dme-mir-4973- Best orthologs

dme-mir-4973	chr2L:20562297-20562448 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 20562305-20562325
   star strand at position 20562424-20562445
   mutations
   read mismatches

Notes: "mature region is deeply conserved, but not the rest of the precursor. Very long stem. "

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:20562282-20562463 +		1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCTGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATCCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droSim1	chr2L:20133895-20134076 +	LASTZ	1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATGCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droSec1	super_18:446156-446334 +	LASTZ	1	GGTCCTTGGGCCA-TCGCTGGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCCGCTGCTG------CTGCG-----------------------------GCTGC------ATCCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droYak2	chr2R:6918558-6918738 +	LASTZ	1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTGC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCTGCT---GCTG------CTGCG-----------------------GC---TGCTGCATCTGCATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAATAGA---CGCGTCGC
droEre2	scaffold_4845:3882318-3882503 -	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTTT--GGA--------CGTTTGG-------------------------------------------ACTGCGCCTCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCCGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droEug1	scf7180000409767:732654-732840 -	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC-----------------------TACTGC-------TACTGAGTCTGCCGCCGCTGCTG------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACTTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droBia1	scf7180000302422:7522699-7522885 -	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------CTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTGCCAC--------------------------CGC-------CACCGCCACTGCTGCTGCTGCTG------CTGCG-----------------------GCAGCTGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droTak1	scf7180000415104:240985-241171 -	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGATGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCCAC--------------------------AGC-------CACTGCGTCTGCCGCTGCTGCTG------CTGCG-----------------------GCAGGCGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGAAGA---CGCGTCGC
droEle1	scf7180000491186:554861-555040 +	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------GTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGC---------------------------------------TACTGCTACTGCGTCTGCTGCTG------CTGTC-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------GC-----CACGG----------------A---CAC---CACGTCGC
droRho1	scf7180000779025:471-665 +	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCAGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC--------------------------TAC-------TACTGCGTCTGCTGCTGCTACTA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------AC-----CACGGCA-------TC---AGAAGTAGA---CGCGTCGC
droFic1	scf7180000453842:74384-74567 +	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TCG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTGT--------------------------TGC-------CACTGCGTCTGCTGCTGCTGCTG------CTGCG-----------------------AC---TGCTGC------ATCT------GCAACCTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droKik1	scf7180000302408:757922-758128 +	LASTZ	5	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCCAGCTCCGGCTCCTGCTC----CAGCT-------------------------------CGTCC-AG--ACGGCTCCTCC-TCCA--------------------------------------------GCT---------------------------------------------GCGGCTGCTGCTGCTGTCA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTACAAC---CTGCCACACTC-A--------CGGACAC---------------------------------CT--CAGCA-----ATGGCA-------CC---AGA-----A---CGTGTCGC
droAna3	scaffold_12916:7065642-7065819 +	LASTZ	5	GG-------GCCA-TGGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CAGCT-------------------------------CTGCC-AGAAATTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTGTGCCTCGGCAATGGCTATTGC-------TACTGTCGCCGCTGCTGCTGCTG------CTGCT-----------------------GC---TACTGC------ATCT------GCAACCTGCAAC--------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396566:247099-247333 +	LASTZ	5	GGTCCTTGGGCCA-TGACTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CTG------------------------------------CC-AGAAGTTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTCTGCTTCGGCG------ATTGC-------TACTGCCATCGCTGCTGCTGCTG------CTGCG-----------------------GCTGCTACTGC------ATCT------GCAACCTGCAACACCCA--TCCAAAC-A-------------------------------------TCGCAT---CCACTGACGC-----CACAGCC-------AC---AGGAGAAGTCGTAACGTCGC
dp4	chr4_group3:7758140-7758314 -	MAF	5	GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTTGTAGGTGGActggtctgctctg-ctccgct------------------ctgct-------------------------------ctgcccag----------------------------------------------------------------------------------------------------------------------cact------gctGTTGCTC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC
droPer1	super_1:9204247-9204421 -	MAF	5	GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTCGTAGGTGGACTGGTGCGGTCTG-ATCCGCT------------------TTGCT-------------------------------CTGCCCAG----------------------------------------------------------------------------------------------------------------------CACT------GCTGTTGATC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC
droWil1	scaffold_180708:1965385-1965667 +	MAF	5	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggcctggtctggtctggcttggac------------------tggactggtctgAAGTTTTTGGCAAGTTTTTTTGCTCTGCC-----------------------------------------------------------------ACTGCCACAACCAGTGTTCTTCAACT------A----------Atgctgcttctactgctaaagctg------ctgct-----------------------gc---tgctgc------ATCT------TC-ACCTGCA---CACATAGCCACGTCGACTCGTCGGGGTCACCAAGGAAAAAATCAACGAAAAATAATAA---TAACTGCT--------------AAAAATGAAAGAAAAAAGAGT---CTCGTCGC
droVir3	scaffold_12963:13534067-13534330 -	MAF	5	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGTCTGGTCTGCTCTG-TGCTGGT------------------CTGC------------------------------------------GCTGCTGCCCA----GATTTTTGCTGCC-ACTGGCACACACTGATTGGGATGCCTctgccgctgctgccg--ttgctgtcgagccgac----gttgctgctga-ttttgctgttgctgttgctgttg------ctgtt-----------------------gc---tgctAC------ATCT-TCC-------------------------------------------------GCAATG----ACGACGACCAACCC---AAA---CT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC
droMoj3	scaffold_6500:24644505-24644771 +	MAF	5	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCgttgcgtgttgtaggtggtctggtctgctctg-gtctggc------------------ctgc------------------------------------------gctgctgttcagcctactttttgatgcc-actgccacacactgatggtgatgccttcgctgctgctgc--------------------------tgc-------tgctgcttctgttgctgctgccg------tcgtt---gctgt-cgtcgctgc-tattgc---tgcCAC------ATCT-TCT-------------------------------------------------ACAACGACCGACGACGACCAACCC---AAACTGCT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC
droGri2	scaffold_15126:6330398-6330651 +	MAF	5	GGTCCTTTCGCAA-TCGTTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggtctggtctgctctg-gtctggt------------------ctAC------------------------------------------GCAGCTGCTCC-CCAAACTTTTGCTGTCTGCTGA-----ACTGAATGTAATGGCTct---gctg---------------------------------------atgctgatgccgccgatgccgctg------atgccgctgctgcCCATCGCTGCCCAATGC---AGCCAC------AGCT-TCG-------------------------------------------------ACAATG----ACGACGACTAACCCACCAAA---CT--------TCTGTTTCAATTG----CTATACGCGA---CGCGACGC

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	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCTGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATCCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droSim1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATGCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droSec1	GGTCCTTGGGCCA-TCGCTGGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCCGCTGCTG------CTGCG-----------------------------GCTGC------ATCCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droYak2	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTGC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCTGCT---GCTG------CTGCG-----------------------GC---TGCTGCATCTGCATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAATAGA---CGCGTCGC
droEre2	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTTT--GGA--------CGTTTGG-------------------------------------------ACTGCGCCTCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCCGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droEug1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC-----------------------TACTGC-------TACTGAGTCTGCCGCCGCTGCTG------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACTTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droBia1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------CTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTGCCAC--------------------------CGC-------CACCGCCACTGCTGCTGCTGCTG------CTGCG-----------------------GCAGCTGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droTak1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGATGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCCAC--------------------------AGC-------CACTGCGTCTGCCGCTGCTGCTG------CTGCG-----------------------GCAGGCGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGAAGA---CGCGTCGC
droEle1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------GTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGC---------------------------------------TACTGCTACTGCGTCTGCTGCTG------CTGTC-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------GC-----CACGG----------------A---CAC---CACGTCGC
droRho1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCAGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC--------------------------TAC-------TACTGCGTCTGCTGCTGCTACTA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------AC-----CACGGCA-------TC---AGAAGTAGA---CGCGTCGC
droFic1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TCG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTGT--------------------------TGC-------CACTGCGTCTGCTGCTGCTGCTG------CTGCG-----------------------AC---TGCTGC------ATCT------GCAACCTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC
droKik1	GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCCAGCTCCGGCTCCTGCTC----CAGCT-------------------------------CGTCC-AG--ACGGCTCCTCC-TCCA--------------------------------------------GCT---------------------------------------------GCGGCTGCTGCTGCTGTCA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTACAAC---CTGCCACACTC-A--------CGGACAC---------------------------------CT--CAGCA-----ATGGCA-------CC---AGA-----A---CGTGTCGC
droAna3	GG-------GCCA-TGGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CAGCT-------------------------------CTGCC-AGAAATTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTGTGCCTCGGCAATGGCTATTGC-------TACTGTCGCCGCTGCTGCTGCTG------CTGCT-----------------------GC---TACTGC------ATCT------GCAACCTGCAAC--------------------------------------------------------------------------------------------------------------------
droBip1	GGTCCTTGGGCCA-TGACTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CTG------------------------------------CC-AGAAGTTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTCTGCTTCGGCG------ATTGC-------TACTGCCATCGCTGCTGCTGCTG------CTGCG-----------------------GCTGCTACTGC------ATCT------GCAACCTGCAACACCCA--TCCAAAC-A-------------------------------------TCGCAT---CCACTGACGC-----CACAGCC-------AC---AGGAGAAGTCGTAACGTCGC
dp4	GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTTGTAGGTGGActggtctgctctg-ctccgct------------------ctgct-------------------------------ctgcccag----------------------------------------------------------------------------------------------------------------------cact------gctGTTGCTC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC
droPer1	GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTCGTAGGTGGACTGGTGCGGTCTG-ATCCGCT------------------TTGCT-------------------------------CTGCCCAG----------------------------------------------------------------------------------------------------------------------CACT------GCTGTTGATC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC
droWil1	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggcctggtctggtctggcttggac------------------tggactggtctgAAGTTTTTGGCAAGTTTTTTTGCTCTGCC-----------------------------------------------------------------ACTGCCACAACCAGTGTTCTTCAACT------A----------Atgctgcttctactgctaaagctg------ctgct-----------------------gc---tgctgc------ATCT------TC-ACCTGCA---CACATAGCCACGTCGACTCGTCGGGGTCACCAAGGAAAAAATCAACGAAAAATAATAA---TAACTGCT--------------AAAAATGAAAGAAAAAAGAGT---CTCGTCGC
droVir3	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGTCTGGTCTGCTCTG-TGCTGGT------------------CTGC------------------------------------------GCTGCTGCCCA----GATTTTTGCTGCC-ACTGGCACACACTGATTGGGATGCCTctgccgctgctgccg--ttgctgtcgagccgac----gttgctgctga-ttttgctgttgctgttgctgttg------ctgtt-----------------------gc---tgctAC------ATCT-TCC-------------------------------------------------GCAATG----ACGACGACCAACCC---AAA---CT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC
droMoj3	GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCgttgcgtgttgtaggtggtctggtctgctctg-gtctggc------------------ctgc------------------------------------------gctgctgttcagcctactttttgatgcc-actgccacacactgatggtgatgccttcgctgctgctgc--------------------------tgc-------tgctgcttctgttgctgctgccg------tcgtt---gctgt-cgtcgctgc-tattgc---tgcCAC------ATCT-TCT-------------------------------------------------ACAACGACCGACGACGACCAACCC---AAACTGCT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC
droGri2	GGTCCTTTCGCAA-TCGTTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggtctggtctgctctg-gtctggt------------------ctAC------------------------------------------GCAGCTGCTCC-CCAAACTTTTGCTGTCTGCTGA-----ACTGAATGTAATGGCTct---gctg---------------------------------------atgctgatgccgccgatgccgctg------atgccgctgctgcCCATCGCTGCCCAATGC---AGCCAC------AGCT-TCG-------------------------------------------------ACAATG----ACGACGACTAACCCACCAAA---CT--------TCTGTTTCAATTG----CTATACGCGA---CGCGACGC

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

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATGCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................AGTCGTCGTTGCGTGTTGTAGG.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	1.67	0.00	1.33	0.00	0.33
.................................................GCCTGGTCTACTGAG-CTC................................................................................................................................................................................................................................................................................................................................................................................................	18	3	1.33	0.00	1.33	0.00	0.00
...................................GCGTGTTGTTGTTGGCCT...............................................................................................................................................................................................................................................................................................................................................................................................................	18	3	1.33	0.00	1.00	0.00	0.33
.........................AGTCGTCGTTGCGTGTTGTAG......................................................................................................................................................................................................................................................................................................................................................................................................................	21	3	0.67	0.00	0.67	0.00	0.00
.........................AGTCGTCGTTGCGTGTTGTAGA.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	0.67	0.00	0.67	0.00	0.00
.................................................................................................................................................................................................................................................................CTGCTG------CAGCG-----------------------CC---TGCTG.................................................................................................................................................	18	48	0.02	0.00	0.00	0.00	0.02
.........................AGTCGTCGTTGCGTGTTG.........................................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
................................................................................................................................................................................................................................................................GCTGCTG------CTGCG-----------------------AC---TGCTG.................................................................................................................................................	19	49	0.02	0.00	0.02	0.00	0.00
...........................................................................................................................................................................................................................................................CAGCTGCTGCTG------CAGCG-----------------------GC---......................................................................................................................................................	19	41	0.02	0.00	0.02	0.00	0.00
............................................................................................................................................................................................................................................................CGCTGCTGCTG------CTGCG-----------------------GC---TG....................................................................................................................................................	20	29	0.03	0.00	0.03	0.00	0.00
.........................AGTCGTCGTTGCGTGTTGTAGGA....................................................................................................................................................................................................................................................................................................................................................................................................................	23	3	0.33	0.00	0.33	0.00	0.00
..................................................................................................................................................................................................................................................CTGCGGCCGTTGCTGCTG................................................................................................................................................................................................	18	241	0.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................CTGCGGCCGCTGCCACTG................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
................................................................................................................................................................................................................................................................GCTGCTA------CTGCG-----------------------TC---TGCTG.................................................................................................................................................	19	38	0.03	0.00	0.00	0.03	0.00
.......................................................................T------------------TGG-------------------------------------------ACTGCTCCTCA-CCCA--------------------------------------------G...............................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
............................................................................................................................................................................................................................................................TGCTGCTGCTG------CTACG-----------------------GC---TG....................................................................................................................................................	20	414	0.00	0.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................CTTCTGCTG------CTGCG-----------------------TC---TG....................................................................................................................................................	18	41	0.02	0.02	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................................................................................................GCA-------AC---AGAAGTAGA---CCCCT...	19	2	0.50	0.00	0.00	0.00	0.50

droSec1

GGTCCTTGGGCCA-TCGCTGGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTA---------------------------------------CTACTGCGGCCGCTGCCGCTGCTG------CTGCG-----------------------------GCTGC------ATCCGC--CTGCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........CA-TCGGTGGT-TCAGTGGT.....................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	3.00	1.00	2.00	0.00
.........................AGTCGTCGTTGCGTGTTGTAGG.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	0.67	0.00	0.33	0.33
............A-TCGGTGGT-TCAGTCGTCGG..................................................................................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00
..........................................................................................................................................................................................................................................................................................................................................TGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------.........................	21	2	0.50	0.00	0.00	0.50
.................................................GCCTGGTCTACTGAG-CTCCGTT------------------TG........................................................................................................................................................................................................................................................................................................................................................................	24	3	0.33	0.00	0.00	0.33
..............................TCGTTGCGTGTTGTAGGTGGCC................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	0.33	0.00	0.00	0.33
...............................................................................................................................................................................................................................................................................................................................................................................................................................CGGCA-------AC---AGAAGTAGA---CGCGTCGC	25	2	0.50	0.00	0.00	0.50
..............TCGGTGGT-TCAGTGGTCG...................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
............A-TCGCTGGT-TCAGTGGTA....................................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
............A-TCGGTGGT-TCAGTCGTAG...................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------A........................	22	2	0.50	0.00	0.00	0.50
.........................AGTCGTCGTCGCGTGTTGTAGG.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	0.33	0.00	0.33	0.00
..........................................................................................................................................................................................................................................................................................................................................TGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AA---....................	23	2	0.50	0.00	0.50	0.00
..........................................................................................................................................................................................................................................................................................................................................TGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AG---....................	23	2	0.50	0.00	0.00	0.50

droYak2

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTT------------------TGG-------------------------------------------ACTGCTCCTGC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCTGCT---GCTG------CTGCG-----------------------GC---TGCTGCATCTGCATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAATAGA---CGCGTCGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................AGTCGTCGTTGCGTGTTGTAGG.....................................................................................................................................................................................................................................................................................................................................................................................................................	22	3	2.00	0.00	0.00	0.00	0.00	2.00
.........................AGTCGTCGTTGCGTGTTGTAG......................................................................................................................................................................................................................................................................................................................................................................................................................	21	3	1.00	0.00	0.33	0.00	0.00	0.67
.................................................GCCTGGTCTACTGAG-CTCCG..............................................................................................................................................................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33	0.00
..........................................................................................................................................................................................................................................................................................................................................TGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------.........................	21	3	0.33	0.00	0.00	0.00	0.33	0.00
.........................AGTCGTCGTTGCGTGTTGT........................................................................................................................................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00	0.00
...............................................................................................................................................................................................................................................................................................................GCTGCATCxACATCT------GCAA............................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
.......................................................................................................................................................................................................................................................................................................................................................................................................................C-----CACAGAA-------AC---AGAAATAGA---........	19	3	0.33	0.33	0.00	0.00	0.00	0.00
..................................................................................................................................................................................................................................................CTGAGGACGCTGCT---GCTG------.......................................................................................................................................................................................	18	8	0.13	0.00	0.00	0.00	0.00	0.13
.........GCCG-TCGCGCGT-TCAG.........................................................................................................................................................................................................................................................................................................................................................................................................................................	16	2	0.50	0.00	0.00	0.00	0.50	0.00
................................................GGCTTGGTCTACTCAG-CTC................................................................................................................................................................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33	0.00

droEre2

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTGAG-CTCCGTTT--GGA--------CGTTTGG-------------------------------------------ACTGCGCCTCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGCCGCTGCTGCTG------CTGCG-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................CTACTGAG-CTCCGTTT--GGA--------CG............................................................................................................................................................................................................................................................................................................................................................................	21	5	0.20	0.00	0.00	0.00	0.20
.............................GTGGTTxCGTGTTGTAGGT....................................................................................................................................................................................................................................................................................................................................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
......................................TGTTGTAGGTGGCCTGGTC...........................................................................................................................................................................................................................................................................................................................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
................................................................................................................................................TCC-TCCA--------------------------------------------ACTA---------------------------------------CTACTGCGGCCGC........................................................................................................................................................................................................	24	5	0.20	0.00	0.00	0.00	0.20
......................................................................................................................................................................................................................................................GACCGCCGGTGCTGCTG------C......................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17

droEug1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC-----------------------TACTGC-------TACTGAGTCTGCCGCCGCTGCTG------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACTTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC

Size

Hit Count

Total Norm

droBia1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------CTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------GCTGCCAC--------------------------CGC-------CACCGCCACTGCTGCTGCTGCTG------CTGCG-----------------------GCAGCTGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC

Size

Hit Count

Total Norm

droTak1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGATGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCCAC--------------------------AGC-------CACTGCGTCTGCCGCTGCTGCTG------CTGCG-----------------------GCAGGCGCTGC------ATCT------GCAACCTGCAACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGAAGA---CGCGTCGC

Size

Hit Count

Total Norm

droEle1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------GTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGC---------------------------------------TACTGCTACTGCGTCTGCTGCTG------CTGTC-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------GC-----CACGG----------------A---CAC---CACGTCGC

Size

Hit Count

Total Norm

droRho1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCAGGTCTACTCAG-CTCCGTT------------------TTG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTAC--------------------------TAC-------TACTGCGTCTGCTGCTGCTACTA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTGCAACACTCACACCCACGC-ACC----------------------------------------------------AC-----CACGGCA-------TC---AGAAGTAGA---CGCGTCGC

Size

Hit Count

Total Norm

droFic1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTACTCAG-CTCCGTT------------------TCG-------------------------------------------ACTGCTCCTCC-TCCA--------------------------------------------ACTGCTGT--------------------------TGC-------CACTGCGTCTGCTGCTGCTGCTG------CTGCG-----------------------AC---TGCTGC------ATCT------GCAACCTGCCACACTCA----------------------------------------------------------------CAC-----CACGGCA-------AC---AGAAGTAGA---CGCGTCGC

Size

Hit Count

Total Norm

droKik1

GGTCCTTGGGCCA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCCAGCTCCGGCTCCTGCTC----CAGCT-------------------------------CGTCC-AG--ACGGCTCCTCC-TCCA--------------------------------------------GCT---------------------------------------------GCGGCTGCTGCTGCTGTCA------CTGCT-----------------------GC---TGCTGC------ATCT------GCAACCTACAAC---CTGCCACACTC-A--------CGGACAC---------------------------------CT--CAGCA-----ATGGCA-------CC---AGA-----A---CGTGTCGC

Size

Hit Count

Total Norm

droAna3

GG-------GCCA-TGGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CAGCT-------------------------------CTGCC-AGAAATTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTGTGCCTCGGCAATGGCTATTGC-------TACTGTCGCCGCTGCTGCTGCTG------CTGCT-----------------------GC---TACTGC------ATCT------GCAACCTGCAAC--------------------------------------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................................................TTGGTCCxCC-TTCA--------------------------------------------ACCGCT..........................................................................................................................................................................................................................................................	19	3	0.67	0.00	0.67	0.00	0.00
..........................................GTAGGTGTCCTGGGCTGC........................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
.........................................TGTAGGTGGCCTGGTCTGCTCAG-CTCA...............................................................................................................................................................................................................................................................................................................................................................................................	27	3	0.33	0.00	0.33	0.00	0.00
............................................AGGTGGCCTGGGCTGCAC......................................................................................................................................................................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
................................................................................................................................................................................................................ATTGTGCCTCGGCAGGGGCT................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.33	0.00
...........................................TAGATGGCCTGGGCTGC........................................................................................................................................................................................................................................................................................................................................................................................................	17	3	0.33	0.00	0.00	0.33	0.00
.................................................................CTCAGCT------------------CAGCT-------------------------------CTGCC-AGAA............................................................................................................................................................................................................................................................................................................................	21	3	0.33	0.00	0.33	0.00	0.00

droBip1

GGTCCTTGGGCCA-TGACTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGCCTGGTCTGCTCAG-CTCAGCT------------------CTG------------------------------------CC-AGAAGTTGCTCCTCC-TTCA--------------------------------------------ACCGCTGCCG--ATTCTGCTTCGGCG------ATTGC-------TACTGCCATCGCTGCTGCTGCTG------CTGCG-----------------------GCTGCTACTGC------ATCT------GCAACCTGCAACACCCA--TCCAAAC-A-------------------------------------TCGCAT---CCACTGACGC-----CACAGCC-------AC---AGGAGAAGTCGTAACGTCGC

Size

Hit Count

Total Norm

dp4

GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTTGTAGGTGGActggtctgctctg-ctccgct------------------ctgct-------------------------------ctgcccag----------------------------------------------------------------------------------------------------------------------cact------gctGTTGCTC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.........................AGTCGTCGTTGCGTGTTG.........................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................A---CACACACAAACGC-G--------CGCA........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................................................................................................ACACACACGCGC-A--------CGCACA......................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
............................................................................................................................................................................................................................................................................................................................................CA---CACACACACACAC-A--------CTCAC.......................................................................................	21	27	0.04	0.00	0.00	0.04	0.00
............................................................................................................................................................................................................................................................................................................................................CA---CACACACACACGA-A--------CAC.........................................................................................	19	24	0.04	0.00	0.04	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TACA---CACACACACACGC-A--------TG..........................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
...................................................................................................................................................................................................................................................................................................................................................CACACACACAC-A--------CGAACAC---------------------------------....................................................	19	24	0.04	0.00	0.04	0.00	0.00
.................................................................CTCCGCT------------------CTGCT-------------------------------CTGCTCTG----------------------------------------------------------------------------------------------------------------------........................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................CATACACACxCGC-A--------CGCACAC---------------------------------....................................................	20	1	1.00	0.00	0.00	1.00	0.00
.........GCCAGGCGCTCGTTGAAGTCG......................................................................................................................................................................................................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................AACA---CACACACACACGA-A--------............................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.........................................TGTAGGTGGACTGGTCTGCTCTG-C..................................................................................................................................................................................................................................................................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00
...........................................................CTCTG-CTCTGCT------------------CTGCT-------------------------------CGG...................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
............................................................................................................................................................................................................................................................................................................................................CA---CACACACACACAC-A--------CGCACAC---------------------------------AC--................................................	25	16	0.06	0.00	0.06	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TACA---CACACACACACGC-T--------CGA.........................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...........................................................CTCCG-CTCTGCT------------------CTGCT-------------------------------CTG...................................................................................................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droPer1

GGTCCTTTCGCCAGGCGCTCGTTTCAGTCGTCGTTGCGTGTCGTAGGTGGACTGGTGCGGTCTG-ATCCGCT------------------TTGCT-------------------------------CTGCCCAG----------------------------------------------------------------------------------------------------------------------CACT------GCTGTTGATC------------------------------CACTGC------ATCT------CTCTCCTaca---cacacacacacgc-a--------cgcacac---------------------------------ac--acgcaagcacacaACA-------GC---AAAAAT-CT---CGCGACGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................................................TTCGCT------------------TTGCT-------------------------------CTGCACA...............................................................................................................................................................................................................................................................................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
.....................................................................................................................................G----------------------------------------------------------------------------------------------------------------------CACT------GCTGTTGAAC------------------------------CACT..................................................................................................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................................................................................................................................................................................................................................................................ACA---CACACACACACGG-A--------AG..........................................................................................	19	3	0.67	0.00	0.00	0.00	0.00	0.67
.......................................................................................................................................................................................................................................................................................................................................................CACACGG-A--------CACACAC---------------------------------AC--A...............................................	18	27	0.07	0.00	0.00	0.00	0.00	0.07
............................................................................................................................................................................................................................................................................................................................................CA---CACACACACACAC-A--------CT..........................................................................................	18	46	0.04	0.00	0.00	0.00	0.00	0.04
.................................................................ATTCGCT------------------TTGCT-------------------------------CTGGCC................................................................................................................................................................................................................................................................................................................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
.....................................................................................................................................................................................................................................................................................................................................................CACACAGGC-A--------CGCACAC---------------------------------AC--C...............................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................................................................................................................................................................................................CACACACACGCGC-A--------CGCACA......................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................ATACACACGC-A--------CGCACAC---------------------------------AA--AC..............................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................................AC---------------------------------AC--ACACAAGCACACAAC.................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................TGTAGGTGGACTGGCGCGG........................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................G---CACACACACACAC-A--------CGCACA......................................................................................	21	21	0.05	0.00	0.05	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................................................................................................TACA---CACACACACACAC-T--------............................................................................................	18	33	0.03	0.00	0.00	0.00	0.00	0.03

droWil1

GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggcctggtctggtctggcttggac------------------tggactggtctgAAGTTTTTGGCAAGTTTTTTTGCTCTGCC-----------------------------------------------------------------ACTGCCACAACCAGTGTTCTTCAACT------A----------Atgctgcttctactgctaaagctg------ctgct-----------------------gc---tgctgc------ATCT------TC-ACCTGCA---CACATAGCCACGTCGACTCGTCGGGGTCACCAAGGAAAAAATCAACGAAAAATAATAA---TAACTGCT--------------AAAAATGAAAGAAAAAAGAGT---CTCGTCGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................................................................................................................................................................................................................................................................................................................TCACGTCGGGGTCACCAA..................................................................................	18	1	14.00	0.00	0.00	0.00	14.00
...............................................................................................................................................................................................................................................................................................................................................................GTCACGTCGGGGTCACCA...................................................................................	18	1	7.00	0.00	1.00	3.00	3.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAATGAAAGAAAAAGAA.............	18	1	6.00	0.00	6.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAAGAAAGAAAAAGGA.............	19	1	1.00	0.00	0.00	1.00	0.00
..............................................................................................................................................................................................................................................................................................................................................................CAACACGTCGGGGTCACCA...................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................................TCTTCGTCAACT------A----------ATGCT................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................AGCTG------CTGTT-----------------------GC---TGTTGC------..........................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................AGTCGTCGTTGCGTGTTG.........................................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................T--------------AAAAAGGAAACAAAAAA...............	18	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................................................CTACAACTG------CTGCT-----------------------GC---TGCT..................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAGAAAGAAAAAAAA.............	18	47	0.02	0.00	0.02	0.00	0.00
..................................................................................................................................................................................................................................................................CGCTA------CTGCT-----------------------GC---TGCTGC------..........................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................CA--------------AAAAATGAGAGAAAAAA...............	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAAAAAGAAAAAAGA.............	18	48	0.02	0.00	0.02	0.00	0.00
..................................................................................................................................................................................................................................................................TGCTG------CTGCT-----------------------GC---TGCTGC------T.........................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
.............................................................................................................................................................................................................................................................................................................................................................TCAACACGTCGGGGTCACCA...................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................GGTCTGGTCTGGTCTGGC..................................................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................GTGTTGTAGGTGGCCTGGTCTGG........................................................................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................................................................................................................................................ACTAAAGTTG------CTGCT-----------------------GC---TG....................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................CT--------------AAAAGTGAAAAAAAAA................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................CTGGCTTGGAC------------------TGGACTGGT.................................................................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................CT--------------AAAAGTGAAAAAAAAAA...............	19	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................TACTG------CTGCT-----------------------GC---TGCTGC------..........................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
............................................................................................................................................................................................................................................................................................................................................................GACGAxTCGTCGGGGTCACCA...................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................................................................................AAGTTG------CTGCT-----------------------Gx---TGCTGC------..........................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................................................................................................................................................................TACTGCTG------CTGCT-----------------------GC---TGC...................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
...............................................................................................................................................................................................................................................................TACTGCTG------CTGCT-----------------------GC---TGCTG.................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................................................................................................................CTGCTCCAGCTG------CTGCT-----------------------GC---TG....................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................A--------------AAAAAAGAAAGAAAAAAGA.............	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................................................................................ATGCTG------CTGCT-----------------------GT---TGCTG.................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAAGGAAGAAAAAAGA.............	19	2	0.50	0.00	0.00	0.50	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAGGAAACAAAAAAGA.............	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................................................................................AGCTG------CTGCT-----------------------GT---CGCTGC------A.........................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAGAAAAAAAAAAGA.............	18	47	0.02	0.00	0.02	0.00	0.00
.....................................................................................................................................................................................................................................................................TG------CTGCT-----------------------GC---TGCTGC------TGCT------................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAAGAAAGAGAAAAGA.............	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAGGAAAAAAAAAAGA.............	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................AATTTTTGGCAAGATTTT...........................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAGTGAAAGAAAAAAAA.............	19	1	1.00	1.00	0.00	0.00	0.00
....................................CTTGTTGTAGATGGCCTGG.............................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................................................................................................................................................................................AACACGTCGGGGTCACCA...................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................................................................................................................................................................................................................................................................................................................AAAAAGGAAAGGAAAAAGA.............	19	1	1.00	0.00	1.00	0.00	0.00
.......................................GTTGTAGGTGGCCTGGTAT..........................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................ACTGGTCTGAAGTTTTTGGCAAG................................................................................................................................................................................................................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................................TCTGCC-----------------------------------------------------------------ACTGCCACAACCAGT.................................................................................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droVir3

GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCGTTGCGTGTTGTAGGTGGTCTGGTCTGCTCTG-TGCTGGT------------------CTGC------------------------------------------GCTGCTGCCCA----GATTTTTGCTGCC-ACTGGCACACACTGATTGGGATGCCTctgccgctgctgccg--ttgctgtcgagccgac----gttgctgctga-ttttgctgttgctgttgctgttg------ctgtt-----------------------gc---tgctAC------ATCT-TCC-------------------------------------------------GCAATG----ACGACGACCAACCC---AAA---CT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................................................................................................................................................................................CTGCTGTTGGTGTTGCTGTTG------.......................................................................................................................................................................................	21	2	2.00	2.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................................CTGTTGTTGTTG------CTGTT-----------------------GC---T.....................................................................................................................................................	20	2	2.00	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................................................................CTGTTGTTGTTGCTGTTG------CT.....................................................................................................................................................................................	20	2	2.00	1.00	0.00	0.00	0.00	1.00
........................................................................................................................................................................................................................................................CTGCTGTTGGTGTTG------CTGTT-----------------------G..........................................................................................................................................................	21	2	2.00	2.00	0.00	0.00	0.00	0.00
................................................................................................................................................................................................................................................................ATTGTTG------CTGTT-----------------------GC---TGCT..................................................................................................................................................	18	1	3.00	0.00	0.00	0.00	3.00	0.00
...............................................................................................................................................................................................................................................................CGCTGTTG------TTGTT-----------------------GC---TGC...................................................................................................................................................	18	2	1.50	0.00	0.00	0.00	0.00	1.50
...............................................................................................................................................................................................................................................................TGTTGTTG------CTGTT-----------------------GT---TGCT..................................................................................................................................................	19	5	0.60	0.00	0.00	0.00	0.60	0.00

droMoj3

GGTCCTTTCGCAA-TCGCTCGT-TCAGTCGTCgttgcgtgttgtaggtggtctggtctgctctg-gtctggc------------------ctgc------------------------------------------gctgctgttcagcctactttttgatgcc-actgccacacactgatggtgatgccttcgctgctgctgc--------------------------tgc-------tgctgcttctgttgctgctgccg------tcgtt---gctgt-cgtcgctgc-tattgc---tgcCAC------ATCT-TCT-------------------------------------------------ACAACGACCGACGACGACCAACCC---AAACTGCT--------TCTGTTTCAATTG----CCGTACGCGA---CGCGACGC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
........................................................................................................................................................................................................CTGC--------------------------TGC-------TGCTGCTGCTGTTGC.....................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
........................................................................................................................................................................................................CTGC--------------------------TGC-------TGCTGCTGATG.........................................................................................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11
.......................................................................................................................................................................................................GCTTC--------------------------TGC-------TGCTGCGTCTG.........................................................................................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................CTGCTGC--------------------------TGC-------TGCTGCTGCT..........................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
.........................................................TGCTCTG-GTCTGGC------------------CTGC------------------------------------------GCTG........................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................................TGTTGCTGCTGCTG------TTGTT---...............................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
......................................................................................................................................................................................................................................TGC-------TGCTGATTCTGTTGTTGCT.................................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................................................CTGCTGCTGC--------------------------TGC-------TGCTGCTGT...........................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
................................................GGGCTGGTCTGGTCTG-G..................................................................................................................................................................................................................................................................................................................................................................................................	17	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................................................................................CGTTGCTGTTGC--------------------------TGC-------TGCTG...............................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................................................................................................................TTACTGCTGCTGC--------------------------TGC-------TG..................................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..................................................................................................................................................................................................TTACTGCTGC--------------------------TGC-------TGCTG...............................................................................................................................................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
........................................................CTGCTCTG-GTCTGGC------------------CTGC------------------------------------------G...........................................................................................................................................................................................................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................................................................................................CGCTGCTGCTGC--------------------------CGC-------CGCT................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
.....TTTTGCAA-TCGCTxGT-TCAG.........................................................................................................................................................................................................................................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................................................................................................GC-------TGCTGCTGCTGTTGTTGC..................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
...........................................................................................................................................................................................................C--------------------------TGC-------TGCTGCTGCTGATG......................................................................................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11
........................................................................................................................................................................................................................................C-------TGCTGCTGCCGTTGCTGC..................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
..........................................................................................................................................................................................................GC--------------------------TGC-------TGCTGCTGTTGTTGC.....................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
..................................................................................................................................................................................................CTGCTGCTGC--------------------------TGC-------TGATG...............................................................................................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11
..................................................................................................................................................................................................CTGCTGCTGC--------------------------TGC-------TGCTGCT.............................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
.....................................................GGGCTGGTCTG-GTCTGG.............................................................................................................................................................................................................................................................................................................................................................................................	17	2	0.50	0.00	0.50	0.00	0.00
........................................................CTGCTCTG-GTCTGGC------------------CTG.......................................................................................................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................GC--------------------------TGT-------TGCTGTTTCTGTTGC.....................................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................................................CTGCTGCTGC--------------------------TGC-------TGCTGTTGC...........................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
.....................................................................................................................................................................................................CTGCTGC--------------------------TGC-------TGCTGCTGCTGT........................................................................................................................................................................................................	22	4	0.25	0.00	0.00	0.00	0.25
.................................................................................................................................................................................................GCTGCTGCTGC--------------------------TGT-------TGTTGC..............................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.00	0.33
..................................................................................................................................................................................................CTGCTGCTGC--------------------------CGT-------TGCTGC..............................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.00	0.33
.....................................................................................................................................................................................................CTGCTGC--------------------------TGC-------TGCTGATG............................................................................................................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11

droGri2

GGTCCTTTCGCAA-TCGTTCGT-TCAGTCGTCGTTGCGTGTTGTAGGtggtctggtctgctctg-gtctggt------------------ctAC------------------------------------------GCAGCTGCTCC-CCAAACTTTTGCTGTCTGCTGA-----ACTGAATGTAATGGCTct---gctg---------------------------------------atgctgatgccgccgatgccgctg------atgccgctgctgcCCATCGCTGCCCAATGC---AGCCAC------AGCT-TCG-------------------------------------------------ACAATG----ACGACGACTAACCCACCAAA---CT--------TCTGTTTCAATTG----CTATACGCGA---CGCGACGC	Size	Hit Count	Total Norm	V109 Male body
.....................................................................................................................................................................................................CTG---------------------------------------ATGCTGATGCTGACGATG...................................................................................................................................................................................................	21	1	2.00	2.00
..............................................................................................................................................................GCTGTCTACGGA-----ACTGAAT..............................................................................................................................................................................................................................................................................	19	1	1.00	1.00
....................................................................................................................................................................................................GCTG---------------------------------------ATGCTGATGCTGACG......................................................................................................................................................................................................	19	1	1.00	1.00

Generated: 04/20/2012 at 05:20:42 EDT

dme-mir-4973

chr2L:20562297-20562448 +

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