Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold291
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: 742724
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 5
Found at i:267264 original size:22 final size:20
Alignment explanation
Indices: 267214--267265 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
267204 ATAAAATATT
267214 TATTTTTATA-AAATTAATA
1 TATTTTTATATAAATTAATA
* **
267233 CATTAATATATAAATCTTAATA
1 TATTTTTATATAAA--TTAATA
267255 TATTTTTATAT
1 TATTTTTATAT
267266 TTATATTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 7 0.29
20 3 0.12
22 14 0.58
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTTTTATATAAATTAATA
Found at i:268069 original size:2 final size:2
Alignment explanation
Indices: 268062--268089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
268052 TATTGCTTTA
268062 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
268090 GAAATTTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:269206 original size:30 final size:29
Alignment explanation
Indices: 269145--269217 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
269135 TTTACTACTT
* * *
269145 TATTTAAATAAATTTTTATATTTTTATTA
1 TATTTAAATAAATTTTAAAATTTTAATTA
269174 TATTTAAATAAATTTTAAAATTTTAAATTA
1 TATTTAAATAAATTTTAAAATTTT-AATTA
*
269204 TATCTAAA-AAATTT
1 TATTTAAATAAATTT
269218 AATATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTTAAATAAATTTTAAAATTTTAATTA
Found at i:269584 original size:22 final size:23
Alignment explanation
Indices: 269559--269608 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
269549 TATTTGAGTG
269559 TAATAAAATAT-AAAATTTATTT
1 TAATAAAATATAAAAATTTATTT
269581 TAATAAAATATAAAAATTTATTT
1 TAATAAAATATAAAAATTTATTT
*
269604 AAATA
1 TAATA
269609 TTTTAACCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAATATAAAAATTTATTT
Found at i:269604 original size:27 final size:27
Alignment explanation
Indices: 269536--269604 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
269526 ATAAAAATAA
269536 AAAATA-AAAAATTTATTTGAGTGTAAT
1 AAAATATAAAAATTTATTT-AGTGTAAT
269563 AAAATAT-AAAATTTA-TT--T-TAAT
1 AAAATATAAAAATTTATTTAGTGTAAT
269585 AAAATATAAAAATTTATTTA
1 AAAATATAAAAATTTATTTA
269605 AATATTTTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
22 11 0.29
23 9 0.24
24 2 0.05
26 2 0.05
27 14 0.37
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (27 bp):
AAAATATAAAAATTTATTTAGTGTAAT
Found at i:269733 original size:5 final size:5
Alignment explanation
Indices: 269693--269785 Score: 61
Period size: 5 Copynumber: 18.6 Consensus size: 5
269683 GCTTGCAACC
* **
269693 TTATA TTTATG TTATA TTA-A TT-TA AAATA TTCATA TTATA TTTATA
1 TTATA -TTATA TTATA TTATA TTATA TTATA TT-ATA TTATA -TTATA
* *
269739 TTA-A TT-T- TTTTA TTATA TTATA TTATAA TTATTT TTATA TTATA TTA
1 TTATA TTATA TTATA TTATA TTATA TTAT-A TTA-TA TTATA TTATA TTA
269786 ACCGTTTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
3 2 0.03
4 8 0.12
5 37 0.54
6 21 0.30
7 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:269739 original size:11 final size:11
Alignment explanation
Indices: 269693--269784 Score: 69
Period size: 11 Copynumber: 9.1 Consensus size: 11
269683 GCTTGCAACC
269693 TTATATT-TAT
1 TTATATTATAT
269703 GTTATATTA-AT
1 -TTATATTATAT
*
269714 TTA-A-AATAT
1 TTATATTATAT
*
269723 TCATATTATAT
1 TTATATTATAT
269734 TTATATTA-AT
1 TTATATTATAT
269744 TT-T-TT-TA-
1 TTATATTATAT
269751 TTATATTATA-
1 TTATATTATAT
*
269761 TTATAATTATTT
1 TTAT-ATTATAT
269773 TTATATTATAT
1 TTATATTATAT
269784 T
1 T
269785 AACCGTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 8 0.12
10 14 0.22
11 32 0.49
12 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
TTATATTATAT
Found at i:269751 original size:20 final size:20
Alignment explanation
Indices: 269728--269800 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
269718 AATATTCATA
269728 TTATATTTATATTAATTTTT
1 TTATATTTATATTAATTTTT
269748 TTATTATATTATATTATAATTATTT
1 TTA-TAT-TTATA-T-TAATT-TTT
**
269773 TTATA-TTATATTAACCGTTT
1 TTATATTTATATTAA-TTTTT
269793 TTATATTT
1 TTATATTT
269801 TAAAATAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
20 14 0.32
21 6 0.14
22 10 0.23
23 1 0.02
24 7 0.16
25 6 0.14
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (20 bp):
TTATATTTATATTAATTTTT
Found at i:269762 original size:22 final size:22
Alignment explanation
Indices: 269704--269786 Score: 80
Period size: 22 Copynumber: 3.6 Consensus size: 22
269694 TATATTTATG
*
269704 TTATATTA-ATTTAAAATATTCATA
1 TTATATTATA-TTAAATTATT--TA
* *
269728 TTATATTTATATTAATTTTTTTA
1 TTATA-TTATATTAAATTATTTA
269751 TTATATTATATTATAATTATTT-
1 TTATATTATATTA-AATTATTTA
269773 TTATATTATATTAA
1 TTATATTATATTAA
269787 CCGTTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.02
22 21 0.41
23 13 0.25
24 5 0.10
25 10 0.20
26 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATTATATTAAATTATTTA
Found at i:270632 original size:12 final size:13
Alignment explanation
Indices: 270612--270645 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
270602 AATAGTTTTT
*
270612 ATATTTTAATTTG
1 ATATTTTAATTTA
270625 AT-TTTTAATTTA
1 ATATTTTAATTTA
270637 ATATTTTAA
1 ATATTTTAA
270646 AAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
ATATTTTAATTTA
Found at i:271035 original size:17 final size:18
Alignment explanation
Indices: 271010--271043 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
271000 TGATAATTTT
271010 TAACGTATT-AAAAATTA
1 TAACGTATTGAAAAATTA
*
271027 TAACTTATTGAAAAATT
1 TAACGTATTGAAAAATT
271044 TTAAGAGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (18 bp):
TAACGTATTGAAAAATTA
Found at i:271187 original size:29 final size:28
Alignment explanation
Indices: 271137--271227 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 28
271127 AAATTTTTTT
*
271137 AAATAAAATAATATTTTAATATAAATTAA
1 AAATAAAA-AATATTTAAATATAAATTAA
271166 ATAATAAAAAATATTTAAATATAAATTAA
1 A-AATAAAAAATATTTAAATATAAATTAA
* *
271195 AAATAAAAATATACTTT-TATTTAAATTAA
1 AAATAAAAA-ATA-TTTAAATATAAATTAA
271224 AAAT
1 AAAT
271228 TATTTTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
28 8 0.14
29 38 0.68
30 10 0.18
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATAAAAAATATTTAAATATAAATTAA
Found at i:271425 original size:21 final size:21
Alignment explanation
Indices: 271386--271425 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
271376 TAAAAAATAT
*
271386 TATTTTATATTAATATTTATA
1 TATTTTATATAAATATTTATA
271407 TATTTTATAATAAAT-TTTA
1 TATTTTAT-ATAAATATTTA
271426 AGTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATATAAATATTTATA
Found at i:273528 original size:124 final size:123
Alignment explanation
Indices: 273309--273556 Score: 424
Period size: 124 Copynumber: 2.0 Consensus size: 123
273299 AGAGATGCAT
* * *
273309 ATCTTTTATTCCATCTTTCCTCAGCCACGGGTACTAGTGATAGTGACCAAAGAGTTGTTAGCGTT
1 ATCTTTTATTCCATCTTTCCTCAGCCACGGGTACTAGTGATAGCGACCAAAGAGTTATTAGCATT
273374 GCTAACATGTTTGTTAGGTGTCTACGGTTCTCTGTTTATCGGGTGTTTTGGATACAGA
66 GCTAACATGTTTGTTAGGTGTCTACGGTTCTCTGTTTATCGGGTGTTTTGGATACAGA
* *
273432 ATCTTTTATTCCATCTTTCCTCAGCCATGGGTTACTAGTGATGGCGACCAAAGAGTTATTAGCAT
1 ATCTTTTATTCCATCTTTCCTCAGCCACGGG-TACTAGTGATAGCGACCAAAGAGTTATTAGCAT
* *
273497 TGCTAACATGTTTGTTTGGTGTTTACGGTTCTCTGTTTATCGGGTGTTTTGGATACAGA
65 TGCTAACATGTTTGTTAGGTGTCTACGGTTCTCTGTTTATCGGGTGTTTTGGATACAGA
273556 A
1 A
273557 CACATAGTTA
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
123 30 0.26
124 87 0.74
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.39
Consensus pattern (123 bp):
ATCTTTTATTCCATCTTTCCTCAGCCACGGGTACTAGTGATAGCGACCAAAGAGTTATTAGCATT
GCTAACATGTTTGTTAGGTGTCTACGGTTCTCTGTTTATCGGGTGTTTTGGATACAGA
Found at i:274467 original size:13 final size:13
Alignment explanation
Indices: 274449--274473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
274439 TTATTTTTTA
274449 AATATTTATATTC
1 AATATTTATATTC
274462 AATATTTATATT
1 AATATTTATATT
274474 TGATGTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTATATTC
Found at i:274547 original size:15 final size:15
Alignment explanation
Indices: 274527--274579 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 15
274517 AAATAAAAAA
274527 ATTAAATATATTTAT
1 ATTAAATATATTTAT
274542 ATTAAAAATATATTTAT
1 ATT--AAATATATTTAT
*
274559 A-T-AAGATATTTAT
1 ATTAAATATATTTAT
274572 ATTTAAAT
1 A-TTAAAT
274580 TTAAATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.35
15 4 0.13
16 3 0.10
17 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:282092 original size:3 final size:3
Alignment explanation
Indices: 282084--282119 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
282074 ATCTCAAGAA
* *
282084 ATT ATT ATT ATT ATT ATT ATA ATT ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
282120 TCATGTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:283941 original size:22 final size:23
Alignment explanation
Indices: 283898--283951 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
283888 AAAAATATGG
283898 TTAAAATATTTTTTTTATTATTT
1 TTAAAATATTTTTTTTATTATTT
283921 TTAAAAT-TTTTTATTTA-TATTT
1 TTAAAATATTTTT-TTTATTATTT
* *
283943 GTACAATAT
1 TTAAAATAT
283952 ATATCTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TTAAAATATTTTTTTTATTATTT
Found at i:284014 original size:21 final size:20
Alignment explanation
Indices: 283990--284032 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
283980 ATTAACCTTA
*
283990 AAAATAAATATAATTAATCAT
1 AAAATAAATATAATAAAT-AT
*
284011 AAAATAAATTTAATAAATAT
1 AAAATAAATATAATAAATAT
284031 AA
1 AA
284033 TTATTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATAAATATAATAAATAT
Found at i:288523 original size:21 final size:21
Alignment explanation
Indices: 288485--288525 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
288475 TAGAAAGGTA
*
288485 CTTAAAAATTAATTTTTTTTT
1 CTTAAAAATTAATATTTTTTT
* *
288506 CTTAAAAGTTTATATTTTTT
1 CTTAAAAATTAATATTTTTT
288526 ATCTCGGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
CTTAAAAATTAATATTTTTTT
Found at i:289034 original size:19 final size:20
Alignment explanation
Indices: 288995--289035 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
288985 AAATTTTTAT
*
288995 TTTTAAATATTTATATAAAA
1 TTTTAAATATGTATATAAAA
*
289015 TTTTAAATA-GTATTTAAAA
1 TTTTAAATATGTATATAAAA
289034 TT
1 TT
289036 AAAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTAAATATGTATATAAAA
Found at i:289951 original size:18 final size:18
Alignment explanation
Indices: 289928--289969 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
289918 TGTTAAGTAA
289928 ATAAATATAATTTATTAT
1 ATAAATATAATTTATTAT
* **
289946 ATAAATTTCTTTTATTAT
1 ATAAATATAATTTATTAT
289964 A-AAATA
1 ATAAATA
289970 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATAAATATAATTTATTAT
Found at i:290749 original size:18 final size:19
Alignment explanation
Indices: 290709--290750 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
290699 TTGAATTTTA
*
290709 AAATTATTTAATACTAATT
1 AAATTATATAATACTAATT
*
290728 -AATTATATAA-ACTATTT
1 AAATTATATAATACTAATT
290745 AAATTA
1 AAATTA
290751 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTATATAATACTAATT
Found at i:293438 original size:16 final size:15
Alignment explanation
Indices: 293419--293520 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 15
293409 ATATAATTTC
293419 ATAAATATAATATTAT
1 ATAAATAT-ATATTAT
*
293435 ATAAATATATATTTT
1 ATAAATATATATTAT
* *
293450 A-AAATTTATATAAT
1 ATAAATATATATTAT
293464 AT-AA-AT-TATTAT
1 ATAAATATATATTAT
*
293476 ATCAA-A-AT-TTAT
1 ATAAATATATATTAT
293488 ATAAATATA-A-TAT
1 ATAAATATATATTAT
*
293501 A-AATATATAAATTAT
1 ATAA-ATATATATTAT
293516 A-AAAT
1 ATAAAT
293521 TTAATTTATT
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
12 17 0.24
13 15 0.21
14 17 0.24
15 13 0.19
16 8 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAAATATATATTAT
Found at i:293460 original size:29 final size:29
Alignment explanation
Indices: 293428--293497 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
293418 CATAAATATA
* * *
293428 ATATTATATAAA-TATATATTTTAAAATTT
1 ATATAATATAAATTAT-TATATCAAAATTT
293457 ATATAATATAAATTATTATATCAAAATTT
1 ATATAATATAAATTATTATATCAAAATTT
293486 ATATAAATATAA
1 ATAT-AATATAA
293498 TATAAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
ATATAATATAAATTATTATATCAAAATTT
Found at i:293502 original size:11 final size:11
Alignment explanation
Indices: 293457--293507 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
293447 TTTAAAATTT
293457 ATATAATATAA
1 ATATAATATAA
*
293468 ATTATTATATCAA
1 A-TATAATAT-AA
*
293481 A-ATTTATATAA
1 ATA-TAATATAA
293492 ATATAATATAA
1 ATATAATATAA
293503 ATATA
1 ATATA
293508 TAAATTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 17 0.50
12 14 0.41
13 3 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATATAATATAA
Found at i:293513 original size:29 final size:30
Alignment explanation
Indices: 293449--293511 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
293439 ATATATATTT
* *
293449 TAAAATTTATAT-AATATAA-ATTATTATA
1 TAAAATTTATATAAATATAATATAAATATA
293477 TCAAAATTTATATAAATATAATATAAATATA
1 T-AAAATTTATATAAATATAATATAAATATA
293508 TAAA
1 TAAA
293512 TTATAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 10 0.33
31 8 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAAATTTATATAAATATAATATAAATATA
Found at i:294911 original size:27 final size:28
Alignment explanation
Indices: 294881--294945 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 28
294871 ATATTTTATC
294881 ATATTATAATAATATTT-ATT-A-TTTAAA
1 ATATTATAAT-AT-TTTAATTAATTTTAAA
*
294908 ATATT-TTATATTTTAATTAATTTTAAA
1 ATATTATAATATTTTAATTAATTTTAAA
294935 ATATTAATAAT
1 ATATT-ATAAT
294946 TCGTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
24 3 0.10
25 5 0.16
26 4 0.13
27 16 0.52
29 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATATTATAATATTTTAATTAATTTTAAA
Found at i:297795 original size:19 final size:19
Alignment explanation
Indices: 297776--297815 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
297766 ATATAATTTT
297776 ATATAAATTATTTATATTTAA
1 ATAT-AATTATTT-TATTTAA
*
297797 ATATATTTATTTTATTTAA
1 ATATAATTATTTTATTTAA
297816 TTAATTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATAATTATTTTATTTAA
Found at i:297810 original size:15 final size:15
Alignment explanation
Indices: 297761--297810 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
297751 TTTATTTATT
* *
297761 TATTTATATAATTT-
1 TATTTAAATTATTTA
*
297775 TATATAAATTATTTA
1 TATTTAAATTATTTA
297790 TATTTAAATATATTTA
1 TATTTAAAT-TATTTA
297806 T-TTTA
1 TATTTA
297811 TTTAATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 11 0.37
15 12 0.40
16 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTAAATTATTTA
Found at i:299145 original size:21 final size:23
Alignment explanation
Indices: 299097--299147 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
299087 ATATTAGTTC
299097 TAATTA-ATGTTTAATTAAATAA
1 TAATTATATGTTTAATTAAATAA
* *
299119 TAATTATAT-TTTATTTAAAT-T
1 TAATTATATGTTTAATTAAATAA
299140 TAATTATA
1 TAATTATA
299148 AAAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATTATATGTTTAATTAAATAA
Found at i:299226 original size:15 final size:17
Alignment explanation
Indices: 299191--299227 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
299181 TATTTCAAAT
*
299191 AATAATTTAAACTTTTA
1 AATAATTTAAACTTATA
299208 AATAATTT-AA-TTATA
1 AATAATTTAAACTTATA
299223 AATAA
1 AATAA
299228 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAATTTAAACTTATA
Found at i:299350 original size:26 final size:27
Alignment explanation
Indices: 299297--299350 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
299287 CATTATTTAA
* *
299297 TAAAAAAATTTAAATCAAACTTTTATT
1 TAAAAAAATTTAAATCAAAATTTGATT
* *
299324 TAAAAAAA-TTCAATTAAAATTTGATT
1 TAAAAAAATTTAAATCAAAATTTGATT
299350 T
1 T
299351 GATATGTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.41
Consensus pattern (27 bp):
TAAAAAAATTTAAATCAAAATTTGATT
Found at i:299991 original size:26 final size:26
Alignment explanation
Indices: 299962--300012 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
299952 TTAATAAGTT
*
299962 TAATTCGAATTTGA-TTTAATTTAAAA
1 TAATTAGAATTT-ATTTTAATTTAAAA
*
299988 TAATTATAATTTATTTTAATTTAAA
1 TAATTAGAATTTATTTTAATTTAAA
300013 TTTAATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
TAATTAGAATTTATTTTAATTTAAAA
Found at i:300586 original size:22 final size:21
Alignment explanation
Indices: 300544--300602 Score: 55
Period size: 24 Copynumber: 2.6 Consensus size: 21
300534 GAAATAAAAA
*
300544 TTAAATTATAAATATTGAGAT
1 TTAAATTAAAAATATTGAGAT
*
300565 TTAAATATAAAAATTATTAGATAT
1 TTAAAT-TAAAAA-TATT-GAGAT
*
300589 TTATATTTAAAAAT
1 TTA-AATTAAAAAT
300603 GATTACATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.19
22 5 0.16
23 5 0.16
24 13 0.42
25 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
TTAAATTAAAAATATTGAGAT
Found at i:300859 original size:20 final size:20
Alignment explanation
Indices: 300831--300890 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
300821 ATAAATTTAA
300831 AATTAAATTTTTATTGATTT
1 AATTAAATTTTTATTGATTT
* *
300851 AATTTAATTTTTTATCGA-TT
1 AA-TTAAATTTTTATTGATTT
* * *
300871 AAATCAATTTTTATTAATTT
1 AATTAAATTTTTATTGATTT
300891 TGTGACTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 10 0.32
20 8 0.26
21 13 0.42
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTAAATTTTTATTGATTT
Found at i:303073 original size:23 final size:23
Alignment explanation
Indices: 303046--303204 Score: 63
Period size: 20 Copynumber: 7.2 Consensus size: 23
303036 TGTAATAATT
303046 TATTTATTTATATTATATTTATA
1 TATTTATTTATATTATATTTATA
* *
303069 TATTT-TATCATATTATA-AT-TA
1 TATTTAT-TTATATTATATTTATA
** *
303090 TATTTA-AAATATTTTA-TT-TA
1 TATTTATTTATATTATATTTATA
* * *
303110 TATTAATTT-TAATATATTAATA
1 TATTTATTTATATTATATTTATA
*
303132 -ATTTATATTATA-TAAATTTTATAA
1 TATTTAT-TTATATTATA-TTTAT-A
** *
303156 TAAATATTTATATCATA-TTATA
1 TATTTATTTATATTATATTTATA
* *
303178 T-TTT-TTTATTTTATATATATTA
1 TATTTATTTATATTATATTTA-TA
303200 TATTT
1 TATTT
303205 GTGTACACGT
Statistics
Matches: 98, Mismatches: 24, Indels: 28
0.65 0.16 0.19
Matches are distributed among these distances:
20 29 0.30
21 16 0.16
22 14 0.14
23 27 0.28
24 6 0.06
25 6 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTTATTTATATTATATTTATA
Found at i:303116 original size:29 final size:28
Alignment explanation
Indices: 303039--303117 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
303029 ACTTAGATGT
*
303039 AATAATTTATTTAT-TTATATTATATTTA
1 AATATTTTATTTATATTA-ATTATATTTA
* *
303067 TATATTTTA-TCATATTATAATTATATTTAA
1 AATATTTTATTTATA-T-TAATTATATTT-A
303097 AATATTTTATTTATATTAATT
1 AATATTTTATTTATATTAATT
303118 TTAATATATT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.07
28 7 0.17
29 15 0.37
30 12 0.29
31 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (28 bp):
AATATTTTATTTATATTAATTATATTTA
Found at i:303150 original size:32 final size:30
Alignment explanation
Indices: 303096--303173 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
303086 ATTATATTTA
* *
303096 AAATATTTTAT-TTATATTAATTTTAATATAT
1 AAATAATTTATATTATATAAATTTT-ATA-AT
*
303127 TAATAATTTATATTATATAAATTTTATAAT
1 AAATAATTTATATTATATAAATTTTATAAT
*
303157 AAAT-ATTTATATCATAT
1 AAATAATTTATATTATAT
303174 TATATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.29
30 5 0.12
31 12 0.29
32 12 0.29
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
AAATAATTTATATTATATAAATTTTATAAT
Found at i:303165 original size:29 final size:31
Alignment explanation
Indices: 303096--303173 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
303086 ATTATATTTA
*
303096 AAATATTT-TATTTATATTAATTTTAATATAT
1 AAATATTTATA-TTATATAAATTTTAATATAT
*
303127 TAATAATTTATATTATATAAATTTT-ATA-AT
1 AAAT-ATTTATATTATATAAATTTTAATATAT
*
303157 AAATATTTATATCATAT
1 AAATATTTATATTATAT
303174 TATATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 12 0.29
30 5 0.12
31 6 0.15
32 16 0.39
33 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (31 bp):
AAATATTTATATTATATAAATTTTAATATAT
Found at i:303661 original size:3 final size:3
Alignment explanation
Indices: 303653--303684 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
303643 CAAGATATTT
303653 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
303685 GATGGCATGT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:305379 original size:17 final size:17
Alignment explanation
Indices: 305353--305387 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
305343 ATATTAAAAT
* *
305353 ATTTACAAATTAAATAA
1 ATTTAAAAATAAAATAA
305370 ATTTAAAAATAAAATAA
1 ATTTAAAAATAAAATAA
305387 A
1 A
305388 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAAAAATAAAATAA
Found at i:305536 original size:24 final size:24
Alignment explanation
Indices: 305482--305536 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
305472 TATCAAATTA
305482 TTAATAATTTTAATCTAAATTATTT
1 TTAAT-ATTTTAATCTAAATTATTT
* * *
305507 TAAATATTTTTATC-AAATTGTGTT
1 TTAATATTTTAATCTAAATTAT-TT
305531 TTAATA
1 TTAATA
305537 AATACACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 6 0.24
24 15 0.60
25 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
TTAATATTTTAATCTAAATTATTT
Found at i:307381 original size:104 final size:101
Alignment explanation
Indices: 307264--307671 Score: 296
Period size: 104 Copynumber: 4.0 Consensus size: 101
307254 ATTATTTGTG
* *
307264 TATAAATTTATACACTAGAAGTTATTCATATCGTGCTATATATTAAAAAAGTATAATTAATATAT
1 TATAAATTTATACACTAGAAG-TA-TCATAT-GTGATACATATTAAAAAAGTATAATTAATATAT
* * *
307329 TTATTCTTAAGAATTTTTTGAATTATTTATTTATTAATA
63 TTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* * * * * * * **
307368 TAAAAATATATACAC-GGACTGTGAATCATAT-TATATCACATATTAAAAAAGTGTAGTTGTTAT
1 TATAAATTTATACACTAGA-AGT--ATCATATGT-GAT-ACATATTAAAAAAGTATAATTAATAT
* * *
307431 ATTTATTTTTAAAAATTTTTACAATTATTTATTTATCAATG
61 ATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* * * *
307472 TATAAATTTATACATTATG-A--ATCATATGATGTTACATATTAAAAAAATATAATTACTATATT
1 TATAAATTTATACACTA-GAAGTATCATATG-TGATACATATTAAAAAAGTATAATTAATATATT
* *
307534 TATTTTTAAAAATATTTAGAAATA-TTATTTATTAATA
64 TATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* ** * * ** * * * *
307571 TATAAATCTATATGCT-GATAGTGAATTATATCATCTTACATTTTAAAAAA-TATAGTT-TTACA
1 TATAAATTTATACACTAGA-AGT--ATCATAT-GTGATACATATTAAAAAAGTATAATTAATATA
* *
307633 -TTATTTTTAAAAATTTTAAAAATTATTTATTTATTAATA
62 TTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
307672 AGGTGTCATT
Statistics
Matches: 238, Mismatches: 49, Indels: 37
0.73 0.15 0.11
Matches are distributed among these distances:
97 1 0.00
99 24 0.10
100 73 0.31
101 17 0.07
102 8 0.03
103 25 0.11
104 88 0.37
105 1 0.00
106 1 0.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (101 bp):
TATAAATTTATACACTAGAAGTATCATATGTGATACATATTAAAAAAGTATAATTAATATATTTA
TTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
Found at i:307532 original size:100 final size:102
Alignment explanation
Indices: 307303--307671 Score: 356
Period size: 100 Copynumber: 3.6 Consensus size: 102
307293 ATCGTGCTAT
* * * * *
307303 ATATTAAAAAAGTATAATTAATATATTTATTCTTAAGAATTTTTTGAATTATTTATTTATTAATA
1 ATATTAAAAAAATATAATTATTATATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* * * * * *
307368 TAAAAATATATACACGGACTGTGAATCATATTATATCAC
66 TATAAATATATATAC--ATTATGAATCATATCATATTAC
* * * * * * *
307407 ATATTAAAAAAGTGTAGTTGTTATATTTATTTTTAAAAATTTTTACAATTATTTATTTATCAATG
1 ATATTAAAAAAATATAATTATTATATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* *
307472 TATAAAT-T-TATACATTATGAATCATATGATGTTAC
66 TATAAATATATATACATTATGAATCATATCATATTAC
* * *
307507 ATATTAAAAAAATATAATTACTATATTTATTTTTAAAAATATTTAGAAATA-TTATTTATTAATA
1 ATATTAAAAAAATATAATTATTATATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
* * * *
307571 TATAAATCTATATGC-TGATAGTGAATTATATCATCTTAC
66 TATAAATATATATACAT--TA-TGAATCATATCATATTAC
* * * * *
307610 AT-TTTAAAAAATATAGTT-TTACA-TTATTTTTAAAAATTTTAAAAATTATTTATTTATTAATA
1 ATATTAAAAAAATATAATTATTATATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
307672 AGGTGTCATT
Statistics
Matches: 220, Mismatches: 39, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
99 18 0.08
100 83 0.38
101 20 0.09
102 20 0.09
103 18 0.08
104 61 0.28
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (102 bp):
ATATTAAAAAAATATAATTATTATATTTATTTTTAAAAATTTTTAGAATTATTTATTTATTAATA
TATAAATATATATACATTATGAATCATATCATATTAC
Found at i:307710 original size:2 final size:2
Alignment explanation
Indices: 307703--307762 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
307693 TATATGCATT
* *
307703 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
307745 TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA
307763 ATAGTTTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:308002 original size:2 final size:2
Alignment explanation
Indices: 307995--308019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
307985 CATCTCCATC
307995 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
308020 ACAAAGTTAA
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:309215 original size:9 final size:9
Alignment explanation
Indices: 309203--309241 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
309193 AAATTCAAAG
309203 TAATTTAAT
1 TAATTTAAT
309212 TAATTTAAAT
1 TAATTT-AAT
309222 TAATTTAAT
1 TAATTTAAT
*
309231 TTATTTAAT
1 TAATTTAAT
309240 TA
1 TA
309242 TCACTTCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTTAAT
Found at i:309219 original size:5 final size:5
Alignment explanation
Indices: 309203--309240 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
309193 AAATTCAAAG
*
309203 TAATT TAA-T TAATT TAAAT TAATT TAATT T-ATT TAATT
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TAATT
309241 ATCACTTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TAATT
Found at i:310353 original size:25 final size:28
Alignment explanation
Indices: 310325--310378 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 28
310315 ATTTATTTTT
310325 TTATA-TTTATTATATATATA--AA-ATA
1 TTATATTTTA-TATATATATATAAATATA
*
310350 TTATATTTTATATTTATATATAAATATA
1 TTATATTTTATATATATATATAAATATA
310378 T
1 T
310379 ATAAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
25 14 0.58
26 4 0.17
27 2 0.08
28 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATATTTTATATATATATATAAATATA
Found at i:310852 original size:13 final size:13
Alignment explanation
Indices: 310832--310865 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
310822 TAAAAATAAA
310832 AAAATTATTCT-T
1 AAAATTATTCTCT
310844 AACAATTATTCTCT
1 AA-AATTATTCTCT
310858 AAAATTAT
1 AAAATTAT
310866 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 15 0.75
14 3 0.15
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTATTCTCT
Found at i:312750 original size:22 final size:21
Alignment explanation
Indices: 312702--312789 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 21
312692 AATTGCGAAA
* *
312702 TTAAAAAAAT-ATATATTTATT
1 TTAAAAAATTAATA-ATATATT
*
312723 TATAAAAAATGTAATAATATTTT
1 T-TAAAAAAT-TAATAATATATT
*
312746 TTAAAAAATTAATAAAATATT
1 TTAAAAAATTAATAATATATT
*
312767 TTAAAATAATATATTAATATATT
1 TTAAAA-AAT-TAATAATATATT
312790 ATATATATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
21 17 0.31
22 18 0.33
23 17 0.31
24 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (21 bp):
TTAAAAAATTAATAATATATT
Found at i:312752 original size:23 final size:22
Alignment explanation
Indices: 312702--312786 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 22
312692 AATTGCGAAA
312702 TTAAAAAAA-T-AT-ATATTTAT
1 TTAAAAAAATTAATAATATTT-T
312722 TTATAAAAAATGTAATAATATTTT
1 TTA-AAAAAAT-TAATAATATTTT
* *
312746 TT-AAAAAATTAATAAAATATT
1 TTAAAAAAATTAATAATATTTT
* *
312767 TTAAAATAATATATTAATAT
1 TTAAAAAAAT-TAATAATAT
312787 ATTATATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
20 3 0.06
21 18 0.34
22 13 0.25
23 8 0.15
24 5 0.09
25 6 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
TTAAAAAAATTAATAATATTTT
Found at i:312966 original size:17 final size:15
Alignment explanation
Indices: 312946--312985 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
312936 TTTTATTAAC
312946 TTTTTATATATTTTATA
1 TTTTTAT-TATTTT-TA
*
312963 TTTTAATTATTTTTA
1 TTTTTATTATTTTTA
312978 TTTTTATT
1 TTTTTATT
312986 TATATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 9 0.43
16 6 0.29
17 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:312982 original size:16 final size:17
Alignment explanation
Indices: 312956--312988 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
312946 TTTTTATATA
312956 TTTTATATTTTAATTAT
1 TTTTATATTTTAATTAT
*
312973 TTTTAT-TTTTATTTAT
1 TTTTATATTTTAATTAT
312989 ATTGTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATATTTTAATTAT
Found at i:318605 original size:5 final size:5
Alignment explanation
Indices: 318573--318620 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
318563 TAGGTTTAGG
* * *
318573 TTTAA TTAAA TTTAA ATTAA TTTGAA TTTAA TTTTA -TTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTT-AA TTTAA TTTAA TTTAA TTTAA TTT
318621 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
4 3 0.09
5 27 0.77
6 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTTAA
Found at i:319407 original size:20 final size:23
Alignment explanation
Indices: 319383--319430 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
319373 TAATTACAAA
*
319383 ATATATATTTTATGAT-ATAATT
1 ATATATATTTTATAATGATAATT
*
319405 ATATATATTTTATAATGATAGTT
1 ATATATATTTTATAATGATAATT
319428 ATA
1 ATA
319431 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (23 bp):
ATATATATTTTATAATGATAATT
Found at i:319589 original size:19 final size:20
Alignment explanation
Indices: 319556--319594 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
319546 AATTAAATTA
*
319556 AAAAATATATTTAAATAAAT
1 AAAAATATATATAAATAAAT
319576 AAAAATA-ATATAAATAAAT
1 AAAAATATATATAAATAAAT
319595 TTAAATAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATATATAAATAAAT
Found at i:319593 original size:23 final size:22
Alignment explanation
Indices: 319549--319594 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
319539 TATTAAAAAT
* **
319549 TAAATTAAAAAATATATTTAAA
1 TAAATAAAAAAATATAAATAAA
319571 TAAATAAAAATAATATAAATAAA
1 TAAATAAAAA-AATATAAATAAA
319594 T
1 T
319595 TTAAATAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATAAAAAAATATAAATAAA
Found at i:319599 original size:10 final size:10
Alignment explanation
Indices: 319558--319683 Score: 57
Period size: 10 Copynumber: 12.6 Consensus size: 10
319548 TTAAATTAAA
*
319558 AAATATATTT
1 AAATAAATTT
**
319568 AAATAAATAA
1 AAATAAATTT
*
319578 AAAT-AATAT
1 AAATAAATTT
319587 AAATAAATTT
1 AAATAAATTT
* *
319597 AAATAGACTT
1 AAATAAATTT
319607 AAATAACTATTT
1 AAATAA--ATTT
*
319619 ATAA-AAA-AT
1 A-AATAAATTT
*
319628 AAATTAATTT
1 AAATAAATTT
319638 AAATAAAAATTT
1 AAAT--AAATTT
* * *
319650 TACTCATATTT
1 AAAT-AAATTT
319661 ---TAAATTT
1 AAATAAATTT
319668 AAATAAATTT
1 AAATAAATTT
319678 AAATAA
1 AAATAA
319684 TCTTGTAAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
7 5 0.06
8 3 0.03
9 12 0.14
10 47 0.54
11 5 0.06
12 13 0.15
13 2 0.02
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (10 bp):
AAATAAATTT
Found at i:322603 original size:3 final size:3
Alignment explanation
Indices: 322595--322623 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
322585 AAGATTGGGT
322595 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
322624 GTTAACATAG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:326197 original size:20 final size:20
Alignment explanation
Indices: 326172--326249 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
326162 TTACTAAATA
326172 ATTATATATATATTATTTAT
1 ATTATATATATATTATTTAT
* * *
326192 ATTATATAAATTTTAATTA-
1 ATTATATATATATTATTTAT
326211 ATTA-ATATAT-TT-TTTAT
1 ATTATATATATATTATTTAT
*
326228 A-TAT-TTTA-ATTATTTTAT
1 ATTATATATATATTA-TTTAT
326246 ATTA
1 ATTA
326250 AATTAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
16 10 0.22
17 3 0.07
18 11 0.24
19 6 0.13
20 16 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATATATATTATTTAT
Found at i:326255 original size:19 final size:19
Alignment explanation
Indices: 326201--326257 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
326191 TATTATATAA
326201 ATTTTA-ATT-AATTAATAT
1 ATTTTATATTAAATTAAT-T
* **
326219 ATTTTTTATATATTTTAATT
1 ATTTTATAT-TAAATTAATT
326239 ATTTTATATTAAATTAATT
1 ATTTTATATTAAATTAATT
326258 TAAATAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 5 0.17
19 10 0.33
20 10 0.33
21 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATTAAATTAATT
Found at i:326880 original size:7 final size:7
Alignment explanation
Indices: 326854--326954 Score: 51
Period size: 8 Copynumber: 13.6 Consensus size: 7
326844 TATAATATAA
326854 ATAAAAT
1 ATAAAAT
*
326861 AATTAAA-
1 -ATAAAAT
326868 ATAAAAT
1 ATAAAAT
326875 ATAAAAATT
1 AT-AAAA-T
* *
326884 TTAAATTT
1 ATAAA-AT
*
326892 ATATAAT
1 ATAAAAT
*
326899 ATAAATT
1 ATAAAAT
*
326906 ATTAATAT
1 A-TAAAAT
326914 ATTAAAAT
1 A-TAAAAT
* *
326922 TTATAAT
1 ATAAAAT
326929 ATAAATAT
1 ATAAA-AT
*
326937 AAAAAAT
1 ATAAAAT
326944 ATAAAAT
1 ATAAAAT
326951 ATAA
1 ATAA
326955 TTATAATAAA
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
6 5 0.07
7 29 0.42
8 33 0.48
9 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATAAAAT
Found at i:326881 original size:13 final size:14
Alignment explanation
Indices: 326840--326882 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
326830 TTATGCATTT
*
326840 TAAATATAATATAAA
1 TAAA-ATAATAAAAA
*
326855 TAAAATAATTAAAA
1 TAAAATAATAAAAA
326869 TAAAAT-ATAAAAA
1 TAAAATAATAAAAA
326882 T
1 T
326883 TTTAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 7 0.28
14 14 0.56
15 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAATAATAAAAA
Found at i:326945 original size:32 final size:32
Alignment explanation
Indices: 326867--326950 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 32
326857 AAATAATTAA
*
326867 AATA-AAATATAAAAAT-T-TTAAATTTATAT
1 AATATAAATATAAAAATATATTAAAATTATAT
**
326896 AATATAAAT-TATTAATATATTAAAATT-TAT
1 AATATAAATATAAAAATATATTAAAATTATAT
326926 AATATAAATATAAAAA-ATA-TAAAAT
1 AATATAAATATAAAAATATATTAAAAT
326951 ATAATTATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
29 15 0.33
30 20 0.43
31 11 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (32 bp):
AATATAAATATAAAAATATATTAAAATTATAT
Found at i:327234 original size:3 final size:3
Alignment explanation
Indices: 327226--327256 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
327216 GCCAATAAAT
327226 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
327257 GGCACTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:327880 original size:18 final size:18
Alignment explanation
Indices: 327853--327890 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
327843 GATTATTTAC
327853 ATTTAAATAAA-TTTAAA
1 ATTTAAATAAATTTTAAA
327870 ATTTAAAATAAATTTTAAA
1 ATTT-AAATAAATTTTAAA
327889 AT
1 AT
327891 ACAACGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 7 0.37
19 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATAAATTTTAAA
Found at i:328698 original size:13 final size:13
Alignment explanation
Indices: 328680--328738 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
328670 TTAAAAAATA
328680 AAATATTATATTT
1 AAATATTATATTT
328693 AAATA-TATATTT
1 AAATATTATATTT
*
328705 -AATAAGTATATTT
1 AAAT-ATTATATTT
*
328718 AAAAAATTATATTT
1 -AAATATTATATTT
*
328732 ATATATT
1 AAATATT
328739 TAAAATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 3 0.08
12 8 0.21
13 17 0.45
14 8 0.21
15 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
AAATATTATATTT
Found at i:328730 original size:14 final size:14
Alignment explanation
Indices: 328678--328732 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
328668 ACTTAAAAAA
*
328678 TAAAATATTATATT
1 TAAAAAATTATATT
*
328692 T-AAATA-TATATT
1 TAAAAAATTATATT
* *
328704 T-AATAAGTATATT
1 TAAAAAATTATATT
328717 TAAAAAATTATATT
1 TAAAAAATTATATT
328731 TA
1 TA
328733 TATATTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.29
13 12 0.34
14 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAAAAATTATATT
Found at i:329963 original size:18 final size:20
Alignment explanation
Indices: 329932--329968 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
329922 ATTCTGTATT
329932 ATATATTTATATAATTTTTG
1 ATATATTTATATAATTTTTG
329952 ATATA-TTA-ATAATTTTT
1 ATATATTTATATAATTTTT
329969 ATTATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATATTTATATAATTTTTG
Found at i:329977 original size:32 final size:33
Alignment explanation
Indices: 329928--330016 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
329918 ATATATTCTG
*
329928 TATTATATATTTATATAATTTTTGATATATTAATA
1 TATT-TATA-TTATATAATTTTTAATATATTAATA
* ** **
329963 -ATTTTTATTATATAAAATTTAATATATTTTTA
1 TATTTATATTATATAATTTTTAATATATTAATA
*
329995 TATTTATATTATATATTTTTTA
1 TATTTATATTATATAATTTTTA
330017 TTGTTATAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
32 20 0.47
33 20 0.47
34 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTTATATTATATAATTTTTAATATATTAATA
Found at i:330030 original size:22 final size:21
Alignment explanation
Indices: 329984--330030 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
329974 ATAAAATTTA
**
329984 ATATATTTTTATATTTATATT
1 ATATATTTTTATATTTATAAC
330005 ATATATTTTT-TATTGTTATAAC
1 ATATATTTTTATA-T-TTATAAC
330027 ATAT
1 ATAT
330031 TATTCTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 11 0.50
22 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATATATTTTTATATTTATAAC
Found at i:330111 original size:19 final size:20
Alignment explanation
Indices: 330087--330126 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
330077 AATTTAATAA
330087 TTTATAT-GTTTATATTATT
1 TTTATATAGTTTATATTATT
* *
330106 TTTATATATTTTATTTTATT
1 TTTATATAGTTTATATTATT
330126 T
1 T
330127 AATCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTATATAGTTTATATTATT
Found at i:330162 original size:26 final size:24
Alignment explanation
Indices: 330117--330164 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
330107 TTATATATTT
* *
330117 TATTTTATTTAATCATATTTAAGA
1 TATTTTATTTAATAAAATTTAAGA
330141 TATTTTATATTATATAAAATTTAA
1 TATTTTAT-TTA-ATAAAATTTAA
330165 TACGTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 3 0.15
26 9 0.45
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTTTATTTAATAAAATTTAAGA
Found at i:330217 original size:33 final size:33
Alignment explanation
Indices: 330140--330217 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
330130 CATATTTAAG
* * *
330140 ATAT-TTTATATTATATAAAATTTAATACGTTA
1 ATATATTTATATTAAATAAAATTTAAAACATTA
* * *
330172 ATA-ATTTATATTAAATAAATTTTAAAATATTT
1 ATATATTTATATTAAATAAAATTTAAAACATTA
330204 ATATATTTATATTA
1 ATATATTTATATTA
330218 TATTTATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 28 0.74
33 10 0.26
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
ATATATTTATATTAAATAAAATTTAAAACATTA
Found at i:330220 original size:19 final size:19
Alignment explanation
Indices: 330086--330236 Score: 73
Period size: 19 Copynumber: 7.9 Consensus size: 19
330076 TAATTTAATA
*
330086 ATTTATATGTTTATATTAT
1 ATTTATATATTTATATTAT
* *
330105 TTTTATATATTT-TATTTT
1 ATTTATATATTTATATTAT
*
330123 ATTTAATCATATTTA-A-GAT
1 ATTT-AT-ATATTTATATTAT
* *
330142 ATTT-TATA-TTATATAAA
1 ATTTATATATTTATATTAT
*
330159 ATTTA-ATACGTTAATAATTTAT
1 ATTTATATA--TTTAT-A-TTAT
* * **
330181 ATTAAATAAATTT-TAAAAT
1 ATT-TATATATTTATATTAT
330200 ATTTATATATTTATATTAT
1 ATTTATATATTTATATTAT
*
330219 ATTTATAATATTTTTATT
1 ATTTAT-ATATTTATATT
330237 TTATCTTCAT
Statistics
Matches: 96, Mismatches: 21, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
15 3 0.03
16 4 0.04
17 9 0.09
18 15 0.16
19 32 0.33
20 21 0.22
21 2 0.02
22 7 0.07
23 1 0.01
24 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:339301 original size:3 final size:3
Alignment explanation
Indices: 339295--339326 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
339285 TATTATTATT
339295 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
339327 TATTATTATT
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:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:340660 original size:28 final size:27
Alignment explanation
Indices: 340614--340680 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
340604 ACTAAATTGT
340614 TAAATAATTATAGAATAAAAATACATACA
1 TAAATAATTATAGAATAAAAATACA-A-A
* *
340643 T-AATAATTA-GGAAGTAAATATACAAA
1 TAAATAATTATAGAA-TAAAAATACAAA
340669 TAAATAATTATA
1 TAAATAATTATA
340681 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.06
27 12 0.38
28 17 0.53
29 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (27 bp):
TAAATAATTATAGAATAAAAATACAAA
Found at i:342358 original size:14 final size:14
Alignment explanation
Indices: 342339--342371 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
342329 TGATTATTTT
*
342339 TATTTTTTGTATTA
1 TATTTTTTATATTA
342353 TATTTTTTATATTA
1 TATTTTTTATATTA
342367 TATTT
1 TATTT
342372 ATATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTTTTATATTA
Found at i:358163 original size:38 final size:38
Alignment explanation
Indices: 358121--358303 Score: 120
Period size: 37 Copynumber: 4.9 Consensus size: 38
358111 TTAACCCTTA
* * *
358121 TGGCATAGGTT-AAAATAAAAATCACTATTCTAATTTGG
1 TGGCAT-GGTTCAAAACAAAAACCACTATTCTAATTCGG
* *
358159 TGGCATGGTTCAGAACAAAAGCCACTATTCTAATTCGG
1 TGGCATGGTTCAAAACAAAAACCACTATTCTAATTCGG
* * * * * * * *
358197 TGGCACGATTTAGAACAAAAACTACTATTTTTACT-GG
1 TGGCATGGTTCAAAACAAAAACCACTATTCTAATTCGG
* ** * ** * * *
358234 TGGTACAGTTCGAAACAAAAATTACTGTTCTCACT-GG
1 TGGCATGGTTCAAAACAAAAACCACTATTCTAATTCGG
* *
358271 TGGCATGGTTCGAAACAAAAACTACTATTCTAA
1 TGGCATGGTTCAAAACAAAAACCACTATTCTAA
358304 ACTGGTAGCA
Statistics
Matches: 115, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
37 60 0.52
38 55 0.48
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (38 bp):
TGGCATGGTTCAAAACAAAAACCACTATTCTAATTCGG
Found at i:358251 original size:37 final size:37
Alignment explanation
Indices: 358210--358301 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
358200 CACGATTTAG
* * *
358210 AACAAAAACTACTATTTTTACTGGTGGTACAGTTCGA
1 AACAAAAACTACTATTCTCACTGGTGGCACAGTTCGA
* * **
358247 AACAAAAATTACTGTTCTCACTGGTGGCATGGTTCGA
1 AACAAAAACTACTATTCTCACTGGTGGCACAGTTCGA
358284 AACAAAAACTACTATTCT
1 AACAAAAACTACTATTCT
358302 AAACTGGTAG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (37 bp):
AACAAAAACTACTATTCTCACTGGTGGCACAGTTCGA
Found at i:362283 original size:34 final size:34
Alignment explanation
Indices: 362222--362405 Score: 235
Period size: 34 Copynumber: 5.4 Consensus size: 34
362212 TAAAAACCAT
* * * *
362222 CATTTAATCAAGAATAGCAACCTACCAAATCTCC
1 CATTTAATCAACAATGGTAAACTACCAAATCTCC
* * * *
362256 CATTTAGTCAACAATGGTAAACCACCAAATCACT
1 CATTTAATCAACAATGGTAAACTACCAAATCTCC
* *
362290 CATTTAATCAATAATGGTAAGCTACCAAATCTCC
1 CATTTAATCAACAATGGTAAACTACCAAATCTCC
* *
362324 CATTTAATCAACAATGGTAAGCTACCAAATTTCC
1 CATTTAATCAACAATGGTAAACTACCAAATCTCC
* *
362358 CATTTAGTCAACAATGGTAAACTACCAAATC-AC
1 CATTTAATCAACAATGGTAAACTACCAAATCTCC
362391 CATTTAATCAACAAT
1 CATTTAATCAACAAT
362406 TCTCCCACTT
Statistics
Matches: 129, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 15 0.12
34 114 0.88
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CATTTAATCAACAATGGTAAACTACCAAATCTCC
Found at i:366069 original size:34 final size:34
Alignment explanation
Indices: 366003--366187 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
365993 AAGTGGGAGA
* *
366003 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
366036 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
366070 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
366104 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
366138 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
366172 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
366188 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:366178 original size:102 final size:101
Alignment explanation
Indices: 366003--366187 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
365993 AAGTGGGAGA
366003 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
366068 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
366104 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
366169 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
366188 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:366548 original size:19 final size:19
Alignment explanation
Indices: 366492--366554 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
366482 TGGTTGTCGA
**
366492 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
366511 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
366530 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
366549 GTTACT
1 GGTACT
366555 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:370687 original size:34 final size:34
Alignment explanation
Indices: 370621--370805 Score: 255
Period size: 34 Copynumber: 5.5 Consensus size: 34
370611 AAGTGAGAGA
* *
370621 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
370654 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
370688 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
370722 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
370756 ATTGTTTACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
370790 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
370806 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
33 13 0.10
34 119 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:371403 original size:34 final size:34
Alignment explanation
Indices: 371357--371467 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 34
371347 GTAAAAACCA
*
371357 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
* *
371391 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATCTC
* *
371425 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCTC
371459 CCATTTAAT
1 CCATTTAAT
371468 GGTGGTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
33 3 0.04
34 61 0.90
35 4 0.06
ACGTcount: A:0.39, C:0.29, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCTC
Found at i:372510 original size:34 final size:34
Alignment explanation
Indices: 372444--372628 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
372434 AAGTGGGAGA
* *
372444 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
372477 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
372511 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
372545 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
372579 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
372613 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
372629 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 13 0.10
34 123 0.90
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:372619 original size:102 final size:101
Alignment explanation
Indices: 372444--372628 Score: 325
Period size: 102 Copynumber: 1.8 Consensus size: 101
372434 AAGTGGGAGA
372444 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
372509 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
372545 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
*
372610 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
372629 TGGTTTTTAC
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 14 0.18
102 65 0.82
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:378118 original size:19 final size:19
Alignment explanation
Indices: 378091--378153 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
378081 TCACGTGTAC
* *
378091 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
378110 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
378129 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
378148 AGTACC
1 AGTACC
378154 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:378506 original size:34 final size:34
Alignment explanation
Indices: 378460--378644 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
378450 GTAAAAACCA
*
378460 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
378494 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
378528 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
378562 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
378596 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
378629 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
378645 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:383791 original size:34 final size:34
Alignment explanation
Indices: 383745--383929 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
383735 GTAAAAACCA
*
383745 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
383779 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
383813 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
383847 CCATTTAATCAACAATGGTAAGCTATCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
383881 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
383914 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
383930 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:383887 original size:102 final size:101
Alignment explanation
Indices: 383745--383929 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 101
383735 GTAAAAACCA
383745 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
383810 CACCCATTTAATCAACAATGGTAAGCTACCAAATCTC
66 CA-CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * *
383847 CCATTTAATCAACAATGGTAAGCTATCAAATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
383912 CACCATTTAATCAACAAT
66 CACCATTTAATCAACAAT
383930 TCTCCCACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 16 0.21
102 62 0.79
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
CACCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:388390 original size:34 final size:34
Alignment explanation
Indices: 388344--388528 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
388334 GTAAAAACCA
*
388344 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
388378 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
388412 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
388446 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
388480 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
388513 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
388529 TCTCTCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:389248 original size:19 final size:19
Alignment explanation
Indices: 389221--389283 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
389211 TCACGTGTAC
* *
389221 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
389240 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
389259 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
389278 AGTACC
1 AGTACC
389284 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:392460 original size:34 final size:34
Alignment explanation
Indices: 392394--392577 Score: 235
Period size: 34 Copynumber: 5.4 Consensus size: 34
392384 AAGTGGGAGA
* *
392394 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
392427 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
392461 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * * *
392495 ATTATTGATTAAATGAGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
392529 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
392563 ATTCTTGATTAAATG
1 ATTGTTGATTAAATG
392578 ATGGTTTTTA
Statistics
Matches: 129, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 13 0.10
34 116 0.90
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:397057 original size:34 final size:34
Alignment explanation
Indices: 396991--397175 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
396981 AAGTGGGAGA
* *
396991 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
397024 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
397058 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
397092 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
397126 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
397160 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
397176 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:398801 original size:34 final size:34
Alignment explanation
Indices: 398744--398956 Score: 259
Period size: 34 Copynumber: 6.3 Consensus size: 34
398734 AAGTGGGAGA
*
398744 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
398777 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
398811 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
398845 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
398879 ATTATTGATTAAATGGGTTATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
398913 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
398947 ATTGTTGATT
1 ATTGTTGATT
398957 CACCACGAAT
Statistics
Matches: 154, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 16 0.10
34 138 0.90
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:398884 original size:102 final size:101
Alignment explanation
Indices: 398744--398956 Score: 336
Period size: 102 Copynumber: 2.1 Consensus size: 101
398734 AAGTGGGAGA
** * * *
398744 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
398809 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
398845 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTTATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
398910 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
398947 ATTGTTGATT
1 ATTGTTGATT
398957 CACCACGAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 15 0.15
102 87 0.85
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:399394 original size:34 final size:34
Alignment explanation
Indices: 399348--399532 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
399338 GTAAAAACCA
*
399348 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
399382 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
399416 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
399450 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
399484 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
399517 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
399533 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:403661 original size:19 final size:19
Alignment explanation
Indices: 403606--403661 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
403596 ACAGTAACCG
* *
403606 TATACTTGAATAGTACCCA
1 TATACGTGAATAGTACCTA
403625 TATACGTGAATAGTACCTA
1 TATACGTGAATAGTACCTA
403644 TATACGTGAATAGTACCT
1 TATACGTGAATAGTACCT
403662 CGACAACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
TATACGTGAATAGTACCTA
Found at i:403840 original size:34 final size:34
Alignment explanation
Indices: 403797--403953 Score: 224
Period size: 34 Copynumber: 4.6 Consensus size: 34
403787 TCGGCTTAAT
* *
403797 TTACCATTGTTGACTAAATGGGAAATTTGGTAGC
1 TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
403831 TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
1 TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
* * * * *
403865 TTACCATTATTGATTAAATGGGTGATTTAGTGGT
1 TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
* *
403899 TTACCATTGTTGACTAAATGGGAGATTTGGTAGG
1 TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
*
403933 TTGCCATTGTTGATTAAATGG
1 TTACCATTGTTGATTAAATGG
403954 TAGTTTTTAC
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 108 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (34 bp):
TTACCATTGTTGATTAAATGGGAGATTTGGTAGC
Found at i:405768 original size:34 final size:34
Alignment explanation
Indices: 405721--405886 Score: 242
Period size: 34 Copynumber: 4.9 Consensus size: 34
405711 TTTTCAAAGG
* * *
405721 TTTGGTAGTTTACCATTGTTGACTAAATGGGAAA
1 TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
405755 TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
1 TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
* *
405789 TTTGGTAGCTTACCATTATTGATTAAATGGGTGA
1 TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
* * *
405823 TTTGGTGGTTTACCATTGTTGACTAAATGGGAGA
1 TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
* *
405857 TTTGGTAGGTTGCCATTGTTGATTAAATGG
1 TTTGGTAGCTTACCATTGTTGATTAAATGG
405887 TGGTTTTTAC
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 118 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TTTGGTAGCTTACCATTGTTGATTAAATGGGAGA
Found at i:406659 original size:33 final size:34
Alignment explanation
Indices: 406590--406676 Score: 110
Period size: 33 Copynumber: 2.6 Consensus size: 34
406580 AAATATTTTA
* *
406590 TTTTCTA--TTTTTTAATTTATAATTGATCTTTT
1 TTTTCTATTTTTTTTAATTTCTAATTGATCTTTC
406622 TTTTCTATTTTTTTTAATTTCTAACTT-ATC-TTC
1 TTTTCTATTTTTTTTAATTTCTAA-TTGATCTTTC
*
406655 TTTTCTATTGTTTTTAATTTCT
1 TTTTCTATTTTTTTTAATTTCT
406677 TTGGGTTTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 7 0.14
33 23 0.47
34 17 0.35
35 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.69
Consensus pattern (34 bp):
TTTTCTATTTTTTTTAATTTCTAATTGATCTTTC
Found at i:408658 original size:31 final size:31
Alignment explanation
Indices: 408620--408686 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
408610 TTGGATGAAC
408620 TTTCTAATTAATACTGT-TTTCTATTTTTTAA
1 TTTCTAATTAAT-CTGTCTTTCTATTTTTTAA
*
408651 TTTCTAATTAATCTTTCTTTCTATTTTTTAA
1 TTTCTAATTAATCTGTCTTTCTATTTTTTAA
408682 TTTCT
1 TTTCT
408687 TTGGGTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.22, C:0.12, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTCTAATTAATCTGTCTTTCTATTTTTTAA
Found at i:409190 original size:28 final size:27
Alignment explanation
Indices: 409135--409226 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
409125 GCCACCCATT
409135 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
409162 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
* * * *
409190 TATTTGTCAAATATGGAGGCT-TGTT-
1 TATTTGTCAAAAATGGTGGTTATTTTG
409215 TATTTGTCAAAA
1 TATTTGTCAAAA
409227 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 20 0.36
28 22 0.39
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:409307 original size:20 final size:20
Alignment explanation
Indices: 409282--409330 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
409272 AAATAGAAGC
409282 TCCCTCTTCCCTCTCAAGTA
1 TCCCTCTTCCCTCTCAAGTA
* **
409302 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGTA
409322 TCCCTCTTC
1 TCCCTCTTC
409331 AATTCTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.10, C:0.47, G:0.04, T:0.39
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGTA
Found at i:413763 original size:28 final size:27
Alignment explanation
Indices: 413708--413799 Score: 100
Period size: 28 Copynumber: 3.4 Consensus size: 27
413698 GCCACCCATT
413708 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
413735 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
* * * *
413763 TATTTGTCAAATATGGAGGCT-TGTT-
1 TATTTGTCAAAAATGGTGGTTATTTTG
413788 TATTTGTCAAAA
1 TATTTGTCAAAA
413800 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.05
27 20 0.36
28 22 0.39
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:413880 original size:20 final size:20
Alignment explanation
Indices: 413855--413903 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
413845 AAATAGAAGC
413855 TCCCTCTTCCCTCTCAAGTA
1 TCCCTCTTCCCTCTCAAGTA
* **
413875 TCCCTCATCCCTCTCTTGTA
1 TCCCTCTTCCCTCTCAAGTA
413895 TCCCTCTTC
1 TCCCTCTTC
413904 AATTCTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.10, C:0.47, G:0.04, T:0.39
Consensus pattern (20 bp):
TCCCTCTTCCCTCTCAAGTA
Found at i:415161 original size:3 final size:3
Alignment explanation
Indices: 415153--415179 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
415143 AATAAATTTC
415153 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
415180 CTATGTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:415786 original size:16 final size:17
Alignment explanation
Indices: 415741--415788 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
415731 CTCTTGACAA
415741 TTTATT-AATGTAATTAT
1 TTTATTAAAT-TAATTAT
415758 TTTATTCATAATTAATT-T
1 TTTATT-A-AATTAATTAT
415776 TTTATTAAATTAA
1 TTTATTAAATTAA
415789 AATATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.21
17 7 0.25
18 7 0.25
19 5 0.18
20 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTATTAAATTAATTAT
Found at i:417240 original size:3 final size:3
Alignment explanation
Indices: 417232--417269 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
417222 ATATATTCAC
417232 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
417270 AATTTTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:421831 original size:23 final size:23
Alignment explanation
Indices: 421779--421831 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
421769 TCTTTCCTTC
* *
421779 TTCTTTCCTTTTTTCCCTCTTTT
1 TTCTTTCCCTCTTTCCCTCTTTT
421802 TGT-TTTCCCTCTTTCCCT-TTGTT
1 T-TCTTTCCCTCTTTCCCTCTT-TT
421825 TTCTTTC
1 TTCTTTC
421832 TTCATTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 3 0.12
23 21 0.84
24 1 0.04
ACGTcount: A:0.00, C:0.30, G:0.04, T:0.66
Consensus pattern (23 bp):
TTCTTTCCCTCTTTCCCTCTTTT
Found at i:423109 original size:22 final size:21
Alignment explanation
Indices: 423081--423122 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
423071 ATAATTATTT
423081 TTATTTTTATATTATAATTTAA
1 TTATTTTTATATTAT-ATTTAA
423103 TTATTTTTATATTATATTTA
1 TTATTTTTATATTATATTTA
423123 TGTTGTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTTTATATTATATTTAA
Found at i:423116 original size:11 final size:11
Alignment explanation
Indices: 423081--423123 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
423071 ATAATTATTT
*
423081 TTATTTTTATA
1 TTATATTTATA
423092 TTATAATTTA-A
1 TTAT-ATTTATA
*
423103 TTATTTTTATA
1 TTATATTTATA
423114 TTATATTTAT
1 TTATATTTAT
423124 GTTGTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 19 0.70
12 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTTATA
Found at i:430485 original size:22 final size:22
Alignment explanation
Indices: 430459--430502 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
430449 AAAAAACAAA
430459 AGATCATTCTAAAAGCATGATG
1 AGATCATTCTAAAAGCATGATG
430481 AGATCATTCTAAAAGCATGATG
1 AGATCATTCTAAAAGCATGATG
430503 CCTATAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (22 bp):
AGATCATTCTAAAAGCATGATG
Found at i:434673 original size:13 final size:13
Alignment explanation
Indices: 434652--434682 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
434642 ATGATTTTTT
*
434652 AAATATATAAAAA
1 AAATTTATAAAAA
434665 AAATTTATAAAAA
1 AAATTTATAAAAA
434678 AAATT
1 AAATT
434683 AAGTATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTTATAAAAA
Found at i:435426 original size:21 final size:22
Alignment explanation
Indices: 435382--435428 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
435372 TTTATATCGT
*
435382 ATTA-TTTTTCATATCGTATAA
1 ATTATTTTTTCATATCATATAA
*
435403 ATTATTTTTTCATATCATGT-A
1 ATTATTTTTTCATATCATATAA
435424 ATTAT
1 ATTAT
435429 ATCATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATTTTTTCATATCATATAA
Found at i:435540 original size:34 final size:34
Alignment explanation
Indices: 435498--435633 Score: 245
Period size: 34 Copynumber: 4.0 Consensus size: 34
435488 CTTTGTTAAG
*
435498 TGTATTTGGTGAGAATGTTAGGTGTGTTAAGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
435532 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
435566 TGTATTTGGTGAAAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
435600 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
435634 GAATGTTAGG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 98 1.00
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Done.