block92371- Best orthologs

block92371	chr2L:6973236-6973348 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 6973248-6973268
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:6973221-6973363 -		1	CGCGCCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATATTC-GGCGAT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC--CATC--------T---CGGATATTACGTGACTTAATGCAAGGCTTTTGGC---------------------------------------------------------------GATTAAAGTCAAG-----------------------CGGAG-------AT
droSim1	chr2L:6769566-6769705 -	LASTZ	4	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCA--CATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droSec1	super_3:2505870-2506008 -	LASTZ	1	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droYak2	chr2L:5936133-5936280 +	LASTZ	3	CC---CCAAGAATACTCACT------------GG----CGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATCCATCC-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTG-G-AGAGA-CGAG----------------------------------------------GAG----------GAGTCGAG-----------------------CAGAG-----ACGC
droEre2	scaffold_4929:15889020-15889155 -	LASTZ	3	CC----CAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATGGCT--GCGGT-------------CC-ATCTTCG-ATC----C-ATCTGTAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTG-G-A----------------------------------------------------------GAG-----GAAAGTCGAG-----------------------AGGAG-------AC
droEug1	scf7180000409463:94621-94763 -	LASTZ	4	CC----CACAAATACTCACT------------TG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------ACC-GCTTTCG-ATC----C-ATCTACAGTCTCA---ATC--------T---CGGATATCACGTGACTTAATGCAAGGCTCC-A-A----------------------------------------------------------AAGCTGCTTGAAAATGCG---------------------AGTCGAG-------AA
droBia1	scf7180000302422:2439201-2439346 +	LASTZ	4	CC-----AAAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAACT--GCTAC------------ACC-GCTTTCG-ATC----C-AACTTCAGTCCCA---ACCTCCA--TTT---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCA-------AG
droTak1	scf7180000416008:231160-231307 -	LASTZ	4	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC-------TTC--TTC-GCTTTCG-ATC----C-ATCTTCAGTCCCA---ATCTC-------ACGTGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCG-------AG
droEle1	scf7180000490640:333648-333793 +	LASTZ	4	CC-----ACAAATACTCACT------------GG----AGAGCCTTGTATTGAATCAACGTAATAGCT--GCGAT------CGTCTAATC-GTCTTCG-ATC----C-ATCTTCAGTCCCA---ATC--------G---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-A----------------------------------------------------------GAGCTGATTGAAAACGCG-----------------------ATACG-------AT
droRho1	scf7180000779930:68908-69048 -	LASTZ	4	CC-----ACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATAGCC--GCGAC------------ATC-GTTTTCG-ATC----C-ATCTTCAGTCCCA---GTC--------C---CGGATATTACGTGGCTTAATGCAAGGCTTA-G-A----------------------------------------------------------GAGCTGCTTGAA-TCGCG---------------------ATACGAG-------AC
droFic1	scf7180000452011:146-285 -	LASTZ	4	CC-----AAAAATACTCACT------------GG----GGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------CTC-GTTTTCG-ATC----C-ATCTTTAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-G----------------------------------------------------------GAGCCGATTGAAGTCGAG-----------------------ACGAG-------AG
droKik1	scf7180000302468:483720-483875 -	LASTZ	4	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATGGTCTCGCGAC-------------AC-GATTTCG-AAC----C-ATCTTCAGTCCCAAATATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTAC-G-A----------------------------------------------------------GAGCTCCTTCAGAACGCG----AC--------AA-AACGTAACGAG-------AC
droAna3	scaffold_12916:53076-53242 -	LASTZ	1	GGCGCTCACAAATACTCACT------------GTAA--TGAGCCTTGCATTGAATCAACGTAATAGCT--GTGTC-------GGC---TCTATTTTGG-TCC----G-AAATTCAGTCCCA---ATC--------T---GGGATATTACGTGGCTTAATGTAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTTGAAGAAATA--AATTTA------AA-AAA----GGAGAAAGACCTT
droBip1	scf7180000392937:103419-103594 -	LASTZ	4	GGCGCCCACAAATACTCACT------------GAAT--AGAGCCTTGCATTGAATCAACGTAATAGCT--GTGAC-------AGC---TC-TATTCCG-GTC----CAAACTTCAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTCGAAAAAAAATTAAAATAACTTTAAAGAAA--AACGCA--AGACCTT
dp4	chr4_group1:3766092-3766263 +	LASTZ	3	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAG--CCA---ATT--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAG------------------------------------------------ACAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droPer1	super_5:1509790-1509963 -	LASTZ	4	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAGC--CA---ATA--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAGAG----------------------------------------------AGAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droWil1	scaffold_180772:7270846-7270981 +	LASTZ	1	TGAACACAAAAAT---AAAA------------AG----TTAGCCTAGCATTGAATCGACGTAATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------GAA---ACT--------T---TGACAATTACGTGACTTAATGCTAAGCTTT-G-T----------------------------------------------------------AA-CAAAATGAA----------AATA------GA-AAAGAAACAAG-------AT
droVir3	scaffold_12963:3413645-3413810 -	LASTZ	3	CCAAAAAAAAAATACTCATTGAAAGCGT-GTTTG----AAAGCTTTGCATTGAATCGCAGTAATCGGCT-GGATT-CACAGAAA--------CCTTAG-AAC----T-CT--ATTATAACT---TTT---TA-AATCAGCTGCAATTACGTGGCTTAATGCAAAGCTTG-G-AATGTGAGGA----------------------------------------------AAAAAGCAGCTTT---------------------------------AT---------G
droMoj3	scaffold_6500:13787240-13787449 -	LASTZ	3	AGAATCATAAAATACTCATTGAGAGCGTTATGCA----AAAGCTTTGCATTGAATCGCCGTAATCGCA--GT--C------------CAC-ACTTTAG-ATA----T-TTT-TTTGTAACC---TTC---GAAAATCAGCTGCAATTACGCGGCTTAATGCAAAGCTTA-T-GATGCAAGAAAAAAAAGAACGAAATATTAATGATAAAATAACAATAAAAAATTAAAAGAAAGCTGCTTT---------------------------------ATG-------AA
droGri2	scaffold_15252:2977193-2977325 -	LASTZ	4	CA----TTAAAAGCTTCATT------------TG----AAAGCTTTGCATTGAATCGCAGTAATCTCG-AGCTAC------------ATA-TCCTTAG-AAC----T-TT--------------ATT--------GCTGTTTTAATTACGTGGCTTAATGCAAAGCTTG-A-AATAAACGA-------------------------------------------------AAAGCTGCTTT---------------------------------ATG-------AA

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	CGCGCCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATATTC-GGCGAT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC--CATC--------T---CGGATATTACGTGACTTAATGCAAGGCTTTTGGC---------------------------------------------------------------GATTAAAGTCAAG-----------------------CGGAG-------AT
droSim1	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCA--CATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droSec1	CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT
droYak2	CC---CCAAGAATACTCACT------------GG----CGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATCCATCC-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTG-G-AGAGA-CGAG----------------------------------------------GAG----------GAGTCGAG-----------------------CAGAG-----ACGC
droEre2	CC----CAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATGGCT--GCGGT-------------CC-ATCTTCG-ATC----C-ATCTGTAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTG-G-A----------------------------------------------------------GAG-----GAAAGTCGAG-----------------------AGGAG-------AC
droEug1	CC----CACAAATACTCACT------------TG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------ACC-GCTTTCG-ATC----C-ATCTACAGTCTCA---ATC--------T---CGGATATCACGTGACTTAATGCAAGGCTCC-A-A----------------------------------------------------------AAGCTGCTTGAAAATGCG---------------------AGTCGAG-------AA
droBia1	CC-----AAAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAACT--GCTAC------------ACC-GCTTTCG-ATC----C-AACTTCAGTCCCA---ACCTCCA--TTT---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCA-------AG
droTak1	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC-------TTC--TTC-GCTTTCG-ATC----C-ATCTTCAGTCCCA---ATCTC-------ACGTGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCG-------AG
droEle1	CC-----ACAAATACTCACT------------GG----AGAGCCTTGTATTGAATCAACGTAATAGCT--GCGAT------CGTCTAATC-GTCTTCG-ATC----C-ATCTTCAGTCCCA---ATC--------G---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-A----------------------------------------------------------GAGCTGATTGAAAACGCG-----------------------ATACG-------AT
droRho1	CC-----ACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATAGCC--GCGAC------------ATC-GTTTTCG-ATC----C-ATCTTCAGTCCCA---GTC--------C---CGGATATTACGTGGCTTAATGCAAGGCTTA-G-A----------------------------------------------------------GAGCTGCTTGAA-TCGCG---------------------ATACGAG-------AC
droFic1	CC-----AAAAATACTCACT------------GG----GGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------CTC-GTTTTCG-ATC----C-ATCTTTAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-G----------------------------------------------------------GAGCCGATTGAAGTCGAG-----------------------ACGAG-------AG
droKik1	CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATGGTCTCGCGAC-------------AC-GATTTCG-AAC----C-ATCTTCAGTCCCAAATATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTAC-G-A----------------------------------------------------------GAGCTCCTTCAGAACGCG----AC--------AA-AACGTAACGAG-------AC
droAna3	GGCGCTCACAAATACTCACT------------GTAA--TGAGCCTTGCATTGAATCAACGTAATAGCT--GTGTC-------GGC---TCTATTTTGG-TCC----G-AAATTCAGTCCCA---ATC--------T---GGGATATTACGTGGCTTAATGTAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTTGAAGAAATA--AATTTA------AA-AAA----GGAGAAAGACCTT
droBip1	GGCGCCCACAAATACTCACT------------GAAT--AGAGCCTTGCATTGAATCAACGTAATAGCT--GTGAC-------AGC---TC-TATTCCG-GTC----CAAACTTCAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTCGAAAAAAAATTAAAATAACTTTAAAGAAA--AACGCA--AGACCTT
dp4	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAG--CCA---ATT--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAG------------------------------------------------ACAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droPer1	TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAGC--CA---ATA--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAGAG----------------------------------------------AGAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA
droWil1	TGAACACAAAAAT---AAAA------------AG----TTAGCCTAGCATTGAATCGACGTAATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------GAA---ACT--------T---TGACAATTACGTGACTTAATGCTAAGCTTT-G-T----------------------------------------------------------AA-CAAAATGAA----------AATA------GA-AAAGAAACAAG-------AT
droVir3	CCAAAAAAAAAATACTCATTGAAAGCGT-GTTTG----AAAGCTTTGCATTGAATCGCAGTAATCGGCT-GGATT-CACAGAAA--------CCTTAG-AAC----T-CT--ATTATAACT---TTT---TA-AATCAGCTGCAATTACGTGGCTTAATGCAAAGCTTG-G-AATGTGAGGA----------------------------------------------AAAAAGCAGCTTT---------------------------------AT---------G
droMoj3	AGAATCATAAAATACTCATTGAGAGCGTTATGCA----AAAGCTTTGCATTGAATCGCCGTAATCGCA--GT--C------------CAC-ACTTTAG-ATA----T-TTT-TTTGTAACC---TTC---GAAAATCAGCTGCAATTACGCGGCTTAATGCAAAGCTTA-T-GATGCAAGAAAAAAAAGAACGAAATATTAATGATAAAATAACAATAAAAAATTAAAAGAAAGCTGCTTT---------------------------------ATG-------AA
droGri2	CA----TTAAAAGCTTCATT------------TG----AAAGCTTTGCATTGAATCGCAGTAATCTCG-AGCTAC------------ATA-TCCTTAG-AAC----T-TT--------------ATT--------GCTGTTTTAATTACGTGGCTTAATGCAAAGCTTG-A-AATAAACGA-------------------------------------------------AAAGCTGCTTT---------------------------------ATG-------AA

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCA--CATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......GAAGAATACTCACT------------GG----AGAGC...................................................................................................................................................................................................................................................	21	1	2.00	0.00	0.00	0.00	2.00
................CACT------------GG----AGAGCCTGGCAA............................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

CC--CCGAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATC----C-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGGAG-------AT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....CGAAGAATACTCACT------------GG----AGAGC...................................................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00
............................................................................................................................................................AATGAAGGGCTTT-GGA----------------------------------------------------------G-----A................................................	18	1	1.00	0.00	1.00	0.00
........................................................................................................................................................................T-GGA----------------------------------------------------------G-----ATCAAAGTCGAG-----------------------CGG...........	20	1	1.00	0.00	0.00	1.00
...........ATACTCACT------------GG----AGAGCCTTGC..............................................................................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00

droYak2

CC---CCAAGAATACTCACT------------GG----CGAGCCTTGCATTGAATCAACGTAATAGCT--GCGGT-------------CC-ATCTACG-ATCCATCC-ATCTATAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCCAGGCTTG-G-AGAGA-CGAG----------------------------------------------GAG----------GAGTCGAG-----------------------CAGAG-----ACGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................................................................ATG-G-AGAxA-CGAG----------------------------------------------GAG----------GAGT.........................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................GGA-CGAG----------------------------------------------GAG----------GAGGCGA......................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................GT-G-AGxGA-CGAG----------------------------------------------GAG----------GAGT.........................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

CC----CAAGAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATGGCT--GCGGT-------------CC-ATCTTCG-ATC----C-ATCTGTAGTCCCC---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTG-G-A----------------------------------------------------------GAG-----GAAAGTCGAG-----------------------AGGAG-------AC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................TTACGTGGCTTAATGCAAGTCTT......................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00

droEug1

CC----CACAAATACTCACT------------TG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------ACC-GCTTTCG-ATC----C-ATCTACAGTCTCA---ATC--------T---CGGATATCACGTGACTTAATGCAAGGCTCC-A-A----------------------------------------------------------AAGCTGCTTGAAAATGCG---------------------AGTCGAG-------AA

Size

Hit Count

Total Norm

droBia1

CC-----AAAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAACT--GCTAC------------ACC-GCTTTCG-ATC----C-AACTTCAGTCCCA---ACCTCCA--TTT---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCA-------AG

Size

Hit Count

Total Norm

droTak1

CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC-------TTC--TTC-GCTTTCG-ATC----C-ATCTTCAGTCCCA---ATCTC-------ACGTGGATATTACGTGGCTTAATGCAAGGCTTC-G-A----------------------------------------------------------GAGCTGCTTGAAAACGCG-----------------------AGGCG-------AG

Size

Hit Count

Total Norm

droEle1

CC-----ACAAATACTCACT------------GG----AGAGCCTTGTATTGAATCAACGTAATAGCT--GCGAT------CGTCTAATC-GTCTTCG-ATC----C-ATCTTCAGTCCCA---ATC--------G---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-A----------------------------------------------------------GAGCTGATTGAAAACGCG-----------------------ATACG-------AT

Size

Hit Count

Total Norm

droRho1

CC-----ACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATAGCC--GCGAC------------ATC-GTTTTCG-ATC----C-ATCTTCAGTCCCA---GTC--------C---CGGATATTACGTGGCTTAATGCAAGGCTTA-G-A----------------------------------------------------------GAGCTGCTTGAA-TCGCG---------------------ATACGAG-------AC

Size

Hit Count

Total Norm

droFic1

CC-----AAAAATACTCACT------------GG----GGAGCCTTGCATTGAATCAACGTAATAGCT--GCGAC------------CTC-GTTTTCG-ATC----C-ATCTTTAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTC-G-G----------------------------------------------------------GAGCCGATTGAAGTCGAG-----------------------ACGAG-------AG

Size

Hit Count

Total Norm

droKik1

CC----CACAAATACTCACT------------GG----AGAGCCTTGCATTGAATCGACGTAATGGTCTCGCGAC-------------AC-GATTTCG-AAC----C-ATCTTCAGTCCCAAATATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTAC-G-A----------------------------------------------------------GAGCTCCTTCAGAACGCG----AC--------AA-AACGTAACGAG-------AC

Size

Hit Count

Total Norm

droAna3

GGCGCTCACAAATACTCACT------------GTAA--TGAGCCTTGCATTGAATCAACGTAATAGCT--GTGTC-------GGC---TCTATTTTGG-TCC----G-AAATTCAGTCCCA---ATC--------T---GGGATATTACGTGGCTTAATGTAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTTGAAGAAATA--AATTTA------AA-AAA----GGAGAAAGACCTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................................................................................................................................................................................................ATA--AATTTA------AA-AGA----CGAGA........	19	1	6.00	4.00	0.00	1.00	1.00
....................................................................................................................................................................................................................................................AAATA--AATTTA------AA-AGA----CGAGA........	21	1	4.00	2.00	0.00	0.00	2.00
.....................................................................................................................................................................................................................................................AATA--AATTTA------AA-AGA----CGAGAA.......	21	1	3.00	1.00	1.00	1.00	0.00
...................................................................................GC---TCTATTTTGG-TCC----G-AAATTC............................................................................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
.....................................................................................................................................................................................................................................................AATA--AATTTA------AA-AGA----CGAGA........	20	1	2.00	2.00	0.00	0.00	0.00
......................................................................................................................................................................................................................................................ATA--AATTTA------AA-AGA----CGAGAA.......	20	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................................................................GCTGCTAGAAGAAATA--GATT...............................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................AAATA--AATTTA------AA-AGA----CGAGAA.......	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................................................................GTGGCTTAATGTAAGGCTTT-G-G----------------------------------------------------------GA.....................................................	24	1	1.00	0.00	1.00	0.00	0.00
........................................AGCCTTGCATTGAATCAACGTAATA.............................................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................................................................................................................ATTTA------AA-GAA----GAAGAAAG.....	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................................................................................TA--AATTTA------AA-AGA----CGAGAA.......	19	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................................................................................TTAA------AA-GAA----GGAGAAAGA....	18	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................AGAAGTA--AATTAA------AA-AAA----.............	18	5	0.20	0.00	0.20	0.00	0.00
........................................................................................................................................................................................................................................................A--AATTTA------AA-AGA----CGAGAAAG.....	20	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................AGTTA------AA-AAA----GGGGAAA......	17	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................GATATTACGTGGCTTAATGTA............................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................................................................................................................................A--AAGTTA------AC-AAA----GGAGAAAGA....	21	1	1.00	1.00	0.00	0.00	0.00

droBip1

GGCGCCCACAAATACTCACT------------GAAT--AGAGCCTTGCATTGAATCAACGTAATAGCT--GTGAC-------AGC---TC-TATTCCG-GTC----CAAACTTCAGTCCCA---ATC--------T---CGGATATTACGTGGCTTAATGCAAGGCTTT-G-G----------------------------------------------------------GAGCTGCTCGAAAAAAAATTAAAATAACTTTAAAGAAA--AACGCA--AGACCTT

Size

Hit Count

Total Norm

dp4

TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAG--CCA---ATT--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAG------------------------------------------------ACAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
............................................................................................................................................................................AGAGAGAG------------------------------------------------ACAGAGGAGCTC..............................................	20	1	5.00	1.00	0.00	0.00	4.00
..................................................................................................................................................................................AG------------------------------------------------ACAGAGCTGCTCGAAA------------------------CGAA..............	22	1	1.00	1.00	0.00	0.00	0.00

droPer1

TGCCCCCCAAAATACTCATT------------GGAGGGAGAGCCTTGCATTGAATCAACGTAATTGCT--GTGAACAAAATCATCTA-TC-GAATCCGAGTC----CAAATGTCAGC--CA---ATA--------ACAGCAGCAATTACGTGGCTTAATGCCAGGCTTT-A-AGAGAGAGAG----------------------------------------------AGAGAGCTGCTCGAAA------------------------CGAAGCGCA-------AA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................................................................................GT-A-AGAGAGAGAG----------------------------------------------AGAGAGC...................................................	20	21	0.19	0.00	0.00	0.00	0.00	0.19
............................................................................................................................................................................AGAGACAGAG----------------------------------------------ACAGAGCT..................................................	18	7	0.29	0.00	0.00	0.00	0.00	0.29
..........................................................................................................................................................................C-AGAGAGAGAG----------------------------------------------AGAGAGC...................................................	18	20	0.10	0.00	0.05	0.00	0.00	0.05
............................................................................................................................................................................AGAGAGAGAG----------------------------------------------AGAGAGCT..................................................	18	17	0.12	0.00	0.00	0.00	0.00	0.12
.......................................................................TGAACAAAATCATCTA-TC-GAATCCGA...........................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................AGAGAGGGAG----------------------------------------------AGAGGGCT..................................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
........................................................................................................................................................................T-G-AGAGAGATAG----------------------------------------------AGAGAGC...................................................	19	17	0.06	0.06	0.00	0.00	0.00	0.00
........................................................................................................................................................................C-A-ATAGAGAGAG----------------------------------------------AGAGAG....................................................	18	41	0.02	0.02	0.00	0.00	0.00	0.00
............................................................................................................................................................................AGAGAGAGAG----------------------------------------------AGAGAGATG.................................................	19	22	0.05	0.05	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GT-A-ACAGAGAGAG----------------------------------------------AGAGA.....................................................	18	26	0.04	0.00	0.04	0.00	0.00	0.00
................................................................................................................................................................CCAGGCTTT-A-AGAGAGAGA.........................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................................A-AGAAAGAGAG----------------------------------------------AGAGAGATG.................................................	20	5	0.20	0.20	0.00	0.00	0.00	0.00
.......................................................................................................................................................................AT-A-AGCGAGAGAG----------------------------------------------AGAGAG....................................................	19	10	0.10	0.10	0.00	0.00	0.00	0.00
....................................................................................................................................................................GCTGT-A-TGAGAGAGAG----------------------------------------------AGA.......................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00
.......................................................................................................................................................................TT-G-AGAGAGATAG----------------------------------------------AGAGAGC...................................................	20	2	0.50	0.00	0.00	0.00	0.00	0.50
....................................................................................................................................................................GCTTG-T-AGAGAGAGAG----------------------------------------------AG........................................................	18	4	0.25	0.25	0.00	0.00	0.00	0.00
......................................................................................................................................................................CTA-A-AGAGAGAGAG----------------------------------------------AGAG......................................................	18	31	0.03	0.00	0.03	0.00	0.00	0.00
.......................................................................................................................................................................GT-A-AGAGAGxGAG----------------------------------------------AGAGAGC...................................................	19	2	0.50	0.00	0.00	0.00	0.00	0.50
............................................................................................................................................................................AGCGAGAGAG----------------------------------------------AGAGAGTT..................................................	18	21	0.05	0.00	0.00	0.00	0.05	0.00
........................................................................................................................................................................A-A-AGAGAGAGAG----------------------------------------------AGCGAGC...................................................	19	22	0.05	0.00	0.00	0.05	0.00	0.00
.............................................................................................................................................................................GAGAGAGAG----------------------------------------------AGAGAGATG.................................................	18	25	0.04	0.04	0.00	0.00	0.00	0.00
.......................................................................................................................................................................AT-A-AGCGAGAGAG----------------------------------------------AGAGA.....................................................	18	11	0.09	0.00	0.09	0.00	0.00	0.00

droWil1

TGAACACAAAAAT---AAAA------------AG----TTAGCCTAGCATTGAATCGACGTAATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------GAA---ACT--------T---TGACAATTACGTGACTTAATGCTAAGCTTT-G-T----------------------------------------------------------AA-CAAAATGAA----------AATA------GA-AAAGAAACAAG-------AT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................AA---ACT--------T---TGACAATTACGTGACT...................................................................................................................................	22	1	21.00	0.00	9.00	1.00	11.00
.............................................................AATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------........................................................................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................................................................................................................................................AATA------GA-AGAGAAAGAAG-------A.	18	3	0.33	0.00	0.00	0.33	0.00
.............................................................................................................................................................................................................................................AAGGAA----------AAGA------GA-AAAGAA..............	18	2	0.50	0.00	0.00	0.50	0.00
..........AAT---AAAA------------AG----TTAGCCTAGC..............................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................AA----------AACA------GA-AAAGAAAAAA..........	18	31	0.03	0.00	0.03	0.00	0.00
...................................................................................................................................................ACGTGACTTAATGCTAAGC........................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
........................................AGCCTAGCATTGAATCGACGTAATA.............................................................................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................A----------AACA------GA-AAAGAAACAAG-------A.	19	2	0.50	0.00	0.50	0.00	0.00
..............................................................ATAGTT--TGAGT-------------TC-AT---AA-ATC----C-ATT-------........................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................ATAAA----------AAGA------GA-AAAGAAA.............	18	15	0.07	0.00	0.07	0.00	0.00
.........................................................................................C-AT---AA-ATC----C-ATT-------GAA---ACT--------T---T..................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................GCCTAGCATTGAATCGACGT.................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................AA---ACT--------T---TGACAATTACGTGAC....................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................AA----------AATA------GA-AGAGAAAGAAG-------A.	20	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................AA---ACT--------T---TGACAATTATGTGACT...................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droVir3

CCAAAAAAAAAATACTCATTGAAAGCGT-GTTTG----AAAGCTTTGCATTGAATCGCAGTAATCGGCT-GGATT-CACAGAAA--------CCTTAG-AAC----T-CT--ATTATAACT---TTT---TA-AATCAGCTGCAATTACGTGGCTTAATGCAAAGCTTG-G-AATGTGAGGA----------------------------------------------AAAAAGCAGCTTT---------------------------------AT---------G	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.......................................................................................................................................................................TG-G-AATGTAAAGA----------------------------------------------AAAAAGCA..................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................TTG-G-AATAAGAGGA----------------------------------------------AAAAA.....................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

AGAATCATAAAATACTCATTGAGAGCGTTATGCA----AAAGCTTTGCATTGAATCGCCGTAATCGCA--GT--C------------CAC-ACTTTAG-ATA----T-TTT-TTTGTAACC---TTC---GAAAATCAGCTGCAATTACGCGGCTTAATGCAAAGCTTA-T-GATGCAAGAAAAAAAAGAACGAAATATTAATGATAAAATAACAATAAAAAATTAAAAGAAAGCTGCTTT---------------------------------ATG-------AA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..................................................................................................................................................................................................ACTGTTAATGATAAAAT...........................................................................	17	1	1.00	0.00	1.00	0.00	0.00

droGri2

CA----TTAAAAGCTTCATT------------TG----AAAGCTTTGCATTGAATCGCAGTAATCTCG-AGCTAC------------ATA-TCCTTAG-AAC----T-TT--------------ATT--------GCTGTTTTAATTACGTGGCTTAATGCAAAGCTTG-A-AATAAACGA-------------------------------------------------AAAGCTGCTTT---------------------------------ATG-------AA

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:17 EDT

block92371

chr2L:6973236-6973348 -

Candidate

three_prime_UTR

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup