Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 23 of 173
Found at i:6234711 original size:20 final size:19
Alignment explanation
Indices: 6234688--6234780 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 19
6234678 ACTCAAACAC
*
6234688 TAAACCTTAAACTCTAAATA
1 TAAACCATAAAC-CTAAATA
*
6234708 TAAATCATAAACCGTAAATA
1 TAAACCATAAACC-TAAATA
*
6234728 TAAACCTTAAACACTATAAT-
1 TAAACCATAAAC-CTA-AATA
* *
6234748 TATATCATAAACCGTAAATA
1 TAAACCATAAACC-TAAATA
*
6234768 TAAACCCTAAACC
1 TAAACCATAAACC
6234781 CTAATAACAA
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
19 5 0.09
20 49 0.84
21 4 0.07
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAACCATAAACCTAAATA
Found at i:6234719 original size:40 final size:39
Alignment explanation
Indices: 6234682--6234779 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 39
6234672 ACCTAAACTC
*
6234682 AAACACTAAACCTTAAACTCTA-AATATAAATCATAAACCG
1 AAACA-TAAACCTTAAACACTATAAT-TAAATCATAAACCG
* *
6234722 TAAATATAAACCTTAAACACTATAATTATATCATAAACCG
1 -AAACATAAACCTTAAACACTATAATTAAATCATAAACCG
* *
6234762 TAAATATAAACCCTAAAC
1 -AAACATAAACCTTAAAC
6234780 CCTAATAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 45 0.87
41 7 0.13
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (39 bp):
AAACATAAACCTTAAACACTATAATTAAATCATAAACCG
Found at i:6234888 original size:14 final size:14
Alignment explanation
Indices: 6234871--6234910 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6234861 CACTAAACAC
* *
6234871 TAAACCTTAAATTA
1 TAAACCCTAAAATA
*
6234885 TAAACCCTAAAATC
1 TAAACCCTAAAATA
6234899 TAAACCCTAAAA
1 TAAACCCTAAAA
6234911 CCATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCCTAAAATA
Found at i:6234902 original size:21 final size:19
Alignment explanation
Indices: 6234864--6234994 Score: 68
Period size: 21 Copynumber: 6.4 Consensus size: 19
6234854 CCTCAAACAC
* *
6234864 TAAACACTAAACCTTAAATTA
1 TAAACCCTAAAAC-TAAA-TA
6234885 TAAACCCTAAAATCTAAACCCTA
1 TAAACCCTAAAA-CTAAA---TA
* *
6234908 -AAACCATAAAAATAAACCT-
1 TAAACCCTAAAACTAAA--TA
* * *
6234927 TAAACCCTACAATTAAACA
1 TAAACCCTAAAACTAAATA
6234946 TAAACCCTAAAACTAGAATTA
1 TAAACCCTAAAACTA-AA-TA
* *
6234967 AAAACCCTAAAACCTAAACA
1 TAAACCCTAAAA-CTAAATA
6234987 TAAACCCT
1 TAAACCCT
6234995 CATTATATCA
Statistics
Matches: 87, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
19 13 0.15
20 26 0.30
21 32 0.37
22 14 0.16
23 2 0.02
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (19 bp):
TAAACCCTAAAACTAAATA
Found at i:6234993 original size:20 final size:20
Alignment explanation
Indices: 6234756--6234994 Score: 79
Period size: 20 Copynumber: 11.9 Consensus size: 20
6234746 ATTATATCAT
*
6234756 AAACCGTAAATATAAACCCTA
1 AAACC-TAAACATAAACCCTA
* *
6234777 AACCCTAATA-ACAAA--CT-
1 AAACCTAA-ACATAAACCCTA
6234794 AAACCATAAACATAAACCCTA
1 AAACC-TAAACATAAACCCTA
** **
6234815 AAATATAAGTATAAACCCT-
1 AAACCTAAACATAAACCCTA
** * *
6234834 AATTCT-ATCCTAAA--CTA
1 AAACCTAAACATAAACCCTA
* *
6234851 TAACCTCAAACACTAAACACT-
1 AAACCT-AAACA-TAAACCCTA
*
6234872 AAACCTTAAATTATAAACCCTA
1 AAACC-TAAA-CATAAACCCTA
* * *
6234894 AAATCTAAACCCTAAAACCATA
1 AAACCTAAA-CAT-AAACCCTA
* *
6234916 AAA-ATAAACCTTAAACCCTA
1 AAACCTAAA-CATAAACCCTA
* *
6234936 CAA-TTAAACATAAACCCTA
1 AAACCTAAACATAAACCCTA
* *
6234955 AAA-CTAGAATTAAAAACCCTA
1 AAACCTA-AA-CATAAACCCTA
6234976 AAACCTAAACATAAACCCT
1 AAACCTAAACATAAACCCT
6234995 CATTATATCA
Statistics
Matches: 161, Mismatches: 38, Indels: 39
0.68 0.16 0.16
Matches are distributed among these distances:
16 2 0.01
17 8 0.05
18 14 0.09
19 20 0.12
20 48 0.30
21 48 0.30
22 21 0.13
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (20 bp):
AAACCTAAACATAAACCCTA
Found at i:6235134 original size:20 final size:21
Alignment explanation
Indices: 6235111--6235163 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6235101 ACTCGAACAC
*
6235111 TAAACACTAAACCTT-AACCA
1 TAAACCCTAAACCTTAAACCA
*
6235131 TAAACCCTAAACCTTAAACCC
1 TAAACCCTAAACCTTAAACCA
6235152 TAAACCCTAAAC
1 TAAACCCTAAAC
6235164 ATTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCCTAAACCTTAAACCA
Found at i:6235148 original size:14 final size:14
Alignment explanation
Indices: 6235126--6235163 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
6235116 ACTAAACCTT
6235126 AACCATAAACCCTA
1 AACCATAAACCCTA
*
6235140 AACCTTAAACCCTA
1 AACCATAAACCCTA
*
6235154 AACCCTAAAC
1 AACCATAAAC
6235164 ATTATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (14 bp):
AACCATAAACCCTA
Found at i:6235222 original size:20 final size:20
Alignment explanation
Indices: 6235194--6235248 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
6235184 CCCAAAAATC
*
6235194 AACCTTAAACACTATAAT-TA
1 AACCATAAACACTA-AATATA
* * *
6235214 TATCATAAACAATAAATATA
1 AACCATAAACACTAAATATA
6235234 AACCATAAACACTAA
1 AACCATAAACACTAA
6235249 TGAAAAACTA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.25
Consensus pattern (20 bp):
AACCATAAACACTAAATATA
Found at i:6235243 original size:40 final size:40
Alignment explanation
Indices: 6235152--6235247 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
6235142 CCTTAAACCC
* * * **
6235152 TAAACCCTAAACATTATAATTATATTATAAACCCCAAAAA
1 TAAACCATAAACACTATAATTATATCATAAACAACAAAAA
* * * *
6235192 TCAACCTTAAACACTATAATTATATCATAAACAATAAATA
1 TAAACCATAAACACTATAATTATATCATAAACAACAAAAA
6235232 TAAACCATAAACACTA
1 TAAACCATAAACACTA
6235248 ATGAAAAACT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (40 bp):
TAAACCATAAACACTATAATTATATCATAAACAACAAAAA
Found at i:6235273 original size:13 final size:13
Alignment explanation
Indices: 6235217--6235280 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
6235207 ATAATTATAT
*
6235217 CATAAACAATAAA
1 CATAAACCATAAA
*
6235230 TATAAACCATAAA
1 CATAAACCATAAA
** *
6235243 CACT-AATGAAAAA
1 CA-TAAACCATAAA
6235256 C-TAAACCATAAA
1 CATAAACCATAAA
*
6235268 CATAAACCCTAAA
1 CATAAACCATAAA
6235281 ATATAAGTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
11 1 0.03
12 7 0.18
13 29 0.76
14 1 0.03
ACGTcount: A:0.61, C:0.20, G:0.02, T:0.17
Consensus pattern (13 bp):
CATAAACCATAAA
Found at i:6235330 original size:21 final size:21
Alignment explanation
Indices: 6235304--6235408 Score: 74
Period size: 20 Copynumber: 5.1 Consensus size: 21
6235294 CCCTAATTAT
6235304 ATCCTAAACCATAAACCCTAA
1 ATCCTAAACCATAAACCCTAA
* *
6235325 ATCCTAAACCATTAAACCTTAT
1 ATCCTAAACCA-TAAACCCTAA
* ** *
6235347 A-CTTAAATTATAAACCTTAA
1 ATCCTAAACCATAAACCCTAA
*
6235367 A--CTCAAACCATCAACCCTAA
1 ATCCT-AAACCATAAACCCTAA
* * *
6235387 AT-ATAAACCTTAAATCCTAA
1 ATCCTAAACCATAAACCCTAA
6235407 AT
1 AT
6235409 TATAAATACT
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
19 1 0.02
20 38 0.58
21 18 0.27
22 9 0.14
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (21 bp):
ATCCTAAACCATAAACCCTAA
Found at i:6235394 original size:20 final size:21
Alignment explanation
Indices: 6235263--6235414 Score: 71
Period size: 20 Copynumber: 7.2 Consensus size: 21
6235253 AAACTAAACC
*
6235263 ATAAA-CATAAACCCTAAAAT
1 ATAAACCATAAACCCTAAATT
**
6235283 AT-AAGTATAAACCCTAATTATAT
1 ATAAACCATAAACCCTAA--AT-T
* *
6235306 CCTAAACCATAAACCCTAAATC
1 -ATAAACCATAAACCCTAAATT
* * * *
6235328 CTAAACCATTAAACCTTATACT
1 ATAAACCA-TAAACCCTAAATT
** * *
6235350 -TAAATTATAAACCTTAAACT
1 ATAAACCATAAACCCTAAATT
* *
6235370 -CAAACCATCAACCCTAAA-T
1 ATAAACCATAAACCCTAAATT
* *
6235389 ATAAACCTTAAATCCTAAATT
1 ATAAACCATAAACCCTAAATT
6235410 ATAAA
1 ATAAA
6235415 TACTAAACCT
Statistics
Matches: 101, Mismatches: 22, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
19 3 0.03
20 52 0.51
21 19 0.19
22 10 0.10
23 3 0.03
24 1 0.01
25 13 0.13
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (21 bp):
ATAAACCATAAACCCTAAATT
Found at i:6235428 original size:14 final size:14
Alignment explanation
Indices: 6235379--6235428 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
6235369 TCAAACCATC
*
6235379 AACCCTAAATA-TA
1 AACCTTAAATACTA
*
6235392 AACCTTAAATCCTA
1 AACCTTAAATACTA
*
6235406 AA-TTATAAATACTA
1 AACCT-TAAATACTA
6235420 AACCTTAAA
1 AACCTTAAA
6235429 CCTTAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 10 0.34
14 18 0.62
15 1 0.03
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (14 bp):
AACCTTAAATACTA
Found at i:6235542 original size:20 final size:19
Alignment explanation
Indices: 6235519--6235563 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
6235509 ACTCAAACAC
6235519 TAAACACTAAATCCTAAATA
1 TAAACA-TAAATCCTAAATA
*
6235539 TAAATCATAAATCGTAAATA
1 TAAA-CATAAATCCTAAATA
6235559 TAAAC
1 TAAAC
6235564 TTTAAACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAACATAAATCCTAAATA
Found at i:6235569 original size:20 final size:20
Alignment explanation
Indices: 6235526--6235615 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
6235516 CACTAAACAC
6235526 TAAATCCTAAATATAAATCA
1 TAAATCCTAAATATAAATCA
* *
6235546 TAAATCGTAAATATAAA-CTT
1 TAAATCCTAAATATAAATC-A
* *
6235566 TAAA-CATTATAAT-TATATCA
1 TAAATC-CTA-AATATAAATCA
* *
6235586 TAAACCCTAAATATAAATCC
1 TAAATCCTAAATATAAATCA
*
6235606 TAAACCCTAA
1 TAAATCCTAA
6235616 TAAAAAACTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
19 5 0.09
20 46 0.82
21 5 0.09
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (20 bp):
TAAATCCTAAATATAAATCA
Found at i:6235750 original size:29 final size:30
Alignment explanation
Indices: 6235729--6235786 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
6235719 TCATGTGTAT
6235729 AATTG-CATTAAATTAAAATTCATGTATCA
1 AATTGACATTAAATTAAAATTCATGTATCA
* *
6235758 AATTGCACATTGAATCAAAATTCATGTAT
1 AATTG-ACATTAAATTAAAATTCATGTAT
6235787 AATTTTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 5 0.20
31 20 0.80
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (30 bp):
AATTGACATTAAATTAAAATTCATGTATCA
Found at i:6235790 original size:29 final size:27
Alignment explanation
Indices: 6235724--6235790 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
6235714 AAATTTCATG
*
6235724 TGTATAATTGCATTAAATTAAAATTCA
1 TGTATAATTGCATTAAATCAAAATTCA
*
6235751 TGTATCAAATTGCACATTGAATCAAAATTCA
1 TGTAT--AATTG--CATTAAATCAAAATTCA
6235782 TGTATAATT
1 TGTATAATT
6235791 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 5 0.15
29 9 0.26
31 20 0.59
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCATTAAATCAAAATTCA
Found at i:6236129 original size:42 final size:42
Alignment explanation
Indices: 6236048--6236134 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
6236038 CTTAAACCCA
* * * * *
6236048 AAATCATGAATCTTAACCCCTAAACCAAGAACACTAAACCTT
1 AAATCAAGAATCTCAACCCCTAAACCAAAAACACAAAACCAT
6236090 AAATCAAGAATCTCAA-CCCTAAAACCAAAAAC-CAAAAACCAT
1 AAATCAAGAATCTCAACCCCT-AAACCAAAAACAC-AAAACCAT
6236132 AAA
1 AAA
6236135 CCATAAGCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 5 0.13
42 33 0.87
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.16
Consensus pattern (42 bp):
AAATCAAGAATCTCAACCCCTAAACCAAAAACACAAAACCAT
Found at i:6236148 original size:14 final size:14
Alignment explanation
Indices: 6236118--6236191 Score: 58
Period size: 14 Copynumber: 5.3 Consensus size: 14
6236108 CTAAAACCAA
* *
6236118 AAACCAAAAACCAT
1 AAACCATAAACCCT
*
6236132 AAACCATAAGCCCT
1 AAACCATAAACCCT
* *
6236146 AAATCATAAACACT
1 AAACCATAAACCCT
* ***
6236160 AAACCTTAAGTTCT
1 AAACCATAAACCCT
*
6236174 AAGCCATAAACCCT
1 AAACCATAAACCCT
6236188 AAAC
1 AAAC
6236192 AAATAAACAT
Statistics
Matches: 43, Mismatches: 17, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.50, C:0.28, G:0.04, T:0.18
Consensus pattern (14 bp):
AAACCATAAACCCT
Found at i:6236305 original size:7 final size:7
Alignment explanation
Indices: 6236295--6236357 Score: 56
Period size: 7 Copynumber: 8.7 Consensus size: 7
6236285 TCTTTAGCCT
*
6236295 AAACCCA
1 AAACCTA
*
6236302 AAACATA
1 AAACCTA
6236309 AAACCTA
1 AAACCTA
6236316 AAA-CTCA
1 AAACCT-A
6236323 AAACCTAA
1 AAACCT-A
6236331 AAACCTAA
1 AAACCT-A
6236339 AAACCTA
1 AAACCTA
* *
6236346 GAACCTT
1 AAACCTA
6236353 AAACC
1 AAACC
6236358 CTAACCCTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
6 2 0.04
7 28 0.60
8 17 0.36
ACGTcount: A:0.57, C:0.29, G:0.02, T:0.13
Consensus pattern (7 bp):
AAACCTA
Found at i:6236335 original size:8 final size:8
Alignment explanation
Indices: 6236308--6236345 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
6236298 CCCAAAACAT
6236308 AAAACCT-
1 AAAACCTA
*
6236315 AAAA-CTC
1 AAAACCTA
6236322 AAAACCTA
1 AAAACCTA
6236330 AAAACCTA
1 AAAACCTA
6236338 AAAACCTA
1 AAAACCTA
6236346 GAACCTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 2 0.07
7 8 0.29
8 18 0.64
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAACCTA
Found at i:6236455 original size:21 final size:21
Alignment explanation
Indices: 6236437--6236478 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
6236427 AACAATAAAG
6236437 CCTAAA-CTTAAACTCATAAC
1 CCTAAACCTTAAACTCATAAC
6236457 CCTAAACCTTAAACTCA-AAC
1 CCTAAACCTTAAACTCATAAC
6236477 CC
1 CC
6236479 ATTACCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (21 bp):
CCTAAACCTTAAACTCATAAC
Found at i:6236489 original size:27 final size:28
Alignment explanation
Indices: 6236425--6236497 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 28
6236415 ACTCTAACAT
* * * *
6236425 ATAACAATAAAGCC-TAAACTTAAACTC
1 ATAACCATAAACCCTTAAACTCAAACCC
*
6236452 ATAACCCTAAA-CCTTAAACTCAAACCC
1 ATAACCATAAACCCTTAAACTCAAACCC
*
6236479 ATTACCATAAACCCTTAAA
1 ATAACCATAAACCCTTAAA
6236498 TTATAAACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.05
27 29 0.76
28 7 0.18
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (28 bp):
ATAACCATAAACCCTTAAACTCAAACCC
Found at i:6236774 original size:28 final size:28
Alignment explanation
Indices: 6236704--6236763 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
6236694 ACATAAATTG
*
6236704 AAACC-AAAACTCT-AAACATTGAACCAC
1 AAACCTAAAA-TCTAAAATATTGAACCAC
* *
6236731 AAACCTTAAATCTAAAATATTGAACCAT
1 AAACCTAAAATCTAAAATATTGAACCAC
6236759 AAACC
1 AAACC
6236764 AAATATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 8 0.29
28 20 0.71
ACGTcount: A:0.52, C:0.25, G:0.03, T:0.20
Consensus pattern (28 bp):
AAACCTAAAATCTAAAATATTGAACCAC
Found at i:6236837 original size:20 final size:21
Alignment explanation
Indices: 6236795--6236838 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
6236785 AATCCCATAA
*
6236795 CCATAACCCTTAAACTTAAAC
1 CCATAACCCTTAAACTCAAAC
6236816 CCATAACCC-TAAACTCAAAC
1 CCATAACCCTTAAACTCAAAC
6236836 CCA
1 CCA
6236839 AAATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (21 bp):
CCATAACCCTTAAACTCAAAC
Found at i:6237013 original size:28 final size:29
Alignment explanation
Indices: 6236982--6237039 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
6236972 CACTTTTAAC
*
6236982 CATAAATATAAACCCTAAACCC-TAAACT
1 CATAAACATAAACCCTAAACCCTTAAACT
* * *
6237010 CATAACCATAAACCTTTAACCCTTAAACT
1 CATAAACATAAACCCTAAACCCTTAAACT
6237039 C
1 C
6237040 GATCTTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (29 bp):
CATAAACATAAACCCTAAACCCTTAAACT
Found at i:6237144 original size:21 final size:20
Alignment explanation
Indices: 6237089--6237131 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
6237079 CTTTAATCGT
6237089 AAACCTTAAAACTTAAACTC
1 AAACCTTAAAACTTAAACTC
* *
6237109 AAACCTTAAATCTTAAATTC
1 AAACCTTAAAACTTAAACTC
6237129 AAA
1 AAA
6237132 ACCCTAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (20 bp):
AAACCTTAAAACTTAAACTC
Found at i:6237723 original size:29 final size:29
Alignment explanation
Indices: 6237664--6237722 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
6237654 TTTAGTCTAA
*
6237664 TGTGCAATTTTATACAAGTATTTTGATTT
1 TGTGCAATTTTATACAAGAATTTTGATTT
* *
6237693 TGTGCAATTTTATGCATGAAATTTTGATTT
1 TGTGCAATTTTATACAAG-AATTTTGATTT
6237723 GGTCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (29 bp):
TGTGCAATTTTATACAAGAATTTTGATTT
Found at i:6237856 original size:31 final size:30
Alignment explanation
Indices: 6237821--6237917 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 30
6237811 GTTTCTTTAA
*
6237821 ATATATATGATTGAATCAAAATTAAAGTTTC
1 ATATATATAATTGAATCAAAATTAAA-TTTC
* * * *
6237852 ATATATACATTTGAACCACAATCTAAATTTC
1 ATATATATAATTGAATCAAAAT-TAAATTTC
* * * *
6237883 ATGTGTATAATTGCATC-AAATTAAAATTC
1 ATATATATAATTGAATCAAAATTAAATTTC
6237912 ATATAT
1 ATATAT
6237918 CAAATTGCAC
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 11 0.22
30 3 0.06
31 32 0.64
32 4 0.08
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.38
Consensus pattern (30 bp):
ATATATATAATTGAATCAAAATTAAATTTC
Found at i:6238317 original size:7 final size:7
Alignment explanation
Indices: 6238305--6238412 Score: 57
Period size: 7 Copynumber: 15.6 Consensus size: 7
6238295 CCCTTAGCCT
6238305 TAAACCA
1 TAAACCA
6238312 TAAACCA
1 TAAACCA
6238319 TAAA-CA
1 TAAACCA
*
6238325 TATAAACA
1 TA-AACCA
*
6238333 TAAACCT
1 TAAACCA
6238340 TAAA-C-
1 TAAACCA
*
6238345 TCAAACCT
1 T-AAACCA
6238353 TAAATCC-
1 TAAA-CCA
6238360 TAAACCA
1 TAAACCA
*
6238367 TAAA-CT
1 TAAACCA
6238373 TAAACCCA
1 TAAA-CCA
*
6238381 T-ATCCA
1 TAAACCA
*
6238387 TAAACTCT
1 TAAAC-CA
*
6238395 TAAGCCA
1 TAAACCA
*
6238402 TAAACCC
1 TAAACCA
6238409 TAAA
1 TAAA
6238413 TAAAAATCTT
Statistics
Matches: 79, Mismatches: 11, Indels: 22
0.71 0.10 0.20
Matches are distributed among these distances:
5 1 0.01
6 19 0.24
7 45 0.57
8 14 0.18
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCA
Found at i:6238323 original size:28 final size:28
Alignment explanation
Indices: 6238250--6238316 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
6238240 CTATAACCAA
* *
6238250 AAACCAAAAACACTAAGCCCTAAGCCTT
1 AAACCATAAACACTAAACCCTAAGCCTT
* * *
6238278 AAAACTTAAACACTAAACCCTTAGCCTT
1 AAACCATAAACACTAAACCCTAAGCCTT
6238306 AAACCATAAAC
1 AAACCATAAAC
6238317 CATAAACATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (28 bp):
AAACCATAAACACTAAACCCTAAGCCTT
Found at i:6238390 original size:27 final size:28
Alignment explanation
Indices: 6238331--6238391 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
6238321 AACATATAAA
* *
6238331 CATAAACCTTAAACTCAAACCTTAAATC
1 CATAAACCATAAACTCAAACCTCAAATC
* *
6238359 C-TAAACCATAAACTTAAACC-CATATC
1 CATAAACCATAAACTCAAACCTCAAATC
6238385 CATAAAC
1 CATAAAC
6238392 TCTTAAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 5 0.18
27 22 0.79
28 1 0.04
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (28 bp):
CATAAACCATAAACTCAAACCTCAAATC
Found at i:6238501 original size:21 final size:21
Alignment explanation
Indices: 6238471--6238580 Score: 75
Period size: 21 Copynumber: 5.2 Consensus size: 21
6238461 CTTAATTCCT
6238471 AACACTAAACCCTAAAACATAA
1 AACA-TAAACCCTAAAACATAA
* *
6238493 AACATAAACCTTAAATCAT-A
1 AACATAAACCCTAAAACATAA
* *
6238513 AACAATAAAGCCT-AAAC-TCTA
1 AAC-ATAAACCCTAAAACAT-AA
* * *
6238534 AACATTAAATCTTAAACCA-AA
1 AACA-TAAACCCTAAAACATAA
**
6238555 AACATAAACCCTAAAACCCAA
1 AACATAAACCCTAAAACATAA
6238576 AACAT
1 AACAT
6238581 TAAATCCAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
19 1 0.01
20 18 0.26
21 42 0.62
22 7 0.10
ACGTcount: A:0.56, C:0.25, G:0.01, T:0.18
Consensus pattern (21 bp):
AACATAAACCCTAAAACATAA
Found at i:6238581 original size:42 final size:42
Alignment explanation
Indices: 6238416--6238586 Score: 136
Period size: 42 Copynumber: 4.1 Consensus size: 42
6238406 CCCTAAATAA
** * *
6238416 AAATCTTAAACCTAAACCCA-AAACCC-AAAACACAAAACCTA
1 AAATCTTAAACC-AAAAACATAAACCCTAAAACACAAAACATT
* * * * *
6238457 AAACCTTAATTCCTAACAC-TAAACCCTAAAACATAAAACA-T
1 AAATCTTAA-ACCAAAAACATAAACCCTAAAACACAAAACATT
* * * * * *
6238498 AAACCTTAAATCATAAACAATAAAGCCT-AAACTCTAAACATT
1 AAATCTTAAACCAAAAAC-ATAAACCCTAAAACACAAAACATT
*
6238540 AAATCTTAAACCAAAAACATAAACCCTAAAACCCAAAACATT
1 AAATCTTAAACCAAAAACATAAACCCTAAAACACAAAACATT
6238582 AAATC
1 AAATC
6238587 CAAAACTCTA
Statistics
Matches: 101, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
40 4 0.04
41 44 0.44
42 53 0.52
ACGTcount: A:0.54, C:0.26, G:0.01, T:0.19
Consensus pattern (42 bp):
AAATCTTAAACCAAAAACATAAACCCTAAAACACAAAACATT
Found at i:6238591 original size:21 final size:21
Alignment explanation
Indices: 6238533--6238615 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
6238523 CCTAAACTCT
** *
6238533 AAACATTAAATCTTAAACCAA
1 AAACATTAAATCCAAAACCCA
*
6238554 AAACA-TAAACCCTAAAACCCA
1 AAACATTAAATCC-AAAACCCA
* *
6238575 AAACATTAAATCCAAAACTCT
1 AAACATTAAATCCAAAACCCA
*
6238596 AAACACTAAA-CCATAAACCC
1 AAACATTAAATCCA-AAACCC
6238616 TATATCTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 8 0.16
21 36 0.72
22 6 0.12
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (21 bp):
AAACATTAAATCCAAAACCCA
Found at i:6238640 original size:42 final size:42
Alignment explanation
Indices: 6238416--6238640 Score: 117
Period size: 42 Copynumber: 5.4 Consensus size: 42
6238406 CCCTAAATAA
* * * *
6238416 AAATCTTAAA-CCTAAACCCA-AAACC-CAAAACACAAAACCTA
1 AAATCTTAAACCCTAAA--CATAAACCATAAAACCCAAAACATT
* ** * **
6238457 AAACCTTAATTCCT-AACACTAAACCCTAAAACATAAAACA-T
1 AAATCTTAAACCCTAAACA-TAAACCATAAAACCCAAAACATT
* * * * *
6238498 AAACCTTAAATCATAAACAATAAAGCC-T-AAACTCTAAACATT
1 AAATCTTAAACCCTAAAC-ATAAA-CCATAAAACCCAAAACATT
** *
6238540 AAATCTTAAACCAAAAACATAAACCCTAAAACCCAAAACATT
1 AAATCTTAAACCCTAAACATAAACCATAAAACCCAAAACATT
** * * *
6238582 AAATCCAAAACTCTAAACACTAAACCAT-AAACCCTATATC-TT
1 AAATCTTAAACCCTAAACA-TAAACCATAAAACCC-AAAACATT
6238624 AAATCTTAAACCCTAAA
1 AAATCTTAAACCCTAAA
6238641 ACCTAATATA
Statistics
Matches: 145, Mismatches: 27, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
39 2 0.01
40 2 0.01
41 42 0.29
42 86 0.59
43 13 0.09
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (42 bp):
AAATCTTAAACCCTAAACATAAACCATAAAACCCAAAACATT
Found at i:6238664 original size:20 final size:20
Alignment explanation
Indices: 6238639--6238686 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
6238629 TTAAACCCTA
6238639 AAACC-TAATATATAAACCAT
1 AAACCTTAAT-TATAAACCAT
* *
6238659 AAACCTTAATTTTAAACCTT
1 AAACCTTAATTATAAACCAT
6238679 AAA-CTTAA
1 AAACCTTAA
6238687 GCACATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.20
20 16 0.64
21 4 0.16
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (20 bp):
AAACCTTAATTATAAACCAT
Found at i:6238773 original size:33 final size:33
Alignment explanation
Indices: 6238735--6238824 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
6238725 CATAAATATT
6238735 AAAACTAAAACACTAAACCATAACACCTTAAACC
1 AAAACTAAAACACTAAACCATAACA-CTTAAACC
* * * * * *
6238769 -AAACTGAAACTCGAACCCATAACATTTAATCC
1 AAAACTAAAACACTAAACCATAACACTTAAACC
* *
6238801 AAAACTCTAAACACTGAACCATAA
1 AAAACT-AAAACACTAAACCATAA
6238825 ATGCTAAATC
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
32 6 0.14
33 25 0.58
34 12 0.28
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (33 bp):
AAAACTAAAACACTAAACCATAACACTTAAACC
Found at i:6238867 original size:21 final size:20
Alignment explanation
Indices: 6238843--6238916 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
6238833 TCTAAAATCT
*
6238843 TAAACCCTAAACCATAACCAA
1 TAAACCTTAAACCATAACC-A
*
6238864 TAAA-CTTGAAGCCATAACCA
1 TAAACCTT-AAACCATAACCA
6238884 TAAACCTTAAACTCA-AACCCA
1 TAAACCTTAAAC-CATAA-CCA
6238905 T-AACCTTAAACC
1 TAAACCTTAAACC
6238917 CTAAACTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.02
20 22 0.48
21 23 0.50
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.19
Consensus pattern (20 bp):
TAAACCTTAAACCATAACCA
Found at i:6238894 original size:27 final size:27
Alignment explanation
Indices: 6238875--6238927 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6238865 AAACTTGAAG
*
6238875 CCATAACCATAAACCTTAAACTCAAAC
1 CCATAACCATAAACCCTAAACTCAAAC
*
6238902 CCATAACCTTAAACCCTAAACTCAAA
1 CCATAACCATAAACCCTAAACTCAAA
6238928 GTTGTACCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (27 bp):
CCATAACCATAAACCCTAAACTCAAAC
Found at i:6243582 original size:51 final size:50
Alignment explanation
Indices: 6243506--6243602 Score: 140
Period size: 51 Copynumber: 1.9 Consensus size: 50
6243496 GATTCTGGTG
* *
6243506 GAGGATGTGTAGCCTATGGGATTGGCACTTAGTGCCTAGGCGTGTTTTTA
1 GAGGATGTGTAGCCTATGGGATTGGCACTTAGTGCCCAGACGTGTTTTTA
* * *
6243556 GAGGAATGTTTAGCCTATGGGCTTGGCATTTAGTGCCCAGACGTGTT
1 GAGG-ATGTGTAGCCTATGGGATTGGCACTTAGTGCCCAGACGTGTT
6243603 CTTGGATGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 4 0.10
51 37 0.90
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (50 bp):
GAGGATGTGTAGCCTATGGGATTGGCACTTAGTGCCCAGACGTGTTTTTA
Found at i:6263742 original size:24 final size:24
Alignment explanation
Indices: 6263715--6263766 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6263705 TTAGTAAGTC
*
6263715 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
6263739 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
6263763 AAAT
1 AAAT
6263767 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:6265711 original size:24 final size:24
Alignment explanation
Indices: 6265684--6265735 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
6265674 TTAGTAAGTC
*
6265684 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
6265708 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
6265732 AAAT
1 AAAT
6265736 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:6266697 original size:13 final size:13
Alignment explanation
Indices: 6266676--6266705 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6266666 TGCACTAGAG
*
6266676 AAGTGCTTTTGAA
1 AAGTACTTTTGAA
6266689 AAGTACTTTTGAA
1 AAGTACTTTTGAA
6266702 AAGT
1 AAGT
6266706 TTAGTTTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (13 bp):
AAGTACTTTTGAA
Found at i:6274580 original size:49 final size:49
Alignment explanation
Indices: 6274503--6274599 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
6274493 AGGATAGAAA
*
6274503 GCATGTGACTTGAAATTAACCTGTCTTCATTAATAACAAATGTAGATAT
1 GCATGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTAGATAT
* *
6274552 GCATGTGATTTGAAATTAACCTGACTTCATTAATAACAAATGTTGATA
1 GCATGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTAGATA
6274600 CAATATTGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (49 bp):
GCATGTGACTTGAAATTAACCTGACTTCATTAATAACAAATGTAGATAT
Found at i:6278712 original size:63 final size:63
Alignment explanation
Indices: 6278575--6278722 Score: 142
Period size: 63 Copynumber: 2.3 Consensus size: 63
6278565 ATCTCTGGAG
* * * *
6278575 AAGGTGTTAATGCAAGGAATGATTATGCGTGTTGTGGTGCTTGTGTAAAATAAAGTGGTACTA
1 AAGGTGATGATGCAGGGAATGATTATGCGTGTTGTGGTGCTTGTGTAAAATAAAGTGATACTA
* * * *
6278638 AATGTGTTGATGTAGGGAATGA-T-TGCGTGTGCTGTGGTGGTTGTGTAAAATAAA-TCAGATA-
1 AAGGTGATGATGCAGGGAATGATTATGCGTGT--TGTGGTGCTTGTGTAAAATAAAGT--GATAC
*
6278699 TG
62 TA
*
6278701 AAGGTGATGATGCGGGGAATGA
1 AAGGTGATGATGCAGGGAATGA
6278723 GTGTGTGTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
61 7 0.10
62 2 0.03
63 58 0.83
64 3 0.04
ACGTcount: A:0.29, C:0.05, G:0.34, T:0.32
Consensus pattern (63 bp):
AAGGTGATGATGCAGGGAATGATTATGCGTGTTGTGGTGCTTGTGTAAAATAAAGTGATACTA
Found at i:6280567 original size:28 final size:28
Alignment explanation
Indices: 6280501--6280567 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
6280491 AACAAAAAAG
* *
6280501 AATTGAGAATTTAGAATAAAAAATCGAG
1 AATTGAGAATTGAGAATAAAAAATCGAA
* *
6280529 AATTGACAATTGAGAATCAAAAAGT-GAA
1 AATTGAGAATTGAGAAT-AAAAAATCGAA
*
6280557 AATTTAGAATT
1 AATTGAGAATT
6280568 AAGTTGAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.27
Consensus pattern (28 bp):
AATTGAGAATTGAGAATAAAAAATCGAA
Found at i:6282629 original size:29 final size:32
Alignment explanation
Indices: 6282597--6282662 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
6282587 TTAAGATGAC
*
6282597 TATATAAAAA-ATT-TTAATAAA-TAAAATAA
1 TATATAAAAATATTAATAATAAATTAAAATAA
*
6282626 TATATAAAAATATTAAATATTAAATTAAAATAA
1 TATATAAAAATATT-AATAATAAATTAAAATAA
6282659 TATA
1 TATA
6282663 AATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.32
30 3 0.10
32 6 0.19
33 12 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
TATATAAAAATATTAATAATAAATTAAAATAA
Found at i:6290639 original size:13 final size:13
Alignment explanation
Indices: 6290621--6290650 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
6290611 AAGCATACAC
6290621 CATAACATAATAT
1 CATAACATAATAT
6290634 CATAACATAATAT
1 CATAACATAATAT
6290647 CATA
1 CATA
6290651 GTTCCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (13 bp):
CATAACATAATAT
Found at i:6291287 original size:10 final size:10
Alignment explanation
Indices: 6291254--6291288 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
6291244 TAAAATCATT
6291254 AAAATTATAA
1 AAAATTATAA
6291264 AAAATGTAT-A
1 AAAAT-TATAA
6291274 AAAATTATAA
1 AAAATTATAA
6291284 AAAAT
1 AAAAT
6291289 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (10 bp):
AAAATTATAA
Found at i:6292740 original size:16 final size:16
Alignment explanation
Indices: 6292721--6292774 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
6292711 AAAAATTTAA
6292721 ATATATAATATATAAT
1 ATATATAATATATAAT
6292737 ATATA-AATGATATAAT
1 ATATATAAT-ATATAAT
6292753 ATAT-TAAT-T-TAAT
1 ATATATAATATATAAT
6292766 A-ATATAATA
1 ATATATAATA
6292775 AAAAAATTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 1 0.03
15 3 0.09
16 19 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATATAATATATAAT
Found at i:6296732 original size:3 final size:3
Alignment explanation
Indices: 6296726--6296757 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6296716 ATTTTTTTAC
6296726 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
6296758 ACATGAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6298361 original size:17 final size:17
Alignment explanation
Indices: 6298341--6298376 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6298331 TAAATAAAGG
*
6298341 TTATTATCAAATGTGGT
1 TTATTATCAAATGGGGT
*
6298358 TTATTATCGAATGGGGT
1 TTATTATCAAATGGGGT
6298375 TT
1 TT
6298377 CGACGTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (17 bp):
TTATTATCAAATGGGGT
Found at i:6301123 original size:16 final size:16
Alignment explanation
Indices: 6301083--6301121 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6301073 AAAAATTTCC
* *
6301083 CAAAATGTCTATCTCT
1 CAAAATTTCCATCTCT
6301099 CAAAATTTCCATCTCT
1 CAAAATTTCCATCTCT
6301115 -AAAATTT
1 CAAAATTT
6301122 TCTTTGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (16 bp):
CAAAATTTCCATCTCT
Found at i:6307180 original size:42 final size:42
Alignment explanation
Indices: 6307128--6307438 Score: 171
Period size: 43 Copynumber: 7.1 Consensus size: 42
6307118 TCCATTTTGG
*
6307128 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTTTATTTCA
1 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTTTATTGCA
* * *
6307170 TTTTAAAGGCCTAGTTGTGA-GATCTATTT-TATGTTTCCATTGCA
1 TTTTAGAGGCCTAGTTGTGAGGTTC-ATTTACAT-TTT--ATTGCA
* * * **
6307214 TTTTAGAGACCTAATTGTGAGGTCCATTTACATTTTGCTGCA
1 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTTTATTGCA
* * * * ** *
6307256 CTTTAGAGGCCTAGTTGTG-TGATCTTTTTATGTTTTTGTTGCA
1 TTTTAGAGGCCTAGTTGTGAGGTTC-ATTTA-CATTTTATTGCA
* ** *
6307299 TTTTAAAAACCTAGTTGTGAGGTCCAATTTTCATTTGCATTTT-TGCTGCA
1 TTTTAGAGGCCTAGTTGTGAGG-------TTCATTTACATTTTAT--TGCA
* * *
6307349 TTTTAGAGGCTTAGTTGTGAGGTTCGTTTACATTTCTATTGCG
1 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTT-TATTGCA
* * * * * * *
6307392 TTTTAGTGACTTAGTTGTGAAGTCCATTTTCATTTCTATTGTA
1 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTT-TATTGCA
6307435 TTTT
1 TTTT
6307439 TGTTTCAAAG
Statistics
Matches: 202, Mismatches: 47, Indels: 39
0.70 0.16 0.14
Matches are distributed among these distances:
41 7 0.03
42 50 0.25
43 77 0.38
44 31 0.15
45 5 0.02
48 1 0.00
49 4 0.02
50 25 0.12
51 2 0.01
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.47
Consensus pattern (42 bp):
TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTTTATTGCA
Found at i:6307232 original size:44 final size:43
Alignment explanation
Indices: 6307168--6307319 Score: 130
Period size: 44 Copynumber: 3.5 Consensus size: 43
6307158 CATTTTATTT
*
6307168 CATTTTAAAGGCCTAGTTGTGAGATCTATTTTATGTTTCCATTG
1 CATTTTAAAGACCTAGTTGTGAGATCTATTTTATGTTTCC-TTG
* * * * * *
6307212 CATTTTAGAGACCTAATTGTGAGGTCCATTTACAT-TTTGC-TG
1 CATTTTAAAGACCTAGTTGTGAGATCTATTT-TATGTTTCCTTG
* * * * **
6307254 CACTTTAGAGGCCTAGTTGTGTGATCT-TTTTATGTTTTTGTTG
1 CATTTTAAAGACCTAGTTGTGAGATCTATTTTATG-TTTCCTTG
*
6307297 CATTTTAAAAACCTAGTTGTGAG
1 CATTTTAAAGACCTAGTTGTGAG
6307320 GTCCAATTTT
Statistics
Matches: 83, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
40 2 0.02
41 3 0.04
42 26 0.31
43 20 0.24
44 30 0.36
45 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (43 bp):
CATTTTAAAGACCTAGTTGTGAGATCTATTTTATGTTTCCTTG
Found at i:6307271 original size:86 final size:85
Alignment explanation
Indices: 6307128--6307334 Score: 261
Period size: 86 Copynumber: 2.4 Consensus size: 85
6307118 TCCATTTTGG
* * * * *
6307128 TTTTAGAGGCCTAGTTGTGAGGTTCATTTACATTTTATTTCATTTTAAAGGCCTAGTTGTGAGAT
1 TTTTAGAGACCTAGTTGTGAGGTCCATTTACATTTTACTGCACTTTAAAGGCCTAGTTGTGAGAT
6307193 CTATTTTATGTTTCCATTGCA
66 CT-TTTTATGTTTCCATTGCA
* * * *
6307214 TTTTAGAGACCTAATTGTGAGGTCCATTTACATTTTGCTGCACTTTAGAGGCCTAGTTGTGTGAT
1 TTTTAGAGACCTAGTTGTGAGGTCCATTTACATTTTACTGCACTTTAAAGGCCTAGTTGTGAGAT
***
6307279 CTTTTTATGTTTTTGTTGCA
66 CTTTTTATGTTTCCATTGCA
* * *
6307299 TTTTAAAAACCTAGTTGTGAGGTCCAATTTTCATTT
1 TTTTAGAGACCTAGTTGTGAGGTCC-ATTTACATTT
6307335 GCATTTTTGC
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 37 0.36
86 67 0.64
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (85 bp):
TTTTAGAGACCTAGTTGTGAGGTCCATTTACATTTTACTGCACTTTAAAGGCCTAGTTGTGAGAT
CTTTTTATGTTTCCATTGCA
Found at i:6309186 original size:200 final size:200
Alignment explanation
Indices: 6308836--6309211 Score: 655
Period size: 200 Copynumber: 1.9 Consensus size: 200
6308826 TTTGGTGTTT
* *
6308836 TAGGGTAATGTAAAGGGATATTTTCTACATAATTCCTTCTACGTCCCGCTTTTTGCAGAAAAGGA
1 TAGGGTAATGTAAAGGGATATTTTCTACATAATTCCTTCTACGTCCAGCCTTTTGCAGAAAAGGA
* *
6308901 TCGCCGTATGGACTAATTGCAGTTCTCGTTCCTCTGCTTTTGATTTCTCCCCGATTTTGAAATTT
66 TCGCCGCATGGACTAATTGCAGTTCTCGTTCCTCTGCTTTTGAATTCTCCCCGATTTTGAAATTT
*
6308966 CAGGCAAATTAATTGCCAAATACGTCCTCTGCTTCTTACATTTTTTTATCCTATTGATTTAGATT
131 CAGGCAAATTAATTGCCAAATACGTACTCTGCTTCTTACATTTTTTTATCCTATTGATTTAGATT
6309031 TCTTA
196 TCTTA
* *
6309036 TAGGGTTATGTAAAGGGATATTTTCTACATAATTCTTTCTACGTCCAGCCTTTTGCAGAAAAGGA
1 TAGGGTAATGTAAAGGGATATTTTCTACATAATTCCTTCTACGTCCAGCCTTTTGCAGAAAAGGA
6309101 TCGCCGCATGGACTAATTGCAGTTCTCG-TCTCTCTGCTTTTGAATTCTCCCCGATTTTGAAATT
66 TCGCCGCATGGACTAATTGCAGTTCTCGTTC-CTCTGCTTTTGAATTCTCCCCGATTTTGAAATT
* *
6309165 TCAGGCAAATTAATTGCCAAATAGGTACTCTGTTTCTTACATTTTTT
130 TCAGGCAAATTAATTGCCAAATACGTACTCTGCTTCTTACATTTTTT
6309212 CTTAACTGCT
Statistics
Matches: 166, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
199 2 0.01
200 164 0.99
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (200 bp):
TAGGGTAATGTAAAGGGATATTTTCTACATAATTCCTTCTACGTCCAGCCTTTTGCAGAAAAGGA
TCGCCGCATGGACTAATTGCAGTTCTCGTTCCTCTGCTTTTGAATTCTCCCCGATTTTGAAATTT
CAGGCAAATTAATTGCCAAATACGTACTCTGCTTCTTACATTTTTTTATCCTATTGATTTAGATT
TCTTA
Found at i:6311119 original size:250 final size:249
Alignment explanation
Indices: 6310677--6311181 Score: 707
Period size: 250 Copynumber: 2.0 Consensus size: 249
6310667 GCTTATTTTG
* *
6310677 AAGTATTAGGATTATTTAAAGTTTTCTCTTTAGCATTGTGTATTTTATCATAGGTTAGCTTCTTT
1 AAGTATTAGGATTATTTAAAGTTTTCTCTTTAGAATTGTGTATTTTATCATAGGTTAGCTTATTT
* *
6310742 TTGAATTTCATACTTTAATTTTTTTTATATTAGGTTTTAAATTAGTTCATTTTAGGATCTTGGAT
66 TTGAATTTCATAC-TT-ATTTTTTTTATATTAGGTTCTAAATTAGTTCATTTTAGGATCTTAGAT
6310807 CTAAATATTAGGTTTATTTTGGTTAAATTTCTAGAAATTAGATTTTAACACTTTTAGATTGTAGG
129 CTAAATATTAGGTTTATTTTGGTTAAATTTCTAGAAATTAGATTTTAACACTTTTAGATTGTAGG
**
6310872 TTTTAAAATTTTTATGTTAAGTTACATATAA-GATTCTATTTT-TTAAAAATTAAATT
194 TTTTAAAA-TTTTATGTTAAGTTACATATAATG-TTCTATTTTAAAAAAAATTAAATT
* * * ** *
6310928 AAGTATTGGGATTATTTGAGGTTTTCTCTTTAGAATTGTGTACTTTTTTATGGTTGGTTAGCTTA
1 AAGTATTAGGATTATTTAAAGTTTTCTCTTTAGAATTGTGTA---TTTTATCATAGGTTAGCTTA
*
6310993 TTTTTGAATTTCAT-C-T-TTTTTTTT-TATTAGGTTCTAAATTAGTTCATTTTAGGATTTTAGA
63 TTTTTGAATTTCATACTTATTTTTTTTATATTAGGTTCTAAATTAGTTCATTTTAGGATCTTAGA
* * * **
6311054 TTTGAATATTAGGCTTTTTTTTCGGTTAAATTTCTAGAAATTAGATTTTAGGACTTTTAGATTGT
128 TCTAAATATTAGG-TTTATTTT-GGTTAAATTTCTAGAAATTAGATTTTAACACTTTTAGATTGT
* *
6311119 AGGTTTTAAAATTTTATGTTAAGTTACATTTAATGTTTTATTTTAAAAAAAATTAAATT
191 AGGTTTTAAAATTTTATGTTAAGTTACATATAATGTTCTATTTTAAAAAAAATTAAATT
6311178 AAGT
1 AAGT
6311182 CTTTTAAACT
Statistics
Matches: 227, Mismatches: 20, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
248 45 0.20
249 44 0.19
250 68 0.30
251 39 0.17
253 1 0.00
254 30 0.13
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (249 bp):
AAGTATTAGGATTATTTAAAGTTTTCTCTTTAGAATTGTGTATTTTATCATAGGTTAGCTTATTT
TTGAATTTCATACTTATTTTTTTTATATTAGGTTCTAAATTAGTTCATTTTAGGATCTTAGATCT
AAATATTAGGTTTATTTTGGTTAAATTTCTAGAAATTAGATTTTAACACTTTTAGATTGTAGGTT
TTAAAATTTTATGTTAAGTTACATATAATGTTCTATTTTAAAAAAAATTAAATT
Found at i:6313643 original size:21 final size:22
Alignment explanation
Indices: 6313600--6313645 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
6313590 TACACCAAAA
*
6313600 TAGGCTTTTAGCGGTGCTTTTT
1 TAGGCCTTTAGCGGTGCTTTTT
6313622 TAGGCCTTTAGCGGTG-TTTTT
1 TAGGCCTTTAGCGGTGCTTTTT
6313643 TAG
1 TAG
6313646 CACCGTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.11, C:0.13, G:0.28, T:0.48
Consensus pattern (22 bp):
TAGGCCTTTAGCGGTGCTTTTT
Found at i:6313865 original size:43 final size:43
Alignment explanation
Indices: 6313756--6313876 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
6313746 AGACCAAGAC
**
6313756 CTTTAGCAACGCTTTCACC-ACAAACGTCGCTAAAGGTCATGGT
1 CTTTAGCGGCGCTTT-ACCAACAAACGTCGCTAAAGGTCATGGT
* * *
6313799 CTTTAGCGGCGCTTTTCCTACAAACGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGCTTTACCAACAAACGTCGCTAAAGGTCATGGT
*
6313842 CTTTAGCGGCGC-TTACCAAACAAATGTCGCTAAAG
1 CTTTAGCGGCGCTTTACC-AACAAACGTCGCTAAAG
6313877 ACAATGACCT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
42 6 0.09
43 62 0.91
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTACCAACAAACGTCGCTAAAGGTCATGGT
Found at i:6319804 original size:25 final size:25
Alignment explanation
Indices: 6319773--6320100 Score: 153
Period size: 25 Copynumber: 13.0 Consensus size: 25
6319763 ATAATTAAGC
*
6319773 TATGTAAGTTATATAAGTTGTGTAT
1 TATGTAAGTTATATAAGTTATGTAT
*
6319798 AATGTAAGTTATGA-AAGTTATGTAT
1 TATGTAAGTTAT-ATAAGTTATGTAT
* **
6319823 TATGTAAGTTATTTAAGTCGTGTAT
1 TATGTAAGTTATATAAGTTATGTAT
* * * *
6319848 TATGTAAGTCATGTAGGCTATGTAT
1 TATGTAAGTTATATAAGTTATGTAT
*
6319873 TATGTAAGTTATAATAAG-TAAG--T
1 TATGTAAGTTAT-ATAAGTTATGTAT
** *
6319896 TATAAAAGTTATATATGTAAGTTATGTGT
1 TATGTAAG-T-TATA--TAAGTTATGTAT
* *
6319925 TGTGTAAGTT-TATATA-TAAAT-T-T
1 TATGTAAGTTATATA-AGT-TATGTAT
6319948 TAT-TCAAGTTATGAATGTAAGTTATGTAAGT
1 TATGT-AAGTTAT--A--TAAGTTATGT-A-T
* * *
6319979 TGTGT--GTAATGTAAGTTATGTAT
1 TATGTAAGTTATATAAGTTATGTAT
* *
6320002 TATGTAAGTTATTTAAGTTGTGTAT
1 TATGTAAGTTATATAAGTTATGTAT
* * * * *
6320027 TATGTAAGTCATGTACGCTATGTGT
1 TATGTAAGTTATATAAGTTATGTAT
*
6320052 TATGTAAGTTATTATAAG-TAAG--T
1 TATGTAAGTTA-TATAAGTTATGTAT
*
6320075 TATGAAAGTTATATATAAGTTATGTA
1 TATGTAAG-T-TATATAAGTTATGTA
6320101 AGTTATTGTG
Statistics
Matches: 227, Mismatches: 44, Indels: 62
0.68 0.13 0.19
Matches are distributed among these distances:
22 1 0.00
23 28 0.12
24 15 0.07
25 142 0.63
26 15 0.07
27 7 0.03
28 5 0.02
29 10 0.04
31 3 0.01
32 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TATGTAAGTTATATAAGTTATGTAT
Found at i:6319834 original size:9 final size:9
Alignment explanation
Indices: 6319768--6320132 Score: 106
Period size: 9 Copynumber: 43.7 Consensus size: 9
6319758 TAAGTATAAT
*
6319768 TAAGCTATG
1 TAAGTTATG
*
6319777 TAAGTTATA
1 TAAGTTATG
*
6319786 TAAGTTGTG
1 TAAGTTATG
*
6319795 T-A-TAATG
1 TAAGTTATG
6319802 TAAGTTATG
1 TAAGTTATG
*
6319811 AAAGTTATG
1 TAAGTTATG
6319820 T-A-TTATG
1 TAAGTTATG
*
6319827 TAAGTTATT
1 TAAGTTATG
**
6319836 TAAGTCGTG
1 TAAGTTATG
6319845 T-A-TTATG
1 TAAGTTATG
*
6319852 TAAGTCATG
1 TAAGTTATG
* *
6319861 TAGGCTATG
1 TAAGTTATG
6319870 T-A-TTATG
1 TAAGTTATG
6319877 TAAGTTA--
1 TAAGTTATG
*
6319884 TAA--TAAG
1 TAAGTTATG
*
6319891 TAAGTTATA
1 TAAGTTATG
*
6319900 AAAGTTA--
1 TAAGTTATG
6319907 T-A--TATG
1 TAAGTTATG
6319913 TAAGTTATG
1 TAAGTTATG
*
6319922 T--GTTGTG
1 TAAGTTATG
*
6319929 TAAGTTTATATA
1 TAAG--T-TATG
*
6319941 TAAATTTTAT-
1 T-AA-GTTATG
6319951 TCAAGTTATG
1 T-AAGTTATG
6319961 --A---ATG
1 TAAGTTATG
6319965 TAAGTTATG
1 TAAGTTATG
*
6319974 TAAGTTGTG
1 TAAGTTATG
*
6319983 T--GTAATG
1 TAAGTTATG
6319990 TAAGTTATG
1 TAAGTTATG
6319999 T-A-TTATG
1 TAAGTTATG
*
6320006 TAAGTTATT
1 TAAGTTATG
*
6320015 TAAGTTGTG
1 TAAGTTATG
6320024 T-A-TTATG
1 TAAGTTATG
*
6320031 TAAGTCATG
1 TAAGTTATG
* *
6320040 TACGCTATG
1 TAAGTTATG
6320049 T--GTTATG
1 TAAGTTATG
6320056 TAAGTTAT-
1 TAAGTTATG
*
6320064 T-A--TAAG
1 TAAGTTATG
6320070 TAAGTTATG
1 TAAGTTATG
* *
6320079 AAAGTTATATA
1 TAAG-T-TATG
6320090 TAAGTTATG
1 TAAGTTATG
6320099 TAAGTTATTGTG
1 TAAGTTA---TG
6320111 TAAGTTATG
1 TAAGTTATG
*
6320120 T--GTTGTG
1 TAAGTTATG
6320127 TAAGTT
1 TAAGTT
6320133 TATATATAAA
Statistics
Matches: 256, Mismatches: 51, Indels: 98
0.63 0.13 0.24
Matches are distributed among these distances:
4 5 0.02
5 4 0.02
6 4 0.02
7 63 0.25
8 12 0.05
9 138 0.54
10 5 0.02
11 10 0.04
12 13 0.05
13 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:6319918 original size:22 final size:23
Alignment explanation
Indices: 6319878--6319920 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
6319868 TGTATTATGT
6319878 AAGTTATAATAAGTAAGTTATAA
1 AAGTTATAATAAGTAAGTTATAA
*
6319901 AAGTTAT-ATATGTAAGTTAT
1 AAGTTATAATAAGTAAGTTAT
6319921 GTGTTGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (23 bp):
AAGTTATAATAAGTAAGTTATAA
Found at i:6319992 original size:16 final size:16
Alignment explanation
Indices: 6319971--6320013 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
6319961 AATGTAAGTT
* *
6319971 ATGTAAGTTGTGTGTA
1 ATGTAAGTTATGTATA
*
6319987 ATGTAAGTTATGTATT
1 ATGTAAGTTATGTATA
6320003 ATGTAAGTTAT
1 ATGTAAGTTAT
6320014 TTAAGTTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (16 bp):
ATGTAAGTTATGTATA
Found at i:6320019 original size:41 final size:41
Alignment explanation
Indices: 6319962--6320074 Score: 126
Period size: 41 Copynumber: 2.8 Consensus size: 41
6319952 CAAGTTATGA
* *
6319962 ATGTAAGTTATGTAAGTTGTGTGTAATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTGTGTATAATGTAAGTCATGTATT
* * *
6320003 ATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGTACGCT
1 ATGTAAGTTATGTAAGTTGTGTATAATGTAAGTCATGTA--TT
*
6320046 ATGT--GTTATGTAAGTTAT-TATAA-GTAAGT
1 ATGTAAGTTATGTAAGTTGTGTATAATGTAAGT
6320075 TATGAAAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
39 6 0.10
40 4 0.06
41 47 0.76
43 5 0.08
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.45
Consensus pattern (41 bp):
ATGTAAGTTATGTAAGTTGTGTATAATGTAAGTCATGTATT
Found at i:6320093 original size:20 final size:22
Alignment explanation
Indices: 6320050--6320120 Score: 85
Period size: 20 Copynumber: 3.3 Consensus size: 22
6320040 TACGCTATGT
6320050 GTTATGTAAGTTATTATAAGTAA
1 GTTATGTAAGTTA-TATAAGTAA
*
6320073 GTTATGAAAGTTATAT-A-TAA
1 GTTATGTAAGTTATATAAGTAA
**
6320093 GTTATGTAAGTTAT-TGTGTAA
1 GTTATGTAAGTTATATAAGTAA
6320114 GTTATGT
1 GTTATGT
6320121 GTTGTGTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
19 1 0.02
20 16 0.37
21 11 0.26
22 3 0.07
23 12 0.28
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (22 bp):
GTTATGTAAGTTATATAAGTAA
Found at i:6320129 original size:96 final size:94
Alignment explanation
Indices: 6320001--6320269 Score: 266
Period size: 96 Copynumber: 2.9 Consensus size: 94
6319991 AAGTTATGTA
* * * * **
6320001 TTATGTAAGTTA-TT-TAAGTTGTGTATTATGTAAGTCATGTACGCTATGTGTTATGTAAGTTAT
1 TTATGTAAGTTATTTGTAAGTTATGTGTTGTGTAAGTCATATA---TAAATGTTATGTAAGTTAT
6320064 -TATAAGTAAGTTAT-GA-AAG-TTATATATAAG
63 GTAT--GTAAGTTATAGATAAGTTTATATATAAG
* * *
6320094 TTATGTAAGTTATTGTGTAAGTTATGTGTTGTGTAAGTTTATATATAAATTTTATTTAAGTTATG
1 TTATGTAAGTTATT-TGTAAGTTATGTGTTGTGTAAG-TCATATATAAATGTTATGTAAGTTATG
*
6320159 TATGTAAGTTATATATAAGTTTATATATAAG
64 TATGTAAGTTATAGATAAGTTTATATATAAG
* * * *
6320190 TTATGTAAGTTATTATGTAAGTTATATGTTGTGTAAGTTTATATATAAAT-TTATATATGTTATG
1 TTATGTAAGTTATT-TGTAAGTTATGTGTTGTGTAAG-TCATATATAAATGTTATGTAAGTTATG
*
6320254 TATGTAAATTAT-GATA
64 TATGTAAGTTATAGATA
6320270 TGATTGATAA
Statistics
Matches: 152, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
93 21 0.14
94 20 0.13
95 30 0.20
96 76 0.50
97 5 0.03
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (94 bp):
TTATGTAAGTTATTTGTAAGTTATGTGTTGTGTAAGTCATATATAAATGTTATGTAAGTTATGTA
TGTAAGTTATAGATAAGTTTATATATAAG
Found at i:6320190 original size:36 final size:36
Alignment explanation
Indices: 6320125--6320196 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
6320115 TTATGTGTTG
*
6320125 TGTAAGTTTATATATAAATTTTATTTAAGTTATGTA
1 TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
*
6320161 TGTAAG-TTATATATAAGTTTATATATAAGTTATGTA
1 TGTAAGTTTATATATAAATTT-TATATAAGTTATGTA
6320197 AGTTATTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (36 bp):
TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
Found at i:6320253 original size:198 final size:195
Alignment explanation
Indices: 6319872--6320255 Score: 429
Period size: 198 Copynumber: 1.9 Consensus size: 195
6319862 AGGCTATGTA
*
6319872 TTATGTAAGTTATAATAAGTAAGTTATAAAAGTTATATATGTAAGTTATGTGTTGTGTAAGTTTA
1 TTATGAAAGTTAT-AT-A-TAAGTTATAAAAGTTATATATGTAAGTTATGTGTTGTGTAAGTTTA
* * * * *
6319937 TATATAAATTTTATTCAAGTTATGAATGTAAGTTATGTAAGTTGTGTGTAATGTAAGTTATGTAT
63 TATATAAATTTTATTCAAGTTATGAATGTAAGTTATATAAGTTATATATAATGTAAGTAATGTAT
* * *
6320002 TATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGTACGCTATGTGTTATGTAAGTTATTAT
128 TATGTAAGTTA-TTAAGTTGTGTATTATATAAG-AATGTA--CTATATGTTATGTAAGTTATTAT
6320067 AAGTAAG
189 AAGTAAG
** *
6320074 TTATGAAAGTTATATATAAGTTATGTAAGTTAT-TGTGTAAGTTATGTGTTGTGTAAGTTTATAT
1 TTATGAAAGTTATATATAAGTTATAAAAGTTATATATGTAAGTTATGTGTTGTGTAAGTTTATAT
* * *
6320138 ATAAATTTTATTTAAGTTATGTATGTAAGTTATATATAAGTTTATATATAA-GTTATGTAA-GTT
66 ATAAATTTTATTCAAGTTATGAATGTAAG-T-TATATAAG-TTATATATAATG-TAAGTAATG-T
* *
6320201 ATTATGTAAGTTA-TATGTTGTGTAAGTTTATATATA-AATTTA-TATATGTTATGTA
126 ATTATGTAAGTTATTAAGTTGTGT-A--TTATATA-AGAATGTACTATATGTTATGTA
6320256 TGTAAATTAT
Statistics
Matches: 156, Mismatches: 17, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
198 69 0.44
199 25 0.16
200 11 0.07
201 32 0.21
202 18 0.12
203 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (195 bp):
TTATGAAAGTTATATATAAGTTATAAAAGTTATATATGTAAGTTATGTGTTGTGTAAGTTTATAT
ATAAATTTTATTCAAGTTATGAATGTAAGTTATATAAGTTATATATAATGTAAGTAATGTATTAT
GTAAGTTATTAAGTTGTGTATTATATAAGAATGTACTATATGTTATGTAAGTTATTATAAGTAAG
Found at i:6320315 original size:19 final size:19
Alignment explanation
Indices: 6320276--6320320 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
6320266 GATATGATTG
*
6320276 ATAAATTTTTCAAATATAT
1 ATAAAATTTTCAAATATAT
6320295 ATAAAATTTT-AATATATAT
1 ATAAAATTTTCAA-ATATAT
6320314 ATTAAAA
1 A-TAAAA
6320321 CTGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTCAAATATAT
Found at i:6320315 original size:21 final size:22
Alignment explanation
Indices: 6320287--6320339 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
6320277 TAAATTTTTC
* *
6320287 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
*
6320308 ATATATAT-TAAAACTGTATAT
1 AAATATATATAAAACTGTATAT
6320329 AAATATATATA
1 AAATATATATA
6320340 TCAAAGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:6324307 original size:43 final size:43
Alignment explanation
Indices: 6324246--6324350 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
6324236 AAATGCCACA
* *
6324246 ATAGATCAGGACTTTTAGCAGCGCATTTCCCACAAACGCCGCT
1 ATAGATCATGACTTTTAGCAGCACATTTCCCACAAACGCCGCT
* * *
6324289 ATAGATCATGACTTTTAGCGGCACTTTTCCTACAAACGCCGCT
1 ATAGATCATGACTTTTAGCAGCACATTTCCCACAAACGCCGCT
* * *
6324332 AAAGAACATGACCTTTAGC
1 ATAGATCATGACTTTTAGC
6324351 GGCGTTTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
ATAGATCATGACTTTTAGCAGCACATTTCCCACAAACGCCGCT
Found at i:6324369 original size:43 final size:43
Alignment explanation
Indices: 6324279--6324376 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
6324269 CATTTCCCAC
* * * ** *
6324279 AAACGCCGCTATAGATCATGACTTTTAGCGGCACTTTTCCTAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCAAAA
**
6324322 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTCAAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCAAAA
*
6324365 AAACGCCACTAA
1 AAACGCCGCTAA
6324377 TTTTGACAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTTCAAAA
Found at i:6324717 original size:21 final size:21
Alignment explanation
Indices: 6324664--6324722 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
6324654 TCCTCTGCTT
* *
6324664 TGCTTCCCTCGCTGCAGCCTC
1 TGCTTCCTTCGCTGCTGCCTC
*
6324685 TGC-TGCTCTCGCTGCTGCCTC
1 TGCTTCCT-TCGCTGCTGCCTC
6324706 TGCTTCCTTCGCTGCTG
1 TGCTTCCTTCGCTGCTG
6324723 TATCAGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.84
22 3 0.09
ACGTcount: A:0.02, C:0.42, G:0.22, T:0.34
Consensus pattern (21 bp):
TGCTTCCTTCGCTGCTGCCTC
Found at i:6330318 original size:25 final size:26
Alignment explanation
Indices: 6330275--6330325 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
6330265 AATATATATT
6330275 TATGTATTAAGTAAATTATGTAAGTTG
1 TATGTATT-AGTAAATTATGTAAGTTG
* *
6330302 TATGTATT-GTAAGTTATGTGAGTT
1 TATGTATTAGTAAATTATGTAAGTT
6330326 ATTTAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
27 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (26 bp):
TATGTATTAGTAAATTATGTAAGTTG
Found at i:6330380 original size:18 final size:18
Alignment explanation
Indices: 6330357--6330618 Score: 72
Period size: 18 Copynumber: 14.6 Consensus size: 18
6330347 ATATAAGTTA
6330357 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTGAG
*
6330375 TTATGTATA-TTATGTGAT
1 TTATGTA-AGTTATGTGAG
* * *
6330393 TTATTTAAGTTAAGGTTTGATA
1 TTATGTAAGTT-A--TGTGA-G
* * *
6330415 TATATATAAGTTGT-TAAG
1 T-TATGTAAGTTATGTGAG
*
6330433 TTATGTAAGTTATCTGAG
1 TTATGTAAGTTATGTGAG
6330451 TTATGT-AGATTATGAT-ATGG
1 TTATGTAAG-TTATG-TGA--G
* * *
6330471 TGCATATAAGTTAT-TAAG
1 T-TATGTAAGTTATGTGAG
* **
6330489 TTAGGTAAGTTATGCAAG
1 TTATGTAAGTTATGTGAG
*
6330507 TTATATAAGTTA--TGA-
1 TTATGTAAGTTATGTGAG
*
6330522 TATATATAAG---T-T--G
1 T-TATGTAAGTTATGTGAG
6330535 TTATGTAAGTTATGTGAG
1 TTATGTAAGTTATGTGAG
6330553 TTATGT-AGATTATGAT-ATG
1 TTATGTAAG-TTATG-TGA-G
* *
6330572 ATATATATAAGTTAT-TAAG
1 -T-TATGTAAGTTATGTGAG
*
6330591 TTAGGTAAGTTATGTGAG
1 TTATGTAAGTTATGTGAG
*
6330609 TTATTTAAGT
1 TTATGTAAGT
6330619 AATGGTATGA
Statistics
Matches: 182, Mismatches: 29, Indels: 66
0.66 0.10 0.24
Matches are distributed among these distances:
12 7 0.04
13 1 0.01
14 1 0.01
15 2 0.01
16 10 0.05
17 34 0.19
18 78 0.43
19 10 0.05
20 6 0.03
21 19 0.10
22 5 0.03
23 9 0.05
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (18 bp):
TTATGTAAGTTATGTGAG
Found at i:6330433 original size:67 final size:69
Alignment explanation
Indices: 6330282--6330445 Score: 173
Period size: 69 Copynumber: 2.4 Consensus size: 69
6330272 ATTTATGTAT
*
6330282 TAAGTAAATTATGTAAG-T-TGTATG-TATTGTA-AGTTATGTGAGTTATTTAAGTAATGGTATG
1 TAAGT-AATTATGTAAGTTATGTAAGTTA-TGTATA-TTATGTGAGTTATTTAAGTAATGGTATG
6330343 ATATATA
63 ATATATA
* * * *
6330350 TAAGTTATTATGTAAGTTATGTGAGTTATGTATATTATGTGATTTATTTAAGTTAA-GGTTTGAT
1 TAAGTAATTATGTAAGTTATGTAAGTTATGTATATTATGTGAGTTATTTAAG-TAATGGTATGAT
6330414 ATATA
65 ATATA
*
6330419 T-A-TAAGT-TGTTAAGTTATGTAAGTTAT
1 TAAGTAATTATG-TAAGTTATGTAAGTTAT
6330446 CTGAGTTATG
Statistics
Matches: 82, Mismatches: 8, Indels: 13
0.80 0.08 0.13
Matches are distributed among these distances:
66 2 0.02
67 29 0.35
68 7 0.09
69 38 0.46
70 6 0.07
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.47
Consensus pattern (69 bp):
TAAGTAATTATGTAAGTTATGTAAGTTATGTATATTATGTGAGTTATTTAAGTAATGGTATGATA
TATA
Found at i:6330439 original size:76 final size:69
Alignment explanation
Indices: 6330315--6330464 Score: 185
Period size: 76 Copynumber: 2.1 Consensus size: 69
6330305 GTATTGTAAG
*
6330315 TTATGTGAGTTATTTAAGTAATGGTATGATATATATAAGTTATTATGTAAGTTATGTGAGTTATG
1 TTATGTGAGTTATTTAAGTAATGGTATGATATATATAAGTTATTATGTAAGTTATCTGAGTTATG
*
6330380 TATA
66 TAGA
* *
6330384 TTATGTGATTTATTTAAGTTAA-GGTTTGATATATATATAAGTTGTTAAGTTATGTAAGTTATCT
1 TTATGTGAGTTATTTAAG-TAATGGTATG--ATATATATAA---GTT-A-TTATGTAAGTTATCT
6330448 GAGTTATGTAGA
58 GAGTTATGTAGA
6330460 TTATG
1 TTATG
6330465 ATATGGTGCA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
69 22 0.32
70 3 0.04
71 10 0.14
74 3 0.04
75 1 0.01
76 30 0.43
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (69 bp):
TTATGTGAGTTATTTAAGTAATGGTATGATATATATAAGTTATTATGTAAGTTATCTGAGTTATG
TAGA
Found at i:6330443 original size:9 final size:9
Alignment explanation
Indices: 6330429--6330618 Score: 95
Period size: 9 Copynumber: 20.6 Consensus size: 9
6330419 TATAAGTTGT
6330429 TAAGTTATG
1 TAAGTTATG
*
6330438 TAAGTTATC
1 TAAGTTATG
*
6330447 TGAGTTATG
1 TAAGTTATG
6330456 T-AGATTATG
1 TAAG-TTATG
* * *
6330465 ATATGGTGCATA
1 -TA-AGT-TATG
6330477 TAAGTTAT-
1 TAAGTTATG
*
6330485 TAAGTTAGG
1 TAAGTTATG
6330494 TAAGTTATG
1 TAAGTTATG
* *
6330503 CAAGTTATA
1 TAAGTTATG
6330512 TAAGTTATG
1 TAAGTTATG
*
6330521 ATATA-TATAAG
1 -TA-AGT-TATG
*
6330532 T-TGTTATG
1 TAAGTTATG
6330540 TAAGTTATG
1 TAAGTTATG
*
6330549 TGAGTTATG
1 TAAGTTATG
6330558 T-AGATTATG
1 TAAG-TTATG
* *
6330567 ATATGATATATA
1 -TAAG-T-TATG
6330579 TAAGTTAT-
1 TAAGTTATG
*
6330587 TAAGTTAGG
1 TAAGTTATG
6330596 TAAGTTATG
1 TAAGTTATG
* *
6330605 TGAGTTATT
1 TAAGTTATG
6330614 TAAGT
1 TAAGT
6330619 AATGGTATGA
Statistics
Matches: 138, Mismatches: 27, Indels: 32
0.70 0.14 0.16
Matches are distributed among these distances:
8 22 0.16
9 88 0.64
10 9 0.07
11 13 0.09
12 6 0.04
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (9 bp):
TAAGTTATG
Found at i:6330553 original size:102 final size:103
Alignment explanation
Indices: 6330432--6330632 Score: 314
Period size: 102 Copynumber: 2.0 Consensus size: 103
6330422 AAGTTGTTAA
* *
6330432 GTTATGTAAGTTATCTGAGTTATGTAGATTATGATATGGTGCATATAAGTTATTAAGTTAGGTAA
1 GTTATGTAAGTTATCTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAA
*
6330497 GTTATGCAAGTTATATAAGTTATGATAT-ATATAAGTT
66 GTTATGCAAGTTATATAAGTAATGATATGATATAAGTT
* *
6330534 GTTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTTATTAAGTTAGGTAA
1 GTTATGTAAGTTATCTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAA
** * *
6330599 GTTATGTGAGTTATTTAAGTAATGGTATGATATA
66 GTTATGCAAGTTATATAAGTAATGATATGATATA
6330633 TATATATAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
102 84 0.94
103 5 0.06
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.43
Consensus pattern (103 bp):
GTTATGTAAGTTATCTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAA
GTTATGCAAGTTATATAAGTAATGATATGATATAAGTT
Found at i:6330555 original size:46 final size:47
Alignment explanation
Indices: 6330488--6330576 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
6330478 AAGTTATTAA
6330488 GTTAGGTAAGTTATGCAAGTTATATA-AGTTATGATAT-ATATAAGTT
1 GTTAGGTAAGTTATGCAAGTTATATAGA-TTATGATATGATATAAGTT
* ** *
6330534 GTTATGTAAGTTATGTGAGTTATGTAGATTATGATATGATATA
1 GTTAGGTAAGTTATGCAAGTTATATAGATTATGATATGATATA
6330577 TATAAGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 31 0.84
47 6 0.16
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.43
Consensus pattern (47 bp):
GTTAGGTAAGTTATGCAAGTTATATAGATTATGATATGATATAAGTT
Found at i:6330628 original size:56 final size:56
Alignment explanation
Indices: 6330414--6330660 Score: 234
Period size: 56 Copynumber: 4.6 Consensus size: 56
6330404 AAGGTTTGAT
* * *
6330414 ATATATATAAGTTGTTAAGTTATGTAAGTTATCTGAGTTATGTAGATTATGATATG
1 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAGATAATGATATG
* ** * ** *
6330470 GTGCATATAAGTTATTAAGTTAGGTAAGTTATGCAAGTTA--T--ATAA-GTTATG
1 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAGATAATGATATG
*
6330521 ATATATATAAG---TT--GTTATGTAAGTTATGTGAGTTATGTAGATTATGATATG
1 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAGATAATGATATG
* * *
6330572 ATATATATAAGTTATTAAGTTAGGTAAGTTATGTGAGTTATTTA-AGTAATGGTATG
1 ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAGA-TAATGATATG
*
6330628 ATATATATATA-TAAGTT-A-TTATGTAAGTTATGT
1 ATATATATA-AGTTA-TTAAGTTATGTAAGTTATGT
6330661 ATATTATGTA
Statistics
Matches: 154, Mismatches: 24, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
46 19 0.12
48 3 0.02
50 3 0.02
51 29 0.19
52 3 0.02
54 3 0.02
55 15 0.10
56 76 0.49
57 3 0.02
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (56 bp):
ATATATATAAGTTATTAAGTTATGTAAGTTATGTGAGTTATGTAGATAATGATATG
Found at i:6330650 original size:102 final size:102
Alignment explanation
Indices: 6330437--6330673 Score: 291
Period size: 102 Copynumber: 2.3 Consensus size: 102
6330427 GTTAAGTTAT
* * *
6330437 GTAAGTTATCTGAGTTATGTAGATTATGATATGGTGCATATAAGTTATTAAGTTAGGTAAGTTAT
1 GTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAAGTTAT
* * *
6330502 GCAAGTTATATAAGTTATGATATATATAAGTTGTTAT
66 GCAAGTTATATAAGTAATGATATATATAAGTTGATAA
*
6330539 GTAAGTTATGTGAGTTATGTAGATTATGATATGATATATATAAGTTATTAAGTTAGGTAAGTTAT
1 GTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAAGTTAT
** * *
6330604 GTGAGTTATTTAAGTAATGGTATGATATATA-TAT-ATAA
66 GCAAGTTATATAAGTAATGATAT-ATATA-AGT-TGATAA
* * *
6330642 GTTA-TTATGTAAGTTATGTATATTATGTATAT
1 GTAAGTTATGTGAGTTATGTAGATTATG-ATAT
6330674 CATTGCTCAC
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
102 100 0.85
103 15 0.13
104 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (102 bp):
GTAAGTTATGTGAGTTATGTAGATTATGATATGATACATATAAGTTATTAAGTTAGGTAAGTTAT
GCAAGTTATATAAGTAATGATATATATAAGTTGATAA
Found at i:6334151 original size:12 final size:12
Alignment explanation
Indices: 6334136--6334169 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
6334126 ACGTTGTGCC
6334136 TGGCCGTGTGGT
1 TGGCCGTGTGGT
6334148 TGGCCGTGTGGT
1 TGGCCGTGTGGT
6334160 TGGCCGTGTG
1 TGGCCGTGTG
6334170 CGAGACATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.50, T:0.32
Consensus pattern (12 bp):
TGGCCGTGTGGT
Found at i:6336489 original size:43 final size:43
Alignment explanation
Indices: 6336435--6336762 Score: 435
Period size: 43 Copynumber: 7.7 Consensus size: 43
6336425 GTTTTTAGAA
* * * *
6336435 ACAAACACCGCTAAAGACAATGACCTTTAGCGGCGCTTCTCCT
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* *
6336478 ACAAACGCCGCTAAAGACCATAACCTTTAGTGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* * *
6336521 ACAAACGCCGCTAAAGACCATGATCTTTAGAGGCGCTTTTCTC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* *
6336564 ACAAACGCCGCTAAAGACCATGATCTTTAGCAGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* *
6336607 ACAAACACCGCTAAAGACCACGACCTTTAGCGGCGCTTTTCCC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* *
6336650 AGAAACGCCGCTAAAGACCACGACCTTTAGCGGCGC-TTTCCC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* * * *
6336692 ACAAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTTCTCGC
1 ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
* * * *
6336735 AAAAACGCCACTAAA-AACATAACCTTTA
1 ACAAACGCCGCTAAAGACCATGACCTTTA
6336763 AAAAAATTTA
Statistics
Matches: 255, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
42 49 0.19
43 206 0.81
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (43 bp):
ACAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCC
Found at i:6340920 original size:9 final size:10
Alignment explanation
Indices: 6340896--6340924 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
6340886 GTTAAATTTA
6340896 ATTTTTTATT
1 ATTTTTTATT
6340906 ATTTTTTATT
1 ATTTTTTATT
6340916 ATTTTTTAT
1 ATTTTTTAT
6340925 AAATTGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:6341316 original size:26 final size:26
Alignment explanation
Indices: 6341287--6341349 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
6341277 AATCTAAATT
* **
6341287 CTAAACCCTAACCCGACCTTGAATCC
1 CTAAACCCTAACCCAACCCAGAATCC
6341313 CTAAACCCTAACCCAACCCAGAATCC
1 CTAAACCCTAACCCAACCCAGAATCC
*
6341339 CTAACCCCTAA
1 CTAAACCCTAA
6341350 ACATTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.44, G:0.05, T:0.16
Consensus pattern (26 bp):
CTAAACCCTAACCCAACCCAGAATCC
Found at i:6341430 original size:15 final size:16
Alignment explanation
Indices: 6341404--6341435 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
6341394 CCTAACCTCT
6341404 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
6341420 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
6341435 A
1 A
6341436 CTGATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:6341666 original size:13 final size:13
Alignment explanation
Indices: 6341648--6341674 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6341638 ATTAAATATT
6341648 TTAAAATTAATAC
1 TTAAAATTAATAC
6341661 TTAAAATTAATAC
1 TTAAAATTAATAC
6341674 T
1 T
6341675 CTAATTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAATTAATAC
Found at i:6342234 original size:41 final size:41
Alignment explanation
Indices: 6342172--6342494 Score: 497
Period size: 41 Copynumber: 7.9 Consensus size: 41
6342162 TTTTATTATT
* * *
6342172 ATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGATCC-GAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-GCCAGAGC
*
6342213 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * *
6342254 ATTAGCGGCGCTTATTTAAAAACGCCGCTAAAGATCC-GAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-GCCAGAGC
*
6342295 ATTAGCGGCGCTTCTTCAAAAACGCTGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
6342336 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
6342377 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * *
6342418 ATTAGCGACGCTTCTTTAAAAACGCCGCTAAAGGCCAGTGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
*
6342459 ATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
6342495 CCAAAAACTT
Statistics
Matches: 258, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.02
41 252 0.98
42 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:6342664 original size:39 final size:39
Alignment explanation
Indices: 6342550--6342664 Score: 112
Period size: 39 Copynumber: 3.0 Consensus size: 39
6342540 CGCTTTTCAG
*
6342550 AAAA-CGCCGCTAATGCT-TATTTTTAGCT-GCGTTTTCGA
1 AAAAGCGCCGCTAATGCTCTATTTTTAG-TGGCGTTTT-TA
** * **
6342588 AAAAGCGCCGCTAATGCTCTACCTTTAGCGGAATTTTTA
1 AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTA
*
6342627 TAAAAGCGCCGC-AATGCTCAATTTTTAGTGGCGTTTTT
1 -AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTT
6342665 TGTTCAAACG
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
38 4 0.07
39 34 0.56
40 23 0.38
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTCTATTTTTAGTGGCGTTTTTA
Found at i:6361054 original size:12 final size:12
Alignment explanation
Indices: 6361037--6361061 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6361027 ACTTAATCAC
6361037 TTTAATATTAAA
1 TTTAATATTAAA
6361049 TTTAATATTAAA
1 TTTAATATTAAA
6361061 T
1 T
6361062 CTTGTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:6361177 original size:12 final size:13
Alignment explanation
Indices: 6361132--6361186 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
6361122 AATAGTCATT
6361132 TTAATATTAAACTA
1 TTAATATTAAA-TA
* *
6361146 TTAAGA-TAAGTA
1 TTAATATTAAATA
6361158 TTAA-ATTAAAT-
1 TTAATATTAAATA
6361169 TTAATATTAAACTA
1 TTAATATTAAA-TA
6361183 TTAA
1 TTAA
6361187 AATAATATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 5 0.15
12 16 0.47
13 4 0.12
14 9 0.26
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (13 bp):
TTAATATTAAATA
Found at i:6361945 original size:15 final size:16
Alignment explanation
Indices: 6361912--6361945 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6361902 TGCAATTCGT
*
6361912 TTTTAAAATCATAATA
1 TTTTAAAATCATAAAA
6361928 TTTTAAAAT-ATAAAA
1 TTTTAAAATCATAAAA
6361943 TTT
1 TTT
6361946 AAATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTAAAATCATAAAA
Found at i:6362697 original size:11 final size:11
Alignment explanation
Indices: 6362681--6362716 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
6362671 CTTCTTGTTG
6362681 TTTTTTGCTAT
1 TTTTTTGCTAT
*
6362692 TTTTTTGTTAT
1 TTTTTTGCTAT
*
6362703 TTTTTTACTAT
1 TTTTTTGCTAT
6362714 TTT
1 TTT
6362717 ACTACCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTGCTAT
Found at i:6365755 original size:23 final size:23
Alignment explanation
Indices: 6365702--6365783 Score: 103
Period size: 23 Copynumber: 3.4 Consensus size: 23
6365692 GAGCCATGAT
6365702 CGGTAAGCTC-ATTCCGAGCTGATAAA
1 CGGTAAGCTCTA-T-CGAGCTG--AAA
6365728 CGGTAAGCTCTATCGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
* *
6365751 CGGTAAGCTCTGTAGAGCTGAAA
1 CGGTAAGCTCTATCGAGCTGAAA
6365774 CGGTAAGCTC
1 CGGTAAGCTC
6365784 ATACAAGCTG
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
23 34 0.64
25 7 0.13
26 11 0.21
27 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCTATCGAGCTGAAA
Found at i:6365792 original size:23 final size:23
Alignment explanation
Indices: 6365702--6365793 Score: 98
Period size: 23 Copynumber: 3.9 Consensus size: 23
6365692 GAGCCATGAT
*
6365702 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
6365728 CGGTAAGCTC-TATCGAGCTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
*
6365751 CGGTAAGCTCTGTA-GAGCTGAAA
1 CGGTAAGCTC-ATACGAGCTGAAA
*
6365774 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACGAGCTG
6365794 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
22 2 0.03
23 37 0.63
24 1 0.02
25 9 0.15
26 10 0.17
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:6368981 original size:18 final size:18
Alignment explanation
Indices: 6368955--6369004 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
6368945 ATCATTGGTT
*
6368955 TCAGATTCCTCTTTATTC
1 TCAGCTTCCTCTTTATTC
*
6368973 TCAGCTTCCTCTTCATTC
1 TCAGCTTCCTCTTTATTC
6368991 TCAGCTTCCTCTTT
1 TCAGCTTCCTCTTT
6369005 GTTATTAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.12, C:0.34, G:0.06, T:0.48
Consensus pattern (18 bp):
TCAGCTTCCTCTTTATTC
Found at i:6370479 original size:41 final size:41
Alignment explanation
Indices: 6370429--6370685 Score: 399
Period size: 41 Copynumber: 6.3 Consensus size: 41
6370419 AATTCATCAT
*
6370429 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* *
6370470 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATA-ACTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
6370510 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
6370551 ATTTAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
6370592 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
6370633 ATTTAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
6370674 ATTCATATCACC
1 ATTCAGATCACC
6370686 AATTCCAAAC
Statistics
Matches: 195, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 37 0.19
41 158 0.81
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:6370634 original size:82 final size:82
Alignment explanation
Indices: 6370435--6370685 Score: 486
Period size: 82 Copynumber: 3.1 Consensus size: 82
6370425 TCATATTCGG
*
6370435 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
6370500 TTTATAA-CTGATTCAT
66 TTTATAACCTGATTCAT
6370516 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
6370581 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6370598 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
6370663 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6370680 ATCACC
1 ATCACC
6370686 AATTCCAAAC
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
81 71 0.42
82 97 0.58
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:6378206 original size:41 final size:41
Alignment explanation
Indices: 6378156--6378413 Score: 417
Period size: 41 Copynumber: 6.3 Consensus size: 41
6378146 AATTCATCAT
* *
6378156 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
6378197 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6378238 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6378279 ATTTAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
* *
6378320 ATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
6378361 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
6378402 ATTCATATCACC
1 ATTCAGATCACC
6378414 AATTCCAAAC
Statistics
Matches: 199, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 199 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:6378299 original size:82 final size:82
Alignment explanation
Indices: 6378162--6378413 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
6378152 TCATATTCGG
6378162 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
6378227 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
*
6378244 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
6378309 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6378326 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
6378391 TTTATAACCTGATTCAT
66 TTTATAACCTGATTCAT
6378408 ATCACC
1 ATCACC
6378414 AATTCCAAAC
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 168 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (82 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
TTTATAACCTGATTCAT
Found at i:6378651 original size:19 final size:19
Alignment explanation
Indices: 6378627--6378663 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6378617 TTGTTCGATC
*
6378627 CACACATATATATATATTA
1 CACACATATACATATATTA
6378646 CACACATATACATATATT
1 CACACATATACATATATT
6378664 CGCACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:6383517 original size:7 final size:7
Alignment explanation
Indices: 6383507--6383531 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6383497 TTTTTTTATT
6383507 TTTTAAA
1 TTTTAAA
6383514 TTTTAAA
1 TTTTAAA
6383521 TTTTAAA
1 TTTTAAA
6383528 TTTT
1 TTTT
6383532 TTAATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:6388694 original size:16 final size:17
Alignment explanation
Indices: 6388673--6388704 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6388663 ATGTGCTTTT
6388673 GATGTATA-TATATATG
1 GATGTATATTATATATG
6388689 GATGTATATTATATAT
1 GATGTATATTATATAT
6388705 AGGCACACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (17 bp):
GATGTATATTATATATG
Found at i:6392152 original size:126 final size:126
Alignment explanation
Indices: 6391994--6392249 Score: 424
Period size: 126 Copynumber: 2.0 Consensus size: 126
6391984 CCTCCCGCCA
* *
6391994 TTAAATGGTTGACATGGTAACTTTTAAAATTGACATAATAGCAACTTTAACACTAACGTTTATAC
1 TTAAATGGTTGACATGATAACTTTTAAAATTGACATAATAACAACTTTAACACTAACGTTTATAC
*
6392059 ATTGTATTAAATTATTCTTGA-TTTAAAAAATTTTAACCTTCAACATCTACACATTTGTAAT
66 ATGGTATTAAATTATTCTTGATTTTAAAAAA-TTTAACCTTCAACATCTACACATTTGTAAT
*
6392120 TTAAATGGTTGACATGATAACTTTTAAAATTGACATAATAACAACTTTAGCACTAACGTTTATAC
1 TTAAATGGTTGACATGATAACTTTTAAAATTGACATAATAACAACTTTAACACTAACGTTTATAC
* * * *
6392185 ATGGTGTTAATTTATTCTTGATTTTAAAAAATTTAACTTTCAACATTTACACATTTGTAAT
66 ATGGTATTAAATTATTCTTGATTTTAAAAAATTTAACCTTCAACATCTACACATTTGTAAT
6392246 TTAA
1 TTAA
6392250 TGTTTTTTGC
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
126 112 0.93
127 9 0.07
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (126 bp):
TTAAATGGTTGACATGATAACTTTTAAAATTGACATAATAACAACTTTAACACTAACGTTTATAC
ATGGTATTAAATTATTCTTGATTTTAAAAAATTTAACCTTCAACATCTACACATTTGTAAT
Found at i:6394974 original size:12 final size:13
Alignment explanation
Indices: 6394954--6394987 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
6394944 AAAATGAATC
*
6394954 AAAACAAAACCG-
1 AAAAGAAAACCGA
6394966 AAAAGAAAACCGA
1 AAAAGAAAACCGA
6394979 AAAAGAAAA
1 AAAAGAAAA
6394988 AAAGGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.15, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAGAAAACCGA
Found at i:6397040 original size:30 final size:31
Alignment explanation
Indices: 6396981--6397040 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
6396971 AGAAATAGAG
* *
6396981 TTTTATGTATATATTTGAACTACAATCAAAA
1 TTTTATGTATATAGTTGAACCACAATCAAAA
* *
6397012 TTTTATGTGTATAGTTGCACCA-AATCAAA
1 TTTTATGTATATAGTTGAACCACAATCAAA
6397041 GGTCATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (31 bp):
TTTTATGTATATAGTTGAACCACAATCAAAA
Found at i:6399098 original size:23 final size:22
Alignment explanation
Indices: 6399038--6399104 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
6399028 TTAGAACATG
6399038 TTAATAATAATTTAAAATAATA
1 TTAATAATAATTTAAAATAATA
* * *
6399060 GT-ATACTACATCTTAAAATCATA
1 TTAATAATA-AT-TTAAAATAATA
*
6399083 TTAATAATAAGTTTAAAGTAAT
1 TTAATAATAA-TTTAAAATAAT
6399105 GTCAAATTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 7
0.71 0.15 0.15
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
23 20 0.59
24 6 0.18
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAATAATAATTTAAAATAATA
Found at i:6399224 original size:3 final size:3
Alignment explanation
Indices: 6399216--6399276 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
6399206 AATTCAAAAT
*
6399216 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6399264 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
6399277 CAACAACAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6401923 original size:19 final size:20
Alignment explanation
Indices: 6401881--6401925 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6401871 ATTAAAAATA
* *
6401881 TTTTAAATTATTTTTATAAT
1 TTTTAAATAAATTTTATAAT
*
6401901 TTTTAAATAAATTTTATATT
1 TTTTAAATAAATTTTATAAT
6401921 TTTTA
1 TTTTA
6401926 GTTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAATAAATTTTATAAT
Found at i:6405483 original size:12 final size:12
Alignment explanation
Indices: 6405418--6405547 Score: 66
Period size: 12 Copynumber: 10.3 Consensus size: 12
6405408 AGTGCTTTTC
6405418 TTTTT-TCAAGT
1 TTTTTATCAAGT
*
6405429 ATTTTTCATCTAGT
1 -TTTTT-ATCAAGT
6405443 TCTTTTATCAAGTT
1 T-TTTTATCAAG-T
*
6405457 TTTAATTACCAAGT
1 TTT--TTATCAAGT
6405471 TTTTTATCAAGT
1 TTTTTATCAAGT
** *
6405483 TTTGCAGCAAGT
1 TTTTTATCAAGT
*
6405495 TCTTTT-TAAAGT
1 T-TTTTATCAAGT
*
6405507 TTTTCATCAAGT
1 TTTTTATCAAGT
* * *
6405519 CTTTTCATAAAAT
1 -TTTTTATCAAGT
**
6405532 TTTCCATCAAGT
1 TTTTTATCAAGT
6405544 TTTT
1 TTTT
6405548 AGTCATTTCG
Statistics
Matches: 90, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
11 3 0.03
12 45 0.50
13 20 0.22
14 15 0.17
15 7 0.08
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTTTATCAAGT
Found at i:6405529 original size:25 final size:24
Alignment explanation
Indices: 6405430--6405548 Score: 89
Period size: 25 Copynumber: 4.8 Consensus size: 24
6405420 TTTTCAAGTA
* *
6405430 TTTTTCATCTAGTTCTTTTATCAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
* * *
6405455 TTTTTAATTACCAAGTTTTTTATCAAG
1 TTTTTCA-T--CAAGTCTTTTATAAAG
* *
6405482 TTTTGCAGCAAGTTCTTTT-TAAAG
1 TTTTTCATCAAG-TCTTTTATAAAG
*
6405506 TTTTTCATCAAGTCTTTTCATAAAA
1 TTTTTCATCAAGTCTTTT-ATAAAG
*
6405531 TTTTCCATCAAGT-TTTTA
1 TTTTTCATCAAGTCTTTTA
6405549 GTCATTTCGT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
23 7 0.09
24 22 0.29
25 27 0.36
26 1 0.01
27 16 0.21
28 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.51
Consensus pattern (24 bp):
TTTTTCATCAAGTCTTTTATAAAG
Found at i:6405547 original size:24 final size:23
Alignment explanation
Indices: 6405466--6405548 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 23
6405456 TTTTAATTAC
* * *
6405466 CAAGTTTTTTATCAAGTTTTGCAG
1 CAAG-TTTTTATAAAGTTTTCCAT
* *
6405490 CAAGTTCTTTTTAAAGTTTTTCAT
1 CAAGTT-TTTATAAAGTTTTCCAT
*
6405514 CAAGTCTTTTCATAAAATTTTCCAT
1 CAAGT-TTTT-ATAAAGTTTTCCAT
6405539 CAAGTTTTTA
1 CAAGTTTTTA
6405549 GTCATTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.06
24 29 0.59
25 17 0.35
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (23 bp):
CAAGTTTTTATAAAGTTTTCCAT
Found at i:6412287 original size:3 final size:3
Alignment explanation
Indices: 6412279--6412335 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
6412269 TTAATTTTCC
* *
6412279 TAT TAT TAT TAT TAT TAT TATT TAT TTT TAC TAT T-T TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* *
6412323 TTT TAT TTT TAT T
1 TAT TAT TAT TAT T
6412336 TTTGCAGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (3 bp):
TAT
Found at i:6412313 original size:19 final size:19
Alignment explanation
Indices: 6412281--6412337 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
6412271 AATTTTCCTA
* *
6412281 TTATTATTATTATTATTA-T
1 TTATTTTTACTATT-TTATT
6412300 TTATTTTTACTATTTTATT
1 TTATTTTTACTATTTTATT
6412319 TTATTTTTA-T-TTTTATT
1 TTATTTTTACTATTTTATT
6412336 TT
1 TT
6412338 TGCAGGAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.26
18 4 0.11
19 22 0.63
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATTTTTACTATTTTATT
Found at i:6412336 original size:6 final size:6
Alignment explanation
Indices: 6412281--6412338 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
6412271 AATTTTCCTA
* *
6412281 TTATTA TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT TTATTT
1 TTATTT TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT TTATTT
6412331 TTATTT TT
1 TTATTT TT
6412339 GCAGGAAACA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.11
6 31 0.66
7 6 0.13
8 5 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:6412338 original size:13 final size:13
Alignment explanation
Indices: 6412287--6412338 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
6412277 CCTATTATTA
* *
6412287 TTATTATTATTAT
1 TTATTTTTATTTT
*
6412300 TTATTTTTACTATT
1 TTATTTTTA-TTTT
6412314 TTA-TTTTA-TTT
1 TTATTTTTATTTT
6412325 TTATTTTTATTTT
1 TTATTTTTATTTT
6412338 T
1 T
6412339 GCAGGAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 5 0.16
12 5 0.16
13 17 0.53
14 5 0.16
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATTTTTATTTT
Found at i:6413792 original size:12 final size:12
Alignment explanation
Indices: 6413702--6413826 Score: 63
Period size: 12 Copynumber: 9.8 Consensus size: 12
6413692 TCTTCAAGTA
*
6413702 TTTTTCATCTAG
1 TTTTTCATCAAG
*
6413714 TTCTTTTATCAAG
1 TT-TTTCATCAAG
*
6413727 TTTTTAATTACCAAG
1 TTTTTCA-T--CAAG
* *
6413742 TTTTTTTATCAAA
1 -TTTTTCATCAAG
*
6413755 TTTTTGCAGCAAG
1 TTTTT-CATCAAG
* *
6413768 TTCTTT-TTAAAG
1 TT-TTTCATCAAG
6413780 TTTTTCATCAAG
1 TTTTTCATCAAG
* *
6413792 TCTTTTCATAAAA
1 T-TTTTCATCAAG
*
6413805 TTTTCCATCAAG
1 TTTTTCATCAAG
*
6413817 TTTTTAATCA
1 TTTTTCATCA
6413827 TTTCGTTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
11 3 0.04
12 37 0.44
13 30 0.36
14 3 0.04
15 5 0.06
16 6 0.07
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.51
Consensus pattern (12 bp):
TTTTTCATCAAG
Done.