dme-mir-4977- Best orthologs

dme-mir-4977	chr2R:3294237-3294342 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	five_prime_UTR

Legend:

   mature strand at position 3294262-3294284
   star strand at position 3294299-3294319
   mutations
   read mismatches

Notes: droWil1 ortholog looks genuine but it is supicious why it diverged so rapidly compared to surrounding species. Better ortholog could not be found by search the genome nor its trace data.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:3294222-3294357 -		1	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGAACGGCCGTA-CAATACCCAAG
droSim1	chrU:460991-461115 -	LASTZ	1	TTTT------------TA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGTTCAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-AACACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droSec1	super_1:944262-944397 -	LASTZ	1	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droYak2	chr2L:15977521-15977656 -	LASTZ	1	TTTTCGTTTACTTG-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAG
droEre2	scaffold_4929:19300554-19300689 +	LASTZ	4	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAAC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droEug1	scf7180000409672:5307008-5307144 -	LASTZ	4	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGCAACCACTTGGAGCGACGAGCACGGCCGTA-CAATACCCAAA
droBia1	scf7180000302292:2853030-2853170 +	LASTZ	4	TTTTGGTTTAATTT-TTGAACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATAC--TT----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droTak1	scf7180000412807:59993-60132 -	LASTZ	4	TTTTCGTTTAATTT-TCC-ACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAA
droEle1	scf7180000491347:110639-110775 -	LASTZ	4	CTTTCGTTTACTTT-TTG---ACC-------CTCCGCT--CGGGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCCAAAGTC-TTGCAACGTTC-----------------CAAAGGA-GAGC-TGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG
droRho1	scf7180000770698:29092-29228 -	LASTZ	4	TTTTCATTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTT-TTGCAACGTTC-----------------CAAAGGA-GAGC-AGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG
droFic1	scf7180000453948:50042-50182 -	LASTZ	4	TTTTCGTTTACTTTCTTA--AACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATTC--TTT---------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGACTAAC-AGCACGTGGAGCGACAAGTACGGCCGTAAAAATACCCAAA
droKik1	scf7180000302670:19296-19422 -	LASTZ	4	TTTTCGTT-AGTTT--------CC-------CTCCGTT--CGCGAGCGTGTTTCCT----TTG-GG--CGTGCAACAC--TT----------------------------------------TTTGCCAAAAGTC-TTGCCACTGTC-----------------CAAAATC-GCGA-AGCACGTCGA---ACGAGTACGGCCGTAAAAATTCCCAAG
droAna3	scaffold_13266:3498798-3498932 -	LASTZ	4	ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGG--CGTGCAAAAC--CC----------------------------------------TTTG--AGAAGTT-TTGCATCGTTC-----------------GAAATTAGGGGC-AGCACCTCGAACA--GTACACGGCCGTA-AAATTCCTAAA
droBip1	scf7180000396427:1965389-1965535 -	LASTZ	4	ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTAGTTTTCGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCCGTGTGG-AAAAGTCGTTGCATCGTTC-----------------GAA--CT-GGAC-AGCACCTCGAACAGC--ATACGGCCGCAAAAATTCCTAAA
dp4	chr3:1570003-1570137 -	LASTZ	4	TTTTTGGTTTTGTT-----------------------T--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTT-----------------CAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA
droPer1	super_2:1744183-1744317 -	LASTZ	4	TTTTTGGTTTTGTT-----------------------T--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTT-----------------CAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA
droWil1	Unknown	MAF	0	TTTTTTTTTTTTGT-TTT---ACC-------TTTTTGT--TGAGGAA---------------------------ACAT--TT------------------------------------------CA--AAAAATT-CT---CCGTTTAAGTGCAAGAAACGTGCTCTG------CC---TACGCCA--AAAGTAATACGGCCGTAAACATTCCAAAA
droVir3	scaffold_12875:10810504-10810650 -	LASTZ	4	TTTTGATTTACTTT---A---ATTTCGTTTGCATCGAT--T-AAAACGTGTT-TG----TTTG-----CGTGCAATCA-CTTTTTCC-ACCGTGTC----------------CCGGC--GTGTGCG-AGAAAGTC-TTGCAACGTAC-----------------AAA-------AC-AACACGTTG----ATAAGCACGGCCGCAAAAATTCCCAAA
droMoj3	scaffold_6496:16132312-16132448 +	LASTZ	4	TTTTG--------------------------CATCGAT--T-AAAACGTGTTT--G---TTTGCG---TTTGCAACAA-CTT-TTTCCACCGTGTCCCCCAC-----------CGGCGTGTGTGCG-AAAAAGTCTTTGCAACGTTC-----------------CAAA-------C-AACACGTCG----ATAAGTACGGCCGCAAAAATTCCTAAA
droGri2	scaffold_15245:3916304-3916452 -	LASTZ	4	TTTTCGTTTGC---------------------ATCGATTGT-GAAACGTGTTT--G---TTTGTAG--CGTGCAACACACTTTTT-C-AC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTG-AAAAAGTCTGTGCAACGTTC-----------------AGAA------AC-AACACGTCGAAC----TCTACGGCCGCAAAAATTCCCAAA

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	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTC----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTCCAAAAGA-GAGC-AGCACGTGGAGCGACGAGAACGGCCGTA-CAATACCCAAG
droSim1	TTTT------------TA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTC----------------------------------------TGTGGTTCAAGTC-TTGCACCGTTCCAAAAGA-GAGC-AACACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droSec1	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTC----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTCCAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droYak2	TTTTCGTTTACTTG-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTC----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTCCAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAG
droEre2	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTT----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTCCAAAAGA-GAAC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droEug1	TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTCCAAAAGA-GAGCAACCACTTGGAGCGACGAGCACGGCCGTA-CAATACCCAAA
droBia1	TTTTGGTTTAATTT-TTGAACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATA--CTT----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTCCAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG
droTak1	TTTTCGTTTAATTT-TCC-ACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATA--CTT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTCCAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAA
droEle1	CTTTCGTTTACTTT-TTG---ACC-------CTCCGCT--CGGGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTT----------------------------------------TGTGGCCAAAGTC-TTGCAACGTTCCAAAGGA-GAGC-TGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG
droRho1	TTTTCATTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATA--CTT----------------------------------------TGTGGCAAAAGTT-TTGCAACGTTCCAAAGGA-GAGC-AGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG
droFic1	TTTTCGTTTACTTTCTTA--AACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATT--CTTT---------------------------------------TGTGGCAAAAGTC-TTGCATCGTTCCAAAAGACTAAC-AGCACGTGGAGCGACAAGTACGGCCGTAAAAATACCCAAA
droKik1	TTTTCGTT-AGTTT--------CC-------CTCCGTT--CGCGAGCGTGTTTCCT----TTG-GG--CGTGCAACA--CTT----------------------------------------TTTGCCAAAAGTC-TTGCCACTGTCCAAAATC-GCGA-AGCACGTCGA---ACGAGTACGGCCGTAAAAATTCCCAAG
droAna3	ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGG--CGTGCAAAA--CCC----------------------------------------TTTG--AGAAGTT-TTGCATCGTTCGAAATTAGGGGC-AGCACCTCGAACA--GTACACGGCCGTA-AAATTCCTAAA
droBip1	ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTAGTTTTCGG--CGTGCAACA--CTTTTTTC----------------------------GCGTCCGTGTGG-AAAAGTCGTTGCATCGTTCGAA--CT-GGAC-AGCACCTCGAACAGC--ATACGGCCGCAAAAATTCCTAAA
dp4	TTTTTGGTTTTGT-----------------------TT--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACA--CTTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTTCAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA
droPer1	TTTTTGGTTTTGT-----------------------TT--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACA--CTTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTTCAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA
droVir3	TTTTGATTTACTTT---A---ATTTCGTTTGCATCGAT--T-AAAACGTGTT-TG----TTTG-----CGTGCAATC-ACTTTTTCC-ACCGTGTC----------------CCGGC--GTGTGCG-AGAAAGTC-TTGCAACGTACAAA-------AC-AACACGTTG----ATAAGCACGGCCGCAAAAATTCCCAAA
droMoj3	TTTTG--------------------------CATCGAT--T-AAAACGTGTTT--G---TTTGCG---TTTGCAACA-ACTT-TTTCCACCGTGTCCCCCAC-----------CGGCGTGTGTGCG-AAAAAGTCTTTGCAACGTTCCAAA-------C-AACACGTCG----ATAAGTACGGCCGCAAAAATTCCTAAA
droGri2	TTTTCGTTTGC---------------------ATCGATTGT-GAAACGTGTTT--G---TTTGTAG--CGTGCAACACACTTTTT-C-AC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTG-AAAAAGTCTGTGCAACGTTCAGAA------AC-AACACGTCGAAC----TCTACGGCCGCAAAAATTCCCAAA

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

TTTT------------TA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGTTCAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-AACACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GAG..........................................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................GTTCAAGAC-TAGCACCGT........................................................................	18	1	1.00	0.00	0.00	1.00	0.00
......................................................................................................................................C-TTGCACCGTTC-----------------CAAAAGA-GAG..........................................	22	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................................................................................GAGC-AACACGTGAAGCGGC.........................	19	1	1.00	1.00	0.00	0.00	0.00

droSec1

TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GA...........................................	22	1	13.00	3.00	9.00	1.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GAG..........................................	23	1	9.00	2.00	5.00	2.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GAGC-........................................	24	1	7.00	1.00	6.00	0.00
......................................................................................................................................C-TTGCACCGTTC-----------------CAAAAGA-GAGC-........................................	23	1	5.00	0.00	2.00	3.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-G............................................	21	1	4.00	1.00	0.00	3.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GT...........................................	22	1	2.00	1.00	1.00	0.00
...........................................................................TAC--GC----------------------------------------TGTGGCAGAGGTC-.................................................................................	18	1	1.00	0.00	0.00	1.00
..................................................................................................................................................................................GCCCGTGGAGCGATGAGC.....................	18	1	1.00	0.00	1.00	0.00
.....................................................................................................................................................................AAAAGT-GAGC-AGCAAGTGG...............................	19	1	1.00	0.00	1.00	0.00
.................................................GGTTTCT---TTCGCGA--AGTG.................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
.............................................................TGCGA--CGTGCAATAC--TC----------------------------------------TGTGGC.........................................................................................	23	1	1.00	1.00	0.00	0.00
............................................AACCTGGTTTTT---TTTGCG........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-.............................................	20	1	1.00	0.00	0.00	1.00
................................TCCGCT--CGAGAACGTGGTT....................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
......................................................................................................................................C-TTGCACCGTTC-----------------CAAAAGA-GAGA-........................................	23	1	1.00	0.00	1.00	0.00
...................................................................................................................................AGTC-TTGCACCGTTC-----------------CAAAAGA-GAGC-........................................	26	1	1.00	1.00	0.00	0.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------TAAAAGA-G............................................	21	1	1.00	0.00	0.00	1.00
...................................................TTTCT---TTTGCGA--CGTGCAATA............................................................................................................................................	21	1	1.00	1.00	0.00	0.00
.....................................................................................................................................................................AAAAGT-GAGC-AGCAAGTG................................	18	1	1.00	0.00	0.00	1.00
......................................................................................................................................C-TTGCACCGTTC-----------------CAAAAGC-GAGC-........................................	23	1	1.00	1.00	0.00	0.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAG...............................................	19	1	1.00	0.00	0.00	1.00

droYak2

TTTTCGTTTACTTG-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TC----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................................C-TTGCATCGTTC-----------------CAAAAGA-GAGC-........................................	23	1	3.00	0.00	0.00	0.00	0.00	3.00
......................................................................................................................................C-TTGCATCGTTC-----------------CAAAAGA-GAGC-T.......................................	24	1	3.00	0.00	0.00	0.00	0.00	3.00
.....................................................................................................................................TC-TTGCATCGTTC-----------------CAAAAGA-G............................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................................................................................................TC-TTGCATCGTTC-----------------CAAAAGA-GAGC-........................................	24	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................................................................ATCGTTC-----------------CAAAAGA-GAGC-AGC.....................................	21	1	2.00	0.00	0.00	2.00	0.00	0.00
.............................................................................................................................................................................AGC-AGCACGTGGAGxGACGATC.....................	21	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAGAAGTC-TTGCACCGTTC-----------------CAAAAGA-GAAC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-G............................................	21	1	5.00	0.00	0.00	0.00	5.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GAA..........................................	23	1	3.00	1.00	0.00	0.00	2.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-GA...........................................	22	1	2.00	0.00	0.00	0.00	2.00
.......................................................................GCAATAC--TT----------------------------------------TGTGGCAGA......................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................TTTCT---TTTGCGA--CGTGCAATAC--.........................................................................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAATA-GT...........................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------CAAAAGA-.............................................	20	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................TC-TTGCAACGTTC-----------------CAAAAGA-GA...........................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................TC-TTGCACCGTTC-----------------AAAAAGA-GAA..........................................	23	1	1.00	0.00	0.00	0.00	1.00
.................................................GGTTTCT---TTTTCGA--CTTGCAATAC--T........................................................................................................................................	25	1	1.00	1.00	0.00	0.00	0.00
........................................................................................................................................TTGCACCGTTC-----------------CAAAAGA-GAAC-A.......................................	23	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................AAGA-xAAC-AGCTCGTGGAG.............................	18	1	1.00	0.00	0.00	0.00	1.00
........................................................................................................................................TTGCACCGCTG-----------------CAAAAGA-GAAC-AG......................................	24	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................TAGAGCGACGAGAACGGC................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TTTTCGTTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGCAACCACTTGGAGCGACGAGCACGGCCGTA-CAATACCCAAA

Size

Hit Count

Total Norm

droBia1

TTTTGGTTTAATTT-TTGAACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATAC--TT----------------------------------------TGTGGCAGAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-CAATACCCAAG

Size

Hit Count

Total Norm

droTak1

TTTTCGTTTAATTT-TCC-ACACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGACGCGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGA-GAGC-AGCACGTGGAGCGACGAGCACGGCCGTA-AAATACCCAAA

Size

Hit Count

Total Norm

droEle1

CTTTCGTTTACTTT-TTG---ACC-------CTCCGCT--CGGGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCCAAAGTC-TTGCAACGTTC-----------------CAAAGGA-GAGC-TGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG

Size

Hit Count

Total Norm

droRho1

TTTTCATTTACTTT-TTA---ACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATAC--TT----------------------------------------TGTGGCAAAAGTT-TTGCAACGTTC-----------------CAAAGGA-GAGC-AGCACGTGGAGCGACGAGTACGGCCGTAAAAATACCCAAG

Size

Hit Count

Total Norm

droFic1

TTTTCGTTTACTTTCTTA--AACC-------CTCCGCT--CGAGAACGTGGTTTCT---TTTGCGA--CGTGCAATTC--TTT---------------------------------------TGTGGCAAAAGTC-TTGCATCGTTC-----------------CAAAAGACTAAC-AGCACGTGGAGCGACAAGTACGGCCGTAAAAATACCCAAA

Size

Hit Count

Total Norm

droKik1

TTTTCGTT-AGTTT--------CC-------CTCCGTT--CGCGAGCGTGTTTCCT----TTG-GG--CGTGCAACAC--TT----------------------------------------TTTGCCAAAAGTC-TTGCCACTGTC-----------------CAAAATC-GCGA-AGCACGTCGA---ACGAGTACGGCCGTAAAAATTCCCAAG

Size

Hit Count

Total Norm

droAna3

ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTTGTTTTCGG--CGTGCAAAAC--CC----------------------------------------TTTG--AGAAGTT-TTGCATCGTTC-----------------GAAATTAGGGGC-AGCACCTCGAACA--GTACACGGCCGTA-AAATTCCTAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................................................TTG--AGAAGTT-TTTCATCGTTC-----------------GAA..................................................	24	1	1.00	1.00	0.00	0.00	0.00

droBip1

ACCCC-TTTATTTT-TAT---TTT-------CACCGTT--CGAGAGGGTGTTCTCTTAGTTTTCGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCCGTGTGG-AAAAGTCGTTGCATCGTTC-----------------GAA--CT-GGAC-AGCACCTCGAACAGC--ATACGGCCGCAAAAATTCCTAAA

Size

Hit Count

Total Norm

dp4

TTTTTGGTTTTGTT-----------------------T--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTT-----------------CAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......TTTTGTT-----------------------T--TGAGGACTTGCCT....................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droPer1

TTTTTGGTTTTGTT-----------------------T--TGAGAACGTGCCTTCTTT-TTTTTGG--CGTGCAACAC--TTTTTTC----------------------------GCGTCTCTGTGG-AAAAGTT-TTGCATCGTTT-----------------CAAAAAAAAAGA-TACACGTCG----ACACATACGGCCGCTAAGATTCCAAAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...................................................................................................................................AGTT-TTGCATCGTTT-----------------CAAA.................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................TTTTC----------------------------GCGTCTCTGTGG-A........................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................AC--TTTTTTC----------------------------GCGTCTCTGTGG-AAA......................................................................................	24	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................................................................................................TTGTATxGTTT-----------------CAAAAAAA.............................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TTTTTTTTTTTTGT-TTT---ACC-------TTTTTGT--TGAGGAA---------------------------ACAT--TT------------------------------------------CA--AAAAATT-CT---CCGTTTAAGTGCAAGAAACGTGCTCTG------CC---TACGCCA--AAAGTAATACGGCCGTAAACATTCCAAAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.ATTTTTTTTTTGT-TAT---ACC-------..........................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
TTTGTTTTTTTTGT-TTT---T...................................................................................................................................................................................................	18	51	0.02	0.00	0.02	0.00	0.00
TTTTTTTTTTTTGT-TCG---ACC-------..........................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................GAAACGTGCTCTG------CC---TACGCC................................	21	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................AATT-CT---CGCTTTAAGTGCA...............................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................................................CAAGAAACGTGCTCTG------CC---TACGCC................................	24	1	1.00	0.00	0.00	1.00	0.00
..TTTTTTTTTTGT-TTT---GCT-------..........................................................................................................................................................................................	18	17	0.06	0.00	0.06	0.00	0.00

droVir3

TTTTGATTTACTTT---A---ATTTCGTTTGCATCGAT--T-AAAACGTGTT-TG----TTTG-----CGTGCAATCA-CTTTTTCC-ACCGTGTC----------------CCGGC--GTGTGCG-AGAAAGTC-TTGCAACGTAC-----------------AAA-------AC-AACACGTTG----ATAAGCACGGCCGCAAAAATTCCCAAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................TTTCxTTTGGATCGAT--T-AAAA...........................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................TG-----CGTGCAATCA-CTTTTTCC-ACCGTGTC----------------.........................................................................................................	28	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

TTTTG--------------------------CATCGAT--T-AAAACGTGTTT--G---TTTGCG---TTTGCAACAA-CTT-TTTCCACCGTGTCCCCCAC-----------CGGCGTGTGTGCG-AAAAAGTCTTTGCAACGTTC-----------------CAAA-------C-AACACGTCG----ATAAGTACGGCCGCAAAAATTCCTAAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................................GTCCCCCAC-----------CGGCGTGTGTGCG-AA........................................................................................	24	1	1.00	0.00	0.00	1.00	0.00

droGri2

TTTTCGTTTGC---------------------ATCGATTGT-GAAACGTGTTT--G---TTTGTAG--CGTGCAACACACTTTTT-C-AC----T--CCCACCCAGCGTGTGT--GTGTGTGTGTG-AAAAAGTCTGTGCAACGTTC-----------------AGAA------AC-AACACGTCGAAC----TCTACGGCCGCAAAAATTCCCAAA	Size	Hit Count	Total Norm	V109 Male body
.........................................................................................................GCGTGCGC--GTGTGTGTGTG-..........................................................................................	19	13	0.08	0.08
..........................................................................................................AGTGTGC--GTGTGTGTGTG-A.........................................................................................	19	22	0.05	0.05
........................................................................................................ACCGTGTGT--GTGTGTGTGCG-..........................................................................................	20	5	0.20	0.20
........................................................................................................CTCGTGTGT--GTGTGTGTGT............................................................................................	19	51	0.02	0.02
..........................................................................................................CGTGTGT--GTGTGTGTGTG-TA........................................................................................	20	32	0.03	0.03
..........................................................................................................CGTGTGT--GTGTGTGTGAG-..........................................................................................	18	18	0.06	0.06
........................................................................................................AGCGTGxGC--GTGTGTGTGTG-..........................................................................................	19	6	0.17	0.17
.........................................................................................................GCGTGTAT--GTGTGTGTGTG-TA........................................................................................	21	33	0.03	0.03
...........................................................................................................GTGCGT--GTGTGTGTGTG-TAAA......................................................................................	21	19	0.05	0.05

Generated: 04/20/2012 at 05:18:07 EDT

dme-mir-4977

chr2R:3294237-3294342 -

Known_mirbase

five_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