Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 14 of 26
Found at i:1902643 original size:25 final size:24
Alignment explanation
Indices: 1902579--1902645 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
1902569 TTTAAAATAT
*
1902579 ATATATTAATTTAAAATATTATTTA
1 ATATATTAA-TTAAAATATTAATTA
1902604 ATAT-TATAATT---ATATTAATTA
1 ATATAT-TAATTAAAATATTAATTA
1902625 ATTATATTAATTAAAATATTA
1 A-TATATTAATTAAAATATTA
1902646 TATATTTACT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
21 10 0.29
22 8 0.23
23 1 0.03
24 3 0.09
25 13 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATATTAATTAAAATATTAATTA
Found at i:1902649 original size:19 final size:20
Alignment explanation
Indices: 1902560--1902651 Score: 80
Period size: 19 Copynumber: 4.3 Consensus size: 20
1902550 AATATAATAA
1902560 ATATATTAATTTAAAATA-T
1 ATATATTAATTTAAAATATT
1902579 ATATATTAATTTAAAATATT
1 ATATATTAATTTAAAATATT
* * *
1902599 ATTTAATATTATAATTATATTAATT
1 A--T-ATATTA-ATTTAAAAT-ATT
1902624 AATTATATTAA-TTAAAATATT
1 -A-TATATTAATTTAAAATATT
1902645 ATATATT
1 ATATATT
1902652 TACTTCAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
19 24 0.39
20 3 0.05
21 3 0.05
22 6 0.10
23 7 0.11
24 12 0.20
25 5 0.08
26 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTAATTTAAAATATT
Found at i:1903040 original size:30 final size:29
Alignment explanation
Indices: 1902987--1903110 Score: 119
Period size: 29 Copynumber: 4.2 Consensus size: 29
1902977 ACCTAAATAA
* *
1902987 AAATTTTGAGTAAAAGT-TATTTATTTTTT
1 AAATTTTTA-TAAAAATATATTTATTTTTT
1903016 AAATTTTTATAATAAATATATTTATTTTTT
1 AAATTTTTATAA-AAATATATTTATTTTTT
* *
1903046 -AATATTTA-AAAAATAATTATTTATTTTTAA
1 AAATTTTTATAAAAAT-A-TATTTATTTTT-T
* *
1903076 AAATTTTGATTAAAAATATATTTATATTTT
1 AAATTTTTA-TAAAAATATATTTATTTTTT
1903106 AAATT
1 AAATT
1903111 AATTTTAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.05
28 6 0.08
29 29 0.37
30 17 0.22
31 16 0.20
32 1 0.01
33 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
AAATTTTTATAAAAATATATTTATTTTTT
Found at i:1903124 original size:34 final size:32
Alignment explanation
Indices: 1903004--1903124 Score: 107
Period size: 29 Copynumber: 3.9 Consensus size: 32
1902994 GAGTAAAAGT
1903004 TATTTATTTTTTAAAT--TTTT--ATAATAAATA
1 TATTTA-TTTTTAAATAATTTTAAATAA-AAATA
*
1903034 TATTTATTTTTTAAT-A-TTTAAA-AAATAAT-
1 TATTTATTTTTAAATAATTTTAAATAAA-AATA
* *
1903063 TATTTATTTTTAAA-AATTTTGATTAAAAATA
1 TATTTATTTTTAAATAATTTTAAATAAAAATA
1903094 TATTTATATTTTAAATTAATTTTAAATAAAA
1 TATTTAT-TTTTAAA-TAATTTTAAATAAAA
1903125 TGATAAAATA
Statistics
Matches: 74, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
29 26 0.35
30 18 0.24
31 11 0.15
32 7 0.09
34 12 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TATTTATTTTTAAATAATTTTAAATAAAAATA
Found at i:1903322 original size:37 final size:39
Alignment explanation
Indices: 1903257--1903337 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
1903247 TTACTGTTAA
* *
1903257 ATTAAATTATTATTAGATTATATTTTAATTTAAGTGTAT
1 ATTAAATTATTATTAAATTATATTTTAATTCAAGTGTAT
* *
1903296 ATTAAA-TATT-TTAAATT-TATTTTTAATTCAATTTTAT
1 ATTAAATTATTATTAAATTATA-TTTTAATTCAAGTGTAT
1903333 ATTAA
1 ATTAA
1903338 CTTTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 2 0.05
37 25 0.68
38 4 0.11
39 6 0.16
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (39 bp):
ATTAAATTATTATTAAATTATATTTTAATTCAAGTGTAT
Found at i:1904670 original size:2 final size:2
Alignment explanation
Indices: 1904663--1904697 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1904653 CAAATGGTTC
1904663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1904698 GGACTTGAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1905277 original size:13 final size:13
Alignment explanation
Indices: 1905261--1905285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1905251 AAAATTTGAG
1905261 TTTTTTAAAATTA
1 TTTTTTAAAATTA
1905274 TTTTTTAAAATT
1 TTTTTTAAAATT
1905286 TTTAAATTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAAATTA
Found at i:1906256 original size:23 final size:22
Alignment explanation
Indices: 1906230--1906276 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
1906220 TTGAATCCGA
*
1906230 TATTCATTTATATAATAAATTTT
1 TATTCAATTATAT-ATAAATTTT
* *
1906253 TATTTAATTATATATATATTTT
1 TATTCAATTATATATAAATTTT
1906275 TA
1 TA
1906277 AAAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTCAATTATATATAAATTTT
Found at i:1906963 original size:13 final size:13
Alignment explanation
Indices: 1906926--1906963 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1906916 TTTCGAGTCT
1906926 AATATATAATA-A
1 AATATATAATACA
**
1906938 AATATATTTTACA
1 AATATATAATACA
1906951 AATATATAATACA
1 AATATATAATACA
1906964 TCGATAGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATATAATACA
Found at i:1909555 original size:2 final size:2
Alignment explanation
Indices: 1909550--1909576 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1909540 AAATTGATTT
1909550 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 T
1909577 TTATTTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1909682 original size:32 final size:32
Alignment explanation
Indices: 1909632--1909716 Score: 79
Period size: 32 Copynumber: 2.7 Consensus size: 32
1909622 CATTTAAAAT
* *
1909632 TTATTATTA-AGTTAA-ATATATGTTTTTATTAA
1 TTATTATTATATTTAATATATAT-TTTATATT-A
*
1909664 TTATTATTATATTTAATATTTATTTTATATTA
1 TTATTATTATATTTAATATATATTTTATATTA
*
1909696 TTA-AATTAATATTTAA-ATATA
1 TTATTATT-ATATTTAATATATA
1909717 ATAAAATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 7 0.16
32 21 0.47
33 12 0.27
34 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (32 bp):
TTATTATTATATTTAATATATATTTTATATTA
Found at i:1909685 original size:26 final size:25
Alignment explanation
Indices: 1909656--1909710 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1909646 AATATATGTT
*
1909656 TTTATTA-ATTATTATTATATTTAATA
1 TTTATTATA-TATTATTA-AATTAATA
*
1909682 TTTATTTTATATTATTAAATTAATA
1 TTTATTATATATTATTAAATTAATA
1909707 TTTA
1 TTTA
1909711 AATATAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 11 0.42
26 14 0.54
27 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTATTATATATTATTAAATTAATA
Found at i:1910227 original size:23 final size:24
Alignment explanation
Indices: 1910201--1910245 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1910191 ATGTTACGTT
1910201 AAAATATTTTATT-TATTTTTTAA
1 AAAATATTTTATTATATTTTTTAA
*
1910224 AAAATTTTTTATTATATTTTTT
1 AAAATATTTTATTATATTTTTT
1910246 TATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
AAAATATTTTATTATATTTTTTAA
Found at i:1910953 original size:31 final size:30
Alignment explanation
Indices: 1910917--1910976 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1910907 ATATGTATTA
1910917 TATTATTAATTTTAAATATAAA-ATTAAAACT
1 TATTATTAATTTTAAAT-TAAATA-TAAAACT
* *
1910948 TATTATTGATTTTTAATTAAATATAAAAC
1 TATTATTAATTTTAAATTAAATATAAAAC
1910977 AATTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (30 bp):
TATTATTAATTTTAAATTAAATATAAAACT
Found at i:1911426 original size:20 final size:19
Alignment explanation
Indices: 1911357--1911433 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 19
1911347 TATTTGTATA
*
1911357 TTTATATTTATTTATATTAT
1 TTTAT-TTTATTTTTATTAT
*
1911377 TTTCATGTTATTTTTAATTTAT
1 TTT-ATTTTATTTTT-A-TTAT
**
1911399 ATAAATTTTATTTTTATTAT
1 -TTTATTTTATTTTTATTAT
1911419 GTTTATTTTATTTTT
1 -TTTATTTTATTTTT
1911434 TTCTCATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 26 0.58
21 4 0.09
22 14 0.31
23 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (19 bp):
TTTATTTTATTTTTATTAT
Found at i:1911434 original size:22 final size:22
Alignment explanation
Indices: 1911406--1911506 Score: 66
Period size: 23 Copynumber: 4.5 Consensus size: 22
1911396 TATATAAATT
1911406 TTATTTTTATTATGTTTATTTTA
1 TTATTTTT-TTATGTTTATTTTA
* * *
1911429 TT-TTTTTCTCATGTTCTGTTTAA
1 TTATTTTT-TTATGTT-TATTTTA
1911452 TTATTTTTTTATG-TTATTTTTA
1 TTATTTTTTTATGTTTA-TTTTA
* * * *
1911474 TGTAATATTTTA-ATTTATTATA
1 T-TATTTTTTTATGTTTATTTTA
1911496 -TATTTTTTTAT
1 TTATTTTTTTAT
1911507 AATTTGTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
20 8 0.14
21 1 0.02
22 21 0.36
23 24 0.41
24 5 0.08
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (22 bp):
TTATTTTTTTATGTTTATTTTA
Found at i:1913543 original size:32 final size:32
Alignment explanation
Indices: 1913500--1913594 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
1913490 ATAGACTCGC
1913500 ACCATTATTAATCATGGGACATCTAGGTCGAT
1 ACCATTATTAATCATGGGACATCTAGGTCGAT
*
1913532 ACCATTTTTAATCATGGGACATCTAGGTCGAT
1 ACCATTATTAATCATGGGACATCTAGGTCGAT
1913564 ACCATTATTAATCATGGGACATCTAGGTCGA
1 ACCATTATTAATCATGGGACATCTAGGTCGA
1913595 GTACGACCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (32 bp):
ACCATTATTAATCATGGGACATCTAGGTCGAT
Found at i:1914475 original size:27 final size:27
Alignment explanation
Indices: 1914437--1914488 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
1914427 GTATACGAGA
1914437 ATTTCTTAATAGTATATATTAAATACT
1 ATTTCTTAATAGTATATATTAAATACT
1914464 ATTTCTTAATAGTATATATTAAATA
1 ATTTCTTAATAGTATATATTAAATA
1914489 GTATACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (27 bp):
ATTTCTTAATAGTATATATTAAATACT
Found at i:1914488 original size:14 final size:14
Alignment explanation
Indices: 1914444--1914493 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1914434 AGAATTTCTT
1914444 AATAGTATATATTA
1 AATAGTATATATTA
* * *
1914458 AATACTATTTCTT-
1 AATAGTATATATTA
1914471 AATAGTATATATTA
1 AATAGTATATATTA
1914485 AATAGTATA
1 AATAGTATA
1914494 CGAGAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (14 bp):
AATAGTATATATTA
Found at i:1915054 original size:33 final size:33
Alignment explanation
Indices: 1914983--1915055 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1914973 ATAATATGAA
* * *
1914983 TATATTATACAAATATATAAATATCTTAAAATT
1 TATATAATACAAATATATAAATATATCAAAATT
* *
1915016 AATATAATACAAAT-TATTAATATATCAAAACTT
1 TATATAATACAAATATATAAATATATCAAAA-TT
1915049 TATATAA
1 TATATAA
1915056 ATATAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (33 bp):
TATATAATACAAATATATAAATATATCAAAATT
Found at i:1915061 original size:6 final size:6
Alignment explanation
Indices: 1915050--1915115 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
1915040 TCAAAACTTT
* * * *
1915050 ATATAA ATATAA A-ATAT CT-TAA ATATAA TTAT-G ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1915095 ATAT-A ATATGAA TATATAA AT
1 ATATAA ATAT-AA -ATATAA AT
1915116 TATCATATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
5 14 0.30
6 25 0.54
7 3 0.07
8 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:1915091 original size:17 final size:17
Alignment explanation
Indices: 1915050--1915115 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
1915040 TCAAAACTTT
1915050 ATATAAATATAAA-AT-
1 ATATAAATATAAATATA
* * *
1915065 ATCTTAAATATAATTATG
1 AT-ATAAATATAAATATA
1915083 ATATAAATATAAATATA
1 ATATAAATATAAATATA
1915100 ATATGAATATATAAAT
1 ATAT-AA-ATATAAAT
1915116 TATCATATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
15 2 0.05
16 9 0.22
17 18 0.44
18 4 0.10
19 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (17 bp):
ATATAAATATAAATATA
Found at i:1915694 original size:12 final size:11
Alignment explanation
Indices: 1915673--1915704 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
1915663 CTGCTAACCT
1915673 TAAAAAAAAAA
1 TAAAAAAAAAA
1915684 TAAATAAAAAAA
1 TAAA-AAAAAAA
1915696 TAAAAAAAA
1 TAAAAAAAA
1915705 TTCTTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:1915817 original size:22 final size:21
Alignment explanation
Indices: 1915792--1915840 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
1915782 ATAGTCATGA
1915792 TATAAAATTATAATTATTATTT
1 TATAAAATTATAATTATTA-TT
** * *
1915814 TATAATTTTATTATTTTTATT
1 TATAAAATTATAATTATTATT
1915835 TATAAA
1 TATAAA
1915841 TATTTATTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATAAAATTATAATTATTATT
Found at i:1916010 original size:7 final size:7
Alignment explanation
Indices: 1916000--1916024 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1915990 TTTATATGAT
1916000 ATATTAA
1 ATATTAA
1916007 ATATTAA
1 ATATTAA
1916014 ATATTAA
1 ATATTAA
1916021 ATAT
1 ATAT
1916025 ATTATAATAT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATTAA
Found at i:1916037 original size:23 final size:22
Alignment explanation
Indices: 1915998--1916056 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
1915988 AATTTATATG
*
1915998 ATATATTA-AATATTAAATATTAA
1 ATATATTATAATA-TAAA-AATAA
1916021 ATATATTATAATATAAAAATAA
1 ATATATTATAATATAAAAATAA
1916043 ATA-A-TATAA-ATAAA
1 ATATATTATAATATAAA
1916057 CAAGACATCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 1 0.03
22 7 0.21
23 12 0.35
24 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATATTATAATATAAAAATAA
Found at i:1916449 original size:3 final size:3
Alignment explanation
Indices: 1916438--1916467 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1916428 TGAAGAAGAA
*
1916438 GCT GAT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1916468 CCTCAGCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:1917646 original size:2 final size:2
Alignment explanation
Indices: 1917641--1917688 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1917631 GTCGCTGGGA
*
1917641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1917683 AT AT AT
1 AT AT AT
1917689 GTATGATGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1918675 original size:17 final size:17
Alignment explanation
Indices: 1918654--1918693 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1918644 GATTTTTAGA
*
1918654 ATTTTTTCT-AATTTTT
1 ATTTTTTTTGAATTTTT
*
1918670 CTTTTTTTTGAATTTTT
1 ATTTTTTTTGAATTTTT
1918687 ATTTTTT
1 ATTTTTT
1918694 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (17 bp):
ATTTTTTTTGAATTTTT
Found at i:1918697 original size:13 final size:13
Alignment explanation
Indices: 1918681--1918705 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1918671 TTTTTTTTGA
1918681 ATTTTTATTTTTT
1 ATTTTTATTTTTT
1918694 ATTTTTATTTTT
1 ATTTTTATTTTT
1918706 AATTATTTAA
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:1926355 original size:12 final size:12
Alignment explanation
Indices: 1926338--1926363 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1926328 TTGCTTTCTT
1926338 TTCTTTCAAATG
1 TTCTTTCAAATG
1926350 TTCTTTCAAATG
1 TTCTTTCAAATG
1926362 TT
1 TT
1926364 AATATAGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCTTTCAAATG
Found at i:1926959 original size:22 final size:23
Alignment explanation
Indices: 1926920--1926962 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1926910 ATTAGATATT
*
1926920 TTAATTTTAATATATTTATTTTA
1 TTAATTTTAAAATATTTATTTTA
*
1926943 TTAA-TTTAAAATTTTTATTT
1 TTAATTTTAAAATATTTATTT
1926963 AAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAATTTTAAAATATTTATTTTA
Found at i:1928396 original size:123 final size:123
Alignment explanation
Indices: 1928087--1928384 Score: 336
Period size: 123 Copynumber: 2.4 Consensus size: 123
1928077 GAAGCACCAC
* * * * *
1928087 CAACGCCATCTCCAACCTCAACAGCAACAGCCCCAGCCCTGATCCTA-CTGAATTCGGGCAAGCG
1 CAACACCATCTCCATCCTCTACAGCAACAGCCCCAGCTCTGGTCCTATC-GAATTCGGGCAAGCG
* * **
1928151 TATTGATAGGATGAGCAGTAGCCTCTCCACTTCCAGTTCTGGTTATACGGAACACTCGG
65 TATTGACAGGATGAGCAGTAGCCTCACCACTTCCAGTTCTGGTTATACGGAACACTCAA
* * * * * *
1928210 CAACACCGTCACCTTCCTCTATAGCAA-TGTCCCCAGCTCTGGTCCTATCCAATTCGGGCAAGCG
1 CAACACCATCTCCATCCTCTACAGCAACAG-CCCCAGCTCTGGTCCTATCGAATTCGGGCAAGCG
** * *
1928274 TATTGACAGGATGTTCAGTAGCCTCACCAGTTCCAGTTCTGG-TACT-GGAGAAGC-CTCAA
65 TATTGACAGGATGAGCAGTAGCCTCACCACTTCCAGTTCTGGTTA-TACG-GAA-CACTCAA
*
1928333 CAACACCATCTCCATCGTCTACAGCAACAGCCCCAGCTCTGGTCCTATCGAA
1 CAACACCATCTCCATCCTCTACAGCAACAGCCCCAGCTCTGGTCCTATCGAA
1928385 CTCTGGGAAG
Statistics
Matches: 143, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
122 4 0.03
123 136 0.95
124 3 0.02
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (123 bp):
CAACACCATCTCCATCCTCTACAGCAACAGCCCCAGCTCTGGTCCTATCGAATTCGGGCAAGCGT
ATTGACAGGATGAGCAGTAGCCTCACCACTTCCAGTTCTGGTTATACGGAACACTCAA
Found at i:1930628 original size:31 final size:31
Alignment explanation
Indices: 1930593--1930655 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1930583 ACCTGTGTTC
1930593 AATGTATATTTGGACAAGGAATGTGGATATG
1 AATGTATATTTGGACAAGGAATGTGGATATG
1930624 AATGTATATTTGGACAAGGAATGTGGATATG
1 AATGTATATTTGGACAAGGAATGTGGATATG
1930655 A
1 A
1930656 GTATGACCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.32
Consensus pattern (31 bp):
AATGTATATTTGGACAAGGAATGTGGATATG
Found at i:1933973 original size:18 final size:18
Alignment explanation
Indices: 1933927--1933975 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
1933917 AAAATTCATA
*
1933927 TTTATTAATTAATAAAAT
1 TTTATTAATAAATAAAAT
* * *
1933945 TTAATT-TTAAATTAAAT
1 TTTATTAATAAATAAAAT
1933962 TTTATTAATAAATA
1 TTTATTAATAAATA
1933976 GTTATTATCT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATTAATAAATAAAAT
Found at i:1934505 original size:10 final size:12
Alignment explanation
Indices: 1934458--1934515 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 12
1934448 ATTAATTAAA
1934458 AATAAAAT-A-T
1 AATAAAATAATT
1934468 AATAAAATAATTTT
1 AATAAAATAA--TT
1934482 AATATAAA-AATT
1 AATA-AAATAATT
1934494 -A-AAAATAATT
1 AATAAAATAATT
1934504 AATAAAATAATT
1 AATAAAATAATT
1934516 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 3 0.08
10 13 0.32
11 3 0.08
12 11 0.28
14 7 0.17
15 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAAAATAATT
Found at i:1935267 original size:22 final size:21
Alignment explanation
Indices: 1935226--1935277 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1935216 TTTTTAATAC
* *
1935226 TTTAATATATTATAATATAAA
1 TTTAATATATAATAAAATAAA
1935247 TTTAATATTATAATAAAATAAA
1 TTTAATA-TATAATAAAATAAA
*
1935269 -TAAATATAT
1 TTTAATATAT
1935278 CAAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 12 0.44
22 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAATATATAATAAAATAAA
Found at i:1935526 original size:228 final size:215
Alignment explanation
Indices: 1935263--1935672 Score: 493
Period size: 215 Copynumber: 1.8 Consensus size: 215
1935253 ATTATAATAA
* * *
1935263 AATAAATAAATATATCAAAATTTTTAAAAAATAAATTTTTAACATATTAAAAATAATATAAATAT
1 AATAAATAAATATATAAAAATTTATAAAAAATAAATTATTAACATATT-AAAATAATATAAATAT
* ** * * ** *
1935328 ATAATATTTTAAATACGATTATGATA-TTAAAAATAATATTAGTACA-ACACGATGATATGTGAT
65 AAAATACATTAAAT-CGATTAT-A-ACGTAAAAATAATA-T-GAACATA-A--AAAAT-TATGAT
*
1935391 ACAAAATTTAAAAATTATTTAAATATTATCAATTAAATTTGATAATTTTAAATAT-AATATAATT
121 ---AAATTTAAAAA-TA-TTAAATAATATCAATTAAATTTGATAATTTTAAATATCAA-ATAATT
1935455 ATACAACAAGATACAAAAATTATAAAATATGACATG
180 ATACAACAAGATACAAAAATTATAAAATATGACATG
* * * *
1935491 AATAGATAAATATATAAAAATTTATATAAAATAAATTATTAATATATTAAAATTATATAAATATA
1 AATAAATAAATATATAAAAATTTATAAAAAATAAATTATTAACATATTAAAATAATATAAATATA
*
1935556 AAATACATTAGATCGATTATAACGTAAAAATAATATGAACATAAAAAATTATGATAAATTTAAAA
66 AAATACATTAAATCGATTATAACGTAAAAATAATATGAACATAAAAAATTATGATAAATTTAAAA
*
1935621 ATATTAAATAATATCAATTAAATTTTATAATTTTAAATATCAAATAATTATA
131 ATATTAAATAATATCAATTAAATTTGATAATTTTAAATATCAAATAATTATA
1935673 TGATATAAAT
Statistics
Matches: 161, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
215 44 0.27
216 4 0.02
217 11 0.07
220 5 0.03
221 3 0.02
223 5 0.03
224 3 0.02
225 12 0.07
226 7 0.04
227 25 0.16
228 42 0.26
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (215 bp):
AATAAATAAATATATAAAAATTTATAAAAAATAAATTATTAACATATTAAAATAATATAAATATA
AAATACATTAAATCGATTATAACGTAAAAATAATATGAACATAAAAAATTATGATAAATTTAAAA
ATATTAAATAATATCAATTAAATTTGATAATTTTAAATATCAAATAATTATACAACAAGATACAA
AAATTATAAAATATGACATG
Found at i:1935543 original size:17 final size:16
Alignment explanation
Indices: 1935502--1935559 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
1935492 ATAGATAAAT
1935502 ATATAAAAATTTATATAA
1 ATAT-AAAA-TTATATAA
1935520 A-AT-AAATTAT-TAA
1 ATATAAAATTATATAA
1935533 TATATTAAAATTATATAA
1 -ATA-TAAAATTATATAA
1935551 ATATAAAAT
1 ATATAAAAT
1935560 ACATTAGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 5 0.14
15 4 0.11
16 7 0.20
17 12 0.34
18 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAAATTATATAA
Found at i:1935704 original size:22 final size:22
Alignment explanation
Indices: 1935679--1935756 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
1935669 TATATGATAT
1935679 AAATATAATATAAAAATAATTA
1 AAATATAATATAAAAATAATTA
* *
1935701 AAATATTATAT-AAAAT--TAA
1 AAATATAATATAAAAATAATTA
*
1935720 AAATATAAT-TACATAATATATTA
1 AAATATAATATA-AAAATA-ATTA
*
1935743 AAAT-TTATATAAAA
1 AAATATAATATAAAA
1935757 TAAATCATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
18 1 0.02
19 10 0.23
20 4 0.09
21 5 0.12
22 15 0.35
23 8 0.19
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATATAATATAAAAATAATTA
Found at i:1935724 original size:41 final size:41
Alignment explanation
Indices: 1935679--1935757 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 41
1935669 TATATGATAT
1935679 AAATATAATATA-AAAATA-ATTAAAATATTATATAAAATTAA
1 AAATATAAT-TACAAAATATATTAAAAT-TTATATAAAATTAA
*
1935720 AAATATAATTACATAATATATTAAAATTTATATAAAAT
1 AAATATAATTACAAAATATATTAAAATTTATATAAAAT
1935758 AAATCATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 2 0.06
41 25 0.71
42 8 0.23
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (41 bp):
AAATATAATTACAAAATATATTAAAATTTATATAAAATTAA
Found at i:1935728 original size:30 final size:29
Alignment explanation
Indices: 1935690--1935747 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
1935680 AATATAATAT
1935690 AAAAATAATTA-A-AATATTATATAAAATTA
1 AAAAATAATTACATAATA-TAT-TAAAATTA
1935719 AAAATATAATTACATAATATATTAAAATT
1 AAAA-ATAATTACATAATATATTAAAATT
1935748 TATATAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 4 0.15
30 14 0.54
31 4 0.15
32 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAAATAATTACATAATATATTAAAATTA
Found at i:1935805 original size:16 final size:15
Alignment explanation
Indices: 1935782--1935837 Score: 71
Period size: 16 Copynumber: 3.7 Consensus size: 15
1935772 TCAAAATTTA
1935782 TATAAATATATAATAT
1 TATAAATATA-AATAT
*
1935798 TTTAAATATAATATAT
1 TATAAATATAA-ATAT
1935814 TATAAA-A-AAATAT
1 TATAAATATAAATAT
1935827 TATAAATATAA
1 TATAAATATAA
1935838 TATAAATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 10 0.29
14 3 0.09
15 4 0.11
16 18 0.51
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATAAATATAAATAT
Found at i:1935811 original size:27 final size:27
Alignment explanation
Indices: 1935781--1935864 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
1935771 ATCAAAATTT
* *
1935781 ATATAAATATATAATATTTTAAATATA
1 ATATAAATAAATAATATTATAAATATA
* *
1935808 ATATATTATAAAAAAATATTATAAATATA
1 ATATA-AAT-AAATAATATTATAAATATA
* * *
1935837 ATATAAATACATAAAATTATAAAAATA
1 ATATAAATAAATAATATTATAAATATA
1935864 A
1 A
1935865 CTAACACTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 21 0.46
28 4 0.09
29 21 0.46
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATAAATAAATAATATTATAAATATA
Found at i:1935852 original size:29 final size:28
Alignment explanation
Indices: 1935781--1935853 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
1935771 ATCAAAATTT
* *
1935781 ATATAAAT-ATATAATATTTTAAATATA
1 ATATAAATAATAAAATATTATAAATATA
* *
1935808 ATATATTATAAAAAAATATTATAAATATA
1 ATATA-AATAATAAAATATTATAAATATA
1935837 ATATAAATACATAAAAT
1 ATATAAATA-ATAAAAT
1935854 TATAAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
27 5 0.14
28 5 0.14
29 27 0.73
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAAATAATAAAATATTATAAATATA
Found at i:1935862 original size:29 final size:29
Alignment explanation
Indices: 1935749--1935863 Score: 71
Period size: 29 Copynumber: 4.1 Consensus size: 29
1935739 ATTAAAATTT
* * * *
1935749 ATATAAAATAAAT-CATTAATTTATCAAA
1 ATATAATATAAATACATAAAATTATAAAA
* * * *
1935777 AT-TTATATAAATATATAATATT-T-TAA
1 ATATAATATAAATACATAAAATTATAAAA
* * *
1935803 ATATAATATATTATA-A-AAAAATATTATAA
1 ATATAATATA-AATACATAAAATTA-TAAAA
1935832 ATATAATATAAATACATAAAATTATAAAA
1 ATATAATATAAATACATAAAATTATAAAA
1935861 ATA
1 ATA
1935864 ACTAACACTT
Statistics
Matches: 65, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
26 8 0.12
27 16 0.25
28 14 0.22
29 21 0.32
30 6 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
ATATAATATAAATACATAAAATTATAAAA
Found at i:1936939 original size:23 final size:22
Alignment explanation
Indices: 1936905--1936989 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 22
1936895 TCGGGATTAA
* * *
1936905 AATATTTGAATTAATTTAGTTT
1 AATATTTAAATTAATTAAATTT
*
1936927 GATCATTTAAATTAATTAAATTT
1 AAT-ATTTAAATTAATTAAATTT
1936950 AATATTTAAATTAA--AAATTT
1 AATATTTAAATTAATTAAATTT
1936970 AAATTATTTTAAATTAATTA
1 -AA-TA-TTTAAATTAATTA
1936990 TTTAAATTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
20 6 0.12
21 2 0.04
22 15 0.29
23 28 0.54
25 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (22 bp):
AATATTTAAATTAATTAAATTT
Found at i:1936992 original size:36 final size:35
Alignment explanation
Indices: 1936931--1936998 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
1936921 TAGTTTGATC
1936931 ATTTAAATTAATTAAATTTAATATTTAAATTAAAA
1 ATTTAAATTAATTAAATTTAATATTTAAATTAAAA
*
1936966 ATTTAAATTATTTTAAA-TTAATTATTTAAATTA
1 ATTTAAATTA-ATTAAATTTAA-TATTTAAATTA
1936999 TTTTGAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (35 bp):
ATTTAAATTAATTAAATTTAATATTTAAATTAAAA
Found at i:1936998 original size:13 final size:12
Alignment explanation
Indices: 1936931--1936998 Score: 65
Period size: 13 Copynumber: 5.8 Consensus size: 12
1936921 TAGTTTGATC
1936931 ATTTAAATT-A-
1 ATTTAAATTAAT
1936941 A-TTAAATTTAAT
1 ATTTAAA-TTAAT
*
1936953 ATTTAAATTAAAA
1 ATTTAAATT-AAT
1936966 ATTTAAATT-AT
1 ATTTAAATTAAT
1936977 -TTTAAATTAATT
1 ATTTAAATTAA-T
1936989 ATTTAAATTA
1 ATTTAAATTA
1936999 TTTTGAGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
9 5 0.10
10 11 0.23
11 3 0.06
12 4 0.08
13 25 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAAATTAAT
Found at i:1937009 original size:23 final size:23
Alignment explanation
Indices: 1936932--1937002 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1936922 AGTTTGATCA
1936932 TTTAAATTAATTAAATTT-AA-TA-
1 TTTAAATTAATT--ATTTAAATTAT
**
1936954 TTTAAATTAAAAATTTAAATTAT
1 TTTAAATTAATTATTTAAATTAT
1936977 TTTAAATTAATTATTTAAATTAT
1 TTTAAATTAATTATTTAAATTAT
1937000 TTT
1 TTT
1937003 GAGTTAAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.10
21 2 0.05
22 12 0.29
23 24 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTAAATTAATTATTTAAATTAT
Found at i:1937667 original size:2 final size:2
Alignment explanation
Indices: 1937660--1937685 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1937650 GACTATAAAA
1937660 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
1937686 TCTTTTAATT
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:1942125 original size:19 final size:21
Alignment explanation
Indices: 1942085--1942125 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1942075 TTTAAAATAT
*
1942085 TTAATATAAAATGAAAATAAA
1 TTAATAAAAAATGAAAATAAA
1942106 TTAATAAAAAAT-AAAA-AAA
1 TTAATAAAAAATGAAAATAAA
1942125 T
1 T
1942126 AAATGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
TTAATAAAAAATGAAAATAAA
Found at i:1942512 original size:21 final size:20
Alignment explanation
Indices: 1942483--1942523 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1942473 AACATTAAAA
1942483 AATAATTTTAT-ATTAATATT
1 AATAATTTTATAATT-ATATT
1942503 AATATATTTTATAATTATATT
1 AATA-ATTTTATAATTATATT
1942524 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 12 0.63
22 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATAATTTTATAATTATATT
Found at i:1942999 original size:2 final size:2
Alignment explanation
Indices: 1942986--1943070 Score: 57
Period size: 2 Copynumber: 42.0 Consensus size: 2
1942976 AATTATAATT
* * **
1942986 TA TA TG TA TA TA TA AA TA TA -A GTA TA TA TA TA TA TA TA GGG T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA
* * * *
1943028 TT TA GCA TA TA TA TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1943071 CTAAAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
1 2 0.03
2 60 0.94
3 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1943274 original size:19 final size:18
Alignment explanation
Indices: 1943250--1943294 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
1943240 TTTTATTAAT
1943250 TTTAATTAAAATATATAAA
1 TTTAATTAAAATATAT-AA
**
1943269 TTTAATTAATTTATATAA
1 TTTAATTAAAATATATAA
1943287 -TTAATTAA
1 TTTAATTAA
1943295 TATTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 2 0.08
19 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAATATATAA
Found at i:1943299 original size:19 final size:18
Alignment explanation
Indices: 1943251--1943309 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
1943241 TTTATTAATT
*
1943251 TTAATTAAA-ATATATAAA
1 TTAATTAAATTTATAT-AA
1943269 TTTAATT-AATTTATATAA
1 -TTAATTAAATTTATATAA
1943287 TTAATTAATATTTA-ATAAA
1 TTAATTAA-ATTTATAT-AA
1943306 TTAA
1 TTAA
1943310 AAAAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 6 0.17
18 7 0.20
19 22 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAATTTATATAA
Found at i:1943635 original size:24 final size:24
Alignment explanation
Indices: 1943614--1943675 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
1943604 AAAGTTTAGT
*
1943614 TATTAAATTAATAATTTTTTTAAA
1 TATTAAATTAAAAATTTTTTTAAA
* *
1943638 TATTAAATTAAAAATTATATTAAA
1 TATTAAATTAAAAATTTTTTTAAA
1943662 -ATATAACATTAAAA
1 TAT-TAA-ATTAAAA
1943676 TAAATATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.06
24 24 0.73
25 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTAAATTAAAAATTTTTTTAAA
Found at i:1943721 original size:19 final size:19
Alignment explanation
Indices: 1943658--1943723 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
1943648 AAAATTATAT
*
1943658 TAAAATAT-AACATTAAAA
1 TAAAATATAAATATTAAAA
* *
1943676 T-AAATATTTAAT-TTAATTA
1 TAAAATA-TAAATATTAA-AA
1943695 TAAAAATATAAATATTAAAA
1 T-AAAATATAAATATTAAAA
1943715 TAAAATATA
1 TAAAATATA
1943724 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
17 5 0.13
18 6 0.16
19 12 0.32
20 6 0.16
21 9 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAATATAAATATTAAAA
Found at i:1943722 original size:13 final size:13
Alignment explanation
Indices: 1943654--1943722 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 13
1943644 ATTAAAAATT
*
1943654 ATATTAAAATATA
1 ATATTAAAATAAA
*
1943667 ACATTAAAAT-AA
1 ATATTAAAATAAA
* * *
1943679 ATATTTAATTTAA
1 ATATTAAAATAAA
* *
1943692 TTATAAAAATATAA
1 ATATTAAAATA-AA
1943706 ATATTAAAATAAA
1 ATATTAAAATAAA
1943719 ATAT
1 ATAT
1943723 ATTTTTTTAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 8 0.19
13 23 0.55
14 11 0.26
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTAAAATAAA
Found at i:1944089 original size:17 final size:17
Alignment explanation
Indices: 1944067--1944102 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1944057 AAAAAAATTA
1944067 TAATTCTTTTATTATTT
1 TAATTCTTTTATTATTT
1944084 TAATTCTTTTATTATTT
1 TAATTCTTTTATTATTT
1944101 TA
1 TA
1944103 TCTTTCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TAATTCTTTTATTATTT
Found at i:1944330 original size:18 final size:16
Alignment explanation
Indices: 1944315--1944354 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1944305 TAAATTTTCA
1944315 TATAAAAATAATTTTT
1 TATAAAAATAATTTTT
*
1944331 TTTAAAAATAATTTATT
1 TATAAAAATAATTT-TT
*
1944348 AATAAAA
1 TATAAAA
1944355 TAGATTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAAAAATAATTTTT
Found at i:1948649 original size:88 final size:91
Alignment explanation
Indices: 1948501--1948666 Score: 216
Period size: 88 Copynumber: 1.9 Consensus size: 91
1948491 AATTCTATAT
* *
1948501 ACTAAAATTATTGGTTGAGAAATTCAACTTCATTCTTTAATAAATAGATTGATTGATTTTATAAA
1 ACTAAAATTATTGGTTGAGAAATTCAACTTCATTCTTTAACAAATAAATTGATTGATTTTATAAA
*
1948566 TTAAATCA-TTTTCATAATTTTATGG
66 CTAAATCACTTTTCATAATTTTATGG
* * * *
1948591 ACTAAAATT-TTGGTT-TGAAATTCAATTTTATT-TTCTAACAAATAAATT-ATTTGATTTTATG
1 ACTAAAATTATTGGTTGAGAAATTCAACTTCATTCTT-TAACAAATAAATTGA-TTGATTTTATA
1948652 AACTAAATCACTTTT
64 AACTAAATCACTTTT
1948667 AAATCATTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
87 3 0.05
88 44 0.67
89 10 0.15
90 9 0.14
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (91 bp):
ACTAAAATTATTGGTTGAGAAATTCAACTTCATTCTTTAACAAATAAATTGATTGATTTTATAAA
CTAAATCACTTTTCATAATTTTATGG
Found at i:1949102 original size:22 final size:24
Alignment explanation
Indices: 1949072--1949135 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 24
1949062 TTAAATTTAA
1949072 AAATAATTTAATTTAAT-TAATT-T
1 AAAT-ATTTAATTTAATATAATTAT
*
1949095 AAATATTT-A-TTAATATATTTAT
1 AAATATTTAATTTAATATAATTAT
* *
1949117 AAATATTAAATTTTATATA
1 AAATATTTAATTTAATATA
1949136 TTTTTAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 5 0.15
22 12 0.35
23 5 0.15
24 7 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATATTTAATTTAATATAATTAT
Found at i:1950863 original size:5 final size:5
Alignment explanation
Indices: 1950853--1950978 Score: 51
Period size: 5 Copynumber: 27.0 Consensus size: 5
1950843 ATATATTTAT
*
1950853 AATTA AATT- AATTA AA-TA AATTA ATTTA AATT- -ATTA AA--A AATTTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA-TTA
** ** * * * *
1950898 TTTTA AATTTA TTTTA ATTTA ATTTAA AATT- TATAA AATTA AA-TA AA-T-
1 AATTA AA-TTA AATTA AATTA AATT-A AATTA AATTA AATTA AATTA AATTA
*
1950946 AATTA AATTA AATT- AATT- AATTA ATTTA AATTA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA
1950979 TTAAAAATTT
Statistics
Matches: 92, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
3 8 0.09
4 24 0.26
5 52 0.57
6 8 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
AATTA
Found at i:1950878 original size:22 final size:22
Alignment explanation
Indices: 1950852--1950976 Score: 70
Period size: 22 Copynumber: 5.8 Consensus size: 22
1950842 TATATATTTA
1950852 TAATTAAATTAATTAAATAAAT
1 TAATTAAATTAATTAAATAAAT
1950874 TAATTTAAATT-ATTAAA-AAATT
1 TAA-TTAAATTAATTAAATAAA-T
* * * *
1950896 TATTTTAAATTTATT--TTAATT
1 TA-ATTAAATTAATTAAATAAAT
* *
1950917 TAATTTAA--AATT-TATAAAAT
1 TAATTAAATTAATTAAAT-AAAT
*
1950937 TAAATAAA-TAATTAAATTAAAT
1 TAATTAAATTAATTAAA-TAAAT
1950959 TAATT-AATTAATTTAAAT
1 TAATTAAATTAA-TTAAAT
1950977 TATTAAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 13 0.16
21 12 0.15
22 34 0.43
23 16 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTAAATTAATTAAATAAAT
Found at i:1950905 original size:11 final size:11
Alignment explanation
Indices: 1950891--1950931 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1950881 AATTATTAAA
1950891 AAATTTATTTT
1 AAATTTATTTT
1950902 AAATTTATTTT
1 AAATTTATTTT
*
1950913 -AATTTAATTTA
1 AAATTT-ATTTT
1950924 AAATTTAT
1 AAATTTAT
1950932 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 5 0.19
11 17 0.63
12 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
AAATTTATTTT
Found at i:1950922 original size:43 final size:42
Alignment explanation
Indices: 1950871--1951005 Score: 121
Period size: 45 Copynumber: 3.0 Consensus size: 42
1950861 TAATTAAATA
1950871 AATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTT
1 AATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTT
* ** * *
1950913 AATTTAATTTAAAATTTATAAAATTAAATAAATAATTAAATTAAATTAATT
1 AA-TTAATTT-AAA-TTATTAAA--AAATTTAT-TTTAAATT-TATT--TT
*
1950964 AATTAATTTAAATTATT-AAAAATTTATTTT-AATTTAATTT
1 AATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTT
1951004 AA
1 AA
1951006 AATTTATAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
40 4 0.05
42 4 0.05
43 11 0.15
44 5 0.07
45 13 0.18
47 8 0.11
48 11 0.15
49 6 0.08
50 7 0.10
51 4 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
AATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTT
Found at i:1950937 original size:21 final size:21
Alignment explanation
Indices: 1950873--1950937 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
1950863 ATTAAATAAA
* *
1950873 TTAATTTAAATTATTAAAAAAT
1 TTAATTTAAAAT-TTATAAAAT
* **
1950895 TT-ATTTTAAATTTATTTTAAT
1 TTAATTTAAAATTTA-TAAAAT
1950916 TTAATTTAAAATTTATAAAAT
1 TTAATTTAAAATTTATAAAAT
1950937 T
1 T
1950938 AAATAAATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.09
21 17 0.52
22 13 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTAATTTAAAATTTATAAAAT
Found at i:1950949 original size:21 final size:21
Alignment explanation
Indices: 1950925--1951032 Score: 73
Period size: 20 Copynumber: 5.3 Consensus size: 21
1950915 TTTAATTTAA
1950925 AATTTATAAAATTAAATAAAT
1 AATTTATAAAATTAAATAAAT
* * * *
1950946 AATTAAATTAAATTAATTAATT
1 AATT-TATAAAATTAAATAAAT
* *
1950968 AATTTA-AATTATTAAA-AATT
1 AATTTATAA-AATTAAATAAAT
* * * *
1950988 TATTT-T-AATTTAATTTAA-
1 AATTTATAAAATTAAATAAAT
1951006 AATTTATAAAATTAAATAAAT
1 AATTTATAAAATTAAATAAAT
1951027 AATTTA
1 AATTTA
1951033 ATTCATAAAT
Statistics
Matches: 62, Mismatches: 18, Indels: 14
0.66 0.19 0.15
Matches are distributed among these distances:
18 8 0.13
19 3 0.05
20 18 0.29
21 16 0.26
22 17 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTATAAAATTAAATAAAT
Found at i:1950972 original size:76 final size:78
Alignment explanation
Indices: 1950857--1951035 Score: 256
Period size: 81 Copynumber: 2.3 Consensus size: 78
1950847 ATTTATAATT
* *
1950857 AAATTAATTAAATAAATTAATTTAAATTATTAAAAAATTT-ATT-TT-AAATTTATTTTAATTTA
1 AAATTAAATAAAT-AATTAAATTAAATTATTAAAAAATTTAATTATTAAAATTTATTTTAATTTA
1950919 ATTTAAAATTTATA
65 ATTTAAAATTTATA
**
1950933 AAATTAAATAAATAATTAAATTAAATTAATTAATTAATTTAAATTATTAAAAATTTATTTTAATT
1 AAATTAAATAAATAATTAAATTAAATT-ATTAAAAAATTT-AATTATT-AAAATTTATTTTAATT
1950998 TAATTTAAAATTTATA
63 TAATTTAAAATTTATA
*
1951014 AAATTAAATAAATAATTTAATT
1 AAATTAAATAAATAATTAAATT
1951036 CATAAATAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
75 13 0.14
76 22 0.24
78 3 0.03
79 2 0.02
81 52 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (78 bp):
AAATTAAATAAATAATTAAATTAAATTATTAAAAAATTTAATTATTAAAATTTATTTTAATTTAA
TTTAAAATTTATA
Found at i:1951033 original size:38 final size:38
Alignment explanation
Indices: 1950910--1951035 Score: 130
Period size: 38 Copynumber: 3.2 Consensus size: 38
1950900 TTAAATTTAT
1950910 TTTAATTTAATTTAAAATTTATAAAATTAAATAAATAA
1 TTTAATTTAATTTAAAATTTATAAAATTAAATAAATAA
* * * * *
1950948 TTAAATTAAATTAATTAATTAATTTA-AATTATTAAA-AATTTAT
1 TTTAATTTAA-T--TTAA--AATTTATAA-AATTAAATAA-ATAA
1950991 TTTAATTTAATTTAAAATTTATAAAATTAAATAAATAA
1 TTTAATTTAATTTAAAATTTATAAAATTAAATAAATAA
1951029 TTTAATT
1 TTTAATT
1951036 CATAAATAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
38 29 0.42
39 5 0.07
40 4 0.06
41 4 0.06
42 5 0.07
43 22 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
TTTAATTTAATTTAAAATTTATAAAATTAAATAAATAA
Found at i:1951047 original size:93 final size:92
Alignment explanation
Indices: 1950851--1951025 Score: 243
Period size: 93 Copynumber: 1.9 Consensus size: 92
1950841 ATATATATTT
* *
1950851 ATAATTAAATT-AATTAAATAAATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTTAA
1 ATAATTAAATTAAATT-AATTAATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTAAA
*
1950915 TTTAATTTAAAATTTATAAAATTAAATAA
65 TTTAA-TTAAAATTAATAAAATTAAATAA
1950944 ATAATTAAATTAAATTAATTAATTAATTTAAATTATT-AAAAATTTATTTT-AATTTAATTTAAA
1 ATAATTAAATTAAATTAATTAATTAATTTAAATTATTAAAAAATTTATTTTAAATTT-ATTT-AA
1951007 ATTT-A-TAAAATTAAATAAA
64 ATTTAATTAAAATT-AATAAA
1951026 TAATTTAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
90 7 0.09
91 10 0.13
92 18 0.24
93 36 0.48
94 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (92 bp):
ATAATTAAATTAAATTAATTAATTAATTTAAATTATTAAAAAATTTATTTTAAATTTATTTAAAT
TTAATTAAAATTAATAAAATTAAATAA
Found at i:1951051 original size:81 final size:82
Alignment explanation
Indices: 1950902--1951056 Score: 251
Period size: 81 Copynumber: 1.9 Consensus size: 82
1950892 AATTTATTTT
* *
1950902 AAATTTATTTTAATTTAATTTAAAATTTATAAAATTAAATAAATAATTAAATTAAATTAATTAAT
1 AAATTTATTTTAATTTAATTTAAAATTTATAAAATTAAATAAATAATTAAATTAAATAAATAAAT
1950967 TAAT-TTAAATTATTAA
66 TAATATTAAATTATTAA
* *
1950983 AAATTTATTTTAATTTAATTTAAAATTTATAAAATTAAATAAATAATTTAATT-CATAAATAAAT
1 AAATTTATTTTAATTTAATTTAAAATTTATAAAATTAAATAAATAATTAAATTAAATAAATAAA-
1951047 TTAATATTAA
65 TTAATATTAA
1951057 TTTTTTAATT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
80 7 0.10
81 57 0.84
82 4 0.06
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (82 bp):
AAATTTATTTTAATTTAATTTAAAATTTATAAAATTAAATAAATAATTAAATTAAATAAATAAAT
TAATATTAAATTATTAA
Found at i:1951341 original size:20 final size:20
Alignment explanation
Indices: 1951316--1951359 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1951306 TTTGAATCCG
* * *
1951316 AATTATTATTTATTTATATT
1 AATTATAATATATTAATATT
1951336 AATTATAATATATTAATATT
1 AATTATAATATATTAATATT
1951356 AATT
1 AATT
1951360 TTTTAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTATAATATATTAATATT
Found at i:1951768 original size:58 final size:58
Alignment explanation
Indices: 1951693--1951808 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
1951683 GAGATGTATA
*
1951693 CTTTAAATATGTCTAATAAATAATAAATAAAACTTATATCATTTTATTAACTTCACTT
1 CTTTAAATATGTCTAATAAATAATAAATAAAACTTATATCACTTTATTAACTTCACTT
* * * * *
1951751 CTTTAAATATTTTTAATATATAATAAATAAAATTTATATCACTTTATTAACTTTACTT
1 CTTTAAATATGTCTAATAAATAATAAATAAAACTTATATCACTTTATTAACTTCACTT
1951809 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.42, C:0.10, G:0.01, T:0.47
Consensus pattern (58 bp):
CTTTAAATATGTCTAATAAATAATAAATAAAACTTATATCACTTTATTAACTTCACTT
Found at i:1956068 original size:2 final size:2
Alignment explanation
Indices: 1956061--1956085 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1956051 TTCGAAGCTT
1956061 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 T
1956086 TCTGAACTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1957822 original size:36 final size:35
Alignment explanation
Indices: 1957731--1957822 Score: 80
Period size: 36 Copynumber: 2.6 Consensus size: 35
1957721 AATAAAAAAA
*
1957731 TATTTATTTT-GTAATAAATAAATAAATAAATAATT
1 TATTTATTTTAATAATAAA-AAATAAATAAATAATT
* ** * *
1957766 TATATTAATTTAATTCT-AAAAATATTATAAATATTTT
1 TAT-TTATTTTAATAATAAAAAATA-AATAAATA-ATT
1957803 TATTTATTTTAATAATAAAA
1 TATTTATTTTAATAATAAAA
1957823 GGCTAATTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
35 8 0.19
36 25 0.58
37 10 0.23
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
TATTTATTTTAATAATAAAAAATAAATAAATAATT
Found at i:1964048 original size:27 final size:27
Alignment explanation
Indices: 1963990--1964055 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
1963980 ACAATTTGTG
*
1963990 TTTGTCAAAAATGGTGGTTCCTTTATG
1 TTTGTCAAAAATGGTGGTTCCTTTATA
* * * *
1964017 CTTGTAAAAAATGGTGGTTCTTTTTTA
1 TTTGTCAAAAATGGTGGTTCCTTTATA
1964044 TTTGTCAAAAAT
1 TTTGTCAAAAAT
1964056 AATAACTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTCCTTTATA
Found at i:1967063 original size:17 final size:18
Alignment explanation
Indices: 1967034--1967068 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1967024 AATTATGCTA
1967034 TTTAAAGAAATATTTATT
1 TTTAAAGAAATATTTATT
1967052 TTTAAA-AAATATTTATT
1 TTTAAAGAAATATTTATT
1967069 GTATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAAGAAATATTTATT
Found at i:1967097 original size:15 final size:16
Alignment explanation
Indices: 1967070--1967100 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1967060 ATATTTATTG
1967070 TATTTTATAATTAAAT
1 TATTTTATAATTAAAT
1967086 TATTTT-TAATTAAAT
1 TATTTTATAATTAAAT
1967101 AATATAATCT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTATAATTAAAT
Found at i:1967477 original size:3 final size:3
Alignment explanation
Indices: 1967469--1967494 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1967459 CAATTCTTGC
1967469 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1967495 CAAAAATAAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1974705 original size:37 final size:37
Alignment explanation
Indices: 1974664--1974738 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
1974654 AGAGCTAAAG
*
1974664 AATGATGAGCTGTGACGGTTGCTGCAAGCATAATTGT
1 AATGATGAGCTGTGACAGTTGCTGCAAGCATAATTGT
* * *
1974701 AATGATGAGTTGTGATAGTTGCTGCAAGCATTATTGT
1 AATGATGAGCTGTGACAGTTGCTGCAAGCATAATTGT
1974738 A
1 A
1974739 CAGGTGTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.33
Consensus pattern (37 bp):
AATGATGAGCTGTGACAGTTGCTGCAAGCATAATTGT
Found at i:1975677 original size:17 final size:17
Alignment explanation
Indices: 1975655--1975698 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1975645 TTTGAATGTT
*
1975655 TATATTTTATAAGTATA
1 TATATTTTATAAATATA
1975672 TATATTTAATATAAATATA
1 TATATTT--TATAAATATA
1975691 TAT-TTTTA
1 TATATTTTA
1975699 ATTTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 7 0.29
18 3 0.12
19 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATATTTTATAAATATA
Found at i:1975690 original size:19 final size:19
Alignment explanation
Indices: 1975662--1975740 Score: 62
Period size: 19 Copynumber: 4.5 Consensus size: 19
1975652 GTTTATATTT
*
1975662 TATAAGTATATATATTTAA
1 TATAAATATATATATTTAA
*
1975681 TATAAATATATATTTTTAA
1 TATAAATATATATATTTAA
***
1975700 T-TTTTTA-ATATATTTAA
1 TATAAATATATATATTTAA
1975717 -A-AAAT-TATATATTT-A
1 TATAAATATATATATTTAA
*
1975732 TATTAATAT
1 TATAAATAT
1975741 TAGAATATGT
Statistics
Matches: 45, Mismatches: 10, Indels: 11
0.68 0.15 0.17
Matches are distributed among these distances:
15 1 0.02
16 10 0.22
17 12 0.27
18 4 0.09
19 18 0.40
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (19 bp):
TATAAATATATATATTTAA
Found at i:1976020 original size:16 final size:17
Alignment explanation
Indices: 1976000--1976040 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1975990 TATATTTTAA
1976000 AATTTAAATAAAAT-AT
1 AATTTAAATAAAATAAT
* *
1976016 TATTT-AATTAAATAAT
1 AATTTAAATAAAATAAT
1976032 AATTTAAAT
1 AATTTAAAT
1976041 TAATTTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 10 0.50
17 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATAAAATAAT
Found at i:1976024 original size:21 final size:22
Alignment explanation
Indices: 1976000--1976048 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
1975990 TATATTTTAA
*
1976000 AATTTAAATAA-AATATT-ATTT
1 AATTTAAATAATAAT-TTAAATT
1976021 AA-TTAAATAATAATTTAAATT
1 AATTTAAATAATAATTTAAATT
1976042 AATTTAA
1 AATTTAA
1976049 TTTAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAAATAATAATTTAAATT
Found at i:1976402 original size:21 final size:20
Alignment explanation
Indices: 1976378--1976427 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1976368 TTTGATAATT
1976378 TATTTTATTTTTATATATAAA
1 TATTTT-TTTTTATATATAAA
**
1976399 TA-TTTTTTTTATATATTTA
1 TATTTTTTTTTATATATAAA
1976418 TATTTTTTTT
1 TATTTTTTTT
1976428 ATTTTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 14 0.54
20 10 0.38
21 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTTTTTTTATATATAAA
Found at i:1976409 original size:19 final size:19
Alignment explanation
Indices: 1976385--1976429 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1976375 ATTTATTTTA
1976385 TTTTTATATATAAATATTT
1 TTTTTATATATAAATATTT
**
1976404 TTTTTATATATTTATATTT
1 TTTTTATATATAAATATTT
1976423 TTTTTAT
1 TTTTTAT
1976430 TTTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTATATATAAATATTT
Found at i:1976455 original size:20 final size:21
Alignment explanation
Indices: 1976399--1976456 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1976389 TATATATAAA
1976399 TATTTTTTTTATATATTTATAT
1 TATTTTTTTTATAT-TTTATAT
*
1976421 T-TTTTTTATTTTATTTT-TAT
1 TATTTTTT-TTATATTTTATAT
*
1976441 TATTTATTTTATATTT
1 TATTTTTTTTATATTT
1976457 AGTAGATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.35
21 14 0.45
22 6 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTTTTTATATTTTATAT
Found at i:1976466 original size:49 final size:47
Alignment explanation
Indices: 1976376--1976470 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 47
1976366 AGTTTGATAA
*
1976376 TTTATTTTATTTTTATATATAAATATTTTTTTTATATATTTATATTTTT
1 TTTATTTTATTTTTATATAT-AATATTTTTTTTATAGATTTA-ATTTTT
*
1976425 TTTATTTTATTTTTAT-TAT-TTATTTTATATTTAGTAGATTTAATTT
1 TTTATTTTATTTTTATATATAATATTTT-T-TTTA-TAGATTTAATTT
1976471 GAAAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 6 0.15
47 1 0.02
48 11 0.27
49 23 0.56
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (47 bp):
TTTATTTTATTTTTATATATAATATTTTTTTTATAGATTTAATTTTT
Found at i:1976722 original size:16 final size:16
Alignment explanation
Indices: 1976696--1976737 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1976686 TTTTAATACA
1976696 TTTATTTATTTTAT-ATT
1 TTTA-TTATTTT-TCATT
1976713 TTTATTATTTTTCATT
1 TTTATTATTTTTCATT
1976729 TTT-TTATTT
1 TTTATTATTT
1976738 AATTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTATTTTTCATT
Found at i:1976743 original size:18 final size:18
Alignment explanation
Indices: 1976696--1976761 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
1976686 TTTTAATACA
*
1976696 TTTATTT-ATTTTATATT
1 TTTATTTAATTTCATATT
* *
1976713 TTTA-TTATTTTTCATTTT
1 TTTATTTA-ATTTCATATT
*
1976731 TTTATTTAATTTCATATC
1 TTTATTTAATTTCATATT
*
1976749 TATATTTTAATTT
1 TTTA-TTTAATTT
1976762 ATCATAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 2 0.05
17 4 0.11
18 21 0.55
19 11 0.29
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTTCATATT
Found at i:1977500 original size:25 final size:26
Alignment explanation
Indices: 1977443--1977519 Score: 120
Period size: 25 Copynumber: 3.0 Consensus size: 26
1977433 TTATCGTTTG
*
1977443 TGTTTGTAAAAAATGGTGGTTTCTTTT
1 TGTTTGTAAAAAATGGTGATTT-TTTT
*
1977470 TGTTTGTCAAAAATGGT-ATTTTTTT
1 TGTTTGTAAAAAATGGTGATTTTTTT
1977495 TGTTTGTAAAAAATGGTGATTTTTT
1 TGTTTGTAAAAAATGGTGATTTTTT
1977520 GTTTATCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.43
26 10 0.22
27 16 0.35
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (26 bp):
TGTTTGTAAAAAATGGTGATTTTTTT
Found at i:1977530 original size:24 final size:25
Alignment explanation
Indices: 1977443--1977536 Score: 102
Period size: 24 Copynumber: 3.7 Consensus size: 25
1977433 TTATCGTTTG
* *
1977443 TGTTTGTAAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAATGGT-GATT-TTTT
1977470 TGTTTGTCAAAAATGGT-ATTTTTTT
1 TGTTTGTCAAAAATGGTGA-TTTTTT
*
1977495 TGTTTGTAAAAAATGGTGA-TTTTT
1 TGTTTGTCAAAAATGGTGATTTTTT
* *
1977519 TGTTTATCAAAATTGGTG
1 TGTTTGTCAAAAATGGTG
1977537 GTTAATTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
24 20 0.34
25 20 0.34
26 3 0.05
27 16 0.27
ACGTcount: A:0.26, C:0.03, G:0.20, T:0.51
Consensus pattern (25 bp):
TGTTTGTCAAAAATGGTGATTTTTT
Found at i:1977530 original size:25 final size:25
Alignment explanation
Indices: 1977443--1977530 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 25
1977433 TTATCGTTTG
*
1977443 TGTTTGT-AAAAAATGGTGGTTTCTTTT
1 TGTTTGTCAAAAAATGGT--ATT-TTTT
1977470 TGTTTGTC-AAAAATGGTATTTTTTT
1 TGTTTGTCAAAAAATGGTA-TTTTTT
1977495 TGTTTGT-AAAAAATGGTGA-TTTTT
1 TGTTTGTCAAAAAATGGT-ATTTTTT
*
1977519 TGTTTATCAAAA
1 TGTTTGTCAAAA
1977531 TTGGTGGTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
24 11 0.20
25 24 0.44
26 3 0.06
27 16 0.30
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.51
Consensus pattern (25 bp):
TGTTTGTCAAAAAATGGTATTTTTT
Found at i:1982022 original size:27 final size:27
Alignment explanation
Indices: 1981991--1982063 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1981981 CAAAAGCCAC
*
1981991 CCTTTGTGTTTGTCAAAAATAGTAGTT
1 CCTTTGTATTTGTCAAAAATAGTAGTT
* *
1982018 CCTTTTTATTTGTCAAAAATAGTGGTT
1 CCTTTGTATTTGTCAAAAATAGTAGTT
* * *
1982045 -CTTTTTATATGTTAAAAAT
1 CCTTTGTATTTGTCAAAAAT
1982064 GGTGGCTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (27 bp):
CCTTTGTATTTGTCAAAAATAGTAGTT
Found at i:1982048 original size:26 final size:27
Alignment explanation
Indices: 1981999--1982068 Score: 97
Period size: 26 Copynumber: 2.6 Consensus size: 27
1981989 ACCCTTTGTG
*
1981999 TTTGTCAAAAATAGTAGTTCCTTTTTA
1 TTTGTCAAAAATAGTGGTTCCTTTTTA
1982026 TTTGTCAAAAATAGTGGTT-CTTTTTA
1 TTTGTCAAAAATAGTGGTTCCTTTTTA
* * *
1982052 TATGTTAAAAATGGTGG
1 TTTGTCAAAAATAGTGG
1982069 CTTGTTGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATAGTGGTTCCTTTTTA
Found at i:1982109 original size:24 final size:24
Alignment explanation
Indices: 1981997--1982114 Score: 74
Period size: 24 Copynumber: 4.7 Consensus size: 24
1981987 CCACCCTTTG
* *
1981997 TGTTTGTCAAAAATAGTAGTTCCTTTT
1 TGTTTGTCAAAAATAGT-G--GCTTAT
* *
1982024 TATTTGTCAAAAATAGTGGTTCTTTT
1 TGTTTGTCAAAAATAGTGG--CTTAT
* * * * *
1982050 TATATGTTAAAAATGGTGGCTTGT
1 TGTTTGTCAAAAATAGTGGCTTAT
* * *
1982074 TGTTTATAAAAAATTGTGGCTTAT
1 TGTTTGTCAAAAATAGTGGCTTAT
*
1982098 TGTTTGTCAAAATTAGT
1 TGTTTGTCAAAAATAGT
1982115 AGCTAATTTT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
24 35 0.48
26 22 0.30
27 16 0.22
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (24 bp):
TGTTTGTCAAAAATAGTGGCTTAT
Found at i:1983979 original size:25 final size:26
Alignment explanation
Indices: 1983911--1983982 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1983901 TTATTTATGT
1983911 TTAATTATAAAATTATAAATATTATTA
1 TTAATTAT-AAATTATAAATATTATTA
** * *
1983938 -TAAAAATAAATTTTAAA-ATTTTTA
1 TTAATTATAAATTATAAATATTATTA
*
1983962 TTAATTATAAATAATAAATAT
1 TTAATTATAAATTATAAATAT
1983983 GAGTAATATA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
24 6 0.17
25 22 0.63
26 7 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAATTATAAATTATAAATATTATTA
Found at i:1986408 original size:14 final size:14
Alignment explanation
Indices: 1986389--1986416 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1986379 AGGGAGTAAG
1986389 TTTTCTTATGACTT
1 TTTTCTTATGACTT
1986403 TTTTCTTATGACTT
1 TTTTCTTATGACTT
1986417 CTCCAAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTCTTATGACTT
Found at i:1988727 original size:20 final size:19
Alignment explanation
Indices: 1988690--1988732 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1988680 ATAATAAATA
1988690 AAAAAATAATAATGATGTTT
1 AAAAAATAATAATGATG-TT
*
1988710 AAAAAATAAT-TTGAATGTT
1 AAAAAATAATAATG-ATGTT
1988729 AAAA
1 AAAA
1988733 TTTTGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (19 bp):
AAAAAATAATAATGATGTT
Found at i:1989740 original size:19 final size:20
Alignment explanation
Indices: 1989716--1989755 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1989706 AAATAAAATT
* *
1989716 TTAAATTAA-TTAATTTAAA
1 TTAAATCAACTTAATTAAAA
1989735 TTAAATCAACTTAATTAAAA
1 TTAAATCAACTTAATTAAAA
1989755 T
1 T
1989756 ATTTACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAATCAACTTAATTAAAA
Found at i:1992546 original size:3 final size:3
Alignment explanation
Indices: 1992538--1992567 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1992528 GTTTGCTTAT
1992538 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1992568 ACACGATTGG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1993009 original size:23 final size:23
Alignment explanation
Indices: 1992983--1993026 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1992973 ATATTAATTT
1992983 TTATATAAATTAT-AAATTATAAA
1 TTATA-AAATTATCAAATTATAAA
*
1993006 TTATAAATTTATCAAATTATA
1 TTATAAAATTATCAAATTATA
1993027 TTATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAAAATTATCAAATTATAAA
Found at i:1993025 original size:8 final size:7
Alignment explanation
Indices: 1992986--1993026 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
1992976 TTAATTTTTA
1992986 TATAAAT
1 TATAAAT
1992993 TATAAAT
1 TATAAAT
1993000 TATAAAT
1 TATAAAT
1993007 TATAAATT
1 TATAAA-T
1993015 TATCAAAT
1 TAT-AAAT
1993023 TATA
1 TATA
1993027 TTATTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 21 0.66
8 8 0.25
9 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAAAT
Found at i:1993037 original size:30 final size:31
Alignment explanation
Indices: 1992987--1993061 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
1992977 TAATTTTTAT
* *
1992987 ATAAATTATA-AATTATAAATTATA-AATTT
1 ATAAATTATATTATTATAAATTATATAATTA
* *
1993016 ATCAAATTATATTATTA-AAATTTTATTATTA
1 AT-AAATTATATTATTATAAATTATATAATTA
1993047 ATAAATTATATTATT
1 ATAAATTATATTATT
1993062 TAAGTTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 28 0.72
31 9 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
ATAAATTATATTATTATAAATTATATAATTA
Found at i:1993042 original size:14 final size:16
Alignment explanation
Indices: 1992987--1993061 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 16
1992977 TAATTTTTAT
*
1992987 ATAAATTATA-AATT-
1 ATAAATTATATTATTA
* *
1993001 ATAAATTATA-AATTT
1 ATAAATTATATTATTA
1993016 ATCAAATTATATTATT-
1 AT-AAATTATATTATTA
*
1993032 A-AAATTTTATTATTA
1 ATAAATTATATTATTA
1993047 ATAAATTATATTATT
1 ATAAATTATATTATT
1993062 TAAGTTAATT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
14 26 0.49
15 3 0.06
16 21 0.40
17 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATTATATTATTA
Found at i:1993157 original size:16 final size:16
Alignment explanation
Indices: 1993121--1993168 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1993111 ATACATAATT
*
1993121 AATTTTTATTATATAT
1 AATTTTTATTATATAA
*
1993137 TATTTTTATTATATAA
1 AATTTTTATTATATAA
* *
1993153 AATTTTAATAATATAA
1 AATTTTTATTATATAA
1993169 TTTAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTTATTATATAA
Found at i:1993611 original size:31 final size:31
Alignment explanation
Indices: 1993531--1993613 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
1993521 GAACAAATAT
1993531 AAAAATTATTT-TTTTTATTATTTAACTTGA
1 AAAAATTATTTATTTTTATTATTTAACTTGA
* * * * *
1993561 AATAATAATTAAATATTTATT-TTTTACTTGA
1 AAAAATTATT-TATTTTTATTATTTAACTTGA
1993592 AAAAATTATTTACTTTTTATTA
1 AAAAATTATTTA-TTTTTATTA
1993614 GATAAAAACG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
30 9 0.22
31 24 0.60
32 7 0.17
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (31 bp):
AAAAATTATTTATTTTTATTATTTAACTTGA
Found at i:1994260 original size:23 final size:22
Alignment explanation
Indices: 1994234--1994286 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
1994224 ATTCGTATCG
1994234 TATTTATATTATTTTTCATAT-TA
1 TATTTATA--ATTTTTCATATCTA
*
1994257 TATTT-TAATTTTTTATATCTA
1 TATTTATAATTTTTCATATCTA
*
1994278 TATATATAA
1 TATTTATAA
1994287 AATTAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 5 0.19
23 5 0.19
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTATAATTTTTCATATCTA
Found at i:1995974 original size:14 final size:14
Alignment explanation
Indices: 1995898--1995982 Score: 72
Period size: 14 Copynumber: 6.3 Consensus size: 14
1995888 TATTATTGAC
1995898 TTATAATATTAAAT
1 TTATAATATTAAAT
*
1995912 TTA-ATTATT---T
1 TTATAATATTAAAT
1995922 TTATAATAATATAAAT
1 TTATAAT-AT-TAAAT
*
1995938 TTATCA-ATTAAAT
1 TTATAATATTAAAT
* * *
1995951 TAATATTATTTAAT
1 TTATAATATTAAAT
1995965 TTATAATATTAAAT
1 TTATAATATTAAAT
1995979 TTAT
1 TTAT
1995983 TTAATATTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
10 4 0.07
11 2 0.04
12 2 0.04
13 14 0.26
14 26 0.48
16 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATAATATTAAAT
Found at i:1996617 original size:17 final size:17
Alignment explanation
Indices: 1996597--1996658 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
1996587 GATATTTATA
1996597 AAAAATAATAATATATT
1 AAAAATAATAATATATT
* * *
1996614 AAAATTTATAATATTTT
1 AAAAATAATAATATATT
* * *
1996631 AAATATAAT-TTATAAT
1 AAAAATAATAATATATT
*
1996647 AAAAATATTAAT
1 AAAAATAATAAT
1996659 GTATAATTAA
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAAATAATAATATATT
Found at i:1996663 original size:19 final size:20
Alignment explanation
Indices: 1996631--1996684 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1996621 ATAATATTTT
*
1996631 AAATA-TAATTTATAA-TAA
1 AAATATTAATATATAATTAA
*
1996649 AAATATTAATGTATAATTAA
1 AAATATTAATATATAATTAA
* *
1996669 TAATATAAATATATAA
1 AAATATTAATATATAA
1996685 ATTATCATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 16 0.53
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AAATATTAATATATAATTAA
Found at i:1996816 original size:20 final size:19
Alignment explanation
Indices: 1996791--1996829 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1996781 TTAATCTTTT
*
1996791 ATTAAATATAATGTTATTAA
1 ATTAAATAT-ATATTATTAA
1996811 ATTAAATATATATTATTAA
1 ATTAAATATATATTATTAA
1996830 GTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTAAATATATATTATTAA
Found at i:1996893 original size:17 final size:18
Alignment explanation
Indices: 1996839--1996896 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
1996829 AGTATTTATT
1996839 TTTTATATTTAATAATTA
1 TTTTATATTTAATAATTA
*
1996857 -TTGATA-TTAATATTATTA
1 TTTTATATTTAATA--ATTA
1996875 TTTTATATTTAA-AATTA
1 TTTTATATTTAATAATTA
1996892 TTTTA
1 TTTTA
1996897 ATTAAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 6 0.18
17 14 0.41
18 4 0.12
19 6 0.18
20 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTATATTTAATAATTA
Found at i:1996901 original size:35 final size:35
Alignment explanation
Indices: 1996824--1996893 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 35
1996814 AAATATATAT
1996824 TATTAAGTATTTATTTTTTATATTTAATAATTATTGA
1 TATTAA-TA-TTATTTTTTATATTTAATAATTATTGA
1996861 TATTAATATTATTATTTTATATTTAA-AATTATT
1 TATTAATATTATT-TTTTATATTTAATAATTATT
1996894 TTAATTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 12 0.38
36 14 0.44
37 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (35 bp):
TATTAATATTATTTTTTATATTTAATAATTATTGA
Found at i:1997048 original size:3 final size:3
Alignment explanation
Indices: 1997040--1997066 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1997030 AATCGGTCAC
1997040 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1997067 GAAAATTTTA
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):
ATT
Found at i:1998291 original size:3 final size:3
Alignment explanation
Indices: 1998283--1998313 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1998273 ATAGATATAA
1998283 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1998314 GAGAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1998834 original size:17 final size:18
Alignment explanation
Indices: 1998814--1998856 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1998804 AATAAAAAAT
*
1998814 ATTAAATAATT-TTTACA
1 ATTAAATAATTATTTAAA
1998831 ATT-AATAATTATTTAAA
1 ATTAAATAATTATTTAAA
*
1998848 AATAAATAA
1 ATTAAATAA
1998857 AAATTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTAAATAATTATTTAAA
Found at i:1998848 original size:45 final size:43
Alignment explanation
Indices: 1998799--1998890 Score: 105
Period size: 48 Copynumber: 2.0 Consensus size: 43
1998789 AGTCTAAATG
*
1998799 TAAA-AAATAAAAAATATTAAATAATTTTTACAATTAATAATTATT
1 TAAATAAATAAAAAATATTAAATAA-TTTTA-AA-AAATAATTATT
* *
1998844 TAAAAATAAATAAAAATTATTATATAATTTTAAAAAATAATTATT
1 T--AAATAAATAAAAAATATTAAATAATTTTAAAAAATAATTATT
1998889 TA
1 TA
1998891 TATTGGACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
43 1 0.02
45 12 0.29
46 2 0.05
47 8 0.20
48 18 0.44
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (43 bp):
TAAATAAATAAAAAATATTAAATAATTTTAAAAAATAATTATT
Done.