Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 8 of 77
Found at i:1169558 original size:22 final size:22
Alignment explanation
Indices: 1169530--1169574 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1169520 AGGTTTATTA
*
1169530 TTATGGTATAGTGACTCATCAC
1 TTATGGTACAGTGACTCATCAC
*
1169552 TTATGGTACGGTGACTCATCAC
1 TTATGGTACAGTGACTCATCAC
1169574 T
1 T
1169575 ATGACTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (22 bp):
TTATGGTACAGTGACTCATCAC
Found at i:1173342 original size:22 final size:22
Alignment explanation
Indices: 1173316--1173366 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1173306 GCTTCGTATT
*
1173316 TTTATTTTAAAATTTTAAATTA
1 TTTATTATAAAATTTTAAATTA
* *
1173338 TTTATTATGATATTTTAAATTA
1 TTTATTATAAAATTTTAAATTA
1173360 TTT-TTAT
1 TTTATTAT
1173367 GGTGGAGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATTATAAAATTTTAAATTA
Found at i:1173613 original size:20 final size:20
Alignment explanation
Indices: 1173588--1173628 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1173578 TCGAGTTTAT
1173588 TATCTATATATAATTATAGA
1 TATCTATATATAATTATAGA
*
1173608 TATCTATATATAGTTATAGA
1 TATCTATATATAATTATAGA
1173628 T
1 T
1173629 TTAGCCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (20 bp):
TATCTATATATAATTATAGA
Found at i:1174478 original size:15 final size:16
Alignment explanation
Indices: 1174443--1174477 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1174433 TTGAATGAAG
*
1174443 TTTTGGTTTTTGTGAT
1 TTTTGGTTTTAGTGAT
*
1174459 TTTTGGTTTTAGTTAT
1 TTTTGGTTTTAGTGAT
1174475 TTT
1 TTT
1174478 GTTATTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.20, T:0.71
Consensus pattern (16 bp):
TTTTGGTTTTAGTGAT
Found at i:1174619 original size:17 final size:17
Alignment explanation
Indices: 1174599--1174631 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1174589 CATTTCTATG
1174599 TTATTTGGA-TTTAAGGA
1 TTATTT-GATTTTAAGGA
1174616 TTATTTGATTTTAAGG
1 TTATTTGATTTTAAGG
1174632 GTTGCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (17 bp):
TTATTTGATTTTAAGGA
Found at i:1174807 original size:2 final size:2
Alignment explanation
Indices: 1174800--1174828 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1174790 ATTGAAGGTG
1174800 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 T
1174829 TTTTTTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1175536 original size:18 final size:18
Alignment explanation
Indices: 1175513--1175548 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1175503 TTCAGATTTC
1175513 AAAGCATATGG-TGATGTA
1 AAAGCATA-GGTTGATGTA
1175531 AAAGCATAGGTTGATGTA
1 AAAGCATAGGTTGATGTA
1175549 GTTTTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.28
Consensus pattern (18 bp):
AAAGCATAGGTTGATGTA
Found at i:1177066 original size:4 final size:4
Alignment explanation
Indices: 1177034--1177078 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
1177024 GACTTTATCT
* * * *
1177034 TATA TAAA TATA AATA TAAA TACA TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA T
1177079 GAAAGTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:1177076 original size:6 final size:6
Alignment explanation
Indices: 1177034--1177078 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
1177024 GACTTTATCT
* * * *
1177034 TATATA AATATA AATATA AATACA TATATA TATATA TATATA TAT
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TAT
1177079 GAAAGTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (6 bp):
TATATA
Found at i:1181305 original size:21 final size:21
Alignment explanation
Indices: 1181281--1181321 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1181271 TTAATTTTGT
1181281 AAAATGATATGAAATTTTAAA
1 AAAATGATATGAAATTTTAAA
* *
1181302 AAAATGTTTTGAAATTTTAA
1 AAAATGATATGAAATTTTAA
1181322 CTTAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (21 bp):
AAAATGATATGAAATTTTAAA
Found at i:1182368 original size:15 final size:16
Alignment explanation
Indices: 1182348--1182380 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1182338 CTATACATTT
1182348 AAATG-TTAAAAAGTA
1 AAATGTTTAAAAAGTA
*
1182363 AAATGTTTAAAAATTA
1 AAATGTTTAAAAAGTA
1182379 AA
1 AA
1182381 TATAAACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (16 bp):
AAATGTTTAAAAAGTA
Found at i:1183269 original size:21 final size:21
Alignment explanation
Indices: 1183245--1183293 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1183235 ATGGTAGAGG
* *
1183245 TGAGATTTGTTACTGTAAAGA
1 TGAGATTAGTTACTATAAAGA
* *
1183266 TGAGATTAGTTACTATAAGGG
1 TGAGATTAGTTACTATAAAGA
1183287 TGAGATT
1 TGAGATT
1183294 GAATACTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (21 bp):
TGAGATTAGTTACTATAAAGA
Found at i:1184512 original size:16 final size:16
Alignment explanation
Indices: 1184488--1184527 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1184478 TTTTATTTTA
1184488 TTTTT-TATTTT-TACT
1 TTTTTGTATTTTGTA-T
1184503 TTTTTGTATTTTGTAT
1 TTTTTGTATTTTGTAT
1184519 TTTTTGTAT
1 TTTTTGTAT
1184528 CTTATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.22
16 16 0.70
17 2 0.09
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (16 bp):
TTTTTGTATTTTGTAT
Found at i:1184569 original size:35 final size:35
Alignment explanation
Indices: 1184529--1184672 Score: 92
Period size: 33 Copynumber: 4.3 Consensus size: 35
1184519 TTTTTGTATC
1184529 TTATTTATTATTACTATTTATTAATATATATATTT
1 TTATTTATTATTACTATTTATTAATATATATATTT
* * * ** *
1184564 TTATTTAGTATT--TATCTGTCGATATATATA-CT
1 TTATTTATTATTACTATTTATTAATATATATATTT
* *
1184596 TTA-TTATTATTTATCTA-TTATTATTAT-TATTATTA
1 TTATTTATTA-TTA-CTATTTATTAATATATA-TATTT
*
1184631 TTA-TTATTATTATTATTTATCT-AT-TA-ATATTT
1 TTATTTATTATTACTATTTAT-TAATATATATATTT
*
1184663 TTATCTATTA
1 TTATTTATTA
1184673 ATATATTATC
Statistics
Matches: 81, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
31 5 0.06
32 13 0.16
33 25 0.31
34 15 0.19
35 23 0.28
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (35 bp):
TTATTTATTATTACTATTTATTAATATATATATTT
Found at i:1184604 original size:3 final size:3
Alignment explanation
Indices: 1184596--1184681 Score: 93
Period size: 3 Copynumber: 27.3 Consensus size: 3
1184586 TATATATACT
1184596 TTA TTA TTA TTTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1184643 TTA TTTA TCTA TTA ATA TTT TTA TCTA TTA ATA -TA TTA T
1 TTA -TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T
1184682 CTTTATTTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.03
3 55 0.76
4 15 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1184649 original size:41 final size:41
Alignment explanation
Indices: 1184596--1184689 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
1184586 TATATATACT
* *
1184596 TTATTATTATTTATCTATTATTATTATTAT-TATTATTATTA
1 TTATTATTATTTATCTATTAATATTATTATCTATTAATA-TA
*
1184637 TTATTATTATTTATCTATTAATATTTTTATCTATTAATATA
1 TTATTATTATTTATCTATTAATATTATTATCTATTAATATA
1184678 TTATCT-TTATTT
1 TTAT-TATTATTT
1184690 TTTATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
41 40 0.83
42 8 0.17
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (41 bp):
TTATTATTATTTATCTATTAATATTATTATCTATTAATATA
Found at i:1185522 original size:5 final size:5
Alignment explanation
Indices: 1185512--1185553 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
1185502 TTAGTATTTC
1185512 TTATT TTATT TTATT TTATTT TTATCT TTA-T TT-TT TTATT TT
1 TTATT TTATT TTATT TTA-TT TTAT-T TTATT TTATT TTATT TT
1185554 CTTTAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
4 6 0.18
5 18 0.55
6 9 0.27
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1185541 original size:12 final size:11
Alignment explanation
Indices: 1185506--1185546 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
1185496 AATTATTTAG
1185506 TATTTCTTATTT
1 TATTT-TTATTT
1185518 TA-TTTTATTT
1 TATTTTTATTT
1185528 TATTTTTATCTT
1 TATTTTTAT-TT
1185540 TATTTTT
1 TATTTTT
1185547 TTATTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.30
11 8 0.30
12 11 0.41
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:1185541 original size:17 final size:16
Alignment explanation
Indices: 1185515--1185558 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1185505 GTATTTCTTA
1185515 TTTTAT-TTTATTTTAT
1 TTTTATCTTTATTTT-T
1185531 TTTTATCTTTATTTTT
1 TTTTATCTTTATTTTT
*
1185547 TTATTTTCTTTA
1 TT-TTATCTTTA
1185559 AATAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATCTTTATTTTT
Found at i:1185611 original size:58 final size:56
Alignment explanation
Indices: 1185549--1185732 Score: 210
Period size: 59 Copynumber: 3.2 Consensus size: 56
1185539 TTATTTTTTT
1185549 ATTTTCTTTAAATAAAATTTCAAAAAAATATATTTTTAAGGAAAAGTTGAAAGTATCA
1 ATTTTCTTTAAATAAAATTTC-AAAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATCA
* * *
1185607 ATTTTCCTTGAAA-ATAACTCTTCAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCA
1 ATTTT-CTTTAAATA-AAAT-TTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCA
* ** *
1185665 GTTTT-TGTTGAAAATAAGTTTTCAAAAAACATATTTTTAAGAAAAAGTTGAAAGTATCA
1 ATTTTCT-TT--AAATAAAATTTCAAAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATCA
1185724 ATTTTCTTT
1 ATTTTCTTT
1185733 GAGAATAATT
Statistics
Matches: 107, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 47 0.44
59 53 0.50
60 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.39
Consensus pattern (56 bp):
ATTTTCTTTAAATAAAATTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCA
Found at i:1185722 original size:59 final size:57
Alignment explanation
Indices: 1185566--1185791 Score: 249
Period size: 58 Copynumber: 3.8 Consensus size: 57
1185556 TTAAATAAAA
*
1185566 TTTCAAAAAAATATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAACT
1 TTTC-AAAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAACT
* * * *
1185626 CTTCAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAGTTTTTGTTGAAAATAAGT
1 TTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTT-TTGAAAATAACT
* * *
1185684 TTTCAAAAAACATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTTGAGAATAATTT
1 TTTCAAAAAA-ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-TTTGAAAATAA-CT
* * *
1185744 TTTTAAAAAAGGGT-TTTTTGCA-GAAAAGTTGAAAGTATCAATTTTTTT
1 TTTCAAAAAA--ATATTTTT-AAGGAAAAGTTGAAAGTATCAATTTTTTT
1185792 TGTATGAAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
58 52 0.36
59 49 0.34
60 41 0.28
61 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (57 bp):
TTTCAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTTTTGAAAATAACT
Found at i:1185900 original size:21 final size:20
Alignment explanation
Indices: 1185852--1185900 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1185842 AGCTGAATCA
**
1185852 TTTTTTTTTGTTTTATTTCT
1 TTTTTTTTTGTTTTATTAAT
*
1185872 TTTCTTTTTTGTTTTCTTGAAT
1 TTT-TTTTTTGTTTTATT-AAT
1185894 TTTTTTT
1 TTTTTTT
1185901 AATGTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTGTTTTATTAAT
Found at i:1196278 original size:24 final size:25
Alignment explanation
Indices: 1196244--1196295 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
1196234 CTTGAATGAA
1196244 AAAAATAAAAAAAAT-AAAAAAAATG
1 AAAAAT-AAAAAAATGAAAAAAAATG
1196269 AAAAAT-AAAAAATGAAAAAAAATG
1 AAAAATAAAAAAATGAAAAAAAATG
1196293 AAA
1 AAA
1196296 GGAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (25 bp):
AAAAATAAAAAAATGAAAAAAAATG
Found at i:1196287 original size:9 final size:9
Alignment explanation
Indices: 1196238--1196295 Score: 61
Period size: 9 Copynumber: 6.8 Consensus size: 9
1196228 ACTATGCTTG
1196238 AATGAAAAA
1 AATGAAAAA
*
1196247 AATAAAAAA
1 AATGAAAAA
*
1196256 AATAAAAAA
1 AATGAAAAA
1196265 AATG--AAA
1 AATGAAAAA
1196272 AAT--AAAA
1 AATGAAAAA
1196279 AATGAAAAAA
1 AATG-AAAAA
1196289 AATGAAA
1 AATGAAA
1196296 GGAAAAAAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 12 0.28
9 23 0.53
10 8 0.19
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (9 bp):
AATGAAAAA
Found at i:1196301 original size:23 final size:24
Alignment explanation
Indices: 1196252--1196308 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1196242 AAAAAAATAA
*
1196252 AAAAAAT-AAAAAAAATGAAAAAT
1 AAAAAATGAAAAAAAATGAAAAAG
*
1196275 AAAAAATGAAAAAAAATG-AAAGG
1 AAAAAATGAAAAAAAATGAAAAAG
1196298 AAAAAA-GAAAA
1 AAAAAATGAAAA
1196309 GTAAAAGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 5 0.16
23 16 0.52
24 10 0.32
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAATGAAAAAAAATGAAAAAG
Found at i:1197465 original size:42 final size:42
Alignment explanation
Indices: 1197308--1197604 Score: 205
Period size: 41 Copynumber: 7.1 Consensus size: 42
1197298 GATGGTCAAT
** * * *
1197308 GAGCAATTTA-TTTTCTGAAGTTG-TGATGCCTCTGTTTAAAG
1 GAGCAATTTATTTTTCAAAAGTCGTTGA-GCCTCTGTTCAGAG
* * *
1197349 GAGCAATCTATTTTTC-AAAGTTG-TGATGTCTCTGATT-AGAG
1 GAGCAATTTATTTTTCAAAAGTCGTTGA-GCCTCTG-TTCAGAG
* * *
1197390 GAGTAATTTACTTTTC-AAAGTCGTTGAGCTTCTGTTCAGAG
1 GAGCAATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTCAGAG
* * *
1197431 GAGCAATTTATTTTTCAAAAGTTGTTGAGCTTCTGTTCAAAG
1 GAGCAATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTCAGAG
* * * * * *
1197473 GAGCAATTTA-TTTTCTAATAGTCATTGAACCTATGATCAGAT
1 GAGCAATTTATTTTTC-AAAAGTCGTTGAGCCTCTGTTCAGAG
** *
1197515 GAGCCTTTTATTTTT-AAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCAATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTCAGAG
** * * * * *
1197556 GAGCTTTGTTTATCTTTTTAAAAGTCGTTAAGCCTTTATTTAGAG
1 GAGC--AATTTAT-TTTTCAAAAGTCGTTGAGCCTCTGTTCAGAG
1197601 GAGC
1 GAGC
1197605 TTTGTTTATT
Statistics
Matches: 208, Mismatches: 37, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
40 2 0.01
41 98 0.47
42 68 0.33
43 9 0.04
44 4 0.02
45 27 0.13
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (42 bp):
GAGCAATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTCAGAG
Found at i:1197636 original size:44 final size:45
Alignment explanation
Indices: 1197525--1197643 Score: 177
Period size: 45 Copynumber: 2.7 Consensus size: 45
1197515 GAGCCTTTTA
* *
1197525 TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTATC
1 TTTTTAAAAGTCGTTGAGCCTTTATTTAGAGGAGCTTTGTTTATC
* *
1197570 TTTTTAAAAGTCGTTAAGCCTTTATTTAGAGGAGCTTTGTTTATT
1 TTTTTAAAAGTCGTTGAGCCTTTATTTAGAGGAGCTTTGTTTATC
* *
1197615 TTTTTGAAATTC-TTGAGCCTTTATTTAGA
1 TTTTTAAAAGTCGTTGAGCCTTTATTTAGA
1197644 AGAGTAATCT
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
44 16 0.24
45 51 0.76
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (45 bp):
TTTTTAAAAGTCGTTGAGCCTTTATTTAGAGGAGCTTTGTTTATC
Found at i:1197973 original size:16 final size:16
Alignment explanation
Indices: 1197942--1198013 Score: 87
Period size: 16 Copynumber: 4.5 Consensus size: 16
1197932 TTCCATTTTA
1197942 TTTTA-TTTTT-TATT
1 TTTTATTTTTTGTATT
1197956 TTTTATTTTTT-TATTT
1 TTTTATTTTTTGTA-TT
1197972 TTTTATTTTTTGTATT
1 TTTTATTTTTTGTATT
*
1197988 TTGTATTTTTTGTATCT
1 TTTTATTTTTTGTAT-T
1198005 TATTTATTT
1 T-TTTATTT
1198014 ATTATTACTA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.10
15 7 0.14
16 29 0.57
17 4 0.08
18 6 0.12
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (16 bp):
TTTTATTTTTTGTATT
Found at i:1197998 original size:9 final size:8
Alignment explanation
Indices: 1197942--1198013 Score: 78
Period size: 8 Copynumber: 9.0 Consensus size: 8
1197932 TTCCATTTTA
1197942 TTTTA-TT
1 TTTTATTT
1197949 TTTTA-TT
1 TTTTATTT
1197956 TTTTATTT
1 TTTTATTT
1197964 TTTTATTT
1 TTTTATTT
1197972 TTTTATTT
1 TTTTATTT
1197980 TTTGTA-TT
1 TTT-TATTT
*
1197988 TTGTATTT
1 TTTTATTT
1197996 TTTGTATCTT
1 TTT-TAT-TT
*
1198006 ATTTATTT
1 TTTTATTT
1198014 ATTATTACTA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
7 14 0.25
8 31 0.54
9 8 0.14
10 4 0.07
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:1198015 original size:8 final size:8
Alignment explanation
Indices: 1197938--1198051 Score: 60
Period size: 8 Copynumber: 14.2 Consensus size: 8
1197928 TTCATTCCAT
1197938 TTTATTTTA
1 TTTA-TTTA
1197947 TTT-TTTA
1 TTTATTTA
1197954 TTT-TTTA
1 TTTATTTA
*
1197961 TTTTTTTA
1 TTTATTTA
*
1197969 TTTTTTTA
1 TTTATTTA
*
1197977 TTTTTTGTA
1 TTTATT-TA
*
1197986 TTT-TGTA
1 TTTATTTA
*
1197993 TTTTTTGTA
1 TTTATT-TA
1198002 TCTTATTTA
1 T-TTATTTA
1198011 TTTA-TTA
1 TTTATTTA
1198018 TTACTATTTA
1 TT--TATTTA
* *
1198028 TTAATATA
1 TTTATTTA
*
1198036 TATA-TT-
1 TTTATTTA
1198042 TTTATTTA
1 TTTATTTA
1198050 TT
1 TT
1198052 ATGTATCTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
6 3 0.03
7 27 0.31
8 31 0.36
9 16 0.19
10 9 0.10
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTATTTA
Found at i:1198046 original size:31 final size:31
Alignment explanation
Indices: 1198011--1198098 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 31
1198001 ATCTTATTTA
*
1198011 TTTATTATTACTATTTATTAATATATATA-TT
1 TTTATTATTA-TATCTATTAATATATATACTT
* *
1198042 TTTATTTATTATGTATCTGTTGATATATATACTT
1 TTTA-TTATTA--TATCTATTAATATATATACTT
1198076 TATTATTATT-TATCTATTAATAT
1 T-TTATTATTATATCTATTAATAT
1198099 TTTTATCTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 15 0.32
32 6 0.13
33 15 0.32
34 8 0.17
35 3 0.06
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTATTATTATATCTATTAATATATATACTT
Found at i:1198105 original size:16 final size:17
Alignment explanation
Indices: 1198079--1198114 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1198069 TATACTTTAT
1198079 TATTATTTATCTATTAA
1 TATTATTTATCTATTAA
1198096 TATT-TTTATCTATTAA
1 TATTATTTATCTATTAA
1198112 TAT
1 TAT
1198115 ATTATCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTATTTATCTATTAA
Found at i:1198109 original size:27 final size:28
Alignment explanation
Indices: 1198035--1198110 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
1198025 TTATTAATAT
*
1198035 ATATATTTTTATTTATTATGTATCTGTTG
1 ATATATTTTTA-TTATTATGTATCTATTG
*
1198064 ATATATATACTTTATTATTATTTATCTATT-
1 ATATAT-T--TTTATTATTATGTATCTATTG
1198094 A-ATATTTTTATCTATTA
1 ATATATTTTTAT-TATTA
1198111 ATATATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
26 5 0.12
27 5 0.12
28 1 0.02
29 10 0.24
30 2 0.05
31 14 0.34
32 4 0.10
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.61
Consensus pattern (28 bp):
ATATATTTTTATTATTATGTATCTATTG
Found at i:1198149 original size:14 final size:14
Alignment explanation
Indices: 1198114--1198157 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
1198104 TCTATTAATA
1198114 TATTATCTTTATTTTT
1 TATT-TCTTT-TTTTT
1198130 TATTTCTTTTCTTTT
1 TATTTCTTTT-TTTT
1198145 T-TTTCTTTTTTTT
1 TATTTCTTTTTTTT
1198158 GATTACCCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 4 0.15
14 9 0.33
15 10 0.37
16 4 0.15
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (14 bp):
TATTTCTTTTTTTT
Found at i:1198425 original size:21 final size:21
Alignment explanation
Indices: 1198385--1198427 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1198375 AGAAAGGTCA
1198385 GAAGTAATTTTAGGATTTTTT
1 GAAGTAATTTTAGGATTTTTT
1198406 GAAG-AATTTTAGGCGATTTTTT
1 GAAGTAATTTTA-G-GATTTTTT
1198428 TCTGGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (21 bp):
GAAGTAATTTTAGGATTTTTT
Found at i:1199013 original size:13 final size:13
Alignment explanation
Indices: 1198995--1199019 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1198985 TTAGTATTTC
1198995 TTATTTTATTTTA
1 TTATTTTATTTTA
1199008 TTATTTTATTTT
1 TTATTTTATTTT
1199020 TTTAAAATAA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:1199184 original size:59 final size:59
Alignment explanation
Indices: 1199035--1199254 Score: 277
Period size: 60 Copynumber: 3.7 Consensus size: 59
1199025 AATAAAATTC
*
1199035 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT-CTTTGAAAATAAATCTT
1 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTGCATTGAAAATAAATCTT
* *
1199093 CAAAAAAAAATATTTTTAAGCAAAAGTTGAAAGTATCAATTTTG-ACTTGAAAATAAGTCTT
1 C--AAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTGCA-TTGAAAATAAATCTT
* *
1199154 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAA-TTTGCATTGAAAATAATTTTTT
1 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTGCATTGAAAATAA-ATCTT
* * * *
1199213 TAAAAAAGGAT-TTTTTGAGAAAAAGTTGAAAGCATCAATTTT
1 CAAAAAA--ATATTTTTAAGGAAAAGTTGAAAGTATCAATTTT
1199255 CCTTGTACGA
Statistics
Matches: 143, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
58 15 0.10
59 45 0.31
60 63 0.44
61 20 0.14
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (59 bp):
CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTGCATTGAAAATAAATCTT
Found at i:1199237 original size:119 final size:119
Alignment explanation
Indices: 1199035--1199254 Score: 334
Period size: 119 Copynumber: 1.8 Consensus size: 119
1199025 AATAAAATTC
* *
1199035 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAATCTTCAAAAAA
1 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTGCATTGAAAATAAATCTTCAAAAAA
* *
1199100 AAATATTTTTAAGCAAAAGTTGAAAGTATCAATTTTGACTTGAAAATAAGTCTT
66 AAATATTTTTAAGAAAAAGTTGAAAGCATCAATTTTGACTTGAAAATAAGTCTT
* * *
1199154 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTGCATTGAAAATAATTTTTTTAAAAA
1 CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTGCATTGAAAATAA-ATCTTCAAAAA
** *
1199219 AGGAT-TTTTTGAGAAAAAGTTGAAAGCATCAATTTT
65 AAAATATTTTTAAGAAAAAGTTGAAAGCATCAATTTT
1199255 CCTTGTACGA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 79 0.88
120 11 0.12
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.35
Consensus pattern (119 bp):
CAAAAAAATATTTTTAAGGAAAAGTTGAAAGTATCAATTTGCATTGAAAATAAATCTTCAAAAAA
AAATATTTTTAAGAAAAAGTTGAAAGCATCAATTTTGACTTGAAAATAAGTCTT
Found at i:1199365 original size:26 final size:25
Alignment explanation
Indices: 1199317--1199371 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1199307 AGCTAAATCA
* * *
1199317 TTTTTCTTTTTTTTTGTTTTATTTC
1 TTTTCCTTTTTTTTTCTTGTATTTC
*
1199342 TTTTCCTTTTTGTTTTCTTGTATTTT
1 TTTTCCTTTTT-TTTTCTTGTATTTC
1199368 TTTT
1 TTTT
1199372 AATGTTAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.04, C:0.09, G:0.05, T:0.82
Consensus pattern (25 bp):
TTTTCCTTTTTTTTTCTTGTATTTC
Found at i:1200910 original size:32 final size:29
Alignment explanation
Indices: 1200871--1200941 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
1200861 ATTTTTTAAA
* *
1200871 ATTTTATTTTCAATTTTTTATATATATTTTTT
1 ATTTTATTTTCAATTCTTT-T-GATA-TTTTT
**
1200903 ATTTTATTTTTGATTCTTTTGATATTTTT
1 ATTTTATTTTCAATTCTTTTGATATTTTT
1200932 ATTTTATTTT
1 ATTTTATTTT
1200942 TGCATAAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.43
30 3 0.09
31 1 0.03
32 16 0.46
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (29 bp):
ATTTTATTTTCAATTCTTTTGATATTTTT
Found at i:1201641 original size:242 final size:244
Alignment explanation
Indices: 1201207--1201687 Score: 607
Period size: 242 Copynumber: 2.0 Consensus size: 244
1201197 AAATTAAGAA
* * * * * * *
1201207 ATTTTCTTAAAAAATTTATCAAAAGTGTCGGGAATATTTTGAGAATTCTTGTATTAAAACTCTTA
1 ATTTTCTAAAAAAATTTACCAAAAATGTCAGGAATATTTTAAGAATTCTTCTAATAAAACTCTTA
* * * * *
1201272 AAAAATATTTTTAAGTATCAAAATAAAATCATAAATAGTGATTTTGTTAAAAATATTCATGCCAA
66 AAAAATATTTTTAACTATCAAAATAAAATCACAAAGAGTGATTTTATTAAAAATATTCATACCAA
* * *
1201337 GAAATTTTTTAAAATATTCTAAAAATGTTAAAAATATATTAAAGTTTTTCAAGCATAAAAAAACC
131 GAAATTTTTTAAAATATTCTAAAAATGTTAAAAATATATTAAAGATTTTCAAACACAAAAAAA-C
* *
1201402 AT-TATTAATAA-A-AAAAATAAAGTGACAAGTGGTGATTTTATTAAGGG
195 ATATATTAATAAGATAAAAATAAAGTCACAAGTGATGATTTTATTAAGGG
* *
1201449 ATTTTCTCAAAAAAATTTACCAAAAATGTTAGGAATATTTTAAGAAATT-TTCTAATAAAACTTT
1 ATTTTCT-AAAAAAATTTACCAAAAATGTCAGGAATATTTTAAG-AATTCTTCTAATAAAACTCT
* * * *
1201513 TATAAAATATTTTTAACTATTAAAATAAAA-CACAAGGGGTGATTTTATTAAAAATATTCATACC
64 TAAAAAATATTTTTAACTATCAAAATAAAATCACAAAGAGTGATTTTATTAAAAATATTCATACC
* *
1201577 AATAAATTTTTTAAAATATTCTAAAAATGTTAGAAATAT-TGTAGAA-ATTTTCAAACACAAAAA
129 AAGAAATTTTTTAAAATATTCTAAAAATGTTAAAAATATAT-TA-AAGATTTTCAAACACAAAAA
* ** *
1201640 AATATATATTAATAAGATAATGATAAAGTCACGAGTGATGATTTTATT
192 AACATATATTAATAAGATAAAAATAAAGTCACAAGTGATGATTTTATT
1201688 GAAATTCCTA
Statistics
Matches: 203, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
241 3 0.01
242 99 0.49
243 72 0.35
244 29 0.14
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.37
Consensus pattern (244 bp):
ATTTTCTAAAAAAATTTACCAAAAATGTCAGGAATATTTTAAGAATTCTTCTAATAAAACTCTTA
AAAAATATTTTTAACTATCAAAATAAAATCACAAAGAGTGATTTTATTAAAAATATTCATACCAA
GAAATTTTTTAAAATATTCTAAAAATGTTAAAAATATATTAAAGATTTTCAAACACAAAAAAACA
TATATTAATAAGATAAAAATAAAGTCACAAGTGATGATTTTATTAAGGG
Found at i:1207101 original size:26 final size:26
Alignment explanation
Indices: 1207052--1207103 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1207042 TATATTCCAA
* *
1207052 CAAAAGTTAAAATATGCAAGAAAAAG
1 CAAAAGTGAAAATATACAAGAAAAAG
*
1207078 CAAAAGTGAAAATGATACAAAAAAAA
1 CAAAAGTGAAAAT-ATACAAGAAAAA
1207104 AAGAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (26 bp):
CAAAAGTGAAAATATACAAGAAAAAG
Found at i:1207976 original size:19 final size:18
Alignment explanation
Indices: 1207937--1207979 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1207927 TTTGGGAAGG
1207937 AAAAAT-AAAATTTTAAT
1 AAAAATAAAAATTTTAAT
*
1207954 -AAAATAAACAATTTTTAT
1 AAAAATAAA-AATTTTAAT
1207972 AAAAATAA
1 AAAAATAA
1207980 GTGACACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.23
17 2 0.09
18 8 0.36
19 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATAAAAATTTTAAT
Found at i:1209087 original size:57 final size:57
Alignment explanation
Indices: 1208947--1209087 Score: 131
Period size: 57 Copynumber: 2.5 Consensus size: 57
1208937 TTGTTCTTTA
* * * * *
1208947 CATTTGCAT-TTTCTCGATGGTGATATTCGAGTTTCCTTCGATGGTGATATCCGAAAT
1 CATTTGCATCTTT-TCGGTGGTGATATCCAAGTTTCCTTCAATGGCGATATCCGAAAT
* * * *** * * **
1209004 CATTTACATCATTTCAGTGACAATATCCAAGTTTTCTTTAATGGCGATATTTGAAAT
1 CATTTGCATCTTTTCGGTGGTGATATCCAAGTTTCCTTCAATGGCGATATCCGAAAT
1209061 CATTTGCATCTTTTCGGTGGTGATATC
1 CATTTGCATCTTTTCGGTGGTGATATC
1209088 TAAAGTTATT
Statistics
Matches: 62, Mismatches: 21, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
57 60 0.97
58 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (57 bp):
CATTTGCATCTTTTCGGTGGTGATATCCAAGTTTCCTTCAATGGCGATATCCGAAAT
Found at i:1211117 original size:20 final size:19
Alignment explanation
Indices: 1211053--1211118 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
1211043 AAGACAAATG
*
1211053 AATAAAAGTAAAAATGAAA
1 AATAAAAGTAAAAATGATA
* * * *
1211072 TAATAAAAATAAAACTTATG
1 -AATAAAAGTAAAAATGATA
1211092 AATAAAAGTAAATAATGATA
1 AATAAAAGTAAA-AATGATA
1211112 AATAAAA
1 AATAAAA
1211119 ATAACAATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 11 0.31
20 25 0.69
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (19 bp):
AATAAAAGTAAAAATGATA
Found at i:1212017 original size:15 final size:16
Alignment explanation
Indices: 1211992--1212022 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1211982 AAAAATTTTC
1211992 AATAATAAAAATAAAA
1 AATAATAAAAATAAAA
1212008 AATAAT-AAAATAAAA
1 AATAATAAAAATAAAA
1212023 GGAGTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAATAAAAATAAAA
Found at i:1219428 original size:25 final size:25
Alignment explanation
Indices: 1219394--1219443 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1219384 AACATTTGGC
*
1219394 TCAATGATAGGTGAATGTCTCCCCT
1 TCAATGATAGGTGAATGTATCCCCT
*
1219419 TCAATGATAGGTGCATGTATCCCCT
1 TCAATGATAGGTGAATGTATCCCCT
1219444 AACCAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (25 bp):
TCAATGATAGGTGAATGTATCCCCT
Found at i:1220848 original size:19 final size:19
Alignment explanation
Indices: 1220809--1220847 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1220799 AACTTTTTAA
*
1220809 TTAATTTTTTCTCACTTTT
1 TTAATTTTTTCACACTTTT
1220828 TTAATTTTTTCACA-TTTT
1 TTAATTTTTTCACACTTTT
1220846 TT
1 TT
1220848 TCTTCATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAATTTTTTCACACTTTT
Found at i:1223300 original size:2 final size:2
Alignment explanation
Indices: 1223293--1223327 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1223283 ACTGATTTAG
1223293 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1223328 CCTCCCTCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1228615 original size:30 final size:29
Alignment explanation
Indices: 1228552--1228662 Score: 91
Period size: 29 Copynumber: 3.8 Consensus size: 29
1228542 TACTTTATTT
* * *
1228552 AAATAAGTCTTTATACTTTT-ATTGCACTC
1 AAATAAGCCCTTA-ACTTTTAATTGCATTC
1228581 AAATAAGCCCTTAACTTTTAATATGCATTC
1 AAATAAGCCCTTAACTTTTAAT-TGCATTC
** * *
1228611 AAAT-AGGGCTTAACCTTTAATTTGTATTC
1 AAATAAGCCCTTAACTTTTAA-TTGCATTC
* * *
1228640 AAATAAGCCTTTTATTTTTAATT
1 AAATAAGCCCTTAACTTTTAATT
1228663 TGTTCCTAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.09
29 38 0.58
30 21 0.32
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.43
Consensus pattern (29 bp):
AAATAAGCCCTTAACTTTTAATTGCATTC
Found at i:1234058 original size:24 final size:24
Alignment explanation
Indices: 1234013--1234059 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1234003 CTTCTCATGC
* *
1234013 AAAAAGAAATTTTTTTTAATTTGT
1 AAAAAGAAACTTGTTTTAATTTGT
1234037 AAAAAGAAACCTTGTTTT-ATTTG
1 AAAAAGAAA-CTTGTTTTAATTTG
1234060 ATTTGTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.45
Consensus pattern (24 bp):
AAAAAGAAACTTGTTTTAATTTGT
Found at i:1235688 original size:15 final size:15
Alignment explanation
Indices: 1235644--1235680 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
1235634 AAAAATAATT
1235644 TATTAATATATTTTAA
1 TATTAATAT-TTTTAA
1235660 TATTAATATTTTTAA
1 TATTAATATTTTTAA
1235675 TGATTA
1 T-ATTA
1235681 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (15 bp):
TATTAATATTTTTAA
Found at i:1235898 original size:16 final size:16
Alignment explanation
Indices: 1235877--1235911 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1235867 TGTCAACTTC
1235877 AATAAAATTTATTTA-A
1 AATAAAATTT-TTTATA
1235893 AATAAAATTTTTTATA
1 AATAAAATTTTTTATA
1235909 AAT
1 AAT
1235912 TTTTTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATAAAATTTTTTATA
Found at i:1235938 original size:26 final size:26
Alignment explanation
Indices: 1235906--1235965 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
1235896 AAAATTTTTT
* *
1235906 ATAAATTTTTTTTAATTACACTTATA
1 ATAAATTTTTTTCAATTACAATTATA
*
1235932 TTAAA-TTTTTTCAATTACAATTATA
1 ATAAATTTTTTTCAATTACAATTATA
1235957 AT-AATTTTT
1 ATAAATTTTT
1235966 ATTATTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 23 0.79
26 4 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (26 bp):
ATAAATTTTTTTCAATTACAATTATA
Found at i:1238067 original size:18 final size:18
Alignment explanation
Indices: 1238040--1238074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1238030 GTCATTTATG
*
1238040 TTGACCTGACATGTTAGA
1 TTGACCTGACATATTAGA
*
1238058 TTGACTTGACATATTAG
1 TTGACCTGACATATTAG
1238075 GTCAGCTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (18 bp):
TTGACCTGACATATTAGA
Found at i:1245590 original size:65 final size:64
Alignment explanation
Indices: 1245521--1245848 Score: 259
Period size: 65 Copynumber: 5.1 Consensus size: 64
1245511 GAGAAGAACT
* * * * *
1245521 CCTTATTTGATTTGGTTTTATAATTTATAAAACCTCAGCAATTATGATGTTTGTTAATATAAATG
1 CCTTAATTGACTTGGTTTTATAATTTATAAAACCT-ATCAATTACGACGTTTGTTAATATAAATG
* * * * * ** * *
1245586 CCTTAATAG-CTTGGTTTT-TGCAATTGATAAAACCTATCAATTATGGCATTTGGGACAGATGAA
1 CCTTAATTGACTTGGTTTTAT--AATTTATAAAACCTATCAATTACGACGTTTGTTA-ATATAAA
1245649 TG
63 TG
** *
1245651 CCTTAATTGAC-ACGTTTTATAATTTATAAAATCTCATCAATTACGACGTTTGTTAATATAAATG
1 CCTTAATTGACTTGGTTTTATAATTTATAAAACCT-ATCAATTACGACGTTTGTTAATATAAATG
* * ** * * * * ** * *
1245715 CCTTTATTGCCAAGTTTTTATAATTGATAAAACCTATCAATTACAACATTTGGAACAAATGAATG
1 CCTTAATTGACTTGGTTTTATAATTTATAAAACCTATCAATTACGACGTTTGTTA-ATATAAATG
* * * * *
1245780 CCTTAATTGACAT-GTTTTATAATTTATAAAACCTTAGCAATTACAACGTTTATTAATATAAATA
1 CCTTAATTGACTTGGTTTTATAATTTATAAAACC-TATCAATTACGACGTTTGTTAATATAAATG
1245844 CCTTA
1 CCTTA
1245849 TTTGCTTTTG
Statistics
Matches: 205, Mismatches: 49, Indels: 19
0.75 0.18 0.07
Matches are distributed among these distances:
63 1 0.00
64 95 0.46
65 107 0.52
66 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (64 bp):
CCTTAATTGACTTGGTTTTATAATTTATAAAACCTATCAATTACGACGTTTGTTAATATAAATG
Found at i:1245692 original size:129 final size:129
Alignment explanation
Indices: 1245491--1245848 Score: 448
Period size: 129 Copynumber: 2.8 Consensus size: 129
1245481 TAAAAAAAAA
* * * ***
1245491 ATCAATTATGGCATTTGGAAGAGAAGAACT-CCTTATTTGATTTGGTTTTATAATTTATAAAACC
1 ATCAATTATGGCATTTGGAACAGATGAA-TGCCTTAATTGA-CACGTTTTATAATTTATAAAACC
* * *** *
1245555 TCAGCAATTATGATGTTTGTTAATATAAATGCCTTAATAGCTTGGTTTTTGCAATTGATAAAACC
64 TCAGCAATTACGACGTTTGTTAATATAAATGCCTTAATAGCCAAGTTTTTACAATTGATAAAACC
1245620 T
129 T
* *
1245621 ATCAATTATGGCATTTGGGACAGATGAATGCCTTAATTGACACGTTTTATAATTTATAAAATCTC
1 ATCAATTATGGCATTTGGAACAGATGAATGCCTTAATTGACACGTTTTATAATTTATAAAACCTC
* * * *
1245686 ATCAATTACGACGTTTGTTAATATAAATGCCTTTATTGCCAAGTTTTTATAATTGATAAAACCT
66 AGCAATTACGACGTTTGTTAATATAAATGCCTTAATAGCCAAGTTTTTACAATTGATAAAACCT
*** * * *
1245750 ATCAATTACAACATTTGGAACAAATGAATGCCTTAATTGACATGTTTTATAATTTATAAAACCTT
1 ATCAATTATGGCATTTGGAACAGATGAATGCCTTAATTGACACGTTTTATAATTTATAAAACCTC
* * *
1245815 AGCAATTACAACGTTTATTAATATAAATACCTTA
66 AGCAATTACGACGTTTGTTAATATAAATGCCTTA
1245849 TTTGCTTTTG
Statistics
Matches: 196, Mismatches: 31, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
129 162 0.83
130 34 0.17
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.39
Consensus pattern (129 bp):
ATCAATTATGGCATTTGGAACAGATGAATGCCTTAATTGACACGTTTTATAATTTATAAAACCTC
AGCAATTACGACGTTTGTTAATATAAATGCCTTAATAGCCAAGTTTTTACAATTGATAAAACCT
Found at i:1248241 original size:19 final size:19
Alignment explanation
Indices: 1248206--1248256 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1248196 GATAATCATC
* *
1248206 ATTATTGTTTTATTTTTTTA
1 ATTATT-TTTAATTTTCTTA
*
1248226 GTTAATTTTTAATTTTCTTA
1 ATT-ATTTTTAATTTTCTTA
1248246 ATTATTTTTAA
1 ATTATTTTTAA
1248257 AATTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.31
20 15 0.58
21 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (19 bp):
ATTATTTTTAATTTTCTTA
Found at i:1250644 original size:16 final size:15
Alignment explanation
Indices: 1250619--1250685 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
1250609 ATTAATATGC
*
1250619 ATTTTTAAAATTTAA
1 ATTTTTAAAATATAA
1250634 ATTTGTTAAAATATAAA
1 ATTT-TTAAAATAT-AA
*
1250651 ATATTTATAAAATAAAA
1 AT-TTT-TAAAATATAA
* *
1250668 ATATTTAAATTA-AA
1 ATTTTTAAAATATAA
1250682 ATTT
1 ATTT
1250686 ATTTACATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 5 0.12
15 10 0.23
16 10 0.23
17 9 0.21
18 9 0.21
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (15 bp):
ATTTTTAAAATATAA
Found at i:1250668 original size:17 final size:18
Alignment explanation
Indices: 1250640--1250674 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1250630 TTAAATTTGT
1250640 TAAAATATAAAATATTTA
1 TAAAATATAAAATATTTA
1250658 TAAAATA-AAAATATTTA
1 TAAAATATAAAATATTTA
1250675 AATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATATAAAATATTTA
Found at i:1250735 original size:9 final size:9
Alignment explanation
Indices: 1250721--1250795 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
1250711 AACAAACTTT
1250721 AAAAAAAT-
1 AAAAAAATA
1250729 AAAAAAATA
1 AAAAAAATA
*
1250738 AAAAGAATA
1 AAAAAAATA
*
1250747 AATAAAATA
1 AAAAAAATA
1250756 GAAATAAAATA
1 -AAA-AAAATA
*
1250767 TAAAAAATA
1 AAAAAAATA
* *
1250776 ATAACAATA
1 AAAAAAATA
* *
1250785 ATAATAATA
1 AAAAAAATA
1250794 AA
1 AA
1250796 TTTTTAAACA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
8 8 0.15
9 36 0.67
10 4 0.07
11 6 0.11
ACGTcount: A:0.77, C:0.01, G:0.03, T:0.19
Consensus pattern (9 bp):
AAAAAAATA
Found at i:1250790 original size:29 final size:29
Alignment explanation
Indices: 1250720--1250791 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
1250710 TAACAAACTT
* *
1250720 TAAAAAAATAAAAAAATAAAAAGAATAAA
1 TAAAATAATAATAAAATAAAAAGAATAAA
1250749 TAAAATAGA-AATAAAATATAAAA-AAT-AA
1 TAAAATA-ATAATAAAATA-AAAAGAATAAA
1250777 TAACAATAATAATAA
1 TAA-AATAATAATAA
1250792 TAAATTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
28 6 0.16
29 26 0.70
30 5 0.14
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (29 bp):
TAAAATAATAATAAAATAAAAAGAATAAA
Found at i:1251088 original size:3 final size:3
Alignment explanation
Indices: 1251082--1251143 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
1251072 GGTCACAAAG
1251082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1251130 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
1251144 ATATATAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1251153 original size:8 final size:7
Alignment explanation
Indices: 1251082--1251153 Score: 72
Period size: 6 Copynumber: 11.4 Consensus size: 7
1251072 GGTCACAAAG
1251082 AATAAT-
1 AATAATA
1251088 AATAAT-
1 AATAATA
1251094 AATAAT-
1 AATAATA
1251100 AATAAT-
1 AATAATA
1251106 AATAAT-
1 AATAATA
1251112 AATAAT-
1 AATAATA
1251118 AATAAT-
1 AATAATA
1251124 AATAAT-
1 AATAATA
1251130 AATAAT-
1 AATAATA
1251136 AATAATA
1 AATAATA
1251143 AATATATA
1 AATA-ATA
1251151 AAT
1 AAT
1251154 GTTATAAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
6 54 0.84
7 4 0.06
8 6 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AATAATA
Found at i:1251670 original size:15 final size:16
Alignment explanation
Indices: 1251650--1251680 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1251640 AAAACCAAAC
1251650 TAAAGACC-ATTTAGT
1 TAAAGACCAATTTAGT
1251665 TAAAGACCAATTTAGT
1 TAAAGACCAATTTAGT
1251681 ACAGCACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TAAAGACCAATTTAGT
Found at i:1252046 original size:9 final size:10
Alignment explanation
Indices: 1252030--1252058 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
1252020 TGATGGTCTA
1252030 ATTTATTATT
1 ATTTATTATT
1252040 A-TTATTATT
1 ATTTATTATT
1252049 ATTTATTATT
1 ATTTATTATT
1252059 TAATATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTTATTATT
Found at i:1252056 original size:7 final size:7
Alignment explanation
Indices: 1252030--1252066 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1252020 TGATGGTCTA
1252030 ATTTATT
1 ATTTATT
1252037 A-TTATT
1 ATTTATT
1252043 A-TTATT
1 ATTTATT
1252049 ATTTATT
1 ATTTATT
*
1252056 ATTTAAT
1 ATTTATT
1252063 ATTT
1 ATTT
1252067 CAAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTATT
Found at i:1252535 original size:13 final size:13
Alignment explanation
Indices: 1252517--1252542 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1252507 ACAACCCTTA
1252517 ACAATATAATTTG
1 ACAATATAATTTG
1252530 ACAATATAATTTG
1 ACAATATAATTTG
1252543 CATTATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAATATAATTTG
Found at i:1253206 original size:11 final size:11
Alignment explanation
Indices: 1253189--1253222 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1253179 TTAGAATAGC
1253189 AAAAATTTTAA
1 AAAAATTTTAA
* *
1253200 TAAAATTATAA
1 AAAAATTTTAA
1253211 AAAAATTTTAA
1 AAAAATTTTAA
1253222 A
1 A
1253223 TAGAATTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:1253215 original size:22 final size:23
Alignment explanation
Indices: 1253189--1253235 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1253179 TTAGAATAGC
1253189 AAAAATTTT-AATAAAATTATAA
1 AAAAATTTTAAATAAAATTATAA
*
1253211 AAAAATTTTAAATAGAATTATAA
1 AAAAATTTTAAATAAAATTATAA
1253234 AA
1 AA
1253236 GTTTTTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAAATTTTAAATAAAATTATAA
Found at i:1254317 original size:22 final size:22
Alignment explanation
Indices: 1254275--1254318 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1254265 GTATATTTTA
* * *
1254275 TTTATAATTTTTTTATTATAAC
1 TTTATAATTATTTAATCATAAC
1254297 TTTATAATTATTTAATCATAAC
1 TTTATAATTATTTAATCATAAC
1254319 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATAATTATTTAATCATAAC
Found at i:1256028 original size:15 final size:14
Alignment explanation
Indices: 1255987--1256036 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
1255977 TTTAATTCTA
1255987 AAATTA-TATTTA-
1 AAATTATTATTTAT
1255999 AAATTAATT-TTTAT
1 AAATT-ATTATTTAT
1256013 AAATTATTATTGTAT
1 AAATTATTATT-TAT
*
1256028 AATTTATTA
1 AAATTATTA
1256037 ATAATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.16
13 8 0.25
14 8 0.25
15 11 0.34
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
AAATTATTATTTAT
Found at i:1256575 original size:34 final size:32
Alignment explanation
Indices: 1256483--1256576 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 32
1256473 AATTATGGGC
* *
1256483 GTTTATATAGAAAACGCCACTAATTTAGTGGT
1 GTTTATATAGAAAATGCCACTAATTTAGCGGT
*
1256515 GTTTGTATAGAAAAATGCCACTAATTTAGCGGT
1 GTTTATATAG-AAAATGCCACTAATTTAGCGGT
*
1256548 GTTTATATATGAAAATGCCCCTAAATTTA
1 GTTTATATA-GAAAATGCCACT-AATTTA
1256577 ATGGCATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 9 0.17
33 38 0.70
34 7 0.13
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
GTTTATATAGAAAATGCCACTAATTTAGCGGT
Found at i:1256637 original size:41 final size:41
Alignment explanation
Indices: 1256571--1256649 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
1256561 AATGCCCCTA
*
1256571 AATTTAATGGCATTTTATGCTACAAATGCCACTAAATTTCG
1 AATTTAATGGCATTTTATGCTACAAATGCCACAAAATTTCG
*
1256612 AATTTAGTGGCATTTT-TGAAC-ACAAATGCCACAAAATT
1 AATTTAATGGCATTTTATG--CTACAAATGCCACAAAATT
1256650 AAGAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 2 0.06
41 31 0.91
42 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (41 bp):
AATTTAATGGCATTTTATGCTACAAATGCCACAAAATTTCG
Found at i:1258096 original size:161 final size:160
Alignment explanation
Indices: 1257881--1258668 Score: 742
Period size: 160 Copynumber: 4.9 Consensus size: 160
1257871 CATTTGGCCC
* * * * * *
1257881 TTTCACACATATCAATCATGGAAACTAAGTTCAATCATTAAAAAAAGTTTAATATTATGTATTGA
1 TTTCACACATATCAATCATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
* * ** * *
1257946 AGCCATCAAAATTGTTAAAATAGATTAATAATAGCAAATTTGTATTTTTGCCTTTTAATGAG-A-
66 AGCTATC-AAACTGTTAAAATAGAACAATAATAACAAATTTGCATTTTTGCCTTTTAATG-GCAC
* ** * *
1258009 AAAATAGTCCTAAGTAGACGTAAACGATAACTT
129 AAAAT-GTCTTAAACAGATGTAAACAATAACTT
* * * **
1258042 TTTCACACATATAAATCATAGAAACCAACTTCAATCATTCGGACAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAATCATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
* * *
1258107 AGCTATCCAAACTGTTAAAATAGAAAAATAATATCAAATTTGCATTTTT-CCTTTTAATGGCATA
66 AGCTAT-CAAACTGTTAAAATAGAACAATAATAACAAATTTGCATTTTTGCCTTTTAATGGCACA
* *** *
1258171 AAATGTCATAAACAGATGTAAATGTTAGCTT
130 AAATGTCTTAAACAGATGTAAACAATAACTT
* * *
1258202 TTTCATACATATCAA-CTATAGAAACCAAGTTCAATTATTCCAACAAGTTTAATATCATGTATTG
1 TTTCACACATATCAATC-ATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTG
* * * * ** **
1258266 AAGCTATGCAAACTGTTAAAATAGAACAATAACAATAAATTTGCATGTTTGTCTCGTAACAGCAC
65 AAGCTAT-CAAACTGTTAAAATAGAACAATAATAACAAATTTGCATTTTTGCCTTTTAATGGCAC
* * *
1258331 AAAAAGTTTTAAACAGAAGTAAACAATAACTT
129 AAAATGTCTTAAACAGATGTAAACAATAACTT
** * * *
1258363 TTTCACACATATCAATTGTGGAAACCAAGTTCAAAAATTCAAACAAGTTTAATATCATGTATTGG
1 TTTCACACATATCAATCATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
* ** ** ** * * *
1258428 AGCTATCAAACTGTTAAAGTAGAACAATTTTTCCAAATTTATATTTTTACCTATTAACGGCACAA
66 AGCTATCAAACTGTTAAAATAGAACAATAATAACAAATTTGCATTTTTGCCTTTTAATGGCACAA
*
1258493 AATGTCTTAAATAGATGTAAACAATAACTT
131 AATGTCTTAAACAGATGTAAACAATAACTT
* * * * * * * * *
1258523 TTTCATACATATAAACCAT-GCAAACTAAGTTGAATAATTTAGATAAGTTTAATATTATGTATTG
1 TTTCACACATATCAATCATAG-AAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTG
* * ** * * *
1258587 AAACTATCAAAACTATTAAAATAGAACAATAACT-GTAAATTTGCATTATTACCTTGTAATGGCA
65 AAGCTATC-AAACTGTTAAAATAGAACAATAA-TAACAAATTTGCATTTTTGCCTTTTAATGGCA
* * *
1258651 TAAAAAGTTTTAAACAGA
128 CAAAATGTCTTAAACAGA
1258669 CATAAATTGC
Statistics
Matches: 513, Mismatches: 105, Indels: 18
0.81 0.17 0.03
Matches are distributed among these distances:
159 3 0.01
160 257 0.50
161 251 0.49
162 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (160 bp):
TTTCACACATATCAATCATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
AGCTATCAAACTGTTAAAATAGAACAATAATAACAAATTTGCATTTTTGCCTTTTAATGGCACAA
AATGTCTTAAACAGATGTAAACAATAACTT
Found at i:1258257 original size:160 final size:160
Alignment explanation
Indices: 1257881--1258668 Score: 732
Period size: 161 Copynumber: 4.9 Consensus size: 160
1257871 CATTTGGCCC
* * * * * *
1257881 TTTCACACATATCAA-TCATGGAAACTAAGTTCAATCATTAAAAAAAGTTTAATATTATGTATTG
1 TTTCACACATATCAACT-ATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTG
* * * ** * *
1257945 AAGCCATCAAAATTGTTAAAATAGATTAATAATAGCAAATTTGTATTTTTGCCTTTTAATGAG-A
65 AAGCTATCCAAACTGTTAAAATAGAACAATAATATCAAATTTGCATTTTT-CCTTTTAATG-GCA
* ** * *
1258009 -AAAATAGTCCTAAGTAGACGTAAACGATAACTT
128 CAAAAT-GTCTTAAACAGATGTAAACAATAACTT
* * * **
1258042 TTTCACACATAT-AAATCATAGAAACCAACTTCAATCATTCGGACAAGTTTAATATCATGTATTG
1 TTTCACACATATCAACT-ATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTG
* *
1258106 AAGCTATCCAAACTGTTAAAATAGAAAAATAATATCAAATTTGCATTTTTCCTTTTAATGGCATA
65 AAGCTATCCAAACTGTTAAAATAGAACAATAATATCAAATTTGCATTTTTCCTTTTAATGGCACA
* *** *
1258171 AAATGTCATAAACAGATGTAAATGTTAGCTT
130 AAATGTCTTAAACAGATGTAAACAATAACTT
* * *
1258202 TTTCATACATATCAACTATAGAAACCAAGTTCAATTATTCCAACAAGTTTAATATCATGTATTGA
1 TTTCACACATATCAACTATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
* * ** **
1258267 AGCTATGCAAACTGTTAAAATAGAACAATAACAAT-AAATTTGCATGTTTGT-CTCGTAACAGCA
66 AGCTATCCAAACTGTTAAAATAGAACAATAA-TATCAAATTTGCAT-TTT-TCCTTTTAATGGCA
* * *
1258330 CAAAAAGTTTTAAACAGAAGTAAACAATAACTT
128 CAAAATGTCTTAAACAGATGTAAACAATAACTT
* * * * *
1258363 TTTCACACATATCAATTGTGGAAACCAAGTTCAAAAATTCAAACAAGTTTAATATCATGTATTGG
1 TTTCACACATATCAACTATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
* * * ** * *
1258428 AGCTAT-CAAACTGTTAAAGTAGAACAAT-TTTTCCAAATTTATATTTTTACCTATTAACGGCAC
66 AGCTATCCAAACTGTTAAAATAGAACAATAATAT-CAAATTTGCATTTTT-CCTTTTAATGGCAC
*
1258491 AAAATGTCTTAAATAGATGTAAACAATAACTT
129 AAAATGTCTTAAACAGATGTAAACAATAACTT
* * * * * * * * *
1258523 TTTCATACATATAAACCAT-GCAAACTAAGTTGAATAATTTAGATAAGTTTAATATTATGTATTG
1 TTTCACACATATCAACTATAG-AAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTG
* * * * * *
1258587 AAACTATCAAAACTATTAAAATAGAACAATAACTGT-AAATTTGCATTATTACCTTGTAATGGCA
65 AAGCTATCCAAACTGTTAAAATAGAACAATAA-TATCAAATTTGCATT-TTTCCTTTTAATGGCA
* * *
1258651 TAAAAAGTTTTAAACAGA
128 CAAAATGTCTTAAACAGA
1258669 CATAAATTGC
Statistics
Matches: 517, Mismatches: 94, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
158 2 0.00
159 5 0.01
160 249 0.48
161 256 0.50
162 3 0.01
163 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (160 bp):
TTTCACACATATCAACTATAGAAACCAAGTTCAATAATTCAAACAAGTTTAATATCATGTATTGA
AGCTATCCAAACTGTTAAAATAGAACAATAATATCAAATTTGCATTTTTCCTTTTAATGGCACAA
AATGTCTTAAACAGATGTAAACAATAACTT
Found at i:1258364 original size:321 final size:321
Alignment explanation
Indices: 1258028--1258668 Score: 790
Period size: 321 Copynumber: 2.0 Consensus size: 321
1258018 CTAAGTAGAC
* ** **
1258028 GTAAACGATAACTTTTTCACACATATAAATCATAGAAACCAACTTCAATCATTCGGACAAGTTTA
1 GTAAACAATAACTTTTTCACACATATAAATCATAGAAACCAACTTCAAAAATTCAAACAAGTTTA
*
1258093 ATATCATGTATTGAAGCTATCCAAACTGTTAAAATAGAAAAATAATAT-CAAATTTGCATTTTT-
66 ATATCATGTATTGAAGCTAT-CAAACTGTTAAAATAGAAAAAT-ATATCCAAATTTACATTTTTA
* * * *** * * *
1258156 CCTTTTAATGGCATAAAATGTCATAAACAGATGTAAATGTTAGCTTTTTCATACATATCAACTAT
129 CCTATTAACGGCACAAAATGTCATAAACAGATGTAAACAATAACTTTTTCATACATATAAACCAT
* * *
1258221 AG-AAACCAAGTTCAATTATTCCA-ACAAGTTTAATATCATGTATTGAAGCTATGC-AAACTGTT
194 -GCAAACCAAGTTCAATAATT-CAGACAAGTTTAATATCATGTATTGAAACTAT-CAAAACTATT
**
1258283 AAAATAGAACAATAACAATAAATTTGCATGT-TTGTCTCGTAACAGCACAAAAAGTTTTAAACAG
256 AAAATAGAACAATAACAATAAATTTGCAT-TATTACCTCGTAACAGCACAAAAAGTTTTAAACAG
1258347 AA
320 AA
* ** * *
1258349 GTAAACAATAACTTTTTCACACATATCAATTGTGGAAACCAAGTTCAAAAATTCAAACAAGTTTA
1 GTAAACAATAACTTTTTCACACATATAAATCATAGAAACCAACTTCAAAAATTCAAACAAGTTTA
* * * * * *
1258414 ATATCATGTATTGGAGCTATCAAACTGTTAAAGTAGAACAATTTTTCCAAATTTATATTTTTACC
66 ATATCATGTATTGAAGCTATCAAACTGTTAAAATAGAAAAATATATCCAAATTTACATTTTTACC
* *
1258479 TATTAACGGCACAAAATGTCTTAAATAGATGTAAACAATAACTTTTTCATACATATAAACCATGC
131 TATTAACGGCACAAAATGTCATAAACAGATGTAAACAATAACTTTTTCATACATATAAACCATGC
* * * * *
1258544 AAACTAAGTTGAATAATTTAGATAAGTTTAATATTATGTATTGAAACTATCAAAACTATTAAAAT
196 AAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAAT
** * ** *
1258609 AGAACAATAACTGTAAATTTGCATTATTACCTTGTAATGGCATAAAAAGTTTTAAACAGA
261 AGAACAATAACAATAAATTTGCATTATTACCTCGTAACAGCACAAAAAGTTTTAAACAGA
1258669 CATAAATTGC
Statistics
Matches: 270, Mismatches: 44, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
319 2 0.01
320 37 0.14
321 231 0.86
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (321 bp):
GTAAACAATAACTTTTTCACACATATAAATCATAGAAACCAACTTCAAAAATTCAAACAAGTTTA
ATATCATGTATTGAAGCTATCAAACTGTTAAAATAGAAAAATATATCCAAATTTACATTTTTACC
TATTAACGGCACAAAATGTCATAAACAGATGTAAACAATAACTTTTTCATACATATAAACCATGC
AAACCAAGTTCAATAATTCAGACAAGTTTAATATCATGTATTGAAACTATCAAAACTATTAAAAT
AGAACAATAACAATAAATTTGCATTATTACCTCGTAACAGCACAAAAAGTTTTAAACAGAA
Found at i:1259855 original size:13 final size:13
Alignment explanation
Indices: 1259820--1259856 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1259810 ATAAAAGCAA
*
1259820 ATATATAAAAAAC
1 ATATATAAAGAAC
*
1259833 ATATGTAAAGAAC
1 ATATATAAAGAAC
1259846 ATATATAAAGA
1 ATATATAAAGA
1259857 TATTGAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:1262105 original size:21 final size:21
Alignment explanation
Indices: 1262081--1262124 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1262071 TCACTTTGCA
* *
1262081 TATCAAGATCAGCAACTTGAG
1 TATCAAGATCACCAACTTAAG
**
1262102 TATCATTATCACCAACTTAAG
1 TATCAAGATCACCAACTTAAG
1262123 TA
1 TA
1262125 ATAAAAGGAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (21 bp):
TATCAAGATCACCAACTTAAG
Found at i:1264767 original size:62 final size:62
Alignment explanation
Indices: 1264677--1265364 Score: 312
Period size: 62 Copynumber: 11.2 Consensus size: 62
1264667 TGTTTGGGGA
* * ** * * **
1264677 ATTATTGAAAGCGTTTTAGGCAGAAAATACCTTTAATAATCCCCTTTAATTTTGGACGAGAG
1 ATTATTGAAGGCATTTTTTGCAAAAAATACCTTCAATAATCCCCTTTAATTTTTTACGAGAG
*** *** * *
1264739 ATTATTGAAGGCATTTTTTGCAAAAAATACCTTCAATAATTTTCTTTAAAAAATTGAAG-GAG
1 ATTATTGAAGGCATTTTTTGCAAAAAATACCTTCAATAATCCCCTTT-AATTTTTTACGAGAG
* * * * *
1264801 ATTATTGAATGC-GTTTTTG-ATTAAAAATGCCTTCAATAATCCCCTTTAATTTTTTTATGGGA-
1 ATTATTGAAGGCATTTTTTGCA--AAAAATACCTTCAATAATCCCCTTTAA-TTTTTTACGAGAG
** * * * * ** * * *
1264863 ATTATTGAAGATATTTTTTTACAGAAAATGCCTTCAATAATCCACTCAAAATTTTTATCAAGGG
1 ATTATTGAAGGCA-TTTTTTGCAAAAAATACCTTCAATAATCCCCTTTAATTTTTTA-CGAGAG
** * * ** ** *
1264927 ATTATTGAAGGTGTTTTTAGTC-AAAAATACCTTCAATAATCTCCTAAAATTTTTTAAAAGAA
1 ATTATTGAAGGCATTTTTTG-CAAAAAATACCTTCAATAATCCCCTTTAATTTTTTACGAGAG
* * * * * *
1264989 ATTATT-AAAG-ATGTATTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC-AGGG
1 ATTATTGAAGGCAT-T-TTTTGCAAAAAATACCTTCAATAATCCCCTTTAATTTTTTA-CGA-GA
1265051 G
62 G
* * * * * *
1265052 ATTATTGAATGTATTTTTTGATAAAAAATACCTTTAATAAT-CCCTTTAAATTTTTTA-AAGAA
1 ATTATTGAAGGCATTTTTTG-CAAAAAATACCTTCAATAATCCCCTTT-AATTTTTTACGAGAG
* * * * * * * *
1265114 ACTATTCAAGGCATTTTTTGTATAAAATGCCTTTAATAATCCCC-TT-ATATTTTGATGAGGAG
1 ATTATTGAAGGCATTTTTTGCAAAAAATACCTTCAATAATCCCCTTTAAT-TTTTTACGA-GAG
* * * ** * * * *
1265176 ATTATTGAATGC-TTTTTAGACTAAAAACGCCTTCAATAATTCCCTTTAATTTTTGAAGA-AA
1 ATTATTGAAGGCATTTTTTG-CAAAAAATACCTTCAATAATCCCCTTTAATTTTTTACGAGAG
* * * *
1265237 ATTA--AAAGATGC-TTTTTTGC-AAAAA-AGCTTCAAT-ATTCCCTTTAAATTTTTA-G-GAG
1 ATTATTGAAG--GCATTTTTTGCAAAAAATACCTTCAATAATCCCCTTTAATTTTTTACGAGAG
* * *
1265293 ATTATTGAAGGTCATTTTTAGTAAAAAATA-CTTTAA-ACAT-CCCTTTAATTTTTTATC-AGAG
1 ATTATTGAAGG-CATTTTTTGCAAAAAATACCTTCAATA-ATCCCCTTTAATTTTTTA-CGAGAG
1265354 ATTATTGAAGG
1 ATTATTGAAGG
1265365 TGTTTTTAGT
Statistics
Matches: 477, Mismatches: 107, Indels: 85
0.71 0.16 0.13
Matches are distributed among these distances:
56 7 0.01
57 17 0.04
58 16 0.03
59 33 0.07
60 11 0.02
61 67 0.14
62 183 0.38
63 93 0.19
64 47 0.10
65 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (62 bp):
ATTATTGAAGGCATTTTTTGCAAAAAATACCTTCAATAATCCCCTTTAATTTTTTACGAGAG
Found at i:1264964 original size:126 final size:127
Alignment explanation
Indices: 1264795--1265346 Score: 416
Period size: 125 Copynumber: 4.5 Consensus size: 127
1264785 TAAAAAATTG
* * * *
1264795 AAGGAGATTATTGAATGCGTTTTT-GATTAAAAATGCCTTCAATAATCCCCTTTAATTTTTTTAT
1 AAGGAGATTATTGAATGTGTTTTTAGATCAAAAATACCTTCAATAATCCCCTTTAATTTTTTTAA
* * * * *
1264859 GGGAATTATTGAAGATATTTTTTTACAGAAAATGCCTTCAATAATCCACTCAAAATTTTTATC
66 AGAAATTATTAAAGATATTTTTTT-CAGAAAATGCCTTCAATAATCCCCTCTAAATTTTTATC
* * ** *
1264922 AAGG-GATTATTGAAGGTGTTTTTAG-TCAAAAATACCTTCAATAATCTCCTAAAATTTTTTAAA
1 AAGGAGATTATTGAATGTGTTTTTAGATCAAAAATACCTTCAATAATCCCCTTTAATTTTTTTAA
* * * ** * *
1264985 AGAAATTATTAAAGATGTATTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC
66 AGAAATTATTAAAGATATTTTTTTCAGAAAATGCCTTCAATAATCCCCTCTAAATTTTTATC
* * * * * *
1265047 -AGGGGATTATTGAATGTATTTTTTGATAAAAAATACCTTTAATAAT-CCCTTTAAATTTTTTAA
1 AAGGAGATTATTGAATGTGTTTTTAGATCAAAAATACCTTCAATAATCCCCTTTAATTTTTTTAA
* * ** * * * *
1265110 AGAAACTATTCAAGGCATTTTTTGT-ATAAAATGCCTTTAATAATCCCCT-TATATTTTGAT-
66 AGAAATTATTAAAGATATTTTTT-TCAGAAAATGCCTTCAATAATCCCCTCTAAATTTTTATC
* * ** * *
1265170 GAGGAGATTATTGAATG-CTTTTTAGA-CTAAAAACGCCTTCAATAATTCCCTTTAA--TTTTTG
1 AAGGAGATTATTGAATGTGTTTTTAGATC-AAAAATACCTTCAATAATCCCCTTTAATTTTTTTA
* * * * *
1265231 AAGAAA--ATTAAAAGATGCTTTTTTGCA-AAAAAG-CTTCAAT-ATTCCCTTTAAA-TTTT-T-
65 AAGAAATTATT-AAAGAT-ATTTTTTTCAGAAAATGCCTTCAATAATCCCCTCTAAATTTTTATC
* * * *
1265288 -AGGAGATTATTGAAGGTCATTTTTAG-TAAAAAATA-CTTTAA-ACAT-CCCTTTAATTTTTT
1 AAGGAGATTATTGAATGT-GTTTTTAGATCAAAAATACCTTCAATA-ATCCCCTTTAATTTTTT
1265347 ATCAGAGATT
Statistics
Matches: 338, Mismatches: 70, Indels: 43
0.75 0.16 0.10
Matches are distributed among these distances:
116 9 0.03
117 22 0.07
118 10 0.03
119 16 0.05
120 12 0.04
121 8 0.02
122 18 0.05
123 22 0.07
124 34 0.10
125 98 0.29
126 84 0.25
127 5 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (127 bp):
AAGGAGATTATTGAATGTGTTTTTAGATCAAAAATACCTTCAATAATCCCCTTTAATTTTTTTAA
AGAAATTATTAAAGATATTTTTTTCAGAAAATGCCTTCAATAATCCCCTCTAAATTTTTATC
Found at i:1265069 original size:125 final size:125
Alignment explanation
Indices: 1264796--1265371 Score: 372
Period size: 126 Copynumber: 4.7 Consensus size: 125
1264786 AAAAAATTGA
** * * * * * **
1264796 AGGAGATTATTGAATGCGTTTTT-GATTAAAAATGCCTTCAATAATCCCCTTTAATTTTTTTATG
1 AGGAGATTATTGAATGTATTTTTAG-TAAAAAATACCTTCAATAATCTCCTTAAATTTTTTAAAA
* * * * ** * * * *
1264860 GGAATTATTGAAGATATTTTTTTACAGAAAATGCCTTCAATAATCCACTCAAAATTTTTATC
65 GAAATTATTAAAGAT-GTTTTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC
* * * *
1264922 AAGG-GATTATTGAAGGTGTTTTTAGTCAAAAATACCTTCAATAATCTCCTAAAATTTTTTAAAA
1 -AGGAGATTATTGAATGTATTTTTAGTAAAAAATACCTTCAATAATCTCCTTAAATTTTTTAAAA
*
1264986 GAAATTATTAAAGATGTATTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC
65 GAAATTATTAAAGATGTTTTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC
* * *
1265047 AGGGGATTATTGAATGTATTTTTTGATAAAAAATACCTTTAATAATC-CCTTTAAATTTTTT-AA
1 AGGAGATTATTGAATGTATTTTTAG-TAAAAAATACCTTCAATAATCTCC-TTAAATTTTTTAAA
* * *** * * * *
1265110 AGAAACTATTCAAGGCATTTTTTGTATAAAATGC-CTTT-AATAATCCCCT-T-ATATTTTGATG
64 AGAAATTATTAAAGATGTTTTTTGCAGAAAA--CACTTTCAATAATCCCCTCTAAT-TTTTTATC
* ** * *
1265171 AGGAGATTATTGAATG-CTTTTTAG-ACTAAAAACGCCTTCAATAAT-TCCCTTTAATTTTTGAA
1 AGGAGATTATTGAATGTATTTTTAGTA--AAAAATACCTTCAATAATCT-CCTTAAATTTTTTAA
* * * *
1265233 GA-AAATTA--AAAGATGCTTTTTTGCA-AAAA-AGC-TTCAAT-ATTCCCTTTAA-ATTTT-T-
63 AAGAAATTATTAAAGATG-TTTTTTGCAGAAAACA-CTTTCAATAATCCCCTCTAATTTTTTATC
* * * **
1265288 AGGAGATTATTGAAGGTCATTTTTAGTAAAAAATA-CTTTAA-ACATC-CCTTTAATTTTTTATC
1 AGGAGATTATTGAATGT-ATTTTTAGTAAAAAATACCTTCAATA-ATCTCCTTAAATTTTTTAAA
* * *
1265350 AGAGATTATTGAAGGTGTTTTT
64 AGAAATTATTAAAGATGTTTTT
1265372 AGTAAAATGC
Statistics
Matches: 357, Mismatches: 66, Indels: 61
0.74 0.14 0.13
Matches are distributed among these distances:
116 15 0.04
117 27 0.08
118 11 0.03
119 23 0.06
120 6 0.02
121 9 0.03
122 8 0.02
123 37 0.10
124 29 0.08
125 93 0.26
126 94 0.26
127 5 0.01
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (125 bp):
AGGAGATTATTGAATGTATTTTTAGTAAAAAATACCTTCAATAATCTCCTTAAATTTTTTAAAAG
AAATTATTAAAGATGTTTTTTGCAGAAAACACTTTCAATAATCCCCTCTAATTTTTTATC
Found at i:1265636 original size:62 final size:62
Alignment explanation
Indices: 1265464--1265767 Score: 245
Period size: 63 Copynumber: 4.8 Consensus size: 62
1265454 TTTAACAATA
* * * * *
1265464 CCTTCAATAATCCCTTGAAGATTCTTAAAGGAAATTATTGAAAGCATTTTTTGT-AGAAAAC-
1 CCTTTAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTAGTCA-AAAACG
* * * ** * * * *
1265525 ACTTTCAGTAATCCCCTCCAATTTTTTATCAGGAGATTATTGAAGGCATTTTTAGTCACAAACG
1 CCTTT-AATAATCCCTTGAAAATTTTTA-AAGGAAATTATTGAAGGCATTTTTAGTCAAAAACG
* ** **
1265589 CCTTTAATAATCCTTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTTCAAAAAATA
1 CCTTTAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTAGTC-AAAAACG
* ** * * ** * *
1265652 CCTTTAGTAATCCTCTCT-AATTTTTTTTATCAGGGAATTATTGAAGGTGTTTTTAGTCACAAAT
1 CCTTTAATAATCC-CT-TGAA-AATTTTTA-AAGGAAATTATTGAAGGCATTTTTAGTCAAAAAC
1265716 G
62 G
* *
1265717 CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGTATTTTT
1 CCTTTAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTT
1265768 TTTTTTATAG
Statistics
Matches: 186, Mismatches: 47, Indels: 19
0.74 0.19 0.08
Matches are distributed among these distances:
61 3 0.02
62 60 0.32
63 66 0.35
64 12 0.06
65 23 0.12
66 22 0.12
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (62 bp):
CCTTTAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTAGTCAAAAACG
Found at i:1265720 original size:128 final size:125
Alignment explanation
Indices: 1265464--1265899 Score: 443
Period size: 128 Copynumber: 3.4 Consensus size: 125
1265454 TTTAACAATA
* * * * *
1265464 CCTTCAATAATCCCTTGAAGATTCTTAAAGGAAATTATTGAAAGCATTTTTTGTAGAAAACACTT
1 CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTTAAAAAACACTT
1265529 TCAGTAATCCCCTCCAATTTTTTATCAGGAGATTATTGAAGGCATTTTTAGTCACAAACG
66 TCAGTAATCCCCTCCAATTTTTTATCAGGAGATTATTGAAGGCATTTTTAGTCACAAACG
* * *
1265589 CCTTTAATAATCCTTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTTCAAAAAATACC
1 CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTT-AAAAAACA-C
* * ** *
1265654 TTT-AGTAATCCTCTCTAATTTTTTTTATCAGG-GAATTATTGAAGGTGTTTTTAGTCACAAATG
64 TTTCAGTAATCCCCTCCAA--TTTTTTATCAGGAG-ATTATTGAAGGCATTTTTAGTCACAAACG
*
1265717 CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGTATTTTTTTTTTTATAGAAAA
1 CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCA---TTTTTTTTA-A-AAAA
* * *** ** * *
1265782 TGAC-TTCAATAATCATTTTTTAA-TTTTTATCAAGAGATTATTGAAGGCATTTTTAGTGA-AAA
61 -CACTTTCAGTAATC-CCCTCCAATTTTTTATCAGGAGATTATTGAAGGCATTTTTAGTCACAAA
*
1265844 TG
124 CG
** * ** *
1265846 CCTT-AATAATCCCTTGATAAAAATTTAGAGGGGATTATTGAAGGTATTTTTTTT
1 CCTTCAATAATCCCTTGA-AAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTT
1265900 GTCAAATGCC
Statistics
Matches: 266, Mismatches: 30, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
125 48 0.18
126 27 0.10
127 5 0.02
128 94 0.35
129 32 0.12
130 31 0.12
131 12 0.05
132 11 0.04
133 6 0.02
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (125 bp):
CCTTCAATAATCCCTTGAAAATTTTTAAAGGAAATTATTGAAGGCATTTTTTTTAAAAAACACTT
TCAGTAATCCCCTCCAATTTTTTATCAGGAGATTATTGAAGGCATTTTTAGTCACAAACG
Found at i:1265740 original size:66 final size:66
Alignment explanation
Indices: 1265546--1265742 Score: 194
Period size: 66 Copynumber: 3.0 Consensus size: 66
1265536 TCCCCTCCAA
* *
1265546 TTTTTTATCA-GGAGATTATTGAAGGCATTTTTAGTCACAAACGCCTTTAATAATCCTTTGAAAA
1 TTTTTTATCAGGGA-ATTATTGAAGGCATTTTTAGTCACAAATGCCTTTAATAATCCCTTGAAAA
1265610 --
65 TT
* * ** * * *
1265610 -TTTTTA-AAGGAAATTATTGAAGGCATTTTTTTTCAAAAAATACCTTTAGTAATCCTCTCT---
1 TTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTC-ACAAATGCCTTTAATAATCC-CT-TGAA
1265670 AATT
63 AATT
** *
1265674 TTTTTTATCAGGGAATTATTGAAGGTGTTTTTAGTCACAAATGCCTTCAATAATCCCTTGAAAAT
1 TTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTCACAAATGCCTTTAATAATCCCTTGAAAAT
1265739 T
66 T
1265740 TTT
1 TTT
1265743 AAAGGAAATT
Statistics
Matches: 103, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
62 23 0.22
63 25 0.24
64 3 0.03
65 23 0.22
66 29 0.28
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (66 bp):
TTTTTTATCAGGGAATTATTGAAGGCATTTTTAGTCACAAATGCCTTTAATAATCCCTTGAAAAT
T
Found at i:1268012 original size:23 final size:21
Alignment explanation
Indices: 1267952--1268012 Score: 52
Period size: 23 Copynumber: 2.7 Consensus size: 21
1267942 TATGATATTA
*
1267952 TTTATTCACTTAATATTTATTTG
1 TTTATT-ACTT-ATATTGATTTG
*
1267975 TTTATTA-TATTTATTGATTTGG
1 TTTATTACT-TATATTGATTT-G
1267997 TTTTATTACTTATATT
1 -TTTATTACTTATATT
1268013 TCATTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 18 0.58
24 1 0.03
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTATTACTTATATTGATTTG
Found at i:1270358 original size:21 final size:21
Alignment explanation
Indices: 1270334--1270410 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 21
1270324 GCTTTTGAGA
1270334 GTTTTTTTTTTTAGGTTTT-TT
1 GTTTTTTTTTTT-GGTTTTATT
* *
1270355 G--TTTTTTTGT-GTTTTCTT
1 GTTTTTTTTTTTGGTTTTATT
*
1270373 GTTTTTTTTTTTTGTTTTATT
1 GTTTTTTTTTTTGGTTTTATT
1270394 GTTTTTTTTTTTTGGTT
1 G-TTTTTTTTTTTGGTT
1270411 GTTTTACAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
17 5 0.11
18 3 0.06
19 8 0.17
20 8 0.17
21 9 0.19
22 14 0.30
ACGTcount: A:0.03, C:0.01, G:0.14, T:0.82
Consensus pattern (21 bp):
GTTTTTTTTTTTGGTTTTATT
Found at i:1270360 original size:8 final size:8
Alignment explanation
Indices: 1270335--1270406 Score: 64
Period size: 8 Copynumber: 9.4 Consensus size: 8
1270325 CTTTTGAGAG
1270335 TTTTT-TT
1 TTTTTGTT
* *
1270342 TTTTAGGT
1 TTTTTGTT
1270350 TTTTTGTT
1 TTTTTGTT
1270358 TTTTTGTGT
1 TTTTTGT-T
1270367 TTTCTTG--
1 TTT-TTGTT
1270374 TTTTT-TT
1 TTTTTGTT
1270381 TTTTTGTT
1 TTTTTGTT
*
1270389 TTATTGTT
1 TTTTTGTT
1270397 TTTTT-TT
1 TTTTTGTT
1270404 TTT
1 TTT
1270407 GGTTGTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
6 2 0.04
7 17 0.32
8 27 0.51
9 4 0.08
10 3 0.06
ACGTcount: A:0.03, C:0.01, G:0.11, T:0.85
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1270361 original size:18 final size:19
Alignment explanation
Indices: 1270338--1270402 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
1270328 TTGAGAGTTT
1270338 TTTTTTTTAG-GTTTT-TTG
1 TTTTTTTT-GTGTTTTCTTG
1270356 -TTTTTTTGTGTTTTCTTG
1 TTTTTTTTGTGTTTTCTTG
* *
1270374 TTTTTTTTTTTTGTTTTATTG
1 --TTTTTTTTGTGTTTTCTTG
1270395 TTTTTTTT
1 TTTTTTTT
1270403 TTTTGGTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 12 0.30
18 3 0.08
19 8 0.20
21 16 0.40
ACGTcount: A:0.03, C:0.02, G:0.12, T:0.83
Consensus pattern (19 bp):
TTTTTTTTGTGTTTTCTTG
Found at i:1270377 original size:23 final size:22
Alignment explanation
Indices: 1270351--1270405 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
1270341 TTTTTAGGTT
*
1270351 TTTTGTTTTTTTGTGTTTTCTTG
1 TTTT-TTTTTTTGTGTTTTATTG
1270374 TTTTTTTTTTT-TGTTTTATTG
1 TTTTTTTTTTTGTGTTTTATTG
1270395 TTTTTTTTTTT
1 TTTTTTTTTTT
1270406 TGGTTGTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 20 0.65
22 7 0.23
23 4 0.13
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (22 bp):
TTTTTTTTTTTGTGTTTTATTG
Found at i:1270412 original size:25 final size:24
Alignment explanation
Indices: 1270350--1270416 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 24
1270340 TTTTTTAGGT
*
1270350 TTTTTGTTTTTTTG-TGTTTTCTTG
1 TTTTT-TTTTTTTGTTGTTTTATTG
1270374 --TTTTTTTTTT-TTGTTTTATTG
1 TTTTTTTTTTTTGTTGTTTTATTG
1270395 TTTTTTTTTTTTGGTTGTTTTA
1 TTTTTTTTTTTT-GTTGTTTTA
1270417 CAAATTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 16 0.43
22 3 0.08
23 10 0.27
25 8 0.22
ACGTcount: A:0.03, C:0.01, G:0.13, T:0.82
Consensus pattern (24 bp):
TTTTTTTTTTTTGTTGTTTTATTG
Found at i:1270748 original size:95 final size:96
Alignment explanation
Indices: 1270559--1270731 Score: 262
Period size: 95 Copynumber: 1.8 Consensus size: 96
1270549 TAAAAAATTG
1270559 TTGAATGCTCCTCATAATAAAGTTGTTGAAACTTTAAAAATTTAAAATATTTTGAAAAGAGGTCT
1 TTGAATGCTCCTCATAATAAAGTTGTTGAAACTTTAAAAATTTAAAATATTTTGAAAAGAGGTCT
1270624 TGGAAATTATGCTCAAAGATATTAAAAATAA
66 TGGAAATTATGCTCAAAGATATTAAAAATAA
** **
1270655 TTGAATGCTCCTTGTAATAAAAG-TGTTGAAACTTT-AAAATTTAAAATATTTTGCCCAAG-GGT
1 TTGAATGCTCCTCATAAT-AAAGTTGTTGAAACTTTAAAAATTTAAAATATTTTG-AAAAGAGGT
*
1270717 TTTGGAAATTATGCT
64 CTTGGAAATTATGCT
1270732 TAGAGGTCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
95 35 0.50
96 31 0.44
97 4 0.06
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (96 bp):
TTGAATGCTCCTCATAATAAAGTTGTTGAAACTTTAAAAATTTAAAATATTTTGAAAAGAGGTCT
TGGAAATTATGCTCAAAGATATTAAAAATAA
Found at i:1278470 original size:19 final size:19
Alignment explanation
Indices: 1278446--1278486 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1278436 GGAGTTATGT
1278446 CAATACATGTTCGTATTGG
1 CAATACATGTTCGTATTGG
1278465 CAATACATGTTCGTATTGG
1 CAATACATGTTCGTATTGG
1278484 CAA
1 CAA
1278487 AGAAAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (19 bp):
CAATACATGTTCGTATTGG
Found at i:1285595 original size:13 final size:14
Alignment explanation
Indices: 1285577--1285606 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1285567 TTTGGCAACC
1285577 TTTCCTCCT-TTTT
1 TTTCCTCCTCTTTT
1285590 TTTCCTCCTCTTTT
1 TTTCCTCCTCTTTT
1285604 TTT
1 TTT
1285607 TTTTTGGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCCTCCTCTTTT
Found at i:1292627 original size:11 final size:11
Alignment explanation
Indices: 1292613--1292639 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1292603 TAAAAAAGAT
1292613 AAAAACAACAA
1 AAAAACAACAA
1292624 AAAAACAACAA
1 AAAAACAACAA
1292635 AAAAA
1 AAAAA
1292640 AAATGAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAACAA
Found at i:1293347 original size:3 final size:3
Alignment explanation
Indices: 1293339--1293382 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1293329 GAGCATGTTA
1293339 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1293383 AAGAAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1294912 original size:33 final size:33
Alignment explanation
Indices: 1294872--1294934 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1294862 AGAAAGATTA
*
1294872 TTAAGCCTAGTTTACCTAGCACTTGATGAAGTC
1 TTAAGCCTAGTTAACCTAGCACTTGATGAAGTC
*
1294905 TTAAGCCTAGTTAACCTGGCACTTGATGAA
1 TTAAGCCTAGTTAACCTAGCACTTGATGAA
1294935 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (33 bp):
TTAAGCCTAGTTAACCTAGCACTTGATGAAGTC
Found at i:1295046 original size:69 final size:64
Alignment explanation
Indices: 1294971--1295147 Score: 156
Period size: 69 Copynumber: 2.6 Consensus size: 64
1294961 ACCAATGAAT
* *
1294971 TTTTAAGTCCTGTTTACCTAGCACCTAATAAAAATTTCAAGCTCAATTTATCTGGCACCAAAAAA
1 TTTTAAG-CCTGTTTACCTAGCACCTGATAAAAATTTCAAGCTCAATTTACCTGGCA-C---AAA
1295036 AGAA
61 AGAA
* * * * * * * * * *
1295040 TTTTAAGCCTAGTTTTCTTGGTACCTGATGAAAATTTTAAACTCAATTTCCCTGGCACTAATGAA
1 TTTTAAGCCT-GTTTACCTAGCACCTGATAAAAATTTCAAGCTCAATTTACCTGGCACAAAAGAA
* *
1295105 TTTCTAAGCCCAGTTTACCTAGCACTTGATAAAAATTTCAAGC
1 TTT-TAAG-CCTGTTTACCTAGCACCTGATAAAAATTTCAAGC
1295148 CTAGTTTATT
Statistics
Matches: 84, Mismatches: 21, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
65 8 0.10
66 27 0.32
67 2 0.02
68 4 0.05
69 43 0.51
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (64 bp):
TTTTAAGCCTGTTTACCTAGCACCTGATAAAAATTTCAAGCTCAATTTACCTGGCACAAAAGAA
Found at i:1295212 original size:135 final size:135
Alignment explanation
Indices: 1294964--1295214 Score: 297
Period size: 135 Copynumber: 1.9 Consensus size: 135
1294954 ACTTGGTACC
* * * *
1294964 AATGAATTTTTAAGTCCTGTTTACCTAGCACCTAATAAAAATTTCAAGCTCAATTTATCTGGCAC
1 AATGAATTTCTAAGCCCAGTTTACCTAGCACCTAATAAAAATTTCAAGCTCAATTTATCTAGCAC
* *** * * *
1295029 CAAAAAAAGAATTTTAAGCCTAGTTTTCTTGGTACCTGATGAAAATTTTAAACTCAATTTCCCTG
66 CAAAAAAAGAATTTTAAGCCGAGTGCACCTAGCACCTGATGAAAATTTTAAACTCAATTTCCCTG
1295094 GCACT
131 GCACT
* * * *
1295099 AATGAATTTCTAAGCCCAGTTTACCTAGCACTTGATAAAAATTTCAAGC-CTAGTTTATTTAGCA
1 AATGAATTTCTAAGCCCAGTTTACCTAGCACCTAATAAAAATTTCAAGCTC-AATTTATCTAGCA
* * * * * *
1295163 CTAAATAACGATTTTTAAGCCGAGTGCACCTAGCACCTGGTGAAGATTTTAA
65 CCAAAAAAAGAATTTTAAGCCGAGTGCACCTAGCACCTGATGAAAATTTTAA
1295215 GGCCCAGTTG
Statistics
Matches: 94, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
134 1 0.01
135 93 0.99
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (135 bp):
AATGAATTTCTAAGCCCAGTTTACCTAGCACCTAATAAAAATTTCAAGCTCAATTTATCTAGCAC
CAAAAAAAGAATTTTAAGCCGAGTGCACCTAGCACCTGATGAAAATTTTAAACTCAATTTCCCTG
GCACT
Found at i:1295420 original size:33 final size:33
Alignment explanation
Indices: 1294872--1296197 Score: 303
Period size: 34 Copynumber: 39.4 Consensus size: 33
1294862 AGAAAGATTA
* * * * *
1294872 TTAAGCCTAGTTTACCTAGCACTTGATGAAGTC
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
* * *
1294905 TTAAGCCTAGTTAACCTGGCACTTGATGAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * * * *
1294939 TTAAAAGCCTAGTTTACTTGGTACC-AATGAATTT
1 TT--AAGCCCAGTTTACCTGGCACCTGATGAAATT
* * * * *
1294973 TTAAGTCCTGTTTACCTAGCACCTAATAAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* * * * ** **
1295007 TCAAGCTCAATTTATCTGGCACCAAAAAAAGAATT
1 TTAAGCCCAGTTTACCTGGCACC-TGATGA-AATT
* * * *
1295042 TTAAGCCTAGTTTTCTTGGTACCTGATGAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * * * *
1295076 TTAAACTCAATTTCCCTGGCA-CTAATG-AATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
* * *
1295107 TCTAAGCCCAGTTTACCTAGCACTTGATAAAAATT
1 T-TAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* * ** * *
1295142 TCAAGCCTAGTTTATTTAGCA-CTAAAT-AACGATTT
1 TTAAGCCCAGTTTACCTGGCACCT-GATGAA--A-TT
* ** * *
1295177 TTAAGCCGAGTGCACCTAGCACCTGGTGAAGATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAA-ATT
* * *
1295211 TTAAGGCCCAGTTGACCTGACACCTGATAAAAATT
1 TTAA-GCCCAGTTTACCTGGCACCTGAT-GAAATT
* * * ** * *** *
1295246 TCAAACTCAGTTTATTTAGCACAAAAAAT-AGATTT
1 TTAAGCCCAGTTTACCTGGCAC--CTGATGA-AATT
** * * * *
1295281 TTAAGCTTAGTTTACTTGGTACGTGATGAAAATA
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * * ** * *
1295315 TTAAACCAAGTTTACTTCTCACC-AATGAATTT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
* * *
1295347 TTAAACCCAGTTTACCTGGTACCTGATAAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* **
1295381 TCAAGCCCAGTTTATTTGGCACCTGATGAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
* * * *
1295414 TTAAGCCTAGTTTACGTAGCACC-AATG-AATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
* ** * * *
1295445 TTAAACCCACCTTACTTGCCACCTGATAAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* * *
1295479 TCAAGCCCAGTTTACTTGGCACATGATGAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * *
1295513 TTAAGTCTAGTTTACCTGGCACCTGATAAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* * * ** * *
1295547 TGAAGCCTAGTTTATCTAACACC-AAAGAAAGATT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AA-ATT
** *
1295581 TTAAAACCAGTTTACCT-GCACTTGATGAAGATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAA-ATT
* * *
1295614 TTAAAGCCTAGTTTACTTGGCA-CTAGA-GAAAGT
1 TT-AAGCCCAGTTTACCTGGCACCT-GATGAAATT
* * ** *
1295647 TTAAGCCTAATTTAATTGGCCCCTGATGAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * * * * ** *
1295681 TCAAGCCTAATTTATCTGGCA--TTAAAAAAGGT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAA-TT
* *
1295713 TTAAGCCTAGTATACCTGGCACCTGATGAAGATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAA-ATT
* * ** ** **
1295747 TTAAGGCCCAGCTTAGCTGGTTCCCAATGAAAAA
1 TTAA-GCCCAGTTTACCTGGCACCTGATGAAATT
* * * * * *
1295781 GTAAGCACAGTTTATCTGGCCCCTTATAAAAATT
1 TTAAGCCCAGTTTACCTGGCACCTGAT-GAAATT
* *
1295815 TTAAGCCCAGTTTA--TGCGACACTTGATAAAAATT
1 TTAAGCCCAGTTTACCTG-G-CACCTGAT-GAAATT
* * * * **
1295849 TTAAGGCTAGTTTATCTGGCA-CTAAAAAAAGATT
1 TTAAGCCCAGTTTACCTGGCACCT-GATGAA-ATT
* * * *
1295883 TTAAACCTAGTTTACTTGGTACCTGATGAAGATT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAA-ATT
* * ** * * *
1295917 TTGAAGCCCAGCTTAGCTAACTCCT-AGTAAAAAT
1 TT-AAGCCCAGTTTACCTGGCACCTGA-TGAAATT
* * * * *
1295951 TTAAGTCCAGTTTATCTAGCCCCTGATGAAAACT
1 TTAAGCCCAGTTTACCTGGCACCTGATG-AAATT
* * * *
1295985 TTAAGTCTAGTTTACCTAGCA-CT-AGTGAAAGT
1 TTAAGCCCAGTTTACCTGGCACCTGA-TGAAATT
** * *
1296017 TTAAGCCCAACTTA-GTAGGCA-CTCAATGAAATT
1 TTAAGCCCAGTTTACCT-GGCACCT-GATGAAATT
** * * * *
1296050 TTAAGCCCAGTTTATTTGGCA-TTAAAGAAAGGAT
1 TTAAGCCCAGTTTACCTGGCACCTGATGAAA--TT
* **
1296084 TTAAGCCCAGTTTATCTAAC-CTCTGATGAAAATT
1 TTAAGCCCAGTTTACCTGGCAC-CTGATG-AAATT
* * *
1296118 TTAAACCCAGTTTATCTGGC-CTCTAATGAAATT
1 TTAAGCCCAGTTTACCTGGCAC-CTGATGAAATT
* * *
1296151 TTAAGCCCAATTTAGCTGGC-CTCTAATGAAATT
1 TTAAGCCCAGTTTACCTGGCAC-CTGATGAAATT
* *
1296184 TTAAGTCCAATTTA
1 TTAAGCCCAGTTTA
1296198 GTTGGCACAT
Statistics
Matches: 942, Mismatches: 283, Indels: 136
0.69 0.21 0.10
Matches are distributed among these distances:
31 29 0.03
32 124 0.13
33 203 0.22
34 417 0.44
35 139 0.15
36 30 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (33 bp):
TTAAGCCCAGTTTACCTGGCACCTGATGAAATT
Found at i:1295474 original size:98 final size:100
Alignment explanation
Indices: 1295289--1295527 Score: 320
Period size: 98 Copynumber: 2.4 Consensus size: 100
1295279 TTTTAAGCTT
* * * * * * **
1295289 AGTTTACTTGGTACGTGATGAAAATATTAAACCAAGTTTACTTCTCACCAATGAATTTTTAAACC
1 AGTTTACTTGGCACATGATGAAAATTTTAAGCCTAGTTTACGTAGCACCAATGAATTTTTAAACC
** **
1295354 CAGTTTACCTGGTACCTGATAAAAATTTCAAGCCC
66 CACCTTACCTGCCACCTGATAAAAATTTCAAGCCC
* *
1295389 AGTTTATTTGGCACCTGATG-AAATTTTAAGCCTAGTTTACGTAGCACCAATGAA-TTTTAAACC
1 AGTTTACTTGGCACATGATGAAAATTTTAAGCCTAGTTTACGTAGCACCAATGAATTTTTAAACC
*
1295452 CACCTTACTTGCCACCTGATAAAAATTTCAAGCCC
66 CACCTTACCTGCCACCTGATAAAAATTTCAAGCCC
*
1295487 AGTTTACTTGGCACATGATGAAAATTTTAAGTCTAGTTTAC
1 AGTTTACTTGGCACATGATGAAAATTTTAAGCCTAGTTTAC
1295528 CTGGCACCTG
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
98 57 0.47
99 47 0.39
100 17 0.14
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (100 bp):
AGTTTACTTGGCACATGATGAAAATTTTAAGCCTAGTTTACGTAGCACCAATGAATTTTTAAACC
CACCTTACCTGCCACCTGATAAAAATTTCAAGCCC
Found at i:1295655 original size:32 final size:32
Alignment explanation
Indices: 1295617--1295721 Score: 90
Period size: 32 Copynumber: 3.2 Consensus size: 32
1295607 GAAGATTTTA
*
1295617 AAGCCTAGTTTACTTGGCACTAGAGAAAGTTT
1 AAGCCTAATTTACTTGGCACTAGAGAAAGTTT
* * *
1295649 AAGCCTAATTTAATTGGCCCCT-GATGAAAATTT
1 AAGCCTAATTTACTTGG-CACTAGA-GAAAGTTT
* *
1295682 CAAGCCTAATTTA-TCTGGCATTA-AAAAAGGTTT
1 -AAGCCTAATTTACT-TGGCACTAGAGAAA-GTTT
1295715 AAGCCTA
1 AAGCCTA
1295722 GTATACCTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
32 27 0.46
33 17 0.29
34 15 0.25
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (32 bp):
AAGCCTAATTTACTTGGCACTAGAGAAAGTTT
Found at i:1295964 original size:170 final size:168
Alignment explanation
Indices: 1295670--1295998 Score: 394
Period size: 170 Copynumber: 1.9 Consensus size: 168
1295660 AATTGGCCCC
* * *
1295670 TGATGAAAATTTCAAGCCTAATTTATCTGGCATTAAAAAAGGTTTAAGCCTAGTATACCTGGCAC
1 TGATAAAAATTTCAAGCCTAATTTATCTGGCATAAAAAAAGGTTTAAACCTAGTATACCTGGCAC
*** *
1295735 CTGATGAAGATTTTAAGGCCCAGCTTAGCTGGTTCCCAATGAAAAAGTAAGCACAGTTTATCTGG
66 CTGATGAAGATTTTAAGGCCCAGCTTAGCTAACTCCCAATGAAAAAGTAAGCACAGTTTATCTAG
* *
1295800 CCCCTTATAAAAATTTTAAGCCCAGTTTATGCGACACT
131 CCCCTGATAAAAACTTTAAGCCCAGTTTATGCGACACT
* * * * * * *
1295838 TGATAAAAATTTTAAGGCTAGTTTATCTGGCACTAAAAAAAGATTTTAAACCTAGTTTACTTGGT
1 TGATAAAAATTTCAAGCCTAATTTATCTGGCA-TAAAAAAAG-GTTTAAACCTAGTATACCTGGC
* * *
1295903 ACCTGATGAAGATTTTGAA-GCCCAGCTTAGCTAACTCCTAGT-AAAAATTTAAGTC-CAGTTTA
64 ACCTGATGAAGATTTT-AAGGCCCAGCTTAGCTAACTCCCAATGAAAAA-GTAAG-CACAGTTTA
* * *
1295965 TCTAGCCCCTGATGAAAACTTTAAGTCTAGTTTA
126 TCTAGCCCCTGATAAAAACTTTAAGCCCAGTTTA
1295999 CCTAGCACTA
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
168 28 0.21
169 13 0.10
170 90 0.67
171 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (168 bp):
TGATAAAAATTTCAAGCCTAATTTATCTGGCATAAAAAAAGGTTTAAACCTAGTATACCTGGCAC
CTGATGAAGATTTTAAGGCCCAGCTTAGCTAACTCCCAATGAAAAAGTAAGCACAGTTTATCTAG
CCCCTGATAAAAACTTTAAGCCCAGTTTATGCGACACT
Found at i:1296121 original size:34 final size:33
Alignment explanation
Indices: 1296010--1296197 Score: 166
Period size: 33 Copynumber: 5.6 Consensus size: 33
1296000 CTAGCACTAG
* * *
1296010 TGAAAGTTTAAGCCCAACTTAGT-AGGCACTC-AA
1 TGAAATTTTAAGCCCAATTTA-TCTGGC-CTCTAA
* * *
1296043 TGAAATTTTAAGCCCAGTTTATTTGGCAT-TAA
1 TGAAATTTTAAGCCCAATTTATCTGGCCTCTAA
* * * ** *
1296075 AGAAAGGATTTAAGCCCAGTTTATCTAACCTCTGA
1 TGAAA--TTTTAAGCCCAATTTATCTGGCCTCTAA
* *
1296110 TGAAAATTTTAAACCCAGTTTATCTGGCCTCTAA
1 TG-AAATTTTAAGCCCAATTTATCTGGCCTCTAA
*
1296144 TGAAATTTTAAGCCCAATTTAGCTGGCCTCTAA
1 TGAAATTTTAAGCCCAATTTATCTGGCCTCTAA
*
1296177 TGAAATTTTAAGTCCAATTTA
1 TGAAATTTTAAGCCCAATTTA
1296198 GTTGGCACAT
Statistics
Matches: 127, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
32 8 0.06
33 69 0.54
34 44 0.35
35 3 0.02
36 3 0.02
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGAAATTTTAAGCCCAATTTATCTGGCCTCTAA
Found at i:1296154 original size:67 final size:66
Alignment explanation
Indices: 1296011--1296187 Score: 173
Period size: 67 Copynumber: 2.7 Consensus size: 66
1296001 TAGCACTAGT
* * * *
1296011 GAAAG-TTTAAGCCCAACTTAG-TAGGCACTC-AATGAAATTTTAAGCCCAGTTTATTTGGCATT
1 GAAAGATTTAAGCCCAATTTAGCTA-AC-CTCTAATGAAATTTTAAACCCAGTTTATCTGGCATT
1296073 AAA
64 AAA
* * * *
1296076 GAAAGGATTTAAGCCCAGTTTATCTAACCTCTGATGAAAATTTTAAACCCAGTTTATCTGGCCTC
1 GAAA-GATTTAAGCCCAATTTAGCTAACCTCTAATG-AAATTTTAAACCCAGTTTATCTGGCAT-
*
1296141 TAAT
63 TAAA
* **
1296145 GAAA-TTTTAAGCCCAATTTAGCTGGCCTCTAATGAAATTTTAA
1 GAAAGATTTAAGCCCAATTTAGCTAACCTCTAATGAAATTTTAA
1296188 GTCCAATTTA
Statistics
Matches: 91, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
65 4 0.04
66 13 0.14
67 41 0.45
68 26 0.29
69 7 0.08
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (66 bp):
GAAAGATTTAAGCCCAATTTAGCTAACCTCTAATGAAATTTTAAACCCAGTTTATCTGGCATTAA
A
Found at i:1296382 original size:36 final size:36
Alignment explanation
Indices: 1296286--1296382 Score: 113
Period size: 36 Copynumber: 2.7 Consensus size: 36
1296276 GATTGTTTTC
* * * *
1296286 TTATTTTTTGACTTACAATGTTATCCTTCTCGTTCT
1 TTATTTTTTGACTTACGATGTTGTCCTACTCATTCT
* * *
1296322 TTATTTTTTGACTTATGATTTTGTCCTAGTCATTCT
1 TTATTTTTTGACTTACGATGTTGTCCTACTCATTCT
* *
1296358 TTATTTTTTGACTTGCGGTGTTGTC
1 TTATTTTTTGACTTACGATGTTGTC
1296383 TTGATATTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.14, C:0.15, G:0.13, T:0.57
Consensus pattern (36 bp):
TTATTTTTTGACTTACGATGTTGTCCTACTCATTCT
Found at i:1296914 original size:18 final size:18
Alignment explanation
Indices: 1296891--1296927 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1296881 GCATTTGCAT
* *
1296891 TTGACATTTTCATTCGCA
1 TTGACATTTCCATTAGCA
1296909 TTGACATTTCCATTAGCA
1 TTGACATTTCCATTAGCA
1296927 T
1 T
1296928 AATATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (18 bp):
TTGACATTTCCATTAGCA
Found at i:1297149 original size:37 final size:36
Alignment explanation
Indices: 1297049--1297369 Score: 268
Period size: 37 Copynumber: 8.7 Consensus size: 36
1297039 AAGATTTTAT
* * * * * *
1297049 TTTTAAAAGTTTCAAAACCTTTATTTATAGGAAGTCA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTA-GGGGAGCCA
* *
1297086 TCTTCAAAGTTTCAAAGCCTCTGTTTAAGGGGAGCCA
1 TTTTAAAAGTTTCAAAGCCTCTGTTT-AGGGGAGCCA
1297123 TTTTAAAAGGTTT-AAAGCCTCTGTTTAGTGGGAGCCA
1 TTTTAAAA-GTTTCAAAGCCTCTGTTTAG-GGGAGCCA
** * * *
1297160 TTTTCCAAGTTTCAAAGCTTCTGTTTGGGGGGAGCTA
1 TTTTAAAAGTTTCAAAGCCTCTGTTT-AGGGGAGCCA
* *
1297197 TTTTAAAAGTTTTAAAGCCTCTATTTAGGGGAAGCCA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAGGGG-AGCCA
* * * *
1297234 TTTTCAACGTTTCAAAGCTTCTGTTTAGGGAGAACCA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAGGG-GAGCCA
* *
1297271 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCA
1 TTTTAAAAGTTTCAAAGCCTCTGTTT-AGGGGAGCCA
* * * * * *
1297308 TTTGCAAAA-TTCCAAAACCTCTGTTGGAGGGAAGTCA
1 TTT-TAAAAGTTTCAAAGCCTCTGTT-TAGGGGAGCCA
* * *
1297345 TCTTCAAAGTTTCAAAGCCTATGTT
1 TTTTAAAAGTTTCAAAGCCTCTGTT
1297370 CGGGAAAAGC
Statistics
Matches: 227, Mismatches: 46, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
36 13 0.06
37 200 0.88
38 14 0.06
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (36 bp):
TTTTAAAAGTTTCAAAGCCTCTGTTTAGGGGAGCCA
Found at i:1297329 original size:111 final size:109
Alignment explanation
Indices: 1297049--1297369 Score: 297
Period size: 111 Copynumber: 2.9 Consensus size: 109
1297039 AAGATTTTAT
* * * * * *
1297049 TTTTAAAAGTTTCAAAACCTTTATTTATAGGAAGTCATCTTCAAAGTTTCAAAGCCTCTGTTTAA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCAT-TTCAAAATTTCAAAGCCTCT-TTT-A
* *
1297114 GGGG-AGCCATTTTAAAAGGTTT-AAAGCCTCTGTTTAGTGGGAGCCA
63 GGGGAAGCCATTTTCAAA-GTTTCAAAGCCTCTGTTTAGTGGGAACCA
** * *** * * * *
1297160 TTTTCCAAGTTTCAAAGCTTCTGTTTGGGGGGAGCTATTTTAAAAGTTTTAAAGCCTCTATTTAG
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCATTTCAAAA-TTTCAAAGCCTCT-TTTAG
* *
1297225 GGGAAGCCATTTTCAACGTTTCAAAGCTTCTGTTTAG-GGAGAACCA
64 GGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTTAGTGG-GAACCA
* * * *
1297271 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCATTTGCAAAATTCCAAAACCTCTGTTGGA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCATTT-CAAAATTTCAAAGCCTCTTTTAG-
* * *
1297336 GGGAAGTCATCTTCAAAGTTTCAAAGCCTATGTT
64 GGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTT
1297370 CGGGAAAAGC
Statistics
Matches: 165, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
110 19 0.12
111 142 0.86
112 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (109 bp):
TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCATTTCAAAATTTCAAAGCCTCTTTTAGGG
GAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTTAGTGGGAACCA
Found at i:1297331 original size:74 final size:74
Alignment explanation
Indices: 1297049--1297369 Score: 333
Period size: 74 Copynumber: 4.3 Consensus size: 74
1297039 AAGATTTTAT
* * * * * *
1297049 TTTTAAAAGTTTCAAAACCTTTATTTATAGGAAGTCATCTTCAAAGTTTCAAAGCCTCTGTTTAA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAGAGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTT-A
1297114 GGG-GAGCCA
65 GGGAGAGCCA
* * * * *
1297123 TTTTAAAAGGTTT-AAAGCCTCTGTTTAGTGGGAGCCATTTTCCAAGTTTCAAAGCTTCTGTTTG
1 TTTTAAAA-GTTTCAAAGCCTCTGTTTAGAGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTTA
* *
1297187 GGGGGAGCTA
65 GGGAGAGCCA
* * * * *
1297197 TTTTAAAAGTTTTAAAGCCTCTATTTAGGGGAAGCCATTTTCAACGTTTCAAAGCTTCTGTTTAG
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAGAGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTTAG
*
1297262 GGAGAACCA
66 GGAGAGCCA
* * * * * *
1297271 TTTTAAAAGTTTCAAAGCCTCTGTTTAAAGGAAGCCATTTGCAAAATTCCAAAACCTCTGTTGGA
1 TTTTAAAAGTTTCAAAGCCTCTGTTTAGAGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTT-TA
*
1297336 GGGA-AGTCA
65 GGGAGAGCCA
* * *
1297345 TCTTCAAAGTTTCAAAGCCTATGTT
1 TTTTAAAAGTTTCAAAGCCTCTGTT
1297370 CGGGAAAAGC
Statistics
Matches: 206, Mismatches: 37, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
73 7 0.03
74 190 0.92
75 9 0.04
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (74 bp):
TTTTAAAAGTTTCAAAGCCTCTGTTTAGAGGAAGCCATTTTCAAAGTTTCAAAGCCTCTGTTTAG
GGAGAGCCA
Found at i:1302176 original size:13 final size:13
Alignment explanation
Indices: 1302158--1302185 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1302148 ATGAGGTATA
1302158 TTTTATTATAATT
1 TTTTATTATAATT
1302171 TTTTATTATAATT
1 TTTTATTATAATT
1302184 TT
1 TT
1302186 ATAATTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTATAATT
Found at i:1303462 original size:36 final size:35
Alignment explanation
Indices: 1303377--1303612 Score: 167
Period size: 36 Copynumber: 6.8 Consensus size: 35
1303367 GCGTCATTGT
* * *
1303377 CTCTGATCAGAGGAGC-TTTTTAAAGTTTCATTGC
1 CTCTGGTCAGAGGAGCTTTTTTAAAGTCTCATAGC
* * *
1303411 CTTTGGT---TGGAGCTTTCTTTAAAGTCTCATAAC
1 CTCTGGTCAGAGGAGCTTT-TTTAAAGTCTCATAGC
* *
1303444 CTCTGGTCAGAGGAGCTTTTTTCAAAATTTCATAGC
1 CTCTGGTCAGAGGAGCTTTTTT-AAAGTCTCATAGC
** ** * * *
1303480 CTCTGGTCAGATAAGCCATTTAAAAGTGTCATTGC
1 CTCTGGTCAGAGGAGCTTTTTTAAAGTCTCATAGC
* * * * *
1303515 CTTTGGTCAGATGAGC-TATTTAAAGTTTCATTGC
1 CTCTGGTCAGAGGAGCTTTTTTAAAGTCTCATAGC
* *
1303549 CTCTGGTTAGGGGAGCTTTCTTTAAAGTCTCATAGC
1 CTCTGGTCAGAGGAGCTTT-TTTAAAGTCTCATAGC
* * * *
1303585 CTTTGGTCAAAGGAACTCTTTTCAAAGT
1 CTCTGGTCAGAGGAGCT-TTTTTAAAGT
1303613 TTTATAGTTT
Statistics
Matches: 155, Mismatches: 38, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
31 5 0.03
32 2 0.01
33 19 0.12
34 31 0.20
35 28 0.18
36 68 0.44
37 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (35 bp):
CTCTGGTCAGAGGAGCTTTTTTAAAGTCTCATAGC
Found at i:1303637 original size:141 final size:138
Alignment explanation
Indices: 1303352--1303652 Score: 395
Period size: 141 Copynumber: 2.2 Consensus size: 138
1303342 TTTTCATTAA
* * * * *
1303352 AGAAGCCATTTGAAAGCGTCATTGTCTCTGATCAGAGGAGCTTTTTAAAGTTTCATTGCCTTTGG
1 AGAAGCCATTTAAAAGTGTCATTGCCTCTGATCAGAGGAGCTATTTAAAGTTTCATTGCCTCTGG
* * *
1303417 TTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAGAGGAGCTTTTTTCAAAATTTCATAGCCT
66 TTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGGAACTCTTTTCAAAATTTCATAGCCT
1303482 CTGGTCAG
131 CTGGTCAG
* * * *
1303490 ATAAGCCATTTAAAAGTGTCATTGCCTTTGGTCAGATGAGCTATTTAAAGTTTCATTGCCTCTGG
1 AGAAGCCATTTAAAAGTGTCATTGCCTCTGATCAGAGGAGCTATTTAAAGTTTCATTGCCTCTGG
* * * *
1303555 TTAGGGGAGCTTTCTTTAAAGTCTCATAGCCTTTGGTCAAAGGAACTCTTTTCAAAGTTTTATAG
66 TT---GGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGGAACTCTTTTCAAAATTTCATAG
** *
1303620 TTTTTGGTCAG
128 CCTCTGGTCAG
*
1303631 AGAAGCCGTTTAAAAGTGTCAT
1 AGAAGCCATTTAAAAGTGTCAT
1303653 AGCCACCGAT
Statistics
Matches: 139, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
138 58 0.42
141 81 0.58
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (138 bp):
AGAAGCCATTTAAAAGTGTCATTGCCTCTGATCAGAGGAGCTATTTAAAGTTTCATTGCCTCTGG
TTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGGAACTCTTTTCAAAATTTCATAGCCT
CTGGTCAG
Found at i:1303677 original size:141 final size:138
Alignment explanation
Indices: 1303395--1303693 Score: 346
Period size: 141 Copynumber: 2.1 Consensus size: 138
1303385 AGAGGAGCTT
* * *
1303395 TTTAAAGTTTCATTGCCTTTGGTTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAGAGGAGC
1 TTTAAAGTTTCATTGCCTCTGGTTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGGAAC
* * * *** *
1303460 TTTTTTCAAAATTTCATAGCCTCTGGTCAGATAAGCCATTTAAAAGTGTCATTGCCTTTGGTCAG
66 TCTTTTCAAAATTTCATAGCCTCTGGTCAGAGAAGCCATTTAAAAGTGTCATAGCCACCGATCAG
** * *
1303525 ATGAGCTA
131 AAAAACCA
* *
1303533 TTTAAAGTTTCATTGCCTCTGGTTAGGGGAGCTTTCTTTAAAGTCTCATAGCCTTTGGTCAAAGG
1 TTTAAAGTTTCATTGCCTCTGGTT---GGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGG
* * ** * *
1303598 AACTCTTTTCAAAGTTTTATAGTTTTTGGTCAGAGAAGCCGTTTAAAAGTGTCATAGCCACCGAT
63 AACTCTTTTCAAAATTTCATAGCCTCTGGTCAGAGAAGCCATTTAAAAGTGTCATAGCCACCGAT
**
1303663 TTGAAAAACCA
128 CAGAAAAACCA
*
1303674 TTTAAAGTTTCATTACCTCT
1 TTTAAAGTTTCATTGCCTCT
1303694 TGTCATAGGA
Statistics
Matches: 133, Mismatches: 25, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
138 23 0.17
141 110 0.83
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (138 bp):
TTTAAAGTTTCATTGCCTCTGGTTGGAGCTTTCTTTAAAGTCTCATAACCTCTGGTCAAAGGAAC
TCTTTTCAAAATTTCATAGCCTCTGGTCAGAGAAGCCATTTAAAAGTGTCATAGCCACCGATCAG
AAAAACCA
Found at i:1303968 original size:3 final size:3
Alignment explanation
Indices: 1303960--1303985 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1303950 AAATAATTTC
1303960 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1303986 ATTTCTCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1304976 original size:3 final size:3
Alignment explanation
Indices: 1304968--1304997 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1304958 TTTTCTATGA
1304968 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1304998 AGAAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1305021 original size:13 final size:14
Alignment explanation
Indices: 1304998--1305039 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1304988 TTATTATTAT
*
1304998 AGAAATAAAAAAAA
1 AGAAGTAAAAAAAA
1305012 A-AAGTAAAAAAAA
1 AGAAGTAAAAAAAA
*
1305025 AGAATTAAAATAAAA
1 AGAAGTAAAA-AAAA
1305040 TGTAGATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (14 bp):
AGAAGTAAAAAAAA
Found at i:1317199 original size:13 final size:14
Alignment explanation
Indices: 1317181--1317213 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1317171 TTAAATTTTC
1317181 TTTTTATT-TGATT
1 TTTTTATTATGATT
1317194 TTTTTATTATGATT
1 TTTTTATTATGATT
*
1317208 ATTTTA
1 TTTTTA
1317214 AAATATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTTTATTATGATT
Found at i:1322635 original size:27 final size:28
Alignment explanation
Indices: 1322605--1322672 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
1322595 ATTAAGTATT
*
1322605 ATATTAATTAATCAATTTAT-AATGTAA
1 ATATTAATTAATAAATTTATAAATGTAA
* * *
1322632 ATATT-ATATAAAAAATTTTTAAATTTAA
1 ATATTAAT-TAATAAATTTATAAATGTAA
1322660 ATATTATATTAAT
1 ATATTA-ATTAAT
1322673 TATTTTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 2 0.06
27 14 0.44
28 11 0.34
29 3 0.09
30 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATATTAATTAATAAATTTATAAATGTAA
Found at i:1322677 original size:28 final size:29
Alignment explanation
Indices: 1322596--1322678 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
1322586 TTAAAATTAA
* *
1322596 TTAAGTATTATATTAATTAATCAATTTATAAT
1 TTAAATATTATATTAATT-AT--TTTTATAAT
* * **
1322628 GTAAATATTATATAAAAAATTTTTA-AAT
1 TTAAATATTATATTAATTATTTTTATAAT
1322656 TTAAATATTATATTAATTATTTT
1 TTAAATATTATATTAATTATTTT
1322679 ATTTTAAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
28 22 0.54
29 4 0.10
31 2 0.05
32 13 0.32
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (29 bp):
TTAAATATTATATTAATTATTTTTATAAT
Done.