sblock181949- 12- and 20-way alignments

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
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chrX:10395810-10395918 -	ATTGTGACAGGTGTACAACACACAGGTGAATGTGTATGT--ATATGTGCGACTACTTACGAGCACATCCACCTGTCT-GGTTTG--CACCTTCAACTAATGC--ATCACTTTAAAG
droSim1	chrX:8074162-8074266 -	ATTGTGACAGGTGTACAGCACACAGGTGAA------TGCGTATATGTACGACTACTTGCGAGCACATCCACCTGTCT-GGTTAG--CACCTTCAACTAATGC--ATCACTTTAAAG
droSec1	super_15:1103035-1103139 -	ATTGTGACAGGTGTACAGCACACAGGTGAA------TGCGTATATGTACGACTACTTACGAGCACATCCACCTGTCT-GGTTAT--CACCTTCAACTAATGC--ATCACTTTAAAG
droYak2	chrX:18969663-18969761 -	ATTGTGACAGGTGTACAACACACGTT----------TGAA--TATATACCTCTACTTACGAGCACATCCACCTGTCT-GGCTTG--CACCTTCAACTAATGC--ATCACTTTAAAG
droEre2	scaffold_4690:4732725-4732818 +	ATTGTGGCAGGTGCACAACACAGTGGT--A------TGCATATATGTACAACTACTTACGAGCACATCCACCTGTCT-GGCTTGGACACCTTCAACTAATGC--A-----------
droAna3	scaffold_13335:2306029-2306106 +	ATTGTGACTGGT------------------------TGCATG---TTGCAGTTGCTTTGTGGCACAATGCTCTCTCTCAGTCTA--GAGCTTTAA---------ATTCCTTGAATG
dp4	chrXL_group1e:5743100-5743145 -	AAGG------------------------------------------------------------CGTACACCTGT--------A--CACCTTGAGGGAAAGGAAGTCGCTTTCAGA
droPer1	super_21:671982-672027 -	AAGG------------------------------------------------------------CGTACACCTGT--------A--CACCTTGAGGGAAAGGAAGTCGCTTTCAGA
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12855:10082495-10082596 +	TATAATACAAAATCGATTGTCTCAAATCGA------TCAAT--ATATAAAGATTTTCAATAGAATAGTCACACCACTTAGAAAA--CAACTTTAAATCTAGC--AC--CCATAAAG
droMoj3	Unknown	--------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:10395810-10395918 -	NA	ATTGTGACAGGTGTACAACACACAG----GTGAATGTGTATGTATATGTG------------------------------------------------------------------------------------------------------------------------------------CGACTACTTACGAGCACATCCACCTGT------CTG--G-TTT--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droSim1	chrX:8074162-8074266 -	1	ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTGCGAGCACATCCACCTGT------CTG--G-TTA--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droSec1	super_15:1103035-1103139 -	1	ATTGTGACAGGTGTACAGCACACAG----GTGAATGCGTATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CGACTACTTACGAGCACATCCACCTGT------CTG--G-TTA--TCACCTTCAACTAATGCATCACTTT------------A-AAG
droYak2	chrX:18969663-18969761 -	1	ATTGTGACAGGTGTACAACACACGT----TTGA----ATATA------TA------------------------------------------------------------------------------------------------------------------------------------CCTCTACTTACGAGCACATCCACCTGT------CTG--G-CTT--GCACCTTCAACTAATGCATCACTTT------------A-AAG
droEre2	scaffold_4690:4732725-4732827 +	1	ATTGTGGCAGGTGCACAACACA--G----TGGTATGCATATA----TGTA------------------------------------------------------------------------------------------------------------------------------------CAACTACTTACGAGCACATCCACCTGT------CTG--G-CTTGGACACCTTCAACTAATGCAGC--CAC------------T-GTA
droEug1	scf7180000409538:335496-335716 +	2	ATTGTGACAGGTGTACAACGC--AG----TTGAATGAGTTTA----TA-----------TTGTG-------GTACTAATACATATACATACATACATATACATACCAAAACATATACATATACATACCTTAACATATACATATACATACCTAAACATATACATATACATACCTAAACATATACACCTACTTATAAGAACATCCACCTGT------CTGCTA-GTCTTGAGACTTAAAATAATGCTTTTCTTT------------A-GTA
droBia1	scf7180000302126:3261824-3261944 -	2	ATTGTGACAGGTGAACAA-ACGCAG----TTGAACGAGCATG----TG-----------GCATG-------GCA-TGATGCAC------------------------------------------------------------------------------------------------ACCCACATACTTACCAGCATATCCAACCGT------CTG--G-CCT--GGGTCTTAATCTAATGCATTTCTTT------------A-AAT
droTak1	scf7180000415394:185406-185501 -	1	ATTGTGACAGGTGTACAGTA----G----GTT------TATA------CA----------------------------------------------------------------------------------------------------------------------------------CCTACATACTTACCAGCACATCCACCTGT------CTG--G-CTT-TGGGTCTTAAACTAATGCATTTCTCT------------G-AAA
droEle1	scf7180000491087:250537-250643 +	2	ATTGTGACAGGTGCACAGTGTACAG----TTGAACGAGTATA------CA------------------------------------------------------------------------------------------------------------------------------------CCTGTACTTACGGGCACATCCACCTGT------CTGTGG-CTTTTGGGCCTTAAGCTAATGCATTTCTTT------------A-AAA
droRho1	scf7180000767464:324-426 -	2	ATTGTGACAGGTGCACAACAC--AG----TTGAGCGAGTACA------CA------------------------------------------------------------------------------------------------------------------------------------CATCTACTTACGGGCACATCCACCTGT------CTG--G-GTTTTTGGCCTTAAGCTAAGGCGTTTCTTT------------A-AAA
droFic1	scf7180000454050:325714-325834 -	1	ATTGTGACAGGTGAACAACTC--CGCCGAACGATGGAGTATA------TA---------TGGAG-------T-----ATATAT-----------------------------------------------------------------------------------------------AGTACACCTACTTACGGGCACATCCACCTGT------CTG--A-CTT--TTGCTCCAGACTAATGCGTTTCTCT------------A-AAA
droKik1	scf7180000302698:739080-739196 +	3	ATTGTGGCAGGTAG----TAGGTAG----GTGGATGTGCTCC----GA---------------AAAAGGTGGC--------AT------------------------------------------------------------------------------------------------AC-CTCCCACTTACCGGCACATCCACCTGTCGTCGTCTG--G-CTT--TTGCCTC--------------TCAGAATATAATATATA-AAA
droAna3	scaffold_13335:2306029-2306106 +	2	ATTGTGACTGGTTG------------------CATGT-----------TG------------------------------------------------------------------------------------------------------------------------------------CAGTTGCTTTGTGGCACAATGCTCTCT------CTC--A-GTCTAGAGCTTTAA--------ATTCCTTG------------A-ATG
droBip1	scf7180000395653:6539-6618 +	2	ATTGTGACAGGTGGC---------------TGTATGT-----------TGCATGTTGCTTTGTG---------------------------------------------------------------------------------------------------------------------------------GAGCACAATAGTCTCC--------A--A-CTA--AGGCTTTAA--------ATTCCTTG------------A-ATA
dp4	chr2:27497880-27497927 +	1	CTTCCTCCAGGTGTACTGTACACAT----GTGTGTGTGTGTG----TGTG------------------------------------------------------------------------------------------------------------------------------------TGT---------------------------------------------------------------------------------GTG
droPer1	super_4:355428-355530 -	2	ATTGCAGCTCTCATTTAAAGC-CCG----ACGATCGTTTACA----AACA----------------------------------------------------------------------------------------------------------------------------------C-TAACTGTCAACAAGCAAATTAATCTGC--------A--G-CTA--AAAGCATATACATATGTACAATTTA------------T-AAA
droWil1	scaffold_181130:766074-766090 +	1	AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCCCTTT------------ATATG
droVir3	scaffold_12855:10082495-10082596 +	1	TATAATACAAAATCGATTGTCTCAA----ATCGATCAATATA------TA------------------------------------------------------------------------------------------------------------------------------------AAGATTTTCAATAGAATAGTCACACCA------CTT--AGAAA--ACAACTTTAAATCTAGCA--CCCAT------------A-AAG
droMoj3	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATTGTGACAGGTGTACAACACACAGGTGAATGTGTATGT--ATATGTGCGACTACTTACGAGCACATCCACCTGTCT-GGTTTG--CACCTTCAACTAATGC--ATCACTTTAAAG

Size

Hit Count

Total Norm

droSim1

ATTGTGACAGGTGTACAGCACACAGGTGAA------TGCGTATATGTACGACTACTTGCGAGCACATCCACCTGTCT-GGTTAG--CACCTTCAACTAATGC--ATCACTTTAAAG

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

ATTGTGACAGGTGTACAGCACACAGGTGAA------TGCGTATATGTACGACTACTTACGAGCACATCCACCTGTCT-GGTTAT--CACCTTCAACTAATGC--ATCACTTTAAAG

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

ATTGTGACAGGTGTACAACACACGTT----------TGAA--TATATACCTCTACTTACGAGCACATCCACCTGTCT-GGCTTG--CACCTTCAACTAATGC--ATCACTTTAAAG

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

ATTGTGGCAGGTGCACAACACAGTGGT--A------TGCATATATGTACAACTACTTACGAGCACATCCACCTGTCT-GGCTTGGACACCTTCAACTAATGC--A-----------

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

ATTGTGACTGGT------------------------TGCATG---TTGCAGTTGCTTTGTGGCACAATGCTCTCTCTCAGTCTA--GAGCTTTAA---------ATTCCTTGAATG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

AAGG------------------------------------------------------------CGTACACCTGT--------A--CACCTTGAGGGAAAGGAAGTCGCTTTCAGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

AAGG------------------------------------------------------------CGTACACCTGT--------A--CACCTTGAGGGAAAGGAAGTCGCTTTCAGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................TGA--------A--CACCGTGAGGGAAAGG..............	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TATAATACAAAATCGATTGTCTCAAATCGA------TCAAT--ATATAAAGATTTTCAATAGAATAGTCACACCACTTAGAAAA--CAACTTTAAATCTAGC--AC--CCATAAAG	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

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image									None		None	None
UNAFold Image									None		None	None

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