Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1448549 original size:20 final size:18
Alignment explanation
Indices: 1448491--1448550 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
1448481 AAAATAAAAC
*
1448491 ATAAAAAAATAATATAAAT
1 ATAAAAAAA-GATATAAAT
*
1448510 ATAAAAAAATATATCAAAAT
1 ATAAAAAAAGATAT--AAAT
1448530 ATATCAAAAAAGATATAAAT
1 ATA--AAAAAAGATATAAAT
1448550 A
1 A
1448551 AATAATTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
18 4 0.11
19 9 0.26
20 12 0.34
22 10 0.29
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAAAAAAAGATATAAAT
Found at i:1448626 original size:10 final size:12
Alignment explanation
Indices: 1448586--1448721 Score: 83
Period size: 12 Copynumber: 11.8 Consensus size: 12
1448576 ATTTTAAATG
*
1448586 TATAAAAAATAA
1 TATAAAATATAA
*
1448598 TAT-AAATATCA
1 TATAAAATATAA
1448609 TATAAAAT-TAA
1 TATAAAATATAA
1448620 T-TAAAATATAA
1 TATAAAATATAA
1448631 TATAAAA-AT-A
1 TATAAAATATAA
*
1448641 TAAAAAATAT-A
1 TATAAAATATAA
* *
1448652 TGT-AAATATTA
1 TATAAAATATAA
* *
1448663 TTTAAATTTATAA
1 TATAAA-ATATAA
**
1448676 TATTTTAA-ATAA
1 TA-TAAAATATAA
*
1448688 TAAAAAATATAA
1 TATAAAATATAA
*
1448700 -ATAAAAACATAA
1 TAT-AAAATATAA
1448712 TATAAAATAT
1 TATAAAATAT
1448722 TTTTTCTTTC
Statistics
Matches: 94, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
10 19 0.20
11 28 0.30
12 38 0.40
13 7 0.07
14 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:1448647 original size:22 final size:23
Alignment explanation
Indices: 1448586--1448651 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
1448576 ATTTTAAATG
*
1448586 TATAAAAA-ATAATATAAATATCA
1 TATAAAAATATAATA-AAATATAA
1448609 TAT-AAAAT-TAATTAAAATATAA
1 TATAAAAATATAA-TAAAATATAA
1448631 TATAAAAATATAA-AAAATATA
1 TATAAAAATATAATAAAATATA
1448652 TGTAAATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
22 25 0.66
23 10 0.26
24 3 0.08
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
TATAAAAATATAATAAAATATAA
Found at i:1453104 original size:21 final size:20
Alignment explanation
Indices: 1453078--1453134 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
1453068 TTAAAAAAAG
1453078 ATGTTTATATATAATTAAGTA
1 ATGTTTATATATAATTAA-TA
* **
1453099 ATGTTTACATATAATCGATA
1 ATGTTTATATATAATTAATA
*
1453119 ATATTT-TATATAATTA
1 ATGTTTATATATAATTA
1453135 TACGTAAAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 7 0.24
20 7 0.24
21 15 0.52
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (20 bp):
ATGTTTATATATAATTAATA
Found at i:1453181 original size:20 final size:19
Alignment explanation
Indices: 1453144--1453220 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
1453134 ATACGTAAAG
*
1453144 ATAATATTTTATAAAATTT
1 ATAATATTTTATATAATTT
1453163 ATAATATTTATATATAA-TT
1 ATAATATTT-TATATAATTT
* *
1453182 AGTTATATTTATATGTAATTT
1 A-TAATATTT-TATATAATTT
*
1453203 ATAATATTTTATGTAATT
1 ATAATATTTTATATAATT
1453221 ATATGTAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
19 21 0.41
20 27 0.53
21 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
ATAATATTTTATATAATTT
Found at i:1453235 original size:29 final size:30
Alignment explanation
Indices: 1453185--1453250 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
1453175 TATAATTAGT
* **
1453185 TATATTTATATGTAATTTATAATATTT-TA
1 TATAATTATATGTAATCAATAATATTTGTA
* *
1453214 TGTAATTATATGTAATCAATAATGTTTGTA
1 TATAATTATATGTAATCAATAATATTTGTA
1453244 TATAATT
1 TATAATT
1453251 TGTAATGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.53
Consensus pattern (30 bp):
TATAATTATATGTAATCAATAATATTTGTA
Found at i:1453321 original size:46 final size:47
Alignment explanation
Indices: 1453216--1453341 Score: 173
Period size: 46 Copynumber: 2.7 Consensus size: 47
1453206 ATATTTTATG
* * * *
1453216 TAATTATATGTAATCAATAATGTTTGTATATAATTTGTAATGTTTTATA
1 TAATTATATGTAA-AAATAATATTT-TATATAATTTGAAATGTTTTACA
*
1453265 TAATTGTATGTAAAAATAATATTTTATATAATTTGAAATG-TTTACA
1 TAATTATATGTAAAAATAATATTTTATATAATTTGAAATGTTTTACA
*
1453311 TAATTATATGTAAAGATAATATTTTATATAA
1 TAATTATATGTAAAAATAATATTTTATATAA
1453342 CTTATAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
46 34 0.49
47 15 0.21
48 9 0.13
49 12 0.17
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.48
Consensus pattern (47 bp):
TAATTATATGTAAAAATAATATTTTATATAATTTGAAATGTTTTACA
Found at i:1453368 original size:20 final size:19
Alignment explanation
Indices: 1453326--1453376 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1453316 ATATGTAAAG
1453326 ATAATATTTTATATAACTT
1 ATAATATTTTATATAACTT
1453345 ATAATATTTATATATAA-TT
1 ATAATATTT-TATATAACTT
*
1453364 AATAATTTTTTAT
1 -ATAATATTTTAT
1453377 GTAAATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATAATATTTTATATAACTT
Found at i:1473473 original size:19 final size:19
Alignment explanation
Indices: 1473451--1473490 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1473441 TTTATTTTTC
1473451 AAAGATTAGAATAAATTAA
1 AAAGATTAGAATAAATTAA
1473470 AAAGATTAGAATAAATTAA
1 AAAGATTAGAATAAATTAA
1473489 AA
1 AA
1473491 TGGGTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (19 bp):
AAAGATTAGAATAAATTAA
Found at i:1474186 original size:2 final size:2
Alignment explanation
Indices: 1474181--1474222 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1474171 TGTGTGTATG
1474181 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1474221 TA
1 TA
1474223 GTAGGGGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1477673 original size:6 final size:6
Alignment explanation
Indices: 1477662--1477701 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1477652 TCATTTAAAA
*
1477662 AAATTT AAATTT AAATTT AAA-TT AAA-TT -AATTA AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
1477702 TTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 8 0.27
6 20 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:1478294 original size:11 final size:11
Alignment explanation
Indices: 1478278--1478334 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
1478268 ATTAATATTT
1478278 TATTTAAATTA
1 TATTTAAATTA
* * *
1478289 TTTTTATATCA
1 TATTTAAATTA
1478300 TATTTAAATTA
1 TATTTAAATTA
* *
1478311 TTTTTATATTA
1 TATTTAAATTA
1478322 TATTTAATATTA
1 TATTTAA-ATTA
1478334 T
1 T
1478335 CAAATTTAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
11 30 0.86
12 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTAAATTA
Found at i:1478303 original size:22 final size:22
Alignment explanation
Indices: 1478278--1478334 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
1478268 ATTAATATTT
1478278 TATTTAAATTATTTTTATATCA
1 TATTTAAATTATTTTTATATCA
*
1478300 TATTTAAATTATTTTTATATTA
1 TATTTAAATTATTTTTATATCA
1478322 TATTTAATATTAT
1 TATTTAA-ATTAT
1478335 CAAATTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTAAATTATTTTTATATCA
Found at i:1478883 original size:6 final size:6
Alignment explanation
Indices: 1478872--1478907 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1478862 AAGAAGGTAG
1478872 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA
1 AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA
1478908 GATGCCGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:1479104 original size:21 final size:21
Alignment explanation
Indices: 1479080--1479150 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1479070 TTTAATTACA
*
1479080 TAAAAAATATAATTATATTAT
1 TAAAATATATAATTATATTAT
*
1479101 T-AAATTTAATAATTA-ATTTAT
1 TAAAATAT-ATAATTATA-TTAT
1479122 TAAAATAT-TAATTATA-TA-
1 TAAAATATATAATTATATTAT
1479140 TAAAAT-TATAA
1 TAAAATATATAA
1479151 AAATATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
17 1 0.02
18 9 0.21
19 2 0.05
20 11 0.26
21 14 0.33
22 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATATATAATTATATTAT
Found at i:1479131 original size:16 final size:18
Alignment explanation
Indices: 1479112--1479145 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1479102 AAATTTAATA
1479112 ATTAATT-TAT-TAAAAT
1 ATTAATTATATATAAAAT
1479128 ATTAATTATATATAAAAT
1 ATTAATTATATATAAAAT
1479146 TATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATTATATATAAAAT
Found at i:1490854 original size:22 final size:23
Alignment explanation
Indices: 1490804--1490854 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
1490794 GAAATTAAAG
* *
1490804 TTTTTATTTATAAATTAAACAAA
1 TTTTTATTAATAAATAAAACAAA
* *
1490827 TATTTATTAAT-AATAAAACATA
1 TTTTTATTAATAAATAAAACAAA
1490849 TTTTTA
1 TTTTTA
1490855 CAATGATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTATTAATAAATAAAACAAA
Found at i:1492146 original size:2 final size:2
Alignment explanation
Indices: 1492139--1492166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1492129 AGATTATTTC
1492139 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
1492167 GTTTGAGACC
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:1499672 original size:2 final size:2
Alignment explanation
Indices: 1499665--1499698 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1499655 TGACATCATA
1499665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1499699 GAGATTTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1500082 original size:17 final size:17
Alignment explanation
Indices: 1500037--1500086 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1500027 TTTTAAATTT
1500037 TATAT-AATAT-AAAT-
1 TATATAAATATAAAATA
1500051 TAT-TAACATATTAAAATA
1 TATATAA-ATA-TAAAATA
1500069 TATATAAATATAAAATA
1 TATATAAATATAAAATA
1500086 T
1 T
1500087 TTAACGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.03
14 4 0.13
15 3 0.10
16 1 0.03
17 12 0.40
18 6 0.20
19 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAAATATAAAATA
Found at i:1500512 original size:23 final size:22
Alignment explanation
Indices: 1500486--1500528 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1500476 GTTGTTTATT
*
1500486 TAAATTTTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1500509 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1500529 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1501257 original size:14 final size:13
Alignment explanation
Indices: 1501240--1501281 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
1501230 TTTTTATTTT
1501240 TAATTAATTATAAA
1 TAATTAA-TATAAA
*
1501254 TAATAAATATAAA
1 TAATTAATATAAA
1501267 TAATATAATATAAA
1 TAAT-TAATATAAA
1501281 T
1 T
1501282 TTAAAATCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTAATATAAA
Found at i:1501266 original size:13 final size:14
Alignment explanation
Indices: 1501248--1501281 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
1501238 TTTAATTAAT
1501248 TATAAATAATA-AA
1 TATAAATAATATAA
1501261 TATAAATAATATAA
1 TATAAATAATATAA
1501275 TATAAAT
1 TATAAAT
1501282 TTAAAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAATAATATAA
Found at i:1502230 original size:47 final size:48
Alignment explanation
Indices: 1502122--1502237 Score: 130
Period size: 47 Copynumber: 2.4 Consensus size: 48
1502112 GTAATATTAA
* **
1502122 ATTATTTATTATTAAAATATTAATATTTTAAAAATAGTTTTTAATAAT
1 ATTATTTATTACTAAAATATTAATATTTTAAAAATAGTTTAAAATAAT
* * *
1502170 AATATTTAATACTAAAATATT-AT-TTTAATATAAATA-TTTAAAATAAT
1 ATTATTTATTACTAAAATATTAATATTT--TAAAAATAGTTTAAAATAAT
*
1502217 ATTATTTATTACTAAAGTATT
1 ATTATTTATTACTAAAATATT
1502238 TATACTAGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
46 3 0.05
47 29 0.51
48 25 0.44
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (48 bp):
ATTATTTATTACTAAAATATTAATATTTTAAAAATAGTTTAAAATAAT
Found at i:1502594 original size:24 final size:23
Alignment explanation
Indices: 1502545--1502594 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1502535 ATGAATTTTT
*
1502545 ATAAATATTTTTAAAATTTAAAA
1 ATAAATATTTTTAAAATATAAAA
* *
1502568 ATAAATATTTTTATTAATATAATA
1 ATAAATATTTTTA-AAATATAAAA
1502592 ATA
1 ATA
1502595 TTCGGCGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATAAATATTTTTAAAATATAAAA
Found at i:1506613 original size:3 final size:3
Alignment explanation
Indices: 1506603--1506637 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1506593 TTGTTGTCAT
1506603 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1506638 GAACAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1511035 original size:17 final size:18
Alignment explanation
Indices: 1511004--1511041 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1510994 AATTACACAT
1511004 AAATATGACACAAAT-TA
1 AAATATGACACAAATATA
* *
1511021 AAATATGATATAAATATA
1 AAATATGACACAAATATA
1511039 AAA
1 AAA
1511042 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAATATGACACAAATATA
Found at i:1511364 original size:2 final size:2
Alignment explanation
Indices: 1511357--1511382 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1511347 GCTTGAAGCC
1511357 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1511383 TTTTATTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1513455 original size:29 final size:30
Alignment explanation
Indices: 1513420--1513480 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
1513410 AGTTAATAGA
* *
1513420 TATTATTATAAAAATAAT-TTTTAATATTT
1 TATTATTATAAAAATAATAATTTAAAATTT
* *
1513449 TATTATTTTATAAATAATAATTTAAAATTT
1 TATTATTATAAAAATAATAATTTAAAATTT
1513479 TA
1 TA
1513481 AGTTAATTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATTATTATAAAAATAATAATTTAAAATTT
Found at i:1515039 original size:26 final size:26
Alignment explanation
Indices: 1514987--1515073 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 26
1514977 TATGTCCGTA
* *
1514987 AAAAATGATGATTTTTTTTTTATTTGTC
1 AAAAATAATGA-TTCTTTTTT-TTTGTC
1515015 AAAAATAATGATTCTTTTTTTTTGT-
1 AAAAATAATGATTCTTTTTTTTTGTC
* * *
1515040 AAAAGATAGTGA--CTTGTTATTTGTC
1 AAAA-ATAATGATTCTTTTTTTTTGTC
*
1515065 AAAATTAAT
1 AAAAATAAT
1515074 AATTAATTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 13 0.26
25 8 0.16
26 11 0.22
27 8 0.16
28 10 0.20
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.49
Consensus pattern (26 bp):
AAAAATAATGATTCTTTTTTTTTGTC
Found at i:1518182 original size:16 final size:17
Alignment explanation
Indices: 1518151--1518184 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
1518141 TACTTTCATA
1518151 AGACATATCATTTTGTTT
1 AGACATAT-ATTTTGTTT
1518169 AGACATAT-TTTTGTTT
1 AGACATATATTTTGTTT
1518185 GAACATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.53
Consensus pattern (17 bp):
AGACATATATTTTGTTT
Found at i:1518296 original size:23 final size:20
Alignment explanation
Indices: 1518233--1518280 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1518223 AATATTTATC
* *
1518233 TTAATTAAAAAATAAAAATA
1 TTAATTATATAATAAAAATA
*
1518253 TTAATTATATAATAATAATA
1 TTAATTATATAATAAAAATA
1518273 TT-ATTATA
1 TTAATTATA
1518281 CATTAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTATATAATAAAAATA
Found at i:1519709 original size:20 final size:20
Alignment explanation
Indices: 1519684--1519761 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
1519674 ATATATTTTA
1519684 AAATTAATAAAAAATTAATT
1 AAATTAATAAAAAATTAATT
1519704 AAATTAAT-AAAAATTAATT
1 AAATTAATAAAAAATTAATT
* *
1519723 ATAATTTATAAAAAATTGATT
1 A-AATTAATAAAAAATTAATT
*
1519744 AAATTGATAAAAAATTAA
1 AAATTAATAAAAAATTAA
1519762 AAATATATTA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 12 0.23
20 29 0.56
21 11 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
AAATTAATAAAAAATTAATT
Found at i:1520720 original size:42 final size:42
Alignment explanation
Indices: 1520668--1520762 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
1520658 AGCTGAGCAG
*
1520668 TGCTTTGAATATGACAATTATTACATCAAAACAATCAAGTAA
1 TGCTATGAATATGACAATTATTACATCAAAACAATCAAGTAA
1520710 TGCTATGAATATGACAATTATTACATCAAAACAATCAAGTAA
1 TGCTATGAATATGACAATTATTACATCAAAACAATCAAGTAA
1520752 TGCTATGAATA
1 TGCTATGAATA
1520763 AGGTGGTTCC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (42 bp):
TGCTATGAATATGACAATTATTACATCAAAACAATCAAGTAA
Found at i:1524766 original size:30 final size:29
Alignment explanation
Indices: 1524732--1524791 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
1524722 TATTTTCTTG
*
1524732 TGATTACACCAAT-TTTATTTTTATATATTT
1 TGATTACA-CAATGTCTATTTTT-TATATTT
* *
1524762 TGATTGCACAATGTCTATTTTTTATTTTT
1 TGATTACACAATGTCTATTTTTTATATTT
1524791 T
1 T
1524792 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.58
Consensus pattern (29 bp):
TGATTACACAATGTCTATTTTTTATATTT
Found at i:1524891 original size:27 final size:27
Alignment explanation
Indices: 1524845--1524912 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1524835 TTCATATAAT
*
1524845 TTTATA-TTATAATAATTTTTAAAATA
1 TTTATATTTATATTAATTTTTAAAATA
*
1524871 TTATATATTTATATTAA-TTTTAATATA
1 TT-TATATTTATATTAATTTTTAAAATA
1524898 TTTATATTATATATT
1 TTTATATT-TATATT
1524913 GTATTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.22
27 21 0.57
28 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATTTATATTAATTTTTAAAATA
Found at i:1524905 original size:33 final size:33
Alignment explanation
Indices: 1524868--1524941 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
1524858 AATTTTTAAA
1524868 ATATTATATATT-TATATTAATTTTAATATATTT
1 ATATTATATATTGTAT-TTAATTTTAATATATTT
* *
1524901 ATATTATATATTGTATTTTATTTTAATTTATTT
1 ATATTATATATTGTATTTAATTTTAATATATTT
1524934 -T-TTATATA
1 ATATTATATA
1524942 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 7 0.18
32 1 0.03
33 27 0.71
34 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (33 bp):
ATATTATATATTGTATTTAATTTTAATATATTT
Found at i:1524946 original size:29 final size:32
Alignment explanation
Indices: 1524868--1524956 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
1524858 AATTTTTAAA
* * *
1524868 ATATTATATATTTATATTAATTTTAATATATTT
1 ATATTATATATATAT-TTTATTTTAATTTATTT
*
1524901 ATATTATATATTGTATTTTATTTTAATTTATTT
1 ATATTATATA-TATATTTTATTTTAATTTATTT
*
1524934 -T-TTATATA-ATATTTT-TTATAATT
1 ATATTATATATATATTTTATTTTAATT
1524957 ATGTATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
28 7 0.14
29 6 0.12
31 7 0.14
32 1 0.02
33 25 0.50
34 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (32 bp):
ATATTATATATATATTTTATTTTAATTTATTT
Found at i:1524958 original size:27 final size:29
Alignment explanation
Indices: 1524914--1524967 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
1524904 TTATATATTG
* * *
1524914 TATTTTATTTTAATTTATTTTTTATATAA
1 TATTTTATTATAATTTATGTATTATATAA
1524943 TATTTT-TTATAA-TTATGTATTATAT
1 TATTTTATTATAATTTATGTATTATAT
1524968 TAAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 5 0.23
29 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (29 bp):
TATTTTATTATAATTTATGTATTATATAA
Found at i:1525186 original size:22 final size:23
Alignment explanation
Indices: 1525160--1525219 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1525150 TATATTATTA
1525160 AATTTAAATTAAAAATTTTAA-TT
1 AATTT-AATTAAAAATTTTAATTT
* *
1525183 -ATTTTATTTAAAA-TTTAATTT
1 AATTTAATTAAAAATTTTAATTT
*
1525204 AATTTATTTAAAAATT
1 AATTTAATTAAAAATT
1525220 AATATTATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.17
21 9 0.31
22 14 0.48
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTTAATTAAAAATTTTAATTT
Found at i:1525197 original size:21 final size:21
Alignment explanation
Indices: 1525171--1525222 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1525161 ATTTAAATTA
*
1525171 AAAATTTTAA-TTATTTTATTT
1 AAAA-TTTAATTTAATTTATTT
1525192 AAAATTTAATTTAATTTATTT
1 AAAATTTAATTTAATTTATTT
*
1525213 AAAAATTAAT
1 AAAATTTAAT
1525223 ATTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAAATTTAATTTAATTTATTT
Found at i:1525225 original size:14 final size:15
Alignment explanation
Indices: 1525208--1525237 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1525198 TAATTTAATT
1525208 TATT-TAAAAATTAA
1 TATTATAAAAATTAA
1525222 TATTATAAAAATTAA
1 TATTATAAAAATTAA
1525237 T
1 T
1525238 TAATTTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTATAAAAATTAA
Found at i:1525257 original size:16 final size:16
Alignment explanation
Indices: 1525238--1525341 Score: 129
Period size: 17 Copynumber: 6.4 Consensus size: 16
1525228 AAAAATTAAT
*
1525238 TAATTTAAACTTAAAA
1 TAATTTAAATTTAAAA
*
1525254 TAATTTAAA-TTAAAT
1 TAATTTAAATTTAAAA
1525269 TAATTTATAATTTAAAA
1 TAATTTA-AATTTAAAA
*
1525286 TAAATTAAATTTAAAA
1 TAATTTAAATTTAAAA
*
1525302 TTATTTTAAATTTAAAA
1 -TAATTTAAATTTAAAA
*
1525319 TAATTTAAACTTAAAAA
1 TAATTTAAA-TTTAAAA
1525336 TAATTT
1 TAATTT
1525342 TTTTATTTTC
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
15 12 0.16
16 28 0.36
17 37 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTAAATTTAAAA
Found at i:1525264 original size:22 final size:20
Alignment explanation
Indices: 1525237--1525333 Score: 68
Period size: 22 Copynumber: 4.5 Consensus size: 20
1525227 TAAAAATTAA
*
1525237 TTAATTTAAACTTAAAATAAT
1 TTAAATTAAA-TTAAAATAAT
*
1525258 TTAAATTAAATTAATTTATAAT
1 TTAAATTAAATTAA--AATAAT
* * *
1525280 TTAAAATAAATTAAATTTAAAA
1 TTAAATTAAATTAAA-AT-AAT
**
1525302 TTATTTTAAATTTAAAATAAT
1 TTAAATTAAA-TTAAAATAAT
1525323 TTAAACTTAAA
1 TTAAA-TTAAA
1525334 AATAATTTTT
Statistics
Matches: 57, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
20 4 0.07
21 15 0.26
22 33 0.58
23 5 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTAAATTAAAATAAT
Found at i:1525296 original size:23 final size:22
Alignment explanation
Indices: 1525253--1525303 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1525243 TAAACTTAAA
*
1525253 ATAATTTAAATTAAATTAATTT
1 ATAATTTAAAATAAATTAATTT
1525275 ATAATTTAAAATAAATTAAATTT
1 ATAATTTAAAATAAATT-AATTT
*
1525298 AAAATT
1 ATAATT
1525304 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAATTTAAAATAAATTAATTT
Found at i:1525314 original size:33 final size:32
Alignment explanation
Indices: 1525235--1525341 Score: 144
Period size: 33 Copynumber: 3.3 Consensus size: 32
1525225 TATAAAAATT
*
1525235 AATTAATTTAAACTTAAAATAATTTAAATT-A
1 AATTAATTTAAATTTAAAATAATTTAAATTAA
*
1525266 AATTAATTTATAATTTAAAATAAATTAAATTTAA
1 AATTAATTTA-AATTTAAAATAATTTAAA-TTAA
*
1525300 AATTATTTTAAATTTAAAATAATTTAAACTTAA
1 AATTAATTTAAATTTAAAATAATTTAAA-TTAA
*
1525333 AAATAATTT
1 AATTAATTT
1525342 TTTTATTTTC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
31 10 0.15
32 16 0.24
33 30 0.45
34 10 0.15
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (32 bp):
AATTAATTTAAATTTAAAATAATTTAAATTAA
Found at i:1525565 original size:15 final size:16
Alignment explanation
Indices: 1525531--1525573 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1525521 TAATGAAAAT
*
1525531 ATATTTAAAATTTTTAA
1 ATATTTAAAA-TTATAA
1525548 ATATTTAAAA-TATAA
1 ATATTTAAAATTATAA
1525563 ATATTTTAAAA
1 ATA-TTTAAAA
1525574 AAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 7 0.29
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTTAAAATTATAA
Found at i:1526205 original size:2 final size:2
Alignment explanation
Indices: 1526195--1526236 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
1526185 TTTATTTAAA
* *
1526195 AT AT TT AT AT AT AT GAC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1526237 AATACATGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1533730 original size:34 final size:34
Alignment explanation
Indices: 1533663--1533878 Score: 274
Period size: 34 Copynumber: 6.4 Consensus size: 34
1533653 CTTCGCAAAC
* * *
1533663 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
1533696 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1533730 TGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1533763 TGTTGATTAAATGGAAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
1533797 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1533831 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1533865 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1533879 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 39 0.24
34 121 0.76
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1533771 original size:67 final size:66
Alignment explanation
Indices: 1533663--1533880 Score: 292
Period size: 67 Copynumber: 3.2 Consensus size: 66
1533653 CTTCGCAAAC
* * *
1533663 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTGCC
1533728 AT
65 AT
* ** * * * *
1533730 TGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGAAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTGCC
1533795 AT
65 AT
* *
1533797 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTGC
1533862 CAT
64 CAT
1533865 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1533881 GTTTTTACCA
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 70 0.54
68 60 0.46
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (66 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGCCA
T
Found at i:1533837 original size:101 final size:101
Alignment explanation
Indices: 1533663--1533878 Score: 335
Period size: 101 Copynumber: 2.1 Consensus size: 101
1533653 CTTCGCAAAC
** * * *
1533663 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1533728 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATGGAAGATTTGGTAGCTTACCAT
*
1533763 TGTTGATTAAATGGAAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATGG-AAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
* * *
1533828 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
65 CATTGTTGACTAAATGGAAGATTTGGTAGCTTACCAT
1533865 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1533879 TGGTTTTTAC
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
100 14 0.13
101 59 0.56
102 32 0.30
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGAAGATTTGGTAGCTTACCAT
Found at i:1538364 original size:34 final size:34
Alignment explanation
Indices: 1538295--1538512 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
1538285 AAGTGGGAGA
* * *
1538295 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1538328 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1538362 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1538395 ATTGTTGATTAAATGGAAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
1538429 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1538463 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1538497 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1538513 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 121 0.75
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1538383 original size:67 final size:66
Alignment explanation
Indices: 1538295--1538514 Score: 296
Period size: 67 Copynumber: 3.3 Consensus size: 66
1538285 AAGTGGGAGA
* * *
1538295 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
1538360 CC
65 CC
* ** * * * *
1538362 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGAAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
1538427 CC
65 CC
* *
1538429 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
1538494 GCC
64 GCC
1538497 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1538515 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.40
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:1538441 original size:101 final size:101
Alignment explanation
Indices: 1538295--1538512 Score: 339
Period size: 101 Copynumber: 2.2 Consensus size: 101
1538285 AAGTGGGAGA
** * * *
1538295 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
1538360 CCATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
*
1538395 ATTGTTGATTAAATGGAAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATGG-AAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTT
* * *
1538460 ACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
1538497 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1538513 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
100 16 0.15
101 59 0.55
102 32 0.30
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
Found at i:1544683 original size:52 final size:51
Alignment explanation
Indices: 1544619--1544908 Score: 319
Period size: 52 Copynumber: 5.6 Consensus size: 51
1544609 ATTCTGTATG
* *
1544619 ACTGATAGTGATGATGTCGTGGTGGCGATTAGGATAGGAGTGACTTGGTGTC
1 ACTGATAGTGATGATGCCATGGTGGCGATTAGGATA-GAGTGACTTGGTGTC
* * * * * *
1544671 ACTAATTGTGATGATGCCATAGTGGCGATTAGAATCGGAGAGACTTGGTGTC
1 ACTGATAGTGATGATGCCATGGTGGCGATTAGGAT-AGAGTGACTTGGTGTC
* * * *
1544723 ACTGATAGTGATGATGCCATGGTGGCAATTAGAATCAGAGTAATTTGGTGTC
1 ACTGATAGTGATGATGCCATGGTGGCGATTAGGAT-AGAGTGACTTGGTGTC
** * * *
1544775 ACTGATAGCAATGATGCCATGGTGGTGGTTAGGATTAGTGTGACTTGGTGTC
1 ACTGATAGTGATGATGCCATGGTGGCGATTAGGA-TAGAGTGACTTGGTGTC
* ** * *
1544827 ACTGATGGTGATGATGAAATGGTGGCGATTAGGATCAAAGTGACTTTGTGTC
1 ACTGATAGTGATGATGCCATGGTGGCGATTAGGAT-AGAGTGACTTGGTGTC
* *
1544879 ACTGATAGTGATGATGCCATGATGCCGATT
1 ACTGATAGTGATGATGCCATGGTGGCGATT
1544909 GGAGGTTTTG
Statistics
Matches: 195, Mismatches: 40, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
51 1 0.01
52 193 0.99
53 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.31
Consensus pattern (51 bp):
ACTGATAGTGATGATGCCATGGTGGCGATTAGGATAGAGTGACTTGGTGTC
Found at i:1553249 original size:2 final size:2
Alignment explanation
Indices: 1553244--1553325 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
1553234 TCTCTCTCTC
1553244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1553286 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1553326 CACAGGTGTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1553372 original size:2 final size:2
Alignment explanation
Indices: 1553365--1553402 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1553355 GATTATATTC
1553365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1553403 CTGTGTGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555112 original size:49 final size:49
Alignment explanation
Indices: 1555059--1555154 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
1555049 TATATATAAT
* * *
1555059 TTTTTATATTCTT-ATATGAATAATGTTTAAGAAAAGGAATTAGAGATTA
1 TTTTTATATT-TTCATATGAACAATCTTTAAAAAAAGGAATTAGAGATTA
* * * *
1555108 TTTTTTTATTTTCATGTGAACGATCTTTAAAAAAAGTAATTAGAGAT
1 TTTTTATATTTTCATATGAACAATCTTTAAAAAAAGGAATTAGAGAT
1555155 CAAATTGATG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 2 0.05
49 37 0.95
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.44
Consensus pattern (49 bp):
TTTTTATATTTTCATATGAACAATCTTTAAAAAAAGGAATTAGAGATTA
Found at i:1555955 original size:43 final size:42
Alignment explanation
Indices: 1555880--1555961 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
1555870 CTAGACCTAT
*
1555880 TTTCCTCTTTGATTGAAAATATAAACAAATAGGTTTAGCCCGC
1 TTTCCTCTTTAATTGAAAATATAAACAAATAGG-TTAGCCCGC
*
1555923 TTTCCTCTTTAATTGAAGAAGTA-AAA-ATATAGGTTAGCC
1 TTTCCTCTTTAATTGAA-AA-TATAAACAAATAGGTTAGCC
1555962 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 6 0.17
43 22 0.63
44 5 0.14
45 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (42 bp):
TTTCCTCTTTAATTGAAAATATAAACAAATAGGTTAGCCCGC
Found at i:1558972 original size:25 final size:29
Alignment explanation
Indices: 1558913--1558979 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
1558903 TTATTTTAAA
1558913 TATAAAAAAATA-ATATAAACATGATATT
1 TATAAAAAAATATATATAAACATGATATT
*
1558941 TATAAAAAAATATTTA-AAACAT-A-ATT
1 TATAAAAAAATATATATAAACATGATATT
*
1558967 TA-AAAATAATATA
1 TATAAAAAAATATA
1558980 CACACAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 9 0.26
26 5 0.14
27 1 0.03
28 18 0.51
29 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
TATAAAAAAATATATATAAACATGATATT
Found at i:1559131 original size:15 final size:14
Alignment explanation
Indices: 1559104--1559157 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
1559094 AATACAAATA
1559104 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
1559118 TTTTTTTCTGTTTTC
1 TTTTTTTCT-TTTTC
* **
1559133 CTCCTTTCTTTTT-
1 TTTTTTTCTTTTTC
1559146 TTTTCTTTCTTT
1 TTTT-TTTCTTT
1559158 CTTTATTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 1 0.03
14 20 0.62
15 11 0.34
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:1559958 original size:28 final size:28
Alignment explanation
Indices: 1559929--1560016 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
1559919 TTGTAATAAT
*
1559929 TTTTAAAATA-TTATATATTTATATTAA
1 TTTTAAAATATTTATATATTAATATTAA
* *
1559956 TTTTAATATATTTATATATTAATA-TCA
1 TTTTAAAATATTTATATATTAATATTAA
* * *
1559983 TATTTATATTATTTATTATATTATATTTTAA
1 T-TTTAAAATATTTA-TATATTA-ATATTAA
1560014 TTT
1 TTT
1560017 ATTATTATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
27 12 0.25
28 22 0.46
29 7 0.15
30 4 0.08
31 3 0.06
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTAAAATATTTATATATTAATATTAA
Found at i:1559991 original size:39 final size:36
Alignment explanation
Indices: 1559943--1560014 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 36
1559933 AAAATATTAT
1559943 ATATTTATATTAATTTTAATATATTTATATATTAATATC
1 ATATTTATATT-A-TTTAATATA-TTATATATTAATATC
* *
1559982 ATATTTATATTATTTATTATATTATATTTTAAT
1 ATATTTATATTATTTAATATATTATATATTAAT
1560015 TTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 11 0.35
37 8 0.26
38 1 0.03
39 11 0.35
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (36 bp):
ATATTTATATTATTTAATATATTATATATTAATATC
Found at i:1560018 original size:20 final size:19
Alignment explanation
Indices: 1559942--1560021 Score: 76
Period size: 20 Copynumber: 4.2 Consensus size: 19
1559932 TAAAATATTA
*
1559942 TATATTTATATTAATTTTAA
1 TATATTTATATTAA-TTTAT
1559962 TATATTTATA-T-ATTAATAT
1 TATATTTATATTAATT--TAT
*
1559981 CATATTTATATT-ATTTAT
1 TATATTTATATTAATTTAT
*
1559999 TATATTATATTTTAATTTAT
1 TATATT-TATATTAATTTAT
1560019 TAT
1 TAT
1560022 TATATAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
17 2 0.04
18 9 0.18
19 17 0.33
20 23 0.45
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTTATATTAATTTAT
Found at i:1560027 original size:20 final size:21
Alignment explanation
Indices: 1559937--1560027 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 21
1559927 ATTTTTAAAA
*
1559937 TATTATATA-TTTATATTAAT
1 TATTATATATTTTATATTTAT
1559957 T-TTA-ATATATTTATA--TAT
1 TATTATATAT-TTTATATTTAT
*
1559975 TAATATCATATTTATATTATTTAT
1 TATTAT-ATATTT-TA-TATTTAT
1559999 TA-TATTATATTTTA-ATTTAT
1 TATTA-TATATTTTATATTTAT
1560019 TATTATATA
1 TATTATATA
1560028 ATATTTTTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
18 6 0.10
19 5 0.09
20 21 0.36
21 8 0.14
22 4 0.07
23 8 0.14
24 6 0.10
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATATATTTTATATTTAT
Found at i:1560032 original size:28 final size:28
Alignment explanation
Indices: 1559949--1560054 Score: 77
Period size: 28 Copynumber: 4.0 Consensus size: 28
1559939 TTATATATTT
*
1559949 ATATTA-ATTTTAATATATT-TATATATTA
1 ATATTATATTTTAATTTATTAT-TATA-TA
* *
1559977 ATATCATA-TTT-A--TATTATT-TATT
1 ATATTATATTTTAATTTATTATTATATA
1560000 ATATTATATTTTAATTTATTATTATATA
1 ATATTATATTTTAATTTATTATTATATA
*
1560028 ATATT-T-TTTTATAATTATGTATTATAT
1 ATATTATATTTTA-ATTTAT-TATTATAT
1560055 TCAAAAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 18
0.74 0.06 0.21
Matches are distributed among these distances:
23 8 0.12
24 5 0.08
25 6 0.09
26 6 0.09
27 14 0.22
28 24 0.38
29 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
ATATTATATTTTAATTTATTATTATATA
Found at i:1560034 original size:23 final size:22
Alignment explanation
Indices: 1559964--1560045 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
1559954 AATTTTAATA
*
1559964 TATTTATATATTAATATCATA-TT
1 TATTTAT-TATT-ATATAATATTT
*
1559987 TATATTATTTATTATATTATATTT
1 TAT-TTA-TTATTATATAATATTT
1560011 TAATTTATTATTATATAATATTT
1 T-ATTTATTATTATATAATATTT
*
1560034 T-TTTATAATTAT
1 TATTTATTATTAT
1560046 GTATTATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
21 10 0.19
23 26 0.50
24 13 0.25
25 3 0.06
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTATTATTATATAATATTT
Found at i:1560045 original size:51 final size:51
Alignment explanation
Indices: 1559936--1560055 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 51
1559926 AATTTTTAAA
1559936 ATATTATATATTTATATTAATTTTAATATATTTATATATTAATATCATATTT
1 ATATTATATA-TTATATTAATTTTAATATATTTATATATTAATATCATATTT
* * * *
1559988 ATATTATTTATTATATTATATTTTAATTTA-TTAT-TATATAATAT-TTTTTT
1 ATATTATATATTATATTA-ATTTTAATATATTTATATAT-TAATATCATATTT
*
1560038 ATAATTATGTATTATATT
1 AT-ATTATATATTATATT
1560056 CAAAAATATT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
50 9 0.15
51 32 0.53
52 19 0.32
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (51 bp):
ATATTATATATTATATTAATTTTAATATATTTATATATTAATATCATATTT
Found at i:1566045 original size:18 final size:18
Alignment explanation
Indices: 1566024--1566059 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1566014 ATTAATTTTT
*
1566024 ATTTCAAATAAAATTTAA
1 ATTTCAAAAAAAATTTAA
*
1566042 ATTTTAAAAAAAATTTAA
1 ATTTCAAAAAAAATTTAA
1566060 TCAAAACTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
ATTTCAAAAAAAATTTAA
Found at i:1570965 original size:18 final size:18
Alignment explanation
Indices: 1570910--1570967 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1570900 CATAGGTGAT
*
1570910 ATTT-TTAAAATATT-AA
1 ATTTATTAATATATTAAA
* **
1570926 ATATATT-ATATAATTATT
1 ATTTATTAATAT-ATTAAA
1570944 ATTTATTAATATATTAAA
1 ATTTATTAATATATTAAA
1570962 ATTTAT
1 ATTTAT
1570968 ATAAATAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 6 0.19
17 5 0.16
18 16 0.52
19 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATTAATATATTAAA
Found at i:1571037 original size:31 final size:32
Alignment explanation
Indices: 1570965--1571037 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
1570955 TATTAAAATT
* *
1570965 TATATAAA-TAAAAAATATTTAAATATTATTA
1 TATATAAATTAAAAAATATATAAATATTATGA
1570996 TA-ATATAATTAAAAAA-ATATAAATA-TATGGA
1 TATATA-AATTAAAAAATATATAAATATTAT-GA
1571027 TATATAAATTA
1 TATATAAATTA
1571038 TTAATGATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
30 6 0.17
31 20 0.56
32 10 0.28
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (32 bp):
TATATAAATTAAAAAATATATAAATATTATGA
Found at i:1572702 original size:16 final size:17
Alignment explanation
Indices: 1572661--1572703 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1572651 TTTTTAATGT
*
1572661 AATAA-AAATAATGTTA
1 AATAATAAATTATGTTA
1572677 AAT-ATAAATTAT-TTA
1 AATAATAAATTATGTTA
1572692 AATAATAAATTA
1 AATAATAAATTA
1572704 AATTATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
AATAATAAATTATGTTA
Found at i:1581587 original size:21 final size:20
Alignment explanation
Indices: 1581508--1581584 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
1581498 TTAAGTTTAA
*
1581508 AAATT-ATTTAATTATTGAT
1 AAATTAATTTATTTATTGAT
* *
1581527 AAATGAA-TAATTTATT--T
1 AAATTAATTTATTTATTGAT
*
1581544 --ATTTATTTATTTATTGAT
1 AAATTAATTTATTTATTGAT
1581562 AAATTAATTTATATTATT-AT
1 AAATTAATTTAT-TTATTGAT
1581582 AAA
1 AAA
1581585 ATTTTTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
15 3 0.07
16 8 0.18
17 1 0.02
18 1 0.02
19 11 0.25
20 15 0.34
21 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
AAATTAATTTATTTATTGAT
Found at i:1583804 original size:17 final size:17
Alignment explanation
Indices: 1583782--1583836 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1583772 GGTATAAAAT
1583782 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
1583799 ATTTTAATATATTA-AT-A
1 ATTTT-ATAT-TTATATAA
1583816 A-TTTATATTT-TATAA
1 ATTTTATATTTATATAA
*
1583831 AATTTA
1 ATTTTA
1583837 AAATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 7 0.21
17 7 0.21
18 6 0.18
19 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:1583834 original size:33 final size:33
Alignment explanation
Indices: 1583779--1583876 Score: 91
Period size: 33 Copynumber: 3.1 Consensus size: 33
1583769 TTTGGTATAA
*
1583779 AATATTTTATA-TTTATATAAATTTTAATATATT
1 AATAATTTATATTTTATA-AAATTTTAATATATT
*
1583812 AATAATTTATATTTTATAAAA-TTTAAAATA-T
1 AATAATTTATATTTTATAAAATTTTAATATATT
* * *
1583843 -AT-ATTTAT-TATTATAATATTTATATTATATT
1 AATAATTTATATTTTATAAAATTT-TAATATATT
1583874 AAT
1 AAT
1583877 TATATATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
28 8 0.15
29 8 0.15
30 7 0.13
31 2 0.04
32 10 0.19
33 13 0.24
34 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
AATAATTTATATTTTATAAAATTTTAATATATT
Found at i:1583897 original size:11 final size:13
Alignment explanation
Indices: 1583862--1583918 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
1583852 ATTATAATAT
*
1583862 TTATATTATATTAA
1 TTATA-TATTTTAA
1583876 TTATATATTTTAA
1 TTATATATTTTAA
1583889 TTAT-T-TTTT-A
1 TTATATATTTTAA
1583899 TT-TATATTATATAA
1 TTATATATT-T-TAA
1583913 TTATAT
1 TTATAT
1583919 TATGATTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
9 1 0.03
10 4 0.11
11 6 0.17
12 2 0.06
13 12 0.33
14 8 0.22
15 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATATATTTTAA
Found at i:1594234 original size:40 final size:39
Alignment explanation
Indices: 1594162--1594239 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
1594152 AATGTAGTTT
* *
1594162 GTGAATCCTTACCTCGGAGCTTTGCTACTCCTTTTATAG
1 GTGAATCCTTACCTAGGAACTTTGCTACTCCTTTTATAG
1594201 GTGAATCCTTACCTTAGGAACTTTGCTACTCCTTTTATA
1 GTGAATCCTTACC-TAGGAACTTTGCTACTCCTTTTATA
1594240 TCTGGCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 13 0.36
40 23 0.64
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (39 bp):
GTGAATCCTTACCTAGGAACTTTGCTACTCCTTTTATAG
Found at i:1595334 original size:2 final size:2
Alignment explanation
Indices: 1595321--1595369 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1595311 ACACTTTATT
* * *
1595321 TA TA TT TA TA TA TA TA TA TA TA TG TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1595363 TA TA TA T
1 TA TA TA T
1595370 TGTTTAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1600370 original size:2 final size:2
Alignment explanation
Indices: 1600363--1600393 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1600353 AAATAAAGAT
1600363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1600394 GAAGTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1600986 original size:25 final size:26
Alignment explanation
Indices: 1600958--1601010 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
1600948 ACATATCATA
1600958 ATTTAAAATTAAAAAAT-ATAAATTT
1 ATTTAAAATTAAAAAATAATAAATTT
*** *
1600983 ATTTTTTATTAAAAAATAATATATTT
1 ATTTAAAATTAAAAAATAATAAATTT
1601009 AT
1 AT
1601011 ATGATACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAAAATTAAAAAATAATAAATTT
Found at i:1601354 original size:23 final size:24
Alignment explanation
Indices: 1601328--1601378 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1601318 TTTAAATATT
*
1601328 ATAAAATTATATTTAT-AAAAAAA
1 ATAAAATTATATATATGAAAAAAA
* *
1601351 ATAAATTTATATATATGATAAAAA
1 ATAAAATTATATATATGAAAAAAA
1601375 ATAA
1 ATAA
1601379 TATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
ATAAAATTATATATATGAAAAAAA
Found at i:1601372 original size:40 final size:40
Alignment explanation
Indices: 1601315--1601400 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
1601305 TAAATTTAAT
* * *
1601315 AATTT-TAAATATTATAAAATTATATTTATAAAAA-AA-ATA
1 AATTTATAAATATGATAAAA-AATA-ATATAAAAATAATATA
*
1601354 AATTTATATATATGATAAAAAATAATATAAAAATAATATA
1 AATTTATAAATATGATAAAAAATAATATAAAAATAATATA
1601394 AATTTAT
1 AATTTAT
1601401 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 8 0.20
39 10 0.25
40 22 0.55
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (40 bp):
AATTTATAAATATGATAAAAAATAATATAAAAATAATATA
Found at i:1601387 original size:11 final size:11
Alignment explanation
Indices: 1601371--1601395 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1601361 ATATATGATA
1601371 AAAAATAATAT
1 AAAAATAATAT
1601382 AAAAATAATAT
1 AAAAATAATAT
1601393 AAA
1 AAA
1601396 TTTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATAATAT
Found at i:1601802 original size:19 final size:19
Alignment explanation
Indices: 1601778--1601834 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
1601768 TTTAATTTAA
1601778 AAAATTAAAAAATTAAATT
1 AAAATTAAAAAATTAAATT
* *
1601797 AAAATT-ATAAATATAAAAT
1 AAAATTAAAAAAT-TAAATT
*
1601816 AAAA-TAAAATATTTAAATT
1 AAAATTAAAA-AATTAAATT
1601835 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 6 0.20
19 22 0.73
20 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAAAAATTAAATT
Found at i:1602084 original size:2 final size:2
Alignment explanation
Indices: 1602005--1602065 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1601995 TCTGAAATCT
* *
1602005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1602047 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1602066 GTATGTATGC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1603935 original size:14 final size:14
Alignment explanation
Indices: 1603916--1603949 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1603906 CAGATATTTC
1603916 AAATTTTAATTTTT
1 AAATTTTAATTTTT
*
1603930 AAATTTAAATTTTT
1 AAATTTTAATTTTT
1603944 -AATTTT
1 AAATTTT
1603950 TTTAAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
AAATTTTAATTTTT
Found at i:1603935 original size:21 final size:21
Alignment explanation
Indices: 1603911--1603950 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1603901 TCAAACAGAT
1603911 ATTTCAAA-TTTTAATTTTTAA
1 ATTT-AAATTTTTAATTTTTAA
1603932 ATTTAAATTTTTAATTTTT
1 ATTTAAATTTTTAATTTTT
1603951 TTAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAAATTTTTAATTTTTAA
Found at i:1607142 original size:34 final size:33
Alignment explanation
Indices: 1607099--1607166 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1607089 TCAAAGGTGC
*
1607099 GATTCTTGATATATCTTCTTTTTTTTCATTTTAA
1 GATTCTTGATATATCTTC-TTTTCTTCATTTTAA
* * *
1607133 GATTGTTGATGTGTCTTCTTTTCTTCATTTTAA
1 GATTCTTGATATATCTTCTTTTCTTCATTTTAA
1607166 G
1 G
1607167 TGCAAGTGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (33 bp):
GATTCTTGATATATCTTCTTTTCTTCATTTTAA
Found at i:1612598 original size:2 final size:2
Alignment explanation
Indices: 1612591--1612634 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1612581 CAATCTGTTA
* *
1612591 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1612633 AT
1 AT
1612635 GGTGTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1615230 original size:27 final size:29
Alignment explanation
Indices: 1615177--1615230 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1615167 TTTTACCAAC
**
1615177 TTTATATATAACTTTTTTTAATAATTAAA
1 TTTATATATAACTTTAATTAATAATTAAA
1615206 TTTATATATAA-TTTAATT-ATAATTA
1 TTTATATATAACTTTAATTAATAATTA
1615231 TAAAAGTGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 5 0.22
29 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTATATATAACTTTAATTAATAATTAAA
Found at i:1615808 original size:23 final size:24
Alignment explanation
Indices: 1615764--1615818 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1615754 TTTAAAAAAT
* *
1615764 ATTAATAATTATATATATTATAAA
1 ATTAATAATAATATATAATATAAA
* *
1615788 ATTAA-AATAATATTTAATATAAT
1 ATTAATAATAATATATAATATAAA
1615811 A-TAATAAT
1 ATTAATAAT
1615819 GCAATAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTAATAATAATATATAATATAAA
Found at i:1618554 original size:33 final size:34
Alignment explanation
Indices: 1618487--1618555 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
1618477 ATCAAAGGTG
*
1618487 AGATTCTTGATATATCTTCTTTTTTTTCATTTTA
1 AGATTCTTGATATATCTTCTTTTTCTTCATTTTA
* *
1618521 AGATTGTTGATGTATCTTC-TTTTCTTCATTTTA
1 AGATTCTTGATATATCTTCTTTTTCTTCATTTTA
1618554 AG
1 AG
1618556 TACAACTGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 15 0.47
34 17 0.53
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (34 bp):
AGATTCTTGATATATCTTCTTTTTCTTCATTTTA
Found at i:1627111 original size:3 final size:3
Alignment explanation
Indices: 1627105--1627136 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1627095 GAAGAAAATA
1627105 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1627137 ATCTTACACT
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:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1627336 original size:4 final size:4
Alignment explanation
Indices: 1627327--1627385 Score: 67
Period size: 4 Copynumber: 16.2 Consensus size: 4
1627317 TCTCCCTCTG
1627327 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA- TTA- TTA- TTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
*
1627370 TTA- TTAT TTAT ATAT T
1 TTAT TTAT TTAT TTAT T
1627386 GCCTTACCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 18 0.35
4 34 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1627518 original size:23 final size:25
Alignment explanation
Indices: 1627482--1627529 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1627472 TGGGAACCCA
1627482 TTATATTTGATTATC-TATTTTTCT
1 TTATATTTGATTATCATATTTTTCT
*
1627506 TTAT-TTTTATTATCATTATTTTTC
1 TTATATTTGATTATCA-TATTTTTC
1627530 CCAATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.21, C:0.08, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATATTTGATTATCATATTTTTCT
Found at i:1630650 original size:20 final size:20
Alignment explanation
Indices: 1630625--1630781 Score: 87
Period size: 22 Copynumber: 7.9 Consensus size: 20
1630615 AATTCAAAAA
1630625 TTTATATTATATTTATATATT
1 TTTATATTATATTTATATA-T
*
1630646 TTATATATTATAATTATAT-T
1 TT-TATATTATATTTATATAT
* * *
1630666 TAAGATATCTTATATTTATATAA
1 T---TTATATTATATTTATATAT
* * *
1630689 ATTATAATATATTAATATAAGT
1 TTTATATTATATTTATAT-A-T
* * *
1630711 TTT-GA-CATATTTATGTA-
1 TTTATATTATATTTATATAT
* *
1630728 CTTATATTATTTTTATAT-T
1 TTTATATTATATTTATATAT
1630747 TTTATATTATATTT-TATA-
1 TTTATATTATATTTATATAT
1630765 -TTATATTATATTTATAT
1 TTTATATTATATTTATAT
1630782 TATATTTAAA
Statistics
Matches: 101, Mismatches: 23, Indels: 27
0.67 0.15 0.18
Matches are distributed among these distances:
17 15 0.15
18 7 0.07
19 21 0.21
20 23 0.23
21 4 0.04
22 31 0.31
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTATATTATATTTATATAT
Found at i:1630751 original size:19 final size:22
Alignment explanation
Indices: 1630729--1630787 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 22
1630719 ATTTATGTAC
1630729 TTATATTAT-TTTTATATT-T-
1 TTATATTATATTTTATATTATA
1630748 TTATATTATATTTTATATTATA
1 TTATATTATATTTTATATTATA
*
1630770 TTATATT-TATATTATATT
1 TTATATTATATTTTATATT
1630788 TAAAGTTACC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 9 0.25
20 9 0.25
21 11 0.31
22 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATATTATATTTTATATTATA
Found at i:1630756 original size:5 final size:5
Alignment explanation
Indices: 1630729--1630787 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
1630719 ATTTATGTAC
*
1630729 TTATA TTATTT TTATA TT-T- TTATA TTATA TTTTATA TTATA TTATA
1 TTATA TTA-TA TTATA TTATA TTATA TTATA --TTATA TTATA TTATA
1630775 TTTATA TTATA TT
1 -TTATA TTATA TT
1630788 TAAAGTTACC
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
3 2 0.04
4 2 0.04
5 28 0.61
6 9 0.20
7 5 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (5 bp):
TTATA
Found at i:1630763 original size:12 final size:12
Alignment explanation
Indices: 1630740--1630782 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1630730 TATATTATTT
1630740 TTATATTTTTATA
1 TTATA-TTTTATA
1630753 TTATATTTTATA
1 TTATATTTTATA
*
1630765 TTATATTATAT-
1 TTATATTTTATA
1630776 TTATATT
1 TTATATT
1630783 ATATTTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 7 0.24
12 17 0.59
13 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:1631283 original size:20 final size:21
Alignment explanation
Indices: 1631260--1631299 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1631250 ATTTTAATAT
1631260 TAAATAAGTAAT-AAATATAA
1 TAAATAAGTAATAAAATATAA
**
1631280 TAAATATTTAATAAAATATA
1 TAAATAAGTAATAAAATATA
1631300 TTTTTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (21 bp):
TAAATAAGTAATAAAATATAA
Found at i:1633364 original size:21 final size:20
Alignment explanation
Indices: 1633340--1633379 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1633330 TATTTGTTTT
*
1633340 TCTTATGATTTCTTTTTATTC
1 TCTTATAATTT-TTTTTATTC
*
1633361 TCTTTTAATTTTTTTTATT
1 TCTTATAATTTTTTTTATT
1633380 ATTGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.10, G:0.03, T:0.72
Consensus pattern (20 bp):
TCTTATAATTTTTTTTATTC
Found at i:1634084 original size:17 final size:17
Alignment explanation
Indices: 1634062--1634095 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1634052 TCCTAAGAAT
1634062 ATTTAT-TATTTATAATA
1 ATTTATATATTTA-AATA
1634079 ATTTATATATTTAAATA
1 ATTTATATATTTAAATA
1634096 TAATAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATATATTTAAATA
Found at i:1640180 original size:13 final size:13
Alignment explanation
Indices: 1640164--1640196 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1640154 ATTTTTTAAA
1640164 AATATTTATATTT
1 AATATTTATATTT
1640177 AATATTTATATTT
1 AATATTTATATTT
1640190 AA-ATTTA
1 AATATTTA
1640197 AATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1640226 original size:19 final size:19
Alignment explanation
Indices: 1640204--1640245 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1640194 TTAAATATAA
*
1640204 AAATAAAATATAAT-TTTTT
1 AAAT-AAATATAATATATTT
*
1640223 AAATATATATAATATATTT
1 AAATAAATATAATATATTT
1640242 AAAT
1 AAAT
1640246 TTGATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATAAATATAATATATTT
Found at i:1640968 original size:13 final size:13
Alignment explanation
Indices: 1640925--1640969 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1640915 CGATTTAAAT
1640925 ATATAAATATATTA
1 ATATAAAT-TATTA
*
1640939 A-AAAAATTATATA
1 ATATAAATTAT-TA
1640952 ATATAAATTATTA
1 ATATAAATTATTA
1640965 ATATA
1 ATATA
1640970 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 3 0.11
13 15 0.56
14 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAAATTATTA
Found at i:1640980 original size:18 final size:17
Alignment explanation
Indices: 1640930--1640977 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1640920 TAAATATATA
**
1640930 AATATATTAAAAAAATT
1 AATATATTAAAATTATT
*
1640947 -ATATAATATAAATTATT
1 AATATATTA-AAATTATT
1640964 AATATATTAAAATT
1 AATATATTAAAATT
1640978 TATAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.28
17 11 0.44
18 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATTAAAATTATT
Found at i:1641421 original size:6 final size:5
Alignment explanation
Indices: 1641409--1641557 Score: 60
Period size: 5 Copynumber: 29.2 Consensus size: 5
1641399 AGTTGATAAT
* * *
1641409 TTATA TATATA TATATA TACATA TTTTA TTATA TTATA TTTATA TTTAAA
1 TTATA T-TATA T-TATA T-TATA TTATA TTATA TTATA -TTATA -TTATA
* * * *
1641459 TTATT TTATA TT-TA TATAAA TT-TT TATATA TTA-A TAAT- TTATA TTATA
1 TTATA TTATA TTATA T-TATA TTATA T-TATA TTATA TTATA TTATA TTATA
* ** *
1641507 TTA-A TTTTA AAATA TT-T- TTATT TTATA TTTTATA TTATA TTCATA
1 TTATA TTATA TTATA TTATA TTATA TTATA --TTATA TTATA TT-ATA
1641552 TTATA T
1 TTATA T
1641558 AATTATAAAA
Statistics
Matches: 109, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
3 2 0.02
4 15 0.14
5 52 0.48
6 35 0.32
7 5 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:1641532 original size:32 final size:32
Alignment explanation
Indices: 1641458--1641540 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
1641448 TTATATTTAA
* *
1641458 ATTATTTTATATTTATATAAATTTTTATATATT
1 ATTATTTTATA-TTATATAAATTTTAAAATATT
* * *
1641491 AATAATTTATATTATATTAATTTTAAAATATT
1 ATTATTTTATATTATATAAATTTTAAAATATT
* *
1641523 TTTATTTTATATTTTATA
1 ATTATTTTATATTATATA
1641541 TTATATTCAT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
32 31 0.77
33 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
ATTATTTTATATTATATAAATTTTAAAATATT
Found at i:1641539 original size:12 final size:12
Alignment explanation
Indices: 1641437--1641557 Score: 66
Period size: 11 Copynumber: 10.9 Consensus size: 12
1641427 ACATATTTTA
1641437 TTATATTATA-T
1 TTATATTATATT
**
1641448 TTATATT-TAAA
1 TTATATTATATT
*
1641459 TTATTTTATA-T
1 TTATATTATATT
*
1641470 TTATA-TAAATT
1 TTATATTATATT
1641481 TT-TA-TATA-T
1 TTATATTATATT
* *
1641490 TAATAATT-TATA
1 TTAT-ATTATATT
1641502 TTATATTA-ATT
1 TTATATTATATT
* *
1641513 TTAAAATAT-TT
1 TTATATTATATT
*
1641524 TTATTTTATATT
1 TTATATTATATT
1641536 TTATATTATA-T
1 TTATATTATATT
*
1641547 TCATATTATAT
1 TTATATTATAT
1641558 AATTATAAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 21
0.68 0.14 0.17
Matches are distributed among these distances:
9 2 0.02
10 11 0.13
11 52 0.63
12 17 0.21
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1641686 original size:16 final size:17
Alignment explanation
Indices: 1641654--1641688 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1641644 ACATGACAAG
1641654 ATTATAATGACAAATGTA
1 ATTATAATGA-AAATGTA
1641672 ATTATAATG-AAATGTA
1 ATTATAATGAAAATGTA
1641688 A
1 A
1641689 ACTATATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (17 bp):
ATTATAATGAAAATGTA
Found at i:1642097 original size:3 final size:3
Alignment explanation
Indices: 1642083--1642117 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1642073 AATTTTGGCC
1642083 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1642118 GAACAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:1643009 original size:14 final size:14
Alignment explanation
Indices: 1642989--1643028 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1642979 TTCAAATTTA
*
1642989 AATTTTTTAAATAT
1 AATTTTTTAAAAAT
*
1643003 TATTTTTTAAAAAT
1 AATTTTTTAAAAAT
*
1643017 AATTATTTAAAA
1 AATTTTTTAAAA
1643029 CAACATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTTTTTAAAAAT
Found at i:1643337 original size:2 final size:2
Alignment explanation
Indices: 1643332--1643361 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1643322 TCCCAACATT
1643332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1643362 AATCATCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1644154 original size:16 final size:16
Alignment explanation
Indices: 1644133--1644167 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1644123 TAAAACTGTT
*
1644133 TTAAATTATTGTTAAA
1 TTAAATTATTATTAAA
1644149 TTAAATTATTATTAAA
1 TTAAATTATTATTAAA
1644165 TTA
1 TTA
1644168 TATTCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTAAATTATTATTAAA
Found at i:1644479 original size:17 final size:17
Alignment explanation
Indices: 1644444--1644482 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1644434 ATAAAAATAT
*
1644444 TTTTTTATTTTAATCAA
1 TTTTTTATTTTAATAAA
1644461 TTTTTTATCTTTAA-AAA
1 TTTTTTAT-TTTAATAAA
1644478 TTTTT
1 TTTTT
1644483 AAAAATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTATTTTAATAAA
Found at i:1644704 original size:21 final size:22
Alignment explanation
Indices: 1644680--1644729 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
1644670 GAATTTTGAA
1644680 AAATATTTAATAT-ATTTAATT
1 AAATATTTAATATAATTTAATT
* *
1644701 AAATA-ATAATTTAATTTAATT
1 AAATATTTAATATAATTTAATT
1644722 --ATATTTAA
1 AAATATTTAA
1644730 ATTTGATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 3 0.12
20 8 0.33
21 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTTAATATAATTTAATT
Found at i:1644714 original size:16 final size:16
Alignment explanation
Indices: 1644684--1644743 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
1644674 TTTGAAAAAT
1644684 ATTTAAT-AT-ATTTA
1 ATTTAATAATAATTTA
*
1644698 ATTAAATAATAATTTA
1 ATTTAATAATAATTTA
*
1644714 ATTTAATTAT-ATTTAA
1 ATTTAATAATAATTT-A
*
1644730 ATTTGATAATAATT
1 ATTTAATAATAATT
1644744 AAAAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.16
15 6 0.16
16 22 0.59
17 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATTTAATAATAATTTA
Found at i:1644743 original size:32 final size:30
Alignment explanation
Indices: 1644684--1644743 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 30
1644674 TTTGAAAAAT
1644684 ATTTAATATATTTAATTAAATAATAATTTA
1 ATTTAATATATTTAATTAAATAATAATTTA
**
1644714 ATTTAATTATATTTAAATTTGATAATAATT
1 ATTTAA-TATATTT-AATTAAATAATAATT
1644744 AAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 7 0.27
32 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTTAATATATTTAATTAAATAATAATTTA
Found at i:1644753 original size:32 final size:31
Alignment explanation
Indices: 1644690--1644753 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
1644680 AAATATTTAA
* **
1644690 TATATTTAATTAAATAATAATTTAATTTAAT
1 TATATTTAATTAAATAATAATTAAAAATAAT
**
1644721 TATATTTAAATTTGATAATAATTAAAAATAAT
1 TATATTT-AATTAAATAATAATTAAAAATAAT
1644753 T
1 T
1644754 TTATAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
TATATTTAATTAAATAATAATTAAAAATAAT
Found at i:1644995 original size:2 final size:2
Alignment explanation
Indices: 1644990--1645027 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1644980 AAGCGAGAGA
1644990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1645028 GTCAAAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.