sblock181949- Best orthologs

sblock181949	chrX:10395825-10395903 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 10395840-10395862
   star strand at position 10395880-10395901
   mutations
   read mismatches

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:10395810-10395918 -		1	ATTGTGACAGGTGTACAACACACAG----GTGAATGTGTATGTATATGTG------------------------------------------------------------------------------------------------------------------------------------CGACTACTTACGAGCACATCCACCTGT------CTG--G-TTT--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droSim1	chrX:8074162-8074266 -	LASTZ	4	ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTGCGAGCACATCCACCTGT------CTG--G-TTA--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droSec1	super_15:1103035-1103139 -	LASTZ	4	ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTACGAGCACATCCACCTGT------CTG--G-TTA--TCACCTTCAACTAATGCATCACTTT------------A-AAG
droYak2	chrX:18969663-18969761 -	LASTZ	5	ATTGTGACAGGTGTACAACACACGT----TTGA----ATATA------TA------------------------------------------------------------------------------------------------------------------------------------CCTCTACTTACGAGCACATCCACCTGT------CTG--G-CTT--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droEre2	scaffold_4690:4732725-4732827 +	LASTZ	5	ATTGTGGCAGGTGCACAACACA--G----TGGTATGCATATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CAACTACTTACGAGCACATCCACCTGT------CTG--G-CTTGGACACCTTCAACTAATGCAGC--CAC------------T-GTA
droEug1	scf7180000409538:335496-335716 +	LASTZ	5	ATTGTGACAGGTGTACAACGC--AG----TTGAATGAGTTTA----TA-----------TTGTG-------GTACTAATACATATACATACATACATATACATACCAAAACATATACATATACATACCTTAACATATACATATACATACCTAAACATATACATATACATACCTAAACATATACACCTACTTATAAGAACATCCACCTGT------CTGCTA-GTCTTGAGACTTAAAATAATGCTTTTCTTT------------A-GTA
droBia1	scf7180000302126:3261824-3261944 -	LASTZ	4	ATTGTGACAGGTGAACAA-ACGCAG----TTGAACGAGCATG----TG-----------GCATG-------GCA-TGATGCAC------------------------------------------------------------------------------------------------ACCCACATACTTACCAGCATATCCAACCGT------CTG--G-CCT--GGGTCTTAATCTAATGCATTTCTTT------------A-AAT
droTak1	scf7180000415394:185406-185501 -	LASTZ	5	ATTGTGACAGGTGTACAGTA----G----GTT------TATA------CA----------------------------------------------------------------------------------------------------------------------------------CCTACATACTTACCAGCACATCCACCTGT------CTG--G-CTT-TGGGTCTTAAACTAATGCATTTCTCT------------G-AAA
droEle1	scf7180000491087:250537-250643 +	LASTZ	5	ATTGTGACAGGTGCACAGTGTACAG----TTGAACGAGTATA------CA------------------------------------------------------------------------------------------------------------------------------------CCTGTACTTACGGGCACATCCACCTGT------CTGTGG-CTTTTGGGCCTTAAGCTAATGCATTTCTTT------------A-AAA
droRho1	scf7180000767464:324-426 -	LASTZ	5	ATTGTGACAGGTGCACAACAC--AG----TTGAGCGAGTACA------CA------------------------------------------------------------------------------------------------------------------------------------CATCTACTTACGGGCACATCCACCTGT------CTG--G-GTTTTTGGCCTTAAGCTAAGGCGTTTCTTT------------A-AAA
droFic1	scf7180000454050:325714-325834 -	LASTZ	5	ATTGTGACAGGTGAACAACTC--CGCCGAACGATGGAGTATA------TA---------TGGAG-------T-----ATATAT-----------------------------------------------------------------------------------------------AGTACACCTACTTACGGGCACATCCACCTGT------CTG--A-CTT--TTGCTCCAGACTAATGCGTTTCTCT------------A-AAA
droKik1	scf7180000302698:739080-739196 +	LASTZ	4	ATTGTGGCAGGTAG----TAGGTAG----GTGGATGTGCTCC----GA---------------AAAAGGTGGC--------AT------------------------------------------------------------------------------------------------AC-CTCCCACTTACCGGCACATCCACCTGTCGTCGTCTG--G-CTT--TTGCCTC--------------TCAGAATATAATATATA-AAA
droAna3	scaffold_13335:2306029-2306106 +	LASTZ	5	ATTGTGACTGGTTG------------------CATGT-----------TG------------------------------------------------------------------------------------------------------------------------------------CAGTTGCTTTGTGGCACAATGCTCTCT------CTC--A-GTCTAGAGCTTTAA--------ATTCCTTG------------A-ATG
droBip1	scf7180000395653:6539-6618 +	LASTZ	5	ATTGTGACAGGTGGC---------------TGTATGT-----------TGCATGTTGCTTTGTG---------------------------------------------------------------------------------------------------------------------------------GAGCACAATAGTCTCC--------A--A-CTA--AGGCTTTAA--------ATTCCTTG------------A-ATA
dp4	chr2:27497880-27497927 +	LASTZ	0	CTTCCTCCAGGTGTACTGTACACAT----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG
droPer1	super_4:355428-355530 -	LASTZ	0	ATTGCAGCTCTCATTTAAAGC-CCG----ACGATCGTTTACA----AACA----------------------------------------------------------------------------------------------------------------------------------C-TAACTGTCAACAAGCAAATTAATCTGC--------A--G-CTA--AAAGCATATACATATGTACAATTTA------------T-AAA
droWil1	scaffold_181130:766074-766090 +	LASTZ	0	AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCCCTTT------------ATATG
droVir3	scaffold_12855:10082495-10082596 +	LASTZ	0	TATAATACAAAATCGATTGTCTCAA----ATCGATCAATATA------TA------------------------------------------------------------------------------------------------------------------------------------AAGATTTTCAATAGAATAGTCACACCA------CTT--AGAAA--ACAACTTTAAATCTAGCA--CCCAT------------A-AAG
droMoj3	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown		0	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend

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

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	ATTGTGACAGGTGTACAACACACAGGTGAA-------------------------------------------------TGTGTATGTATAT------------------------------------------------------------------------------------------------------------------GTGCG--ACTACTTACGAGCACATCCACCTGT------CTG----GTTT--GCACCTTCAACTAATGC-----AT-CACTTT------------AAAG
droSim1	ATTGTGACAGGTGTACAGCACACAGGTGAA-------------------------------------------------TGCGTAT----AT------------------------------------------------------------------------------------------------------------------GTACG--ACTACTTGCGAGCACATCCACCTGT------CTG----GTTA--GCACCTTCAACTAATGC-----AT-CACTTT------------AAAG
droSec1	ATTGTGACAGGTGTACAGCACACAGGTGAA-------------------------------------------------TGCGTAT----AT------------------------------------------------------------------------------------------------------------------GTACG--ACTACTTACGAGCACATCCACCTGT------CTG----GTTA--TCACCTTCAACTAATGC-----AT-CACTTT------------AAAG
droYak2	ATTGTGACAGGTGTACAACACACGTTTGAA-----------------------------------------------------TAT------------------------------------------------------------------------------------------------------------------------ATACC--TCTACTTACGAGCACATCCACCTGT------CTG----GCTT--GCACCTTCAACTAATGC-----AT-CACTTT------------AAAG
droEre2	ATTGTGGCAGGTGCACAACACA--GTGGTA-------------------------------------------------TGCATAT----AT------------------------------------------------------------------------------------------------------------------GTACA--ACTACTTACGAGCACATCCACCTGT------CTG----GCTTGGACACCTTCAACTAATGC-----AGCCACTGT------------A---
droEug1	ATTGTGACAGGTGTACAACGC--AGTTGAA-------------------------------------------------TGAGTTT----ATATTGTGGTACTAATACATATACATACATACATATACATACCAAAACATATACATATACATACCTTAACATATACATATACATACCTAAACATATACATATACATACCTAAACATATACA--CCTACTTATAAGAACATCCACCTGT------CTGCTAGTCTT--GAGACTTAAAATAATGC-----TT-TTCTTT------------AGTA
droBia1	ATTGTGACAGGTGAACAA-ACGCAGTTGAA-------------------------------------------------CGAGCAT----GTGGCATGGCA-TGATGC--------------------------------------------------------------------------------------------------ACACCCACATACTTACCAGCATATCCAACCGT------CTG----GCCT--GGGTCTTAATCTAATGC-----AT-TTCTTT------------AAAT
droTak1	ATTGTGACAGGTGTACAGTA----GGTTT-------------------------------------------------------AT------------------------------------------------------------------------------------------------------------------------ACACCTACATACTTACCAGCACATCCACCTGT------CTG----GCTT-TGGGTCTTAAACTAATGC-----AT-TTCTCT------------GAAA
droEle1	ATTGTGACAGGTGCACAGTGTACAGTTGAA-------------------------------------------------CGAGTAT------------------------------------------------------------------------------------------------------------------------ACACC--TGTACTTACGGGCACATCCACCTGT------CTGTG--GCTTTTGGGCCTTAAGCTAATGC-----AT-TTCTTT------------AAAA
droRho1	ATTGTGACAGGTGCACAACAC--AGTTGAG-------------------------------------------------CGAGTAC------------------------------------------------------------------------------------------------------------------------ACACA--TCTACTTACGGGCACATCCACCTGT------CTG----GGTTTTTGGCCTTAAGCTAAGGC-----GT-TTCTTT------------AAAA
droFic1	ATTGTGACAGGTGAACAACTC--CGCCGAACGATGGAGTATATATGGAGTATATATA-----------------------------------------------------------------------------------------------------------------------------------------------------GTACA--CCTACTTACGGGCACATCCACCTGT------CTG----ACTT--TTGCTCCAGACTAATGC-----GT-TTCTCT------------AAAA
droKik1	ATTGTGGCAGGTAG----TAGGTAGGTGGA--------------------------------TGT-GCTCCGAAAAAGGT-G--GC------------------------------------------------------------------------------------------------------------------------ATACCT-CCCACTTACCGGCACATCCACCTGTCGTCGTCTG----GCTT--TTGCCT--------------------CTCAGAATATAATATATAAAA
droAna3	ATTGTGACTGGTTG--------------CA-------------------------TG-----------------------------------------------------------------------------------------------------------------------------------------------------TTGCA--GTTGCTTTGTGGCACAATGCTCTCT------CTC--AGTCTA--GAGCTTTAA-------------AT-TCCTTG------------AATG
droBip1	ATTGTGACAGGTGGC-----------TGTA-------------------------TGTTGCATGTTGCT------------------------TTGTG----------------------------------------------------------------------------------------------------------------------------GAGCACAAT---------------------------AGTCTCCAACTAAGGCTTTAAAT-TCCTTG------------AATA

20-way Secondary Structure

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

Small RNA-seq read pileup

Species

Alignment

droSim1

ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTGCGAGCACATCCACCTGT------CTG--G-TTA--GCACCTTCAACTAATGCATCACTTT------------A-AAG

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTACGAGCACATCCACCTGT------CTG--G-TTA--TCACCTTCAACTAATGCATCACTTT------------A-AAG

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

ATTGTGACAGGTGTACAACACACGT----TTGA----ATATA------TA------------------------------------------------------------------------------------------------------------------------------------CCTCTACTTACGAGCACATCCACCTGT------CTG--G-CTT--GCACCTTCAACTAATGCATCACTTT------------A-AAG

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

ATTGTGGCAGGTGCACAACACA--G----TGGTATGCATATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CAACTACTTACGAGCACATCCACCTGT------CTG--G-CTTGGACACCTTCAACTAATGCAGC--CAC------------T-GTA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droEug1

ATTGTGACAGGTGTACAACGC--AG----TTGAATGAGTTTA----TA-----------TTGTG-------GTACTAATACATATACATACATACATATACATACCAAAACATATACATATACATACCTTAACATATACATATACATACCTAAACATATACATATACATACCTAAACATATACACCTACTTATAAGAACATCCACCTGT------CTGCTA-GTCTTGAGACTTAAAATAATGCTTTTCTTT------------A-GTA

Size

Hit Count

Total Norm

droBia1

ATTGTGACAGGTGAACAA-ACGCAG----TTGAACGAGCATG----TG-----------GCATG-------GCA-TGATGCAC------------------------------------------------------------------------------------------------ACCCACATACTTACCAGCATATCCAACCGT------CTG--G-CCT--GGGTCTTAATCTAATGCATTTCTTT------------A-AAT

Size

Hit Count

Total Norm

droTak1

ATTGTGACAGGTGTACAGTA----G----GTT------TATA------CA----------------------------------------------------------------------------------------------------------------------------------CCTACATACTTACCAGCACATCCACCTGT------CTG--G-CTT-TGGGTCTTAAACTAATGCATTTCTCT------------G-AAA

Size

Hit Count

Total Norm

droEle1

ATTGTGACAGGTGCACAGTGTACAG----TTGAACGAGTATA------CA------------------------------------------------------------------------------------------------------------------------------------CCTGTACTTACGGGCACATCCACCTGT------CTGTGG-CTTTTGGGCCTTAAGCTAATGCATTTCTTT------------A-AAA

Size

Hit Count

Total Norm

droRho1

ATTGTGACAGGTGCACAACAC--AG----TTGAGCGAGTACA------CA------------------------------------------------------------------------------------------------------------------------------------CATCTACTTACGGGCACATCCACCTGT------CTG--G-GTTTTTGGCCTTAAGCTAAGGCGTTTCTTT------------A-AAA

Size

Hit Count

Total Norm

droFic1

ATTGTGACAGGTGAACAACTC--CGCCGAACGATGGAGTATA------TA---------TGGAG-------T-----ATATAT-----------------------------------------------------------------------------------------------AGTACACCTACTTACGGGCACATCCACCTGT------CTG--A-CTT--TTGCTCCAGACTAATGCGTTTCTCT------------A-AAA

Size

Hit Count

Total Norm

droKik1

ATTGTGGCAGGTAG----TAGGTAG----GTGGATGTGCTCC----GA---------------AAAAGGTGGC--------AT------------------------------------------------------------------------------------------------AC-CTCCCACTTACCGGCACATCCACCTGTCGTCGTCTG--G-CTT--TTGCCTC--------------TCAGAATATAATATATA-AAA

Size

Hit Count

Total Norm

droAna3

ATTGTGACTGGTTG------------------CATGT-----------TG------------------------------------------------------------------------------------------------------------------------------------CAGTTGCTTTGTGGCACAATGCTCTCT------CTC--A-GTCTAGAGCTTTAA--------ATTCCTTG------------A-ATG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

ATTGTGACAGGTGGC---------------TGTATGT-----------TGCATGTTGCTTTGTG---------------------------------------------------------------------------------------------------------------------------------GAGCACAATAGTCTCC--------A--A-CTA--AGGCTTTAA--------ATTCCTTG------------A-ATA

Size

Hit Count

Total Norm

dp4

CTTCCTCCAGGTGTACTGTACACAT----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	24	35	0.71	0.11	0.00	0.60	0.00
..............................TGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	24	35	0.71	0.11	0.00	0.60	0.00
.............................GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	25	28	0.29	0.04	0.00	0.25	0.00
.................................GTACGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	20	6	1.33	0.00	1.33	0.00	0.00
.......................GT----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	25	28	0.29	0.04	0.00	0.25	0.00
.......................GT----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------G..	23	41	0.15	0.00	0.00	0.15	0.00
.............................GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	23	41	0.15	0.00	0.00	0.15	0.00
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	25	27	0.22	0.04	0.00	0.19	0.00
...............................GTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	23	41	0.15	0.00	0.00	0.15	0.00
..............................TGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	25	27	0.22	0.04	0.00	0.19	0.00
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	26	22	0.23	0.00	0.00	0.23	0.00
.............................GTACGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TG.....................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
.................................GTACGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	19	46	0.11	0.04	0.04	0.02	0.00
...............................GTACGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------G..	19	46	0.11	0.04	0.04	0.02	0.00
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTT	24	17	0.24	0.00	0.06	0.18	0.00
..............................TGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	22	49	0.08	0.00	0.00	0.08	0.00
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------G..	22	49	0.08	0.00	0.00	0.08	0.00
................................TGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	22	49	0.08	0.00	0.00	0.08	0.00
................................TGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	24	17	0.24	0.00	0.06	0.18	0.00
................................TGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GT.	19	35	0.09	0.03	0.00	0.06	0.00
..............................TGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------...	19	35	0.09	0.03	0.00	0.06	0.00
................................TTTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------G..	18	49	0.06	0.02	0.02	0.02	0.00
..............................TTTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TG.....................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
..................................TTTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	18	49	0.06	0.02	0.02	0.02	0.00
.................................GTACGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG	21	4	0.75	0.00	0.50	0.25	0.00
........................T----TTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------.......................................................................................	18	49	0.06	0.02	0.02	0.02	0.00
........................T----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------T......................................................................................	19	35	0.09	0.03	0.00	0.06	0.00

droPer1

ATTGCAGCTCTCATTTAAAGC-CCG----ACGATCGTTTACA----AACA----------------------------------------------------------------------------------------------------------------------------------C-TAACTGTCAACAAGCAAATTAATCTGC--------A--G-CTA--AAAGCATATACATATGTACAATTTA------------T-AAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................................................................................................................................................................................ATATxTGTAGAATTTA------------T-AA.	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCCCTTT------------ATATG

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TATAATACAAAATCGATTGTCTCAA----ATCGATCAATATA------TA------------------------------------------------------------------------------------------------------------------------------------AAGATTTTCAATAGAATAGTCACACCA------CTT--AGAAA--ACAACTTTAAATCTAGCA--CCCAT------------A-AAG	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....ATACxAAATCGATTGTCACA.....................................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

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

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:14:12 EDT

sblock181949

chrX:10395825-10395903 -

Candidate

intron

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