Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 10 of 190
Found at i:1434612 original size:13 final size:12
Alignment explanation
Indices: 1434594--1434640 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1434584 CAAAAAATTA
1434594 ATTTATGTTAAAG
1 ATTTAT-TTAAAG
*
1434607 ATTTATTTAAAT
1 ATTTATTTAAAG
* *
1434619 A-TAAATTAAAG
1 ATTTATTTAAAG
1434630 ATTTATTTAAA
1 ATTTATTTAAA
1434641 TAAAAACTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
11 8 0.30
12 13 0.48
13 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (12 bp):
ATTTATTTAAAG
Found at i:1434627 original size:23 final size:23
Alignment explanation
Indices: 1434601--1434656 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1434591 TTAATTTATG
*
1434601 TTAAAGATTTATTTAAATATAAA
1 TTAAAGATTTATTTAAATAAAAA
1434624 TTAAAGATTTATTTAAATAAAAA
1 TTAAAGATTTATTTAAATAAAAA
*
1434647 CTAAA-ATTTA
1 TTAAAGATTTA
1434657 AAAGCTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TTAAAGATTTATTTAAATAAAAA
Found at i:1434752 original size:30 final size:28
Alignment explanation
Indices: 1434615--1434756 Score: 92
Period size: 30 Copynumber: 4.8 Consensus size: 28
1434605 AGATTTATTT
1434615 AAATATAAA-TTAAAGATTTATTTAAATAA
1 AAATA-AAATTTAAA-ATTTATTTAAATAA
* **
1434644 AAACTAAAATTTAAAAGCTTATTTAGGTACA
1 AAA-TAAAATTTAAAA-TTTATTTAAATA-A
* * * *
1434675 AAGTAAAAGTTATAAATTTATTTGAGT-A
1 AAATAAAATTTA-AAATTTATTTAAATAA
* *
1434703 TAATAAAAATATAAAAATTTATTTAAATAA
1 AAAT-AAAAT-TTAAAATTTATTTAAATAA
1434733 AATGATAAAATTTAAAATTT-TTTA
1 AA--ATAAAATTTAAAATTTATTTA
1434757 TTATTTTAGT
Statistics
Matches: 87, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
28 3 0.03
29 27 0.31
30 44 0.51
31 11 0.13
32 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (28 bp):
AAATAAAATTTAAAATTTATTTAAATAA
Found at i:1436276 original size:24 final size:24
Alignment explanation
Indices: 1436237--1436308 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1436227 TTATTTTTAT
*
1436237 TATTATTT-TTATTTATCTATTAA
1 TATTTTTTATTATTTATCTATTAA
*
1436260 TATTTTTTATTATTTATCTATTAT
1 TATTTTTTATTATTTATCTATTAA
* *
1436284 TATTTTATTATCTATATATTTATTA
1 TATTTT-TTAT-TATTTATCTATTA
1436309 TTTATCTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 7 0.17
24 20 0.48
25 4 0.10
26 11 0.26
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTTTTATTATTTATCTATTAA
Found at i:1436305 original size:15 final size:13
Alignment explanation
Indices: 1436223--1436362 Score: 89
Period size: 15 Copynumber: 10.3 Consensus size: 13
1436213 AAGATGGGCC
1436223 TATT-TTATT-TT
1 TATTATTATTATT
1436234 TATTATTATT-TT
1 TATTATTATTATT
1436246 TATTTATCTATTAATAT
1 TA-TTAT-TATT-AT-T
1436263 T-TT-TTATTATT
1 TATTATTATTATT
1436274 TATCTATTATTATTT
1 TAT-TATTATTA-TT
1436289 TATTATCTATATATT
1 TATTAT-TAT-TATT
1436304 TATTATTTATCTATT
1 TATTA-TTAT-TATT
*
1436319 AATATATTTTATTATT
1 --TAT-TATTATTATT
1436335 TATCTATTATT-TT
1 TAT-TATTATTATT
1436348 TATT-TT-TTATT
1 TATTATTATTATT
1436359 TATT
1 TATT
1436363 TATTTTTTGA
Statistics
Matches: 108, Mismatches: 4, Indels: 34
0.74 0.03 0.23
Matches are distributed among these distances:
10 2 0.02
11 14 0.13
12 13 0.12
13 14 0.13
14 23 0.21
15 24 0.22
16 8 0.07
17 9 0.08
18 1 0.01
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:1436313 original size:4 final size:4
Alignment explanation
Indices: 1436244--1436367 Score: 66
Period size: 4 Copynumber: 31.8 Consensus size: 4
1436234 TATTATTATT
* *
1436244 TTTA TTTA TCTA TTAATA TTT- TTTA -TTA TTTA TCTA -TTA -TTA TTT-
1 TTTA TTTA TTTA TT--TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
1436289 TATTA TCTA TATA TTTA -TTA TTTA TCTA TTAA TATA TTT- TATTA TTTA
1 T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA
* *
1436337 TCTA TTATT TTTA TTT- TTTA TTTA TTTA TTT
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTT
1436368 TTTGACTTCA
Statistics
Matches: 91, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
3 19 0.21
4 63 0.69
5 5 0.05
6 4 0.04
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:1436315 original size:37 final size:39
Alignment explanation
Indices: 1436265--1436350 Score: 126
Period size: 37 Copynumber: 2.3 Consensus size: 39
1436255 ATTAATATTT
1436265 TTTATTATTTATCTATT-AT-TATTTTATTATCTATATA
1 TTTATTATTTATCTATTAATATATTTTATTATCTATATA
* *
1436302 TTTATTATTTATCTATTAATATATTTTATTATTTATCTA
1 TTTATTATTTATCTATTAATATATTTTATTATCTATATA
1436341 -TTATT-TTTAT
1 TTTATTATTTAT
1436351 TTTTTATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 22 0.49
38 7 0.16
39 16 0.36
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (39 bp):
TTTATTATTTATCTATTAATATATTTTATTATCTATATA
Found at i:1436317 original size:61 final size:59
Alignment explanation
Indices: 1436222--1436367 Score: 200
Period size: 61 Copynumber: 2.6 Consensus size: 59
1436212 GAAGATGGGC
*
1436222 CTATT-TTA-TTT-TTATTATTATTT-TTATTTATCTATTAATATTTTTTATTATTTAT
1 CTATTATTATTTTATTATTATTATTTATTATTTATCTATTAATATATTTTATTATTTAT
1436277 CTATTATTATTTTATTATCTATATATTTATTATTTATCTATTAATATATTTTATTATTTAT
1 CTATTATTATTTTATTAT-TAT-TATTTATTATTTATCTATTAATATATTTTATTATTTAT
1436338 CTATTA-T-TTTTATT-TT-TTATTTATTTATTT
1 CTATTATTATTTTATTATTATTATTTA-TTATTT
1436368 TTTGACTTCA
Statistics
Matches: 83, Mismatches: 1, Indels: 13
0.86 0.01 0.13
Matches are distributed among these distances:
55 11 0.13
56 10 0.12
57 4 0.05
58 5 0.06
59 10 0.12
60 6 0.07
61 37 0.45
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (59 bp):
CTATTATTATTTTATTATTATTATTTATTATTTATCTATTAATATATTTTATTATTTAT
Found at i:1436334 original size:24 final size:24
Alignment explanation
Indices: 1436296--1436366 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
1436286 TTTTATTATC
*
1436296 TATATATTTATTATTTATCTATTA
1 TATATATTTTTTATTTATCTATTA
1436320 -ATATATTTTATTATTTATCTATTA
1 TATATATTTT-TTATTTATCTATTA
* * *
1436344 TTTTTATTTTTTATTTATTTATT
1 TATATATTTTTTATTTATCTATT
1436367 TTTTGACTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.20
24 26 0.63
25 7 0.17
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (24 bp):
TATATATTTTTTATTTATCTATTA
Found at i:1447602 original size:16 final size:17
Alignment explanation
Indices: 1447570--1447607 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1447560 ACTATGCTTT
1447570 AAAAA-ATGAAAATATG
1 AAAAATATGAAAATATG
1447586 AAAAATATGAAAA-ATG
1 AAAAATATGAAAATATG
1447602 AAAAAT
1 AAAAAT
1447608 GAGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (17 bp):
AAAAATATGAAAATATG
Found at i:1447604 original size:7 final size:7
Alignment explanation
Indices: 1447571--1447614 Score: 52
Period size: 7 Copynumber: 5.7 Consensus size: 7
1447561 CTATGCTTTA
1447571 AAAAATG
1 AAAAATG
1447578 AAAATATG
1 AAAA-ATG
1447586 AAAAATATG
1 -AAAA-ATG
1447595 AAAAATG
1 AAAAATG
1447602 AAAAATG
1 AAAAATG
1447609 AGAAAA
1 A-AAAA
1447615 AAAGACTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 15 0.44
8 11 0.32
9 8 0.24
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:1447613 original size:16 final size:16
Alignment explanation
Indices: 1447571--1447615 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1447561 CTATGCTTTA
*
1447571 AAAAATGA-AAATATG
1 AAAAATGAGAAAAATG
1447586 AAAAAT-ATGAAAAATG
1 AAAAATGA-GAAAAATG
1447602 AAAAATGAGAAAAA
1 AAAAATGAGAAAAA
1447616 AAGACTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 6 0.23
16 18 0.69
17 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAAATGAGAAAAATG
Found at i:1449042 original size:41 final size:41
Alignment explanation
Indices: 1448991--1449213 Score: 284
Period size: 41 Copynumber: 5.4 Consensus size: 41
1448981 GTCAAAAAGT
* * * * *
1448991 AATTTATTTTCAAAAGTTATGGTGCCTCTCTTTGGAAAAAC
1 AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* *
1449032 AATTTATTTTCAAAAATTGTGGTGCCTTTGTTTAGAAGAGC
1 AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* * *
1449073 AATTTATTTTCAAAAGTTGTAGTGCCGCTGTTTAGATGAGC
1 AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* *
1449114 AATTTATTTTTAAAAGTTGTGGTGCCTCTGTTTAGAGGAGC
1 AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
* * * * *
1449155 AATTTACTTTCAAAAGTTGTGGTACTTCTATTTAGAGGAGC
1 AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
1449196 AATTTACTTTTCAAAAGT
1 AATTTA-TTTTCAAAAGT
1449214 CATTGAGCTT
Statistics
Matches: 159, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 149 0.94
42 10 0.06
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (41 bp):
AATTTATTTTCAAAAGTTGTGGTGCCTCTGTTTAGAAGAGC
Found at i:1449232 original size:42 final size:41
Alignment explanation
Indices: 1449104--1449232 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
1449094 GTGCCGCTGT
* * * ** * * **
1449104 TTAGATGAGCAATTTATTTTTAAAAGTTGTGGTGCCTCTGT
1 TTAGAGGAGCAATTTACTTTCAAAAGTCATGGTACTTCTAC
** *
1449145 TTAGAGGAGCAATTTACTTTCAAAAGTTGTGGTACTTCTAT
1 TTAGAGGAGCAATTTACTTTCAAAAGTCATGGTACTTCTAC
*
1449186 TTAGAGGAGCAATTTACTTTTCAAAAGTCATTG-AGCTTCTAC
1 TTAGAGGAGCAATTTAC-TTTCAAAAGTCATGGTA-CTTCTAC
1449228 TTAGA
1 TTAGA
1449233 TGAGTTTTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
41 53 0.70
42 23 0.30
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (41 bp):
TTAGAGGAGCAATTTACTTTCAAAAGTCATGGTACTTCTAC
Found at i:1449318 original size:44 final size:44
Alignment explanation
Indices: 1449242--1449344 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
1449232 ATGAGTTTTG
* * **
1449242 TTTATTTTTTCAAA-TCATCGAGCCTTTGTTTAGAGGAGCCTTA
1 TTTATTTTTTCAAAGTCATCAAACCCATGTTTAGAGGAGCCTTA
* *
1449285 TTTATTTTTTCAAAGTCATTAAACCCATGTTTAGAGGAGCCTTG
1 TTTATTTTTTCAAAGTCATCAAACCCATGTTTAGAGGAGCCTTA
*
1449329 TTTATTTTTTAAAAGT
1 TTTATTTTTTCAAAGT
1449345 TGTTGAGCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 14 0.27
44 38 0.73
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTCATCAAACCCATGTTTAGAGGAGCCTTA
Found at i:1449594 original size:21 final size:20
Alignment explanation
Indices: 1449564--1449661 Score: 80
Period size: 20 Copynumber: 4.8 Consensus size: 20
1449554 TATTTTATTT
1449564 TTAT-TTTTTTATTTATCTA
1 TTATATTTTTTATTTATCTA
*
1449583 TTA-A-TATTT-TTTATCTA
1 TTATATTTTTTATTTATCTA
*
1449600 TATATATTTATTATTTATCTA
1 T-TATATTTTTTATTTATCTA
*
1449621 TTAATATATTTTATTATTTATTTA
1 -T--TATATTTT-TTATTTATCTA
1449645 TTAT-TTTTATTATTTAT
1 TTATATTTT-TTATTTAT
1449662 TTTTGACATC
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.14
18 6 0.09
19 4 0.06
20 16 0.24
21 11 0.17
22 1 0.02
23 9 0.14
24 10 0.15
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATTTTTTATTTATCTA
Found at i:1449597 original size:17 final size:17
Alignment explanation
Indices: 1449575--1449638 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
1449565 TATTTTTTTA
1449575 TTTATCTATTAATATTT
1 TTTATCTATTAATATTT
*
1449592 TTTATCTATATATATTTATTA
1 TTTATCTAT-TA-A--TATTT
*
1449613 TTTATCTATTAATATAT
1 TTTATCTATTAATATTT
1449630 TTTAT-TATT
1 TTTATCTATT
1449639 TATTTATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
16 4 0.10
17 17 0.43
18 2 0.05
19 2 0.05
20 2 0.05
21 13 0.32
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATCTATTAATATTT
Found at i:1449611 original size:4 final size:4
Alignment explanation
Indices: 1449563--1449663 Score: 57
Period size: 4 Copynumber: 24.8 Consensus size: 4
1449553 CTATTTTATT
* * *
1449563 TTTA TTTT TTTA TTTA TCTA TTAATA TTT- TTTA TCTATA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT--TA TTTA TTTA T-T-TA TTTA TTTA
* * * *
1449610 -TTA TTTA TCTA TTAA TATA TTT- TATTA TTTA TTTA -TTA TTTT TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA T-TTA
1449657 TTTA TTT
1 TTTA TTT
1449664 TTGACATCAT
Statistics
Matches: 73, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
3 10 0.14
4 51 0.70
5 5 0.07
6 7 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:1449621 original size:38 final size:35
Alignment explanation
Indices: 1449554--1449650 Score: 133
Period size: 38 Copynumber: 2.7 Consensus size: 35
1449544 AAGATGGGCC
*
1449554 TATTTTATT-TTTATTTTTTTATTTATCTATTAATA
1 TATTTTATTATTTA-TTTATTATTTATCTATTAATA
*
1449589 TTTTTTATCTATATATATTTATTATTTATCTATTAATA
1 TATTTTAT-TAT-T-TATTTATTATTTATCTATTAATA
1449627 TATTTTATTATTTATTTATTATTT
1 TATTTTATTATTTATTTATTATTT
1449651 TTATTATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
35 19 0.35
36 2 0.04
37 4 0.07
38 28 0.51
39 2 0.04
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (35 bp):
TATTTTATTATTTATTTATTATTTATCTATTAATA
Found at i:1450433 original size:3 final size:3
Alignment explanation
Indices: 1450417--1450464 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1450407 CTTCATTTAT
* **
1450417 TTA TTA TT- TATA TTA TTA TTA TTA TTA TTA TTA GTA GAA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1450462 TTA
1 TTA
1450465 GAATTATTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 37 0.95
4 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1450466 original size:12 final size:12
Alignment explanation
Indices: 1450431--1450472 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1450421 TATTTATATT
**
1450431 ATTATTATTATT
1 ATTATTATTAGA
*
1450443 ATTATTAGTAGA
1 ATTATTATTAGA
1450455 ATTATTATTAGA
1 ATTATTATTAGA
1450467 ATTATT
1 ATTATT
1450473 TGGTATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (12 bp):
ATTATTATTAGA
Found at i:1450513 original size:18 final size:19
Alignment explanation
Indices: 1450476--1450513 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1450466 AATTATTTGG
**
1450476 TATTTTATTTTAATTTTTT
1 TATTTTATTTTAATGATTT
1450495 TATTTT-TTTTAATGATTT
1 TATTTTATTTTAATGATTT
1450513 T
1 T
1450514 CCTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
TATTTTATTTTAATGATTT
Found at i:1450654 original size:56 final size:56
Alignment explanation
Indices: 1450509--1450625 Score: 141
Period size: 56 Copynumber: 2.1 Consensus size: 56
1450499 TTTTTTAATG
* ** * *
1450509 ATTTTCCT-AAAATAAAAAA-TTCCAAAAAAAA-ATTAAGGAAAAGTTAAAAGTATCA
1 ATTTTCCTGAAAATAAAAAAGTT--AAAAAAAATTTTTGGGAAAAATTAAAAATATCA
*
1450564 ATTTTCCTGAAAATAAAAAAGTTAAAAAATATTTTTGGGAAAAATTAAAAATATCA
1 ATTTTCCTGAAAATAAAAAAGTTAAAAAAAATTTTTGGGAAAAATTAAAAATATCA
1450620 ATTTTC
1 ATTTTC
1450626 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
55 15 0.28
56 36 0.68
57 2 0.04
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (56 bp):
ATTTTCCTGAAAATAAAAAAGTTAAAAAAAATTTTTGGGAAAAATTAAAAATATCA
Found at i:1451443 original size:132 final size:128
Alignment explanation
Indices: 1451275--1451623 Score: 360
Period size: 132 Copynumber: 2.6 Consensus size: 128
1451265 GTTATGACAG
* * * *
1451275 ATACTTTTAACTTTT-CCTTAAATTTTTTTTTCTAAAATTTTAATTTCAAGGAAATTTGATACCT
1 ATACTTTTAACTTTTCCCTAAAAATATTTTTT-TAAAATTTTATTTTCAAGGAAA-TTGATA-CT
* * * * *
1451339 TTCAATTTTCCTC-AAAATACTTTTCTTGATAATTTTTATTTTAGAAATTTTATTTTCAAGGAAA
63 TTCAACTTTCCCCTAAAATAC-ATT-TAGA-AATTTTTATTTTAGAAATTTTATTTTCAAGAAAA
1451403 ATTA
125 ATTA
* * * *
1451407 ATACTTTCAACTTTTCCCTAAAAATATATTTTTAAAACCTTTTTATTTTCATGAAAAATTGATAC
1 ATACTTTTAACTTTTCCCTAAAAATATTTTTTTAAAA---TTTTATTTTCAAG-GAAATTGATAC
* *
1451472 TTTCAACTTTCCCCTAAAATACATTTAGAAATTTTTATTTTATAAATTTTATTTTTAAGAAAAAT
62 TTTCAACTTTCCCCTAAAATACATTTAGAAATTTTTATTTTAGAAATTTTATTTTCAAGAAAAAT
*
1451537 TG
127 TA
* * * **
1451539 ATAGTTTTAATTTTTCCTTAAAAAAATATTTTTTTAACCTTTTTATTTTCAAAGGAAATTGATAC
1 ATACTTTTAACTTTTCCCT--AAAAATATTTTTTTAA-AATTTTATTTTC-AAGGAAATTGATAC
1451604 TTTCAACTTTCCCCTCAAAA
62 TTTCAACTTTCCCCT-AAAA
1451624 CTTATTTTTT
Statistics
Matches: 181, Mismatches: 25, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
132 103 0.57
133 21 0.12
134 30 0.17
135 24 0.13
136 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.48
Consensus pattern (128 bp):
ATACTTTTAACTTTTCCCTAAAAATATTTTTTTAAAATTTTATTTTCAAGGAAATTGATACTTTC
AACTTTCCCCTAAAATACATTTAGAAATTTTTATTTTAGAAATTTTATTTTCAAGAAAAATTA
Found at i:1451707 original size:59 final size:61
Alignment explanation
Indices: 1451641--1451756 Score: 182
Period size: 59 Copynumber: 1.9 Consensus size: 61
1451631 TTTTATTAAA
1451641 AAAAATTGATACATTCAACTTTCCTTCAAAAA-A-TATTTTTTTAAAATTTTATTTTCAAG
1 AAAAATTGATACATTCAACTTTCCTTCAAAAATATTATTTTTTTAAAATTTTATTTTCAAG
* * * *
1451700 AAAAATTGATCCTTTCAACTTTTCTTCAAAAATATTATTTTTTTGAAATTTTATTTT
1 AAAAATTGATACATTCAACTTTCCTTCAAAAATATTATTTTTTTAAAATTTTATTTT
1451757 AGGAAAATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 29 0.57
60 1 0.02
61 21 0.41
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (61 bp):
AAAAATTGATACATTCAACTTTCCTTCAAAAATATTATTTTTTTAAAATTTTATTTTCAAG
Found at i:1451764 original size:59 final size:58
Alignment explanation
Indices: 1451627--1451763 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 58
1451617 CTCAAAACTT
* *
1451627 ATTTTTTTATTAAAAAAAATTGATACATTCAACTTTCCTTCAAAAAATATTTTTTTAAA
1 ATTTTATT-TTAAGAAAAATTGATACATTCAACTTTCCTTCAAAAAATATTTTTTTAAA
* * * *
1451686 ATTTTATTTTCAAGAAAAATTGATCCTTTCAACTTTTCTTCAAAAATATTATTTTTTTGAA
1 ATTTTATTTT-AAGAAAAATTGATACATTCAACTTTCCTTCAAAAA-A-TATTTTTTTAAA
*
1451747 ATTTTATTTTAGGAAAA
1 ATTTTATTTTAAGAAAA
1451764 TCATTAAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.03
59 38 0.56
60 7 0.10
61 21 0.31
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (58 bp):
ATTTTATTTTAAGAAAAATTGATACATTCAACTTTCCTTCAAAAAATATTTTTTTAAA
Found at i:1451788 original size:12 final size:12
Alignment explanation
Indices: 1451773--1451799 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1451763 ATCATTAAAA
1451773 AAAAATTAAATT
1 AAAAATTAAATT
1451785 AAAAATTAAATT
1 AAAAATTAAATT
1451797 AAA
1 AAA
1451800 TAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:1451795 original size:17 final size:17
Alignment explanation
Indices: 1451766--1451810 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1451756 TAGGAAAATC
*
1451766 ATTAAAAA-AAAATTAA
1 ATTAAAAATTAAATTAA
1451782 ATTAAAAATTAAATTAA
1 ATTAAAAATTAAATTAA
*
1451799 ATAAAAAATTAA
1 ATTAAAAATTAA
1451811 GAATACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAATTAAATTAA
Found at i:1451844 original size:3 final size:3
Alignment explanation
Indices: 1451836--1451873 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
1451826 CTAATTTAGA
*
1451836 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT A
1451874 TAAAAAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1455327 original size:2 final size:2
Alignment explanation
Indices: 1455320--1455347 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1455310 GAATTTGAGC
1455320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1455348 TTTTGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1457500 original size:2 final size:2
Alignment explanation
Indices: 1457493--1457526 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1457483 GGTCATTAGA
1457493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1457527 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1460311 original size:2 final size:2
Alignment explanation
Indices: 1460304--1460329 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1460294 ATCCTAATTG
1460304 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1460330 CTTTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1460346 original size:5 final size:6
Alignment explanation
Indices: 1460329--1460356 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1460319 TATATATATA
1460329 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT
1460357 CCATTGAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TCTTTT
Found at i:1461112 original size:27 final size:27
Alignment explanation
Indices: 1461073--1461131 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
1461063 GTTTTAATCC
*
1461073 ATTTTTTA-TAAAACATATTCAATCAT
1 ATTTTTTAGAAAAACATATTCAATCAT
* *
1461099 ATTTTTATAGAAAAAATATATTTAATCAT
1 ATTTTT-TAG-AAAAACATATTCAATCAT
1461128 ATTT
1 ATTT
1461132 ATTAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.22
27 2 0.07
29 19 0.70
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTTTTAGAAAAACATATTCAATCAT
Found at i:1461617 original size:33 final size:35
Alignment explanation
Indices: 1461580--1461646 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 35
1461570 ATCTTTTTGT
*
1461580 TGATTATTCATTTATTTATTT-TTTG-TTTATCTC
1 TGATTATTCAGTTATTTATTTATTTGATTTATCTC
* * *
1461613 TGATTTTTCAGTTGTTTTTTTATTTGATTTATCT
1 TGATTATTCAGTTATTTATTTATTTGATTTATCT
1461647 TTTGTTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 17 0.61
34 4 0.14
35 7 0.25
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.67
Consensus pattern (35 bp):
TGATTATTCAGTTATTTATTTATTTGATTTATCTC
Found at i:1462517 original size:17 final size:17
Alignment explanation
Indices: 1462497--1462552 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1462487 ATTTTGGTAT
1462497 TTTTATTATTATT-TTTA
1 TTTTATTATT-TTATTTA
*
1462514 TTTTTTTATTTTATTTA
1 TTTTATTATTTTATTTA
* *
1462531 TTCTATT-TATTTATTTG
1 TTTTATTAT-TTTATTTA
1462548 TTTTA
1 TTTTA
1462553 AGTATTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 3 0.09
17 29 0.91
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTATTATTTTATTTA
Found at i:1462552 original size:9 final size:8
Alignment explanation
Indices: 1462494--1462542 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
1462484 CCTATTTTGG
1462494 TATTTTTAT
1 TATTTTT-T
1462503 TATTATTTT
1 TATT-TTTT
1462512 TATTTTTT
1 TATTTTTT
1462520 TATTTTATT
1 TATTTT-TT
*
1462529 TATTCTATT
1 TATT-TTTT
1462538 TATTT
1 TATTT
1462543 ATTTGTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 11 0.31
9 21 0.58
10 4 0.11
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (8 bp):
TATTTTTT
Found at i:1462552 original size:13 final size:13
Alignment explanation
Indices: 1462494--1462545 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
1462484 CCTATTTTGG
1462494 TATTTTTA-TTAT
1 TATTTTTATTTAT
1462506 TATTTTTATTT-T
1 TATTTTTATTTAT
*
1462518 TTTATTTTATTTAT
1 TAT-TTTTATTTAT
* *
1462532 TCTATTTATTTAT
1 TATTTTTATTTAT
1462545 T
1 T
1462546 TGTTTTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 11 0.32
13 20 0.59
14 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTATTTAT
Found at i:1462552 original size:26 final size:25
Alignment explanation
Indices: 1462497--1462552 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1462487 ATTTTGGTAT
* *
1462497 TTTTATTATTATTTTTATTTTTTTA
1 TTTTATTATTATATTTATTTATTTA
* *
1462522 TTTTATTTATTCTATTTATTTATTTG
1 TTTTA-TTATTATATTTATTTATTTA
1462548 TTTTA
1 TTTTA
1462553 AGTATTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTTATTATTATATTTATTTATTTA
Found at i:1463243 original size:175 final size:175
Alignment explanation
Indices: 1462834--1463303 Score: 617
Period size: 175 Copynumber: 2.7 Consensus size: 175
1462824 AATTAAATAC
* * *
1462834 TAATTACCTAAGAATGAGATTCTT-GAAAATTTCAAATGGTAAATTTTTTAAAAAATCTTTGGGT
1 TAATTACCCAA-AATGAGATTCTTAG-AAATTTCAAATGGTAAATTTTTTAAAAAATCTCTAGGT
* * * **
1462898 GAGAAATTTTTTTAAATTTGTCACAAA-TGATGAAATAATTTAAATGAAATTTCAATAAAAGTAA
64 GAGAAATTTATTTAAATTTGTCTCAAATTG-TGGAATAATTTAAATGAAATTTCAATAAAAACAA
1462962 TTGTATTTTTTTCTAAATAAGAAATTTTTTTGGTTGGAAAATATTTGA
128 TTGTATTTTTTTCTAAATAAGAAATTTTTTTGGTTGGAAAATATTTGA
* * * * *
1463010 TAATTACCCAAAGATAAGATTATTAGAAATTTCAAATGGTAAATTTTCTAAGAAATCTCTAGGTA
1 TAATTACCCAAA-ATGAGATTCTTAGAAATTTCAAATGGTAAATTTTTTAAAAAATCTCTAGGTG
* *
1463075 AGAAATTTATTTAAATTTGTCTTAAATTGTGGAATAATTTAAATGAAATTTTAATAAAAACAATT
65 AGAAATTTATTTAAATTTGTCTCAAATTGTGGAATAATTTAAATGAAATTTCAATAAAAACAATT
* *
1463140 GTATTCTTTTTC-AAATAA-AATTTTTTTTGGTTGGAAATTATTTGA
130 GTATT-TTTTTCTAAATAAGAAATTTTTTTGGTTGGAAAATATTTGA
* * *
1463185 TAATTACCCAATAATGAGATTCTTAGGAATTTCAAATAGTAAATTTTTTAAAAAATCTCTAAGTG
1 TAATTACCCAA-AATGAGATTCTTAGAAATTTCAAATGGTAAATTTTTTAAAAAATCTCTAGGTG
* * * * *
1463250 AGAAATTTCTTTAAATATGT-TCCAAATGGTGGAAGAATTTAAATGAAACTTCAA
65 AGAAATTTATTTAAATTTGTCT-CAAATTGTGGAATAATTTAAATGAAATTTCAA
1463304 ACAATAATTA
Statistics
Matches: 256, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
174 1 0.00
175 126 0.49
176 120 0.47
177 9 0.04
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (175 bp):
TAATTACCCAAAATGAGATTCTTAGAAATTTCAAATGGTAAATTTTTTAAAAAATCTCTAGGTGA
GAAATTTATTTAAATTTGTCTCAAATTGTGGAATAATTTAAATGAAATTTCAATAAAAACAATTG
TATTTTTTTCTAAATAAGAAATTTTTTTGGTTGGAAAATATTTGA
Found at i:1464226 original size:2 final size:2
Alignment explanation
Indices: 1464219--1464377 Score: 318
Period size: 2 Copynumber: 79.5 Consensus size: 2
1464209 TTTAGTTAAC
1464219 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1464261 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1464303 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1464345 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1464378 TCCCGAAATG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 157 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1471051 original size:17 final size:19
Alignment explanation
Indices: 1471029--1471076 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1471019 TTTGATAAAA
1471029 ATTTTAAAT-AA-ATGAAT
1 ATTTTAAATGAATATGAAT
*
1471046 ATTTT-AATGAATTTGAAT
1 ATTTTAAATGAATATGAAT
1471064 ATTTT-AATGAATA
1 ATTTTAAATGAATA
1471077 ATACTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 3 0.11
17 7 0.26
18 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTTAAATGAATATGAAT
Found at i:1471064 original size:18 final size:18
Alignment explanation
Indices: 1471041--1471075 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1471031 TTTAAATAAA
1471041 TGAATATTTTAATGAATT
1 TGAATATTTTAATGAATT
1471059 TGAATATTTTAATGAAT
1 TGAATATTTTAATGAAT
1471076 AATACTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (18 bp):
TGAATATTTTAATGAATT
Found at i:1478371 original size:3 final size:3
Alignment explanation
Indices: 1478365--1478391 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1478355 GCTAAAGGTT
1478365 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1478392 AGCTTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1502838 original size:23 final size:24
Alignment explanation
Indices: 1502812--1502864 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
1502802 CGATTCGATC
*
1502812 TAAAATTA-ATAAAATATTATTTT
1 TAAAATAATATAAAATATTATTTT
1502835 TAAAA-AATATAAAATATTATTTT
1 TAAAATAATATAAAATATTATTTT
*
1502858 TTAAATA
1 TAAAATA
1502865 TAAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 24 0.92
24 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TAAAATAATATAAAATATTATTTT
Found at i:1502863 original size:21 final size:22
Alignment explanation
Indices: 1502820--1502872 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
1502810 TCTAAAATTA
1502820 ATAAAATATTATTTTTAAAAAAT
1 ATAAAATATTATTTTT-AAAAAT
*
1502843 ATAAAATATTATTTTT-TAAAT
1 ATAAAATATTATTTTTAAAAAT
1502864 AT-AAATATT
1 ATAAAATATT
1502873 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
23 16 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTATTTTTAAAAAT
Found at i:1502907 original size:30 final size:30
Alignment explanation
Indices: 1502835--1502908 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
1502825 ATATTATTTT
* * *
1502835 TAAA-AAATATAAAATATTATTTTTTAAATA
1 TAAATAAATA-AAAATATCATTATATAAATA
**
1502865 TAAATATTTAAAAATATCATTATATAAATA
1 TAAATAAATAAAAATATCATTATATAAATA
*
1502895 TATATAAATAAAAA
1 TAAATAAATAAAAA
1502909 ATTAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATAAATAAAAATATCATTATATAAATA
Found at i:1503676 original size:18 final size:18
Alignment explanation
Indices: 1503636--1503683 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
1503626 AAATTTAATC
* *
1503636 AAATTTGAACTTTTAAATTT
1 AAATTT-AA-TTTAAAATAT
1503656 AAATTTAATTTAAAATAT
1 AAATTTAATTTAAAATAT
*
1503674 AAATTAAATT
1 AAATTTAATT
1503684 ATTCGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.68
19 2 0.08
20 6 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATTTAATTTAAAATAT
Found at i:1507983 original size:19 final size:20
Alignment explanation
Indices: 1507948--1507991 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
1507938 ATGACTAAAA
1507948 TTAATATTTTAATATTA-TT
1 TTAATATTTTAATATTACTT
*
1507967 TTAA-ATTTTATTAATTACTT
1 TTAATATTTTAAT-ATTACTT
1507987 TTAAT
1 TTAAT
1507992 TTGAGTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.33
19 8 0.38
20 6 0.29
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATATTTTAATATTACTT
Found at i:1514940 original size:14 final size:14
Alignment explanation
Indices: 1514916--1514948 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1514906 CTCTCTCTGT
1514916 CCTCT-TCCTTCTC
1 CCTCTCTCCTTCTC
1514929 CCTCTCTCCTTCTC
1 CCTCTCTCCTTCTC
*
1514943 CTTCTC
1 CCTCTC
1514949 CGCCTACCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (14 bp):
CCTCTCTCCTTCTC
Found at i:1524321 original size:25 final size:24
Alignment explanation
Indices: 1524280--1524330 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
1524270 TTAATAATTT
* *
1524280 AAAATATAATATGATATGATATAA
1 AAAATATAAAATGATATAATATAA
*
1524304 AAAATATCAAAATGATATAATTTAA
1 AAAATAT-AAAATGATATAATATAA
1524329 AA
1 AA
1524331 TTATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (24 bp):
AAAATATAAAATGATATAATATAA
Found at i:1524391 original size:31 final size:29
Alignment explanation
Indices: 1524348--1524434 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 29
1524338 AATTATTATA
* *
1524348 TATATTTAATAAA-ATAATATTTTATATTTT
1 TATATTGAATAAATATAATA-TATAT-TTTT
1524378 TATATTGATATAAATTATAATATATATTTTT
1 TATATTGA-ATAAA-TATAATATATATTTTT
**
1524409 TATATAAAATATAATATAAATATATA
1 TATATTGAATA-AATAT-AATATATA
1524435 AAATTTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
30 13 0.27
31 25 0.52
32 4 0.08
33 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
TATATTGAATAAATATAATATATATTTTT
Found at i:1524714 original size:26 final size:27
Alignment explanation
Indices: 1524667--1524719 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1524657 CTTTTTTTAT
*
1524667 TTATTTATTTATTTTAGAT-AAATAAA
1 TTATTTATTTATTTTAAATAAAATAAA
1524693 TTATTTATTT-TTTTAAATTAAAATAAA
1 TTATTTATTTATTTTAAA-TAAAATAAA
1524720 ATATGTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 6 0.25
26 11 0.46
27 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTATTTATTTATTTTAAATAAAATAAA
Found at i:1525592 original size:13 final size:13
Alignment explanation
Indices: 1525574--1525623 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
1525564 TGGGTTCAAG
1525574 TTAAATTTAAATA
1 TTAAATTTAAATA
* *
1525587 TTAAATGTATATA
1 TTAAATTTAAATA
*
1525600 TTAAATTTGAAT-
1 TTAAATTTAAATA
*
1525612 TAAAATTTAAAT
1 TTAAATTTAAAT
1525624 TAAAATATCA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
TTAAATTTAAATA
Found at i:1525713 original size:16 final size:16
Alignment explanation
Indices: 1525694--1525762 Score: 50
Period size: 18 Copynumber: 4.0 Consensus size: 16
1525684 TTATATTGTT
1525694 TAAAATTTTTATTAAA
1 TAAAATTTTTATTAAA
*
1525710 TAAAATAATTATT-TTATA
1 TAAAAT--TT-TTATTAAA
* *
1525728 TAAAAGTTTTTAAATATAT
1 TAAAA-TTTTT-ATTA-AA
1525747 TAAAATTTTTATTAAA
1 TAAAATTTTTATTAAA
1525763 ATAATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
16 9 0.22
17 5 0.12
18 18 0.45
19 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (16 bp):
TAAAATTTTTATTAAA
Found at i:1526646 original size:13 final size:14
Alignment explanation
Indices: 1526616--1526650 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1526606 ATTGAGATAT
1526616 AAAATTATTATTAA
1 AAAATTATTATTAA
*
1526630 AAAATTATT-TTAC
1 AAAATTATTATTAA
1526643 AAAATTAT
1 AAAATTAT
1526651 CAATATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTATTATTAA
Found at i:1529295 original size:30 final size:30
Alignment explanation
Indices: 1529236--1529296 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1529226 CATGGATGAT
* * *
1529236 TGTAGGTTGCATTTATTAATCTCAGATAAG
1 TGTAAGTTGCATTTAATAATCTCAAATAAG
* *
1529266 TGTAAGTTGCATTTAATGATTTCAAATAAG
1 TGTAAGTTGCATTTAATAATCTCAAATAAG
1529296 T
1 T
1529297 TAAAGGTCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (30 bp):
TGTAAGTTGCATTTAATAATCTCAAATAAG
Found at i:1529557 original size:167 final size:163
Alignment explanation
Indices: 1529281--1529579 Score: 508
Period size: 167 Copynumber: 1.8 Consensus size: 163
1529271 GTTGCATTTA
1529281 ATGATTTCAAATAAGTTAAAGGTCAGTTGATCTTATTTTGAAGTAATACCTCAATGAAACGTTAA
1 ATGATTTCAAATAAGTTAAAGGTCAGTTGATCTTATTTTGAAGTAATACCTCAATGAAACGTTAA
*
1529346 TGGAGGTAGTTGGGCGAACGAGCCTACTTTGTGGCAAGGATTATAGATATCATCTCTCATGTGCG
66 TGGAGGTAGTTGGGCAAACGAGCCTACTTTGTGGCAAGGATTAT--ATAT-ATC-CTCATGTGCG
1529411 ATGATACAACAATGGAGTATTCATTGATTTAGCAATT
127 ATGATACAACAATGGAGTATTCATTGATTTAGCAATT
* * *
1529448 ATGATTTCAAATAAGTTAAAGGTCAGTTGATCTTATTTTGAAGTAATATCTCAATGAAATGTTAG
1 ATGATTTCAAATAAGTTAAAGGTCAGTTGATCTTATTTTGAAGTAATACCTCAATGAAACGTTAA
* *
1529513 TGGAGGTAGTTGGGCAAATGAGCCTACTTTGTGGCAAGGATTATATATATCCTCATGTGCGGTGA
66 TGGAGGTAGTTGGGCAAACGAGCCTACTTTGTGGCAAGGATTATATATATCCTCATGTGCGATGA
1529578 TA
131 TA
1529580 TAATAGTCTA
Statistics
Matches: 126, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
163 15 0.12
164 3 0.02
165 4 0.03
167 104 0.83
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (163 bp):
ATGATTTCAAATAAGTTAAAGGTCAGTTGATCTTATTTTGAAGTAATACCTCAATGAAACGTTAA
TGGAGGTAGTTGGGCAAACGAGCCTACTTTGTGGCAAGGATTATATATATCCTCATGTGCGATGA
TACAACAATGGAGTATTCATTGATTTAGCAATT
Found at i:1529805 original size:27 final size:26
Alignment explanation
Indices: 1529768--1529835 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 26
1529758 TTTACATTCG
*
1529768 AATA-CATATTTTTATTATTAACTTT
1 AATATCATATTTTTATAATTAACTTT
* *
1529793 AATATCATAATTTTAATAATTAATTTT
1 AATATCAT-ATTTTTATAATTAACTTT
* *
1529820 ACTGTCATCATTTTTA
1 AATATCAT-ATTTTTA
1529836 ATATCCTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 27 0.79
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (26 bp):
AATATCATATTTTTATAATTAACTTT
Found at i:1530666 original size:12 final size:12
Alignment explanation
Indices: 1530642--1530677 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1530632 TCTTTTATCA
1530642 AAAATAATTTAAT
1 AAAA-AATTTAAT
*
1530655 AAAAATTTTAAT
1 AAAAAATTTAAT
1530667 AAAAAATTTAA
1 AAAAAATTTAA
1530678 ATCGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAAAATTTAAT
Found at i:1536106 original size:41 final size:41
Alignment explanation
Indices: 1536061--1536145 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
1536051 GACTCGACAC
*
1536061 AAACATGATATAAAAATAAAATATGAAAATAACATGATTTA
1 AAACATGATATAAAAATAAAACATGAAAATAACATGATTTA
*
1536102 AAACATGATATAAAAATAAAACATGAAAATAACATGGTTTA
1 AAACATGATATAAAAATAAAACATGAAAATAACATGATTTA
1536143 AAA
1 AAA
1536146 TTTTAATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (41 bp):
AAACATGATATAAAAATAAAACATGAAAATAACATGATTTA
Found at i:1536123 original size:18 final size:18
Alignment explanation
Indices: 1536061--1536127 Score: 62
Period size: 18 Copynumber: 3.4 Consensus size: 18
1536051 GACTCGACAC
1536061 AAACATGATATAAAAATA
1 AAACATGATATAAAAATA
* * *
1536079 AAATATGAAAATAACATGATTTA
1 AAACATG-ATATAA-A--A-ATA
1536102 AAACATGATATAAAAATA
1 AAACATGATATAAAAATA
1536120 AAACATGA
1 AAACATGA
1536128 AAATAACATG
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 16 0.42
19 6 0.16
20 1 0.03
21 1 0.03
22 6 0.16
23 8 0.21
ACGTcount: A:0.63, C:0.06, G:0.07, T:0.24
Consensus pattern (18 bp):
AAACATGATATAAAAATA
Found at i:1540980 original size:31 final size:35
Alignment explanation
Indices: 1540945--1541008 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 35
1540935 GTAATAATTA
1540945 TATATATTTA-A-TAAAATAAA-AAT-ATATATTT
1 TATATATTTATATTAAAATAAATAATGATATATTT
* *
1540976 TATATTTTTATATTAATATAAATAATGATATAT
1 TATATATTTATATTAAAATAAATAATGATATAT
1541009 AATTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 9 0.33
32 1 0.04
33 8 0.30
34 3 0.11
35 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
TATATATTTATATTAAAATAAATAATGATATATTT
Found at i:1540988 original size:37 final size:39
Alignment explanation
Indices: 1540947--1541019 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
1540937 AATAATTATA
1540947 TATATTTAATA-AAATAAAAATATAT-A-TTTTATATTTT
1 TATA-TTAATATAAATAAAAATATATAATTTTTATATTTT
**
1540984 TATATTAATATAAATAATGATATATAATTTTTATAT
1 TATATTAATATAAATAAAAATATATAATTTTTATAT
1541020 AAATTACGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 6 0.19
37 16 0.52
38 1 0.03
39 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (39 bp):
TATATTAATATAAATAAAAATATATAATTTTTATATTTT
Found at i:1541503 original size:22 final size:23
Alignment explanation
Indices: 1541439--1541505 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
1541429 GATTGATTAT
*
1541439 AATATAATTAAAAATATTAATAAA
1 AATATAATAAAAAAT-TTAATAAA
* *
1541463 AATAATTATAATTATAATTTAA-AAA
1 AAT-ATAATAA--AAAATTTAATAAA
1541488 AATATAATAAAAAATTTA
1 AATATAATAAAAAATTTA
1541506 TATTAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
22 7 0.20
24 9 0.26
25 11 0.31
26 4 0.11
27 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATATAATAAAAAATTTAATAAA
Found at i:1542164 original size:7 final size:7
Alignment explanation
Indices: 1542152--1542176 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1542142 TTCATTCGGT
1542152 TTTTAAA
1 TTTTAAA
1542159 TTTTAAA
1 TTTTAAA
1542166 TTTTAAA
1 TTTTAAA
1542173 TTTT
1 TTTT
1542177 TTATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:1542292 original size:21 final size:20
Alignment explanation
Indices: 1542277--1542314 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1542267 TATTTCATTG
1542277 AATTTT-TTTAAAATTTTTA
1 AATTTTATTTAAAATTTTTA
1542296 AATTTTGATTTAAAATTTT
1 AATTTT-ATTTAAAATTTT
1542315 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTATTTAAAATTTTTA
Found at i:1542725 original size:6 final size:6
Alignment explanation
Indices: 1542701--1542740 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1542691 TGGCAGTAGC
* * *
1542701 CATTAT TATTAT TATTAT CACTAT CATTAT CATTAT CATT
1 CATTAT CATTAT CATTAT CATTAT CATTAT CATTAT CATT
1542741 TCTGCTGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTAT
Found at i:1544086 original size:28 final size:28
Alignment explanation
Indices: 1544047--1544140 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
1544037 TTGTTACACC
* *
1544047 TAAATAAGTTTTTAACTTTTAATTTACAT
1 TAAATAAATTTTTAAATTTTAATTTA-AT
* * *
1544076 TAAA-AAATTTTAAAATTTAAATTATATT
1 TAAATAAATTTTTAAATTTTAATT-TAAT
*
1544104 TAAATAAATTTTT-ATTTTTAATTTATAT
1 TAAATAAATTTTTAAATTTTAATTTA-AT
1544132 CTAAATAAA
1 -TAAATAAA
1544141 CGCTTAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.04
28 29 0.56
29 21 0.40
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (28 bp):
TAAATAAATTTTTAAATTTTAATTTAAT
Found at i:1544180 original size:18 final size:18
Alignment explanation
Indices: 1544160--1544193 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1544150 TAAATTAATT
*
1544160 TTTTGTTTA-AAATAAAA
1 TTTTATTTATAAATAAAA
1544177 TTTTATTTATAAATAAA
1 TTTTATTTATAAATAAA
1544194 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTATTTATAAATAAAA
Found at i:1544287 original size:2 final size:2
Alignment explanation
Indices: 1544282--1544306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1544272 TATTTTACTC
1544282 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1544307 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1550525 original size:12 final size:14
Alignment explanation
Indices: 1550503--1550534 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1550493 TAAGAAGCAG
1550503 ATTTATTAATA-TT
1 ATTTATTAATATTT
1550516 ATTT-TTAATATTT
1 ATTTATTAATATTT
1550529 ATTTAT
1 ATTTAT
1550535 CATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 10 0.59
14 1 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTATTAATATTT
Found at i:1550975 original size:4 final size:4
Alignment explanation
Indices: 1550954--1550999 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
1550944 ATTTTAATCA
*
1550954 AATT AATT GATT AA-- AATT AATT AATT AATT AATT -ATT AAATT AATT
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT AATT -AATT AATT
1551000 TTGAATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 2 0.06
3 3 0.08
4 28 0.78
5 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1562009 original size:14 final size:14
Alignment explanation
Indices: 1561992--1562025 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1561982 CAAATCTTAT
*
1561992 AAAAATAATATATA
1 AAAAATAATAAATA
1562006 AAAAATAATAAATA
1 AAAAATAATAAATA
*
1562020 ATAAAT
1 AAAAAT
1562026 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAATAAATA
Found at i:1562087 original size:20 final size:20
Alignment explanation
Indices: 1562045--1562090 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1562035 TAATGAACCG
***
1562045 AATCAAAAAAATTTTATTGA
1 AATCAAAAAAATTTTAAAAA
*
1562065 AATCAAAACAATTTTAAAAA
1 AATCAAAAAAATTTTAAAAA
1562085 AATCAA
1 AATCAA
1562091 TTTGAATTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (20 bp):
AATCAAAAAAATTTTAAAAA
Found at i:1562591 original size:16 final size:16
Alignment explanation
Indices: 1562572--1562623 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
1562562 TTAAAAAATT
1562572 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
1562588 TTTAAATTTAA-TAAA
1 TTTAAATTTAATTAAA
* * *
1562603 TATAAAATTAAATCAAA
1 T-TTAAATTTAATTAAA
1562620 TTTA
1 TTTA
1562624 TAATGAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:1562608 original size:15 final size:16
Alignment explanation
Indices: 1562574--1562613 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1562564 AAAAAATTTT
*
1562574 TAAATTTAATTAAATT
1 TAAATTTAATTAAATA
1562590 TAAATTTAA-TAAATA
1 TAAATTTAATTAAATA
*
1562605 TAAAATTAA
1 TAAATTTAA
1562614 ATCAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTAAATA
Found at i:1562991 original size:14 final size:14
Alignment explanation
Indices: 1562972--1563006 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1562962 GTTTAGATTA
*
1562972 ATTTATATAAATTT
1 ATTTATATAAAATT
*
1562986 ATTTATGTAAAATT
1 ATTTATATAAAATT
1563000 ATTTATA
1 ATTTATA
1563007 AATTTATAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (14 bp):
ATTTATATAAAATT
Found at i:1565674 original size:2 final size:2
Alignment explanation
Indices: 1565667--1565700 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1565657 TTATTGATTT
1565667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1565701 TATGATTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1572238 original size:8 final size:8
Alignment explanation
Indices: 1572227--1572267 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
1572217 AATTATTTTT
1572227 TATTTATA
1 TATTTATA
1572235 TATTTATA
1 TATTTATA
*
1572243 TAATTATA
1 TATTTATA
*
1572251 TATTTAAA
1 TATTTATA
1572259 TATTTATA
1 TATTTATA
1572267 T
1 T
1572268 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTATA
Found at i:1572266 original size:14 final size:16
Alignment explanation
Indices: 1572230--1572285 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
1572220 TATTTTTTAT
*
1572230 TTATATATTTATATAA
1 TTATATATTTAAATAA
1572246 TTATATATTTAAAT-A
1 TTATATATTTAAATAA
*
1572261 TT-TATATTTAAAAAA
1 TTATATATTTAAATAA
*
1572276 TAATAT-TTTA
1 TTATATATTTA
1572286 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 16 0.46
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATTTAAATAA
Found at i:1572287 original size:21 final size:22
Alignment explanation
Indices: 1572257--1572309 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
1572247 TATATATTTA
1572257 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
*
1572277 AATATTTTATATTTTTTAAAAAT
1 AATATTTTATA-TTTTAAAAAAT
1572300 AATATTTTAT
1 AATATTTTAT
1572310 TAATTTCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
23 19 0.66
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:1572760 original size:19 final size:19
Alignment explanation
Indices: 1572724--1572775 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
1572714 TATTATTTTA
* *
1572724 ATATATTTAAATAA-ATTT
1 ATATATTAAAAAAATATTT
1572742 ATATATTAAAAAAATATTT
1 ATATATTAAAAAAATATTT
* * *
1572761 TTATTTTATAAAAAT
1 ATATATTAAAAAAAT
1572776 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATTAAAAAAATATTT
Found at i:1572788 original size:18 final size:17
Alignment explanation
Indices: 1572767--1572805 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1572757 ATTTTTATTT
1572767 TATAAAAATTTAAAAAAA
1 TATAAAAA-TTAAAAAAA
*
1572785 TATAAAAATTAATAAAA
1 TATAAAAATTAAAAAAA
1572802 TATA
1 TATA
1572806 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TATAAAAATTAAAAAAA
Found at i:1572791 original size:17 final size:17
Alignment explanation
Indices: 1572771--1572811 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1572761 TTATTTTATA
1572771 AAAATTTAAAAAAATAT
1 AAAATTTAAAAAAATAT
* *
1572788 AAAAATTAATAAAATAT
1 AAAATTTAAAAAAATAT
*
1572805 ATAATTT
1 AAAATTT
1572812 TATTTGATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTTAAAAAAATAT
Found at i:1580364 original size:79 final size:79
Alignment explanation
Indices: 1580270--1580428 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
1580260 AAGCCTCCTT
* *
1580270 AAAGGTAGTCCTTTTTTGTATTATTTTGTTTATCAACTCAATCCTCATATAGCAATTCACTACAG
1 AAAGGTAGCCCTTTTTTATATTATTTTGTTTATCAACTCAATCCTCATATAGCAATTCACTACAG
1580335 ATCCAATGTCACTA
66 ATCCAATGTCACTA
1580349 AAAGGTAGCCCTTTTTTATATTATTTTGTTTATCAACTCAATCCTCATATAGCAATTCACTACAG
1 AAAGGTAGCCCTTTTTTATATTATTTTGTTTATCAACTCAATCCTCATATAGCAATTCACTACAG
*
1580414 ATCCAATGTTACTA
66 ATCCAATGTCACTA
1580428 A
1 A
1580429 CAGACTTCTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (79 bp):
AAAGGTAGCCCTTTTTTATATTATTTTGTTTATCAACTCAATCCTCATATAGCAATTCACTACAG
ATCCAATGTCACTA
Found at i:1583947 original size:17 final size:17
Alignment explanation
Indices: 1583925--1583958 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1583915 AAATAAAAGT
*
1583925 CCAAAACAAGCAAGGAC
1 CCAAAACAAGAAAGGAC
*
1583942 CCAAAAGAAGAAAGGAC
1 CCAAAACAAGAAAGGAC
1583959 AAACAGGGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.24, G:0.21, T:0.00
Consensus pattern (17 bp):
CCAAAACAAGAAAGGAC
Found at i:1586198 original size:13 final size:14
Alignment explanation
Indices: 1586175--1586204 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1586165 AATAATTATT
1586175 TAAATATATAAAAA
1 TAAATATATAAAAA
1586189 TAAA-ATATAAAAA
1 TAAATATATAAAAA
1586202 TAA
1 TAA
1586205 TATTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAATATATAAAAA
Found at i:1586299 original size:37 final size:37
Alignment explanation
Indices: 1586219--1586303 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 37
1586209 ATTTAAAGGT
*
1586219 TTAATA-AAATAAAATAATATATTTTAAAATTTTATA
1 TTAATATAAATAAAATAATATATTTTAAAATTTCATA
*
1586255 TTAATATAAATAATAATAA-ATAATTTTAATATTTCATA
1 TTAATATAAATAA-AATAATAT-ATTTTAAAATTTCATA
1586293 TT-ATATAAATA
1 TTAATATAAATA
1586304 TAGAATCGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 6 0.14
37 17 0.39
38 21 0.48
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (37 bp):
TTAATATAAATAAAATAATATATTTTAAAATTTCATA
Found at i:1587094 original size:20 final size:22
Alignment explanation
Indices: 1587034--1587101 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 22
1587024 AATTATGTTT
*
1587034 TTTTTTTTTACATCTAAAACATTTA
1 TTTTTTTATACAT-TAAAA-A-TTA
* *
1587059 TTTTTTTATA-TTTTAAAATTA
1 TTTTTTTATACATTAAAAATTA
1587080 TTTTTTTA-ACATTAAAAATTA
1 TTTTTTTATACATTAAAAATTA
1587101 T
1 T
1587102 GAAACTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 21 0.57
22 1 0.03
23 4 0.11
24 1 0.03
25 9 0.24
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTTATACATTAAAAATTA
Found at i:1600279 original size:3 final size:3
Alignment explanation
Indices: 1600271--1600320 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
1600261 GTCACCACTC
* ** *
1600271 TCA TCA TCA TCA TCC TCA TCA TTG TCA TCG TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1600319 TC
1 TC
1600321 TTCAAGACAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.26, C:0.34, G:0.04, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:1603331 original size:19 final size:20
Alignment explanation
Indices: 1603307--1603349 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1603297 AGTTTTATTT
*
1603307 TATAAAAATTTA-AAAAATA
1 TATAAAAATTAATAAAAATA
1603326 TAT-AAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
1603345 TATAA
1 TATAA
1603350 TTAAGTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 13 0.62
20 1 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:1603351 original size:17 final size:18
Alignment explanation
Indices: 1603319--1603353 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1603309 TAAAAATTTA
1603319 AAAAATATATAAAATTAAT
1 AAAAATATAT-AAATTAAT
1603338 AAAAATATAT-AATTAA
1 AAAAATATATAAATTAA
1603354 GTTTGGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATATAAATTAAT
Found at i:1608866 original size:29 final size:30
Alignment explanation
Indices: 1608844--1608902 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
1608834 TTTACATTTT
*
1608844 TATTGCATTCAAATAAATTTTTAATCTTTC
1 TATTGCAATCAAATAAATTTTTAATCTTTC
* *
1608874 TTTTGTAATCAAATAAATTTTTAATCTTT
1 TATTGCAATCAAATAAATTTTTAATCTTT
1608903 AATTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (30 bp):
TATTGCAATCAAATAAATTTTTAATCTTTC
Found at i:1608888 original size:30 final size:30
Alignment explanation
Indices: 1608852--1608919 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
1608842 TTTATTGCAT
*
1608852 TCAAATAAATTTTTAATCTTT-CTTTTGTAA
1 TCAAATAAATTTTTAATCTTTAATTTT-TAA
*
1608882 TCAAATAAATTTTTAATCTTTAATTTTTAT
1 TCAAATAAATTTTTAATCTTTAATTTTTAA
1608912 TCAAATAA
1 TCAAATAA
1608920 GTCCTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.51
Consensus pattern (30 bp):
TCAAATAAATTTTTAATCTTTAATTTTTAA
Found at i:1609055 original size:29 final size:30
Alignment explanation
Indices: 1608982--1609057 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
1608972 TTCATTTGAA
* *
1608982 ATAAGAATTTATTTGAATATAAATCAAAAT
1 ATAAAAATTTATTTAAATATAAATCAAAAT
1609012 ATAAAAATTTATTTAAATAT-AAT-AAAATT
1 ATAAAAATTTATTTAAATATAAATCAAAA-T
*
1609041 TTAAAAATTTATTTAAA
1 ATAAAAATTTATTTAAA
1609058 AAAATAATTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.10
29 20 0.48
30 18 0.43
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAAAAATTTATTTAAATATAAATCAAAAT
Found at i:1617723 original size:52 final size:52
Alignment explanation
Indices: 1617667--1617775 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 52
1617657 AGAGTGATAT
* * * *
1617667 TATTTAAAATTTTAATAATAATTATATATAAATTTAATGTAATTAAAAAA-TA
1 TATTTAAAATTTTAAT-ATAATCAAAAATAAATTTAATGTAATCAAAAAATTA
* * * **
1617719 TATTTTATATTTTAATATGATCAAAAATAAATTTAATGTGGTCAAAAAATTA
1 TATTTAAAATTTTAATATAATCAAAAATAAATTTAATGTAATCAAAAAATTA
1617771 TATTT
1 TATTT
1617776 TATATTTTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 26 0.55
52 21 0.45
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (52 bp):
TATTTAAAATTTTAATATAATCAAAAATAAATTTAATGTAATCAAAAAATTA
Found at i:1617817 original size:31 final size:30
Alignment explanation
Indices: 1617765--1617847 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 30
1617755 TGTGGTCAAA
* * * *
1617765 AAATTATATTTTAT-ATTTTTATGTTAATAT
1 AAATTATAATATATAATTTTTAT-ATAAAAT
1617795 AAATTATAATATATAATTTTTATATAAAAT
1 AAATTATAATATATAATTTTTATATAAAAT
*
1617825 ATAA-TATAAATATATAAATTTTA
1 A-AATTAT-AATATATAATTTTTA
1617848 AAATTTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
AAATTATAATATATAATTTTTATATAAAAT
Found at i:1618912 original size:19 final size:20
Alignment explanation
Indices: 1618888--1618930 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1618878 CTAAGATCGT
*
1618888 TATTTATATATTTT-TAATA
1 TATTTATAAATTTTATAATA
1618907 TATTTATAAATTTTATAATA
1 TATTTATAAATTTTATAATA
1618927 TATT
1 TATT
1618931 GATTTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTATAAATTTTATAATA
Found at i:1624926 original size:23 final size:24
Alignment explanation
Indices: 1624900--1624972 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 24
1624890 ATTAAATATG
1624900 AAATATATTTTTTAATTTTTA-TA
1 AAATATATTTTTTAATTTTTATTA
* *
1624923 AAATGTA-TTTATAATTTTTATTA
1 AAATATATTTTTTAATTTTTATTA
*
1624946 AAATTTTATTTTTTAGATTTTTTATTA
1 AAA-TATATTTTTTA-A-TTTTTATTA
1624973 CTATTATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 12 0.29
23 11 0.27
24 3 0.07
25 5 0.12
26 1 0.02
27 9 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
AAATATATTTTTTAATTTTTATTA
Found at i:1628423 original size:17 final size:18
Alignment explanation
Indices: 1628401--1628450 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 18
1628391 AACAAGTTAT
1628401 TCTTTTTGAT-CAAT-TTC
1 TCTTTTTG-TCCAATCTTC
1628418 TCTTTTTGTCCAATCTTC
1 TCTTTTTGTCCAATCTTC
1628436 TCTCTTTTGTACCAA
1 TCT-TTTTGT-CCAA
1628451 ACACCAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.03
17 12 0.41
18 6 0.21
19 6 0.21
20 4 0.14
ACGTcount: A:0.16, C:0.24, G:0.06, T:0.54
Consensus pattern (18 bp):
TCTTTTTGTCCAATCTTC
Found at i:1629122 original size:2 final size:2
Alignment explanation
Indices: 1629115--1629149 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1629105 AAGTACCCTC
1629115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1629150 CTATCAGATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1630837 original size:15 final size:15
Alignment explanation
Indices: 1630814--1630859 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1630804 ACTACTGGGA
*
1630814 CAACAACAGGGACTC
1 CAACCACAGGGACTC
*
1630829 CACCCACAGGGA---
1 CAACCACAGGGACTC
1630841 CAACCACAGGGACTC
1 CAACCACAGGGACTC
1630856 CAAC
1 CAAC
1630860 AGTTTTTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
12 11 0.44
15 14 0.56
ACGTcount: A:0.37, C:0.39, G:0.20, T:0.04
Consensus pattern (15 bp):
CAACCACAGGGACTC
Found at i:1634312 original size:19 final size:19
Alignment explanation
Indices: 1634265--1634312 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1634255 AAAACCATCG
1634265 ATTTATAAAAAATTTTATAA
1 ATTTAT-AAAAATTTTATAA
* *
1634285 ATCTT-TAAAAATTTTTTGA
1 AT-TTATAAAAATTTTATAA
1634304 ATTTATAAA
1 ATTTATAAA
1634313 TTATTAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 17 0.71
20 3 0.12
21 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTTATAAAAATTTTATAA
Found at i:1635071 original size:12 final size:12
Alignment explanation
Indices: 1635056--1635080 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1635046 AACAATTTTG
1635056 TTTAAAATTGGT
1 TTTAAAATTGGT
1635068 TTTAAAATTGGT
1 TTTAAAATTGGT
1635080 T
1 T
1635081 CATTTATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTTAAAATTGGT
Found at i:1635197 original size:15 final size:14
Alignment explanation
Indices: 1635177--1635230 Score: 81
Period size: 15 Copynumber: 3.7 Consensus size: 14
1635167 AAGATTTATT
*
1635177 TTTATTTGTTTAAA
1 TTTATTTATTTAAA
1635191 GTTTATTTATTTAAA
1 -TTTATTTATTTAAA
1635206 TTTATTTATTTATAA
1 TTTATTTATTTA-AA
1635221 TTTATTTATT
1 TTTATTTATT
1635231 GTTCATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
14 12 0.32
15 25 0.68
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (14 bp):
TTTATTTATTTAAA
Found at i:1636912 original size:100 final size:100
Alignment explanation
Indices: 1636739--1636934 Score: 329
Period size: 100 Copynumber: 2.0 Consensus size: 100
1636729 TGTATTTCGG
* *
1636739 GAACAACGTCGAAGCGGGGCGGGCGGTGAGGGTGAGGATTTTTCGTCACGAGGGAGTGGAATTAG
1 GAACAACGTCGAAGCCGGGCGGGCGGTGAGGGTGAGGATTTTTCGTCACCAGGGAGTGGAATTAG
*
1636804 CGTCGCCTGTGGGCTGCCTCCTCCATGAAGTAAAT
66 CGTCGCCTGGGGGCTGCCTCCTCCATGAAGTAAAT
** * *
1636839 GAACAACGTCGGCGCCGGGCTGGCTGTGAGGGTGAGGATTTTTCGTCACCAGGGAGTGGAATTAG
1 GAACAACGTCGAAGCCGGGCGGGCGGTGAGGGTGAGGATTTTTCGTCACCAGGGAGTGGAATTAG
1636904 CGTCGCCTGGGGGCTGCCTCCTCCATGAAGT
66 CGTCGCCTGGGGGCTGCCTCCTCCATGAAGT
1636935 GAGTGATTGA
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.21
Consensus pattern (100 bp):
GAACAACGTCGAAGCCGGGCGGGCGGTGAGGGTGAGGATTTTTCGTCACCAGGGAGTGGAATTAG
CGTCGCCTGGGGGCTGCCTCCTCCATGAAGTAAAT
Found at i:1638419 original size:16 final size:16
Alignment explanation
Indices: 1638394--1638427 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1638384 TTGCTTGTAC
1638394 AATAGAAAATGAATCA
1 AATAGAAAATGAATCA
*
1638410 AATAGGAAATGAATCA
1 AATAGAAAATGAATCA
1638426 AA
1 AA
1638428 CATTTCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (16 bp):
AATAGAAAATGAATCA
Found at i:1643217 original size:18 final size:19
Alignment explanation
Indices: 1643194--1643236 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1643184 CGTCAAATTG
1643194 AATTATTAAAAAAAT-AAA
1 AATTATTAAAAAAATAAAA
1643212 AATTA-TAAAAAAATAAAA
1 AATTATTAAAAAAATAAAA
1643230 AATTATT
1 AATTATT
1643237 GAGTTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 13 0.57
19 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTATTAAAAAAATAAAA
Found at i:1669119 original size:23 final size:23
Alignment explanation
Indices: 1669093--1669137 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1669083 GACCACCTTA
*
1669093 TTTGACAAGGAGTTAACTTACTT
1 TTTGAAAAGGAGTTAACTTACTT
*
1669116 TTTGAAAAGGAGTTACCTTACT
1 TTTGAAAAGGAGTTAACTTACT
1669138 ACAATGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (23 bp):
TTTGAAAAGGAGTTAACTTACTT
Found at i:1673804 original size:2 final size:2
Alignment explanation
Indices: 1673797--1673822 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1673787 TGTTTTGAGC
1673797 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1673823 CTGCTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1685189 original size:25 final size:26
Alignment explanation
Indices: 1685160--1685213 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
1685150 TAATATAATA
1685160 AAAATTT-TAAATTT-AAATTTAATTT
1 AAAATTTAT-AATTTGAAATTTAATTT
* *
1685185 AAAATTTATTATTTGAAATTTGATTT
1 AAAATTTATAATTTGAAATTTAATTT
1685211 AAA
1 AAA
1685214 TTGGACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (26 bp):
AAAATTTATAATTTGAAATTTAATTT
Found at i:1685362 original size:18 final size:18
Alignment explanation
Indices: 1685326--1685364 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1685316 TATATTTAAT
*
1685326 TTTAAATTCAATTATATA
1 TTTAAATTCAATCATATA
1685344 TTTAAATTCGAATCAATATA
1 TTTAAATTC-AATC-ATATA
1685364 T
1 T
1685365 ATATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (18 bp):
TTTAAATTCAATCATATA
Found at i:1689828 original size:13 final size:13
Alignment explanation
Indices: 1689806--1689841 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1689796 GACACGTTAT
*
1689806 ATGAACATAAAAA
1 ATGAATATAAAAA
1689819 ATGAATATAAAAA
1 ATGAATATAAAAA
1689832 ATGAATATAA
1 ATGAATATAA
1689842 CGTAACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (13 bp):
ATGAATATAAAAA
Found at i:1695118 original size:2 final size:2
Alignment explanation
Indices: 1695111--1695141 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1695101 ATTTTGCCTT
1695111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1695142 CAATTTGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1698646 original size:2 final size:2
Alignment explanation
Indices: 1698639--1698666 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1698629 TATTTGTTGC
1698639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1698667 TCTCATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1702665 original size:29 final size:31
Alignment explanation
Indices: 1702633--1702697 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 31
1702623 TGTGTCACAA
* * *
1702633 ATTTTTGAG-AATTTAATCTTTTTAATGT-T
1 ATTTTTAAGAAATTTAATCTTTGTAATATAT
1702662 A-TTTTAAGAAATTTAATCTTTGTAATATAT
1 ATTTTTAAGAAATTTAATCTTTGTAATATAT
1702692 ATTTTT
1 ATTTTT
1702698 TTAAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 6 0.20
29 18 0.60
30 2 0.07
31 4 0.13
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.57
Consensus pattern (31 bp):
ATTTTTAAGAAATTTAATCTTTGTAATATAT
Found at i:1702968 original size:16 final size:17
Alignment explanation
Indices: 1702947--1702983 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1702937 ATTAATTATA
1702947 TATATATTTT-AATTTT
1 TATATATTTTAAATTTT
1702963 TATATATTTTAAATTTT
1 TATATATTTTAAATTTT
1702980 TATA
1 TATA
1702984 ATATAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTTTAAATTTT
Found at i:1702968 original size:18 final size:18
Alignment explanation
Indices: 1702945--1702987 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1702935 GAATTAATTA
*
1702945 TATATATATTTTAATTTT
1 TATATATATTTAAATTTT
1702963 TATATAT-TTTAAATTTT
1 TATATATATTTAAATTTT
1702980 TATA-ATAT
1 TATATATAT
1702988 AAATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATATATTTAAATTTT
Found at i:1702990 original size:15 final size:17
Alignment explanation
Indices: 1702947--1702992 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
1702937 ATTAATTATA
*
1702947 TATATATT-TTAATTTT
1 TATATATTATAAATTTT
*
1702963 TATATATTTTAAATTTT
1 TATATATTATAAATTTT
1702980 TATA-A-TATAAATT
1 TATATATTATAAATT
1702993 AATTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 9 0.33
17 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATTATAAATTTT
Done.