dme-mir-303- Best orthologs

dme-mir-303	chrX:4260212-4260281 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 4260252-4260273
   star strand at position 4260218-4260239
   mutations
   read mismatches

Notes: droBia1 and earlier orthologs look questionable. Talked about in Lu 2008 paper as newly evolved.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:4260197-4260296 -		1	AAAACCAAATTGAT--A-----TCTTGGTTTAGGTT----------TC----------------------------ACAGGAAAC-------------------------------------------TGGTTTAATAACGAAAACTAGTTTCCTCTAAAATCC------------------------------------------------------------TAATCAAGACA-TCA----------TGTGTCGTCG
droSim1	chrX:3275244-3275342 -	LASTZ	1	AAAACCAATGTGAT--C-----TCTTGCTTTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTT------------------------------------------------------------CAAACAATACA-TCA----------TGTGTCGTCG
droSec1	super_4:2464323-2464421 +	LASTZ	1	AAAACCAATGTGAT--C-----TCTTGCTTTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTGATTACGAAAACTAGTTTCCTCTAAGGTTT------------------------------------------------------------TAAACATTACA-TCA----------TGTGTCGTCG
droYak2	chrX:4177737-4177835 +	LASTZ	1	GAACTCAAA-TAATCTG-----CCTTGCTTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGTTTGTTTACAAAAACTATTTACCCCTAAAATTC------------------------------------------------------------TAATCTAGTCA-GCA----------TTA--TTTCG
droEre2	scaffold_4690:1630987-1631073 -	LASTZ	0	GAACCAAAAAATGT--G-----CTTTGTTTAGAATT----------TTAGCG------AGGAATCATTACAAATAT------------------------------------------------------GGATGTGAACTTAAAGT--------------ACT------------------------------------------------------------CACT----GC-----------------AAGAAACG
droEug1	scf7180000409076:260374-260485 -	LASTZ	0	AAAGTTGTTC--AT---------------TTAACAT----------T-----------------------------TAAAGAA--------------------------------------------------------------------------------TAATTTAAAAAAAGTGATGGTTTTATAGTGTTTTTTGGCCCACTGTTGAATTGTTTTTTTTTAAGCAAAACA-TTT----------AGTAGTTGTC
droBia1	scf7180000301703:497690-497799 +	LASTZ	0	GAAAAATTACTCGT--G-----CCTGGCACCCAATG----------TC----------------------------CAGGGATTC-------------------------------------------TTATTTACCCATACACATAACGATCTTTGGACATTG------------------------------------------------------------TGAAGCGAATC-GCGAAAACATTGCTGCGGTGCCG
droTak1	scf7180000415394:1162865-1162940 +	LASTZ	0	ACAAAAAAAGTGAT--A-----TTTATTCTTGGTTT----------TTAA-T-CGATAAATAT---------------------------------------------------------------------TTATTAATTGA-C-----------------------------------------------------------------------------------C-AAACACCAC----------GATTTAATAA
droEle1	scf7180000491011:2115170-2115267 +	LASTZ	0	ATAACAATCTTTCG--A-----TTTTGGTAAGTAGT----------TCA------------------------------GACTGC-------------------------------------------TGTCTTCTTATCATAAATTGTTTCGTTTTAATAAAA------------------------------------------------------------TTATTTGGTTA-TTG----------TGATTGGAAT
droRho1	scf7180000779334:418422-418514 +	LASTZ	0	AAGATTACATTTTT-----------TAGTGAA------------------------TGTATTC-------------TCATTAGAC-------------------------------------------TGGTTCAACTACAACAATTAACAACATTTGAAGATT------------------------------------------------------------TATT----ATA-AAA----------TGTATAATAT
droFic1	scf7180000453901:212284-212435 +	LASTZ	0	GTAACCATTACTGA--CAACACGCTGCTTATTTCAT----------A-----------------------------AAACAGTGTTAATCTGAAAGTTAAAACTAAAGTTCAAACATATTGAGTCAACAAGTCAAAAAACAACAATGCACAA------------------------------------TCATGCTAGGTACTCCT-------------------TAGTCAAAATA-TTA----------TTATTCATTA
droKik1	scf7180000302610:1791618-1791727 +	LASTZ	0	AAAAGGAAAATAAT----------TAAAC-----AAGAAAAGAAAATTAT-TACAATAAAAAATTATTAAAAAAAT----------------------------------------------------AAACCCCTCAAAAACAACCC-------AC-AAAATC------------------------------------------------------------CATGAAAAACA-CAA----------CTT--TTCTT
droAna3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181150:2098814-2098829 +	LASTZ	0	AAATCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCGTCAACT
droVir3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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	AAAACCAAATTGATAT--CTTGGTTTAGGTTTCACAGGAAACTGGTTTAATAACGAAAACTAGTTTCCTCTAAAATCCTAATCAAGACATCATGTGTCGTCG
droSim1	AAAACCAATGTGATCT--CTTGCTTTGGCATT-AAAGGAAGCTAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTTCAAACAATACATCATGTGTCGTCG
droSec1	AAAACCAATGTGATCT--CTTGCTTTGGCTTT-AAAGGAATCTAGTTTGATTACGAAAACTAGTTTCCTCTAAGGTTTTAAACATTACATCATGTGTCGTCG
droYak2	GAACTCAA-ATAATCTGCCTTGCTTAGAATTTTAAGAGCAAAAAGTTTGTTTACAAAAACTATTTACCCCTAAAATTCTAATCTAGTCAGCATTAT--TTCG

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

AAAACCAATGTGAT--C-----TCTTGCTTTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGTTTAATTACGAAAACTAGTTTCCTCTAACGTTT------------------------------------------------------------CAAACAATACA-TCA----------TGTGTCGTCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................TTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGTT..............................................................................................................................	22	1	6.00	1.00	0.00	5.00	0.00
.............................TTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGT...............................................................................................................................	21	1	4.00	1.00	1.00	2.00	0.00
.............................TTGGCAT----------T-----------------------------AAAGGAATC-------------------------------------------TAG................................................................................................................................	20	1	3.00	0.00	0.00	3.00	0.00
.............................TTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAG................................................................................................................................	20	1	3.00	0.00	0.00	3.00	0.00
.................................................................................................................................................CTAGTTTCCTCTAACGTTT------------------------------------------------------------CA.................................	21	1	2.00	0.00	0.00	2.00	0.00
.................................................................................................................................................CTAGTTTCCTCTAACGTTT------------------------------------------------------------CAAA...............................	23	1	2.00	0.00	0.00	0.00	2.00
.............................TTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGTTA.............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
..AACCAATGTGAT--C-----TCTTGCT......................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
....CCAATGTGAT--C-----TCTTGCT......................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................CTAGTTTCCTCTAACGTTT------------------------------------------------------------CAA................................	22	1	1.00	0.00	0.00	1.00	0.00
.............................TTGGCAT----------T-----------------------------AAAGGAAGC-------------------------------------------TAGTTC.............................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.AAACCAATGTGAT--C-----TCTTGCT......................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00

droSec1

AAAACCAATGTGAT--C-----TCTTGCTTTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTGATTACGAAAACTAGTTTCCTCTAAGGTTT------------------------------------------------------------TAAACATTACA-TCA----------TGTGTCGTCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	961.00	807.00	70.00	84.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTT.............................................................................................................................	23	1	298.00	278.00	2.00	18.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGT...............................................................................................................................	21	1	142.00	126.00	4.00	12.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAG................................................................................................................................	20	1	75.00	70.00	0.00	5.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTA.............................................................................................................................	23	1	25.00	20.00	4.00	1.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTT............................................................................................................................	24	1	18.00	16.00	0.00	2.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TCGTT..............................................................................................................................	22	1	7.00	7.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTA............................................................................................................................	24	1	6.00	6.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTA..............................................................................................................................	22	1	6.00	6.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TCGTTT.............................................................................................................................	23	1	5.00	5.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TTGTTT.............................................................................................................................	23	1	4.00	4.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTCT............................................................................................................................	24	1	4.00	4.00	0.00	0.00
.............................TTGGCCT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	4.00	3.00	0.00	1.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTTT...........................................................................................................................	25	1	4.00	4.00	0.00	0.00
..................................TT----------T-----------------------------AAAGGTATC-------------------------------------------TAGTTT.............................................................................................................................	18	1	4.00	0.00	4.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TGGTT..............................................................................................................................	22	1	4.00	4.00	0.00	0.00
.............................TTGGATT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	3.00	2.00	1.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TGGTTT.............................................................................................................................	23	1	3.00	3.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TTGTT..............................................................................................................................	22	1	3.00	3.00	0.00	0.00
..............................TGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	21	1	3.00	3.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAACC-------------------------------------------TAGTT..............................................................................................................................	22	1	3.00	2.00	1.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTAA.............................................................................................................................	23	1	2.00	2.00	0.00	0.00
.............................TTCGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	1.00	0.00	1.00
.............................TTGGCTT----------T-----------------------------AAAGGACTC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TCGT...............................................................................................................................	21	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGGATC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	1.00	1.00	0.00
.............................TTGGCxT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	21	1	2.00	2.00	0.00	0.00
.............................TTTGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	1.00	1.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAA................................................................................................................................	20	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTC..............................................................................................................................	22	1	2.00	2.00	0.00	0.00
.............................TTGGCTC----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TGGTTTT............................................................................................................................	24	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TATTT..............................................................................................................................	22	1	2.00	2.00	0.00	0.00
..............................TTGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	21	1	2.00	2.00	0.00	0.00
.............................CTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTAT.............................................................................................................................	23	1	2.00	1.00	0.00	1.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTAT............................................................................................................................	24	1	2.00	2.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTAA............................................................................................................................	24	1	1.00	0.00	1.00	0.00
.............................TTGCCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
............................CTTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTCA............................................................................................................................	24	1	1.00	1.00	0.00	0.00
...................................T----------T-----------------------------AAAGGTATC-------------------------------------------TAGTTTT............................................................................................................................	18	1	1.00	0.00	1.00	0.00
.............................TTGGCxT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTT.............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAT................................................................................................................................	20	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATT-------------------------------------------TAGT...............................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................TTAGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTT.............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTC.............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGCCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGT...............................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTATT............................................................................................................................	24	1	1.00	1.00	0.00	0.00
..............................TGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTA.............................................................................................................................	22	1	1.00	0.00	0.00	1.00
.............................TTCGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TCGTTT.............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------AAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGGTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.................................TTT----------T-----------------------------AAAGGTATC-------------------------------------------TAGTTT.............................................................................................................................	19	1	1.00	0.00	1.00	0.00
.............................GTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AACGGAATC-------------------------------------------TAGT...............................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAGGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTG............................................................................................................................	24	1	1.00	1.00	0.00	0.00
.............................TTGACTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTAAA...........................................................................................................................	25	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTTAA..........................................................................................................................	26	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TTGTTTA............................................................................................................................	24	1	1.00	1.00	0.00	0.00
.............................TTCGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTA............................................................................................................................	24	1	1.00	1.00	0.00	0.00
.............................TTGGTTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAAGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TCG................................................................................................................................	20	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAATT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AGAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	0.00	0.00	1.00
.............................TTGGCTT----------A-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------ACAGGAATC-------------------------------------------TAGT...............................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TACTT..............................................................................................................................	22	1	1.00	1.00	0.00	0.00
.............................TTGGCCT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTT.............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATT-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	0.00	1.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGGATC-------------------------------------------TAGTTTT............................................................................................................................	24	1	1.00	1.00	0.00	0.00
..................................................................................................................................................TAGTTTCCTCTAAGGTTT------------------------------------------------------------TAAA...............................	22	1	1.00	1.00	0.00	0.00
...............................GGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTT..............................................................................................................................	20	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAAAC-------------------------------------------TAGTT..............................................................................................................................	22	1	1.00	0.00	1.00	0.00
.............................TTGGCTT----------T-----------------------------AACGGAATC-------------------------------------------TAGTTT.............................................................................................................................	23	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGTTTC............................................................................................................................	24	1	1.00	1.00	0.00	0.00
.............................TTGGCTT----------x-----------------------------xAAGGAATC-------------------------------------------TAGTTT.............................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................TGGGCTT----------T-----------------------------AAAGGAATC-------------------------------------------TAGT...............................................................................................................................	21	1	1.00	1.00	0.00	0.00

droYak2

GAACTCAAA-TAATCTG-----CCTTGCTTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGTTTGTTTACAAAAACTATTTACCCCTAAAATTC------------------------------------------------------------TAATCTAGTCA-GCA----------TTA--TTTCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAG................................................................................................................................	22	1	5.00	0.00	0.00	5.00	0.00	0.00
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGT...............................................................................................................................	23	1	4.00	1.00	0.00	2.00	0.00	1.00
..................................................................................................................................................TATTTACCCCTAAAATTC------------------------------------------------------------TAATC..............................	23	1	3.00	1.00	0.00	0.00	0.00	2.00
............................TTAGAATT----------TTAG-G---------------------------AGCAAA-------------------------------------------AAG................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGTT..............................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------A..................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................................................................TATTCACCCCTAAAATTC------------------------------------------------------------TAAT...............................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AA.................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
............................TTAGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGA...............................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................................................TATTTACCCCTAAAATTC------------------------------------------------------------TAATCA.............................	24	1	1.00	1.00	0.00	0.00	0.00	0.00
..............................AGAATT----------TTAA-G---------------------------AGCAAA-------------------------------------------AAGTT..............................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................CTTGCxTAAAATT----------TTAA-G---------------------------A...................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.......................CTTGCTAAGATTT----------TTAA-G---------------------------....................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GAACCAAAAAATGT--G-----CTTTGTTTAGAATT----------TTAGCG------AGGAATCATTACAAATAT------------------------------------------------------GGATGTGAACTTAAAGT--------------ACT------------------------------------------------------------CACT----GC-----------------AAGAAACG

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

AAAGTTGTTC--AT---------------TTAACAT----------T-----------------------------TAAAGAA--------------------------------------------------------------------------------TAATTTAAAAAAAGTGATGGTTTTATAGTGTTTTTTGGCCCACTGTTGAATTGTTTTTTTTTAAGCAAAACA-TTT----------AGTAGTTGTC

Size

Hit Count

Total Norm

droBia1

GAAAAATTACTCGT--G-----CCTGGCACCCAATG----------TC----------------------------CAGGGATTC-------------------------------------------TTATTTACCCATACACATAACGATCTTTGGACATTG------------------------------------------------------------TGAAGCGAATC-GCGAAAACATTGCTGCGGTGCCG

Size

Hit Count

Total Norm

droTak1

ACAAAAAAAGTGAT--A-----TTTATTCTTGGTTT----------TTAA-T-CGATAAATAT---------------------------------------------------------------------TTATTAATTGA-C-----------------------------------------------------------------------------------C-AAACACCAC----------GATTTAATAA

Size

Hit Count

Total Norm

droEle1

ATAACAATCTTTCG--A-----TTTTGGTAAGTAGT----------TCA------------------------------GACTGC-------------------------------------------TGTCTTCTTATCATAAATTGTTTCGTTTTAATAAAA------------------------------------------------------------TTATTTGGTTA-TTG----------TGATTGGAAT

Size

Hit Count

Total Norm

droRho1

AAGATTACATTTTT-----------TAGTGAA------------------------TGTATTC-------------TCATTAGAC-------------------------------------------TGGTTCAACTACAACAATTAACAACATTTGAAGATT------------------------------------------------------------TATT----ATA-AAA----------TGTATAATAT

Size

Hit Count

Total Norm

droFic1

GTAACCATTACTGA--CAACACGCTGCTTATTTCAT----------A-----------------------------AAACAGTGTTAATCTGAAAGTTAAAACTAAAGTTCAAACATATTGAGTCAACAAGTCAAAAAACAACAATGCACAA------------------------------------TCATGCTAGGTACTCCT-------------------TAGTCAAAATA-TTA----------TTATTCATTA

Size

Hit Count

Total Norm

droKik1

AAAAGGAAAATAAT----------TAAAC-----AAGAAAAGAAAATTAT-TACAATAAAAAATTATTAAAAAAAT----------------------------------------------------AAACCCCTCAAAAACAACCC-------AC-AAAATC------------------------------------------------------------CATGAAAAACA-CAA----------CTT--TTCTT

Size

Hit Count

Total Norm

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

Size

Hit Count

Total Norm

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AAATCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCGTCAACT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:12:11 EDT

dme-mir-303

chrX:4260212-4260281 -

Known_mirbase

intergenic

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