dme-mir-955- 12- and 20-way alignments

dme-mir-955	chr3L:3299055-3299151 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3299072-3299094
   star strand at position 3299113-3299134
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:3299040-3299166 +	TAAGGAACACT-TTTTGGC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------AC-AATT----
droSim1	chr3L:2834561-2834687 +	TAAAGAACTCT-TTTTGGC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------GA-AATT----
droSec1	super_2:3291343-3291466 +	TAATAAACACT-TTTTGGT---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA---------------------------------------------AA-AATT----
droYak2	chr3L:3844747-3844868 +	TAAAGT-------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGTG----TGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------AT-GAGTATAT
droEre2	scaffold_4784:5981990-5982116 +	AAGGAA-TACACTTTTGTC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------GC-AAGT----
droAna3	scaffold_13337:7606422-7606539 +	TGAAGGATGTT-TTTTGAG---AAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT-----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA----------------------------------------------------------
dp4	chrXR_group8:3252997-3253027 -	T--------------------------------------CCTGCAGGGGTTTGAGGGTCCTGTG----TCTTG----------------------------------------------------------------------------------------------------------------
droPer1	super_65:53567-53597 -	T--------------------------------------CCTGCAGGAGTTCGAGGATCCTGGG----TCTTG----------------------------------------------------------------------------------------------------------------
droWil1	Unknown	AA----ATACT-TTTGCGTTA-AGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTC-GTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA---------------------------------------------AA-AATT----
droVir3	scaffold_12758:855537-855672 -	CA----------------T---CAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGAG----TTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAACTAATACGGGTTGGGGCAA----GCCAA----------------AGA-AAAG----
droMoj3	scaffold_6680:1909566-1909725 -	TCCAAT-------------AT-GGGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGTG----T-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAACTGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGA-AATA----
droGri2	scaffold_15110:657062-657177 +	TTTAAT-------------AA-AGGTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGAG----T-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA---------------------------------------------AACAATC----

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:3299040-3299166 +	NA	TAAGGA--ACACTTT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTA------------------------------------AAA----------------------------------------------CAATT
droSim1	chr3L:2834561-2834687 +	5	TAAAGA--ACTCTTT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGCACGGTAGAGATGGTA-CGCTTAGAAACAACCTA------------------------------------AAG----------------------------------------------AAATT
droSec1	super_2:3291343-3291466 +	5	TAATAA--ACACTTT-----T-TGGTCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTTTTGCCTAA-TCGCATTCAATTTCTGCAG---AGAGATGGTA-CGCTTAGAAACAACCTA------------------------------------CAA----------------------------------------------AAATT
droYak2	chr3L:3844747-3844864 +	3	TAAAGT-----------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGT---GTGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTA------------------------------------AAA----------------------------------------------TGAGT
droEre2	scaffold_4784:5981989-5982116 +	4	AAGGAA--TACACTT-----T-TGTCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTGTTGCCTAA-TCGCATTCAATTTCTGAACGGTAGAGATGGTA-CGCTTAGAAACAACCTA------------------------------------AAG----------------------------------------------CAAGT
droEug1	scf7180000409466:1024712-1024826 +	5	T-------------T-----T-TTGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GACTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-AGCTTAAAAGCAACCTA------------------------------------AAG------------------------------------------------ACT
droBia1	scf7180000302428:2658402-2658538 +	2	CAGGAT--TTGCTTT-TCGTT-TGGTCAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCCTGT---ATCTTGCCAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTC-TGCTTCAAAGCAACATA------------------------------------AAACATT---------------------------AA-------------AAACA
droTak1	scf7180000415378:64765-64932 -	2	TACAGG--GTATTTT-TTGTTTCGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTCGACAAA-TCGCATTCAATCTCTGAACGGTAGAGATGGTA-TGCTCAAAAGCAACATAAATAAATTCCTAATTCCTAAAAATTCCTAAAAAAAATTG----------------------------------------------CAATT
droEle1	scf7180000491249:1960492-1960621 -	2	TGTGGAAGGTATTTG-----T-CGGCCAGCTTTTCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGCCAAT-TCGCATTCAATCTCTGAACGATAGAGATGGTC-AGCTTAAAAGCAACATA------------------------------------AGAT---------------------------------------------CAAAA
droRho1	scf7180000769770:13927-14066 -	2	ATATGA--AGACTTT-----C-TGGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGCCAAT-CCGCATTCAATCTTTGAACGATAGATATGGTC-AGCTTAAATGCAACCTA------------------------------------AACA-TC---------------------TATTCGAAAT-----------TCAGA
droFic1	scf7180000454105:1620302-1620432 +	4	TGAAGC--AACCTTT-----T-CAGCTAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGT---GTCTTGTCAAATTCGCATTCAATCTCTGAACGGTAGAGATGGTGGAGCTATAGATCAGCCTAAATAT--------------------------------------------------------------------------------ATACA
droKik1	scf7180000302391:414346-414467 +	1	TTCGA-------CAT-----T-TGGCCAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGT---GTATTGCCAAA-TCGCATTCAACCTCTGAACGGTAGAGATGGTG-AGCTTTAGAGCAACCTA------------------------------------AAT----------------------------------------------TTATA
droAna3	scaffold_13337:7606422-7606539 +	1	TGAAGG--ATGTTTT-----T-TGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT---TT-TTAACCAT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAGAAAGCAACCTA------------------------------------------------------------------------------------------
droBip1	scf7180000395543:273565-273688 +	1	GAAGGC--TGTTTTT-----T-TGAGAAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTC-TAT---TTTTTAACCTT-TCGCATTCAACCTTTGGACGGTAGAGATGGTC-AGTGAAAAAGCAACCTA------------------------------------AAA------------------------------------------------AAG
dp4	chr4_group1:2379981-2380081 +	1	AAT-----------------T-TAAAAAAATGAATAAATTCAAATGACAAAAATGTAAATGAATTAA-----------AAA-ATAAATTCAAATGATAAAAAGTAAA-----TG-AATAAAAAAATAAAGTA-------------------------------------------------------------------------------------AAATT
droPer1	Unknown	NA	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180698:10215726-10215851 +	1	ATTCAA--ATACTTTTGCG-T---TAAGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTCGTTTGTTTTCTCTAA-TGGCATTCAACCTTGGAGCGATAGAGACGGCC-AATCGAGAAACAGCCTA------------------------------------AA----------------------------------------------------
droVir3	scaffold_12758:855562-855687 -	3	TATGTA--TGGATCT-----C-TCATCAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGA---GTTTTTCCTAG-TGGCATTCAACCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTA------------------------------------AAC----------------------------------------------TAATA
droMoj3	scaffold_6680:1909563-1909732 -	1	TCAGGT--ATCCAAT-----A-TG---GGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGT---GTT-TGGCTAG-TCGCATTCAGCCTTTGAACGGTAGAGATGGCC-AACTGAAAAGCGACCTAACTGAA-------------------------------AG---CGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGAAATAGTT
droGri2	scaffold_15110:657067-657177 +	2	TAAAG-----------------------GTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGA---GT-TTGCCAAG-TGGCATTCAGCCCCTGGACGCTAGAGATGGCC-AACTGAAAAGCAACCTA------------------------------------AAAA---------------------------------------------CAATC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TAAGGAACACT-TTTTGGC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------AC-AATT----

Size

Hit Count

Total Norm

droSim1

TAAAGAACTCT-TTTTGGC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGCACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------GA-AATT----	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................CATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	836.00	395.00	5.00	0.00	436.00
.....................................ATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	22	1	154.00	29.00	1.00	0.00	124.00
....................................CATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	127.00	84.00	2.00	0.00	41.00
.................................................................................CATTCAATTTCTGCACGGTAGT..................................................................................	22	1	95.00	4.00	5.00	1.00	85.00
....................................CATCGTGCAGAGGTTTGAGTG................................................................................................................................	21	1	76.00	60.00	3.00	0.00	13.00
...............TGGC---CAGCTAATCAACTC.....................................................................................................................................................	18	1	64.00	0.00	0.00	0.00	64.00
.................................................................................CATTCAATTTCTGCACGG......................................................................................	18	1	50.00	0.00	0.00	0.00	50.00
..............TTGGC---CAGCTAATCAACTC.....................................................................................................................................................	19	1	33.00	1.00	0.00	0.00	32.00
.................................................................................CATTCAATTTCTGCACGGTAGA..................................................................................	22	1	31.00	17.00	0.00	0.00	14.00
...............TGGC---CAGCTAATCAACTCC....................................................................................................................................................	19	1	16.00	8.00	0.00	0.00	8.00
.....................................ATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	21	1	14.00	4.00	2.00	0.00	8.00
.................................................................................CATTCAATTTCTGCACGGTAG...................................................................................	21	1	14.00	0.00	0.00	0.00	14.00
....................................CATCGTGCAGAGGTTTGAGTGG...............................................................................................................................	22	1	13.00	0.00	2.00	0.00	11.00
.....................................ATCGTGCAGAGGTTTGAGTGTCC.............................................................................................................................	23	1	12.00	6.00	1.00	0.00	5.00
.............TTTGGC---CAGCTAATCAACTC.....................................................................................................................................................	20	1	12.00	0.00	0.00	0.00	12.00
....................................CATCGTGCAGAGGTTTGAG..................................................................................................................................	19	1	8.00	0.00	2.00	0.00	6.00
.................................................................................CATTCAATTTCTGCACGGTAGG..................................................................................	22	1	8.00	1.00	1.00	0.00	6.00
....................................CATCGTGCAGCGGTTTGAGTGTC..............................................................................................................................	23	1	6.00	6.00	0.00	0.00	0.00
............TTTTGGC---CAGCTAATCAACTC.....................................................................................................................................................	21	1	6.00	0.00	0.00	0.00	6.00
.....................................ATCGTGCAGAGGTTTGAGTGTCCTG...........................................................................................................................	25	1	6.00	2.00	0.00	0.00	4.00
....................................CATCGTGCAGAGGTTTGAGGGTC..............................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
....................................CATCGTGCAGATGTTTGAGTGTC..............................................................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
....................................CATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	24	1	5.00	2.00	0.00	0.00	3.00
....................................CATCGTGCAGAGGTTTGAGCGTC..............................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
..............TTGGC---CAGCTAATCAACTCC....................................................................................................................................................	20	1	5.00	0.00	0.00	0.00	5.00
.....................................ATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	23	1	5.00	1.00	0.00	0.00	4.00
....................................CATCTTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
.................................................................................CATTCAATTTCTGCACGGTAGC..................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
....................................CATCGTGCATAGGTTTGAGTGTC..............................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
.....................................ATCGTGCAGAGGTTTGAGTGTCCT............................................................................................................................	24	1	3.00	1.00	0.00	0.00	2.00
....................................CATCGTGCAGAGGTTTGAGT.................................................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGC...............................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
....................................CATCGTGCAGAGGTTTGAGTGAC..............................................................................................................................	23	1	3.00	0.00	0.00	0.00	3.00

droSec1

TAATAAACACT-TTTTGGT---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCCTGTG----TTTTGCCTAATCGCATTCAATTTCTGCAG---AGAGATGGTACGCTTAGAAACAACCTACA---------------------------------------------AA-AATT----	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................CTTTCxGCAG---AGAGATGGT............................................................................	18	1	4.00	0.00	3.00	1.00
.......................................................................................CTTTCxGCAG---AGAGATGGTA...........................................................................	19	1	2.00	0.00	2.00	0.00
.........................................CGCAGCGGTTTGAGTGTC..............................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TAAAGT-------------AAACAGCTAATCAACTCCATCGTGCAGAAGTTTGAGTGTCCTGTG----TGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------AT-GAGTATAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....................................CATCGTGCAGAAGTTTGAGTGTC..............................................................................................................................	23	1	293.00	206.00	0.00	15.00	4.00	68.00
....................................CATCGTGCAGAAGTTTGAGTGT...............................................................................................................................	22	1	96.00	16.00	8.00	33.00	12.00	27.00
....................................CATCGTGCAGAAGTTTGAGTGTCT.............................................................................................................................	24	1	16.00	0.00	0.00	3.00	1.00	12.00
....................................CATCGTGCAGAAGTTTGAGTG................................................................................................................................	21	1	7.00	1.00	0.00	5.00	1.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGC...............................................................................................................................	22	1	6.00	0.00	0.00	2.00	0.00	4.00
.....................................ATCGTGCAGAAGTTTGAGTGTC..............................................................................................................................	22	1	5.00	4.00	0.00	0.00	0.00	1.00
.....................................ATCGTGCAGAAGTTTGAGTGTCT.............................................................................................................................	23	1	3.00	0.00	0.00	0.00	0.00	3.00
....................................CATCGTGCAGCAGTTTGAGTGTC..............................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGTCC.............................................................................................................................	24	1	2.00	0.00	0.00	1.00	0.00	1.00
.....T-------------AAACAGCTAAGCGACTCCAT..................................................................................................................................................	21	1	2.00	0.00	0.00	2.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGTT..............................................................................................................................	23	1	2.00	0.00	0.00	2.00	0.00	0.00
.................................................................................CATTCAATTTCTGAACGGTAGA..................................................................................	22	1	2.00	2.00	0.00	0.00	0.00	0.00
....................................CATCGCGCAGAAGTTTGAGTGTC..............................................................................................................................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGT.................................................................................................................................	20	1	2.00	0.00	0.00	2.00	0.00	0.00
....................................CATCGTGTAGAAGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................CATCGTGCAGAAGTTTGAGTGAC..............................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................CATCGTGCAGACGTTTGAGTGT...............................................................................................................................	22	1	2.00	0.00	0.00	0.00	1.00	1.00
..................................................................................ATTCAATTTCTGAACGGTAGAGT................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................CATCGTGCAGAAGTTTGAGTGG...............................................................................................................................	22	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................CATCGGGCAGAAGTTTGAGTGTC..............................................................................................................................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
....................................CATCGTGCCGAAGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	0.00	0.00	0.00	2.00
....................................CATCGTGCAGAAGTTTGAGTGTG..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAATTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................CATCGTGCAGAAGTTTGAGAGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGCTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................CATCGGGCAGAAGTTTGAGCG................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAAGTTTAAGTGTA..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.....T-------------AAACAGCTAATCAACTCC....................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGTGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CAACGTGCAGAAGTTTCAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAATTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................CATCGTGCAGAAGTTTCAGTGAC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................ATCGTGCAGAAGTTTGAGTGTCC.............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
...................AAACAGCTAAGCGACTCCATC.................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCCGACGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGTCA.............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
...................AAACAGCTAAACGACTCCATC.................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................CCATCGTGCAGAAGTTTGAGTGT...............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTCAG..................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGTCTT............................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAAGTTTGAGTT................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGA.................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAATCTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGAGCAGACGTTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGGTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................TCGTGCAGAAGTTTGAGTGTCCTG...........................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................ATCGTGCAGAAGTTTGAGTGTCCTG...........................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGTAGTTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGA...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGGGTG................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGCTGTTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAAGTTTGAGTATC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCTTGCAGAAGTTTGAGTGAC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................ATTGTGCAGAAGxTTGAGTGT...............................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...................AAACAGCTAAGCGACTCCAT..................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAAGCTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

AAGGAA-TACACTTTTGTC---CAGCTAATCAACTCCATCGTGCAGAGGTTTGAGTGTCTTGTG----TGTTGCCTAATCGCATTCAATTTCTGAACGGTAGAGATGGTACGCTTAGAAACAACCTAAA---------------------------------------------GC-AAGT----	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................CATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	289.00	57.00	18.00	0.00	214.00
....................................CATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	260.00	228.00	1.00	0.00	31.00
....................................CATCGTGCAGAGGTTTGAGTG................................................................................................................................	21	1	201.00	41.00	9.00	0.00	151.00
....................................CATCGTGCACAGGTTTGAGTGTT..............................................................................................................................	23	1	49.00	5.00	0.00	44.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	24	1	27.00	6.00	1.00	0.00	20.00
....................................CATCGTGCAGAGGTTTGAGT.................................................................................................................................	20	1	16.00	2.00	1.00	0.00	13.00
....................................CATCGTGCACAGGTTTGAGTGT...............................................................................................................................	22	1	14.00	0.00	0.00	13.00	1.00
....................................CATCGTGCAGAGGTTTTAGTGTC..............................................................................................................................	23	1	9.00	9.00	0.00	0.00	0.00
.....................................ATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	23	1	5.00	2.00	0.00	0.00	3.00
....................................CATCGTGCATAGGTTTGAGTGTC..............................................................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
....................................CATCGTGCAGCGGTTTGAGTGTC..............................................................................................................................	23	1	4.00	3.00	0.00	0.00	1.00
....................................AATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
....................................CATCGTGCAGATGTTTGAGTGT...............................................................................................................................	22	1	4.00	0.00	0.00	0.00	4.00
.....................................ATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
....................................CATCGTGCAGAGGTTTGATTGT...............................................................................................................................	22	1	3.00	1.00	0.00	0.00	2.00
....................................CATCGTTCAGAGGTTTGAGTGT...............................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00

droAna3

TGAAGGATGTT-TTTTGAG---AAGCTCATCAGCTCCATCGTGCAGAGGTTTGAGTGTCTAAT-----TTTTAACCATTCGCATTCAACCTTTGGACGGTAGAGATGGTCAGTGAGAAAGCAACCTA----------------------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
....................................CATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	124.00	62.00	40.00	19.00	3.00
....................................CATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	60.00	21.00	18.00	8.00	13.00
....................................CATCGTGCAGAGGTTTGAGTG................................................................................................................................	21	1	41.00	21.00	16.00	2.00	2.00
....................................CATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	24	1	37.00	16.00	13.00	2.00	6.00
....................................CATCGTGCAGAGGTTTGAGT.................................................................................................................................	20	1	9.00	5.00	1.00	3.00	0.00
.................................................................................CATTCAACCTTTGGACGGTAGA..................................................................................	22	1	7.00	4.00	1.00	1.00	1.00
....................................CATCGTGCAGAGGTTTGAGTGTT..............................................................................................................................	23	1	6.00	3.00	2.00	1.00	0.00
...................................................................................TTCAACCTTTGGACGGTAGAG.................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTTAGTGTC..............................................................................................................................	23	1	4.00	0.00	2.00	0.00	2.00
....................................CATCGTGCAGAGGTTTGAGTTTC..............................................................................................................................	23	1	3.00	0.00	1.00	0.00	2.00
.....................................ATCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTT................................................................................................................................	21	1	2.00	1.00	0.00	0.00	1.00
....................................CATCGTGCAGAGGTTAGAGTGT...............................................................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
...................................CCATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	23	1	2.00	1.00	1.00	0.00	0.00
...................................................................................TTCAACCTTTGGACGGTAGAGT................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
....................................CATCGGGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	0.00	1.00	1.00
....................................AATGGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAGCGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................AATCGTGCAGAGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...................................................................................TTCAACCTTTGGACGATAGAGA................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CCTCGTGCAGAGGTTTGAGT.................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCACGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
....................................CATCTTGCATAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...................................................................................TTCAACCTTTGGACGGTAGA..................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCATAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGCGGTTTGAGTATC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTTGGT.................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................GATCGTGCAGAGGTTTGAG..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................CATTCAACCTTTGTACGATAGA..................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATAGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...............................................................................CGCATTCAACCTTTGGACGGTAG...................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTTCAGAGGTTTGCGTG................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAAGTTTGAGTGTCT.............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTAAGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGCGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGCTTGAGTGTCT.............................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
......................................TCGTGCAGAGGTTTGAGTGTCT.............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGCTTTGAGTG................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
....................................CATTGTGCAGAGGTTTGAGTT................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTA................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGTGGTTTGTGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................TGGTAAGTGAGAAAGCAAGC............................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAT..................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGG...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTTAGT.................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGTCTA............................................................................................................................	25	1	1.00	0.00	0.00	0.00	1.00
...................................................................................TTCAACCTTTGGAAGGTAGAG.................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................................................................CATTCAACCTTTGGACGGTGGA..................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGGGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGTTT.............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGCTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCAGCGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
...................................................................................TTCAACCTTTGAACGGTAGAGT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTATC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................AATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGCTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGATTTGAGTGTCT.............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.....................................ATCGTGCAGAGGTTTGAGTGTCA.............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
......................................TCGTGCGGAGGTTTGAGTGTCT.............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTTCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGTGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCAGAGGTTTGAGTGC...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................................CATTCAACCTTTGGACGGTAG...................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTGGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CAACGTGCAGAGGTTTGAGCGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCATAGGTTTTAGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
......................................TCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGCGCAGAGGTTTGAGTG................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAGTTTCT.............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTCTC..............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.....................................ATCGTGCAGAGGTTTGAGTG................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCATAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCAGAGTTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...................................................................................TTCAACCTTTGGACGGTAGAGA................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAAGGTC..............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCAGAGGTTTGAG..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

dp4

T--------------------------------------CCTGCAGGGGTTTGAGGGTCCTGTG----TCTTG----------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

T--------------------------------------CCTGCAGGAGTTCGAGGATCCTGGG----TCTTG----------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................CTGCAGGAGATCCAGGATC..............................................................................................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00

droWil1

AA----ATACT-TTTGCGTTA-AGGTTGGCTGGCTCCATCGTGCTTAGGTTTGAGTGTCTTC-GTTTGTTTTCTCTAATGGCATTCAACCTTGGAGCGATAGAGACGGCCAATCGAGAAACAGCCTAAA---------------------------------------------AA-AATT----	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................CATCGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	673.00	2.00	653.00	11.00	7.00
....................................CATCGTGCTTAGGTTTGAGTGT...............................................................................................................................	22	1	116.00	2.00	68.00	14.00	32.00
....................................CATCGTGCTTAGGTTTGAGTG................................................................................................................................	21	1	41.00	1.00	28.00	2.00	10.00
....................................CATCGTGCTTAGGTTTGAGTGTCT.............................................................................................................................	24	1	29.00	0.00	10.00	4.00	15.00
.................................................................................CATTCAACCTTGGAGCGATAGA..................................................................................	22	1	9.00	0.00	9.00	0.00	0.00
.....................................ATCGTGCTTAGGTTTGAGTGTC..............................................................................................................................	22	1	5.00	0.00	5.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGTCC.............................................................................................................................	24	1	4.00	0.00	2.00	0.00	2.00
....................................CATCGTGCTTAGGTTTTAGTGTC..............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
....................................CATCGTGCTTAGGCTTGAGTGTC..............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
....................................CATCGTGCTTATGTTTGAGTGTC..............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGTCA.............................................................................................................................	24	1	3.00	0.00	2.00	1.00	0.00
....................................CATCTTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGC...............................................................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
....................................CATCGTGCTTAGGTTTGATTGTC..............................................................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
........................................GTGCTTAGGTTTGAGTGTC..............................................................................................................................	19	1	2.00	0.00	2.00	0.00	0.00
.....................................ATCGTGCTTAGGTTTGAGTGT...............................................................................................................................	21	1	2.00	0.00	1.00	1.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGTCAA............................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGT.................................................................................................................................	20	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGCC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTTCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGG...............................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
....................................CATCGCGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGCGTCT.............................................................................................................................	24	1	2.00	0.00	1.00	0.00	1.00
....................................CATCGTGCTTAGATTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................CATTGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
.....................................ATCGTGCTTAGGTTTGAGTGTCT.............................................................................................................................	23	1	2.00	0.00	1.00	1.00	0.00
....................................CATCGTGCTTAGGTTTGAGAGTC..............................................................................................................................	23	1	2.00	0.00	2.00	0.00	0.00
....................................CATCGTGCTTAGGxTTGAGTGTC..............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
..............................................................................TGGCATTCAACCTTGGAGCGATA....................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................GCGATAGAxACGGCAAATCG......................................................................	19	1	1.00	1.00	0.00	0.00	0.00
........................................GTGCTTAGGTTTGAGTGT...............................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCTTAGGCTTGAGTG................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................AATCGTGCTTAGGTTTGAGTG................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................CCATCGTGCTTAGGTTTGAGTG................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGCGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTTAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................CATTCAACCTTGGAGCGATAG...................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
......................................................................................AACCTTAGAGAGATAGAGA................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGACTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATGGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGCTTGAGTGTCA.............................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
....................................TATCGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAATGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...................................CCATCGTGCTTAGGTTTGAGTGTC..............................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
...................................CCATCGTGCTTAGGGTTGAGTG................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTACGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGTCG.............................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCTTAGGTTTGAGTCTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATTGTGCTTAGGTTTGAGTG................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAATGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTxCTTAGGTTTGAGTGTC..............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................AATCGTGCTTAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CGTCGTGCTTAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCCTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAG..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTGATTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCCTAGGTTTGAATGTC..............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATAGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.............................................................................ATGGCATTCAACCTTGGAGCGATAGAA.................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
....................................CATCCTGCTTAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCTTGGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCAGAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
....................................CACCGTGCTTAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTTCTTAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCTTAGGTTTGAGTGTT..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
......ATACT-TTTGCGxTC-AGGTTG.............................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
....................................CGTCGTGCTTAGGTTTGAGTGTC..............................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droVir3

CA----------------T---CAGTTAGCTAGCTCCATCGTGCACAGGTTTGAGTGTT-TGAG----TTTTTCCTAGTGGCATTCAACCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAAACTAATACGGGTTGGGGCAA----GCCAA----------------AGA-AAAG----	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................CATCGTGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	46.00	1.00	0.00	44.00	1.00	0.00
....................................CATCGTGCACAGGTTTGAGTGT...............................................................................................................................	22	1	23.00	5.00	5.00	13.00	0.00	0.00
.................................................................................CATTCAACCTTTGAACGGTAGA..................................................................................	22	1	2.00	0.00	1.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTTAGTGT...............................................................................................................................	22	1	2.00	0.00	0.00	2.00	0.00	0.00
....................................CAGCGTGCACAGGTTTTAGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGAGTGTT-A............................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGATTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGGGCTCAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
....................................CATGGTGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................................AGTGGCCAACTGAAAAGCG...............................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................GTGCAGAGGTTTGAGTGTC-T............................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................CATCGTGCACAGGTTTGAGTGTT-T............................................................................................................................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCCCAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................ATCGTGCAGAGGTTTGAGTGTC-.............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.................................................................................CATTCAACCTCTGAACGGTAGA..................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGAACAGGTTTGAGTGTT-T............................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CGTCGTGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTTAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACCGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................CATCGTGCACAGGTTTGA...................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGAGCGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTCTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGGGCACAGGTTTGAGGGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGAGTATT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGAGTTTT-.............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

TCCAAT-------------AT-GGGTTAGCGAGCTCCATCGTGCACAGGTTTGAGTGTT-TGTG----T-TTGGCTAGTCGCATTCAGCCTTTGAACGGTAGAGATGGCCAACTGAAAAGCGACCTAACTGAAAGCGAATCAAGGGAACTAGGCCAATAGGCGAGAATCATATAGA-AATA----	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
....................................CATCGTGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	200.00	22.00	2.00	0.00	176.00
....................................CATCGTGCACAGGTTTGAGTGT...............................................................................................................................	22	1	65.00	37.00	12.00	5.00	11.00
.................................................................................CATTCAGCCTTTGAACGGTAGA..................................................................................	22	1	18.00	4.00	0.00	0.00	14.00
....................................CATCGTGCACAGGTTTGAGTGTT-T............................................................................................................................	24	1	12.00	6.00	3.00	1.00	2.00
....................................CATCGTGCAGAGGTTTGAGTGT...............................................................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
....................................CATCGTGCACAGGTTTGAGT.................................................................................................................................	20	1	2.00	1.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAGTGTT-TGTG----.....................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGGGCACAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
....................................CATCGTCCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGGGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
........................................GTGCACAGGTTTGAGTGTT-.............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAGTGGT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGGGAACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAAGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
..CAAT-------------AT-GGGTTAGCGAGCTC.....................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAGTG................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGCGCACAGGTTTGAGTGGT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
................................................GTTTGAATGTG-TGTG----T-TTGG...............................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
....................................CAGCGTGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAGTGTT-TGTT----.....................................................................................................................	27	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGTGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAATGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTTAGTG................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGCGCACAGGTTTGAGGGTT-T............................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGCGTGT...............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
....................................CATCGTGCACAGGTTTGAGTTTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...AAT-------------AT-GGGTTAGCGAGCTC.....................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGGTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGCGCACAGGTTTGAGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.................................................................................CATTCAGCCTTCGAACGGTAGA..................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAGTGTT-C............................................................................................................................	24	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGGGCACAGGTTTGGGTGTT-T............................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGCGCACAGGTTTGAGTGT...............................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
....................................CATCGTGCACAGGTTTGCGTGTT-.............................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
....................................CATCGTGCACAGGTTTGAG..................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

TTTAAT-------------AA-AGGTTGGCGAACTCCATCGTGCACGGGTTTGAGTGTC-TGAG----T-TTGCCAAGTGGCATTCAGCCCCTGGACGCTAGAGATGGCCAACTGAAAAGCAACCTAAA---------------------------------------------AACAATC----	Size	Hit Count	Total Norm	V109 Male body
....................................CATCGTGCACGGGTTTGAGTG................................................................................................................................	21	1	44.00	44.00
....................................CATCGTGCACGGGTTTGAGTGT...............................................................................................................................	22	1	41.00	41.00
....................................CATCGTGCACGGGTTTGAGT.................................................................................................................................	20	1	16.00	16.00
....................................CATCGTGCACGGGTTTGAGTGTC-.............................................................................................................................	23	1	5.00	5.00
....................................CATCGTGCACGGGTTTGAGTGA...............................................................................................................................	22	1	2.00	2.00
....................................CAACGTGCACGGGTTTGAGT.................................................................................................................................	20	1	2.00	2.00
.....................................ATCGTGCACGGGTTTGAGTG................................................................................................................................	20	1	1.00	1.00
....................................CATCGTGCACGGGTTTGAGTGTC-T............................................................................................................................	24	1	1.00	1.00
....................................CATCGTGCCCGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00
....................................CATCGAGCACGGGTTTGAGT.................................................................................................................................	20	1	1.00	1.00
.....................................ATGGTGCACGGGTTTGAGT.................................................................................................................................	19	1	1.00	1.00
....................................CATCGTGCACGGGTTTGAGTGTC-A............................................................................................................................	24	1	1.00	1.00
.....................................ATCGTGCACAGGxTTGAGTGTC-.............................................................................................................................	21	1	1.00	1.00
....................................CATCGTGCATGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00
.....................................ATCGTGCACGGGTTTGAGTGTC-.............................................................................................................................	22	1	1.00	1.00
....................................CATCGCGCACGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00
....................................CATCGTGCGCGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00
....................................CACCGTGCACGGGTTTGAGTG................................................................................................................................	21	1	1.00	1.00
....................................CATCGTACACGGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00
....................................CATCGTGCACGGGTTTGAATG................................................................................................................................	21	1	1.00	1.00
....................................CATAGTGCACGGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00
....................................CATCGTGCACGGGTTTGCGTGT...............................................................................................................................	22	1	1.00	1.00
....................................CATCGTGCACCGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00
....................................TATCGTGCACGGGTTTGAGTGT...............................................................................................................................	22	1	1.00	1.00
....................................CATCGTGCACGGGTTTGGGTG................................................................................................................................	21	1	1.00	1.00

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

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