Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold189
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2243555
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:1209471 original size:22 final size:23
Alignment explanation
Indices: 1209441--1209484 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1209431 TATAATTATT
1209441 TTTTAAAATTT-AATATTTAATAA
1 TTTTAAAATTTAAAT-TTTAATAA
1209464 TTTT-AAATTTAAATTTTAATA
1 TTTTAAAATTTAAATTTTAATA
1209485 TTTATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTAAAATTTAAATTTTAATAA
Found at i:1210049 original size:2 final size:2
Alignment explanation
Indices: 1210039--1210074 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1210029 AATGTGTGTG
*
1210039 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1210075 GGGTTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1217316 original size:20 final size:21
Alignment explanation
Indices: 1217291--1217344 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
1217281 AATAGAAATG
*
1217291 AAATAATAAAATT-TTTTGTA
1 AAATAATAAAATTATTTTATA
1217311 AAATAATAAATAATTATTTTATA
1 AAATAAT-AA-AATTATTTTATA
*
1217334 TAATAATAAAA
1 AAATAATAAAA
1217345 ATAAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 4 0.14
22 6 0.21
23 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AAATAATAAAATTATTTTATA
Found at i:1217329 original size:25 final size:25
Alignment explanation
Indices: 1217312--1217362 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1217302 TTTTTTGTAA
1217312 AATAATAAATAATTATTTTATATAAT
1 AATAA-AAATAATTATTTTATATAAT
**
1217338 AATAAAAATAAAAATTTTATA-AAT
1 AATAAAAATAATTATTTTATATAAT
1217362 A
1 A
1217363 TTATTAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 14 0.61
26 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
AATAAAAATAATTATTTTATATAAT
Found at i:1218277 original size:31 final size:32
Alignment explanation
Indices: 1218214--1218283 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1218204 AATAATTAAA
1218214 ATATTATTATGTTATATATATATTAAAATATTT
1 ATATT-TTATGTTATATATATATTAAAATATTT
* *
1218247 ATATTTTATGATTA-AT-TATATTAGAGTATTT
1 ATATTTTATG-TTATATATATATTAAAATATTT
*
1218278 AAATTT
1 ATATTT
1218284 ATTAAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 18 0.55
32 7 0.21
33 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (32 bp):
ATATTTTATGTTATATATATATTAAAATATTT
Found at i:1219395 original size:24 final size:24
Alignment explanation
Indices: 1219339--1219387 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
1219329 TTATTAAAAT
* *
1219339 ATTAATTTTATATTAATATTTATA
1 ATTAAATTTATATTAATATATATA
1219363 ATTAAATTTA-ATTAA-ATATATA
1 ATTAAATTTATATTAATATATATA
1219385 ATT
1 ATT
1219388 TAAAATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 5 0.22
24 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTAAATTTATATTAATATATATA
Found at i:1220355 original size:2 final size:2
Alignment explanation
Indices: 1220348--1220378 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1220338 ATAAATATGT
1220348 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1220379 TTAACTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1229160 original size:20 final size:20
Alignment explanation
Indices: 1229119--1229172 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
1229109 TTTTGTTTCC
*
1229119 AAAAAAAAAA-AAAACAATG
1 AAAAAAAAAAGAAAACAAGG
1229138 AAAAAAATAAAGAAAA-AAGG
1 AAAAAAA-AAAGAAAACAAGG
*
1229158 AAAGAAAGAAAGAAA
1 AAA-AAAAAAAGAAA
1229173 CGAAACTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 7 0.23
20 16 0.53
21 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAAAAAAGAAAACAAGG
Found at i:1230716 original size:21 final size:18
Alignment explanation
Indices: 1230685--1230731 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
1230675 TTTATCTAAA
1230685 TTTAATTATAAAATATATAAT
1 TTTAA-TATAAAATA-AT-AT
1230706 TATTAATATAAAATAATAT
1 T-TTAATATAAAATAATAT
1230725 TTTAATA
1 TTTAATA
1230732 ATAATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
20 2 0.08
21 10 0.40
22 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAATATAAAATAATAT
Found at i:1234291 original size:7 final size:7
Alignment explanation
Indices: 1234276--1234311 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1234266 TTGCAAAATT
*
1234276 ACTGAAC
1 ACTGTAC
1234283 ACTGTAC
1 ACTGTAC
1234290 ACTGTAC
1 ACTGTAC
*
1234297 ACCGTAC
1 ACTGTAC
1234304 ACTGTAC
1 ACTGTAC
1234311 A
1 A
1234312 AGCAATGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (7 bp):
ACTGTAC
Found at i:1234733 original size:2 final size:2
Alignment explanation
Indices: 1234726--1234750 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1234716 ATGGCAAATC
1234726 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1234751 CGTGTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1235276 original size:45 final size:45
Alignment explanation
Indices: 1235225--1235347 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 45
1235215 ATTTAATTAA
*
1235225 AATATAATTTAAAATAATATATGATATAAAAAATTTTATAAATAT
1 AATATAATTTAAAATAATATATAATATAAAAAATTTTATAAATAT
* * * * *
1235270 AATATAATATAAAATACTA-A-CATATTAAAATTTTTATAAATAT
1 AATATAATTTAAAATAATATATAATATAAAAAATTTTATAAATAT
1235313 -ATA-ATATTTCAAATATAAT-TATAATATATAAAAAT
1 AATATA-ATTT-AAA-ATAATATATAATATA-AAAAAT
1235348 ATATTTAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
41 1 0.02
42 6 0.10
43 23 0.37
44 6 0.10
45 21 0.34
46 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (45 bp):
AATATAATTTAAAATAATATATAATATAAAAAATTTTATAAATAT
Found at i:1235337 original size:20 final size:19
Alignment explanation
Indices: 1235312--1235370 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
1235302 TTTATAAATA
1235312 TATAATATTTCAAATATAAT
1 TATAATATTT-AAATATAAT
* *
1235332 TATAATATATAAAAATATAT
1 TATAATATTTAAATATA-AT
*
1235352 T-TAAATATTTAAATCTAAT
1 TAT-AATATTTAAATATAAT
1235371 AAGTTTTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.28
20 23 0.72
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATTTAAATATAAT
Found at i:1238570 original size:2 final size:2
Alignment explanation
Indices: 1238563--1238633 Score: 51
Period size: 2 Copynumber: 37.5 Consensus size: 2
1238553 TAAATATGAA
* * *
1238563 AT AT AT AT CT AT A- AT AT AA AT AT AT AT -T AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1238602 AT -T AT AG AT AA AT AT GT AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1238634 AAATATTAAC
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
1 4 0.08
2 48 0.92
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1238613 original size:16 final size:15
Alignment explanation
Indices: 1238576--1238607 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1238566 TATATCTATA
1238576 ATATAAATATATATT
1 ATATAAATATATATT
1238591 ATATAAA-ATATATT
1 ATATAAATATATATT
1238605 ATA
1 ATA
1238608 GATAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATAAATATATATT
Found at i:1256674 original size:21 final size:21
Alignment explanation
Indices: 1256650--1256734 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 21
1256640 TTATCTGTAG
1256650 ATATAATTTTGATAATTTTTA
1 ATATAATTTTGATAATTTTTA
* *
1256671 ATATAATTTTAATAATATTTA
1 ATATAATTTTGATAATTTTTA
*
1256692 ATA-AAATTT-ATATATCATTTTA
1 ATATAATTTTGATA-AT--TTTTA
1256714 TATATAATTTTGATAATTTTT
1 -ATATAATTTTGATAATTTTT
1256735 TTATATATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.06
20 7 0.13
21 22 0.42
22 8 0.15
23 3 0.06
24 7 0.13
25 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (21 bp):
ATATAATTTTGATAATTTTTA
Found at i:1256763 original size:26 final size:26
Alignment explanation
Indices: 1256708--1256765 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1256698 TTTATATATC
***
1256708 ATTT-TATATATAATTTTGATAATTT
1 ATTTATATATATAATTTTGATAAAAA
*
1256733 TTTTATATATATAATTTTGATAAAAA
1 ATTTATATATATAATTTTGATAAAAA
1256759 ATTTATA
1 ATTTATA
1256766 ATAATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 3 0.11
26 24 0.89
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (26 bp):
ATTTATATATATAATTTTGATAAAAA
Found at i:1256814 original size:21 final size:21
Alignment explanation
Indices: 1256759--1256817 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1256749 TTGATAAAAA
* *
1256759 ATTTATAATAATTTTAATAGT
1 ATTTATAATAATTTTAGTAAT
* **
1256780 CTTTCAT-ACCATTTTAGTAAT
1 ATTT-ATAATAATTTTAGTAAT
1256801 ATTTATAATAATTTTAG
1 ATTTATAATAATTTTAG
1256818 AAATTTTCTC
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTATAATAATTTTAGTAAT
Found at i:1256816 original size:11 final size:11
Alignment explanation
Indices: 1256652--1256774 Score: 60
Period size: 12 Copynumber: 10.8 Consensus size: 11
1256642 ATCTGTAGAT
1256652 ATAATTTTGATA
1 ATAATTTT-ATA
1256664 AT--TTTTA-A
1 ATAATTTTATA
1256672 TATAATTTTAATA
1 -ATAATTTT-ATA
*
1256685 AT-ATTTAATA
1 ATAATTTTATA
1256695 A-AA-TTTATA
1 ATAATTTTATA
*
1256704 TATCATTTTATA
1 -ATAATTTTATA
1256716 TATAATTTTGATA
1 -ATAATTTT-ATA
**
1256729 ATTTTTTTATATA
1 A-TAATTT-TATA
1256742 TATAATTTTGATA
1 -ATAATTTT-ATA
* *
1256755 AAAAATTTATA
1 ATAATTTTATA
1256766 ATAATTTTA
1 ATAATTTTA
1256775 ATAGTCTTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
8 1 0.01
9 8 0.09
10 10 0.12
11 19 0.22
12 27 0.32
13 18 0.21
14 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (11 bp):
ATAATTTTATA
Found at i:1256934 original size:23 final size:21
Alignment explanation
Indices: 1256885--1256976 Score: 89
Period size: 21 Copynumber: 4.3 Consensus size: 21
1256875 TTTTACTAAC
**
1256885 TTTTTTATATAATCGTGATAA
1 TTTTTTATATAATTTTGATAA
1256906 TTTTTTATATAATTTTGATAA
1 TTTTTTATATAATTTTGATAA
1256927 TATATTTTA-ATAAATTTT-ATAA
1 T-T-TTTTATAT-AATTTTGATAA
** * *
1256949 TTTTCGATATTATTTTGGTAA
1 TTTTTTATATAATTTTGATAA
1256970 TTTTTTA
1 TTTTTTA
1256977 AAAGATTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
20 8 0.14
21 31 0.53
22 8 0.14
23 11 0.19
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTTTATATAATTTTGATAA
Found at i:1256949 original size:43 final size:41
Alignment explanation
Indices: 1256902--1256985 Score: 98
Period size: 43 Copynumber: 2.0 Consensus size: 41
1256892 TATAATCGTG
**
1256902 ATAATTTTTTATATAATTTTGATAATATATTTTAATAA-ATTTT
1 ATAATTTTCGATATAATTTTGATAAT-T-TTTTAA-AAGATTTT
* *
1256945 ATAATTTTCGATATTATTTTGGTAATTTTTTAAAAGATTTT
1 ATAATTTTCGATATAATTTTGATAATTTTTTAAAAGATTTT
1256986 GTATTCTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.06
41 11 0.31
42 1 0.03
43 22 0.61
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (41 bp):
ATAATTTTCGATATAATTTTGATAATTTTTTAAAAGATTTT
Found at i:1256976 original size:31 final size:32
Alignment explanation
Indices: 1256902--1256976 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 32
1256892 TATAATCGTG
1256902 ATAATTTTTTATATAATTTTGATAATATATTTTA
1 ATAA-TTTTT-TATAATTTTGATAATATATTTTA
* *
1256936 ATAA-ATTTTATAATTTTCGAT-AT-TATTTTG
1 ATAATTTTTTATAATTTT-GATAATATATTTTA
*
1256966 GTAATTTTTTA
1 ATAATTTTTTA
1256977 AAAGATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
30 9 0.26
31 16 0.46
32 6 0.17
34 4 0.11
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (32 bp):
ATAATTTTTTATAATTTTGATAATATATTTTA
Found at i:1257758 original size:32 final size:32
Alignment explanation
Indices: 1257722--1257808 Score: 174
Period size: 32 Copynumber: 2.7 Consensus size: 32
1257712 TTTTGATATA
1257722 TTAATAATTCGTATTATATAAATATTGATTCG
1 TTAATAATTCGTATTATATAAATATTGATTCG
1257754 TTAATAATTCGTATTATATAAATATTGATTCG
1 TTAATAATTCGTATTATATAAATATTGATTCG
1257786 TTAATAATTCGTATTATATAAAT
1 TTAATAATTCGTATTATATAAAT
1257809 TTTAATACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (32 bp):
TTAATAATTCGTATTATATAAATATTGATTCG
Found at i:1257841 original size:64 final size:64
Alignment explanation
Indices: 1257722--1257845 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
1257712 TTTTGATATA
* * * * *
1257722 TTAATAATTCGTATTATATAAATATTGATTCGTTAATAATTCGTATTATATAAATATTGATTCG
1 TTAATAATTCGTATTATATAAATATTAATACATAAATAATTCATATTATATAAATATTGATTCG
* *
1257786 TTAATAATTCGTATTATATAAATTTTAATACATAAGAGT-ATTCATATTGTA-AAATATTGA
1 TTAATAATTCGTATTATATAAATATTAATACATAA-A-TAATTCATATTATATAAATATTGA
1257846 ACTTTCACTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
64 39 0.76
65 11 0.22
66 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (64 bp):
TTAATAATTCGTATTATATAAATATTAATACATAAATAATTCATATTATATAAATATTGATTCG
Found at i:1258206 original size:20 final size:21
Alignment explanation
Indices: 1258146--1258297 Score: 111
Period size: 20 Copynumber: 7.5 Consensus size: 21
1258136 TTGATGTTCG
***
1258146 ATATAATTTTAATAAACATTA
1 ATATAATTTTAATAATTTTTA
* *
1258167 ATATAACTTTGATCAATTTTTA
1 ATATAATTTTAAT-AATTTTTA
* *
1258189 ATTTAATTTTAA-AATTTTTT
1 ATATAATTTTAATAATTTTTA
*
1258209 ATATAATTTTAATAATTTTTT
1 ATATAATTTTAATAATTTTTA
* **
1258230 ATATTA-TTTAATAAACTTT-
1 ATATAATTTTAATAATTTTTA
*
1258249 A-A-AATTATAATAAATTTTT-
1 ATATAATTTTAAT-AATTTTTA
*
1258268 ATATAATTTTGATAA-TTTTA
1 ATATAATTTTAATAATTTTTA
*
1258288 TTATAATTTT
1 ATATAATTTT
1258298 TTTTCTTCCT
Statistics
Matches: 104, Mismatches: 20, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.01
18 6 0.06
19 11 0.11
20 41 0.39
21 31 0.30
22 14 0.13
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (21 bp):
ATATAATTTTAATAATTTTTA
Found at i:1258209 original size:21 final size:22
Alignment explanation
Indices: 1258146--1258286 Score: 88
Period size: 21 Copynumber: 6.9 Consensus size: 22
1258136 TTGATGTTCG
***
1258146 ATATAATTTTAATAA-ACATTA
1 ATATAATTTTAATAATTTTTTA
* *
1258167 ATATAACTTTGATCAA-TTTTTA
1 ATATAATTTTAAT-AATTTTTTA
*
1258189 ATTTAATTTTAA-AATTTTTT-
1 ATATAATTTTAATAATTTTTTA
1258209 ATATAATTTTAATAATTTTTT-
1 ATATAATTTTAATAATTTTTTA
* **
1258230 ATATTA-TTTAATAA-ACTTT-
1 ATATAATTTTAATAATTTTTTA
* *
1258249 A-A-AATTATAATAAATTTTT-
1 ATATAATTTTAATAATTTTTTA
*
1258268 ATATAATTTTGATAATTTT
1 ATATAATTTTAATAATTTT
1258287 ATTATAATTT
Statistics
Matches: 94, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
17 1 0.01
18 8 0.09
19 8 0.09
20 22 0.23
21 41 0.44
22 14 0.15
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (22 bp):
ATATAATTTTAATAATTTTTTA
Found at i:1258218 original size:11 final size:11
Alignment explanation
Indices: 1258204--1258298 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 11
1258194 ATTTTAAAAT
1258204 TTTTTATATAA
1 TTTTTATATAA
1258215 -TTTTA-ATAA
1 TTTTTATATAA
1258224 TTTTT-TAT-A
1 TTTTTATATAA
1258233 TTATTTA-ATAA
1 TT-TTTATATAA
**
1258244 ACTTTA-A-AA
1 TTTTTATATAA
* *
1258253 TTATAATA-AA
1 TTTTTATATAA
1258263 TTTTTATATAA
1 TTTTTATATAA
*
1258274 -TTTT-GATAA
1 TTTTTATATAA
1258283 -TTTTATTATAA
1 TTTTTA-TATAA
1258294 TTTTT
1 TTTTT
1258299 TTTCTTCCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
9 19 0.30
10 34 0.53
11 7 0.11
12 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTTATATAA
Found at i:1258526 original size:10 final size:10
Alignment explanation
Indices: 1258513--1258687 Score: 136
Period size: 9 Copynumber: 17.8 Consensus size: 10
1258503 TTTTATTTTA
1258513 ATATAAAATT
1 ATATAAAATT
1258523 ATATAAAAATT
1 ATAT-AAAATT
*
1258534 AT-TAAAATA
1 ATATAAAATT
*
1258543 ATCTTAAAATT
1 AT-ATAAAATT
1258554 AT-TAAAATT
1 ATATAAAATT
*
1258563 ATATAAAATA
1 ATATAAAATT
* *
1258573 ATAAAAAAAT
1 ATATAAAATT
1258583 ATTATAAAATT
1 A-TATAAAATT
1258594 ATATAAAAATT
1 ATAT-AAAATT
1258605 AT-TAAAATT
1 ATATAAAATT
* *
1258614 A-ATTATA-T
1 ATATAAAATT
*
1258622 CTA-AAAATT
1 ATATAAAATT
1258631 AT-TAAAATT
1 ATATAAAATT
1258640 ATA-AAAATT
1 ATATAAAATT
1258649 AT-TAAAATT
1 ATATAAAATT
*
1258658 ATATAAAA-A
1 ATATAAAATT
1258667 ACTATTAAAATT
1 A-TA-TAAAATT
1258679 ATATGAAAA
1 ATAT-AAAA
1258688 AATCAAAATT
Statistics
Matches: 132, Mismatches: 16, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
8 3 0.02
9 54 0.41
10 31 0.23
11 43 0.33
12 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (10 bp):
ATATAAAATT
Found at i:1258533 original size:11 final size:11
Alignment explanation
Indices: 1258513--1258688 Score: 107
Period size: 11 Copynumber: 16.8 Consensus size: 11
1258503 TTTTATTTTA
1258513 ATAT-AAAATT
1 ATATAAAAATT
1258523 ATATAAAAATT
1 ATATAAAAATT
*
1258534 AT-T-AAAATA
1 ATATAAAAATT
* *
1258543 ATCTTAAAATT
1 ATATAAAAATT
1258554 AT-T-AAAATT
1 ATATAAAAATT
*
1258563 ATAT-AAAATA
1 ATATAAAAATT
*
1258573 ATA-AAAAAAT
1 ATATAAAAATT
1258583 AT-TATAAAATT
1 ATATA-AAAATT
1258594 ATATAAAAATT
1 ATATAAAAATT
1258605 AT-TAAAATTAATT
1 ATAT-AAA--AATT
1258618 ATATCTAAAAATT
1 ATA--TAAAAATT
1258631 AT-T-AAAA-T
1 ATATAAAAATT
1258639 -TATAAAAATT
1 ATATAAAAATT
1258649 AT-T-AAAATT
1 ATATAAAAATT
1258658 ATATAAAAA--
1 ATATAAAAATT
*
1258667 ACTATTAAAATT
1 A-TATAAAAATT
1258679 ATATGAAAAA
1 ATAT-AAAAA
1258689 ATCAAAATTC
Statistics
Matches: 134, Mismatches: 8, Indels: 46
0.71 0.04 0.24
Matches are distributed among these distances:
7 1 0.01
8 2 0.01
9 32 0.24
10 35 0.26
11 41 0.31
12 7 0.05
13 12 0.09
15 3 0.02
16 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (11 bp):
ATATAAAAATT
Found at i:1258630 original size:26 final size:24
Alignment explanation
Indices: 1258519--1258679 Score: 109
Period size: 21 Copynumber: 7.0 Consensus size: 24
1258509 TTTAATATAA
1258519 AATTATATAAAAATTATTAAAA-T
1 AATTATATAAAAATTATTAAAATT
*
1258542 AA-TCT-T-AAAATTATTAAAATT
1 AATTATATAAAAATTATTAAAATT
* * *
1258563 ATATAAAATAATAAAAAAATATTATAA--
1 A-AT--TAT-AT-AAAAATTATTAAAATT
1258590 AATTATATAAAAATTATTAAAATT
1 AATTATATAAAAATTATTAAAATT
1258614 AATTATATCTAAAAATTATT--AA--
1 AATTATA--TAAAAATTATTAAAATT
1258636 AA-T-TATAAAAATTATTAAAATT
1 AATTATATAAAAATTATTAAAATT
*
1258658 -A-TATA-AAAAACTATTAAAATT
1 AATTATATAAAAATTATTAAAATT
1258679 A
1 A
1258680 TATGAAAAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 39
0.70 0.06 0.25
Matches are distributed among these distances:
18 11 0.10
20 17 0.15
21 21 0.19
22 19 0.17
23 4 0.04
24 11 0.10
25 1 0.01
26 13 0.12
27 2 0.02
29 11 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTATATAAAAATTATTAAAATT
Found at i:1258695 original size:19 final size:20
Alignment explanation
Indices: 1258652--1258697 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1258642 AAAAATTATT
*
1258652 AAAATTATATAAAAAACTATT
1 AAAATTATATAAAAAAC-ATC
*
1258673 AAAATTATATGAAAAA-ATC
1 AAAATTATATAAAAAACATC
1258692 AAAATT
1 AAAATT
1258698 CCATGGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
21 15 0.65
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAATTATATAAAAAACATC
Found at i:1264833 original size:2 final size:2
Alignment explanation
Indices: 1264826--1264856 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1264816 ATATTATTTG
1264826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1264857 TCTAGTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1267564 original size:23 final size:24
Alignment explanation
Indices: 1267529--1267573 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1267519 TATAAATTAT
* *
1267529 TATTTTAATATAAATAT-ATAACA
1 TATTTAAACATAAATATCATAACA
*
1267552 TATTTAAACATAATTATCATAA
1 TATTTAAACATAAATATCATAA
1267574 AAAAATAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (24 bp):
TATTTAAACATAAATATCATAACA
Found at i:1268265 original size:49 final size:50
Alignment explanation
Indices: 1268158--1268266 Score: 141
Period size: 49 Copynumber: 2.2 Consensus size: 50
1268148 CGTTCACATT
* * * *
1268158 TGAATCCAAGTAACATAATTAGGTGTAATAGTATGAATGTACTAAAAACC
1 TGAATCCAAATAACATAACTAGGTATAACAGTATGAATGTACTAAAAACC
* * *
1268208 -GAATCCAAATAACATAACTAGGTATAACAGTATGAATGTGCTGAAAGCC
1 TGAATCCAAATAACATAACTAGGTATAACAGTATGAATGTACTAAAAACC
1268257 TGAA-CCAAAT
1 TGAATCCAAAT
1268267 TTGTCTTGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 48 0.94
50 3 0.06
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (50 bp):
TGAATCCAAATAACATAACTAGGTATAACAGTATGAATGTACTAAAAACC
Found at i:1277065 original size:29 final size:29
Alignment explanation
Indices: 1277032--1277090 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1277022 TTAGAAAATA
1277032 AATTTAATGTTTAAATCCGAACATCTTCG
1 AATTTAATGTTTAAATCCGAACATCTTCG
1277061 AATTTAATGTTTAAATCCGAACATCTTCG
1 AATTTAATGTTTAAATCCGAACATCTTCG
1277090 A
1 A
1277091 CCTTTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (29 bp):
AATTTAATGTTTAAATCCGAACATCTTCG
Found at i:1281340 original size:15 final size:15
Alignment explanation
Indices: 1281286--1281351 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 15
1281276 TTTTATTGAT
*
1281286 AATTATTGGTAAATA
1 AATTATTGGTAATTA
* *
1281301 ATTTCTTGGTAATTATTA
1 AATTATTGGT-A--ATTA
1281319 GAATTATTGGTAATTA
1 -AATTATTGGTAATTA
*
1281335 AATTATTAGTAATTA
1 AATTATTGGTAATTA
1281350 AA
1 AA
1281352 GTATAAAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
15 24 0.59
16 5 0.12
18 4 0.10
19 8 0.20
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (15 bp):
AATTATTGGTAATTA
Found at i:1282916 original size:2 final size:2
Alignment explanation
Indices: 1282909--1282940 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1282899 CCACATGCTT
1282909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1282941 GGTAATATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1283112 original size:2 final size:2
Alignment explanation
Indices: 1283105--1283131 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1283095 TTAAATATTG
1283105 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1283132 AATAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1287815 original size:18 final size:17
Alignment explanation
Indices: 1287792--1287868 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 17
1287782 AATTACATAA
1287792 TATATTTTATATAAATAT
1 TATATTTTATATAAAT-T
*
1287810 TATATTTATATTAAAAATTT
1 TATATTT-TA-TATAAA-TT
1287830 TAATATATTTA-AT-AATT
1 T-ATAT-TTTATATAAATT
* *
1287847 TATATTTTATTTATATT
1 TATATTTTATATAAATT
1287864 TATAT
1 TATAT
1287869 GAGTAATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.08
16 5 0.10
17 11 0.23
18 9 0.19
19 3 0.06
20 7 0.15
21 7 0.15
22 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATAAATT
Found at i:1290653 original size:35 final size:35
Alignment explanation
Indices: 1290614--1290680 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1290604 TAACTCATTT
* * *
1290614 TATTATTTTAATATTTATAATTA-AATTTAAATAAA
1 TATTAATTTAATATATA-AATAATAATTTAAATAAA
*
1290649 TATTAATTTATTATATAAATAATAATTTAAAT
1 TATTAATTTAATATATAAATAATAATTTAAAT
1290681 TTAAAACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 4 0.15
35 23 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
TATTAATTTAATATATAAATAATAATTTAAATAAA
Found at i:1290658 original size:16 final size:16
Alignment explanation
Indices: 1290637--1290680 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
1290627 TTTATAATTA
*
1290637 AATTTAAATAAATATT
1 AATTTAAATAAATAAT
1290653 AATTTATTATATAAATAAT
1 AATTTA--A-ATAAATAAT
1290672 AATTTAAAT
1 AATTTAAAT
1290681 TTAAAACATT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 8 0.33
17 1 0.04
18 1 0.04
19 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATAAATAAT
Found at i:1290696 original size:13 final size:13
Alignment explanation
Indices: 1290678--1290723 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1290668 TAATAATTTA
1290678 AATTTA-AAACATT
1 AATTTATAAA-ATT
1290691 AATTTATAAAA-T
1 AATTTATAAAATT
1290703 AATTTATAAAAATT
1 AATTTAT-AAAATT
1290717 AAATTTA
1 -AATTTA
1290724 ATGTGGGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.28
13 11 0.38
14 4 0.14
15 6 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTTATAAAATT
Found at i:1295107 original size:19 final size:19
Alignment explanation
Indices: 1295085--1295125 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1295075 AGAATGCTTC
1295085 AGAGAGCTCAATAACTTTT
1 AGAGAGCTCAATAACTTTT
*
1295104 AGAGAGCTCAATAGCTTTT
1 AGAGAGCTCAATAACTTTT
1295123 AGA
1 AGA
1295126 TCAGTGCAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (19 bp):
AGAGAGCTCAATAACTTTT
Found at i:1299159 original size:14 final size:13
Alignment explanation
Indices: 1299140--1299183 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1299130 TAATTAATTT
*
1299140 TAATTATTTTAAAA
1 TAATTATTAT-AAA
1299154 TAATTATTATAAA
1 TAATTATTATAAA
1299167 TAATATATTATATAA
1 TAAT-TATTATA-AA
1299182 TA
1 TA
1299184 TCAAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 16 0.59
15 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTATTATAAA
Found at i:1302358 original size:17 final size:18
Alignment explanation
Indices: 1302323--1302358 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1302313 AAATTTTTTC
1302323 ATATTTAAAAATTTATATT
1 ATATTTAAAAA-TTATATT
1302342 ATATTTAAAAA-TATATT
1 ATATTTAAAAATTATATT
1302359 TAATCGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTTAAAAATTATATT
Found at i:1309962 original size:4 final size:4
Alignment explanation
Indices: 1309953--1309978 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1309943 GATGGACAAA
1309953 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1309979 TCATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1314604 original size:3 final size:3
Alignment explanation
Indices: 1314596--1314624 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1314586 GTCCTTTTCA
1314596 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1314625 TGTTGATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1325381 original size:17 final size:17
Alignment explanation
Indices: 1325348--1325397 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1325338 TATTTATATT
* *
1325348 TATATAAATAATAATAA
1 TATAAAAATAATTATAA
* *
1325365 TTTAAATATAATTATAA
1 TATAAAAATAATTATAA
1325382 TATAAAAATAA-TATAA
1 TATAAAAATAATTATAA
1325398 AGATAATAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TATAAAAATAATTATAA
Found at i:1325398 original size:28 final size:27
Alignment explanation
Indices: 1325349--1325418 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
1325339 ATTTATATTT
* * *
1325349 ATATAA-ATAATAATAATTTAAATATA
1 ATATAATATAAAAATAATATAAAGATA
1325375 ATTATAATATAAAAATAATATAAAGATA
1 A-TATAATATAAAAATAATATAAAGATA
*
1325403 ATAGTAATATATAAAT
1 ATA-TAATATAAAAAT
1325419 TACAAAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 7 0.19
28 29 0.78
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
ATATAATATAAAAATAATATAAAGATA
Found at i:1335368 original size:14 final size:14
Alignment explanation
Indices: 1335345--1335401 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1335335 ATTAAAATAC
*
1335345 TTTATATTTATTTA
1 TTTATTTTTATTTA
1335359 TTTATTTTTATTTTA
1 TTTATTTTTA-TTTA
1335374 TATTATTTTTATTATA
1 T-TTATTTTTATT-TA
*
1335390 TTT-TTATTATTT
1 TTTATTTTTATTT
1335402 TTCATGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.03
14 16 0.42
15 9 0.24
16 12 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:1335373 original size:25 final size:27
Alignment explanation
Indices: 1335345--1335397 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1335335 ATTAAAATAC
1335345 TTTATATT-TATTTATT-TATTTTTAT
1 TTTATATTATATTTATTATATTTTTAT
*
1335370 TTTATATTATTTTTATTATATTTTTAT
1 TTTATATTATATTTATTATATTTTTAT
1335397 T
1 T
1335398 ATTTTTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.32
26 7 0.28
27 10 0.40
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTATATTATATTTATTATATTTTTAT
Found at i:1335399 original size:25 final size:24
Alignment explanation
Indices: 1335345--1335397 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 24
1335335 ATTAAAATAC
1335345 TTTATATTTATTTATTTATTTTTA
1 TTTATATTTATTTATTTATTTTTA
*
1335369 TTTTATATTATTTTTATTATATTTTTA
1 -TTTATATT-TATTTATT-TATTTTTA
1335396 TT
1 TT
1335398 ATTTTTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 9 0.36
27 8 0.32
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTATATTTATTTATTTATTTTTA
Found at i:1335411 original size:11 final size:9
Alignment explanation
Indices: 1335346--1335403 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 9
1335336 TTAAAATACT
*
1335346 TTATATTTA
1 TTATTTTTA
*
1335355 TTTATTTATTT
1 -TTATTT-TTA
1335366 TTATTTTATA
1 TTATTTT-TA
1335376 TTATTTTTA
1 TTATTTTTA
1335385 TTATATTTTTA
1 -T-TATTTTTA
1335396 TTATTTTT
1 TTATTTTT
1335404 CATGTATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 10 0.24
10 21 0.51
11 10 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1335411 original size:20 final size:21
Alignment explanation
Indices: 1335346--1335403 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
1335336 TTAAAATACT
1335346 TTATA-TTTAT-TTATTTATT-
1 TTATATTTTATATTATTT-TTA
1335365 TT-TATTTTATATTATTTTTA
1 TTATATTTTATATTATTTTTA
1335385 TTATATTTT-TATTATTTTT
1 TTATATTTTATATTATTTTT
1335404 CATGTATTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 18 0.51
21 6 0.17
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATATTTTATATTATTTTTA
Found at i:1345028 original size:13 final size:14
Alignment explanation
Indices: 1344986--1345029 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1344976 ATCCTATTTA
1344986 TAAATATAATAGTAT
1 TAAATATAATA-TAT
1345001 TAAATATAATA-AT
1 TAAATATAATATAT
*
1345014 TAACTA-AATATAT
1 TAAATATAATATAT
1345027 TAA
1 TAA
1345030 GTGAACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 4 0.15
13 12 0.44
15 11 0.41
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (14 bp):
TAAATATAATATAT
Found at i:1348915 original size:34 final size:31
Alignment explanation
Indices: 1348858--1348923 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 31
1348848 AATCGAGTAA
1348858 ATTAAAAATTTTAATTTATTATTTAAAATAAT
1 ATTAAAAATTTTAATTTATTATTT-AAATAAT
*
1348890 ATTAAAAATTTTATTTTTTATTATTTAAATAAT
1 ATTAAAAATTTTA--ATTTATTATTTAAATAAT
1348923 A
1 A
1348924 ATTTAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 13 0.42
33 8 0.26
34 10 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTAAAAATTTTAATTTATTATTTAAATAAT
Found at i:1349898 original size:13 final size:15
Alignment explanation
Indices: 1349877--1349913 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1349867 ATATATATAT
1349877 ATATTAATTAATTA-
1 ATATTAATTAATTAG
*
1349891 AT-TTAATTGATTAG
1 ATATTAATTAATTAG
1349905 ATATTAATT
1 ATATTAATT
1349914 TAAAAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
ATATTAATTAATTAG
Found at i:1350016 original size:15 final size:15
Alignment explanation
Indices: 1349983--1350033 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1349973 ATTTTTTAAT
*
1349983 AAATTAACTCAAATT-
1 AAATTAAAT-AAATTA
*
1349998 AAATTAAATTAATTA
1 AAATTAAATAAATTA
*
1350013 AAATTTAATAAATTCA
1 AAATTAAATAAATT-A
1350029 AAATT
1 AAATT
1350034 TTGACAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 4 0.13
15 20 0.67
16 6 0.20
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAATAAATTA
Found at i:1350272 original size:5 final size:5
Alignment explanation
Indices: 1350262--1350353 Score: 56
Period size: 5 Copynumber: 19.6 Consensus size: 5
1350252 ATATAATAAA
* *
1350262 TATAT TATAT TA-AT CATAT T-TAAT T-TAT TATAT CATAT T-TAT TATAT
1 TATAT TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TATAT
* * * *
1350309 TATTTT TATAT T-TAT T-TAA TATA- TACAT CATAT T-TAT TATAT TAT
1 TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1350354 TTTTATATCT
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
4 25 0.37
5 39 0.57
6 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1350294 original size:14 final size:13
Alignment explanation
Indices: 1350262--1350374 Score: 72
Period size: 14 Copynumber: 8.4 Consensus size: 13
1350252 ATATAATAAA
*
1350262 TATATTATATTAAT
1 TATATT-TATTTAT
*
1350276 CATATTTAATTTAT
1 TATATTT-ATTTAT
*
1350290 TATATCATATTTAT
1 TATAT-TTATTTAT
1350304 TATA-TTATTT-T
1 TATATTTATTTAT
1350315 TATATTTATTTAAT
1 TATATTTATTT-AT
*
1350329 ATATACATCATATTTAT
1 -TAT--AT-TTATTTAT
1350346 TATA-TTATTT-T
1 TATATTTATTTAT
* *
1350357 TATATCTATTTAA
1 TATATTTATTTAT
1350370 TATAT
1 TATAT
1350375 ACCTCATATT
Statistics
Matches: 79, Mismatches: 9, Indels: 23
0.71 0.08 0.21
Matches are distributed among these distances:
11 10 0.13
12 21 0.27
13 6 0.08
14 26 0.33
15 4 0.05
16 3 0.04
17 4 0.05
18 5 0.06
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:1350298 original size:19 final size:19
Alignment explanation
Indices: 1350264--1350353 Score: 94
Period size: 19 Copynumber: 4.6 Consensus size: 19
1350254 ATAATAAATA
1350264 TATTATATTA-ATCATATT
1 TATTATATTATATCATATT
1350282 TAATT-TATTATATCATATT
1 T-ATTATATTATATCATATT
* *
1350301 TATTATATTATTTTTATATT
1 TATTATATTA-TATCATATT
*
1350321 TATTTAATATATACATCATATT
1 TA-TT-ATAT-TATATCATATT
1350343 TATTATATTAT
1 TATTATATTAT
1350354 TTTTATATCT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
18 9 0.15
19 19 0.32
20 13 0.22
21 4 0.07
22 12 0.20
23 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATATTATATCATATT
Found at i:1350317 original size:11 final size:12
Alignment explanation
Indices: 1350284--1350374 Score: 69
Period size: 12 Copynumber: 6.9 Consensus size: 12
1350274 ATCATATTTA
1350284 ATTTATTATATCAT
1 ATTTATTATAT--T
1350298 ATTTATTATATT
1 ATTTATTATATT
1350310 ATTT-TTATATTT
1 ATTTATTATA-TT
1350322 ATTTAATATATACATCAT
1 ATTT-AT-TAT--AT--T
1350340 ATTTATTATATT
1 ATTTATTATATT
1350352 ATTT-TTATATCT
1 ATTTATTATAT-T
*
1350364 ATTTAATATAT
1 ATTTATTATAT
1350375 ACCTCATATT
Statistics
Matches: 66, Mismatches: 1, Indels: 21
0.75 0.01 0.24
Matches are distributed among these distances:
11 11 0.17
12 21 0.32
13 5 0.08
14 14 0.21
15 3 0.05
16 4 0.06
17 3 0.05
18 5 0.08
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTTATTATATT
Found at i:1350350 original size:9 final size:9
Alignment explanation
Indices: 1350264--1350351 Score: 51
Period size: 9 Copynumber: 10.0 Consensus size: 9
1350254 ATAATAAATA
1350264 TATTATATT
1 TATTATATT
* *
1350273 AATCATATT
1 TATTATATT
1350282 TAATT-TATT
1 T-ATTATATT
*
1350291 ATATCATATT
1 -TATTATATT
1350301 TATTATA-T
1 TATTATATT
1350309 TATT-T-TT
1 TATTATATT
1350316 ATATT-TATT
1 -TATTATATT
* *
1350325 TAATATATA
1 TATTATATT
* *
1350334 CATCATATT
1 TATTATATT
1350343 TATTATATT
1 TATTATATT
1350352 ATTTTTATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
7 2 0.03
8 13 0.22
9 36 0.62
10 7 0.12
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATATT
Found at i:1350408 original size:30 final size:30
Alignment explanation
Indices: 1350351--1350411 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
1350341 TTTATTATAT
* *
1350351 TATTTTTATATCTATTTAATATATACCTCA
1 TATTTTTATATCTATTCAAAATATACCTCA
1350381 TATTTTTATATCTATTCCAAAAT-TACCTCA
1 TATTTTTATATCTATT-CAAAATATACCTCA
1350411 T
1 T
1350412 CTATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTTATATCTATTCAAAATATACCTCA
Found at i:1350847 original size:13 final size:16
Alignment explanation
Indices: 1350829--1350868 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1350819 CTGAGAGGGC
1350829 TTTTTAT-TTT-T-CT
1 TTTTTATATTTGTACT
1350842 TTTTTATATTTGTACTT
1 TTTTTATATTTGTAC-T
1350859 TTTTTATATT
1 TTTTTATATT
1350869 AAACAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 1 0.04
16 1 0.04
17 11 0.48
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTATATTTGTACT
Found at i:1351206 original size:2 final size:2
Alignment explanation
Indices: 1351201--1351230 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1351191 TTCTTTTTTA
1351201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1351231 CAAGGGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351923 original size:22 final size:23
Alignment explanation
Indices: 1351891--1351934 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1351881 TGCTTTTCAT
1351891 TTTGATC-AAAATTAAGATGAAG
1 TTTGATCAAAAATTAAGATGAAG
*
1351913 TTTGATTAAAAATTAAGATGAA
1 TTTGATCAAAAATTAAGATGAA
1351935 CATTCCTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.48, C:0.02, G:0.16, T:0.34
Consensus pattern (23 bp):
TTTGATCAAAAATTAAGATGAAG
Found at i:1360583 original size:20 final size:22
Alignment explanation
Indices: 1360548--1360592 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1360538 TTAAAAAATT
*
1360548 TTAAAAATATATATTA-TATGA
1 TTAAAAATATAAATTATTATGA
1360569 TTAAAAA-ATAAATTATTATGA
1 TTAAAAATATAAATTATTATGA
1360590 TTA
1 TTA
1360593 TATTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TTAAAAATATAAATTATTATGA
Found at i:1360693 original size:38 final size:38
Alignment explanation
Indices: 1360624--1360706 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
1360614 TTTAAAATTA
**
1360624 ATTTTTAAATTATAATTATATTTTTTTATTTTAAAAAAAT
1 ATTTTTAAATTAT-ATTATATTTTTAAATTTT-AAAAAAT
* * *
1360664 ATTTTTATATTAT-TTTTATTTTTAAATTTTAAAATAT
1 ATTTTTAAATTATATTATATTTTTAAATTTTAAAAAAT
1360701 ATTTTT
1 ATTTTT
1360707 TTTAATATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
37 12 0.32
38 14 0.37
40 12 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (38 bp):
ATTTTTAAATTATATTATATTTTTAAATTTTAAAAAAT
Found at i:1360707 original size:38 final size:39
Alignment explanation
Indices: 1360614--1360707 Score: 95
Period size: 38 Copynumber: 2.4 Consensus size: 39
1360604 AAATATATAA
* **
1360614 TTTAAAAT-TAATTTTTAAATTATAATTATATTTTTTTAT
1 TTTAAAATATATTTTTTAAATTAT-ATTATATTTTTAAAT
* * *
1360653 TTTAAAA-AAATATTTTTATATTAT-TTTTATTTTTAAAT
1 TTTAAAATATAT-TTTTTAAATTATATTATATTTTTAAAT
1360691 TTTAAAATATATTTTTT
1 TTTAAAATATATTTTTT
1360708 TTAATATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
38 23 0.51
39 11 0.24
40 11 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTAAAATATATTTTTTAAATTATATTATATTTTTAAAT
Found at i:1361048 original size:24 final size:23
Alignment explanation
Indices: 1361007--1361051 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1360997 TGGAGTCGAA
*
1361007 TTTAAATTTGAATGAGTTTTAGT
1 TTTAAATTTAAATGAGTTTTAGT
*
1361030 TTTAATATTTAAATTAGTTTTA
1 TTTAA-ATTTAAATGAGTTTTA
1361052 AGATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (23 bp):
TTTAAATTTAAATGAGTTTTAGT
Found at i:1361061 original size:18 final size:18
Alignment explanation
Indices: 1361025--1361063 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1361015 TGAATGAGTT
* **
1361025 TTAGTTTTAATATTTAAA
1 TTAGTTTTAAGATAAAAA
1361043 TTAGTTTTAAGATAAAAA
1 TTAGTTTTAAGATAAAAA
1361061 TTA
1 TTA
1361064 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
TTAGTTTTAAGATAAAAA
Found at i:1363474 original size:11 final size:11
Alignment explanation
Indices: 1363455--1363489 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1363445 AAAAATTAAA
1363455 AATTAAAAATT
1 AATTAAAAATT
*
1363466 AATTGAAAATT
1 AATTAAAAATT
*
1363477 ATTTAAAAATT
1 AATTAAAAATT
1363488 AA
1 AA
1363490 ATATGTTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:1364012 original size:2 final size:2
Alignment explanation
Indices: 1363999--1364028 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1363989 TGTTGAATTG
*
1363999 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1364029 TATCTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1371056 original size:28 final size:28
Alignment explanation
Indices: 1371024--1371082 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
1371014 TATTTACTTG
1371024 GACCTACACACTACCGAAACAGAAGTGT
1 GACCTACACACTACCGAAACAGAAGTGT
1371052 GACCTACACACTACCGAAACAGAAGTGT
1 GACCTACACACTACCGAAACAGAAGTGT
1371080 GAC
1 GAC
1371083 TCAGTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.14
Consensus pattern (28 bp):
GACCTACACACTACCGAAACAGAAGTGT
Found at i:1386184 original size:2 final size:2
Alignment explanation
Indices: 1386177--1386212 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1386167 GAAGCAGCAA
1386177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1386213 CTTGCTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1386553 original size:2 final size:2
Alignment explanation
Indices: 1386546--1386594 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1386536 ACGTAGAATA
*
1386546 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1386587 TT AT AT AT
1 AT AT AT AT
1386595 CTGCCACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1387237 original size:2 final size:2
Alignment explanation
Indices: 1387230--1387276 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1387220 TTTTAATGGA
1387230 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1387272 AG AG A
1 AG AG A
1387277 CTCTCTCATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1388151 original size:4 final size:4
Alignment explanation
Indices: 1388142--1388171 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1388132 GTAATTTCAT
1388142 TATG TATG TATGG TATG TATG TATG TATG T
1 TATG TATG TAT-G TATG TATG TATG TATG T
1388172 TCTTTCCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1390067 original size:7 final size:7
Alignment explanation
Indices: 1390055--1390083 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1390045 CCGTCTACAT
1390055 AGGCGAA
1 AGGCGAA
1390062 AGGCGAA
1 AGGCGAA
1390069 AGGCGAA
1 AGGCGAA
1390076 AGGCGAA
1 AGGCGAA
1390083 A
1 A
1390084 TCTAGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.41, T:0.00
Consensus pattern (7 bp):
AGGCGAA
Found at i:1393548 original size:2 final size:2
Alignment explanation
Indices: 1393541--1393569 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1393531 CATGAGTGAT
1393541 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1393570 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1393574 original size:2 final size:2
Alignment explanation
Indices: 1393569--1393605 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1393559 ACACACACAC
1393569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1393606 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1393610 original size:2 final size:2
Alignment explanation
Indices: 1393605--1393651 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1393595 ATATATATAT
1393605 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1393647 AG AG A
1 AG AG A
1393652 AAGGGACCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1398836 original size:13 final size:12
Alignment explanation
Indices: 1398803--1398856 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1398793 GAATATATTA
*
1398803 AAAATTATTTTT
1 AAAATTAATTTT
*
1398815 AAAAATAATTTT
1 AAAATTAATTTT
1398827 ATAAATTAA--TT
1 A-AAATTAATTTT
1398838 -AAATTAAATTTT
1 AAAATT-AATTTT
1398850 AAAATTA
1 AAAATTA
1398857 TTCAATCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
9 5 0.15
10 2 0.06
11 2 0.06
12 14 0.41
13 11 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAATTAATTTT
Found at i:1398868 original size:21 final size:22
Alignment explanation
Indices: 1398820--1398869 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1398810 TTTTTAAAAA
1398820 TAATTTTATAAATTAATTAAAT
1 TAATTTTATAAATTAATTAAAT
*
1398842 TAAATTTTA-AAATT-ATTCAAT
1 T-AATTTTATAAATTAATTAAAT
1398863 CTAATTT
1 -TAATTT
1398870 GAAGCTGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 11 0.44
22 7 0.28
23 7 0.28
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTTATAAATTAATTAAAT
Found at i:1399552 original size:18 final size:18
Alignment explanation
Indices: 1399531--1399568 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1399521 CCCCCAAACG
*
1399531 AAGCCCAATCACCAACCC
1 AAGCCCAATCAACAACCC
1399549 AAGCCCAATCAACAACCC
1 AAGCCCAATCAACAACCC
1399567 AA
1 AA
1399569 ATTCAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.45, G:0.05, T:0.05
Consensus pattern (18 bp):
AAGCCCAATCAACAACCC
Found at i:1399636 original size:13 final size:13
Alignment explanation
Indices: 1399613--1399648 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1399603 TTTAGTAATG
*
1399613 ATTCAACACCCAA
1 ATTCAAAACCCAA
*
1399626 ATTCACAACCCAA
1 ATTCAAAACCCAA
1399639 ATTCAAAACC
1 ATTCAAAACC
1399649 GTCGGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (13 bp):
ATTCAAAACCCAA
Found at i:1410638 original size:2 final size:2
Alignment explanation
Indices: 1410631--1410673 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1410621 GCCATAACCC
1410631 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1410673 C
1 C
1410674 ACAGCTTACG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1413400 original size:2 final size:2
Alignment explanation
Indices: 1413393--1413419 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1413383 TATTTTGGTT
1413393 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1413420 CGCATCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1413840 original size:123 final size:122
Alignment explanation
Indices: 1413685--1414386 Score: 671
Period size: 123 Copynumber: 5.6 Consensus size: 122
1413675 TTTGCAATCG
* * ** * * *
1413685 CGGCAGCAATTCCTGTAGAGCTTGGCAGGCTTTGGGCGGCGTCTTTAAACACTGAAGTTACCTTG
1 CGGCAGC-ATTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTG
*
1413750 TTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTC-CGCTGCACACTAT
65 TTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTC-CTGCACACTGT
*
1413808 CGGCAGTAATTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTG
1 CGGCAG-CATTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTG
* * * * * * *
1413873 TTGAACTGTTCAGGGGACGGTGCTTCAGCCCATGAC-AAAGCAGTATCCTTCAAACTCT
65 TTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAA-CAGTCTCCTGCACACTGT
* * * * * **
1413931 TGGCAGCA-TCAGCTGCAGAGCTTGATAGGCTTAGAGCGGCGTCGCTGATATCTGAAGTAACCTT
1 CGGCAGCATTC--CTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTT
** * *
1413995 GTTTACCTGTTCACCGGAAGGTGCTTCAGCCCATGACGAAACAGTCT-CAGTCACACCGT
64 GTTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTG-CACACTGT
*
1414054 CGGCAGCATCTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTG
1 CGGCAGCAT-TCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTG
* * *
1414119 TTGAACTGTTCAGGGGAAGGTGCTTCAGGCCCTTCAGCCCAGGACGAAACAGTCTCC-GTCACAC
65 TTTACCTGTTCAGGGGAA-G-G--T---G--CTTCAGCCCATGACGAAACAGTCTCCTG-CACAC
*
1414183 GGT
120 TGT
* * * * *
1414186 CGGCAGCATCTCCTGCCGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCCCTGAAGTAGCCATG
1 CGGCAGCAT-TCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTG
** * ** * ** * *
1414251 TTTACCTGTTCAGGGGAAAATGCTGCAAACAATGACGAGGCGGTCTCCTTCACACTGT
65 TTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTGCACACTGT
* * * ** * *
1414309 CGGCAGCATCTCCTGCAGAGCTTGACAGACCTAGGGCGAAGTCACTCAA-CTGC-GAAGTAGCCT
1 CGGCAGCAT-TCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCT-AATC-GCTGAAGTAACCT
1414372 TGTTTACCTGTTCAG
63 TGTTTACCTGTTCAG
1414387 AGGTAAATGC
Statistics
Matches: 479, Mismatches: 78, Indels: 44
0.80 0.13 0.07
Matches are distributed among these distances:
121 2 0.00
122 5 0.01
123 349 0.73
124 8 0.02
125 4 0.01
127 1 0.00
128 1 0.00
130 1 0.00
132 107 0.22
133 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.24
Consensus pattern (122 bp):
CGGCAGCATTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTGT
TTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTGCACACTGT
Found at i:1414260 original size:132 final size:132
Alignment explanation
Indices: 1414018--1414268 Score: 403
Period size: 132 Copynumber: 1.9 Consensus size: 132
1414008 CCGGAAGGTG
*
1414018 CTTCAGCCCATGACGAAACAGTCTCAGTCACACCGTCGGCAGCATCTCCTGCAGAGCTTGACAGG
1 CTTCAGCCCAGGACGAAACAGTCTCAGTCACACCGTCGGCAGCATCTCCTGCAGAGCTTGACAGG
* *
1414083 CTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTGTTGAACTGTTCAGGGGAAGGTGCTTCAGG
66 CTTTGGGCGGCGTCGCTAATCCCTGAAGAAACCATGTTGAACTGTTCAGGGGAAGGTGCTTCAGG
1414148 CC
131 CC
* * * *
1414150 CTTCAGCCCAGGACGAAACAGTCTCCGTCACACGGTCGGCAGCATCTCCTGCCGAGCTTGATAGG
1 CTTCAGCCCAGGACGAAACAGTCTCAGTCACACCGTCGGCAGCATCTCCTGCAGAGCTTGACAGG
* * * *
1414215 CTTTGGGCGGCGTCGCTAATCCCTGAAGTAGCCATGTTTACCTGTTCAGGGGAA
66 CTTTGGGCGGCGTCGCTAATCCCTGAAGAAACCATGTTGAACTGTTCAGGGGAA
1414269 AATGCTGCAA
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 108 1.00
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.22
Consensus pattern (132 bp):
CTTCAGCCCAGGACGAAACAGTCTCAGTCACACCGTCGGCAGCATCTCCTGCAGAGCTTGACAGG
CTTTGGGCGGCGTCGCTAATCCCTGAAGAAACCATGTTGAACTGTTCAGGGGAAGGTGCTTCAGG
CC
Found at i:1414313 original size:255 final size:245
Alignment explanation
Indices: 1413685--1414336 Score: 756
Period size: 246 Copynumber: 2.6 Consensus size: 245
1413675 TTTGCAATCG
* ** ** *
1413685 CGGCAGCAAT-TCCTGTAGAGCTTGGCAGGCTTTGGGCGGCGTCTTTAAACACTGAAGTTACCTT
1 CGGCAGC-ATCTCCTGCAGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCACTGAAG-TACCTT
* *
1413749 GTTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTC-CGCTGCACACTATCGGCA
64 GTTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTC-CTTCACACTGTCGGCA
* *
1413813 GTAAT-TCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGTAACCTTGTTGA
128 G-CATCTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTGTTGA
* * *
1413877 ACTGTTCAGGGGACGGTGCTTCAGCCCATGACAAAGCAGTATCCTTCAAACTCT
192 ACTGTTCAGGGGACGGTGCTTCAGCCCAGGACAAAGCAGTATCCGTCAAACGCT
* ** * * *
1413931 TGGCAGCATCAGCTGCAGAGCTTGATAGGCTTAGAGCGGCGTCGCTGAT-ATCTGAAGTAACCTT
1 CGGCAGCATCTCCTGCAGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCA-CTGAAGT-ACCTT
** ** *
1413995 GTTTACCTGTTCACCGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCAGTCACACCGTCGGCAG
64 GTTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTTCACACTGTCGGCAG
1414060 CATCTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTGTTGAAC
129 CATCTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTGTTGAAC
* * * *
1414125 TGTTCAGGGGAAGGTGCTTCAGGCCCTTCAGCCCAGGACGAAA-CAGTCTCCGTCACACGGT
194 TGTTCAGGGG-ACG-G--T---G--CTTCAGCCCAGGAC-AAAGCAGTATCCGTCAAACGCT
* * *
1414186 CGGCAGCATCTCCTGCCGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCCCTGAAGTAGCCATG
1 CGGCAGCATCTCCTGCAGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCACTGAAGTA-CCTTG
** * ** * ** *
1414251 TTTACCTGTTCAGGGGAAAATGCTGCAAACAATGACGAGGCGGTCTCCTTCACACTGTCGGCAGC
65 TTTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTTCACACTGTCGGCAGC
1414316 ATCTCCTGCAGAGCTTGACAG
130 ATCTCCTGCAGAGCTTGACAG
1414337 ACCTAGGGCG
Statistics
Matches: 338, Mismatches: 51, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
245 6 0.02
246 171 0.51
247 3 0.01
248 1 0.00
250 1 0.00
253 1 0.00
254 1 0.00
255 151 0.45
256 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (245 bp):
CGGCAGCATCTCCTGCAGAGCTTGATAGGCTTTGGGCGGCGTCGCTAATCACTGAAGTACCTTGT
TTACCTGTTCAGGGGAAGGTGCTTCAGCCCATGACGAAACAGTCTCCTTCACACTGTCGGCAGCA
TCTCCTGCAGAGCTTGACAGGCTTTGGGCGGCGTCGCTAATCGCTGAAGAAACCTTGTTGAACTG
TTCAGGGGACGGTGCTTCAGCCCAGGACAAAGCAGTATCCGTCAAACGCT
Found at i:1415653 original size:19 final size:19
Alignment explanation
Indices: 1415616--1415653 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1415606 ATAATTAAAT
*
1415616 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
1415635 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
1415654 ATTTGAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:1423773 original size:16 final size:16
Alignment explanation
Indices: 1423733--1423775 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1423723 TTATTAAATT
*
1423733 TTAA-AATTATTATTA
1 TTAATAATTTTTATTA
*
1423748 TAAATAATTTTTATTA
1 TTAATAATTTTTATTA
1423764 TTAATAATTTTT
1 TTAATAATTTTT
1423776 TATCCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 3 0.12
16 21 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATAATTTTTATTA
Found at i:1425827 original size:2 final size:2
Alignment explanation
Indices: 1425820--1425853 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1425810 TAAGTTGGTG
1425820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1425854 GTTATTGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1428037 original size:2 final size:2
Alignment explanation
Indices: 1428030--1428060 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1428020 CTCTTCCATT
1428030 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1428061 TTGTATAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1436962 original size:14 final size:13
Alignment explanation
Indices: 1436929--1436966 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
1436919 TAAAATGTTG
1436929 AATAGATATAA-A
1 AATAGATATAATA
1436941 AATA-ATATAATA
1 AATAGATATAATA
1436953 AATATGATATAATA
1 AATA-GATATAATA
1436967 TAATTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.26
12 9 0.39
14 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (13 bp):
AATAGATATAATA
Found at i:1436984 original size:19 final size:19
Alignment explanation
Indices: 1436942--1436987 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1436932 AGATATAAAA
*
1436942 ATAATATAATAAATATGAT
1 ATAATATAATAAATAAGAT
*
1436961 ATAATATAATTATATAAGAT
1 ATAATATAA-TAAATAAGAT
1436981 -TAATATA
1 ATAATATA
1436988 GGTATCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
ATAATATAATAAATAAGAT
Found at i:1438422 original size:2 final size:2
Alignment explanation
Indices: 1438415--1438452 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1438405 CTTCAGGAAG
1438415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1438453 TCATGGTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1439403 original size:21 final size:20
Alignment explanation
Indices: 1439379--1439445 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1439369 ATTGATACAT
*
1439379 TTTTAGTAATATTTAATATTA
1 TTTT-GTAATATTTAATATAA
*
1439400 TTTTGATAATATTTTATATAA
1 TTTTG-TAATATTTAATATAA
*
1439421 TTTTGGTAAGT-TTTATTATAA
1 TTTT-GTAA-TATTTAATATAA
1439442 TTTT
1 TTTT
1439446 TTATAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTGTAATATTTAATATAA
Found at i:1439449 original size:10 final size:10
Alignment explanation
Indices: 1439378--1439459 Score: 51
Period size: 10 Copynumber: 7.7 Consensus size: 10
1439368 CATTGATACA
1439378 TTTTTAGTAAT
1 TTTTTA-TAAT
* *
1439389 ATTTAAT-AT
1 TTTTTATAAT
1439398 TATTTTGATAAT
1 T-TTTT-ATAAT
1439410 ATTTTATATAAT
1 -TTTT-TATAAT
* *
1439422 TTTGGTA-AGT
1 TTT-TTATAAT
1439432 TTTATTATAAT
1 TTT-TTATAAT
1439443 TTTTTATAAT
1 TTTTTATAAT
1439453 TTTTTAT
1 TTTTTAT
1439460 TTTATTTTGT
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
9 2 0.04
10 25 0.45
11 16 0.29
12 10 0.18
13 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:1439466 original size:22 final size:22
Alignment explanation
Indices: 1439431--1439498 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
1439421 TTTTGGTAAG
*
1439431 TTTTATTATAATTTTTTATAATT
1 TTTTATT-TTATTTTTTATAATT
*
1439454 TTTTATTTTATTTTGTTA-ACTT
1 TTTTATTTTATTTT-TTATAATT
**
1439476 TAATATTTT-TTTTTTGATAATT
1 TTTTATTTTATTTTTT-ATAATT
1439498 T
1 T
1439499 ATGATATAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.05
21 5 0.14
22 20 0.54
23 10 0.27
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTTATTTTATTTTTTATAATT
Found at i:1439499 original size:22 final size:21
Alignment explanation
Indices: 1439442--1439499 Score: 55
Period size: 23 Copynumber: 2.7 Consensus size: 21
1439432 TTTATTATAA
**
1439442 TTTTTT-ATAATTTTTTATTT
1 TTTTTTGATAATTTAATATTT
* *
1439462 TATTTTGTTAACTTTAATATTTT
1 TTTTTTGATAA-TTTAATA-TTT
1439485 TTTTTTGATAATTTA
1 TTTTTTGATAATTTA
1439500 TGATATAACT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 5 0.17
21 3 0.10
22 9 0.31
23 12 0.41
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTTTTGATAATTTAATATTT
Found at i:1439741 original size:12 final size:12
Alignment explanation
Indices: 1439726--1439762 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1439716 TTCAATATAA
1439726 TTTTGATAATTT
1 TTTTGATAATTT
1439738 TTTTG-TAATTAT
1 TTTTGATAATT-T
1439750 TTTT-ATAATTT
1 TTTTGATAATTT
1439761 TT
1 TT
1439763 AAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTGATAATTT
Found at i:1439772 original size:21 final size:21
Alignment explanation
Indices: 1439712--1439836 Score: 56
Period size: 21 Copynumber: 5.8 Consensus size: 21
1439702 TTATCTTAAC
* *
1439712 ATTTTTCAATATAATTTTGATA
1 ATTTTT-AAAATAATTTTTATA
** *
1439734 ATTTTTTTGTAATTATTTTTATA
1 A--TTTTTAAAATAATTTTTATA
*
1439757 ATTTTTAAAATAATTTTAATA
1 ATTTTTAAAATAATTTTTATA
** * * * *
1439778 ACATTTAATATAACTTCTCACA
1 ATTTTTAAAATAA-TTTTTATA
*
1439800 ACTTTTT-ATATAA-TTTTATTA
1 A-TTTTTAAAATAATTTTTA-TA
*
1439821 ATTTTTAAAATGATTT
1 ATTTTTAAAATAATTT
1439837 GGTAACCTAA
Statistics
Matches: 74, Mismatches: 22, Indels: 14
0.67 0.20 0.13
Matches are distributed among these distances:
20 8 0.11
21 32 0.43
22 15 0.20
23 14 0.19
24 5 0.07
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTTAAAATAATTTTTATA
Found at i:1439783 original size:23 final size:23
Alignment explanation
Indices: 1439708--1439783 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 23
1439698 AATATTATCT
* *
1439708 TAACATTTTTCAATATAATTTTGA
1 TAACATTTTT-AAAATAATTTTAA
** ** * *
1439732 TAATTTTTTTGTAATTATTTTTA
1 TAACATTTTTAAAATAATTTTAA
1439755 T-A-ATTTTTAAAATAATTTTAA
1 TAACATTTTTAAAATAATTTTAA
1439776 TAACATTT
1 TAACATTT
1439784 AATATAACTT
Statistics
Matches: 38, Mismatches: 12, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
21 15 0.39
22 2 0.05
23 13 0.34
24 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
TAACATTTTTAAAATAATTTTAA
Found at i:1444232 original size:4 final size:4
Alignment explanation
Indices: 1444223--1444250 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1444213 AGATTGACTG
1444223 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1444251 TTGCATATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:1445017 original size:259 final size:259
Alignment explanation
Indices: 1444558--1445331 Score: 1437
Period size: 259 Copynumber: 3.0 Consensus size: 259
1444548 TTCCAACAGA
1444558 AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
1 AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
* * *
1444623 TTGACAATACGTATATGCATCTCTATAATATGAATATGGCACTTGTATTAAACCTATCGTGTTAT
66 TTGACAATATGTATATGCATCTCTATAATATGAATATGACACTTGTATTAAACATATCGTGTTAT
* *
1444688 ATATTACATTATTTTAATTTGAGCTTGCCAAAATACCCACCGTTATAGAACAGTTCTTACAACAA
131 ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
1444753 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
196 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
*
1444817 AACATTAAAACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
1 AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
*
1444882 TTGACAATATGTATATGCATCTCTATAATATGAATATGACACTTGTATTAAACATGTCGTGTTAT
66 TTGACAATATGTATATGCATCTCTATAATATGAATATGACACTTGTATTAAACATATCGTGTTAT
1444947 ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
131 ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
*
1445012 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGACGTCTTTGAGTCAATCAGTAAC
196 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
*
1445076 AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAGTAGAT
1 AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
*
1445141 TTGACAATATGTATATGCATCTCTATAATATGAATATAACACTTG---TAAACATATCGTGTTAT
66 TTGACAATATGTATATGCATCTCTATAATATGAATATGACACTTGTATTAAACATATCGTGTTAT
1445203 ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
131 ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
1445268 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
196 CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
1445332 CTCACTGCAC
Statistics
Matches: 502, Mismatches: 13, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
256 144 0.29
259 358 0.71
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (259 bp):
AACATTAACACGTGTATCGTCACTAAATTATTCTGTAGAACTTCTTTGCAAGGATTTTAATAGAT
TTGACAATATGTATATGCATCTCTATAATATGAATATGACACTTGTATTAAACATATCGTGTTAT
ATATTACATTATTTTAATTTGAGCTTGCAAAAATACCCACCATTATAGAACAGTTCTTACAACAA
CGAACTACTAGAACAAAACATATGTAGTTTTATGTTTATGGATGTCTTTGAGTCAATCAGTAAC
Found at i:1447913 original size:2 final size:2
Alignment explanation
Indices: 1447908--1447938 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1447898 TTTTTCCCCC
1447908 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1447939 CGGACTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1450607 original size:23 final size:24
Alignment explanation
Indices: 1450576--1450624 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
1450566 TGGTACATTT
* *
1450576 CCTAGTCATACTTCCA-AAATTACC
1 CCTAGTCAT-CTCCCACAAAATACC
1450600 CCTA-TCATCTCCCACAAAATACC
1 CCTAGTCATCTCCCACAAAATACC
1450623 CC
1 CC
1450625 AAATTACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.24
Consensus pattern (24 bp):
CCTAGTCATCTCCCACAAAATACC
Found at i:1450830 original size:5 final size:5
Alignment explanation
Indices: 1450816--1450849 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
1450806 TTCCCTCCAT
* *
1450816 CTTTC GTTTC CTTTC CTTTC CCTTC CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
1450850 TTTTTTTCCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.03, T:0.59
Consensus pattern (5 bp):
CTTTC
Found at i:1456502 original size:96 final size:96
Alignment explanation
Indices: 1456338--1456537 Score: 391
Period size: 96 Copynumber: 2.1 Consensus size: 96
1456328 TTAAAATCAA
*
1456338 ACAAATATATATGTTGCCAATATTTAAGGCTCCTCGTGAGAAAGGTGTTAATAACAGAATACTGA
1 ACAAATATATATGTTGCCAATATTTAAGGCCCCTCGTGAGAAAGGTGTTAATAACAGAATACTGA
1456403 TACTCCCATCAAAGTAATCTTCATTTGAAAT
66 TACTCCCATCAAAGTAATCTTCATTTGAAAT
1456434 ACAAATATATATGTTGCCAATATTTAAGGCCCCTCGTGAGAAAGGTGTTAATAACAGAATACTGA
1 ACAAATATATATGTTGCCAATATTTAAGGCCCCTCGTGAGAAAGGTGTTAATAACAGAATACTGA
1456499 TACTCCCATCAAAGTAATCTTCATTTGAAAT
66 TACTCCCATCAAAGTAATCTTCATTTGAAAT
1456530 ACAAATAT
1 ACAAATAT
1456538 TTGTTAATTT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 103 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (96 bp):
ACAAATATATATGTTGCCAATATTTAAGGCCCCTCGTGAGAAAGGTGTTAATAACAGAATACTGA
TACTCCCATCAAAGTAATCTTCATTTGAAAT
Found at i:1459514 original size:25 final size:26
Alignment explanation
Indices: 1459462--1459522 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
1459452 TAATTAAAAA
* *
1459462 TAAATTTAATT-TTTATATTAAATTT
1 TAAATTTAATTATTTACATTAAATCT
*
1459487 TAAATTTAATTATTTACATTACA-CT
1 TAAATTTAATTATTTACATTAAATCT
1459512 T-AA-TTAATTAT
1 TAAATTTAATTAT
1459523 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 8 0.25
24 2 0.06
25 13 0.41
26 9 0.28
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (26 bp):
TAAATTTAATTATTTACATTAAATCT
Found at i:1460643 original size:27 final size:26
Alignment explanation
Indices: 1460613--1460687 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
1460603 TTATTAATAT
* *
1460613 ATATTTATTAATTAAATTTAAATAAAA
1 ATATATATT-ATTAAAATTAAATAAAA
* *
1460640 ATATATATTTTTAAAATTAAATTAAA
1 ATATATATTATTAAAATTAAATAAAA
*
1460666 ATA-A-AATATTAAATATTAAATA
1 ATATATATTATTAAA-ATTAAATA
1460688 CATCAAGGTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.17
25 8 0.20
26 17 0.43
27 8 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATATATTATTAAAATTAAATAAAA
Found at i:1460674 original size:31 final size:31
Alignment explanation
Indices: 1460608--1460671 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
1460598 ATTTTTTATT
*
1460608 AATATATATTTATTAATTAAATTTAAATAAA
1 AATATATATTTATTAATTAAATTAAAATAAA
1460639 AATATATATTT-TTAAAATTAAATTAAAATAAA
1 AATATATATTTATT--AATTAAATTAAAATAAA
1460671 A
1 A
1460672 TATTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 2 0.07
31 11 0.37
32 17 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
AATATATATTTATTAATTAAATTAAAATAAA
Found at i:1460685 original size:31 final size:32
Alignment explanation
Indices: 1460622--1460685 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
1460612 TATATTTATT
* * *
1460622 AATTAAATTTAAATAAAAATATATATTTTTAA
1 AATTAAATTAAAATAAAAATATATAATATTAA
1460654 AATTAAATTAAAAT-AAAATAT-TAAATATTAA
1 AATTAAATTAAAATAAAAATATAT-AATATTAA
1460685 A
1 A
1460686 TACATCAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.04
31 14 0.50
32 13 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTAAATTAAAATAAAAATATATAATATTAA
Found at i:1468484 original size:18 final size:17
Alignment explanation
Indices: 1468443--1468485 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1468433 ATTATATATT
*
1468443 TTTTAATTTCATAAAAA
1 TTTTAATTTAATAAAAA
*
1468460 TAATTAATTTAATATAAAA
1 T-TTTAATTTAATA-AAAA
1468479 TTTTAAT
1 TTTTAAT
1468486 AAAAATTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 15 0.71
19 5 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAATTTAATAAAAA
Found at i:1483396 original size:21 final size:20
Alignment explanation
Indices: 1483357--1483407 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1483347 TATATATTTT
*
1483357 ATAATTATATTTAAATAAAAA
1 ATAATTTTA-TTAAATAAAAA
* *
1483378 ATATATTTTATTAATTAAATA
1 ATA-ATTTTATTAAATAAAAA
1483399 ATAATTTTA
1 ATAATTTTA
1483408 ATTGAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.23
21 15 0.58
22 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTTTATTAAATAAAAA
Found at i:1485215 original size:18 final size:19
Alignment explanation
Indices: 1485183--1485219 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1485173 TCCAGTAAAT
*
1485183 CCCTTGATCATAAATGGAA
1 CCCTTGATCACAAATGGAA
1485202 CCCTT-ATCACAAATGGAA
1 CCCTTGATCACAAATGGAA
1485220 TCCTCCATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (19 bp):
CCCTTGATCACAAATGGAA
Found at i:1488304 original size:2 final size:2
Alignment explanation
Indices: 1488297--1488329 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1488287 TAACAACTAC
1488297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1488330 CCTTTATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.