	1	1.00	0.00	1.00	0.00

droYak2

AACCGCGTTTATTTGCCAAAATGCTGC---TCCGAGCT-------------------------------------CTACCACTTC----------------------TGCTCACACTCTGTGTGTTGGTCCTCTCC-------AACGACGACACGGATGCAGATGAAGAAGAGGAAGAGGACGAC-----------------------GACTGCAACAAGGCGACTCTTGGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................AGAAGAAGAGGACGAC-----------------------GACT....................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
............................................................................................................................................................................GGAAGAGGACGAC-----------------------GAGCG...................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................AGAAGACGAAGAGGAGGA................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................GGAAGAAGAGGAAGAGGAGGA................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................................GAGGACGAGGACGAC-----------------------GATT....................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................................................................................AAGAAGATGAAGAAGAGGA.........................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....GTTTTTAxTTGCCAAAATG.................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................................................................................................................CGATGAAGATGAGGAAGAGGA...................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................GATGAAGAAGAGGAGGAGGATG.................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................GAGGACGAGGAAGAGGAC..................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................GAGGAGGACGAGGACGAC-----------------------........................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................................................................................AGAGGAAGAGGAGGAG-----------------------GA......................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................ATGAAGATGAGGCAGAG.....................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................................................................................................................................................AAGAGGAAGAGGAGGAG-----------------------G.......................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................GATGAAGAGGAGGAGGACG.................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................................TGAAGAAAAGGAGGAGGA...................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................GATGAAGAGGAGGAGGAGG....................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................GATGAGGACGAGGAAGAGG....................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................GAAGAAGAGGAAGAGGAGGAG-----------------------GA......................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AACCACGTTTATTTGCCATAATGCTGC---TCCGAACT-------------------------------------CTGCTC----------------------------CTTACGCTCTTCGTGTTTGTCCTTGCC-------AAAAACGATACGATTGCAGAAGTAGAGGAAGAGTCGGACGAGGACGAA-----------------GGATGCAACAAGGCGACTCTTGGT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

GTCCAATCCAGTTACTCACCATGTCTC---CTCGTCTG-------------------------CTGATCTTGGTGCTGCAGCTCC----------------------TGCTCCTGCCCTCCATTTTGGC----GCAAGAACGTAAAAAGGGAAAGGAGAAGAATAAAGAGCCCTCGCAGGACGTCAAGATG-----------------GAGTGCGACAATGCTACCATTGGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................................AAAAAGGGAAAGAAGAAGC......................................................................	19	1	7.00	2.00	2.00	3.00	0.00
..................................................................................................................................................AAGGGAAAGAAGAAAAAT....................................................................	18	1	2.00	0.00	2.00	0.00	0.00
........................................................................................................................................................AAGAAGAAGAAGAAAGAG..............................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................ACAGGGAAGGGAGAAGAA.....................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................................TAAAGGAGxAGAATAAAGA...............................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................GAAAAGGAAAAGGAGAAGAA.....................................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................AAAAGGGAAAGAAGAAGC......................................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................AAAAGGGxAAGAAGAAGAA.....................................................................	18	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................AAAAAGAAAAGGAGAAGAA.....................................................................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................AAAAAGGAAAGAAGAAGA......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................AAAAAGGCAAAGAAGAAGA......................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................AAAAAGGGxAAGGAGAAAAA.....................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................AGGAGAAGAAGAAAGAGG.............................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................AGAACGAAAAAAGGAAAA..............................................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................................................................AAAAGAGAAAGGAAAAGA......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................AAAAAAGGAAAGGAAAAGA......................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................................................AGGAAAAGGAGAAGAAAAA..................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................AGGTAGAAAGGGAAAGGA...........................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................ACGTTAAAAAGGAAAGGAG..........................................................................	19	1	1.00	1.00	0.00	0.00	0.00
................................................................................................................................................AAAAGAGAAAGGAGAAAA......................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................ATGGAAAAAGGGAAAGGAGA.........................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................................................................................................................................AAAAAGGAAAAGGAAAAGA......................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................AAAAAGGGACAGGATAAGA......................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................TAAAAAGGAAGAGGAGAAG.......................................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................................AAAAGGGAAAGGAAAAGG......................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................AACGxAAAAAGGGAAAGGC...........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................AAGAAAGTAAAAAGGGGA...............................................................................	18	1	1.00	1.00	0.00	0.00	0.00

dp4

AAGCAA-TTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCGAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTT------TAGTAAC-----------------------------------------TCCCAGAACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.............................................................................................................................................................................................TGAACAAAGCTCGATCCGCGTT.....................	22	1	1.00	1.00	0.00	0.00	0.00

droPer1

AAGCAA-TTAGTTTGCCATTTGCCATCTTATCGGGGTAATACCCAATCCAATTTATTGACCAATTCAAGATAGTCCCAAAGCTTTTCGCTGATTGCAACGATCCATTCCAAAGAAATTT------TAGTAGC-----------------------------------------TCCCAGAACAACAAAATGAACAAAGCTCGATCCGCGTTCGCCGCCGCCCTTCTTTTGCT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.....................................................................ATAGTCCCAAAGCTTTTCGCTGATTG.........................................................................................................................................	26	1	4.00	0.00	0.00	0.00	0.00	4.00
..............................................................................................................................................................................................GAACAAAGCTCGATCCGCGTT.....................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.............................................................................................................................................................................................TGAACAAAGCTCGATCCG.........................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................GCTCGATCCGCGTTCTGCGCC..............	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.............................ATCGGGGxAATACGCAATC........................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

ACCCATTTTATTTTACTG-------------------------------------------------------------------------------ATAATCCATTTAGATTCATGTT------TGGTCATTTGA-------AGAAGT-----------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTGGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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

20-way Secondary Structure

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