Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 187 of 322
Found at i:61578913 original size:31 final size:31
Alignment explanation
Indices: 61578870--61578937 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
61578860 CGGGTGTGTG
61578870 GGCCCACACTGGTGAACATCATAGACTTGTA
1 GGCCCACACTGGTGAACATCATAGACTTGTA
* *
61578901 GGCCTACACTGGTGAACATCATAGGCTTGTA
1 GGCCCACACTGGTGAACATCATAGACTTGTA
61578932 GGCCCA
1 GGCCCA
61578938 TTTTTACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.22
Consensus pattern (31 bp):
GGCCCACACTGGTGAACATCATAGACTTGTA
Found at i:61585626 original size:26 final size:26
Alignment explanation
Indices: 61585590--61585639 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
61585580 CTAATGTAAA
61585590 AGGGGTTGCTAAGTGC-AGATTCCCTT
1 AGGGGTTGCTAAGTGCTA-ATTCCCTT
61585616 AGGGGTTGCTAAGTGCTAATTCCC
1 AGGGGTTGCTAAGTGCTAATTCCC
61585640 CAAATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTAATTCCCTT
Found at i:61585680 original size:42 final size:42
Alignment explanation
Indices: 61585619--61585764 Score: 125
Period size: 42 Copynumber: 3.5 Consensus size: 42
61585609 TTCCCTTAGG
* * * ** * *
61585619 GGTTGCTAAGTGCTAATTCCCCAAATTATTGATTCTAAAGGT
1 GGTTGCTAAATACTGATTCCCCGTATCATTGATTATAAAGGT
*
61585661 GGTTGCTAAATACTGATTCCACCGTATCATTGATTGTGAAAGG-
1 GGTTGCTAAATACTGATTCC-CCGTATCATTGATTAT-AAAGGT
** * * * *
61585704 GGTTGCTATGTGCTGAATCCCCGTATCACTGAATAT-AAGGT
1 GGTTGCTAAATACTGATTCCCCGTATCATTGATTATAAAGGT
*
61585745 GGTTGCTAAATAGTGATTCC
1 GGTTGCTAAATACTGATTCC
61585765 ACCGAGTAAC
Statistics
Matches: 82, Mismatches: 19, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
40 4 0.05
41 15 0.18
42 30 0.37
43 28 0.34
44 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAATACTGATTCCCCGTATCATTGATTATAAAGGT
Found at i:61585708 original size:43 final size:43
Alignment explanation
Indices: 61585646--61585768 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
61585636 TCCCCAAATT
*
61585646 ATTGATTCTAAAGGTGGTTGCTAAATACTGATTCCACCGTATC
1 ATTGATTATAAAGGTGGTTGCTAAATACTGATTCCACCGTATC
* ** * *
61585689 ATTGATTGTGAAAGG-GGTTGCTATGTGCTGAATCC-CCGTATC
1 ATTGATTAT-AAAGGTGGTTGCTAAATACTGATTCCACCGTATC
* * *
61585731 ACTGAATAT-AAGGTGGTTGCTAAATAGTGATTCCACCG
1 ATTGATTATAAAGGTGGTTGCTAAATACTGATTCCACCG
61585769 AGTAACGATT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
40 4 0.06
41 15 0.23
42 16 0.25
43 24 0.38
44 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (43 bp):
ATTGATTATAAAGGTGGTTGCTAAATACTGATTCCACCGTATC
Found at i:61602474 original size:15 final size:18
Alignment explanation
Indices: 61602440--61602475 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
61602430 CTTAATTTTA
61602440 TTTTAAATTATAGAATTT
1 TTTTAAATTATAGAATTT
61602458 TTTTAAA-TATA-AATTT
1 TTTTAAATTATAGAATTT
61602474 TT
1 TT
61602476 AAAGCACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 4 0.22
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAATTATAGAATTT
Found at i:61603226 original size:28 final size:28
Alignment explanation
Indices: 61603166--61603230 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
61603156 AAATTGGAAG
61603166 AATTTTAA-ATATTTTTTAATGTTTAAT
1 AATTTTAATATATTTTTTAATGTTTAAT
* *
61603193 ATTTTTAATATTATTTTTT-AT-TTTTAT
1 AATTTTAATA-TATTTTTTAATGTTTAAT
61603220 AAATTTTAATA
1 -AATTTTAATA
61603231 ATGCTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 12 0.38
28 12 0.38
29 8 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
AATTTTAATATATTTTTTAATGTTTAAT
Found at i:61603821 original size:29 final size:30
Alignment explanation
Indices: 61603781--61603971 Score: 199
Period size: 30 Copynumber: 6.4 Consensus size: 30
61603771 CTTGTTTAAA
* * *
61603781 AAAATTATATTTTAACCCTTAAACTTT-TT
1 AAAATTACATTTTAACCCCTAAAATTTCTT
** *
61603810 AAAATTACATTTCGACCCCTAAAATTTCTC
1 AAAATTACATTTTAACCCCTAAAATTTCTT
* *
61603840 AGAATTACATTTCAACCCCTAAAATTT-TCT
1 AAAATTACATTTTAACCCCTAAAATTTCT-T
*
61603870 -AAATTACATTTTAATCCCTAAAATTTCTT
1 AAAATTACATTTTAACCCCTAAAATTTCTT
* * * * *
61603899 GAAATTACATTTTGACCACTAAACTTTTTT
1 AAAATTACATTTTAACCCCTAAAATTTCTT
* * *
61603929 GAAATTACATTTTGACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAAATTTCTT
61603959 AAAATTACATTTT
1 AAAATTACATTTT
61603972 GGCCCCAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
29 47 0.34
30 91 0.66
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAAATTTCTT
Found at i:61603957 original size:60 final size:60
Alignment explanation
Indices: 61603781--61604004 Score: 245
Period size: 59 Copynumber: 3.8 Consensus size: 60
61603771 CTTGTTTAAA
* * * * *
61603781 AAAATTATATTTTAACCCTTAAACTTTT-TAAAATTACATTTCGACCCCTAAAATTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTTCTGAAATTACATTTTGACCCCTAAAATTTCTT
* * * * *
61603840 AGAATTACATTTCAACCCCTAAAATTTTCT-AAATTACATTTTAATCCCTAAAATTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTTCTGAAATTACATTTTGACCCCTAAAATTTCTT
* * * * *
61603899 GAAATTACATTTTGACCACTAAACTTTTTTGAAATTACATTTTGACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTTCTGAAATTACATTTTGACCCCTAAAATTTCTT
** * * *
61603959 AAAATTACATTTTGGCCCCAAAACTTTTACTGTATTTACATTTTGA
1 AAAATTACATTTTAACCCCTAAACTTTT-CTGAAATTACATTTTGA
61604005 TCCTTCTGAT
Statistics
Matches: 136, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
59 71 0.52
60 51 0.38
61 14 0.10
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTTCTGAAATTACATTTTGACCCCTAAAATTTCTT
Found at i:61604175 original size:15 final size:16
Alignment explanation
Indices: 61604145--61604186 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
61604135 TGGGCAGCCA
61604145 AAAAAGAAAAACCAAG
1 AAAAAGAAAAACCAAG
61604161 CAAAAA-AAAAA-CAAG
1 -AAAAAGAAAAACCAAG
61604176 AAAAAGCAAAA
1 AAAAAG-AAAA
61604187 GAAATCAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 9 0.39
17 5 0.22
ACGTcount: A:0.79, C:0.12, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAACCAAG
Found at i:61604186 original size:20 final size:22
Alignment explanation
Indices: 61604158--61604201 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
61604148 AAGAAAAACC
61604158 AAGCAAAAAAAAAACAAG-AAA
1 AAGCAAAAAAAAAACAAGCAAA
* *
61604179 AAGC-AAAAGAAATCAAGCAAA
1 AAGCAAAAAAAAAACAAGCAAA
61604200 AA
1 AA
61604202 CAGTAGCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.75, C:0.11, G:0.11, T:0.02
Consensus pattern (22 bp):
AAGCAAAAAAAAAACAAGCAAA
Found at i:61604458 original size:18 final size:17
Alignment explanation
Indices: 61604435--61604529 Score: 69
Period size: 18 Copynumber: 5.8 Consensus size: 17
61604425 GGGGCCGAAC
61604435 AAGGAAGAAGAAGAAAGA
1 AAGGAAGAAGAA-AAAGA
61604453 AAGGAAGAAGAAAAAG-
1 AAGGAAGAAGAAAAAGA
61604469 AA-GAAG--GAAAAAGA
1 AAGGAAGAAGAAAAAGA
**
61604483 AAGGGGGAAAGAAAAAAGA
1 AAGGAAG-AAG-AAAAAGA
*
61604502 AA--AAGAA-AAAAACA
1 AAGGAAGAAGAAAAAGA
* *
61604516 AAGAAAAAAGAAAA
1 AAGGAAGAAGAAAA
61604530 TTTTTTTACA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
13 7 0.11
14 10 0.16
15 6 0.10
16 8 0.13
17 9 0.15
18 13 0.21
19 9 0.15
ACGTcount: A:0.73, C:0.01, G:0.26, T:0.00
Consensus pattern (17 bp):
AAGGAAGAAGAAAAAGA
Found at i:61604510 original size:5 final size:6
Alignment explanation
Indices: 61604442--61604529 Score: 54
Period size: 6 Copynumber: 14.2 Consensus size: 6
61604432 AACAAGGAAG
* * * ** **
61604442 AAGAAGA AAG-AA AGGAAG AAGAAA AAGAAGA AGGAAA AAGAAA GGGGGA
1 AAGAA-A AAGAAA AAGAAA AAGAAA AAGAA-A AAGAAA AAGAAA AAGAAA
61604491 AAGAAAA AAGAAA AAGAAA AA-AACA AAGAAAA AAGAAA A
1 AAG-AAA AAGAAA AAGAAA AAGAA-A AAG-AAA AAGAAA A
61604530 TTTTTTTACA
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
5 5 0.08
6 38 0.62
7 16 0.26
8 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:61604680 original size:18 final size:19
Alignment explanation
Indices: 61604659--61604726 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 19
61604649 AGTAGGCCAG
* *
61604659 AAAAAAAGAGAGAAGA-AA
1 AAAAAAAGAAAAAAGAGAA
*
61604677 AAAAAGAGAAAAAAGAGAA
1 AAAAAAAGAAAAAAGAGAA
*
61604696 AAAAACAA-AAAAAA-ATAA
1 AAAAA-AAGAAAAAAGAGAA
61604714 AAAGAAAAGAAAA
1 AAA-AAAAGAAAA
61604727 GTTCAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 21 0.51
19 19 0.46
20 1 0.02
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (19 bp):
AAAAAAAGAAAAAAGAGAA
Found at i:61604697 original size:8 final size:9
Alignment explanation
Indices: 61604657--61604699 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
61604647 GAAGTAGGCC
61604657 AGAAAAAA-
1 AGAAAAAAG
* *
61604665 AGAGAGAAG
1 AGAAAAAAG
*
61604674 AAAAAAAAG
1 AGAAAAAAG
61604683 AGAAAAAAG
1 AGAAAAAAG
61604692 AGAAAAAA
1 AGAAAAAA
61604700 ACAAAAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 6 0.21
9 22 0.79
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:61604706 original size:9 final size:9
Alignment explanation
Indices: 61604671--61604727 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
61604661 AAAAAGAGAG
61604671 AAGAAAAAA
1 AAGAAAAAA
*
61604680 AAGAGAAAA
1 AAGAAAAAA
61604689 AAGAGAAAAA
1 AAGA-AAAAA
*
61604699 AA-CAAAAA
1 AAGAAAAAA
*
61604707 AA-AATAAA
1 AAGAAAAAA
61604715 AAGAAAAGAA
1 AAGAAAA-AA
61604725 AAG
1 AAG
61604728 TTCAATTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 13 0.33
9 15 0.38
10 11 0.28
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:61604716 original size:11 final size:11
Alignment explanation
Indices: 61604657--61604726 Score: 59
Period size: 12 Copynumber: 5.9 Consensus size: 11
61604647 GAAGTAGGCC
*
61604657 AGAAAAAAAGAG
1 AGAAAAAAA-AA
61604669 AGAAGAAAAAAA
1 AGAA-AAAAAAA
* *
61604681 AGAGAAAAAAG
1 AGAAAAAAAAA
61604692 AGAAAAAAACAA
1 AGAAAAAAA-AA
*
61604704 AAAAAAATAAAA
1 AGAAAAA-AAAA
61604716 AGAAAAGAAAA
1 AGAAAA-AAAA
61604727 GTTCAATTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
11 14 0.30
12 25 0.53
13 8 0.17
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:61604887 original size:13 final size:15
Alignment explanation
Indices: 61604831--61604887 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 15
61604821 TGCTATTTCG
*
61604831 TTTTAATATTATTAGTA
1 TTTT-ATATTTTTA-TA
61604848 TTTTATGCATTTTTATA
1 TTTTAT--ATTTTTATA
61604865 TTTTATATTTTTAT-
1 TTTTATATTTTTATA
61604879 TTTTA-ATTT
1 TTTTATATTT
61604888 AACTCAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 8 0.22
16 2 0.05
17 12 0.32
18 6 0.16
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTATATTTTTATA
Found at i:61605316 original size:18 final size:18
Alignment explanation
Indices: 61605257--61605326 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
61605247 AAATTTCATG
*
61605257 TTTTCGTATTTTCAACAAA
1 TTTTCGTGTTTTCAA-AAA
* * *
61605276 TTCTCATGTCTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
61605293 AATTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
61605311 TTTTCGTG-TTTCAAAA
1 TTTTCGTGTTTTCAAAA
61605327 CAAAAAGTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
17 18 0.46
18 13 0.33
19 8 0.21
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:61605357 original size:17 final size:18
Alignment explanation
Indices: 61605288--61605365 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
61605278 CTCATGTCTT
*
61605288 AAAAAAATTCGTGTTTTC
1 AAAAAAATTCGTGTTTTA
** *
61605306 AAAAATTTTCGTGTTTCAA
1 AAAAAAATTCGTGTTT-TA
*
61605325 AACAAAAAGTTAGTGTTTTA
1 AA-AAAAA-TTCGTGTTTTA
*
61605345 AAAAAAATT-GTGTTTCA
1 AAAAAAATTCGTGTTTTA
61605362 AAAA
1 AAAA
61605366 TCCTCATGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
17 11 0.23
18 16 0.33
19 7 0.15
20 6 0.12
21 8 0.17
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (18 bp):
AAAAAAATTCGTGTTTTA
Found at i:61605358 original size:38 final size:39
Alignment explanation
Indices: 61605289--61605364 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
61605279 TCATGTCTTA
* * **
61605289 AAAAAATTCGTGTTTTCAAAAATTTTCGTGTTTCAAAAC
1 AAAAAATTAGTGTTTTAAAAAAAATTCGTGTTTCAAAAC
*
61605328 AAAAAGTTAGTGTTTTAAAAAAAATT-GTGTTTCAAAA
1 AAAAAATTAGTGTTTTAAAAAAAATTCGTGTTTCAAAA
61605365 ATCCTCATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 11 0.34
39 21 0.66
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (39 bp):
AAAAAATTAGTGTTTTAAAAAAAATTCGTGTTTCAAAAC
Found at i:61605530 original size:37 final size:35
Alignment explanation
Indices: 61605482--61605618 Score: 98
Period size: 37 Copynumber: 3.7 Consensus size: 35
61605472 CGTGCTTCGT
*
61605482 AAATTTTCGTGTTTTCAAAAATTCTCGCATTTTCAAA
1 AAATTCTCGTGTTTTCAAAAATT-TCGC-TTTTCAAA
* * *
61605519 AAATTCTCGTG-TTTCACAAATTTTTGTGTTTTCAAAAAA
1 AAATTCTCGTGTTTTCA-AAAATTTCG-CTTTTC---AAA
* * *
61605558 AAATCCTCATGTTTTCAAAAAATTTCTCTTGTT-ACAA
1 AAATTCTCGTGTTTTC-AAAAATTTCGCTT-TTCA-AA
*
61605595 AAATTTTCGTGTTTTCAAAAATTT
1 AAATTCTCGTGTTTTCAAAAATTT
61605619 TCGTGTTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
36 21 0.27
37 30 0.38
39 14 0.18
40 12 0.15
41 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (35 bp):
AAATTCTCGTGTTTTCAAAAATTTCGCTTTTCAAA
Found at i:61605634 original size:17 final size:18
Alignment explanation
Indices: 61605408--61605632 Score: 161
Period size: 18 Copynumber: 12.2 Consensus size: 18
61605398 AATTTAAAAA
*
61605408 AAAAATTTCTCTTG-TTTC
1 AAAAATTT-TCGTGTTTTC
61605426 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** *
61605444 GTAAATTTTCGTGTATTC
1 AAAAATTTTCGTGTTTTC
* *
61605462 AAAAAATTCTCGTG-CTTC
1 -AAAAATTTTCGTGTTTTC
**
61605480 GTAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* **
61605498 AAAAATTCTCGCATTTTC
1 AAAAATTTTCGTGTTTTC
*
61605516 AAAAAATTCTCGTG-TTTC
1 -AAAAATTTTCGTGTTTTC
* *
61605534 ACAAATTTTTGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** *
61605552 AAAAAAAAATCCTCATGTTTTC
1 ----AAAAATTTTCGTGTTTTC
* *
61605574 AAAAAATTTCTCTTG-TTAC
1 -AAAAATTT-TCGTGTTTTC
61605593 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
61605611 AAAAATTTTCGTGTTTTT
1 AAAAATTTTCGTGTTTTC
61605629 AAAA
1 AAAA
61605633 TTCTTGTAAC
Statistics
Matches: 162, Mismatches: 34, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
17 28 0.17
18 86 0.53
19 31 0.19
20 4 0.02
22 13 0.08
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:61616758 original size:10 final size:10
Alignment explanation
Indices: 61616743--61616799 Score: 69
Period size: 10 Copynumber: 5.7 Consensus size: 10
61616733 TGTTATGCCT
* *
61616743 AAAAAAATAG
1 AAAAAAACAA
61616753 AAAAAAACAA
1 AAAAAAACAA
61616763 AAAAAAACAA
1 AAAAAAACAA
* *
61616773 AAAAAAATAT
1 AAAAAAACAA
*
61616783 AAAGAAACAA
1 AAAAAAACAA
61616793 AAAAAAA
1 AAAAAAA
61616800 TGAAAAATCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.86, C:0.05, G:0.04, T:0.05
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:61616768 original size:20 final size:20
Alignment explanation
Indices: 61616743--61616806 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
61616733 TGTTATGCCT
* * *
61616743 AAAAAAATAGAAAAAAACAA
1 AAAAAAACAAAAAAAAATAA
*
61616763 AAAAAAACAAAAAAAAATAT
1 AAAAAAACAAAAAAAAATAA
*
61616783 AAAGAAACAAAAAAAAATGAA
1 AAAAAAACAAAAAAAAAT-AA
61616804 AAA
1 AAA
61616807 TCAAGATGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 33 0.89
21 4 0.11
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.06
Consensus pattern (20 bp):
AAAAAAACAAAAAAAAATAA
Found at i:61616806 original size:30 final size:30
Alignment explanation
Indices: 61616743--61616799 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
61616733 TGTTATGCCT
61616743 AAAAAAATAGAAAAAAACAAAAAAAAACAA
1 AAAAAAATAGAAAAAAACAAAAAAAAACAA
* *
61616773 AAAAAAATATAAAGAAACAAAAAAAAA
1 AAAAAAATAGAAAAAAACAAAAAAAAA
61616800 TGAAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.86, C:0.05, G:0.04, T:0.05
Consensus pattern (30 bp):
AAAAAAATAGAAAAAAACAAAAAAAAACAA
Found at i:61617739 original size:29 final size:29
Alignment explanation
Indices: 61617697--61617759 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
61617687 CATATTGCGA
61617697 GAGGTGAGTTGAGCCTCGAGTCACATGCC
1 GAGGTGAGTTGAGCCTCGAGTCACATGCC
61617726 GAGGTGAGTTGAGCCTCGAGTCACATGCC
1 GAGGTGAGTTGAGCCTCGAGTCACATGCC
61617755 GAGGT
1 GAGGT
61617760 ATTCTCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.37, T:0.21
Consensus pattern (29 bp):
GAGGTGAGTTGAGCCTCGAGTCACATGCC
Found at i:61618130 original size:157 final size:151
Alignment explanation
Indices: 61617726--61618272 Score: 690
Period size: 157 Copynumber: 3.5 Consensus size: 151
61617716 GTCACATGCC
61617726 GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTCTCTTCAATTTCTGTTTTTTCAAAAAAA
1 GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATT-T-TTCAATTTCTG-TTTTTC--AAAAA
61617791 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACACGCCGAGGTATTTTTCAATTTCTA
61 TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTC--
*
61617855 TTTTTTCAACAAATCAACTCATATTGCGA
124 TGTTTTCAA-AAATCAACTCATATTGCGA
* * ** *
61617884 GAGGTGAGTTGAGTCTCGAGTTAC--GCTAAGGTATTTTTCAATTTCTGCTTTTCAAAAATCAAC
1 GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
* * *
61617947 TCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAAGTATTTCTTTTAAATTTCTGTT
66 TCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTA--T-TTTTCAATTTCTGTT
* *
61618012 TTGAAAAATCAACTCATATTGTGA
128 TTCAAAAATCAACTCATATTGCGA
*
61618036 GAGGTGAGTTGAGCCTC-AGGTCACATGCCGAGGTATTTCTTTTAAGTTTCTGTTTTTCAAAAAT
1 GAGGTGAGTTGAGCCTCGA-GTCACATGCCGAGGTA-TT-TTTCAA-TTTCTGTTTTTCAAAAAT
* * * *
61618100 AAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTCAATTTCTGT
62 CAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTG-
*
61618165 CTTTTTCATAAATCAACTCATATTGCGA
126 --TTTTCAAAAATCAACTCATATTGCGA
* * * * * *
61618193 GAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TTTTAAATTTATGTTTTTCTAAAATCAAC
1 GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
61618257 TCATATTGCGAGAGGT
66 TCATATTGCGAGAGGT
61618273 CTGTTTTTCT
Statistics
Matches: 339, Mismatches: 36, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
151 42 0.12
152 50 0.15
153 45 0.13
154 36 0.11
155 15 0.04
156 14 0.04
157 115 0.34
158 22 0.06
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (151 bp):
GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
TCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTGTTTTC
AAAAATCAACTCATATTGCGA
Found at i:61618148 original size:79 final size:76
Alignment explanation
Indices: 61617726--61618272 Score: 690
Period size: 78 Copynumber: 7.1 Consensus size: 76
61617716 GTCACATGCC
* *
61617726 GAGGTGAGTTGAGCCTCGAGTCACATGCCGAGGTATTCTCTTCAATTTCTGTTTTTTCAAAAAAA
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATT-T-TTCAATTTCTG-TTTTTC--AAAAA
61617791 TCAACTCATATTGCGA
61 TCAACTCATATTGCGA
*
61617807 GAGGTGAGTTGAGCCTCGGG-CACACGCCGAGGTATTTTTCAATTTCTATTTTTTCAACAAATCA
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCT-GTTTTTCAA-AAATCA
61617871 ACTCATATTGCGA
64 ACTCATATTGCGA
* * * ** *
61617884 GAGGTGAGTTGAGTCTCGAGT--TACGCTAAGGTATTTTTCAATTTCTGCTTTTCAAAAATCAAC
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
61617947 TCATATTGCGA
66 TCATATTGCGA
* * * *
61617958 GAGGTGAGTTGAGCCTCGGGTCACATGCCGAAGTATTTCTTTTAAATTTCTG-TTTTGAAAAATC
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTA--T-TTTTCAATTTCTGTTTTTCAAAAATC
*
61618022 AACTCATATTGTGA
63 AACTCATATTGCGA
* * * *
61618036 GAGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTCTTTTAAGTTTCTGTTTTTCAAAAATA
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTA-TT-TTTCAA-TTTCTGTTTTTCAAAAATC
*
61618101 AACTCATATTGCTA
63 AACTCATATTGCGA
* * *
61618115 GAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTCAATTTCTGTCTTTTTCATAAATCA
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTG--TTTTTCAAAAATCA
61618180 ACTCATATTGCGA
64 ACTCATATTGCGA
* * * *
61618193 GAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TTTTAAATTTATGTTTTTCTAAAATCAAC
1 GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
61618257 TCATATTGCGA
66 TCATATTGCGA
61618268 GAGGT
1 GAGGT
61618273 CTGTTTTTCT
Statistics
Matches: 413, Mismatches: 40, Indels: 32
0.85 0.08 0.07
Matches are distributed among these distances:
74 38 0.09
75 37 0.09
76 38 0.09
77 60 0.15
78 140 0.34
79 66 0.16
80 15 0.04
81 19 0.05
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (76 bp):
GAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTGTTTTTCAAAAATCAAC
TCATATTGCGA
Found at i:61618285 original size:35 final size:35
Alignment explanation
Indices: 61618239--61618307 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
61618229 TTTAAATTTA
61618239 TGTTTTTCTAAAATCAACTCATATTGCGAGAGGTC
1 TGTTTTTCTAAAATCAACTCATATTGCGAGAGGTC
61618274 TGTTTTTCTAAAATCAACTCATATTGCGAGAGGT
1 TGTTTTTCTAAAATCAACTCATATTGCGAGAGGT
61618308 GAGTTGAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (35 bp):
TGTTTTTCTAAAATCAACTCATATTGCGAGAGGTC
Found at i:61618401 original size:188 final size:189
Alignment explanation
Indices: 61618084--61618463 Score: 568
Period size: 188 Copynumber: 2.0 Consensus size: 189
61618074 CTTTTAAGTT
* *
61618084 TCTGTTTTTCAAAAATAAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
1 TCTGTTTTTCAAAAATAAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGAT
*
61618149 ATTTTTCAATTTCTGTCTTTTTCATAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
66 ATTTTTCAATTTCTGTCTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
61618214 CACACGCTGAGGTA-TTTTAAATTTATGTTTTTCTAA-AATCAACTCATATTGCGAGAGG
131 CACACGCTGAGGTATTTTTAAATTTATGTTTTTC-AAGAATCAACTCATATTGCGAGAGG
* * * *
61618272 TCTGTTTTTCTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGAT
1 TCTGTTTTTCAAAAATAAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGAT
* *
61618337 ATTTTTCAATTTTTGT-TTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGG
66 ATTTTTCAATTTCTGTCTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
* * * * * *
61618401 TCATATGCTGAGGTATTCTTTTCAATTTCTTTTTTTCAAGAATCAACTCATGTTGCGAGAGG
130 TCACACGCTGAGGTA-T-TTTTAAATTTATGTTTTTCAAGAATCAACTCATATTGCGAGAGG
61618463 T
1 T
61618464 GAGTTGAGCC
Statistics
Matches: 172, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
187 6 0.03
188 126 0.73
190 2 0.01
191 38 0.22
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (189 bp):
TCTGTTTTTCAAAAATAAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGAT
ATTTTTCAATTTCTGTCTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
CACACGCTGAGGTATTTTTAAATTTATGTTTTTCAAGAATCAACTCATATTGCGAGAGG
Found at i:61618480 original size:266 final size:267
Alignment explanation
Indices: 61618016--61618495 Score: 729
Period size: 266 Copynumber: 1.8 Consensus size: 267
61618006 TCTGTTTTGA
* * * *
61618016 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGTCACATGCCGAGGTATTTCTTTTAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGATATTTCTTTCAA
61618081 GTTTCTGTTTTTCAAAAATAAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTGA
66 GTTTCTGTTTTTCAAAAATAAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTGA
61618146 GGTATTTTTCAATTTCTGTCTTTTTCATAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
131 GGTATTTTTCAATTTCTGTCTTTTTCATAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* *
61618211 GGTCACACGCTGAGGTATTTTAAATTTATGTTTTTCTAAAATCAACTCATATTGCGAGAGGTCTG
196 GGTCACACGCCGAGCTATTTTAAATTTATGTTTTTCTAAAATCAACTCATATTGCGAGAGGTCTG
61618276 TTTTTCT
261 TTTTTCT
* * *
61618283 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGATA-TT-TTTCAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGATATTTCTTTCAA
* * * * *
61618346 -TTTTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCATATGCT
66 GTTTCTG-TTTTTC-AAAAATAAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCT
*
61618410 GAGGTATTCTTTTCAATTTCT-T-TTTTTCA-AGAATCAACTCATGTTGCGAGAGGTGAGTTGAG
129 GAGGTA-T-TTTTCAATTTCTGTCTTTTTCATA-AATCAACTCATATTGCGAGAGGTGAGTTGAG
*
61618472 CCTCGGGTCGCACGCCGAGCTATT
191 CCTCGGGTCACACGCCGAGCTATT
61618496 CTTGATTTCT
Statistics
Matches: 192, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
264 5 0.03
265 12 0.06
266 112 0.58
267 51 0.27
268 12 0.06
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35
Consensus pattern (267 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGATATTTCTTTCAA
GTTTCTGTTTTTCAAAAATAAACTCATATTGCTAGAAGTGAGTTGAGCCTCGGGTCACACGCTGA
GGTATTTTTCAATTTCTGTCTTTTTCATAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
GGTCACACGCCGAGCTATTTTAAATTTATGTTTTTCTAAAATCAACTCATATTGCGAGAGGTCTG
TTTTTCT
Found at i:61618496 original size:78 final size:79
Alignment explanation
Indices: 61618272--61618498 Score: 318
Period size: 78 Copynumber: 2.9 Consensus size: 79
61618262 TTGCGAGAGG
*
61618272 TCTG-TTTTTCTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGA
1 TCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGA
61618336 TA-T-TTTTCAATT
66 TATTCTTTTCAATT
* * ** *
61618348 TTTGTTTTTTCAAAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCGGGTCATATGCTGAG
1 TCTGTTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAG
*
61618413 GTATTCTTTTCAATT
65 ATATTCTTTTCAATT
* * * *
61618428 TCT-TTTTTTCAAGAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCCGAGC
1 TCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGA
61618492 TATTCTT
66 TATTCTT
61618499 GATTTCTGCT
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
76 3 0.02
77 6 0.05
78 103 0.79
79 8 0.06
80 11 0.08
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (79 bp):
TCTGTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGA
TATTCTTTTCAATT
Found at i:61618685 original size:30 final size:29
Alignment explanation
Indices: 61618650--61618805 Score: 197
Period size: 30 Copynumber: 5.2 Consensus size: 29
61618640 CGTGTTTAAA
*
61618650 AAAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTTAACCCCTAAAC-TTTCT
*
61618680 AAAATTACATTTTAATCCCTAAACTTTCT
1 AAAATTACATTTTAACCCCTAAACTTTCT
* *
61618709 CAAAATTATATTTCAACCCCTAAACTTTTCT
1 -AAAATTACATTTTAACCCCTAAAC-TTTCT
* *
61618740 -AAATTACATTTTGACCCTTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTC-T
*
61618769 AAAATTACATTTTAACCCTTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTC-T
61618799 AAAATTA
1 AAAATTA
61618806 GGTTTTGGCT
Statistics
Matches: 112, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.04
29 25 0.22
30 78 0.70
31 5 0.04
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (29 bp):
AAAATTACATTTTAACCCCTAAACTTTCT
Found at i:61618773 original size:59 final size:60
Alignment explanation
Indices: 61618650--61618805 Score: 219
Period size: 59 Copynumber: 2.6 Consensus size: 60
61618640 CGTGTTTAAA
*
61618650 AAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAATCCCTAAACTTTCTC
1 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAATCCCTAAACTTTCTC
* * * *
61618710 AAAATTATATTTCAACCCCTAAACTTTTCT-AAATTACATTTTGA-CCCTTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAATCCC-TAAACTTTCTC
*
61618769 AAAATTACATTTTAACCCTTAAAC-TTTCTTAAAATTA
1 AAAATTACATTTTAACCCCTAAACTTTTC-TAAAATTA
61618806 GGTTTTGGCT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
58 7 0.08
59 45 0.53
60 33 0.39
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAATCCCTAAACTTTCTC
Found at i:61619293 original size:18 final size:17
Alignment explanation
Indices: 61619270--61619321 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
61619260 GGGGCCAAAC
61619270 AAGGAAGAAGAAGAAAGA
1 AAGGAAGAAGAA-AAAGA
61619288 AAGGAAGAAGAAAAAGA
1 AAGGAAGAAGAAAAAGA
61619305 AA--AAG--GAAAAAGA
1 AAGGAAGAAGAAAAAGA
61619318 AAGG
1 AAGG
61619322 GGGAAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.31
15 3 0.09
17 7 0.22
18 12 0.38
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AAGGAAGAAGAAAAAGA
Found at i:61619313 original size:13 final size:13
Alignment explanation
Indices: 61619297--61619346 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
61619287 AAAGGAAGAA
61619297 GAAAAAGAAAAAG
1 GAAAAAGAAAAAG
*
61619310 GAAAAAG-AAAGG
1 GAAAAAGAAAAAG
** *
61619322 GGGAAAGAAAAAA
1 GAAAAAGAAAAAG
61619335 GAAAAAGAAAAA
1 GAAAAAGAAAAA
61619347 ATTGTTTTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAAG
Found at i:61619345 original size:5 final size:6
Alignment explanation
Indices: 61619277--61619346 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
61619267 AACAAGGAAG
* * ** **
61619277 AAGAAGA AAG-AA AGGAAG AAGAAA AAGAAA AAGGAAA AAGAAA GGGGGA
1 AAGAA-A AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA
61619326 AAGAAAA AAGAAA AAGAAA AA
1 AAG-AAA AAGAAA AAGAAA AA
61619347 ATTGTTTTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
5 3 0.06
6 32 0.67
7 13 0.27
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:61619504 original size:10 final size:10
Alignment explanation
Indices: 61619485--61619555 Score: 76
Period size: 10 Copynumber: 7.0 Consensus size: 10
61619475 AAAAAGAGAG
61619485 AAGA-AAAAA
1 AAGAGAAAAA
61619494 AAGAGAAAAA
1 AAGAGAAAAA
61619504 AAGAGAAAAA
1 AAGAGAAAAA
61619514 AAGAGAAAAGAAA
1 AAGAG--AA-AAA
*
61619527 AAAAGAAAAA
1 AAGAGAAAAA
61619537 AA-AGAAAAGA
1 AAGAGAAAA-A
61619547 AA-AGAAAAA
1 AAGAGAAAAA
61619556 TTCAATTTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
9 11 0.20
10 34 0.61
11 2 0.04
12 2 0.04
13 7 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AAGAGAAAAA
Found at i:61619512 original size:36 final size:34
Alignment explanation
Indices: 61619471--61619555 Score: 120
Period size: 36 Copynumber: 2.5 Consensus size: 34
61619461 GAAGCATGCC
*
61619471 AGAAAAAAAGAGAGAAGAAAAAAAAGAGAAAAAAAG
1 AGAAAAAAAGAGAAAAG-AAAAAAAGA-AAAAAAAG
61619507 AGAAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAG
1 AGAAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAG
61619541 A-AAAGAAAAGA-AAAA
1 AGAAA-AAAAGAGAAAA
61619556 TTCAATTTGC
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 7 0.15
34 15 0.32
35 9 0.19
36 16 0.34
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (34 bp):
AGAAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAG
Found at i:61619519 original size:34 final size:33
Alignment explanation
Indices: 61619473--61619555 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 33
61619463 AGCATGCCAG
*
61619473 AAAAAAAGAGAGAAGAAAAAAAAGAGAAAAAAAGA
1 AAAAAAAGAGAAAAG-AAAAAAAGA-AAAAAAAGA
61619508 GAAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAGA
1 -AAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAGA
61619542 AAAGAAAAGA-AAAA
1 AAA-AAAAGAGAAAA
61619556 TTCAATTTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
33 7 0.16
34 15 0.33
35 9 0.20
36 14 0.31
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (33 bp):
AAAAAAAGAGAAAAGAAAAAAAGAAAAAAAAGA
Found at i:61619527 original size:22 final size:21
Alignment explanation
Indices: 61619476--61619555 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 21
61619466 ATGCCAGAAA
61619476 AAAAGAGAGAAGAAAAAAAAGAG
1 AAAAGA-A-AAGAAAAAAAAGAG
61619499 -AAA-AAAAGAGAAAAAAAGAG
1 AAAAGAAAAGA-AAAAAAAGAG
* *
61619519 AAAAGAAAAAAAGAAAAAAAAG
1 AAAAGAAAAGAA-AAAAAAGAG
61619541 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
61619556 TTCAATTTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.08
20 11 0.22
21 8 0.16
22 27 0.54
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAGAAAAAAAAGAG
Found at i:61619766 original size:17 final size:17
Alignment explanation
Indices: 61619709--61620079 Score: 156
Period size: 18 Copynumber: 20.5 Consensus size: 17
61619699 GTTTTCGTAT
*
61619709 TTTCAAAAAATTCTCGTG
1 TTTC-AAAAATTTTCGTG
* ** *
61619727 TCTTAAAAAAAATTCCTG
1 T-TTCAAAAATTTTCGTG
61619745 TTTTCAAAAATTTTCGTG
1 -TTTCAAAAATTTTCGTG
***
61619763 TTTCAAAACAAAAAATCTGTG
1 TTTC--AA-AAATTTTC-GTG
* *** *
61619784 TTTTAAAAAAAATCGTT
1 TTTCAAAAATTTTCGTG
**
61619801 TTTCAAAAATCCTCGTG
1 TTTCAAAAATTTTCGTG
* *
61619818 TTTTCAAAAATTCTGGTG
1 -TTTCAAAAATTTTCGTG
61619836 TTTCAAAAATTTT--TG
1 TTTCAAAAATTTTCGTG
* * *
61619851 TTTAAAAAAAAATTCTCATG
1 TTT---CAAAAATTTTCGTG
* *
61619871 TTTCAGAATTTTTCGTG
1 TTTCAAAAATTTTCGTG
*
61619888 TTTTCAAAAATTCTCACGT-
1 -TTTCAAAAATT-T-TCGTG
*
61619907 TTTCAAAAAATTCTCGTG
1 TTTC-AAAAATTTTCGTG
* *
61619925 TTTCACAAATTTTTTGTG
1 TTTCA-AAAATTTTCGTG
**
61619943 TTTTCAAAAAAAAATCCTCGTG
1 -TTTC----AAAAATTTTCGTG
* *
61619965 TTTTCAAAAAAATTCTCTTG
1 -TTTC--AAAAATTTTCGTG
*
61619985 TTACAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
61620002 TTTTCAAAAATTTTCGTG
1 -TTTCAAAAATTTTCGTG
*
61620020 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
* * *
61620037 -TTCTTAAAATTCTCGTA
1 TTTC-AAAAATTTTCGTG
*
61620054 TTTCAAAAGTTTTCGTG
1 TTTCAAAAATTTTCGTG
61620071 TTTCAAAAA
1 TTTCAAAAA
61620080 AAATTCTCAC
Statistics
Matches: 270, Mismatches: 57, Indels: 53
0.71 0.15 0.14
Matches are distributed among these distances:
15 5 0.02
16 2 0.01
17 97 0.36
18 98 0.36
19 22 0.08
20 26 0.10
21 6 0.02
22 13 0.05
23 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:61619840 original size:35 final size:35
Alignment explanation
Indices: 61619700--61620079 Score: 227
Period size: 35 Copynumber: 10.5 Consensus size: 35
61619690 AAATTTCATG
* *
61619700 TTTTCGTATTTTCAAAAAATTCTCGTGTCTTAAAAAA
1 TTTTCGTGTTTTC-AAAAATTCTCGTGT-TTCAAAAA
** * *
61619737 AATTCCTGTTTTCAAAAATTTTCGTGTTTCAAAACAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTC--AA-AAA
*** *** *
61619775 AAATCTGTGTTTT-AAAAAAAATCGTTTTTCAAAAA
1 TTTTC-GTGTTTTCAAAAATTCTCGTGTTTCAAAAA
** *
61619810 TCCTCGTGTTTTCAAAAATTCTGGTGTTTCAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAA
** * * *
61619845 TTTT--TGTTTAAAAAAAAATTCTCATGTTTCAGAAT
1 TTTTCGTGTTT--TCAAAAATTCTCGTGTTTCAAAAA
61619880 TTTTCGTGTTTTCAAAAATTCTCACGT-TTTCAAAAAA
1 TTTTCGTGTTTTCAAAAATTCT--CGTGTTTC-AAAAA
* * * *
61619917 TTCTCGTG-TTTCACAAATTTTTTGTGTTTTCAAAAAAAAA
1 TTTTCGTGTTTTCA-AAAATTCTCGTG-TTTC----AAAAA
** * *
61619957 TCCTCGTGTTTTCAAAAAAATTCTCTTGTTACAAAAA
1 TTTTCGTGTTTTC--AAAAATTCTCGTGTTTCAAAAA
* *
61619994 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTAAAAA
1 TTTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAA
* *
61620029 TTTTCGTGTTCTT--AAAATTCTCGTATTTCAAAAG
1 TTTTCGTGTT-TTCAAAAATTCTCGTGTTTCAAAAA
61620063 TTTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
61620080 AAATTCTCAC
Statistics
Matches: 266, Mismatches: 53, Indels: 51
0.72 0.14 0.14
Matches are distributed among these distances:
32 2 0.01
33 6 0.02
34 36 0.14
35 87 0.33
36 26 0.10
37 54 0.20
38 20 0.08
39 6 0.02
40 13 0.05
41 7 0.03
42 8 0.03
43 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTTCGTGTTTTCAAAAATTCTCGTGTTTCAAAAA
Found at i:61620043 original size:18 final size:17
Alignment explanation
Indices: 61619989--61620079 Score: 112
Period size: 17 Copynumber: 5.3 Consensus size: 17
61619979 CTCTTGTTAC
61619989 AAAAATTTTCGTGTTTT
1 AAAAATTTTCGTGTTTT
61620006 CAAAAATTTTCGTGTTTT
1 -AAAAATTTTCGTGTTTT
61620024 AAAAATTTTCGTGTTCTT
1 AAAAATTTTCGTGTT-TT
* * *
61620042 -AAAATTCTCGTATTTC
1 AAAAATTTTCGTGTTTT
* *
61620058 AAAAGTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTT
61620075 AAAAA
1 AAAAA
61620080 AAATTCTCAC
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 1 0.02
17 44 0.69
18 19 0.30
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTT
Found at i:61621021 original size:6 final size:6
Alignment explanation
Indices: 61621010--61621043 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
61621000 AAAAATATTT
61621010 TAAAAA TAAAAAA TAAAAAA TAAAAA TAAAAA TA
1 TAAAAA T-AAAAA T-AAAAA TAAAAA TAAAAA TA
61621044 TTTTTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 14 0.52
7 13 0.48
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:61621023 original size:7 final size:7
Alignment explanation
Indices: 61621011--61621041 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
61621001 AAAATATTTT
61621011 AAAAATA
1 AAAAATA
61621018 AAAAATA
1 AAAAATA
61621025 AAAAAT-
1 AAAAATA
61621031 AAAAATA
1 AAAAATA
61621038 AAAA
1 AAAA
61621042 TATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:61621026 original size:13 final size:14
Alignment explanation
Indices: 61621011--61621041 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
61621001 AAAATATTTT
61621011 AAAAATAAAAAATA
1 AAAAATAAAAAATA
61621025 AAAAAT-AAAAATA
1 AAAAATAAAAAATA
61621038 AAAA
1 AAAA
61621042 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAATA
Found at i:61623335 original size:16 final size:16
Alignment explanation
Indices: 61623307--61623359 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
61623297 TTGGTTCGCT
61623307 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
* * *
61623323 GTAATTGATTAGATGC
1 GTAATGGAATAGAGGC
61623339 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
61623355 GTAAT
1 GTAAT
61623360 AGGTAACTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.36, C:0.06, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:61623394 original size:46 final size:44
Alignment explanation
Indices: 61623341--61623430 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
61623331 TTAGATGCGT
* * *
61623341 AATGGAATAGAGGCGTAATAGGTAACTCTTTTGTTTGGTTGAATGG
1 AATGGAATAAAGGCGTAAT-GGT-ACTCTTGTGTTTAGTTGAATGG
*
61623387 AATGGAATAAAGGCGTAATGGTATTCTTGTGTTTAGTTGAATGG
1 AATGGAATAAAGGCGTAATGGTACTCTTGTGTTTAGTTGAATGG
61623431 GATAGAGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 19 0.47
45 3 0.08
46 18 0.45
ACGTcount: A:0.29, C:0.06, G:0.30, T:0.36
Consensus pattern (44 bp):
AATGGAATAAAGGCGTAATGGTACTCTTGTGTTTAGTTGAATGG
Found at i:61623623 original size:18 final size:18
Alignment explanation
Indices: 61623600--61623753 Score: 71
Period size: 18 Copynumber: 7.9 Consensus size: 18
61623590 TTATTATTAA
61623600 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
61623618 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* ****
61623636 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
61623655 ATATGAATTTAAT-AAAAT
1 ATAT-AATTTAATAAAAAT
* *
61623673 CATATTATATAATACTATAAA-
1 -ATATAATTTAATA--A-AAAT
*
61623694 ATATAATTTAAAATAATTATTATTAA
1 ATATAATTT--AATAA--A--A--AT
61623720 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
61623738 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
61623754 TTCTTAATAT
Statistics
Matches: 104, Mismatches: 15, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
17 4 0.04
18 44 0.42
19 14 0.13
20 12 0.12
21 6 0.06
22 8 0.08
23 1 0.01
24 5 0.05
25 1 0.01
26 9 0.09
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:61623710 original size:120 final size:121
Alignment explanation
Indices: 61623580--61623831 Score: 461
Period size: 120 Copynumber: 2.1 Consensus size: 121
61623570 TTAATCATAT
*
61623580 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
* *
61623645 -AAATATTCTTATATGAATTTAATAAAATCATATTATATAATACTATAAAATATAA
66 AAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
61623700 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
*
61623765 AAAATATTCTTAAATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
61623821 TTTAAAATAAT
1 TTTAAAATAAT
61623832 AAAATTTGAA
Statistics
Matches: 127, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
120 64 0.50
121 63 0.50
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (121 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
AAAATATTCTTAAATGAATTTAATAAAATCATAATATATAATACTATAAAATATAA
Found at i:61623766 original size:18 final size:17
Alignment explanation
Indices: 61623723--61623777 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
61623713 TTATTAAATA
* *
61623723 TAATTTAATAAAAATAT
1 TAATTTAATAAAATTCT
61623740 ATAATTTAATAAAATTCT
1 -TAATTTAATAAAATTCT
*
61623758 TAATATTAA-AATATTCT
1 TAAT-TTAATAAAATTCT
61623775 TAA
1 TAA
61623778 ATGAATTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 14 0.42
18 19 0.58
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTTAATAAAATTCT
Found at i:61623876 original size:20 final size:20
Alignment explanation
Indices: 61623829--61623867 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61623819 AATTTAAAAT
*
61623829 AATAAAATTTGAATCGATTA
1 AATAATATTTGAATCGATTA
* *
61623849 AATGATATTTGAATTGATT
1 AATAATATTTGAATCGATT
61623868 TGATAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.41
Consensus pattern (20 bp):
AATAATATTTGAATCGATTA
Found at i:61627173 original size:19 final size:18
Alignment explanation
Indices: 61627151--61627196 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
61627141 AGAAATCTGG
61627151 AGAAAAGAAAATAGAGAAA
1 AGAAAAGAAAAT-GAGAAA
* *
61627170 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGAGAAA
61627187 AGAAAAGAAA
1 AGAAAAGAAA
61627197 CGTACCGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.46
18 6 0.25
19 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGAGAAA
Found at i:61640260 original size:41 final size:40
Alignment explanation
Indices: 61640203--61640522 Score: 329
Period size: 41 Copynumber: 7.8 Consensus size: 40
61640193 ATTTTTTAAC
*
61640203 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GAT
* *
61640244 CTTTAGCGGCATTTTTGTCTATGCGCCGCTAATGCTCGAGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGA-T
* * *
61640285 CTTTAGCGGCGTTTTCGTGTAGGCGCCGCTAATGCTCGAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCG-AT
*
61640326 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GAT
* *
61640367 CTTTAGCGGCGTTTTTATAC-AAGCGCCGCTAATACTCGGAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTC-GAT
** * * *
61640408 CTTTAGCGGCGTTTTTAACTGAGCGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC--GAT
* * * * * * *
61640449 CTTCAGCGGCATTTGTATCTAAGCGCCGCTAATGTATTGAC
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATG-CTCGAT
** *
61640490 CTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
61640523 AGTAACAAAA
Statistics
Matches: 238, Mismatches: 33, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
40 4 0.02
41 229 0.96
42 5 0.02
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGAT
Found at i:61641051 original size:15 final size:15
Alignment explanation
Indices: 61641030--61641067 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
61641020 TTTAAGGTTA
61641030 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
61641045 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
61641060 ATTTAGGG
1 ATTTAGGG
61641068 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:61642386 original size:37 final size:38
Alignment explanation
Indices: 61642316--61642387 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
61642306 AAATTTGATG
**
61642316 TTTAGGGGTTAGGGGGATTTAAGGTTTAAGGGTTATAC
1 TTTAGGGGTTAGGGGGATTTAAGGGGTAAGGGTTATAC
61642354 TTTAGGGGTTA-GGGGATTT-AGGGGTAATGGGTTA
1 TTTAGGGGTTAGGGGGATTTAAGGGGTAA-GGGTTA
61642388 GGGGGTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 6 0.19
37 14 0.45
38 11 0.35
ACGTcount: A:0.22, C:0.01, G:0.40, T:0.36
Consensus pattern (38 bp):
TTTAGGGGTTAGGGGGATTTAAGGGGTAAGGGTTATAC
Found at i:61642597 original size:35 final size:36
Alignment explanation
Indices: 61642558--61642627 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
61642548 AATTTATTTA
* *
61642558 TTTAT-CAATAAAATTAAATATTATAA-ATTTCAAAC
1 TTTATACAA-AAAAATAAATATTATAATATTACAAAC
61642593 TTTATACAAAAAAATAAATATTATAATATTACAAA
1 TTTATACAAAAAAATAAATATTATAATATTACAAA
61642628 TTAAAAGTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (36 bp):
TTTATACAAAAAAATAAATATTATAATATTACAAAC
Found at i:61650502 original size:42 final size:42
Alignment explanation
Indices: 61650455--61650616 Score: 175
Period size: 43 Copynumber: 3.8 Consensus size: 42
61650445 AGGTGTTGGC
*
61650455 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGG
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGG
* ** * *
61650497 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATA-GT
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGAT-A-AGGG
* *
61650540 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGG
1 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGG
* **
61650582 TCTATT-GTGGCGTTTGAGGGGAAAGCGCCGCTAAA
1 -CT-TTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAA
61650617 AACCCTGATC
Statistics
Matches: 98, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 33 0.34
43 61 0.62
44 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (42 bp):
CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTAAAGATAAGGG
Found at i:61650642 original size:86 final size:85
Alignment explanation
Indices: 61650455--61650685 Score: 261
Period size: 86 Copynumber: 2.7 Consensus size: 85
61650445 AGGTGTTGGC
*
61650455 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGCTTTAGCGGCGTTTGTGGAAAAA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGCTTTAGCGGCGTTTGAGGAAAAA
* *
61650520 GCGCCACTAAAGATCATAGT
66 GCGCCACTAAAAACCATAGT
* * **
61650540 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATT-GTGGCGTTTGAGGGGA
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGG-CT-TTAGCGGCGTTTGAGGAAA
* *
61650604 AAGCGCCGCTAAAAACCCT-GAT
64 AAGCGCCACTAAAAACCATAG-T
** * * * *
61650626 CTTTAGTGATGTTTTTGG-GAGAAGCGCCGCTAAAGATAAGGATCTTTAGCAGCATTTGAG
1 CTTTAGTGGCGTTTTTGGTCA-AAGCGCCGCTAAAGATAAGG-GCTTTAGCGGCGTTTGAG
61650686 AGAGAAGCAC
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
85 45 0.37
86 76 0.62
87 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (85 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGCTTTAGCGGCGTTTGAGGAAAAA
GCGCCACTAAAAACCATAGT
Found at i:61650670 original size:43 final size:42
Alignment explanation
Indices: 61650455--61650704 Score: 159
Period size: 43 Copynumber: 5.9 Consensus size: 42
61650445 AGGTGTTGGC
* * *
61650455 CTTTAGTGGCGTTTTTGGTCA-AAGCGCCGCTAAAGATAAGGG
1 CTTTAGTGGCGTTTGTGG-GAGAAGCGCCGCTAAAGATAAGGT
* * * *
61650497 CTTTAGCGGCGTTTGTGGAAAAAGCGCCACTAAAGATCATA-GT
1 CTTTAGTGGCGTTTGTGGGAGAAGCGCCGCTAAAGAT-A-AGGT
* * *
61650540 CTTTAGTGGCGTTTTTGGTCA-AAGCGCCGCTAAAGATCAGGGT
1 CTTTAGTGGCGTTTGTGG-GAGAAGCGCCGCTAAAGAT-AAGGT
* * *** *
61650583 CTATT-GTGGCGTTTGAGGG-GAAAGCGCCGCTAAAAACCCTGAT
1 CT-TTAGTGGCGTTTGTGGGAG-AAGCGCCGCTAAAGA-TAAGGT
** *
61650626 CTTTAGTGATGTTTTTGGGAGAAGCGCCGCTAAAGATAAGGAT
1 CTTTAGTGGCGTTTGTGGGAGAAGCGCCGCTAAAGATAAGG-T
** * * * *
61650669 CTTTAGCAGCATTTGAGAGAGAAGCACCGCTAAAGA
1 CTTTAGTGGCGTTTGTGGGAGAAGCGCCGCTAAAGA
61650705 CCCTTGTCTT
Statistics
Matches: 160, Mismatches: 36, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
41 1 0.01
42 34 0.21
43 120 0.75
44 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (42 bp):
CTTTAGTGGCGTTTGTGGGAGAAGCGCCGCTAAAGATAAGGT
Found at i:61650699 original size:86 final size:86
Alignment explanation
Indices: 61650455--61650717 Score: 232
Period size: 86 Copynumber: 3.1 Consensus size: 86
61650445 AGGTGTTGGC
* * * * * *
61650455 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGG-GCT-TTAGCGGCGTTTGTGGAAA
1 CTTTAGTGACGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGATCTATT-GCAGCATTTGAGGAGA
* * * * * *
61650518 AAGCGCCACTAAAGATCATAGT
65 AAGCACCGCTAAAAACCCTTGT
* * * ** * *
61650540 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGTCTATTGTGGCGTTTGAGGGGAA
1 CTTTAGTGACGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGATCTATTGCAGCATTTGAGGAGAA
*
61650605 AGCGCCGCTAAAAACCC-TGAT
66 AGCACCGCTAAAAACCCTTG-T
* *
61650626 CTTTAGTGATGTTTTTGG-GAGAAGCGCCGCTAAAGATAAGGATCT-TTAGCAGCATTTGA-GAG
1 CTTTAGTGACGTTTTTGGTCA-AAGCGCCGCTAAAGATAAGGATCTATT-GCAGCATTTGAGGAG
*
61650688 AGAAGCACCGCTAAAGACCCTTGT
64 A-AAGCACCGCTAAAAACCCTTGT
61650712 CTTTAG
1 CTTTAG
61650718 CGGCGCTTCT
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
85 47 0.32
86 98 0.66
87 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (86 bp):
CTTTAGTGACGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGATCTATTGCAGCATTTGAGGAGAA
AGCACCGCTAAAAACCCTTGT
Found at i:61651388 original size:60 final size:60
Alignment explanation
Indices: 61651315--61651439 Score: 241
Period size: 60 Copynumber: 2.1 Consensus size: 60
61651305 CTCTTTTATA
61651315 ATTTCTTTGTATTTACTATCATTTAGGCATCCATAACACCAAACATGTTCTTAATTAGCC
1 ATTTCTTTGTATTTACTATCATTTAGGCATCCATAACACCAAACATGTTCTTAATTAGCC
*
61651375 ATTTCTTTGTATTTACTATCATTTAGGCATTCATAACACCAAACATGTTCTTAATTAGCC
1 ATTTCTTTGTATTTACTATCATTTAGGCATCCATAACACCAAACATGTTCTTAATTAGCC
61651435 ATTTC
1 ATTTC
61651440 AATAGCTAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.42
Consensus pattern (60 bp):
ATTTCTTTGTATTTACTATCATTTAGGCATCCATAACACCAAACATGTTCTTAATTAGCC
Found at i:61651751 original size:4 final size:4
Alignment explanation
Indices: 61651734--61651772 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
61651724 ACTCGCTTCT
* * *
61651734 TTAC TTAC TCAC TTAC TTAT TTAC TTAC TTGC TTAC TTA
1 TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTAC TTA
61651773 AATAACTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.51
Consensus pattern (4 bp):
TTAC
Found at i:61652052 original size:49 final size:49
Alignment explanation
Indices: 61651989--61652263 Score: 205
Period size: 50 Copynumber: 5.4 Consensus size: 49
61651979 GCTATGTCCT
* *
61651989 AGACATAGTCTTACATGGGATGTTTTC-TATAC-TGCCAATGCCAT-ATCCC
1 AGACATGGTCTTACATGGGA-GTTCTCATAT-CGTGCCAATGCCATGA-CCC
* *
61652038 AGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGACCC
1 AGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATGACCC
** *** * ** *
61652088 AGACATGGTCTTACGGGGGACCCCTCATCTCGGTGCCAACACCATGTCCC
1 AGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATGACCC
** ** * *
61652138 AGACATGGTCTTACATGGGACCTCTCACCTCGGTGCCAACGCCATGTCCC
1 AGACATGGTCTTACATGGGAGTTCTCATATC-GTGCCAATGCCATGACCC
** * *
61652188 AGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCTAATGCCATGTCCC
1 AGACATGGTCTTACATGGGAGTTCTCAT-A--TC---G-TGCCAATGCCATGACCC
61652244 AGACATGGTCTTACATGGGA
1 AGACATGGTCTTACATGGGA
61652264 TCTCATTCCC
Statistics
Matches: 191, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
48 6 0.03
49 21 0.11
50 125 0.65
51 1 0.01
53 2 0.01
55 1 0.01
56 35 0.18
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (49 bp):
AGACATGGTCTTACATGGGAGTTCTCATATCGTGCCAATGCCATGACCC
Found at i:61652090 original size:50 final size:50
Alignment explanation
Indices: 61652021--61652263 Score: 245
Period size: 50 Copynumber: 4.7 Consensus size: 50
61652011 TTTTCTATAC
* * **
61652021 TGCCAATGCCAT-ATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGA-CCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** * *
61652071 TGCCCATGCCATGACCCAGACATGGTCTTACGGGGGACCCCTCATCTCGG
1 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * **
61652121 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCACCTCGG
1 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
61652171 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
61652227 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGACCCAGACATGGTCTTACATGGGA
61652264 TCTCATTCCC
Statistics
Matches: 164, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
50 125 0.76
51 1 0.01
53 2 0.01
56 36 0.22
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (50 bp):
TGCCAACGCCATGACCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:61652148 original size:100 final size:104
Alignment explanation
Indices: 61652029--61652263 Score: 280
Period size: 100 Copynumber: 2.3 Consensus size: 104
61652019 ACTGCCAATG
* * ** * * *
61652029 CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGACCCAGACAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCACATCGGTGCCAACGCCATGACCCAGACAT
* * *
61652094 GGTCTTACGGGGGACC-C-C-TCATCTC-GGTGCCAACA
66 GGTCTTACAGGGGACCTCTCATAATCTCAGATGCCAACA
* *
61652129 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCACCTCGGTGCCAACGCCATGTCCCAGACAT
1 CCATGTCCCAGACATGGTCTTACATGGGACCTCTCACATCGGTGCCAACGCCATGACCCAGACAT
* * **
61652194 GGTCTTACATGGGACCTCTCATAATCTCAATGATGCTAATG
66 GGTCTTACAGGGGACCTCTCATAATCTC-A-GATGCCAACA
61652235 CCATGTCCCAGACATGGTCTTACATGGGA
1 CCATGTCCCAGACATGGTCTTACATGGGA
61652264 TCTCATTCCC
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
100 70 0.62
101 1 0.01
102 1 0.01
103 6 0.05
106 35 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (104 bp):
CCATGTCCCAGACATGGTCTTACATGGGACCTCTCACATCGGTGCCAACGCCATGACCCAGACAT
GGTCTTACAGGGGACCTCTCATAATCTCAGATGCCAACA
Found at i:61654272 original size:3 final size:3
Alignment explanation
Indices: 61654266--61654292 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
61654256 TATCATATTA
61654266 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
61654293 TATTATTACT
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:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:61654482 original size:14 final size:14
Alignment explanation
Indices: 61654460--61654489 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61654450 ATTTATATAC
*
61654460 ATATCTATATCTAT
1 ATATATATATCTAT
61654474 ATATATATATCTAT
1 ATATATATATCTAT
61654488 AT
1 AT
61654490 GCATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATATCTAT
Found at i:61654489 original size:104 final size:102
Alignment explanation
Indices: 61654350--61654594 Score: 228
Period size: 104 Copynumber: 2.4 Consensus size: 102
61654340 GTTATACATA
* * * *
61654350 TATATACATACATACATACATTTTTATA-ATATATAT-ACACGTGCATAATTTT-ATAATTTATT
1 TATATACAT--ATATATACATATATATACATATATATCACACGTGCATAATTTTCATAA---ATG
* *
61654412 TTTATATATACATACTTATATATGTTTTATATTTTATAA-TT
61 TATATATATACATACTTATATATATTTTATATTTTATAATTT
* * * * ** *** *
61654453 TATATACATATCTATATCTATATATATATATCTATATGCATATTTTTTTCATTTTCATAAATGTA
1 TATATACATATATATA-C-ATATATATACATATATAT-CACACGTGCATAATTTTCATAAATGTA
*
61654518 TATATGTACATACTTATATATATTTTATATTTTATAATTTT
63 TATATATACATACTTATATATATTTTATATTTTATAA-TTT
61654559 TATATACATATATATACATATATATACATATATATC
1 TATATACATATATATACATATATATACATATATATC
61654595 TTTTTATATT
Statistics
Matches: 115, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
101 5 0.04
102 1 0.01
103 17 0.15
104 61 0.53
105 1 0.01
106 26 0.23
107 4 0.03
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (102 bp):
TATATACATATATATACATATATATACATATATATCACACGTGCATAATTTTCATAAATGTATAT
ATATACATACTTATATATATTTTATATTTTATAATTT
Found at i:61654574 original size:10 final size:10
Alignment explanation
Indices: 61654559--61654593 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
61654549 TTATAATTTT
61654559 TATATACATA
1 TATATACATA
61654569 TATATACATA
1 TATATACATA
61654579 TATATACATA
1 TATATACATA
61654589 TATAT
1 TATAT
61654594 CTTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (10 bp):
TATATACATA
Found at i:61654602 original size:20 final size:21
Alignment explanation
Indices: 61654550--61654603 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
61654540 TTTTATATTT
*
61654550 TATAATTTTTATATACATATA
1 TATACTTTTTATATACATATA
* *
61654571 TATAC-ATATATATACATATA
1 TATACTTTTTATATACATATA
61654591 TAT-CTTTTTATAT
1 TATACTTTTTATAT
61654604 TTTTATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.81
21 4 0.15
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
TATACTTTTTATATACATATA
Found at i:61655089 original size:74 final size:73
Alignment explanation
Indices: 61654968--61655112 Score: 227
Period size: 74 Copynumber: 2.0 Consensus size: 73
61654958 ATCTTTTCCA
* * * * *
61654968 CTCAAGTTTTATATGATCTCGGGAATTAAGAAGAGATCGTGTTCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
61655033 TTTTTTTC
66 TTTTTTTC
*
61655041 CTCAAGTTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTTGGCATGATCC
1 CTCAAG-TTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCC
61655106 CTTTTTT
65 CTTTTTT
61655113 AAACTGAGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
73 6 0.09
74 59 0.91
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTTC
Found at i:61667041 original size:50 final size:50
Alignment explanation
Indices: 61666977--61667143 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
61666967 TCGACAATAG
* * * * *
61666977 CGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCCATAACGA
1 CGAATCTTGCTTCCCCGGAGGTGCAGTGGAAAAGATTGAAGCCACAACGA
* ** ** ** *
61667027 CGAATCTTGTTTCCCCAAAATTGCAGTTAAAAAGATTGAAGCCACAATGA
1 CGAATCTTGCTTCCCCGGAGGTGCAGTGGAAAAGATTGAAGCCACAACGA
* * * * *
61667077 TGAATCTTCCTTCCCCGGAGGTGCAGTGGAATAGATTGAAGCTACAACGG
1 CGAATCTTGCTTCCCCGGAGGTGCAGTGGAAAAGATTGAAGCCACAACGA
61667127 CGAATCTTGCTTCCCCG
1 CGAATCTTGCTTCCCCG
61667144 ACATTGCAGT
Statistics
Matches: 89, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
CGAATCTTGCTTCCCCGGAGGTGCAGTGGAAAAGATTGAAGCCACAACGA
Found at i:61667150 original size:100 final size:100
Alignment explanation
Indices: 61666978--61667158 Score: 272
Period size: 100 Copynumber: 1.8 Consensus size: 100
61666968 CGACAATAGC
* * * *
61666978 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCCATAACGACGAATCTTGTTTCCCC
1 GAATCTTACTTCCCCGGAGGTGCAGTGGAACAGATTGAAGCCACAACGACGAATCTTGCTTCCCC
61667043 AAAATTGCAGTTAAAAAGATTGAAGCCACAATGAT
66 AAAATTGCAGTTAAAAAGATTGAAGCCACAATGAT
* * * *
61667078 GAATCTTCCTTCCCCGGAGGTGCAGTGGAATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCC
1 GAATCTTACTTCCCCGGAGGTGCAGTGGAACAGATTGAAGCCACAACGACGAATCTTGCTTCCCC
* *
61667143 GACATTGCAGTTAAAA
66 AAAATTGCAGTTAAAA
61667159 TGATCTAAGC
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (100 bp):
GAATCTTACTTCCCCGGAGGTGCAGTGGAACAGATTGAAGCCACAACGACGAATCTTGCTTCCCC
AAAATTGCAGTTAAAAAGATTGAAGCCACAATGAT
Found at i:61669192 original size:33 final size:33
Alignment explanation
Indices: 61669115--61669201 Score: 88
Period size: 33 Copynumber: 2.6 Consensus size: 33
61669105 CAAATTTCGT
* *
61669115 TATACATATATATACATACATACATTTTTATAA
1 TATATATATATATACATACATACATTGTTATAA
*
61669148 TATATAGATATATACA-A-ATACATAATGTTATAA
1 TATATATATATATACATACATACAT--TGTTATAA
*
61669181 TTTATTTATATATATACATAC
1 --TATATATATATATACATAC
61669202 TTATATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 6 0.14
32 1 0.02
33 21 0.49
35 14 0.33
36 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (33 bp):
TATATATATATATACATACATACATTGTTATAA
Found at i:61669241 original size:47 final size:44
Alignment explanation
Indices: 61669175--61669365 Score: 146
Period size: 45 Copynumber: 4.2 Consensus size: 44
61669165 ATACATAATG
*
61669175 TTATAATTTAT-TTATATATATACATACTTATATATGTTTTATATT
1 TTATAATTTATATCATATATAT-CATACTTATATAT-TTTTATATT
*
61669220 TTATAATTTATATACATATATATCTATA-TGCATA-ATTTTT-TCATT
1 TTATAATTTATAT-CATATATATC-ATACT-TATATATTTTTAT-ATT
* *
61669265 TTCATAA-ATGTAT-ATATATA-CATACTTATATATATTTTATATT
1 TT-ATAATTTATATCATATATATCATACTTATATAT-TTTTATATT
* *
61669308 TTATAATTTTTATATACATATATAT-ATACAAATATATCTTTTTATATTT
1 TTATAA--TTTATAT-CATATATATCATAC--TTATATATTTTTATA-TT
61669357 TTATAATTT
1 TTATAATTT
61669366 TATTTTCTTT
Statistics
Matches: 118, Mismatches: 9, Indels: 36
0.72 0.06 0.22
Matches are distributed among these distances:
41 6 0.05
42 8 0.07
43 16 0.14
44 2 0.02
45 28 0.24
46 9 0.08
47 28 0.24
48 7 0.06
49 14 0.12
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (44 bp):
TTATAATTTATATCATATATATCATACTTATATATTTTTATATT
Found at i:61669309 original size:51 final size:48
Alignment explanation
Indices: 61669254--61669366 Score: 118
Period size: 51 Copynumber: 2.3 Consensus size: 48
61669244 TATATGCATA
* ** *
61669254 ATTTTTTCATTTTCATAAATGTATATATATACATACTTATATATATTTTAT
1 ATTTTTTAATTTTCATAAACATATATATATACA-A-ATATATAT-TTTTAT
* * * *
61669305 ATTTTATAATTTTTATATACATATATATATACAAATATATCTTTTTAT
1 ATTTTTTAATTTTCATAAACATATATATATACAAATATATATTTTTAT
61669353 ATTTTTATAATTTT
1 ATTTTT-TAATTTT
61669367 ATTTTCTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 11 0.21
49 13 0.25
50 1 0.02
51 27 0.52
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (48 bp):
ATTTTTTAATTTTCATAAACATATATATATACAAATATATATTTTTAT
Found at i:61669831 original size:74 final size:73
Alignment explanation
Indices: 61669720--61669864 Score: 272
Period size: 74 Copynumber: 2.0 Consensus size: 73
61669710 TCTTTTCAAA
*
61669720 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGCCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGCCATGATCCC
61669785 TTTTTTTC
66 TTTTTTTC
61669793 CTCAAGTTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGCCATGATCC
1 CTCAAG-TTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGCCATGATCC
61669858 CTTTTTT
65 CTTTTTT
61669865 AAACCCGAGA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
73 6 0.09
74 64 0.91
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (73 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGCCATGATCCC
TTTTTTTC
Found at i:61672289 original size:37 final size:37
Alignment explanation
Indices: 61672248--61672423 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
61672238 TTTGAGTACT
61672248 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
61672285 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
61672322 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
61672359 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
61672396 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
61672424 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:61672495 original size:45 final size:46
Alignment explanation
Indices: 61672386--61672509 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
61672376 GTGATAAGTG
* *
61672386 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
61672432 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
61672477 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
61672510 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:61674945 original size:25 final size:25
Alignment explanation
Indices: 61674916--61674999 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 25
61674906 GCCCTCTCTC
**
61674916 GAGCCATATAACGGGAATCTTATGT
1 GAGCCATATAACGGGAATCTTATAA
* * * **
61674941 GAGCCATGTAAGGGGAAGCTTATCC
1 GAGCCATATAACGGGAATCTTATAA
* ** *
61674966 GGGCTGTATAACGGGAATCTCATAA
1 GAGCCATATAACGGGAATCTTATAA
61674991 GAGCCATAT
1 GAGCCATAT
61675000 TTAGGGAGCT
Statistics
Matches: 42, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (25 bp):
GAGCCATATAACGGGAATCTTATAA
Found at i:61675057 original size:24 final size:24
Alignment explanation
Indices: 61675015--61675152 Score: 59
Period size: 26 Copynumber: 5.6 Consensus size: 24
61675005 GAGCTTATAT
* * *
61675015 GAGCCAATAACGAGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
61675039 GAGCCATTAACGGGAAGCTTCGGA
1 GAGCCATTAACGGGAAGCTCCGAA
* *
61675063 GAACCATATATC-GG--GCTCC-AGA
1 GAGCCAT-TAACGGGAAGCTCCGA-A
*** *
61675085 GAGCCATTATTTAGGAAGCTCACAAA
1 GAGCCATTA-ACGGGAAGCTC-CGAA
* *
61675111 GAGCCTTTAATCAGGAAGCTCACGAA
1 GAGCCATTAA-CGGGAAGCTC-CGAA
*
61675137 GAGCCATATATCGGGA
1 GAGCCAT-TAACGGGA
61675153 CGTTCATAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
21 2 0.02
22 12 0.14
23 2 0.02
24 27 0.31
25 7 0.08
26 33 0.38
27 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCGAA
Found at i:61675113 original size:26 final size:26
Alignment explanation
Indices: 61675084--61675143 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
61675074 CGGGCTCCAG
* *
61675084 AGAGCCATTATTTAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* *
61675110 AGAGCCTTTAATCAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
61675136 AGAGCCAT
1 AGAGCCAT
61675144 ATATCGGGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:61677939 original size:16 final size:16
Alignment explanation
Indices: 61677903--61677941 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
61677893 GCTTGGTTCA
*
61677903 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
61677919 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
61677935 CTGTAAT
1 CTGTAAT
61677942 CAATAATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.31, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:61679350 original size:104 final size:104
Alignment explanation
Indices: 61679155--61679526 Score: 593
Period size: 105 Copynumber: 3.6 Consensus size: 104
61679145 TTGTACATAA
** *
61679155 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
**
61679220 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
61679259 AGGGGTTGCTAAGTGCTGATTCCCCTATTTCATTGGTTGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
61679324 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * * *
61679363 ACGGATTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAATGCGATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
61679428 TGAAATGAAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATG-AAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
61679468 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCG
61679527 ATAACGGTTA
Statistics
Matches: 246, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
103 42 0.17
104 78 0.32
105 126 0.51
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:61680003 original size:21 final size:21
Alignment explanation
Indices: 61679977--61680017 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
61679967 GAGTCTATTT
*
61679977 TTATTATAAACAAGCAAAACA
1 TTATTAGAAACAAGCAAAACA
61679998 TTATTAGAAACAAGCAAAAC
1 TTATTAGAAACAAGCAAAAC
61680018 CATTTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (21 bp):
TTATTAGAAACAAGCAAAACA
Found at i:61680983 original size:20 final size:20
Alignment explanation
Indices: 61680958--61681014 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
61680948 TAATTATTAA
61680958 ATATAATTTAATAACATAAT
1 ATATAATTTAATAACATAAT
61680978 ATATAATTTAATAACATAAT
1 ATATAATTTAATAACATAAT
61680998 ATATAATTTAATAACAT
1 ATATAATTTAATAACAT
61681015 TCTTAATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAATTTAATAACATAAT
Found at i:61684293 original size:13 final size:13
Alignment explanation
Indices: 61684275--61684319 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
61684265 AGCACACAGG
61684275 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
61684288 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
*
61684301 TGTGTGGCTTGGC
1 CGTGTGGCTTGGC
*
61684314 CATGTG
1 CGTGTG
61684320 ACCCAAGTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.44, T:0.33
Consensus pattern (13 bp):
CGTGTGGCTTGGC
Found at i:61693244 original size:15 final size:16
Alignment explanation
Indices: 61693218--61693250 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
61693208 ATGGATTAGG
*
61693218 GAAAAATCAAGAAGAA
1 GAAAAATCAAGAAAAA
61693234 GAAAAAT-AAGAAAAA
1 GAAAAATCAAGAAAAA
61693249 GA
1 GA
61693251 CGAAAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.73, C:0.03, G:0.18, T:0.06
Consensus pattern (16 bp):
GAAAAATCAAGAAAAA
Found at i:61696630 original size:43 final size:43
Alignment explanation
Indices: 61696564--61696662 Score: 162
Period size: 43 Copynumber: 2.3 Consensus size: 43
61696554 CTATGCTTTT
* *
61696564 AATTTATAATTAATTATTTTAAAATTATTGATATATTATCATC
1 AATTTTTAATTAATTATTTTAAAATTATTGATATATTATCATA
* *
61696607 ATTTTTTAATTATTTATTTTAAAATTATTGATATATTATCATA
1 AATTTTTAATTAATTATTTTAAAATTATTGATATATTATCATA
61696650 AATTTTTAATTAA
1 AATTTTTAATTAA
61696663 ATCTCCTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (43 bp):
AATTTTTAATTAATTATTTTAAAATTATTGATATATTATCATA
Found at i:61699625 original size:13 final size:13
Alignment explanation
Indices: 61699603--61699634 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
61699593 TTTCTGTTAT
61699603 TATA-ATTGTGTG
1 TATATATTGTGTG
61699615 TATATATTGTGTG
1 TATATATTGTGTG
61699628 TATATAT
1 TATATAT
61699635 ATTATATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (13 bp):
TATATATTGTGTG
Found at i:61706786 original size:180 final size:180
Alignment explanation
Indices: 61706475--61706819 Score: 521
Period size: 180 Copynumber: 1.9 Consensus size: 180
61706465 TGTACCTAAT
* * * *
61706475 GGAGGACTACTATTGGCTATAGACGAAGGAAGTAAAAGAGGTCGGGACTGAGATTGGGCTGAGTG
1 GGAGGACTACTATTGGCTAGAGACAAAGGAAGCAAAAGAGGTCGGGACTGAGATCGGGCTGAGTG
* * * *
61706540 AGAGCTTTCTTGAGGTGAGAAAATGAGAAGGTAAAATGGAAACGATAGAGCTATTCAATGGGTAT
66 AGAGCTTTCTTGAGGTGAGAAAACGAAAAGGTAAAATGGAAACAAAAGAGCTATTCAATGGGTAT
* *
61706605 TCAATGGGGGTGAAACAAAA-TAGGAATTTCCCCTAATAAAGGTTTAATTA
131 TCAATGAGGGTGAAACAAAAGT-GGAATGTCCCCTAATAAAGGTTTAATTA
* * * **
61706655 GGAGGATTGCTATTGGCTGGAGACAAAGGAAGCAAGGGAGGTCGGGACTGAGATCGGGCTGAGTG
1 GGAGGACTACTATTGGCTAGAGACAAAGGAAGCAAAAGAGGTCGGGACTGAGATCGGGCTGAGTG
*
61706720 AGAGCTTTCTTGAGGTGAGAAAACGAAAAGGTAAAATGGAAATAAAAGAGCTATTCAATGGGTAT
66 AGAGCTTTCTTGAGGTGAGAAAACGAAAAGGTAAAATGGAAACAAAAGAGCTATTCAATGGGTAT
*
61706785 TCATTGAGGGTGAAACAAAAGTGGAATGTCCCCTA
131 TCAATGAGGGTGAAACAAAAGTGGAATGTCCCCTA
61706820 TTACATGCTT
Statistics
Matches: 147, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 146 0.99
181 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.32, T:0.22
Consensus pattern (180 bp):
GGAGGACTACTATTGGCTAGAGACAAAGGAAGCAAAAGAGGTCGGGACTGAGATCGGGCTGAGTG
AGAGCTTTCTTGAGGTGAGAAAACGAAAAGGTAAAATGGAAACAAAAGAGCTATTCAATGGGTAT
TCAATGAGGGTGAAACAAAAGTGGAATGTCCCCTAATAAAGGTTTAATTA
Found at i:61717554 original size:16 final size:14
Alignment explanation
Indices: 61717532--61717575 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
61717522 TTTTTAAAGG
61717532 TTAATTAAGTAATT
1 TTAATTAAGTAATT
61717546 TGATAATTAAGTTAAATT
1 T--TAATTAAG-T-AATT
61717564 TTAATTAAGTAA
1 TTAATTAAGTAA
61717576 AAGATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 1 0.04
16 16 0.62
17 1 0.04
18 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
TTAATTAAGTAATT
Found at i:61730022 original size:11 final size:11
Alignment explanation
Indices: 61730008--61730032 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61729998 CGACACTCGA
61730008 TTTTCACTCAT
1 TTTTCACTCAT
61730019 TTTTCACTCAT
1 TTTTCACTCAT
61730030 TTT
1 TTT
61730033 CTCCCAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTCACTCAT
Found at i:61730991 original size:43 final size:43
Alignment explanation
Indices: 61730903--61731207 Score: 445
Period size: 43 Copynumber: 7.1 Consensus size: 43
61730893 AAAAAAGCCA
61730903 GCTAAAGAACC-AGACCTTTAGCGGCGC-TTTCCCACAAACGCC
1 GCTAAAG-ACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* *
61730945 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCTACAAACGAC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
61730988 GCTAAAGAACAAGACCTTTAGCAGCGCTTCTCCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
61731031 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * *
61731074 GCTAAAAACCAAGACCTTTAACGGCGCTTTTTCCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
*
61731117 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCACAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
* * * ** *
61731160 GCTATAGATCAA-ACCTTTAGCGGCGCTTCTAGCAAAAACGCC
1 GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
61731202 GCTAAA
1 GCTAAA
61731208 AACATAACCT
Statistics
Matches: 239, Mismatches: 22, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 3 0.01
42 55 0.23
43 181 0.76
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (43 bp):
GCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGCC
Found at i:61737959 original size:13 final size:13
Alignment explanation
Indices: 61737941--61737966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61737931 TTCGTAAGCG
61737941 AGTAATACATTAT
1 AGTAATACATTAT
61737954 AGTAATACATTAT
1 AGTAATACATTAT
61737967 TTGATATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AGTAATACATTAT
Found at i:61741783 original size:13 final size:13
Alignment explanation
Indices: 61741765--61741791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61741755 AACACAAAAA
61741765 TTGAATCATGAAT
1 TTGAATCATGAAT
61741778 TTGAATCATGAAT
1 TTGAATCATGAAT
61741791 T
1 T
61741792 ACTAGAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGAATCATGAAT
Found at i:61742661 original size:19 final size:18
Alignment explanation
Indices: 61742619--61742661 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
61742609 TTCTGAACGG
61742619 ACTAAGGTTCCTAAGTCT
1 ACTAAGGTTCCTAAGTCT
*
61742637 AGTAAGGTATCCTAAGATC-
1 ACTAAGGT-TCCTAAG-TCT
61742656 ACTAAG
1 ACTAAG
61742662 TCATTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 12 0.57
20 2 0.10
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (18 bp):
ACTAAGGTTCCTAAGTCT
Found at i:61744003 original size:20 final size:20
Alignment explanation
Indices: 61743978--61744016 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
61743968 ATTTAGCCAT
*
61743978 TTTTTATTTTTATTTTAATA
1 TTTTTATTTTTAATTTAATA
61743998 TTTTTATTTTTAATTTAAT
1 TTTTTATTTTTAATTTAAT
61744017 TGTTACATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTATTTTTAATTTAATA
Found at i:61748378 original size:45 final size:45
Alignment explanation
Indices: 61748278--61748475 Score: 188
Period size: 45 Copynumber: 4.5 Consensus size: 45
61748268 TACACGGTGG
* * * *
61748278 ATCAGCACACAGC-ACCACCCTTATAGTCAATAGTA-CTGGTGAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTATCGGGTGAA
* *
61748321 ATCAGCACATAGCAACCACCTTTATACTCAATGGTACCGGGTGAA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTATCGGGTGAA
* * * * * *
61748366 ATCAGCAGATAGCAACCACC-ATATTACT-ATTGGTATCTGATGAA
1 ATCAGCACATAGCAACCACCTTTA-TACTCAATAGTATCGGGTGAA
* ** * * *
61748410 ATCAACACATAGCAACCACCTTTATTTTCATTAATATCGGGTGGA
1 ATCAGCACATAGCAACCACCTTTATACTCAATAGTATCGGGTGAA
*
61748455 ATCAGCACATAGCATCCACCT
1 ATCAGCACATAGCAACCACCT
61748476 ATATTTCCAA
Statistics
Matches: 127, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
43 12 0.09
44 53 0.42
45 62 0.49
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATACTCAATAGTATCGGGTGAA
Found at i:61748451 original size:89 final size:90
Alignment explanation
Indices: 61748317--61748480 Score: 231
Period size: 89 Copynumber: 1.8 Consensus size: 90
61748307 ATAGTACTGG
* ** *
61748317 TGAAATCAGCACATAGCAACCACCTTTATACTCAATGGTACCGGGTGAAATCAGCAGATAGCAAC
1 TGAAATCAACACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGCAAC
61748382 CACC-ATATTACTATTGGTATCTGA
66 CACCTATATTACTATTGGTATCTGA
** * * * *
61748406 TGAAATCAACACATAGCAACCACCTTTATTTTCATTAATATCGGGTGGAATCAGCACATAGCATC
1 TGAAATCAACACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGCAAC
61748471 CACCTATATT
66 CACCTATATT
61748481 TCCAACGATA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
89 59 0.92
90 5 0.08
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (90 bp):
TGAAATCAACACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGCAAC
CACCTATATTACTATTGGTATCTGA
Found at i:61750127 original size:22 final size:21
Alignment explanation
Indices: 61750081--61750134 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
61750071 CACTTTACTG
* *
61750081 TTATTTTTTTGATTGTTTTCC
1 TTATTTTTTTGATTCTTTACC
*
61750102 -TATTTTTTTTATCTCTTTACC
1 TTATTTTTTTGAT-TCTTTACC
61750123 TTATTTTATTTG
1 TTATTTT-TTTG
61750135 TTGTTTATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.42
21 6 0.23
22 6 0.23
23 3 0.12
ACGTcount: A:0.13, C:0.11, G:0.06, T:0.70
Consensus pattern (21 bp):
TTATTTTTTTGATTCTTTACC
Found at i:61750141 original size:21 final size:20
Alignment explanation
Indices: 61750081--61750141 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 20
61750071 CACTTTACTG
*
61750081 TTATTTTTTTGATTGTTTTCC
1 TTATTTTTTTG-TTGTTTACC
* *
61750102 -TATTTTTTTTATCTCTTTACC
1 TTA-TTTTTTTGT-TGTTTACC
61750123 TTATTTTATTTGTTGTTTA
1 TTATTTT-TTTGTTGTTTA
61750142 TCTTCTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
20 3 0.10
21 22 0.71
22 6 0.19
ACGTcount: A:0.13, C:0.10, G:0.07, T:0.70
Consensus pattern (20 bp):
TTATTTTTTTGTTGTTTACC
Found at i:61751871 original size:27 final size:27
Alignment explanation
Indices: 61751817--61751871 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
61751807 ACAATAATAT
*
61751817 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
* *
61751844 AATTATTAAAAT-ATTGAATTTTAATTA
1 AATTA-TAAAATAATTAAATTGTAATTA
61751871 A
1 A
61751872 TTTTATAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:61755682 original size:43 final size:42
Alignment explanation
Indices: 61755635--61755772 Score: 136
Period size: 43 Copynumber: 3.2 Consensus size: 42
61755625 TCTCAAATAG
*
61755635 GGTCTTACACAAAAATCTCAATCGAGGCCTGTGTCCCAGACAC
1 GGTCTTACAC-AAAATCTCAATCGAGGCCTGTGTCCCAAACAC
* * ** *
61755678 GGTCTTACACGAAA--TCAGATACGATGCCCATGTCCCAAACAT
1 GGTCTTACACAAAATCTCA-AT-CGAGGCCTGTGTCCCAAACAC
* **
61755720 GGTCTTATATGTAAATCTCAATCGAGGCCTGTGTCCCAAACAC
1 GGTCTTACA-CAAAATCTCAATCGAGGCCTGTGTCCCAAACAC
*
61755763 AGTCTTACAC
1 GGTCTTACAC
61755773 GATGTCTCAG
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
40 3 0.04
41 2 0.03
42 27 0.36
43 37 0.50
44 2 0.03
45 3 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTCTTACACAAAATCTCAATCGAGGCCTGTGTCCCAAACAC
Found at i:61759760 original size:39 final size:39
Alignment explanation
Indices: 61759716--61759804 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
61759706 TTAAGCCTGA
*
61759716 ATATAATACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
1 ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
*
61759755 ATATAACACCAGCACGAATGCCTTCGGGGCTTAGCCCGG
1 ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
61759794 ATATAACACCA
1 ATATAACACCA
61759805 AATCATATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.19
Consensus pattern (39 bp):
ATATAACACCAGCACAAATGCCTTCGGGGCTTAGCCCGG
Found at i:61760181 original size:19 final size:19
Alignment explanation
Indices: 61760157--61760197 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
61760147 GTTATAATAT
*
61760157 TAATATTCCTTTAATATTA
1 TAATATTCATTTAATATTA
*
61760176 TAATATTCATTTCATATTA
1 TAATATTCATTTAATATTA
61760195 TAA
1 TAA
61760198 AACAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTCATTTAATATTA
Found at i:61760995 original size:15 final size:15
Alignment explanation
Indices: 61760947--61761029 Score: 91
Period size: 15 Copynumber: 5.7 Consensus size: 15
61760937 TAAAGATAAC
*
61760947 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
* *
61760961 AAGAAATCTA-AGATA
1 AAGAAACCCAGA-ATA
*
61760976 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
61760991 AAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
61761006 AAGAAATCCAGAATA
1 AAGAAACCCAGAATA
61761021 AAG-AACCCA
1 AAGAAACCCA
61761030 AGATACAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
14 13 0.22
15 44 0.76
16 1 0.02
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.10
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:61762118 original size:14 final size:14
Alignment explanation
Indices: 61762099--61762136 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
61762089 TATGTATATA
61762099 TCATAATTTTTTAT
1 TCATAATTTTTTAT
61762113 TCATAATTTTTTAT
1 TCATAATTTTTTAT
*
61762127 TCATACTTTT
1 TCATAATTTT
61762137 CTGAATCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (14 bp):
TCATAATTTTTTAT
Found at i:61767553 original size:13 final size:13
Alignment explanation
Indices: 61767535--61767559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61767525 TAATGGTATA
61767535 TTGAATCCATGAC
1 TTGAATCCATGAC
61767548 TTGAATCCATGA
1 TTGAATCCATGA
61767560 AAATTTAGTA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:61768143 original size:27 final size:27
Alignment explanation
Indices: 61768105--61768282 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
61768095 TAAATTGTAC
*
61768105 AGCACTAAGTGTGCGGTTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
61768132 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
61768158 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
61768186 GGCGCTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
61768214 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
61768241 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
61768268 AGCACTGAGGGTGCG
1 AGCACTAAGTGTGCG
61768283 GACTCAATAT
Statistics
Matches: 125, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
27 103 0.82
28 22 0.18
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:61768219 original size:82 final size:81
Alignment explanation
Indices: 61768109--61768261 Score: 227
Period size: 82 Copynumber: 1.9 Consensus size: 81
61768099 TTGTACAGCA
* *
61768109 CTAAGTGTGCGGTTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGC
1 CTAAGTGTGCGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTGTGC
61768173 GAATTGACCATGCGGCG
65 GAATTGACCATGCGGCG
** *
61768190 CTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGC
1 CTAAGTGTGCG-GTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGC
*
61768255 GAGTTGA
65 GAATTGA
61768262 TTATATAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 11 0.17
82 52 0.81
83 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.30
Consensus pattern (81 bp):
CTAAGTGTGCGGTTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGTGCG
AATTGACCATGCGGCG
Found at i:61770995 original size:50 final size:51
Alignment explanation
Indices: 61770871--61771059 Score: 200
Period size: 50 Copynumber: 3.7 Consensus size: 51
61770861 AACCATGTCT
* * * *
61770871 TACACATAGTGGCCTGCACTTAGTACTACACATGTGATCGAAGCTATCGGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* * *
61770922 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CCATCTGG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
* * * * ****
61770972 TACACATAATAGCTTGCACTTAGTACTACACACGTGACCTAAAACCATTTTA
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCT-AAGCCATCGGG
* * *
61771024 AACACATAGTATCCTGCACATAGTACTACACATGTG
1 TACACATAGTAGCCTGCACTTAGTACTACACATGTG
61771060 TTCTCACAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
50 41 0.36
51 39 0.34
52 35 0.30
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACTTAGTACTACACATGTGACCTAAGCCATCGGG
Found at i:61773663 original size:65 final size:65
Alignment explanation
Indices: 61773559--61773688 Score: 215
Period size: 65 Copynumber: 2.0 Consensus size: 65
61773549 CATGCATAAG
*
61773559 TTACTTGTATTTTGATGGTTTATGGAAGAATATGAAAGTTGGACGTGTGTTAAACATCTTTCCCT
1 TTACTTGTATTTTGATGGTTTATGGAAGAATATGAAAGTTGGACGTGTGTTAAACAACTTTCCCT
* * * *
61773624 TTACTTGTATTTTGATGTTTTATGGAGGAATATGAAAGTTTGAGGTGTGTTAAACAACTTTCCCT
1 TTACTTGTATTTTGATGGTTTATGGAAGAATATGAAAGTTGGACGTGTGTTAAACAACTTTCCCT
61773689 AGGTGATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (65 bp):
TTACTTGTATTTTGATGGTTTATGGAAGAATATGAAAGTTGGACGTGTGTTAAACAACTTTCCCT
Found at i:61778831 original size:27 final size:27
Alignment explanation
Indices: 61778801--61778855 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
61778791 ATCTCATATC
*
61778801 TGTAGGCTA-ATATTACTGAAATGCCCT
1 TGTAGGCTAGA-ATTACTGAAATACCCT
*
61778828 TGTAGGGTAGAATTACTGAAATACCCT
1 TGTAGGCTAGAATTACTGAAATACCCT
61778855 T
1 T
61778856 AGTTTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (27 bp):
TGTAGGCTAGAATTACTGAAATACCCT
Found at i:61778868 original size:27 final size:27
Alignment explanation
Indices: 61778838--61779130 Score: 116
Period size: 27 Copynumber: 10.9 Consensus size: 27
61778828 TGTAGGGTAG
*
61778838 AATTACTGAAATACCCTTAGTTTACAA
1 AATTACTGAAATACCCTTAGTTTATAA
** * * *
61778865 AATTACCAAAATACTCCTGA-TTTGTGA
1 AATTACTGAAATAC-CCTTAGTTTATAA
* * ** *
61778892 AATTACCGAAATACCC-TCGACCTGTAA
1 AATTACTGAAATACCCTTAG-TTTATAA
**
61778919 AATTACTGAAATACCCTT-GACCTATAA
1 AATTACTGAAATACCCTTAG-TTTATAA
** * * ***
61778946 AATTACCAAAATACTCTCAACCTATAA
1 AATTACTGAAATACCCTTAGTTTATAA
*
61778973 AATTA-TCGAAATACCCTT-GATTTGTAA
1 AATTACT-GAAATACCCTTAG-TTTATAA
** * * **
61779000 AATTACCAAAATACCCCTAATTTGGAA
1 AATTACTGAAATACCCTTAGTTTATAA
* * **
61779027 AATTACCGAAATACCCTTAATTTGGAA
1 AATTACTGAAATACCCTTAGTTTATAA
* *
61779054 AATTA-TAGAAATACCCTTGACTTTAAAA
1 AATTACT-GAAATACCCTT-AGTTTATAA
* * * *
61779082 AATTA-TAAAATACCATTGGTTTACAA
1 AATTACTGAAATACCCTTAGTTTATAA
*
61779108 AATTA-TCGAAATACCCTTGGTTT
1 AATTACT-GAAATACCCTTAGTTT
61779131 GTAGATTTAC
Statistics
Matches: 209, Mismatches: 45, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
26 14 0.07
27 178 0.85
28 17 0.08
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
AATTACTGAAATACCCTTAGTTTATAA
Found at i:61778921 original size:54 final size:54
Alignment explanation
Indices: 61778863--61779058 Score: 207
Period size: 54 Copynumber: 3.6 Consensus size: 54
61778853 CTTAGTTTAC
* * * * *
61778863 AAAATTACCAAAATACTCC-TGATTTGTGAAATTACCGAAATACCCTCGACCTGT
1 AAAATTACCGAAATAC-CCTTGATTTGTAAAATTACCAAAATACCCTCAACCTAT
* ** * *
61778917 AAAATTACTGAAATACCCTTGACCTATAAAATTACCAAAATACTCTCAACCTAT
1 AAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAACCTAT
* ** **
61778971 AAAATTATCGAAATACCCTTGATTTGTAAAATTACCAAAATACCC-CTAATTTGG
1 AAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTC-AACCTAT
* *
61779025 AAAATTACCGAAATACCCTTAATTTGGAAAATTA
1 AAAATTACCGAAATACCCTTGATTTGTAAAATTA
61779059 TAGAAATACC
Statistics
Matches: 117, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
53 3 0.03
54 114 0.97
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (54 bp):
AAAATTACCGAAATACCCTTGATTTGTAAAATTACCAAAATACCCTCAACCTAT
Found at i:61778976 original size:81 final size:81
Alignment explanation
Indices: 61778838--61779015 Score: 198
Period size: 81 Copynumber: 2.2 Consensus size: 81
61778828 TGTAGGGTAG
** * ** * *
61778838 AATTACTGAAATACCCTTAGTTTACAAAATTACCAAAATACTCCTGATTTGTGAAATTACCGAAA
1 AATTACTGAAATACCCTTAGCCTACAAAATTACCAAAATACTCCTAACCTATAAAATTACCGAAA
61778903 TACCCTCGACCTGTAA
66 TACCCTCGACCTGTAA
* *
61778919 AATTACTGAAATACCCTT-GACCTATAAAATTACCAAAATACT-CTCAACCTATAAAATTATCGA
1 AATTACTGAAATACCCTTAG-CCTACAAAATTACCAAAATACTCCT-AACCTATAAAATTACCGA
* **
61778982 AATACCCTTGATTTGTAA
64 AATACCCTCGACCTGTAA
**
61779000 AATTACCAAAATACCC
1 AATTACTGAAATACCC
61779016 CTAATTTGGA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
80 3 0.04
81 78 0.96
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (81 bp):
AATTACTGAAATACCCTTAGCCTACAAAATTACCAAAATACTCCTAACCTATAAAATTACCGAAA
TACCCTCGACCTGTAA
Found at i:61779029 original size:81 final size:81
Alignment explanation
Indices: 61778944--61779095 Score: 189
Period size: 81 Copynumber: 1.9 Consensus size: 81
61778934 CTTGACCTAT
* * * **
61778944 AAAATTACCAAAATACTCTCAACCTATAAAATTATCGAAATACCCTTGA-TTTGTAAAATTACCA
1 AAAATTACCAAAATACCCTCAACCTAGAAAATTATAGAAATACCCTTGACTTTAAAAAATTA-CA
61779008 AAATACCCCTAATTTGG
65 AAATACCCCTAATTTGG
* * ** * *
61779025 AAAATTACCGAAATACCCTTAATTTGGAAAATTATAGAAATACCCTTGACTTTAAAAAATTATAA
1 AAAATTACCAAAATACCCTCAACCTAGAAAATTATAGAAATACCCTTGACTTTAAAAAATTACAA
61779090 AATACC
66 AATACC
61779096 ATTGGTTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
81 49 0.83
82 10 0.17
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTCAACCTAGAAAATTATAGAAATACCCTTGACTTTAAAAAATTACAA
AATACCCCTAATTTGG
Done.