Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold320
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: 2598547
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:151095 original size:78 final size:78
Alignment explanation
Indices: 150914--151116 Score: 234
Period size: 78 Copynumber: 2.6 Consensus size: 78
150904 TCGTTATTTC
* * *
150914 ACCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
1 ACCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCT-AAAT
* *
150979 ATTGATTTCTCATA
65 ATCGATTTCTCACA
** * *
150993 ATTGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTCTTT-TT-CT-AA
1 ACCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG--GCTTTATTCCTAAA
151055 TCATCGATTTCTCACA
64 T-ATCGATTTCTCACA
* *
151071 ACCGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACC
1 ACCGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACC
151117 TCGTTATTAT
Statistics
Matches: 106, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
77 8 0.08
78 47 0.44
79 45 0.42
80 2 0.02
81 4 0.04
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (78 bp):
ACCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCTAAATA
TCGATTTCTCACA
Found at i:156035 original size:17 final size:17
Alignment explanation
Indices: 156013--156045 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
156003 TGATTAGCAA
156013 ATTTAAATTTTATTTTC
1 ATTTAAATTTTATTTTC
*
156030 ATTTAATTTTTATTTT
1 ATTTAAATTTTATTTT
156046 GATTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAAATTTTATTTTC
Found at i:157855 original size:33 final size:33
Alignment explanation
Indices: 157812--157874 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
157802 AACAAAAAAA
*
157812 AATGATATGGTGAAAAAGTAACGGAGAGAATAT
1 AATGAAATGGTGAAAAAGTAACGGAGAGAATAT
*
157845 AATGAAATGGTGAAAAAGTAATGGAGAGAA
1 AATGAAATGGTGAAAAAGTAACGGAGAGAA
157875 AAAAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.51, C:0.02, G:0.29, T:0.19
Consensus pattern (33 bp):
AATGAAATGGTGAAAAAGTAACGGAGAGAATAT
Found at i:157894 original size:33 final size:33
Alignment explanation
Indices: 157818--157882 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
157808 AAAAAATGAT
*
157818 ATGGTGAAAAAGTAACGGAGAGAATATAATGAA
1 ATGGTGAAAAAGTAACGGAGAGAATATAAAGAA
*
157851 ATGGTGAAAAAGTAATGGAGAGAA-A-AAAGAA
1 ATGGTGAAAAAGTAACGGAGAGAATATAAAGAA
157882 A
1 A
157883 GATGGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.20
32 1 0.03
33 23 0.77
ACGTcount: A:0.55, C:0.02, G:0.28, T:0.15
Consensus pattern (33 bp):
ATGGTGAAAAAGTAACGGAGAGAATATAAAGAA
Found at i:157907 original size:2 final size:2
Alignment explanation
Indices: 157900--157926 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
157890 AAAAATGTTT
157900 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
157927 GTATGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162771 original size:20 final size:20
Alignment explanation
Indices: 162746--162925 Score: 115
Period size: 20 Copynumber: 8.9 Consensus size: 20
162736 TCACAATTTG
162746 TCATTGTATCGATACATTGT
1 TCATTGTATCGATACATTGT
162766 TCATTGTATCGATACATTGT
1 TCATTGTATCGATACATTGT
* * **
162786 TTATTATATTAATACATTG-
1 TCATTGTATCGATACATTGT
* *
162805 T-ATTG-ATAC-ATTC-TGGGTT
1 TCATTGTAT-CGATACAT-TG-T
*
162824 TACCTAGATGTATCGATACATT-T
1 T--C-A-TTGTATCGATACATTGT
*
162847 TGCATTATATCGATACATTGCT
1 T-CATTGTATCGATACATTG-T
*
162869 T-ATTGTATCGATACATTGC
1 TCATTGTATCGATACATTGT
162888 TCATTGTATCGATACATT-T
1 TCATTGTATCGATACATTGT
* *
162907 TACAATATATCGATACATT
1 T-CATTGTATCGATACATT
162926 CAGGCATTTT
Statistics
Matches: 125, Mismatches: 19, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
16 1 0.01
17 6 0.05
18 3 0.02
19 4 0.03
20 95 0.76
21 1 0.01
22 3 0.02
23 3 0.02
24 3 0.02
25 5 0.04
26 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (20 bp):
TCATTGTATCGATACATTGT
Found at i:165750 original size:21 final size:21
Alignment explanation
Indices: 165703--165743 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
165693 GAGGTGCTGG
165703 ACATGGCTCAAAATGCATGAA
1 ACATGGCTCAAAATGCATGAA
165724 ACATGGCTCAAAATGCATGA
1 ACATGGCTCAAAATGCATGA
165744 TCCATGGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
ACATGGCTCAAAATGCATGAA
Found at i:166700 original size:13 final size:13
Alignment explanation
Indices: 166682--166706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
166672 CAAAGATCAG
166682 TGTATCGATACAA
1 TGTATCGATACAA
166695 TGTATCGATACA
1 TGTATCGATACA
166707 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:166785 original size:13 final size:13
Alignment explanation
Indices: 166767--166792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166757 TACAAAACTT
166767 ATGTATCGATACA
1 ATGTATCGATACA
166780 ATGTATCGATACA
1 ATGTATCGATACA
166793 TCACTTTATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:166790 original size:32 final size:33
Alignment explanation
Indices: 166749--166813 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
166739 TAGCTTAAAT
166749 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
**
166781 TGTATCGATACATCACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
166814 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:167587 original size:52 final size:52
Alignment explanation
Indices: 167498--167665 Score: 194
Period size: 53 Copynumber: 3.2 Consensus size: 52
167488 TATTGGGTTC
* * *
167498 AAAGATGAGAAAAAAGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTT
1 AAAGATGAG--AAAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT
* * **
167553 AAAGATGAGAAAAATGCCAATGTGCTAATTCAAGGCCAACAACATTGGGTTTT
1 AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGACTT
* * *
167606 AAAGATGATG-AAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT
1 AAAGATGA-GAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT
167658 AAAGATGA
1 AAAGATGA
167666 AGGTGAGAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
52 41 0.42
53 46 0.47
54 1 0.01
55 9 0.09
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (52 bp):
AAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTT
Found at i:167833 original size:29 final size:29
Alignment explanation
Indices: 167795--168137 Score: 481
Period size: 29 Copynumber: 11.7 Consensus size: 29
167785 CTGAAAGTTA
* *
167795 CCACTGACTTGTGGGCTTT-TAAAGAGATA
1 CCACTGACTTGTGGGCTTTGGAAA-AGATG
* *
167824 CCATTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
167854 CCACTGACTTGTGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
*
167883 CCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
* *
167913 CCACTGACTTGTGGGCTTTTGAAAAGATA
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
* *
167942 CCACTGACTTGTGGGCTTTGAAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
*
167972 CCACTGACTTGTGAGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
*
168001 CCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
* *
168031 CCACTGACTTGTGGGCTTTTGAAAAGATA
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
*
168060 CCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAA-GATG
* *
168090 TCACTGACTTATGGGCTTTGGAAAAGATG
1 CCACTGACTTGTGGGCTTTGGAAAAGATG
168119 CCACTGACTTGTGGGCTTT
1 CCACTGACTTGTGGGCTTT
168138 TGAAGGGTGA
Statistics
Matches: 278, Mismatches: 30, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
29 145 0.52
30 133 0.48
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (29 bp):
CCACTGACTTGTGGGCTTTGGAAAAGATG
Found at i:167871 original size:59 final size:59
Alignment explanation
Indices: 167795--168137 Score: 571
Period size: 59 Copynumber: 5.8 Consensus size: 59
167785 CTGAAAGTTA
* *
167795 CCACTGACTTGTGGGCTTT-TAAAGAGATACCATTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAA-AGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
*
167854 CCACTGACTTGTGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
* *
167913 CCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGAAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
* *
167972 CCACTGACTTGTGAGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
*
168031 CCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
* * *
168090 TCACTGACTTATGGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTT
1 CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTT
168138 TGAAGGGTGA
Statistics
Matches: 266, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
59 263 0.99
60 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (59 bp):
CCACTGACTTGTGGGCTTTGGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTG
Found at i:169609 original size:13 final size:12
Alignment explanation
Indices: 169586--169652 Score: 55
Period size: 13 Copynumber: 5.5 Consensus size: 12
169576 CTTTTTGTTG
*
169586 TTGTTGTTTTTT
1 TTGTTTTTTTTT
**
169598 TT-TTTGGTTTT
1 TTGTTTTTTTTT
*
169609 TTGTTTTGTCTTT
1 TTGTTTT-TTTTT
169622 TTGTTTTTTTTT
1 TTGTTTTTTTTT
**
169634 ATTCCTTTTTTTT
1 -TTGTTTTTTTTT
169647 TTGTTT
1 TTGTTT
169653 ATTATTATTA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
11 8 0.20
12 13 0.32
13 20 0.49
ACGTcount: A:0.01, C:0.04, G:0.12, T:0.82
Consensus pattern (12 bp):
TTGTTTTTTTTT
Found at i:169610 original size:8 final size:7
Alignment explanation
Indices: 169577--169630 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
169567 ATCCGGACCC
169577 TTTTTGT
1 TTTTTGT
169584 TGTTGTTGT
1 T-TT-TTGT
169593 TTTTT-T
1 TTTTTGT
*
169599 TTTTGGT
1 TTTTTGT
169606 TTTTTG-
1 TTTTTGT
169612 -TTTTGT
1 TTTTTGT
169618 CTTTTTGT
1 -TTTTTGT
169626 TTTTT
1 TTTTT
169631 TTTATTCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
5 5 0.13
6 5 0.13
7 14 0.36
8 10 0.26
9 5 0.13
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (7 bp):
TTTTTGT
Found at i:169612 original size:20 final size:20
Alignment explanation
Indices: 169576--169652 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
169566 CATCCGGACC
169576 CTTTTTGTTGTTGTTGTTTT-T
1 CTTTTTGTT-TT-TTGTTTTGT
*
169597 TTTTTTGGTTTTTTGTTTTGT
1 CTTTTT-GTTTTTTGTTTTGT
169618 CTTTTTGTTTTTT-TTTAT-T
1 CTTTTTGTTTTTTGTTT-TGT
*
169637 CCTTTT-TTTTTTGTTT
1 CTTTTTGTTTTTTGTTT
169653 ATTATTATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.12
19 12 0.24
20 15 0.31
21 13 0.27
22 3 0.06
ACGTcount: A:0.01, C:0.05, G:0.13, T:0.81
Consensus pattern (20 bp):
CTTTTTGTTTTTTGTTTTGT
Found at i:169647 original size:25 final size:24
Alignment explanation
Indices: 169619--169670 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
169609 TTGTTTTGTC
* * *
169619 TTTTTGTTTTTTTTTATTCCTTTTT
1 TTTTTGTTTATTATTATT-ATTTTT
169644 TTTTTGTTTATTATTATTATTTTT
1 TTTTTGTTTATTATTATTATTTTT
169668 TTT
1 TTT
169671 GTGGAGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.83
Consensus pattern (24 bp):
TTTTTGTTTATTATTATTATTTTT
Found at i:182452 original size:21 final size:21
Alignment explanation
Indices: 182394--182445 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
182384 GACATGCTAT
182394 AAATGCATGAAACATGGCTCA
1 AAATGCATGAAACATGGCTCA
182415 AAATGCATGAAACATGGCTCA
1 AAATGCATGAAACATGGCTCA
182436 AAATGCATGA
1 AAATGCATGA
182446 TCCATGGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (21 bp):
AAATGCATGAAACATGGCTCA
Found at i:183409 original size:13 final size:13
Alignment explanation
Indices: 183391--183415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183381 CAAAGATCAG
183391 TGTATCGATACAA
1 TGTATCGATACAA
183404 TGTATCGATACA
1 TGTATCGATACA
183416 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:183494 original size:13 final size:13
Alignment explanation
Indices: 183476--183501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
183466 TACAAAACTT
183476 ATGTATCGATACA
1 ATGTATCGATACA
183489 ATGTATCGATACA
1 ATGTATCGATACA
183502 TCACTTTATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:183499 original size:32 final size:33
Alignment explanation
Indices: 183458--183522 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
183448 TAGCTTAAAT
183458 TGTATCGATACAAAAC-TTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
**
183490 TGTATCGATACATCACTTTATGTATCGATACAA
1 TGTATCGATACAAAACTTTATGTATCGATACAA
183523 ATCGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAACTTTATGTATCGATACAA
Found at i:185588 original size:51 final size:51
Alignment explanation
Indices: 185498--185676 Score: 157
Period size: 51 Copynumber: 3.5 Consensus size: 51
185488 AAATTTCTAG
* * * **
185498 ATTTTTCAT-CTCGGGGATACTCTAA-TCCCGGTTCCATTTCCAAAACATCA
1 ATTTTTCATAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATCA
* * * * *
185548 ATTTTTCTTAATCGAGGATACTCCAACTCCGATTTTATTTCTAAAGCATCG
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCA
** ** * * *
185599 ATTTACCGCAATCGGGGATATTCCAACTCTGATTTTATTTTCAAAACA-CTA
1 ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC-A
*
185650 ATTTTTCATAATTGGGGATACTCCAAC
1 ATTTTTCATAATCGGGGATACTCCAAC
185677 CCCGTTATTT
Statistics
Matches: 99, Mismatches: 27, Indels: 5
0.76 0.21 0.04
Matches are distributed among these distances:
50 9 0.09
51 89 0.90
52 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (51 bp):
ATTTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCA
Found at i:185696 original size:28 final size:26
Alignment explanation
Indices: 185663--185736 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 26
185653 TTTCATAATT
185663 GGGGATACTCCAACCCCGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTC--C
*
185691 GGGGATACCCCAACCCCGTTATTTCC
1 GGGGATACTCCAACCCCGTTATTTCC
*
185717 GAGTCGATACTCCAACCCCG
1 G-G-GGATACTCCAACCCCG
185737 GCTTTATATC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 1 0.02
28 38 0.93
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGTTATTTCC
Found at i:185823 original size:110 final size:108
Alignment explanation
Indices: 185651--185893 Score: 283
Period size: 110 Copynumber: 2.2 Consensus size: 108
185641 AAAACACTAA
* * * *
185651 TTTTTCATAATTGGGGATACTCCAACCCCGTTATTTCATCGGGGATACCCCAACCCCGTTATTTC
1 TTTTTCATAATAGGGGATACTCCAACCCCGTTATGTCATCGAGGATACCCCAACCCCATTATTTC
*
185716 CG-AGTCGATACTCCAACCCCGGCTTTATATCTAAAACATTGAT
66 CGAAG-CGATACTCCAACCCCGACTTTATATCTAAAACATTGAT
* * * *
185759 TTTTTCCATAATCAGGGGGTACTCCAACCCCGTTATGTCCTCGAGGATACTCCAATCCCATTATT
1 TTTTT-CATAAT-AGGGGATACTCCAACCCCGTTATGTCATCGAGGATACCCCAACCCCATTATT
* * * * * * *
185824 TCCGAAGGGATACTCCAGCCCCGATTTTATTTCTAAAATA-TCAA
64 TCCGAAGCGATACTCCAACCCCGACTTTATATCTAAAACATTGAT
* *
185868 TTTTTCACAATCGGGGATACTCCAAC
1 TTTTTCATAATAGGGGATACTCCAAC
185894 TCCGATTTTA
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
107 13 0.12
108 10 0.09
109 13 0.12
110 75 0.66
111 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (108 bp):
TTTTTCATAATAGGGGATACTCCAACCCCGTTATGTCATCGAGGATACCCCAACCCCATTATTTC
CGAAGCGATACTCCAACCCCGACTTTATATCTAAAACATTGAT
Found at i:185899 original size:51 final size:51
Alignment explanation
Indices: 185830--185948 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 51
185820 TATTTCCGAA
* * *
185830 GGGATACTCCAGCCCCGATTTTA-TTTCTAAAATATCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTTCACAATCG
*
185881 GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
*
185932 GGGGTACTCCAACCCCG
1 GGGATACTCCAACCCCG
185949 TTATTTTCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 57 0.93
52 4 0.07
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTTCACAATCG
Found at i:185965 original size:79 final size:78
Alignment explanation
Indices: 185882--186184 Score: 243
Period size: 79 Copynumber: 3.8 Consensus size: 78
185872 TCACAATCGG
* *
185882 GGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTCACAATCGGGGGTACTCCAACCC
1 GGATACTCCAAC-CCGATTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
185947 CGTTATTTTC-ACAA
65 CGTTATTTTCGA-AA
* *** * *** *
185961 GGATACTTCAAACCCGGCCTTA-TTTCTAAAGCATTGATTTTCCACAATCGGGGATACTCCAACT
1 GGATAC-TCCAACCCGATTTTATTTTC-AAAACACCAATTTTCCACAATCGGGGATACTCCAACC
**
186025 CCGTTATTTTCGAGG
64 CCGTTATTTTCGAAA
* ** * * * *
186040 GGATACTCCAACCCCGATTTTATTTTCAAAATACGGATTTTCTATAATCAGGGATACTCCATCCC
1 GGATACTCCAA-CCCGATTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCC
* * **
186105 TGTTATTTCCGAGG
65 CGTTATTTTCGAAA
* * * * * * *
186119 GGATACTCCAACCCCGGTCTTATTTCCAGAACA-CAGATTTTCCATAATCGGTGATACTCCAGCC
1 GGATACTCCAA-CCCGATTTTATTTTCAAAACACCA-ATTTTCCACAATCGGGGATACTCCAACC
186183 CC
64 CC
186185 ATTGTTATCT
Statistics
Matches: 178, Mismatches: 40, Indels: 12
0.77 0.17 0.05
Matches are distributed among these distances:
78 8 0.04
79 160 0.90
80 10 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (78 bp):
GGATACTCCAACCCGATTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCCAACCCC
GTTATTTTCGAAA
Found at i:186061 original size:158 final size:158
Alignment explanation
Indices: 185880--186179 Score: 374
Period size: 158 Copynumber: 1.9 Consensus size: 158
185870 TTTCACAATC
* * *
185880 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTT-TCACAATCGGGGGTACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCT-ACAATCAGGGATACTCCAA
* * **
185944 CCCCGTTATTTTCAC-A-AGGATACTTCAAACCCGGCCTTATTTCTA-AAGCATTGATTTTCCAC
65 CCCCGTTA-TTTC-CGAGAGGATACTCCAAACCCGGCCTTATTTCCAGAA-CACAGATTTTCCAC
186006 AATCGGGGATACTCCAACTCCGTTATTTTCGA
127 AATCGGGGATACTCCAACTCCGTTATTTTCGA
* ** * *
186038 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACGGATTTTCTATAATCAGGGATACTCCATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAAC
* * * * *
186103 CCTGTTATTTCCGAGGGGATACTCCAACCCCGGTCTTATTTCCAGAACACAGATTTTCCATAATC
66 CCCGTTATTTCCGAGAGGATACTCCAAACCCGGCCTTATTTCCAGAACACAGATTTTCCACAATC
*
186168 GGTGATACTCCA
131 GGGGATACTCCA
186180 GCCCCATTGT
Statistics
Matches: 120, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
156 1 0.01
157 5 0.04
158 111 0.93
159 3 0.03
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (158 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATCAGGGATACTCCAAC
CCCGTTATTTCCGAGAGGATACTCCAAACCCGGCCTTATTTCCAGAACACAGATTTTCCACAATC
GGGGATACTCCAACTCCGTTATTTTCGA
Found at i:187323 original size:2 final size:2
Alignment explanation
Indices: 187316--187350 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
187306 TGCTATCAAG
*
187316 AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
187351 AATACACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:194534 original size:2 final size:2
Alignment explanation
Indices: 194529--194562 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
194519 CTTCCCCCCT
194529 TC TC TC TC TC TC TAC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC T-C TC TC TC TC TC TC TC TC TC T
194563 TTTCCGGCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:198026 original size:15 final size:15
Alignment explanation
Indices: 198008--198074 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
197998 CCCCCCCATG
198008 ACCACCCCCCACCAC
1 ACCACCCCCCACCAC
*
198023 ACCA--CCCAACCAC
1 ACCACCCCCCACCAC
**
198036 ACC-CACCCCTGCCAC
1 ACCAC-CCCCCACCAC
*
198051 ACCGACCCCCCCCCAAC
1 ACC-ACCCCCCACC-AC
198068 ACCACCC
1 ACCACCC
198075 ACCCCCCCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
13 11 0.27
15 14 0.34
16 10 0.24
17 6 0.15
ACGTcount: A:0.27, C:0.69, G:0.03, T:0.01
Consensus pattern (15 bp):
ACCACCCCCCACCAC
Found at i:198069 original size:17 final size:17
Alignment explanation
Indices: 198016--198081 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
198006 TGACCACCCC
*
198016 CCACCACACCACCCAAC-
1 CCACC-CACCCCCCAACA
198033 CACACCCACCCCTGCC-ACA
1 C-CACCCACCCC--CCAACA
198052 CCGACCC-CCCCCCAACA
1 CC-ACCCACCCCCCAACA
198069 CCACCCACCCCCC
1 CCACCCACCCCCC
198082 CTCCAACCGC
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
16 6 0.15
17 17 0.41
18 11 0.27
19 7 0.17
ACGTcount: A:0.26, C:0.70, G:0.03, T:0.02
Consensus pattern (17 bp):
CCACCCACCCCCCAACA
Found at i:198073 original size:20 final size:20
Alignment explanation
Indices: 198050--198101 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
198040 ACCCCTGCCA
198050 CACCGACCCCCCC-CCAACAC-
1 CACC-ACCCCCCCTCCAAC-CG
198070 CACCCACCCCCCCTCCAACCG
1 CA-CCACCCCCCCTCCAACCG
198091 CACCACCCCCC
1 CACCACCCCCC
198102 AACCCTCGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.21, C:0.73, G:0.04, T:0.02
Consensus pattern (20 bp):
CACCACCCCCCCTCCAACCG
Found at i:198082 original size:21 final size:20
Alignment explanation
Indices: 198056--198101 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
198046 GCCACACCGA
198056 CCCCCCCCCAACAC-CACCCAC
1 CCCCCCCCCAAC-CGCA-CCAC
*
198077 CCCCCCTCCAACCGCACCAC
1 CCCCCCCCCAACCGCACCAC
198097 CCCCC
1 CCCCC
198102 AACCCTCGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.20, C:0.76, G:0.02, T:0.02
Consensus pattern (20 bp):
CCCCCCCCCAACCGCACCAC
Found at i:198107 original size:24 final size:25
Alignment explanation
Indices: 198067--198114 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
198057 CCCCCCCCAA
*
198067 CACCACCCACCCCCCCTC-CAACCG
1 CACCACCCACCCACCCTCGCAACCG
198091 CACCACCC-CCCAACCCTCGCAACC
1 CACCACCCACCC-ACCCTCGCAACC
198115 AACACGCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.23, C:0.69, G:0.04, T:0.04
Consensus pattern (25 bp):
CACCACCCACCCACCCTCGCAACCG
Found at i:201195 original size:2 final size:2
Alignment explanation
Indices: 201188--201225 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
201178 TTTCTAAATA
201188 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
201226 CACATTAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:202513 original size:27 final size:28
Alignment explanation
Indices: 202478--202536 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
202468 TTTAAGTTTA
202478 GGGAAAATA-AAAATATGCCTAAATTTG
1 GGGAAAATATAAAATATGCCTAAATTTG
*
202505 GGGATAATATAAAATATGCCTAAATTTG
1 GGGAAAATATAAAATATGCCTAAATTTG
202533 GGGA
1 GGGA
202537 CCACATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGAAAATATAAAATATGCCTAAATTTG
Found at i:202544 original size:28 final size:28
Alignment explanation
Indices: 202487--202544 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
202477 AGGGAAAATA
* *
202487 AAAATATGCCTAAATTTGGGGATAATAT
1 AAAATATGCCTAAATTTGGGGACAACAT
*
202515 AAAATATGCCTAAATTTGGGGACCACAT
1 AAAATATGCCTAAATTTGGGGACAACAT
202543 AA
1 AA
202545 GTAATTAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAATATGCCTAAATTTGGGGACAACAT
Found at i:204354 original size:16 final size:16
Alignment explanation
Indices: 204305--204355 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
204295 AGTATGAATA
*
204305 TATTAATATATCAAAA
1 TATTAATATATCAAAT
204321 T-TTATATAATAT-AAAT
1 TATTA-AT-ATATCAAAT
204337 TATTAATATATCAAAT
1 TATTAATATATCAAAT
204353 TAT
1 TAT
204356 ATATAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTAATATATCAAAT
Found at i:204985 original size:26 final size:24
Alignment explanation
Indices: 204956--205016 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
204946 AAATTTAACA
204956 TTAATTTTTATATAAATTATAAATAT
1 TTAATTTTTAT-TAAATTAT-AATAT
* *
204982 TTAA-TTTTATTAACTTATATTAT
1 TTAATTTTTATTAAATTATAATAT
*
205005 TAAATTTTTATT
1 TTAATTTTTATT
205017 GTTAAAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 7 0.23
24 14 0.45
25 6 0.19
26 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TTAATTTTTATTAAATTATAATAT
Found at i:205010 original size:23 final size:25
Alignment explanation
Indices: 204955--205012 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
204945 TAAATTTAAC
*
204955 ATTAATTTTTATATAAATTATAAAT
1 ATTAAATTTTATATAAATTATAAAT
* * *
204980 ATTTAATTTTAT-TAACTTAT-ATT
1 ATTAAATTTTATATAAATTATAAAT
205003 ATTAAATTTT
1 ATTAAATTTT
205013 TATTGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 11 0.39
24 7 0.25
25 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTAAATTTTATATAAATTATAAAT
Found at i:210765 original size:76 final size:76
Alignment explanation
Indices: 210678--210924 Score: 289
Period size: 76 Copynumber: 3.2 Consensus size: 76
210668 ACTATTATCG
* * * * *
210678 AAATAACCCTAATAGACATGTTACAACATGAAAGTTCTCATATGATCTTATACTCGATTGTAAGA
1 AAATAACCCTAATAGACATGTTTCAACATGAAAGTTCCCATATGATCTTATACTTGATTTTAAGG
210743 TATTTTTACCT
66 TATTTTTACCT
* * * * * * ** *
210754 AACTAACCCTAATAGACATGTTTTAACATGAATGTTCCCACATGACCCTAGGCTTGATTTTGAGG
1 AAATAACCCTAATAGACATGTTTCAACATGAAAGTTCCCATATGATCTTATACTTGATTTTAAGG
* **
210819 TATTATTACGG
66 TATTTTTACCT
* *
210830 AAATAACCCTAATAAACATGTTTCAACATG-AAGATTCCCATATGATCTTATACTTAATTTTAAG
1 AAATAACCCTAATAGACATGTTTCAACATGAAAG-TTCCCATATGATCTTATACTTGATTTTAAG
*
210894 GTACTTTTACCT
65 GTATTTTTACCT
*
210906 AAATACCCCTAATAGACAT
1 AAATAACCCTAATAGACAT
210925 ATTTTGATAG
Statistics
Matches: 136, Mismatches: 34, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
75 2 0.01
76 134 0.99
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (76 bp):
AAATAACCCTAATAGACATGTTTCAACATGAAAGTTCCCATATGATCTTATACTTGATTTTAAGG
TATTTTTACCT
Found at i:210954 original size:152 final size:151
Alignment explanation
Indices: 210649--210979 Score: 396
Period size: 152 Copynumber: 2.2 Consensus size: 151
210639 CCACGTGATT
* * *
210649 CTAAACTCGATTTTGAGGTACTATTATCGAAATAACCCTAATAGACATGTTACAACATGAAAGTT
1 CTAAACTTGATTTTGAGGTATTATTA-CGAAATAACCCTAATAAACATGTTACAACATGAAAGTT
* * * * *
210714 CTCATATGATCTTATACTCGATTGTAAGATATTTTTACCTAACTAACCCTAATAGACATGTTTTA
65 CCCATATGATCTTATACTCAATTGTAAGATACTTTTACCTAAATAACCCTAATAGACATATTTTA
* * *
210779 ACATGAATGTTCCCACATGACC
130 ACATGAAAGATCCCACATAACC
** *
210801 CTAGGCTTGATTTTGAGGTATTATTACGGAAATAACCCTAATAAACATGTTTCAACATG-AAGAT
1 CTAAACTTGATTTTGAGGTATTATTAC-GAAATAACCCTAATAAACATGTTACAACATGAAAG-T
* * * *
210865 TCCCATATGATCTTATACTTAATTTTAAGGTACTTTTACCTAAATACCCCTAATAGACATATTTT
64 TCCCATATGATCTTATACTCAATTGTAAGATACTTTTACCTAAATAACCCTAATAGACATATTTT
* * **
210930 GATA-GAAAAGATCTTACATAACC
129 AACATG-AAAGATCCCACATAACC
* *
210953 CTAAACTTGATTTTAAGGCATTATTAC
1 CTAAACTTGATTTTGAGGTATTATTAC
210980 TAAAATATCT
Statistics
Matches: 150, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
151 5 0.03
152 145 0.97
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (151 bp):
CTAAACTTGATTTTGAGGTATTATTACGAAATAACCCTAATAAACATGTTACAACATGAAAGTTC
CCATATGATCTTATACTCAATTGTAAGATACTTTTACCTAAATAACCCTAATAGACATATTTTAA
CATGAAAGATCCCACATAACC
Found at i:211396 original size:20 final size:20
Alignment explanation
Indices: 211348--211421 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 20
211338 TTCAACAATT
* * *
211348 TGTATTGATACAATAAGTGAA
1 TGTATCGATAC-ATAGGTAAA
*
211369 TATATCGATACATAGGTAAA
1 TGTATCGATACATAGGTAAA
*
211389 TGTATCGATACAT-GTTTGAAA
1 TGTATCGATACATAG-GT-AAA
211410 TGTATCGATACA
1 TGTATCGATACA
211422 AGATCATGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 20 0.44
21 24 0.53
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATAGGTAAA
Found at i:211541 original size:51 final size:52
Alignment explanation
Indices: 211457--211580 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
211447 TTTGGAATGA
* *
211457 AAATGTATCGATAAATTTCTATATTGTATCGATACATTCTAGG-TTTTGACCC
1 AAATGTATCGATACA-TTCTTTATTGTATCGATACATTCTAGGTTTTTGACCC
* *
211509 AAATGTATCGATACATTCTTTATTGTATCGATACATTTTAGGTTTTTGAGCC
1 AAATGTATCGATACATTCTTTATTGTATCGATACATTCTAGGTTTTTGACCC
* *
211561 AAATATATTGATACATTCTT
1 AAATGTATCGATACATTCTT
211581 CAGTGAATCG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 25 0.38
52 40 0.62
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (52 bp):
AAATGTATCGATACATTCTTTATTGTATCGATACATTCTAGGTTTTTGACCC
Found at i:211591 original size:52 final size:51
Alignment explanation
Indices: 211484--211593 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 51
211474 TCTATATTGT
* * * *
211484 ATCGATACATTCTAGGTTTTGACCCAAATGTATCGATACATTCTTTATTGT
1 ATCGATACATTCTAGGTTTTGACCCAAATATATCGATACATTCTTCAGTGA
* * *
211535 ATCGATACATTTTAGGTTTTTGAGCCAAATATATTGATACATTCTTCAGTGA
1 ATCGATACATTCTAGG-TTTTGACCCAAATATATCGATACATTCTTCAGTGA
211587 ATCGATA
1 ATCGATA
211594 TATGCAGGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 15 0.29
52 36 0.71
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (51 bp):
ATCGATACATTCTAGGTTTTGACCCAAATATATCGATACATTCTTCAGTGA
Found at i:216873 original size:51 final size:51
Alignment explanation
Indices: 216818--216946 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 51
216808 TCCCGGTTCC
** * *
216818 ATTTCCAAAACATCAATTTTTCTTAATCGAGGATACTCTAACTCTGATTTT
1 ATTTCCAAAACATCAATTTTTCGCAATCGAGGATACTCCAACTCCGATTTT
* * ** *
216869 ATTTCTAAAGCATCAATTTGCCGCAATCGGGGATACTCCAACTCCGATTTT
1 ATTTCCAAAACATCAATTTTTCGCAATCGAGGATACTCCAACTCCGATTTT
*
216920 ATTTCCAAAACA-CTAATTTTTCACAAT
1 ATTTCCAAAACATC-AATTTTTCGCAAT
216947 TGGGACCCCA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
50 1 0.02
51 62 0.98
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.36
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCGCAATCGAGGATACTCCAACTCCGATTTT
Found at i:217358 original size:79 final size:77
Alignment explanation
Indices: 217166--217423 Score: 220
Period size: 79 Copynumber: 3.3 Consensus size: 77
217156 AATCGAAGAC
* ** * * *
217166 ACTCCAACTCCGATTTTATTTTCAAAACACTAATTTCTCACAATCG-GGGGTACTCCAACCCTGT
1 ACTCCAACCCCGATTTTA-TTTCAAAACACCGATTTTTCACAATCGAGGAG-ACTCTAA-CCTGT
217230 TATTTTT-ACGGGGAT
63 TATTTTTGA-GGGGAT
* ** * *
217245 ACTTCAAACCCCG-CCTTATTTCTAAAGCATCGATTTTTCACAATCGAGGAGACTCTAACTCTGT
1 AC-TCCAACCCCGATTTTATTTC-AAAACACCGATTTTTCACAATCGAGGAGACTCTAAC-CTGT
217309 TATTTTTGAGGGGAT
63 TATTTTTGAGGGGAT
* * * *
217324 ACTCCAACCCCGATTTTATCTTCAAAATACCGA-TTTTCTATAATCAAGGATG-CTCTATCCTTG
1 ACTCCAACCCCGATTTTAT-TTCAAAACACCGATTTTTC-ACAATCGAGGA-GACTCTAACC-TG
*
217387 TTATTTCTGAGGGGAT
62 TTATTTTTGAGGGGAT
* *
217403 ACTCCAACCCCGGTCTTATTT
1 ACTCCAACCCCGATTTTATTT
217424 TTAGAACACA
Statistics
Matches: 146, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
78 22 0.15
79 108 0.74
80 16 0.11
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (77 bp):
ACTCCAACCCCGATTTTATTTCAAAACACCGATTTTTCACAATCGAGGAGACTCTAACCTGTTAT
TTTTGAGGGGAT
Found at i:218604 original size:2 final size:2
Alignment explanation
Indices: 218597--218633 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
218587 TGCTATCAAG
218597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218634 AATACACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223365 original size:3 final size:3
Alignment explanation
Indices: 223359--223387 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
223349 TAGCATGAGT
223359 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
223388 CCCATGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:223838 original size:2 final size:2
Alignment explanation
Indices: 223831--223857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
223821 CTCTCGTAAA
223831 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
223858 AATTGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:224664 original size:2 final size:2
Alignment explanation
Indices: 224657--224702 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
224647 TTTGTTGCAT
* * *
224657 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
224699 TA TA
1 TA TA
224703 AGAGCATCTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:227475 original size:29 final size:29
Alignment explanation
Indices: 227423--227499 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 29
227413 TATTTTATAA
* * *
227423 AATAAATGAAATATATAATAAATTTTTAATTT
1 AATATATGAAA-A-ATAA-AAAATTTCAATTT
* *
227455 AATGTAT-AAAATTAAAAAATTTCAATTT
1 AATATATGAAAAATAAAAAATTTCAATTT
227483 AATATATGAAAAATAAA
1 AATATATGAAAAATAAA
227500 TTCTTTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 17 0.46
29 11 0.30
30 1 0.03
31 3 0.08
32 5 0.14
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (29 bp):
AATATATGAAAAATAAAAAATTTCAATTT
Found at i:228777 original size:18 final size:17
Alignment explanation
Indices: 228748--228782 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
228738 TGTATATATC
228748 AAATTAAAAATTAAAAT
1 AAATTAAAAATTAAAAT
*
228765 AAATTATAAAATTTAAAT
1 AAATTA-AAAATTAAAAT
228783 GTATATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTAAAAATTAAAAT
Found at i:232366 original size:22 final size:20
Alignment explanation
Indices: 232340--232379 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
232330 TAAATTCATG
232340 TAATTTCTATAAGGATGAATTC
1 TAATTT-TA-AAGGATGAATTC
*
232362 TAATTTTAGAGGATGAAT
1 TAATTTTAAAGGATGAAT
232380 ATCTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
TAATTTTAAAGGATGAATTC
Found at i:233377 original size:23 final size:24
Alignment explanation
Indices: 233343--233392 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
233333 CATATGTGTT
* *
233343 TAAATTTAAATATAACAA-TAAAA
1 TAAATTTAAATAAAAAAATTAAAA
233366 TAAA-TTATAATAAAAAAATTAAAA
1 TAAATTTA-AATAAAAAAATTAAAA
233390 TAA
1 TAA
233393 TCATTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 12 0.52
24 8 0.35
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAATTTAAATAAAAAAATTAAAA
Found at i:233386 original size:14 final size:15
Alignment explanation
Indices: 233349--233392 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
233339 TGTTTAAATT
233349 TAAATATAACAATAAAA
1 TAAAT-TAA-AATAAAA
*
233366 TAAATTATAATAAAA
1 TAAATTAAAATAAAA
233381 -AAATTAAAATAA
1 TAAATTAAAATAA
233393 TCATTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 11 0.44
15 7 0.28
16 2 0.08
17 5 0.20
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATTAAAATAAAA
Found at i:233505 original size:25 final size:24
Alignment explanation
Indices: 233467--233513 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
233457 TATTTATACT
233467 TAAAAATAAATTAATAAAATAAATA
1 TAAAAATAAATTAA-AAAATAAATA
* *
233492 TAAAAATAATTTAAAAATTAAA
1 TAAAAATAAATTAAAAAATAAA
233514 AAAAGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
TAAAAATAAATTAAAAAATAAATA
Found at i:233506 original size:11 final size:12
Alignment explanation
Indices: 233466--233509 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
233456 ATATTTATAC
233466 TTAAAAATAAAT
1 TTAAAAATAAAT
*
233478 TAATAAAATAAAT
1 TTA-AAAATAAAT
*
233491 ATAAAAAT-AAT
1 TTAAAAATAAAT
233502 TTAAAAAT
1 TTAAAAAT
233510 TAAAAAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 10 0.37
12 7 0.26
13 10 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TTAAAAATAAAT
Found at i:234106 original size:31 final size:32
Alignment explanation
Indices: 234068--234144 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
234058 ACATTTTTAT
234068 TGTATCGATACATTCT-GAG-TTTTAATCCAAA
1 TGTATCGATACATTCTAG-GTTTTTAATCCAAA
* *
234099 TGTATCGATACATCCTAGGTTTTTGATCCAAA
1 TGTATCGATACATTCTAGGTTTTTAATCCAAA
*
234131 TGTATTGATACATT
1 TGTATCGATACATT
234145 ATTTATTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 16 0.40
32 24 0.60
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTCTAGGTTTTTAATCCAAA
Found at i:234158 original size:20 final size:20
Alignment explanation
Indices: 234133--234181 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
234123 GATCCAAATG
*
234133 TATTGATACATTATTTATTA
1 TATTGATACATTATTTAATA
* *
234153 TATTGATATATTTTTTAATA
1 TATTGATACATTATTTAATA
234173 TATTGATAC
1 TATTGATAC
234182 GTCTAGTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (20 bp):
TATTGATACATTATTTAATA
Found at i:237121 original size:22 final size:23
Alignment explanation
Indices: 237078--237121 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
237068 CCCCATCTTT
*
237078 CTGGATTCATTTTTTATTAAAAC
1 CTGGATTCATTTTTTATCAAAAC
237101 CTGGATTCATTTTTT-TCAAAA
1 CTGGATTCATTTTTTATCAAAA
237122 TTCATGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (23 bp):
CTGGATTCATTTTTTATCAAAAC
Found at i:238477 original size:37 final size:34
Alignment explanation
Indices: 238421--238494 Score: 78
Period size: 37 Copynumber: 2.1 Consensus size: 34
238411 TATTATTTTT
* *
238421 AAAATATATAAAAAGT-AAAATAAGATCAATATTA
1 AAAATATATAAAAAATAAAAATAAGA-CAATAATA
*
238455 AAAATAATATAAATTAAATAAAAATACGACAATAATA
1 AAAAT-ATATAAA--AAATAAAAATAAGACAATAATA
238492 AAA
1 AAA
238495 GTTAAATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.15
35 7 0.21
37 13 0.39
38 8 0.24
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (34 bp):
AAAATATATAAAAAATAAAAATAAGACAATAATA
Found at i:240169 original size:12 final size:12
Alignment explanation
Indices: 240152--240177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
240142 TGTATTAAAT
240152 AAATAATTTATA
1 AAATAATTTATA
240164 AAATAATTTATA
1 AAATAATTTATA
240176 AA
1 AA
240178 TTATCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATTTATA
Found at i:240950 original size:13 final size:13
Alignment explanation
Indices: 240934--240958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240924 ATTATTTATT
240934 AAAATTTTATTTC
1 AAAATTTTATTTC
240947 AAAATTTTATTT
1 AAAATTTTATTT
240959 TATTATTAAA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATTTTATTTC
Found at i:241022 original size:29 final size:30
Alignment explanation
Indices: 240990--241064 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
240980 ATTAAAATAA
240990 TTTATAATTAAATTTAAATAA-AATAT-ATT
1 TTTATAATT-AATTTAAATAATAATATAATT
*
241019 TTTACAA-T-ATTTAAATAATAATATAAATT
1 TTTATAATTAATTTAAATAATAATAT-AATT
*
241048 ATTAT-ATTAATTTAAAT
1 TTTATAATTAATTTAAAT
241065 TATCAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
26 10 0.26
27 5 0.13
28 2 0.05
29 13 0.34
30 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTATAATTAATTTAAATAATAATATAATT
Found at i:241061 original size:56 final size:56
Alignment explanation
Indices: 240959--241064 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
240949 AATTTTATTT
* *
240959 TATTATTAAAATATTTAAAATATTAAAATAATTTATAATTAAATTTAAATAAAATA
1 TATTATTAAAATATTTAAAATAATAAAATAAATTATAATTAAATTTAAATAAAATA
* * *
241015 TATTTTTACAATATTT-AAATAATAATATAAATTATTATATT-AATTTAAAT
1 TATTATTAAAATATTTAAAATAATAAAATAAATTA-TA-ATTAAATTTAAAT
241065 TATCAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
55 15 0.35
56 25 0.58
57 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (56 bp):
TATTATTAAAATATTTAAAATAATAAAATAAATTATAATTAAATTTAAATAAAATA
Found at i:241352 original size:4 final size:4
Alignment explanation
Indices: 241327--241375 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
241317 ATTTGCACGT
* * * *
241327 TATA -ATA TCTA TCTA TACA TATA TATA TATA TATA TATA TATT TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
241374 TA
1 TA
241376 GAAAAGAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:241358 original size:10 final size:10
Alignment explanation
Indices: 241327--241375 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
241317 ATTTGCACGT
*
241327 TATA-ATATC
1 TATATATATA
* *
241336 TATCTATACA
1 TATATATATA
241346 TATATATATA
1 TATATATATA
241356 TATATATATA
1 TATATATATA
*
241366 TATTTATATA
1 TATATATATA
241376 GAAAAGAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 3 0.09
10 30 0.91
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (10 bp):
TATATATATA
Found at i:245423 original size:24 final size:22
Alignment explanation
Indices: 245395--245455 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
245385 ATTTTATTAT
245395 TATTTATTTAATAATA-ATAAAA
1 TATTTATTTAATAATATAT-AAA
245417 TAAATTTAATTTAA-AATATATAAA
1 T--ATTT-ATTTAATAATATATAAA
*
245441 TATTTAATTAATAAT
1 TATTTATTTAATAAT
245456 TTAAGTTCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
21 5 0.15
22 8 0.24
24 12 0.36
25 8 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTTATTTAATAATATATAAA
Found at i:246211 original size:9 final size:9
Alignment explanation
Indices: 246197--246250 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
246187 AACTTGAAAG
246197 AATTAAAAA
1 AATTAAAAA
*
246206 AATTAAAAG
1 AATTAAAAA
*
246215 GATTAAAAA
1 AATTAAAAA
*
246224 AATT-TAAA
1 AATTAAAAA
* *
246232 AATTTAAAG
1 AATTAAAAA
246241 AATTAAAAA
1 AATTAAAAA
246250 A
1 A
246251 TACAAAATAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
8 7 0.20
9 28 0.80
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAAAAA
Found at i:246222 original size:17 final size:17
Alignment explanation
Indices: 246197--246251 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
246187 AACTTGAAAG
*
246197 AATTAAAAAAATTAAAA
1 AATTAAAAGAATTAAAA
* * *
246214 GGATTAAAAAAATTTAAA
1 -AATTAAAAGAATTAAAA
*
246232 AATTTAAAGAATTAAAA
1 AATTAAAAGAATTAAAA
246249 AAT
1 AAT
246252 ACAAAATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AATTAAAAGAATTAAAA
Found at i:246250 original size:18 final size:18
Alignment explanation
Indices: 246193--246248 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
246183 TAAAAACTTG
246193 AAAGAATTAAAAAAATTA
1 AAAGAATTAAAAAAATTA
* *
246211 AAAGGATTAAAAAAATTT
1 AAAGAATTAAAAAAATTA
* *
246229 AAA-AATTTAAAGAATTA
1 AAAGAATTAAAAAAATTA
246246 AAA
1 AAA
246249 AATACAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 13 0.41
18 19 0.59
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AAAGAATTAAAAAAATTA
Found at i:250208 original size:7 final size:7
Alignment explanation
Indices: 250196--250225 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
250186 AATATACTTT
250196 TTATTAA
1 TTATTAA
250203 TTATTAA
1 TTATTAA
250210 TTATTAA
1 TTATTAA
250217 TTATTAA
1 TTATTAA
250224 TT
1 TT
250226 TTTTTTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATTAA
Found at i:250941 original size:12 final size:12
Alignment explanation
Indices: 250924--250948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
250914 AAATAATTGG
250924 AGAAAAAATAAA
1 AGAAAAAATAAA
250936 AGAAAAAATAAA
1 AGAAAAAATAAA
250948 A
1 A
250949 ACAAATAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AGAAAAAATAAA
Found at i:251364 original size:67 final size:61
Alignment explanation
Indices: 251279--251440 Score: 141
Period size: 67 Copynumber: 2.6 Consensus size: 61
251269 AGGGAAAACT
* *
251279 AAATTATTTTTTAAAAAAT-TCTTAAAATAATGAAATATAGGAAAATATAAGAAAGTATGAAAAA
1 AAATAATTTTTTAAAAAATGT-TTAAAATAATAAAATATAGG-AAATATAA-AAA-TA--AAAAA
251343 GA
60 GA
* * * *
251345 AAATAATTTTTTACGAAAATGTTTACAGTAATAAAATATATGAAATATAAAAATAAAAAAGA
1 AAATAATTTTTTA-AAAAATGTTTAAAATAATAAAATATAGGAAATATAAAAATAAAAAAGA
** * *
251407 AAA-AA-TAATTAAAAACTTGTTTATAATAATAAAA
1 AAATAATTTTTTAAAAA-ATGTTTAAAATAATAAAA
251441 AGAAAAAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
59 3 0.04
60 19 0.23
61 2 0.02
62 10 0.12
64 2 0.02
65 3 0.04
66 20 0.25
67 21 0.26
68 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (61 bp):
AAATAATTTTTTAAAAAATGTTTAAAATAATAAAATATAGGAAATATAAAAATAAAAAAGA
Found at i:251517 original size:11 final size:13
Alignment explanation
Indices: 251491--251522 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
251481 AAGAAAACAT
251491 AGGAAAATATAAA
1 AGGAAAATATAAA
251504 AGGAAAA-A-AAA
1 AGGAAAATATAAA
251515 AGGAAAAT
1 AGGAAAAT
251523 GGAAAACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.56
12 1 0.06
13 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (13 bp):
AGGAAAATATAAA
Found at i:254789 original size:2 final size:2
Alignment explanation
Indices: 254747--254776 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
254737 ATGTGTGTGC
254747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254777 CATTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256082 original size:2 final size:2
Alignment explanation
Indices: 256075--256118 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
256065 CTAGTTTAAA
256075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256117 AT
1 AT
256119 TAGTGAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:262537 original size:20 final size:22
Alignment explanation
Indices: 262512--262567 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
262502 AAAAACCCAG
262512 AATGTATCGATACAA-TG-AAA
1 AATGTATCGATACAATTGTAAA
262532 AATGTATCGATACAATTGTAAA
1 AATGTATCGATACAATTGTAAA
*
262554 CATGTATCGATACA
1 AATGTATCGATACA
262568 TTTTATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 15 0.45
21 2 0.06
22 16 0.48
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (22 bp):
AATGTATCGATACAATTGTAAA
Found at i:264164 original size:43 final size:43
Alignment explanation
Indices: 264102--264188 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
264092 TAATCTATAT
* *
264102 TATATATAAAATTTATAATTAAGTTTAGTGTCATTGAGTCAAG
1 TATATATAAAATTTATAATTAAATTTAGTGTCAATGAGTCAAG
* *
264145 TATATATAAAATTTTTAATTAAATTTAGTGTTAATGAGTCAAG
1 TATATATAAAATTTATAATTAAATTTAGTGTCAATGAGTCAAG
264188 T
1 T
264189 GACACCAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (43 bp):
TATATATAAAATTTATAATTAAATTTAGTGTCAATGAGTCAAG
Found at i:264421 original size:13 final size:13
Alignment explanation
Indices: 264405--264438 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
264395 ATTAAATAAT
264405 TATTTTAAAAAAA
1 TATTTTAAAAAAA
264418 TATTTTCTAAAAAAA
1 TA-TTT-TAAAAAAA
264433 TATTTT
1 TATTTT
264439 TCTTTACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.16
14 6 0.32
15 10 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TATTTTAAAAAAA
Found at i:264441 original size:16 final size:15
Alignment explanation
Indices: 264410--264438 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
264400 ATAATTATTT
264410 TAAAAAAATATTTTC
1 TAAAAAAATATTTTC
264425 TAAAAAAATATTTT
1 TAAAAAAATATTTT
264439 TCTTTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAAAAATATTTTC
Found at i:265093 original size:3 final size:3
Alignment explanation
Indices: 265085--265115 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
265075 AATCCCAGCT
265085 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
265116 CTCTCGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:266698 original size:28 final size:29
Alignment explanation
Indices: 266659--266732 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 29
266649 AAAAGTTAAG
* * *
266659 TAAAATATAATAAAAATATATTTTG-ATA
1 TAAAAAATAATAAAAATATAATATGAATA
*
266687 TAAAAAATAATATAAATATAATATGAATA
1 TAAAAAATAATAAAAATATAATATGAATA
266716 TATAAAAAT-ATAAAAAT
1 TA-AAAAATAATAAAAAT
266733 TTATCTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 21 0.54
29 12 0.31
30 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
TAAAAAATAATAAAAATATAATATGAATA
Found at i:267872 original size:2 final size:2
Alignment explanation
Indices: 267867--267897 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
267857 TTTGCTTAAT
*
267867 TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
267898 TGCTTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:268136 original size:13 final size:14
Alignment explanation
Indices: 268112--268165 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
268102 AAATTTAAAT
268112 AAATATAAATATAA
1 AAATATAAATATAA
268126 AAATA-AAATATAA
1 AAATATAAATATAA
* *
268139 ATATAT-TATATTAA
1 AAATATAAATA-TAA
268153 TAAATAT-AATATA
1 -AAATATAAATATA
268166 TTACATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 15 0.45
14 10 0.30
15 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATAAATATAA
Found at i:268136 original size:19 final size:18
Alignment explanation
Indices: 268108--268143 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
268098 TTATAAATTT
268108 AAATAAATATAAATATAA
1 AAATAAATATAAATATAA
268126 AAATAAAATATAAATATA
1 AAAT-AAATATAAATATA
268144 TTATATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAATATAAATATAA
Found at i:268149 original size:7 final size:7
Alignment explanation
Indices: 268139--268224 Score: 52
Period size: 7 Copynumber: 12.0 Consensus size: 7
268129 TAAAATATAA
268139 ATATATT
1 ATATATT
*
268146 ATATTAAT
1 ATA-TATT
* *
268154 AAATATA
1 ATATATT
268161 ATATATT
1 ATATATT
*
268168 ACAT-TT
1 ATATATT
268174 AAATATAATT
1 --ATAT-ATT
268184 A-ATATT
1 ATATATT
268190 ATATATT
1 ATATATT
268197 ATAT-TT
1 ATATATT
*
268203 ATATTTT
1 ATATATT
*
268210 ATAATTTT
1 AT-ATATT
268218 ATATATT
1 ATATATT
268225 TAATAATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
6 12 0.19
7 32 0.52
8 16 0.26
10 2 0.03
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:268157 original size:17 final size:17
Alignment explanation
Indices: 268135--268182 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 17
268125 AAAATAAAAT
*
268135 ATAAATATATTATATTA
1 ATAAATATAATATATTA
268152 ATAAATATAATATATTA
1 ATAAATATAATATATTA
268169 CATTTAAATATAAT
1 -A--TAAATATAAT
268183 TAATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.59
18 1 0.04
20 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATATAATATATTA
Found at i:268161 original size:6 final size:6
Alignment explanation
Indices: 268110--268143 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
268100 ATAAATTTAA
*
268110 ATAAAT ATAAAT ATAAAA ATAAAAT ATAAAT ATA
1 ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATA
268144 TTATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
ATAAAT
Found at i:268178 original size:24 final size:22
Alignment explanation
Indices: 268106--268188 Score: 70
Period size: 24 Copynumber: 3.8 Consensus size: 22
268096 TTTTATAAAT
268106 TTAAATAAATATAA-ATA-TAA
1 TTAAATAAATATAATATATTAA
268126 --AAATAAAATATAAATATATTATA
1 TTAAAT-AAATAT-AATATATTA-A
268149 TT-AATAAATATAATATATTACA
1 TTAAATAAATATAATATATTA-A
268171 TTTAAATATAAT-TAATAT
1 -TTAAATA-AATATAATAT
268189 TATATATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 16
0.75 0.01 0.23
Matches are distributed among these distances:
18 4 0.08
19 6 0.12
20 2 0.04
21 3 0.06
22 12 0.23
23 9 0.17
24 13 0.25
25 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAATAAATATAATATATTAA
Found at i:268189 original size:22 final size:21
Alignment explanation
Indices: 268110--268182 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 21
268100 ATAAATTTAA
* * *
268110 ATAAATATAA-ATATAAAAAT
1 ATAAATATAATATATTACATT
*
268130 A-AAATATAAATATATTATATT
1 ATAAATAT-AATATATTACATT
268151 AATAAATATAATATATTACATT
1 -ATAAATATAATATATTACATT
268173 -TAAATATAAT
1 ATAAATATAAT
268183 TAATATTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.13
20 13 0.29
21 7 0.16
22 13 0.29
23 6 0.13
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAAATATAATATATTACATT
Found at i:268211 original size:13 final size:15
Alignment explanation
Indices: 268183--268233 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 15
268173 TAAATATAAT
* *
268183 TAATATTATATATTA
1 TAATTTTATATTTTA
268198 T-A-TTTATATTTTA
1 TAATTTTATATTTTA
268211 TAATTTTATATATTTAA
1 TAATTTTATAT-TTT-A
268228 TAATTT
1 TAATTT
268234 AAATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 8 0.27
16 3 0.10
17 7 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATTTTATATTTTA
Found at i:268850 original size:21 final size:22
Alignment explanation
Indices: 268826--268872 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
268816 TTTTTAAAAT
*
268826 AAAAAACTA-CC-TATTTATATA
1 AAAAAACTATCCATATATA-ATA
268847 AAAAAACTATCCATATATAATA
1 AAAAAACTATCCATATATAATA
268869 AAAA
1 AAAA
268873 TTTATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAAACTATCCATATATAATA
Found at i:271380 original size:21 final size:21
Alignment explanation
Indices: 271351--271414 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
271341 ATTTTACAAT
271351 TAATTTTAAAATAATAATATA
1 TAATTTTAAAATAATAATATA
*
271372 TACA-TTTAAATATAATAA-AAA
1 TA-ATTTTAAA-ATAATAATATA
271393 TAATTTTAAAAATAA-AATATA
1 TAATTTT-AAAATAATAATATA
271414 T
1 T
271415 GATAATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
20 3 0.08
21 22 0.61
22 11 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTTTAAAATAATAATATA
Found at i:285382 original size:20 final size:20
Alignment explanation
Indices: 285357--285415 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
285347 ATTGCCAAAG
285357 AAATGTATCGATACATTATT
1 AAATGTATCGATACATTATT
* **
285377 AAATGTATCGATACCTGCTT
1 AAATGTATCGATACATTATT
285397 ACAATTGTATCGATACATT
1 A-AA-TGTATCGATACATT
285416 TCTCATTGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 12 0.38
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (20 bp):
AAATGTATCGATACATTATT
Found at i:293730 original size:20 final size:20
Alignment explanation
Indices: 293702--293776 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
293692 TTTTACCTTG
293702 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
293722 ATATATCGATATATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
293742 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
293762 ATGTATCGATACATT
1 ATGTATCGATACATT
293777 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:302254 original size:27 final size:27
Alignment explanation
Indices: 302217--302899 Score: 1042
Period size: 27 Copynumber: 25.0 Consensus size: 27
302207 GTGGCATTTT
* *
302217 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
302245 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302272 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302299 CTTTTAAGTCTACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302326 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
302354 CTTTTAAGTCCACAACTTCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
302382 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302409 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302436 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302463 CTTTTAAGTCCACAACTCTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
302491 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * **
302518 CTTTTAAGTCCACCACTCTGTGGCATT
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302545 CTTTTAAGTCCACAACTCCGTGGCACA
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
302572 TTTTTAAGTCCACAACTCTGTGGCACA
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302599 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302626 CTTTTAAGTCCACAACTCCATGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
302654 CTTTTAAGACCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302681 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
302708 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
302736 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302763 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
302791 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302818 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
302845 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
302872 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
302899 C
1 C
302900 ATTCCAAAGC
Statistics
Matches: 605, Mismatches: 45, Indels: 11
0.92 0.07 0.02
Matches are distributed among these distances:
27 450 0.74
28 155 0.26
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:302765 original size:300 final size:298
Alignment explanation
Indices: 302217--302897 Score: 1098
Period size: 300 Copynumber: 2.3 Consensus size: 298
302207 GTGGCATTTT
302217 CTTTTAAAGTCCACAACTCTGTGGCATCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTAAGTC
1 CTTTT-AAGTCCACAACTCTGTGGCATC-TTTTAAGTCCACAACTCCGTGGCA-CTTTTTAAGTC
* * * *
302282 CACAACTCCGTGGCACCCTTTTAAGTCTACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGT
63 CACAACTCTGTGGCACACTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCAT
* *
302347 GGCATCCCTTTTAAGTCCACAACTTCGTGGCATCTCTTTTAAGTCCACAACTCCGTGGCACCCTT
128 GGCATCCCTTTTAAGACCACAACTTCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTT
302412 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCAC
193 TTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCAC
*
302476 AACTCTGTGGCATCCCTTTTAAGACCACAACTCCGTGGCACC
258 AACTCCGTGGCA-CCCTTTTAAGACCACAACTCCGTGGCACC
*
302518 CTTTTAAGTCCACCACTCTGTGGCATTCTTTTAAGTCCACAACTCCGTGGCACATTTTTAAGTCC
1 CTTTTAAGTCCACAACTCTGTGGCA-TCTTTTAAGTCCACAACTCCGTGGCAC-TTTTTAAGTCC
*
302583 ACAACTCTGTGGCACATTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATG
64 ACAACTCTGTGGCACACTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATG
*
302648 GCATCCCTTTTAAGACCACAAC-TCTGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACCCTT
129 GCATCCCTTTTAAGACCACAACTTC-GTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTT
* * *
302711 TTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCA
193 TTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCA
302776 CAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACC
257 CAACTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACC
* * * *
302818 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAATCC
1 CTTTTAAGTCCACAACTCTGTGGCA-TCTTTTAAGTCCACAACTCCGTGGCA-CTTTTTAAGTCC
302883 ACAACTCTGTGGCAC
64 ACAACTCTGTGGCAC
302898 CCATTCCAAA
Statistics
Matches: 355, Mismatches: 19, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
299 54 0.15
300 274 0.77
301 27 0.08
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (298 bp):
CTTTTAAGTCCACAACTCTGTGGCATCTTTTAAGTCCACAACTCCGTGGCACTTTTTAAGTCCAC
AACTCTGTGGCACACTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCATGGC
ATCCCTTTTAAGACCACAACTTCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
AGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAAC
TCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACC
Found at i:302933 original size:32 final size:31
Alignment explanation
Indices: 302882--303659 Score: 736
Period size: 32 Copynumber: 26.0 Consensus size: 31
302872 CTTTTAAATC
* * *
302882 CACAACTCTGTGGCACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
302913 CGCAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
302945 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
302977 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
303009 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
* *
303041 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
303073 CACAAGTC-GATGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAG-TGGC-ACCCATTTCAAAGCCCA
* *
303105 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCAGTGGC-ACCCATTTCAAAGCCCA
*
303137 CACAAGTCAGTGGCACCC-TTTCGAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
303165 CACAAGTCAGTGGCACCC-TTTCGAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
** *
303193 CACAAGTCAGTGGCA-CCATCGCGAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
303221 CACAATTCAGTAGCACTC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
303249 CACAAGTCAGCGGCACCC-TTTTAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
303279 CACAAGTTAGTGGCACCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
303309 CACAAGTCAGTGGCACTCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAC-CCATTTCAAAGCCCA
*
303340 CGCAAGTCAGTGGCACTCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAC-CCATTTCAAAGCCCA
*
303371 CGCAAGTCAGTGGCACTCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCAC-CCATTTCAAAGCCCA
* * *
303402 CGCAAGTCAGTGGCA-CCTTTTTAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
303430 CACGAGTCAGTGGCACTC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
303458 CACAAGTCAGTGGCACTC-TTTC-AAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
303485 CACGAGTCAGTGGTA-CCTTTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
*
303513 CACGAGTCAGTGGCA-CC-TTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
**
303540 CACAAGTCAGTGGCA-CTTTTTCAAAG-CC-
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* *
303568 CACGAGTCAGTGGCATCC-TTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* * *
303598 CGCAAGTCAGTGGCACCC-TTTTAAAACCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
* ** * *
303628 CGCAAGTCAGTAACACTCTTTTCAAAGCCCA
1 CACAAGTCAGTGGCACCCATTTCAAAGCCCA
303659 C
1 C
303660 CTGTGTCAGT
Statistics
Matches: 679, Mismatches: 51, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
26 1 0.00
27 49 0.07
28 188 0.28
29 13 0.02
30 95 0.14
31 117 0.17
32 215 0.32
33 1 0.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.18
Consensus pattern (31 bp):
CACAAGTCAGTGGCACCCATTTCAAAGCCCA
Found at i:303173 original size:28 final size:28
Alignment explanation
Indices: 303137--303618 Score: 342
Period size: 28 Copynumber: 16.8 Consensus size: 28
303127 CCAAAGCCCA
* *
303137 CACAAGTCAGTGGCACCCTTTCGAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* *
303165 CACAAGTCAGTGGCACCCTTTCGAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* * ** *
303193 CACAAGTCAGTGGCACCATCGCGAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* * * *
303221 CACAATTCAGTAGCACTCTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* *
303249 CACAAGTCAGCGGCACCCTTT-TAAAGCCC
1 CACAACTCAGTGGCACCCTTTCT-AAG-CC
* * *
303278 ACACAAGTTAGTGGCACCCTTTCAAAGCCC
1 -CACAACTCAGTGGCACCCTTTCTAAG-CC
* *
303308 ACACAAGTCAGTGGCACTCCTTTCAAAGCC
1 -CACAACTCAGTGGCAC-CCTTTCTAAGCC
* *
303338 CACGCAAGTCAGTGGCACTCCTTTCAAAGCC
1 CA--CAACTCAGTGGCAC-CCTTTCTAAGCC
* *
303369 CACGCAAGTCAGTGGCACTCCTTTCAAAGCC
1 CA--CAACTCAGTGGCAC-CCTTTCTAAGCC
* *
303400 CACGCAAGTCAGTGGCA-CCTTTTTAAAGCC
1 CA--CAACTCAGTGGCACCCTTTCT-AAGCC
* * * *
303430 CACGAGTCAGTGGCACTCTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* *
303458 CACAAGTCAGTGGCACTCTTTC-AAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* * * * *
303485 CACGAGTCAGTGGTACCTTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* * *
303513 CACGAGTCAGTGGCA-CCTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* ** *
303540 CACAAGTCAGTGGCACTTTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
* * * *
303568 CACGAGTCAGTGGCATCCTTTCAAAGCC
1 CACAACTCAGTGGCACCCTTTCTAAGCC
*
303596 CACGCAAGTCAGTGGCACCCTTT
1 CA--CAACTCAGTGGCACCCTTT
303619 TAAAACCCAC
Statistics
Matches: 400, Mismatches: 41, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
27 48 0.12
28 187 0.47
29 13 0.03
30 67 0.17
31 85 0.21
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (28 bp):
CACAACTCAGTGGCACCCTTTCTAAGCC
Found at i:304296 original size:20 final size:20
Alignment explanation
Indices: 304268--304338 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
304258 TTTTACCTTG
304268 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * * *
304288 ATATATCGATATATGTATGA
1 ATGTATCGATATATTTTTCA
* *
304308 ATGTATCGATATATTCTACA
1 ATGTATCGATATATTTTTCA
304328 ATGTATCGATA
1 ATGTATCGATA
304339 CATTATGTCT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:319050 original size:11 final size:11
Alignment explanation
Indices: 319034--319102 Score: 50
Period size: 11 Copynumber: 5.9 Consensus size: 11
319024 AGTGTTATGA
319034 TATATTAGCTG
1 TATATTAGCTG
*
319045 TATATTAACTG
1 TATATTAGCTG
319056 TAGATATTGAG-TG
1 T--ATATT-AGCTG
* *
319069 TGTTATGAGCTG
1 T-ATATTAGCTG
319081 TATAATTAGCTG
1 TAT-ATTAGCTG
*
319093 TACATTAGCT
1 TATATTAGCT
319103 ATAAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 21 0.46
12 16 0.35
13 8 0.17
14 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (11 bp):
TATATTAGCTG
Found at i:321989 original size:5 final size:5
Alignment explanation
Indices: 321974--322110 Score: 62
Period size: 5 Copynumber: 27.8 Consensus size: 5
321964 TTAATTAAAA
321974 ATAATT ATAAT ATAAT ATAAAAT ATAAT ATAAT ATAA- A-AA- ATAAT
1 ATAA-T ATAAT ATAAT AT--AAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
322019 ATAAT A-AAA AT-AT ATAAT TTTAT ATAAT ATTAATT ATTAAT -TAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAA-T A-TAAT ATAAT
* * *
322064 -TAAAT TTTAT ATAA- AT-AT ATAAT ACT-TT A-AAT ATAATT ATAAT
1 AT-AAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAA-T ATAAT
322107 ATAA
1 ATAA
322111 AAATAATACA
Statistics
Matches: 104, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
3 4 0.04
4 20 0.19
5 54 0.52
6 15 0.14
7 11 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:321999 original size:12 final size:12
Alignment explanation
Indices: 321965--322032 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
321955 AATTATTTAT
321965 TAAT-TAAAA-A
1 TAATATAAAATA
*
321975 TAAT-TATAATA
1 TAATATAAAATA
321986 TAATATAAAATA
1 TAATATAAAATA
321998 TAATAT--AATA
1 TAATATAAAATA
*
322008 TAA-AAAATAATA
1 TAATATAA-AATA
322020 TAATA-AAAATA
1 TAATATAAAATA
322031 TA
1 TA
322033 TAATTTTATA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
9 1 0.02
10 15 0.31
11 11 0.22
12 21 0.43
13 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:321999 original size:17 final size:17
Alignment explanation
Indices: 321979--322032 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
321969 TAAAAATAAT
321979 TATAATATAATATAAAA
1 TATAATATAATATAAAA
321996 TATAATATAATATAAAA
1 TATAATATAATATAAAA
*
322013 AATAATATAATA-AAAA
1 TATAATATAATATAAAA
322029 TATA
1 TATA
322033 TAATTTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 7 0.20
17 28 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TATAATATAATATAAAA
Found at i:322031 original size:40 final size:40
Alignment explanation
Indices: 321970--322048 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
321960 TTTATTAATT
*
321970 AAAAATAATTATAATATAATATAAAATATAATATAATATA
1 AAAAATAATTATAATAAAATATAAAATATAATATAATATA
* * *
322010 AAAAATAA-TATAATAAAAATATATAATTTTATATAATAT
1 AAAAATAATTATAAT-AAAATATAAAATATAATATAATAT
322049 TAATTATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (40 bp):
AAAAATAATTATAATAAAATATAAAATATAATATAATATA
Found at i:322116 original size:17 final size:17
Alignment explanation
Indices: 321980--322117 Score: 67
Period size: 17 Copynumber: 8.3 Consensus size: 17
321970 AAAAATAATT
321980 ATAA-TATAATATAAAA
1 ATAATTATAATATAAAA
321996 TATAA-TATAATATAAAAA
1 -ATAATTATAATAT-AAAA
*
322014 ATAA-TATAATAAAAATA
1 ATAATTATAATATAAA-A
* *
322031 TATAATT-TTATATAATA
1 -ATAATTATAATATAAAA
* **
322048 TTAATTATTAAT-TAATT
1 ATAATTA-TAATATAAAA
* *
322065 A-AATT-TTATATAAAT
1 ATAATTATAATATAAAA
* * * *
322080 AT-ATAATACTTTAAAT
1 ATAATTATAATATAAAA
322096 ATAATTATAATATAAAA
1 ATAATTATAATATAAAA
322113 ATAAT
1 ATAAT
322118 ACAAATAGAT
Statistics
Matches: 93, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
14 3 0.03
15 7 0.08
16 21 0.23
17 44 0.47
18 17 0.18
19 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTATAATATAAAA
Found at i:322438 original size:19 final size:18
Alignment explanation
Indices: 322393--322442 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
322383 TTTGTAAGTA
322393 ATTTTTTAAAAAATACAT
1 ATTTTTTAAAAAATACAT
**
322411 ATTCATTAAAAAATTA-ATT
1 ATTTTTTAAAAAA-TACA-T
322430 ATTTTTTAAAAAA
1 ATTTTTTAAAAAA
322443 ATCACTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTTTAAAAAATACAT
Found at i:323678 original size:20 final size:19
Alignment explanation
Indices: 323649--323693 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
323639 TCATGTGGAC
323649 TTTTTTTTTTCTTTCTTCT
1 TTTTTTTTTTCTTTCTTCT
*
323668 TTTTTTATTT-TTT-TTCT
1 TTTTTTTTTTCTTTCTTCT
323685 TTATTTTTT
1 TT-TTTTTT
323694 CGTCCCTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 8 0.35
19 9 0.39
ACGTcount: A:0.04, C:0.09, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTCTTTCTTCT
Found at i:323973 original size:13 final size:14
Alignment explanation
Indices: 323957--323998 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
323947 AAATAATTAA
323957 AAAAATTTT-AAAT
1 AAAAATTTTAAAAT
*
323970 AAAATTTTTAAAAT
1 AAAAATTTTAAAAT
*
323984 AAAAA-TATAAAAT
1 AAAAATTTTAAAAT
323997 AA
1 AA
323999 GAGTGTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAATTTTAAAAT
Found at i:324089 original size:22 final size:21
Alignment explanation
Indices: 324039--324137 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 21
324029 AATTATTTAA
*
324039 TTTTTTATTTGAAAAAAATCATTAA
1 TTTTTTATTT-AAAAAAAT-A--AC
324064 TTTTCTTATTTAAAAAAATAAC
1 TTTT-TTATTTAAAAAAATAAC
*
324086 TTTTTATTTTTTATTTTAAAAAAATCAA-
1 ----T-T-TTTTATTTAAAAAAA-T-AAC
324114 TTTTTTATTTAAAAAAATAAC
1 TTTTTTATTTAAAAAAATAAC
324135 TTT
1 TTT
324138 CAATTTATTT
Statistics
Matches: 61, Mismatches: 3, Indels: 24
0.69 0.03 0.27
Matches are distributed among these distances:
20 2 0.03
21 4 0.07
22 15 0.25
23 1 0.02
24 2 0.03
25 12 0.20
26 7 0.11
27 13 0.21
28 3 0.05
29 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (21 bp):
TTTTTTATTTAAAAAAATAAC
Found at i:324143 original size:20 final size:21
Alignment explanation
Indices: 324100--324144 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
324090 TATTTTTTAT
* **
324100 TTTAAAAAAATCAATTTTTTA
1 TTTAAAAAAATCAACTTTCAA
324121 TTTAAAAAAAT-AACTTTCAA
1 TTTAAAAAAATCAACTTTCAA
324141 TTTA
1 TTTA
324145 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAAAAAATCAACTTTCAA
Found at i:324152 original size:28 final size:27
Alignment explanation
Indices: 324037--324157 Score: 123
Period size: 28 Copynumber: 4.7 Consensus size: 27
324027 TTAATTATTT
*
324037 AATTTTTTATTTGAAAAAAAT--CATT-
1 AATTTTTTATTT-AAAAAAATAACTTTC
*
324062 AATTTTCTTATTTAAAAAAATAACTTTT
1 AATTTT-TTATTTAAAAAAATAACTTTC
* *
324090 TATTTTTTATTT-TAAAAA-AA---TC
1 AATTTTTTATTTAAAAAAATAACTTTC
324112 AATTTTTTATTTAAAAAAATAACTTTC
1 AATTTTTTATTTAAAAAAATAACTTTC
324139 AATTTATTTATTTAAAAAA
1 AATTT-TTTATTTAAAAAA
324158 CTACTACTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 17
0.78 0.06 0.17
Matches are distributed among these distances:
22 12 0.15
23 5 0.06
24 2 0.03
25 16 0.20
26 11 0.14
27 16 0.20
28 18 0.22
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.50
Consensus pattern (27 bp):
AATTTTTTATTTAAAAAAATAACTTTC
Found at i:324153 original size:49 final size:50
Alignment explanation
Indices: 324037--324157 Score: 165
Period size: 49 Copynumber: 2.4 Consensus size: 50
324027 TTAATTATTT
*
324037 AATTTTTTATTTGAAAAAAATCATTAATTTTCTTATTTAAAAAAATAACTTTT
1 AATTTTTTATTT-AAAAAAATC--TAATTTTCTTATTTAAAAAAATAACTTTC
*
324090 TATTTTTTATTTTAAAAAAATC-AATTTT-TTATTTAAAAAAATAACTTTC
1 AATTTTTTA-TTTAAAAAAATCTAATTTTCTTATTTAAAAAAATAACTTTC
324139 AATTTATTTATTTAAAAAA
1 AATTT-TTTATTTAAAAAA
324158 CTACTACTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
49 33 0.52
50 10 0.16
53 17 0.27
54 3 0.05
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.50
Consensus pattern (50 bp):
AATTTTTTATTTAAAAAAATCTAATTTTCTTATTTAAAAAAATAACTTTC
Found at i:327510 original size:29 final size:28
Alignment explanation
Indices: 327461--327517 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
327451 AACCATCACA
* *
327461 CATTTTATTATGCATAGATATTCTTAAT
1 CATTTTATTAAGCATAGATATTCGTAAT
*
327489 CATTTTATTTAAGCATATATATTCGTAAT
1 CATTTTA-TTAAGCATAGATATTCGTAAT
327518 AATATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (28 bp):
CATTTTATTAAGCATAGATATTCGTAAT
Found at i:328310 original size:20 final size:20
Alignment explanation
Indices: 328287--328359 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
328277 ACAATTCAAA
328287 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
328307 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
328328 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
328348 GTATCGATACAT
1 GTATCGATACAT
328360 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:328331 original size:21 final size:21
Alignment explanation
Indices: 328305--328380 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
328295 ACATGTTGCA
328305 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
328326 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
328346 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
328367 ATGTATCGATACAT
1 ATGTATCGATACAT
328381 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:328338 original size:41 final size:41
Alignment explanation
Indices: 328287--328380 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
328277 ACAATTCAAA
*
328287 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
328328 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
328369 GTATCGATACAT
1 GTATCGATACAT
328381 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:328437 original size:13 final size:13
Alignment explanation
Indices: 328419--328444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
328409 TACAGCAAGT
328419 ATGTATCGATACA
1 ATGTATCGATACA
328432 ATGTATCGATACA
1 ATGTATCGATACA
328445 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.