Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold804.1
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: 734204
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.34
Warning! 17016 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:550 original size:18 final size:18
Alignment explanation
Indices: 526--655 Score: 98
Period size: 18 Copynumber: 6.7 Consensus size: 18
516 TCAGCTCTGG
526 TGAGCTTCAGTTAGCCTT
1 TGAGCTTCAGTTAGCCTT
* *
544 CGAGCTTCCGTTTAGCACTT
1 TGAGCTTCAG-TTAGC-CTT
* *
564 CTGTGCTTCAGTCAGCCTT
1 -TGAGCTTCAGTTAGCCTT
* *
583 TGGGCTTCCGTTTAGCACTT
1 TGAGCTTCAG-TTAGC-CTT
*
603 GTGTGCTTCAGTTAGCCTT
1 -TGAGCTTCAGTTAGCCTT
*
622 TGAGCTTCCGTTTAGCACTT
1 TGAGCTTCAG-TTAGC-CTT
*
642 GTGTGCTTCAGTTA
1 -TGAGCTTCAGTTA
656 AGTTAGCCTC
Statistics
Matches: 88, Mismatches: 15, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
18 24 0.27
19 20 0.23
20 21 0.24
21 23 0.26
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (18 bp):
TGAGCTTCAGTTAGCCTT
Found at i:575 original size:39 final size:39
Alignment explanation
Indices: 529--696 Score: 219
Period size: 39 Copynumber: 4.2 Consensus size: 39
519 GCTCTGGTGA
*
529 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTGTGT
* * *
568 GCTTCAGTCAGCCTTTGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTGTGT
*
607 GCTTCAGTTAGCCTTTGAGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTGTGT
* * *
646 GCTTCAGTTAAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTC-----AGTTAGCCTTCGAGCTTCCGTTTAGCACTTGTGT
690 GCTTCAG
1 GCTTCAG
697 CTAAACTTCG
Statistics
Matches: 114, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
39 79 0.69
44 35 0.31
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGAGCTTCCGTTTAGCACTTGTGT
Found at i:712 original size:83 final size:78
Alignment explanation
Indices: 541--712 Score: 209
Period size: 83 Copynumber: 2.1 Consensus size: 78
531 TTCAGTTAGC
** *
541 CTTCGAGCTTCCGTTTAGCACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGCACTTGTG
1 CTTCGAGCTTCCGTTTAGCACTTCTGTGCTTCAGTCAGCCTCCGGGCTTCCGTTTAGCACTTATG
* **
606 TGCTTCAGTTAGC
66 TGCTTCAGCTAAA
* * *
619 CTTTGAGCTTCCGTTTAGCACTTGTGTGCTTCAGTTAAGTTAGCCTCCGGGCTTCCGTTTAGCAC
1 CTTCGAGCTTCCGTTTAGCACTTCTGTGCTTC-----AGTCAGCCTCCGGGCTTCCGTTTAGCAC
684 TTATGTGCTTCAGCTAAA
61 TTATGTGCTTCAGCTAAA
*
702 CTTCGGGCTTC
1 CTTCGAGCTTC
713 AGATCACAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 30 0.38
83 48 0.62
ACGTcount: A:0.13, C:0.26, G:0.23, T:0.38
Consensus pattern (78 bp):
CTTCGAGCTTCCGTTTAGCACTTCTGTGCTTCAGTCAGCCTCCGGGCTTCCGTTTAGCACTTATG
TGCTTCAGCTAAA
Found at i:6272 original size:88 final size:90
Alignment explanation
Indices: 6114--6291 Score: 261
Period size: 88 Copynumber: 2.0 Consensus size: 90
6104 AGCAAAACCG
* *
6114 GAGCCACAACCACCTGGAACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTC
1 GAGCCACAACCACCTAGAACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACACCTC
*
6179 GACATGTAGAAGATCGCATGAGGCA
66 AACATGTAGAAGATCGCATGAGGCA
* * * *
6204 GAGCCACATCGACCTAG-ACAAAACATGATCAAATGAT-AAACATATTGCAATGGCATACGCCTC
1 GAGCCACAACCACCTAGAACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACACCTC
* *
6267 AACATGTCGAAGATCGTATGAGGCA
66 AACATGTAGAAGATCGCATGAGGCA
6292 AAGCATAGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 45 0.57
89 20 0.25
90 14 0.18
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (90 bp):
GAGCCACAACCACCTAGAACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACACCTC
AACATGTAGAAGATCGCATGAGGCA
Found at i:13188 original size:20 final size:20
Alignment explanation
Indices: 13163--13211 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
13153 CCAAGAAATA
* * *
13163 AGATCCGGATGCTTGTAGTT
1 AGATCCAGATGCTTCTACTT
13183 AGATCCAGATGCTTCTACTT
1 AGATCCAGATGCTTCTACTT
13203 AGATCCAGA
1 AGATCCAGA
13212 AGCTCGTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
AGATCCAGATGCTTCTACTT
Found at i:14111 original size:23 final size:22
Alignment explanation
Indices: 14082--14124 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
14072 GGTTTTGCCA
14082 ATTTGGGGTTTGGATTGTTTTTT
1 ATTTGGGGTTTGG-TTGTTTTTT
*
14105 ATTTGGGTTTTGGTTGTTTT
1 ATTTGGGGTTTGGTTGTTTT
14125 ATGACCAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (22 bp):
ATTTGGGGTTTGGTTGTTTTTT
Found at i:14112 original size:22 final size:23
Alignment explanation
Indices: 14082--14124 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
14072 GGTTTTGCCA
14082 ATTTGGGG-TTTGGATTGTTTTTT
1 ATTTGGGGTTTTGG-TTGTTTTTT
14105 ATTT-GGGTTTTGGTTGTTTT
1 ATTTGGGGTTTTGGTTGTTTT
14125 ATGACCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.07, C:0.00, G:0.30, T:0.63
Consensus pattern (23 bp):
ATTTGGGGTTTTGGTTGTTTTTT
Found at i:16570 original size:9 final size:9
Alignment explanation
Indices: 16531--16677 Score: 59
Period size: 9 Copynumber: 15.6 Consensus size: 9
16521 TACAAATATA
16531 AAAAATTGAT
1 AAAAATT-AT
*
16541 ATAAACTTAT
1 A-AAAATTAT
**
16551 AAAAACAAT
1 AAAAATTAT
16560 AAAAATTAT
1 AAAAATTAT
16569 -AAAATTAT
1 AAAAATTAT
16577 -AAAATTA-
1 AAAAATTAT
16584 ATAAAATATATT
1 A-AAAAT-TA-T
*
16596 AAAATTTTAT
1 AAAA-ATTAT
**
16606 AAAAACAAAT
1 AAAAA-TTAT
*
16616 TAAAATT-T
1 AAAAATTAT
16624 AAAAAATGTAT
1 -AAAAAT-TAT
* *
16635 TAAAAGTAT
1 AAAAATTAT
*
16644 TAAAATTGAT
1 AAAAATT-AT
* *
16654 ATAAACTTGT
1 A-AAAATTAT
16664 AAAAATTAT
1 AAAAATTAT
16673 AAAAA
1 AAAAA
16678 AAACATAAAA
Statistics
Matches: 102, Mismatches: 22, Indels: 27
0.68 0.15 0.18
Matches are distributed among these distances:
8 16 0.16
9 42 0.41
10 26 0.25
11 16 0.16
12 2 0.02
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16572 original size:8 final size:8
Alignment explanation
Indices: 16561--16601 Score: 55
Period size: 8 Copynumber: 4.8 Consensus size: 8
16551 AAAAACAATA
16561 AAAATTAT
1 AAAATTAT
16569 AAAATTAT
1 AAAATTAT
16577 AAAATTAAT
1 AAAATT-AT
16586 AAAATATATT
1 AAAAT-TA-T
16596 AAAATT
1 AAAATT
16602 TTATAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.47
9 9 0.30
10 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:16576 original size:26 final size:25
Alignment explanation
Indices: 16540--16627 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 25
16530 AAAAAATTGA
*
16540 TATAAACTTATAAAAACAATAAAAAT
1 TATAAAATTATAAAAACAAT-AAAAT
**
16566 TATAAAATTATAAAATTAATAAAAT
1 TATAAAATTATAAAAACAATAAAAT
16591 ATATTAAAATTTTATAAAAACAAATTAAAAT
1 -TA-TAAAA--TTATAAAAAC-AA-TAAAAT
16622 T-TAAAA
1 TATAAAA
16628 AATGTATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
25 5 0.10
26 19 0.37
27 5 0.10
28 5 0.10
29 8 0.16
30 3 0.06
31 6 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (25 bp):
TATAAAATTATAAAAACAATAAAAT
Found at i:16582 original size:16 final size:19
Alignment explanation
Indices: 16561--16649 Score: 69
Period size: 19 Copynumber: 4.7 Consensus size: 19
16551 AAAAACAATA
16561 AAAATT-ATAAAAT-TA-T
1 AAAATTAATAAAATATATT
16577 AAAATTAATAAAATATATT
1 AAAATTAATAAAATATATT
* * *
16596 AAAATTTTATAAAAACAAATT
1 AAAA-TTAAT-AAAATATATT
*
16617 AAAATTTAA-AAAATGTATT
1 AAAA-TTAATAAAATATATT
* *
16636 AAAAGTATTAAAAT
1 AAAATTAATAAAAT
16650 TGATATAAAC
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
16 6 0.10
17 7 0.12
18 4 0.07
19 21 0.36
20 4 0.07
21 16 0.28
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTAATAAAATATATT
Found at i:17149 original size:23 final size:24
Alignment explanation
Indices: 17107--17151 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
17097 TTTATAAATT
*
17107 TTTTATAATTTATTATATTTTTCA
1 TTTTATAATATATTATATTTTTCA
17131 TTTTATAATAT-TTATATTTTT
1 TTTTATAATATATTATATTTTT
17152 ATAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTATAATATATTATATTTTTCA
Found at i:17168 original size:16 final size:17
Alignment explanation
Indices: 17108--17171 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
17098 TTATAAATTT
*
17108 TTTATAA-TTTATTATA
1 TTTATAAGTTTATAATA
* * *
17124 TTTTTCATTTTATAATA
1 TTTATAAGTTTATAATA
**
17141 TTTATATTTTTATAA-A
1 TTTATAAGTTTATAATA
17157 TTTATAAGTTTATAA
1 TTTATAAGTTTATAA
17172 CAATTTTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
16 19 0.49
17 20 0.51
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTATAAGTTTATAATA
Found at i:17193 original size:14 final size:15
Alignment explanation
Indices: 17174--17203 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17164 GTTTATAACA
17174 ATTTTA-ATATTTTT
1 ATTTTATATATTTTT
17188 ATTTTATATATTTTT
1 ATTTTATATATTTTT
17203 A
1 A
17204 ATGATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATATATTTTT
Found at i:18552 original size:14 final size:14
Alignment explanation
Indices: 18533--18568 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18523 TATGTCGATT
18533 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
* *
18547 AAAAAGAGAGAAAA
1 AAAAAGAAAAAAAA
18561 AAAAAGAA
1 AAAAAGAA
18569 GGGGAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:21463 original size:13 final size:13
Alignment explanation
Indices: 21445--21474 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
21435 GTGTAGTTGA
21445 GATATTTTAGATG
1 GATATTTTAGATG
21458 GATATTTTAGATG
1 GATATTTTAGATG
21471 GATA
1 GATA
21475 AACTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (13 bp):
GATATTTTAGATG
Found at i:32854 original size:37 final size:37
Alignment explanation
Indices: 32797--32901 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
32787 TATGATCACT
*
32797 TATCACT-TGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
* * *
32832 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
32869 TATCACTCTGTCTCTTGATCAGATAAGTGTAGC
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGC
32902 TAAAGCTATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 7 0.11
36 3 0.05
37 53 0.84
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (37 bp):
TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:32944 original size:52 final size:52
Alignment explanation
Indices: 32865--33035 Score: 288
Period size: 52 Copynumber: 3.2 Consensus size: 52
32855 TAAGTGTAGC
* * **
32865 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCACT-TGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
32918 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
32970 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
33022 CACTTTGTCACTTG
1 CACTTT-TCACTTG
33036 ATCAGAAGTA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
52 96 0.85
53 17 0.15
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:36222 original size:49 final size:50
Alignment explanation
Indices: 36167--36370 Score: 241
Period size: 49 Copynumber: 4.0 Consensus size: 50
36157 TTCGTTTTCT
*
36167 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* * *
36216 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* *
36265 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACATAC
* * *
36323 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACAT
36371 GTTCACATGT
Statistics
Matches: 136, Mismatches: 10, Indels: 17
0.83 0.06 0.10
Matches are distributed among these distances:
49 74 0.54
50 7 0.05
51 7 0.05
52 1 0.01
55 1 0.01
56 6 0.04
57 1 0.01
58 39 0.29
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (50 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
Found at i:36337 original size:58 final size:59
Alignment explanation
Indices: 36251--36369 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
36241 TACACGAAAT
36251 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
36309 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
36368 CA
1 CA
36370 TGTTCACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 54 0.90
59 6 0.10
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (59 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
Found at i:36350 original size:28 final size:28
Alignment explanation
Indices: 36260--36350 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
36250 TCACATATCA
36260 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
36288 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
36318 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
36346 CTTAC
1 CTTAC
36351 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:37684 original size:37 final size:37
Alignment explanation
Indices: 37623--37807 Score: 320
Period size: 37 Copynumber: 5.1 Consensus size: 37
37613 TACGTATGAT
*
37623 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
* *
37658 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
37695 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
37732 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
37769 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
37806 CA
1 CA
37808 AAGCTATCAC
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
35 9 0.06
36 4 0.03
37 130 0.91
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:37848 original size:52 final size:52
Alignment explanation
Indices: 37769--37985 Score: 293
Period size: 52 Copynumber: 4.2 Consensus size: 52
37759 TAAGTGTAGC
* *
37769 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
*
37822 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
37874 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
37920 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
37972 CACTTTGTCACTTG
1 CACTTT-TCACTTG
37986 ATCAGAAGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
52 86 0.59
53 15 0.10
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
Found at i:37935 original size:98 final size:98
Alignment explanation
Indices: 37768--37991 Score: 376
Period size: 98 Copynumber: 2.3 Consensus size: 98
37758 ATAAGTGTAG
* * *
37768 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
*
37833 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
* * *
37866 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
*
37931 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
37964 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
37992 AGTACTCAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 117 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATCACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTGTAGCCAAAGCTA
Found at i:41488 original size:25 final size:25
Alignment explanation
Indices: 41434--41488 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
41424 ACAAAAATAA
* * *
41434 AATATTTTTTAAAAATTTCAAATTT
1 AATATTTTTAAAAAATTTCAAAATG
*
41459 TATATTTTTAAAAAA-TTCTAAAATG
1 AATATTTTTAAAAAATTTC-AAAATG
41484 AATAT
1 AATAT
41489 AAAAAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (25 bp):
AATATTTTTAAAAAATTTCAAAATG
Found at i:42939 original size:6 final size:6
Alignment explanation
Indices: 42930--42958 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42920 TTGATGTTGA
42930 TTTGTT TTTGTT TTTGTT TTT-TT TTTGTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT
42959 CGCGAAACGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (6 bp):
TTTGTT
Found at i:52294 original size:8 final size:8
Alignment explanation
Indices: 52281--52311 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
52271 AGATTTTTGT
52281 ATATATAC
1 ATATATAC
52289 ATATATAC
1 ATATATAC
52297 ATATATAC
1 ATATATAC
*
52305 ACATATA
1 ATATATA
52312 AATTTAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (8 bp):
ATATATAC
Found at i:52445 original size:14 final size:15
Alignment explanation
Indices: 52426--52455 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52416 AAATAAATAA
52426 ATAAAA-AACAACTG
1 ATAAAAGAACAACTG
52440 ATAAAAGAACAACTG
1 ATAAAAGAACAACTG
52455 A
1 A
52456 AAACAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ATAAAAGAACAACTG
Found at i:52694 original size:21 final size:21
Alignment explanation
Indices: 52670--52711 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
52660 CCCATTTTAT
52670 GTATAAAACCTCAATAGTATG
1 GTATAAAACCTCAATAGTATG
*
52691 GTATGAAACCTCAATAGTATG
1 GTATAAAACCTCAATAGTATG
52712 AAAACCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (21 bp):
GTATAAAACCTCAATAGTATG
Found at i:54763 original size:19 final size:19
Alignment explanation
Indices: 54721--54787 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
54711 ATATTAAAAA
*
54721 ATAAAAATTGATATAAAT-TT
1 ATAAATATT-ATA-AAATATT
54741 ATAAATATTATAAAATATT
1 ATAAATATTATAAAATATT
***
54760 ATAAGCGTTATAAAAATATT
1 ATAAATATTAT-AAAATATT
*
54780 AAAAATAT
1 ATAAATAT
54788 AAGAAATCTA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 20 0.54
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (19 bp):
ATAAATATTATAAAATATT
Found at i:60468 original size:39 final size:39
Alignment explanation
Indices: 60414--60493 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
60404 ACTTCCTTAT
*
60414 CCGTGAAAACTATATAAAATCTCGATTTTTCTAGTTAAG
1 CCGTGAAAACTATATAAAATATCGATTTTTCTAGTTAAG
60453 CCGTGAAAACTATATAAAATATCGATTTTTCTAGTTAAG
1 CCGTGAAAACTATATAAAATATCGATTTTTCTAGTTAAG
60492 CC
1 CC
60494 AAATTTCATG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (39 bp):
CCGTGAAAACTATATAAAATATCGATTTTTCTAGTTAAG
Found at i:63516 original size:19 final size:19
Alignment explanation
Indices: 63492--63529 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
63482 AGTACATTGT
63492 GTATTTTATACTCGAACCC
1 GTATTTTATACTCGAACCC
63511 GTATTTTATACTCGAACCC
1 GTATTTTATACTCGAACCC
63530 TCCACTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (19 bp):
GTATTTTATACTCGAACCC
Found at i:68818 original size:30 final size:31
Alignment explanation
Indices: 68782--68841 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
68772 TTATATATAT
* *
68782 AAATTTTGATTTTATGTAATT-TTATGCATG
1 AAATTTTAATTTGATGTAATTCTTATGCATG
* *
68812 AAATTTTAATTTGATTTAATTCTTTTGCAT
1 AAATTTTAATTTGATGTAATTCTTATGCAT
68842 TATTAACACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (31 bp):
AAATTTTAATTTGATGTAATTCTTATGCATG
Found at i:69604 original size:65 final size:65
Alignment explanation
Indices: 69526--69656 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
69516 TTCGATTAGT
*
69526 ACATTCGGTTTAATTAATTAATTTATTAAAAAATTATAAAAATAAAAATGTATATCAAAAATCCG
1 ACATTCGGTTTAATTAAATAATTTATTAAAAAATTATAAAAATAAAAATGTATATCAAAAATCCG
69591 ACATTCGGTTTAATTAAATAATTTATTAAAAAATTATAAAAATAAAAATGTATATCAAAAATCCG
1 ACATTCGGTTTAATTAAATAATTTATTAAAAAATTATAAAAATAAAAATGTATATCAAAAATCCG
69656 A
1 A
69657 TTCAACCGGT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (65 bp):
ACATTCGGTTTAATTAAATAATTTATTAAAAAATTATAAAAATAAAAATGTATATCAAAAATCCG
Found at i:90588 original size:23 final size:22
Alignment explanation
Indices: 90561--90603 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
90551 CCGAAATTTC
* *
90561 AAAATTTAGAAAATTTAAAAATT
1 AAAATTGAG-AAATTAAAAAATT
90584 AAAATTGAGAAATTAAAAAA
1 AAAATTGAGAAATTAAAAAA
90604 ATAGGAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAATTGAGAAATTAAAAAATT
Found at i:91028 original size:95 final size:95
Alignment explanation
Indices: 90863--91051 Score: 360
Period size: 95 Copynumber: 2.0 Consensus size: 95
90853 ATTAGATTAG
90863 AACTCATAACACATTCAGAGAATTTTATGTTTACGTTTGAGGGTTCTTTGTTTTACGGGTTTTCG
1 AACTCATAACACATTCAGAGAATTTTATGTTTACGTTTGAGGGTTCTTTGTTTTACGGGTTTTCG
90928 AGGTTTAGTTTTTATCTCCATCTTTTGTAA
66 AGGTTTAGTTTTTATCTCCATCTTTTGTAA
*
90958 AACTCATAACACATTCAGAGAATTTTGTGTTTACGTTTGAGGGTTCTTTGTTTTACGGGTTTTCG
1 AACTCATAACACATTCAGAGAATTTTATGTTTACGTTTGAGGGTTCTTTGTTTTACGGGTTTTCG
*
91023 GGGTTTAGTTTTTATCTCCATCTTTTGTA
66 AGGTTTAGTTTTTATCTCCATCTTTTGTA
91052 CTCTTCATTC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (95 bp):
AACTCATAACACATTCAGAGAATTTTATGTTTACGTTTGAGGGTTCTTTGTTTTACGGGTTTTCG
AGGTTTAGTTTTTATCTCCATCTTTTGTAA
Found at i:92198 original size:27 final size:27
Alignment explanation
Indices: 92160--92214 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
92150 GTCCTCAAAA
* * * *
92160 ATTTTTTAAAAATTGATTAGATCCCTT
1 ATTTTTAAAAAATTCATTAAACCCCTT
92187 ATTTTTAAAAAATTCATTAAACCCCTT
1 ATTTTTAAAAAATTCATTAAACCCCTT
92214 A
1 A
92215 AAAATTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTTTTAAAAAATTCATTAAACCCCTT
Found at i:103145 original size:13 final size:13
Alignment explanation
Indices: 103127--103165 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
103117 ACCTGGTCAC
103127 CTACTTTTATAAT
1 CTACTTTTATAAT
103140 CTACTTTTATAAT
1 CTACTTTTATAAT
103153 CTACTTTTATAAT
1 CTACTTTTATAAT
103166 GTTATTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
CTACTTTTATAAT
Found at i:104832 original size:1 final size:1
Alignment explanation
Indices: 104826--104863 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
104816 AGAATCTGGG
* *
104826 TTTTTTTTTCTGTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
104864 GGCAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.03, T:0.95
Consensus pattern (1 bp):
T
Found at i:112200 original size:27 final size:28
Alignment explanation
Indices: 112170--112232 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
112160 TTTAATAAGC
*
112170 TTTTAAAATTTGGA-ATATTTTTTTTAT
1 TTTTAAAATTTGGAGATATTTTGTTTAT
* *
112197 TTTTTAAATTTTGAGATATTTTGTTTAT
1 TTTTAAAATTTGGAGATATTTTGTTTAT
112225 TTTTAAAA
1 TTTTAAAA
112233 AAATTTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (28 bp):
TTTTAAAATTTGGAGATATTTTGTTTAT
Found at i:115727 original size:5 final size:5
Alignment explanation
Indices: 115717--115745 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
115707 TGTTCACATG
115717 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
115746 GGATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:121457 original size:23 final size:23
Alignment explanation
Indices: 121430--121476 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
121420 TAAATACATC
121430 AGTTCAAATTAGTTTTTTGATTT
1 AGTTCAAATTAGTTTTTTGATTT
121453 AGTTCAAATTAGTTTTTTGATTT
1 AGTTCAAATTAGTTTTTTGATTT
121476 A
1 A
121477 CTCGGTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (23 bp):
AGTTCAAATTAGTTTTTTGATTT
Found at i:128335 original size:28 final size:28
Alignment explanation
Indices: 128295--128350 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
128285 TCTTCATTCA
128295 TTTCATTTTAAGTGATAGAAGTAAAAGG
1 TTTCATTTTAAGTGATAGAAGTAAAAGG
128323 TTTCATTTTAAGTGATAGAAGTAAAAGG
1 TTTCATTTTAAGTGATAGAAGTAAAAGG
128351 ATTTGGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (28 bp):
TTTCATTTTAAGTGATAGAAGTAAAAGG
Found at i:129766 original size:24 final size:24
Alignment explanation
Indices: 129739--129788 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
129729 CTTACTAATC
* *
129739 GAACAATTCCAAACTACAACTGAG
1 GAACAATTCCAAACCACAACCGAG
129763 GAACAATTCCAAACCACAACCGAG
1 GAACAATTCCAAACCACAACCGAG
129787 GA
1 GA
129789 TACGGGTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.28, G:0.14, T:0.12
Consensus pattern (24 bp):
GAACAATTCCAAACCACAACCGAG
Found at i:130624 original size:27 final size:28
Alignment explanation
Indices: 130589--130648 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
130579 AAAAAATATC
**
130589 TTTTGGGGGCTAGAATTGAATTTTAATT
1 TTTTGGGGGCTAGAATTGAATAGTAATT
*
130617 TTTTGGGGGTTAGAATTGAATAGTAATT
1 TTTTGGGGGCTAGAATTGAATAGTAATT
130645 TTTT
1 TTTT
130649 AGGTCAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (28 bp):
TTTTGGGGGCTAGAATTGAATAGTAATT
Found at i:133443 original size:137 final size:137
Alignment explanation
Indices: 133197--133583 Score: 756
Period size: 137 Copynumber: 2.8 Consensus size: 137
133187 ATATTTGGGG
133197 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
1 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
133262 AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCATCAGACACCTTCGAATC
66 AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCATCAGACACCTTCGAATC
133327 AAAGGGA
131 AAAGGGA
133334 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
1 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
133399 AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCATCAGACACCTTCGAATC
66 AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCATCAGACACCTTCGAATC
133464 AAAGGGA
131 AAAGGGA
133471 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
1 CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
* *
133536 AAAACACCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGTAGCCA
66 AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCA
133584 ACACCTTCAA
Statistics
Matches: 248, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 248 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (137 bp):
CAATGCAAGGAAACTTAGTGGGAAAACCATGAAGAACATCTAGAGCGTCAACGAAAATCATGAAG
AAAACATCACCTCCGAAATATGCCGCCCTTTTAATTTCTTGGCAGCCATCAGACACCTTCGAATC
AAAGGGA
Found at i:141058 original size:31 final size:31
Alignment explanation
Indices: 141022--141081 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
141012 TTACAAAATG
*
141022 GTCACTGGACTATTTGAAAGTTTTCATTTAA
1 GTCACTGAACTATTTGAAAGTTTTCATTTAA
*
141053 GTCACTGAACTATTTGAAAGTTTTTATTT
1 GTCACTGAACTATTTGAAAGTTTTCATTT
141082 GAGCCACTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (31 bp):
GTCACTGAACTATTTGAAAGTTTTCATTTAA
Found at i:142684 original size:109 final size:109
Alignment explanation
Indices: 142490--142795 Score: 447
Period size: 109 Copynumber: 2.8 Consensus size: 109
142480 TAAATTCAAT
* * * * * *
142490 AGGATATTTGGCAATTTGATTAAACGAG--AAATCGAAACCCAGTACCTTAGGGCACG-TTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
* *
142552 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAA
66 GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
* * * * *
142596 AGGATATTTAGCTATTTGGTTGAATGAGAAAAATCTATACCCAGTACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
*
142661 GAATTTCCAAACACAAAATATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
*
142705 ATGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
*
142770 GAATTTCCAAACGCTAAATATTGCCT
66 GAATTTCCAAACGCAAAATATTGCCT
142796 CAATCGAAAA
Statistics
Matches: 177, Mismatches: 20, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
106 23 0.13
108 25 0.14
109 129 0.73
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (109 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTAAA
Found at i:143333 original size:17 final size:17
Alignment explanation
Indices: 143311--143345 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
143301 AAATAGGTAC
143311 AAGTGTATA-AATTAAAA
1 AAGTGTATATAA-TAAAA
143328 AAGTGTATATAATAAAA
1 AAGTGTATATAATAAAA
143345 A
1 A
143346 TAGTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (17 bp):
AAGTGTATATAATAAAA
Found at i:153672 original size:26 final size:26
Alignment explanation
Indices: 153642--153694 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
153632 TCGTGGAGTG
153642 ATAGAATTATTTTTCGTAGAAACGAC
1 ATAGAATTATTTTTCGTAGAAACGAC
153668 ATAGAATTATTTTTCGTAGAAACGAC
1 ATAGAATTATTTTTCGTAGAAACGAC
153694 A
1 A
153695 GCTCAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (26 bp):
ATAGAATTATTTTTCGTAGAAACGAC
Found at i:158772 original size:2 final size:2
Alignment explanation
Indices: 158765--158789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158755 ACATTAACCC
158765 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
158790 AAATATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158805 original size:15 final size:15
Alignment explanation
Indices: 158765--158805 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
158755 ACATTAACCC
*
158765 ATATATATAT-ATAT
1 ATATATATATAAAAT
158779 ATATATATATAAAAT
1 ATATATATATAAAAT
158794 ATCATATA-ATAA
1 AT-ATATATATAA
158806 TTGGGATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATATATATAAAAT
Found at i:159389 original size:29 final size:30
Alignment explanation
Indices: 159357--159414 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
159347 TAAAATTTAA
*
159357 AATTTAGTCTTTATACTTTT-ATTTTTAGG
1 AATTTAATCTTTATACTTTTAATTTTTAGG
*
159386 AATTTAATCTTTCTACTTTTCAATTTTTA
1 AATTTAATCTTTATACTTTT-AATTTTTA
159415 AAATTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.72
31 7 0.28
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (30 bp):
AATTTAATCTTTATACTTTTAATTTTTAGG
Found at i:159559 original size:12 final size:13
Alignment explanation
Indices: 159537--159565 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
159527 ATGTCACACT
159537 AAAAAATTTTAAC
1 AAAAAATTTTAAC
159550 AAAAAA-TTTAAC
1 AAAAAATTTTAAC
159562 AAAA
1 AAAA
159566 TTAACAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAAATTTTAAC
Found at i:163950 original size:28 final size:27
Alignment explanation
Indices: 163907--163959 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
163897 CTAAAAATTG
163907 TATAAAAAAATTAAATATACTAAAAAACC
1 TATAAAAAAATTAAATAT--TAAAAAACC
*
163936 TATAATAAAA-TAAATATTAAAAAA
1 TATAAAAAAATTAAATATTAAAAAA
163960 GATAACAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
28 7 0.30
29 9 0.39
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (27 bp):
TATAAAAAAATTAAATATTAAAAAACC
Found at i:169880 original size:10 final size:10
Alignment explanation
Indices: 169865--169895 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
169855 TCTGGTTTTT
169865 GTTGATGAAA
1 GTTGATGAAA
*
169875 GTTGATGGAA
1 GTTGATGAAA
169885 GTTGATGAAA
1 GTTGATGAAA
169895 G
1 G
169896 AGAATGGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (10 bp):
GTTGATGAAA
Found at i:170440 original size:9 final size:9
Alignment explanation
Indices: 170427--170477 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
170417 GTCACCTCCT
170427 TCACCATCA
1 TCACCATCA
*
170436 ACACCATCA
1 TCACCATCA
*
170445 TCATCATCA
1 TCACCATCA
*
170454 TCATCATCA
1 TCACCATCA
*
170463 TCATCATCA
1 TCACCATCA
170472 TCACCA
1 TCACCA
170478 CCACCTTCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.35, C:0.39, G:0.00, T:0.25
Consensus pattern (9 bp):
TCACCATCA
Found at i:170448 original size:3 final size:3
Alignment explanation
Indices: 170440--170474 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
170430 CCATCAACAC
170440 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
170475 CCACCACCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:170493 original size:3 final size:3
Alignment explanation
Indices: 170487--170516 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
170477 ACCACCTTCA
*
170487 CCT CCT CCT CCT CCT TCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
170517 GAGGAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (3 bp):
CCT
Found at i:170628 original size:39 final size:39
Alignment explanation
Indices: 170584--170663 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
170574 TCACCGTCAC
170584 CATCACCGCCACCTCCTAAG-AAACAATCATCACCACCTT
1 CATCACCGCCACCTCCTAAGCAAA-AATCATCACCACCTT
* *
170623 CATCACCTCCTCCTCCTAAGCAAAAATCATCACCACCTT
1 CATCACCGCCACCTCCTAAGCAAAAATCATCACCACCTT
170662 CA
1 CA
170664 GATAGCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.33, C:0.44, G:0.04, T:0.20
Consensus pattern (39 bp):
CATCACCGCCACCTCCTAAGCAAAAATCATCACCACCTT
Found at i:173331 original size:15 final size:15
Alignment explanation
Indices: 173311--173341 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
173301 GAGAAGAGAC
173311 TAAACTATTGGTAGT
1 TAAACTATTGGTAGT
173326 TAAACTATTGGTAGT
1 TAAACTATTGGTAGT
173341 T
1 T
173342 TTAGGCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.42
Consensus pattern (15 bp):
TAAACTATTGGTAGT
Found at i:179606 original size:33 final size:33
Alignment explanation
Indices: 179564--179631 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
179554 TTCAATATTT
* *
179564 CCATTTCCATGGA-TTCTAAATCCTCTAAGATCC
1 CCATTTCCATGCACTT-TAAATCCTCTAACATCC
*
179597 CCATTTCCATGCACTTTAAATCCTTTAACATCC
1 CCATTTCCATGCACTTTAAATCCTCTAACATCC
179630 CC
1 CC
179632 GTGCTTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.26, C:0.34, G:0.06, T:0.34
Consensus pattern (33 bp):
CCATTTCCATGCACTTTAAATCCTCTAACATCC
Found at i:182426 original size:22 final size:23
Alignment explanation
Indices: 182401--182450 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
182391 TATGAGTTCA
*
182401 TTTAATTAAAAATCATAGTTA-T
1 TTTAATAAAAAATCATAGTTAGT
* *
182423 TTTAATAAAAAATCTTATTTAGT
1 TTTAATAAAAAATCATAGTTAGT
182446 TTTAA
1 TTTAA
182451 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
TTTAATAAAAAATCATAGTTAGT
Found at i:189223 original size:257 final size:257
Alignment explanation
Indices: 188767--189250 Score: 826
Period size: 257 Copynumber: 1.9 Consensus size: 257
188757 TGGCGTCGAA
*
188767 GGAAAAACTGCGAGACGATGCCGGATCTTCTTCTCGACCTCTGTTTAGGTACCCTAATTACTTGC
1 GGAAAAACTGCGAGACGATGCCAGATCTTCTTCTCGACCTCTGTTTAGGTACCCTAATTACTTGC
* *
188832 ATAATTATCATGTTTAAATATTACTTTAATTGTTTGTTTAAAAAGCATGCGCCGAATCGTTTGCT
66 ATAATTATCATGTTTAAATATTACTTGAATTGTTTGTTTAAAAAGCATGCACCGAATCGTTTGCT
* * * *
188897 TGCTTGAATTCTTTATTTTCCCCCTTAGTTTAAGTGATTTTGAATCGGTCTGGTTAATGATAGAA
131 TGCTTGAATTCTTTATTTTCCCCCTTAATATAAGTGATTTTGAATCGGTCTGGTGAACGATAGAA
*
188962 TCATAATAGTTGTAATGATCTTGAATTCTATATGGATCAGTGGCGTCGAAAGAAAAACCAAG
196 TCATAATAGTTGTAAGGATCTTGAATTCTATATGGATCAGTGGCGTCGAAAGAAAAACCAAG
*
189024 GGAAAAACTGCGAGACGATGCCAGATCTTCTTCTCGATCTCTGTTTAGGTACCCTAATTACTTGC
1 GGAAAAACTGCGAGACGATGCCAGATCTTCTTCTCGACCTCTGTTTAGGTACCCTAATTACTTGC
*
189089 ATGATTATCATGTTTAAATATTACTTGAATTGTTTGTTTAAAAAGCATGCACCGAATCGTTTGCT
66 ATAATTATCATGTTTAAATATTACTTGAATTGTTTGTTTAAAAAGCATGCACCGAATCGTTTGCT
***
189154 TGCTTGAATTCCTTT-TTTTCTTTCTTAATATAAGTGATTTTGAATCGGTCTGGTGAACGATAGA
131 TGCTTGAATT-CTTTATTTTCCCCCTTAATATAAGTGATTTTGAATCGGTCTGGTGAACGATAGA
*
189218 ATCATAGTAGTTGTAAGGATCTTGAATTCTATA
195 ATCATAATAGTTGTAAGGATCTTGAATTCTATA
189251 AGGAATATTG
Statistics
Matches: 212, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
257 208 0.98
258 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (257 bp):
GGAAAAACTGCGAGACGATGCCAGATCTTCTTCTCGACCTCTGTTTAGGTACCCTAATTACTTGC
ATAATTATCATGTTTAAATATTACTTGAATTGTTTGTTTAAAAAGCATGCACCGAATCGTTTGCT
TGCTTGAATTCTTTATTTTCCCCCTTAATATAAGTGATTTTGAATCGGTCTGGTGAACGATAGAA
TCATAATAGTTGTAAGGATCTTGAATTCTATATGGATCAGTGGCGTCGAAAGAAAAACCAAG
Found at i:196618 original size:18 final size:18
Alignment explanation
Indices: 196586--196620 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
196576 TTATATTTTT
196586 AAATCTAAAAGTAAAAAA
1 AAATCTAAAAGTAAAAAA
196604 AAATCATAAAA-TAAAAA
1 AAATC-TAAAAGTAAAAA
196621 TAAAGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCTAAAAGTAAAAAA
Found at i:196912 original size:51 final size:52
Alignment explanation
Indices: 196852--196958 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
196842 CTTCTTGTGA
* * *
196852 ATTTTGGTCGGGAATTCTTTA-TTTATTGAAAAAGAGTTCTTTCAGGGGTCC
1 ATTTTGGTCGGGAATTCTTTATTTTACTGAAAAAGAGTTATTGCAGGGGTCC
* *
196903 ATTTTGGTCGGGATTTCTTTATTTTACTGAAAAAGGGTTATTGCAGGGGTCC
1 ATTTTGGTCGGGAATTCTTTATTTTACTGAAAAAGAGTTATTGCAGGGGTCC
196955 ATTT
1 ATTT
196959 ACATGCCACA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 20 0.40
52 30 0.60
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.42
Consensus pattern (52 bp):
ATTTTGGTCGGGAATTCTTTATTTTACTGAAAAAGAGTTATTGCAGGGGTCC
Found at i:202883 original size:30 final size:30
Alignment explanation
Indices: 202836--202979 Score: 173
Period size: 30 Copynumber: 4.8 Consensus size: 30
202826 ACTTTTCTCA
*
202836 ACTAGCCAC-CCTTTTCCACCACCAACTCC
1 ACTAGCCACACTTTTTCCACCACCAACTCC
*
202865 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACTTTTTCCACCACCAACTCC
* *
202895 ACTAGCCACACCTTTTCCACCACCAAATCC
1 ACTAGCCACACTTTTTCCACCACCAACTCC
** ** *
202925 ACTAGCCACACTTGCTCCATTACCTACTCC
1 ACTAGCCACACTTTTTCCACCACCAACTCC
* **
202955 ACTAACCACACTTGCTCCACCACCA
1 ACTAGCCACACTTTTTCCACCACCA
202980 CTTGTACCTA
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 9 0.09
30 90 0.91
ACGTcount: A:0.26, C:0.47, G:0.04, T:0.22
Consensus pattern (30 bp):
ACTAGCCACACTTTTTCCACCACCAACTCC
Found at i:206797 original size:12 final size:12
Alignment explanation
Indices: 206780--206815 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
206770 AACATTTTGA
206780 CATTCATACATT
1 CATTCATACATT
**
206792 CATTCATGTATT
1 CATTCATACATT
206804 CATTCATACATT
1 CATTCATACATT
206816 GCATATCCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (12 bp):
CATTCATACATT
Found at i:208467 original size:27 final size:27
Alignment explanation
Indices: 208437--208491 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
208427 CCGAAATGGT
*
208437 ACGATCCAAACGCTAGTTGTGCATACC
1 ACGATCCAAACACTAGTTGTGCATACC
208464 ACGATCCAAACACTAGTTGTGCATACC
1 ACGATCCAAACACTAGTTGTGCATACC
208491 A
1 A
208492 TGCGGGGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (27 bp):
ACGATCCAAACACTAGTTGTGCATACC
Found at i:218749 original size:16 final size:15
Alignment explanation
Indices: 218725--218772 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
218715 TAATTATTAT
*
218725 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
218741 TATTTTAATATTTTA
1 TATTTTAATATTTTA
218756 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
218772 T
1 T
218773 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:218760 original size:7 final size:8
Alignment explanation
Indices: 218725--218776 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
218715 TAATTATTAT
*
218725 TATTCTAA
1 TATTTTAA
*
218733 TATTTTGA
1 TATTTTAA
218741 TATTTTAA
1 TATTTTAA
218749 TATTTT-A
1 TATTTTAA
218756 TATTTTATA
1 TATTTTA-A
*
218765 TATTTTAT
1 TATTTTAA
218773 TATT
1 TATT
218777 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:219620 original size:14 final size:14
Alignment explanation
Indices: 219578--219620 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
219568 GATAGTGAAA
219578 TTTATAAATATATT
1 TTTATAAATATATT
* *
219592 TTCAT--ATAAATT
1 TTTATAAATATATT
219604 TTTATAAATATATT
1 TTTATAAATATATT
219618 TTT
1 TTT
219621 TATGTAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAAATATATT
Found at i:222279 original size:29 final size:29
Alignment explanation
Indices: 222246--222305 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
222236 CACAAAAATT
222246 ACACTCAGTTTCGTATTTCGAAAATACAA
1 ACACTCAGTTTCGTATTTCGAAAATACAA
222275 ACACTCAGTTTCGTATTTCGAAAATACAA
1 ACACTCAGTTTCGTATTTCGAAAATACAA
222304 AC
1 AC
222306 TGATGAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.30
Consensus pattern (29 bp):
ACACTCAGTTTCGTATTTCGAAAATACAA
Found at i:223524 original size:14 final size:14
Alignment explanation
Indices: 223505--223532 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
223495 ACAAATTTAC
223505 TATAGTAAAAATAT
1 TATAGTAAAAATAT
223519 TATAGTAAAAATAT
1 TATAGTAAAAATAT
223533 ACAACTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TATAGTAAAAATAT
Found at i:230701 original size:38 final size:40
Alignment explanation
Indices: 230657--230748 Score: 125
Period size: 38 Copynumber: 2.3 Consensus size: 40
230647 AAAAATTATA
*
230657 TTTAATAAAATAAAACATTTATTATATTTAT-TTGTG-TT
1 TTTAATAAAATAAAACATTTATTATATTTATGTAGTGTTT
* *
230695 TTTAATATAATAAAATATTTATTATATTTATGGTAGTGTTT
1 TTTAATAAAATAAAACATTTATTATATTTAT-GTAGTGTTT
230736 TTTAATATAAATA
1 TTTAATA-AAATA
230749 CTTTTTAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
38 29 0.63
40 4 0.09
41 9 0.20
42 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (40 bp):
TTTAATAAAATAAAACATTTATTATATTTATGTAGTGTTT
Found at i:232446 original size:70 final size:70
Alignment explanation
Indices: 232336--232474 Score: 251
Period size: 70 Copynumber: 2.0 Consensus size: 70
232326 TTTCATTTAT
* *
232336 AAAATCAAAAGTTCGATGGTATTATTATATTTTTGGGTATTTTAATGATAATTATTGTTTTACTA
1 AAAATCAAAAGTTCGATAGTATTATTATATTTTTGAGTATTTTAATGATAATTATTGTTTTACTA
232401 AAATC
66 AAATC
*
232406 AAAATTAAAAGTTCGATAGTATTATTATATTTTTGAGTATTTTAATGATAATTATTGTTTTACTA
1 AAAATCAAAAGTTCGATAGTATTATTATATTTTTGAGTATTTTAATGATAATTATTGTTTTACTA
232471 AAAT
66 AAAT
232475 AATTGTATGA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (70 bp):
AAAATCAAAAGTTCGATAGTATTATTATATTTTTGAGTATTTTAATGATAATTATTGTTTTACTA
AAATC
Found at i:234028 original size:10 final size:11
Alignment explanation
Indices: 234012--234036 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
234002 TTAATTATAC
234012 AAAAAAAAAAG
1 AAAAAAAAAAG
234023 AAAAAAAAAAG
1 AAAAAAAAAAG
234034 AAA
1 AAA
234037 GGGTTTGCCT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:234379 original size:34 final size:35
Alignment explanation
Indices: 234309--234379 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
234299 AGTTGTAATT
234309 TTTATAGTTTTTGATGGACCCCGTACATTAAAATC
1 TTTATAGTTTTTGATGGACCCCGTACATTAAAATC
* *
234344 TTTATAGTTTTTGTTGGACGCC-TA-ATTTAAAATC
1 TTTATAGTTTTTGATGGACCCCGTACA-TTAAAATC
234378 TT
1 TT
234380 ATCATTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 1 0.03
34 12 0.36
35 20 0.61
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (35 bp):
TTTATAGTTTTTGATGGACCCCGTACATTAAAATC
Found at i:235276 original size:20 final size:19
Alignment explanation
Indices: 235221--235298 Score: 72
Period size: 20 Copynumber: 4.2 Consensus size: 19
235211 TTTTAAAAAT
**
235221 AATTTTTTATTTAAATTTT
1 AATTTTTTATTTAAATTCG
* *
235240 AA-TTTGTA--TAAACTCG
1 AATTTTTTATTTAAATTCG
235256 AATTTTTTATGTTAAATTCG
1 AATTTTTTAT-TTAAATTCG
* *
235276 AATATTTTATTTAAATTTG
1 AATTTTTTATTTAAATTCG
235295 AATT
1 AATT
235299 AAATAATAGT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
16 7 0.15
17 5 0.11
18 5 0.11
19 13 0.28
20 16 0.35
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (19 bp):
AATTTTTTATTTAAATTCG
Found at i:236228 original size:5 final size:5
Alignment explanation
Indices: 236181--236214 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
236171 CTGCCCATGA
* *
236181 ATATT ATATT ATATT ACATT ATATT TTATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
236215 AAAACATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:238787 original size:17 final size:18
Alignment explanation
Indices: 238767--238806 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
238757 TCTAAAATAA
*
238767 TAAATAAATCTA-AATTT
1 TAAATAAATCTACAAATT
*
238784 TAAATAAATTTACAAATT
1 TAAATAAATCTACAAATT
238802 TAAAT
1 TAAAT
238807 GTTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATAAATCTACAAATT
Found at i:238800 original size:25 final size:24
Alignment explanation
Indices: 238772--238824 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
238762 AATAATAAAT
*
238772 AAATCTAAATTTTA-AATAAATTTAC
1 AAATCTAAATGTTATAA-AAA-TTAC
*
238797 AAATTTAAATGTTATAAAAATTAC
1 AAATCTAAATGTTATAAAAATTAC
238821 AAAT
1 AAAT
238825 ATTCAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 15 0.60
26 2 0.08
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATCTAAATGTTATAAAAATTAC
Found at i:238805 original size:18 final size:17
Alignment explanation
Indices: 238757--238806 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
238747 AGATTTGGAT
*
238757 TCTAAAATAATAAATAAA
1 TCTAAAAT-TTAAATAAA
*
238775 TCTAAATTTTAAATAAA
1 TCTAAAATTTAAATAAA
*
238792 TTTACAAATTTAAAT
1 TCTA-AAATTTAAAT
238807 GTTATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TCTAAAATTTAAATAAA
Found at i:239432 original size:17 final size:17
Alignment explanation
Indices: 239410--239442 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
239400 TATGATTTAC
239410 AAAATTAAAAATAAATT
1 AAAATTAAAAATAAATT
*
239427 AAAATTAAAATTAAAT
1 AAAATTAAAAATAAAT
239443 ATTATTAGGA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAAAATAAATT
Found at i:241431 original size:204 final size:204
Alignment explanation
Indices: 241018--241725 Score: 971
Period size: 204 Copynumber: 3.5 Consensus size: 204
241008 GTTAGTTCTA
* * * * * *
241018 TTTCTCCTTCTAGATCTAGCTGTTCGTTTCAAAGTTCATCGATATTTCCCTTTTTTTTAGTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCCCTTTTTTTAGTTTGA
* *
241083 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATCTT-TCGTTCTAGATCTCGCTCTTCGT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAAT-TTCTCGTTCTAGATCTCGCTATTCAT
*
241147 TTATATTTCCTTTTTTTTAAA--TGATTTATAATAGTATTTCTTTGCTGATTAGTTTGAATTCAT
130 TTATATTTCC-TTTTTTTAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCAT
*
241210 TTTTAGCTCAC
194 TTTTAGCTCAT
* * * **
241221 TTTCTCCTTCCAGACCTCGTTATTCATTTCGAAGTTCATCTATATTTCCGGTTTTTTTAGTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCCCTTTTTTTAGTTTGA
* * * *
241286 -TTGTATTAATGTTTCTTTGCTGATTACTTTGTTCAATTTCTCGTCCTAGGTCTCGCTATTCATT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTTCTCGTTCTAGATCTCGCTATTCATT
241350 TATATTTCCTTTTTTTAAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATT
131 TATATTTCCTTTTTTT-AAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATT
*
241415 TTTAGCTTAT
195 TTTAGCTCAT
* *
241425 TTTCTCCTTCTAGACCTGGTTATTCATTTCAAAGTTCATCGATATTTCCCCTTTTTTTACTTTGA
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCCCTTTTTTTAGTTTGA
* * * *
241490 TTTGAATTAGTGTTTCTTTGCTCATTAATTTGTTCAATTTCTCCTTCTAGATCTCGTTATTCATT
66 TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTTCTCGTTCTAGATCTCGCTATTCATT
*
241555 TATATTTCCTTTTTGTT-AATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTGATT
131 TATATTTCCTTTTT-TTAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATT
**
241619 TCGAG-TCAT
195 TTTAGCTCAT
** * * * *
241628 TTTCTCCTTCTAGACCTCG-TATTGGTTTCGAAGTTCATCAACATTTCCTCTCTTTTTTTAGTTC
1 TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCC-C-CTTTTTTTAGTTT
* * *
241692 GATTTTTATTGGTGTTTCTTTTCTGATTAATTTG
64 GATTTGTATTAGTGTTTCTTTGCTGATTAATTTG
241726 AATTGATTTT
Statistics
Matches: 446, Mismatches: 51, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
201 9 0.02
202 91 0.20
203 77 0.17
204 197 0.44
205 70 0.16
206 2 0.00
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (204 bp):
TTTCTCCTTCTAGACCTCGTTATTCATTTCAAAGTTCATCGATATTTCCCCTTTTTTTAGTTTGA
TTTGTATTAGTGTTTCTTTGCTGATTAATTTGTTCAATTTCTCGTTCTAGATCTCGCTATTCATT
TATATTTCCTTTTTTTAAATTTGATTTATAATAGTTTTTCTTTGCTGATTAGTTTGAATTCATTT
TTAGCTCAT
Found at i:241974 original size:120 final size:120
Alignment explanation
Indices: 241706--242020 Score: 345
Period size: 120 Copynumber: 2.6 Consensus size: 120
241696 TTTATTGGTG
* *
241706 TTTCTTTTCTGATTAATTTGAATTGATTTTTAGTTCAATTTCTCGCTCTAGATCTTGCTATTCAT
1 TTTCTTTGCTGATTAATTTGAATTGATTTTTAGTTCAATTTCTC-CTCTAGATCTCGCTATTCAT
** * * * *
241771 TTCAAAGTTCGTCAATATTTTCTTCTTCTTAAAAAATAAAAATTGATTTGTGTTAGTA
65 TTCAAAGTTCACCAATATATTATTCGTCTT--AAAATAAAAATTGATTTGTGTTAGCA
* *
241829 TTTCTTTGCTGATAAATTTGAA-T--TTTTTAGTTCAATTTCTCACTCTAGATCTGGCTATTCAT
1 TTTCTTTGCTGATTAATTTGAATTGATTTTTAGTTCAATTTCTC-CTCTAGATCTCGCTATTCAT
* *** **
241891 TTCAAAGTTCACCATTATATTATT-GTCTT-TTTTAAAGTTTGATTTGTGTTAGCA
65 TTCAAAGTTCACCAATATATTATTCGTCTTAAAATAAAAATTGATTTGTGTTAGCA
* * * *
241945 TTTCTTTGGTGATTAATTTGAATTGATTTTTAGTTC-ATTGTGTCCTTCTTGATCTCGCTTTTCA
1 TTTCTTTGCTGATTAATTTGAATTGATTTTTAGTTCAATT-TCTCC-TCTAGATCTCGCTATTCA
*
242009 TTTTAAAGTTCA
64 TTTCAAAGTTCA
242021 GTAATGTCAT
Statistics
Matches: 164, Mismatches: 23, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
116 39 0.24
117 1 0.01
118 4 0.02
119 43 0.26
120 56 0.34
122 1 0.01
123 20 0.12
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (120 bp):
TTTCTTTGCTGATTAATTTGAATTGATTTTTAGTTCAATTTCTCCTCTAGATCTCGCTATTCATT
TCAAAGTTCACCAATATATTATTCGTCTTAAAATAAAAATTGATTTGTGTTAGCA
Found at i:246562 original size:80 final size:80
Alignment explanation
Indices: 246465--246627 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
246455 TTACATTTCA
*
246465 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCGAAGCAAAATCCATCACAAACTAATAGTA
1 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
246530 AATTTTGACAATCAC
66 AATTTTGACAATCAC
246545 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
1 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
246610 AATTTTGACAATCAC
66 AATTTTGACAATCAC
246625 AAA
1 AAA
246628 ACAAGATTAC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (80 bp):
AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
AATTTTGACAATCAC
Found at i:246716 original size:99 final size:99
Alignment explanation
Indices: 246545--246750 Score: 394
Period size: 99 Copynumber: 2.1 Consensus size: 99
246535 TGACAATCAC
246545 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
1 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
246610 AATTTTGACAATCACAAAACAAGATTACATTTCA
66 AATTTTGACAATCACAAAACAAGATTACATTTCA
*
246644 AAACATCTCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
1 AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
*
246709 AATTTTGACAATCACAAAACAATATTACATTTCA
66 AATTTTGACAATCACAAAACAAGATTACATTTCA
246743 AAACATCC
1 AAACATCC
246751 TTTAAAAAAA
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 104 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.27
Consensus pattern (99 bp):
AAACATCCCTAAAACAACATTACTTCTAAGCTTTTCAAAGCAAAATCCATCACAAACTAATAGTA
AATTTTGACAATCACAAAACAAGATTACATTTCA
Found at i:247798 original size:30 final size:30
Alignment explanation
Indices: 247752--247845 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
247742 TTTTATTATG
*
247752 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
247783 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
247813 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
247843 CCA
1 CCA
247846 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:247807 original size:15 final size:15
Alignment explanation
Indices: 247762--247839 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
247752 CCAATATCTC
247762 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
247777 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
247792 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
247807 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
247822 GATACCCATATCTTT
1 GATACCCATATCTTT
247837 GAT
1 GAT
247840 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:256634 original size:37 final size:36
Alignment explanation
Indices: 256585--256657 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
256575 TGATTTATTT
*
256585 ATTTATAAATAAA-TCATTGCAATAT-ATGTAAAAATA
1 ATTTAAAAATAAATTCATT--AATATAATGTAAAAATA
*
256621 ATTTAAAATATAAATTTATTAATATAATGTAAAAATA
1 ATTTAAAA-ATAAATTCATTAATATAATGTAAAAATA
256658 GTTTTTCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 12 0.38
37 16 0.50
38 4 0.12
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (36 bp):
ATTTAAAAATAAATTCATTAATATAATGTAAAAATA
Found at i:256760 original size:19 final size:21
Alignment explanation
Indices: 256732--256774 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
256722 CTAAACACCA
*
256732 AAAAAGTAAATTATTTT-CAG
1 AAAAAGTAAATCATTTTCCAG
256752 AAAAA-TAAATCATTTTCCAG
1 AAAAAGTAAATCATTTTCCAG
256772 AAA
1 AAA
256775 TTATTTTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAAGTAAATCATTTTCCAG
Found at i:258389 original size:173 final size:175
Alignment explanation
Indices: 258024--258738 Score: 832
Period size: 175 Copynumber: 4.1 Consensus size: 175
258014 CAATTAGCTA
* * * * * * *
258024 CCACTTGGTGGTTGACGATGTTTTCTTTTTCAACGTTTGTTTGCGAAGCGATTGATCTGCCGACA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTTCGCGAAGCGATTGGTATGCCGACA
* *
258089 TTTTATTGACAGAGAATGTTTTATGGAGATGTCA-TGATCAAGTTGATTAATTATTTAGTGGTTT
66 TTTTATTGACAGAGAATGTTTTATGAAGATGT-AGTGA--AA-TTGATTAATTATTTAGTGGTCT
* * *
258153 GTCATATTATCATGTTTGCTTTTTACTATGTTAAGAACTTGTTTCTTGC
127 GCCATATTATCATGTTTGCTTTTTACTATGTTAGGAACTTGTTTCCTGC
* * *
258202 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTCCGCGAAGCGATTGGTATGTCGAAA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTTCGCGAAGCGATTGGTATGCCGACA
*
258267 TTTTATTGACAGAGAATGTTTTATGAAGATGT-G-GAAATTGATTAATTATTTTGTGGTCTGCCA
66 TTTTATTGACAGAGAATGTTTTATGAAGATGTAGTGAAATTGATTAATTATTTAGTGGTCTGCCA
*
258330 TATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGC
131 TATTATCATGTTTGCTTTTTACTATGTTAGGAACTTGTTTCCTGC
* * * * * * * *
258375 CCACTTGCTGGTTGGCCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTGGTATGTCGATA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTTCGCGAAGCGATTGGTATGCCGACA
* * ** * * *
258440 TTTTATTAACAGCGAATGTTTTATGAAGACATGGTGAAATTGATTAATTATTTAGTGGTTTGTCA
66 TTTTATTGACAGAGAATGTTTTATGAAGATGTAGTGAAATTGATTAATTATTTAGTGGTCTGCCA
* *
258505 TATTATCATGTTTGCTTTTTACTACGTTAGGAACTTGTTTCTTGC
131 TATTATCATGTTTGCTTTTTACTATGTTAGGAACTTGTTTCCTGC
* * * * * *
258550 CCACTTGGCGATTGGCAACGTTTTCTTTTTGAACAATTGTTCGTGAAGTGATTGGTATGCCGACA
1 CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTTCGCGAAGCGATTGGTATGCCGACA
* * * * * * *
258615 TTTTATTGACAAAGCATGTTTTGTGGAA-ACGTGGTGAAGTTGATTAATT-TTTCAATGG-CT-C
66 TTTTATTGACAGAGAATGTTTTAT-GAAGATGTAGTGAAATTGATTAATTATTT-AGTGGTCTGC
* * * * *
258676 CTTATATTATAATGTTTGCTTCTTACTATGTTAGGAATTTTTTTTCTGC
129 C--ATATTATCATGTTTGCTTTTTACTATGTTAGGAACTTGTTTCCTGC
*
258725 CCAGTTGGTGGTTG
1 CCACTTGGTGGTTG
258739 ATGATATTCG
Statistics
Matches: 464, Mismatches: 66, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
173 151 0.33
174 7 0.02
175 215 0.46
176 5 0.01
178 86 0.19
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.43
Consensus pattern (175 bp):
CCACTTGGTGGTTGGCGACGTTTTCTTTTTGAACATTTGTTCGCGAAGCGATTGGTATGCCGACA
TTTTATTGACAGAGAATGTTTTATGAAGATGTAGTGAAATTGATTAATTATTTAGTGGTCTGCCA
TATTATCATGTTTGCTTTTTACTATGTTAGGAACTTGTTTCCTGC
Found at i:259036 original size:25 final size:24
Alignment explanation
Indices: 259008--259068 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
258998 AATCTGAAAC
259008 CTAAAGCTCTATATAAACCCTAAAT
1 CTAAA-CTCTATATAAACCCTAAAT
* * *
259033 CTAAAACCCAATATAAATCCTAAAT
1 CT-AAACTCTATATAAACCCTAAAT
259058 CATAAACTCTA
1 C-TAAACTCTA
259069 ACCCAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.26
Consensus pattern (24 bp):
CTAAACTCTATATAAACCCTAAAT
Found at i:263267 original size:56 final size:56
Alignment explanation
Indices: 263181--263294 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
263171 TATTTCAAAG
263181 TAGGAAAAGGGACCACAAGCAAATAAAAATTATTCTAATCATAACTCAATCTCTCA
1 TAGGAAAAGGGACCACAAGCAAATAAAAATTATTCTAATCATAACTCAATCTCTCA
263237 TAGGAAAAGGGACCACAAGCAAATAAAAATTATTCTAATCATAACTCAATCTCTCA
1 TAGGAAAAGGGACCACAAGCAAATAAAAATTATTCTAATCATAACTCAATCTCTCA
263293 TA
1 TA
263295 AACATTTTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (56 bp):
TAGGAAAAGGGACCACAAGCAAATAAAAATTATTCTAATCATAACTCAATCTCTCA
Found at i:263490 original size:18 final size:17
Alignment explanation
Indices: 263467--263504 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
263457 TAATGGACAG
263467 AAAGTAAATTATAAAATT
1 AAAGTAAATTAT-AAATT
263485 AAAGTAAATTATAAATT
1 AAAGTAAATTATAAATT
263502 AAA
1 AAA
263505 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAGTAAATTATAAATT
Found at i:264093 original size:333 final size:333
Alignment explanation
Indices: 263487--264142 Score: 1276
Period size: 333 Copynumber: 2.0 Consensus size: 333
263477 ATAAAATTAA
263487 AGTAAATTATAAATTAAAATTATAAAAATTATAAGATGTGGAAATTGATTAATTATTTAGTGGCC
1 AGTAAATTATAAATTAAAATTATAAAAATTATAAGATGTGGAAATTGATTAATTATTTAGTGGCC
263552 TGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGCCCACTTGCTGGTTGG
66 TGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGCCCACTTGCTGGTTGG
* **
263617 CCACGTTTTCTTTTTGAACATTTGTTTGCAAAGTGATTGGTATGTCGATATTTTATTAACAGCGA
131 CCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTGGTATGTCGATATTTTATTAACAGCGA
*
263682 ATGTTTTATGAAGACATGGTGGAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGC
196 ATGTTTTATGAAGACATGGTGAAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGC
263747 TTCTTACTATGTTAGGAATTTGTTTCTTGCCCACTTGGCGATTGGCAACGTTTTCTTTTTGAAAA
261 TTCTTACTATGTTAGGAATTTGTTTCTTGCCCACTTGGCGATTGGCAACGTTTTCTTTTTGAAAA
263812 CATTTGTT
326 CATTTGTT
263820 AGTAAATTATAAATTAAAATTATAAAAATTATAAGATGTGGAAATTGATTAATTATTTAGTGGCC
1 AGTAAATTATAAATTAAAATTATAAAAATTATAAGATGTGGAAATTGATTAATTATTTAGTGGCC
263885 TGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGCCCACTTGCTGGTTGG
66 TGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGCCCACTTGCTGGTTGG
263950 CCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTGGTATGTCGATATTTTATTAACAGCGA
131 CCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTGGTATGTCGATATTTTATTAACAGCGA
264015 ATGTTTTATGAAGACATGGTGAAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGC
196 ATGTTTTATGAAGACATGGTGAAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGC
264080 TTCTTACTATGTTAGGAATTTGTTTCTTGCCCACTTGGCGATTGGCAACGTTTTCTTTTTGAA
261 TTCTTACTATGTTAGGAATTTGTTTCTTGCCCACTTGGCGATTGGCAACGTTTTCTTTTTGAA
264143 CAATTGTTCG
Statistics
Matches: 319, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
333 319 1.00
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (333 bp):
AGTAAATTATAAATTAAAATTATAAAAATTATAAGATGTGGAAATTGATTAATTATTTAGTGGCC
TGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATTTGTTTCCTGCCCACTTGCTGGTTGG
CCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTGGTATGTCGATATTTTATTAACAGCGA
ATGTTTTATGAAGACATGGTGAAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGC
TTCTTACTATGTTAGGAATTTGTTTCTTGCCCACTTGGCGATTGGCAACGTTTTCTTTTTGAAAA
CATTTGTT
Found at i:264161 original size:175 final size:176
Alignment explanation
Indices: 263860--264292 Score: 586
Period size: 175 Copynumber: 2.5 Consensus size: 176
263850 ATAAGATGTG
* *
263860 GAAATTGATTAATTATTTAGTGGCCTGTCATATTATCATGTTTGCTTTTTACTATGTTAGGAATT
1 GAAATTGATTAATTATTTAGTGGCTTGTCATATTATCATGTTTGCTTCTTACTATGTTAGGAATT
* * * *
263925 TGTTTCCTGCCCACTT-GCTGGTTGGCCACGTTTTCTTCTTGAACATTTGTTCACAAAGTGATTG
66 TGTTTCTTGCCCACTTGGCTGATTGGCAACGTTTTCTTCTTGAACAATTGTTCACAAAGTGATTG
* * ** *
263989 GTATGTCGATATTTTATTAACAGCGAATGTTTTATGAAGACATGGT
131 GTATGCCGACATTTTATTAACAAAGAATGTTTTATGAAAACATGGT
*
264035 GAAATTGATTAATTATTTAGTGGTTTGTCATATTATCATGTTTGCTTCTTACTATGTTAGGAATT
1 GAAATTGATTAATTATTTAGTGGCTTGTCATATTATCATGTTTGCTTCTTACTATGTTAGGAATT
* ***
264100 TGTTTCTTGCCCACTTGGC-GATTGGCAACGTTTTCTTTTTGAACAATTGTTCGTGAAGTGATTG
66 TGTTTCTTGCCCACTTGGCTGATTGGCAACGTTTTCTTCTTGAACAATTGTTCACAAAGTGATTG
* * *
264164 GTATGCCGACATTTTATTGACAAAGCATGTTTTATGAAAACGTGGT
131 GTATGCCGACATTTTATTAACAAAGAATGTTTTATGAAAACATGGT
* ** * *
264210 GAAATTGATTAATT-TTTCAATGGCTCCTTATATTATAATGTTTGCTTCTTACTATGTTAGGAAT
1 GAAATTGATTAATTATTT-AGTGGCTTGTCATATTATCATGTTTGCTTCTTACTATGTTAGGAAT
* *
264274 TT-TTTTTCTGCCCAGTTGG
65 TTGTTTCT-TGCCCACTTGG
264293 TGGTTGATGA
Statistics
Matches: 228, Mismatches: 27, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
174 7 0.03
175 219 0.96
176 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (176 bp):
GAAATTGATTAATTATTTAGTGGCTTGTCATATTATCATGTTTGCTTCTTACTATGTTAGGAATT
TGTTTCTTGCCCACTTGGCTGATTGGCAACGTTTTCTTCTTGAACAATTGTTCACAAAGTGATTG
GTATGCCGACATTTTATTAACAAAGAATGTTTTATGAAAACATGGT
Found at i:264596 original size:25 final size:24
Alignment explanation
Indices: 264568--264628 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
264558 AATCTGAAAC
264568 CTAAAGCTCTATATAAACCCTAAAT
1 CTAAA-CTCTATATAAACCCTAAAT
* * *
264593 CTAAAACCCAATATAAATCCTAAAT
1 CT-AAACTCTATATAAACCCTAAAT
264618 CATAAACTCTA
1 C-TAAACTCTA
264629 ACCCAAAACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.26
Consensus pattern (24 bp):
CTAAACTCTATATAAACCCTAAAT
Found at i:267606 original size:31 final size:31
Alignment explanation
Indices: 267536--267596 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
267526 CCTGGAAAAA
*
267536 AAACATTAAAACAAAACTCAGGTACCAAATT
1 AAACATTAAAACAAAACTCAAGTACCAAATT
*
267567 AAACATTAAAACCAAACTCAAGTACCAAAT
1 AAACATTAAAACAAAACTCAAGTACCAAAT
267597 AGTATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.21, G:0.05, T:0.18
Consensus pattern (31 bp):
AAACATTAAAACAAAACTCAAGTACCAAATT
Found at i:268696 original size:68 final size:67
Alignment explanation
Indices: 268615--268748 Score: 241
Period size: 68 Copynumber: 2.0 Consensus size: 67
268605 CTTTTAAAAA
* *
268615 TTTTAAAAAATATAAATGATCCATAAATAATATAAATTTATTTTTTTAAGTCGTATTTCTGAATT
1 TTTTAAAAAATATAAATAATCCATAAATAATATAAATTTATCTTTTTAAGTCGTATTTCTGAATT
268680 CT
66 CT
268682 TTTTAAAAATATATAAATAATCCATAAATAATATAAATTTATCTTTTTAAGTCGTATTTCTGAAT
1 TTTTAAAAA-ATATAAATAATCCATAAATAATATAAATTTATCTTTTTAAGTCGTATTTCTGAAT
268747 TC
65 TC
268749 GTCGTTGTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
67 9 0.14
68 55 0.86
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (67 bp):
TTTTAAAAAATATAAATAATCCATAAATAATATAAATTTATCTTTTTAAGTCGTATTTCTGAATT
CT
Found at i:269267 original size:25 final size:25
Alignment explanation
Indices: 269233--269284 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
269223 AAATAACTTG
269233 TAATAATAATAACTAGGTTATGACA
1 TAATAATAATAACTAGGTTATGACA
269258 TAATAATAATAACTAGGTTATGACA
1 TAATAATAATAACTAGGTTATGACA
269283 TA
1 TA
269285 TCCACTGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (25 bp):
TAATAATAATAACTAGGTTATGACA
Found at i:271295 original size:47 final size:46
Alignment explanation
Indices: 271211--271303 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 46
271201 TATAACGTTA
271211 ATACTACAATTTTTGAGGTTAATTGATTTCTTGAGTAAGATTGTTT
1 ATACTACAATTTTTGAGGTTAATTGATTTCTTGAGTAAGATTGTTT
271257 ATACTACAATTTTTGAGGTTTAATTGATTTCTTGAGTAAGATTGTTT
1 ATACTACAATTTTTGAGG-TTAATTGATTTCTTGAGTAAGATTGTTT
271304 TGATGGGAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 18 0.39
47 28 0.61
ACGTcount: A:0.28, C:0.06, G:0.17, T:0.48
Consensus pattern (46 bp):
ATACTACAATTTTTGAGGTTAATTGATTTCTTGAGTAAGATTGTTT
Found at i:280733 original size:26 final size:26
Alignment explanation
Indices: 280667--280733 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 26
280657 TGGATTCTCT
*
280667 GAAGCTAGTGTTAGCAACATTGTATC
1 GAAGCTAGTGTTAGCAACACTGTATC
* *
280693 -AAGATACTGTTAGCAATC-CTG-ATC
1 GAAGCTAGTGTTAGCAA-CACTGTATC
280717 AGAAGCTAGTGTTAGCA
1 -GAAGCTAGTGTTAGCA
280734 GCCTGAATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 3 0.09
25 16 0.48
26 14 0.42
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (26 bp):
GAAGCTAGTGTTAGCAACACTGTATC
Found at i:282945 original size:19 final size:19
Alignment explanation
Indices: 282923--282962 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
282913 TTTATTTTTA
282923 TATTATTAAAT-TATATTAT
1 TATT-TTAAATATATATTAT
*
282942 TATTTTTAATATATATTAT
1 TATTTTAAATATATATTAT
282961 TA
1 TA
282963 ACCCTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTAAATATATATTAT
Found at i:286919 original size:26 final size:28
Alignment explanation
Indices: 286890--286942 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
286880 TTATTTTTTT
*
286890 ATTTTAAAAATAC-TTT-TTTATAAATA
1 ATTTAAAAAATACATTTGTTTATAAATA
286916 ATTTAAAAAATACATTTGTTTATAAAT
1 ATTTAAAAAATACATTTGTTTATAAAT
286943 TAAGATGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 3 0.12
28 9 0.38
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (28 bp):
ATTTAAAAAATACATTTGTTTATAAATA
Found at i:302865 original size:14 final size:14
Alignment explanation
Indices: 302846--302874 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
302836 GGACTGAAAC
302846 TAGAATTCGACCTA
1 TAGAATTCGACCTA
302860 TAGAATTCGACCTA
1 TAGAATTCGACCTA
302874 T
1 T
302875 TATGTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (14 bp):
TAGAATTCGACCTA
Found at i:313443 original size:87 final size:86
Alignment explanation
Indices: 313291--313543 Score: 321
Period size: 87 Copynumber: 2.9 Consensus size: 86
313281 ATTCCTATTT
* * * *
313291 AACATAAAAGAATCTAGAAAAAAAAAGTATC-GAGTAACTTCAAATACTTAAACACGAAGTGAAT
1 AACATAAAAGAATCTAGAAAAAAAAAGT-GCAGAGTAATTTCAACTACTTAAACACAAAGTGAAT
*
313355 CAGTTCCTTACTAATGGTATGC
65 CAGTTCCTTACTAATAGTATGC
* * *
313377 AACATAAAAGAATCTAGAGAAAAAGAAGTGCAGACTAATTTCAACTACTTAAACACAAAGTAAAT
1 AACATAAAAGAATCTAGA-AAAAAAAAGTGCAGAGTAATTTCAACTACTTAAACACAAAGTGAAT
*
313442 CAGCTCCTTACTAATAGTATGC
65 CAGTTCCTTACTAATAGTATGC
* * * * *
313464 AACATACAAGAATCTAGAAAAAAAATAGTGCCA-AGTAATTTGAACTGCTTCACCACAAAGTGAA
1 AACATAAAAGAATCTAGAAAAAAAA-AGTG-CAGAGTAATTTCAACTACTTAAACACAAAGTGAA
*
313528 TCAATTCCTTACTAAT
64 TCAGTTCCTTACTAAT
313544 CGTTGTAAGA
Statistics
Matches: 144, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
86 25 0.17
87 117 0.81
88 2 0.01
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (86 bp):
AACATAAAAGAATCTAGAAAAAAAAAGTGCAGAGTAATTTCAACTACTTAAACACAAAGTGAATC
AGTTCCTTACTAATAGTATGC
Found at i:327307 original size:15 final size:15
Alignment explanation
Indices: 327287--327319 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
327277 TGAGGCTTTG
327287 GCTGCTTCCTTTT-CT
1 GCTGCTT-CTTTTGCT
327302 GCTGCTTCTTTTGCT
1 GCTGCTTCTTTTGCT
327317 GCT
1 GCT
327320 ATCCTCTCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.30, G:0.18, T:0.52
Consensus pattern (15 bp):
GCTGCTTCTTTTGCT
Found at i:334714 original size:18 final size:18
Alignment explanation
Indices: 334687--334728 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
334677 TCCTCTAAAC
*
334687 TTTATAGAGAAATATTAT
1 TTTATAGAGAAATACTAT
* *
334705 TTTATTGAGAAATCCTAT
1 TTTATAGAGAAATACTAT
334723 TTTATA
1 TTTATA
334729 AAAACCTTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (18 bp):
TTTATAGAGAAATACTAT
Found at i:335125 original size:18 final size:20
Alignment explanation
Indices: 335081--335126 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
335071 TAAAAATTAA
335081 AATTATATAATATATTATTCT
1 AATTA-ATAATATATTATTCT
*
335102 ACATTAATAAT-TATT-TTTT
1 A-ATTAATAATATATTATTCT
335121 AATTAA
1 AATTAA
335127 ATTTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 4 0.17
21 6 0.26
22 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTAATAATATATTATTCT
Found at i:339136 original size:68 final size:68
Alignment explanation
Indices: 339027--339163 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
339017 TTTTGTCTGG
*
339027 ACCATTACATCGCTAAAACTTTGGTGAATGATTTTTTTTTTCATTGAACAAATATTTAGGCATTT
1 ACCATTACATCGCTAAAACTTTGGAGAATGATTTTTTTTTTCATTGAACAAATATTTAGGCATTT
339092 TCA
66 TCA
*
339095 ACCATTACGTCGCTAAAACTTTGGAGAATGATTTTTTTTTTCATTGAACAAATATTTAGGCATTT
1 ACCATTACATCGCTAAAACTTTGGAGAATGATTTTTTTTTTCATTGAACAAATATTTAGGCATTT
339160 TCA
66 TCA
339163 A
1 A
339164 TTTATTAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (68 bp):
ACCATTACATCGCTAAAACTTTGGAGAATGATTTTTTTTTTCATTGAACAAATATTTAGGCATTT
TCA
Found at i:339541 original size:26 final size:26
Alignment explanation
Indices: 339494--339544 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
339484 TGGTACCTGA
* *
339494 TTTTTTCAATTTGATACTTGAGTTTT
1 TTTTTTCAATTAGATACATGAGTTTT
339520 TTTTTTCAATTA-AGTACATGAGTTT
1 TTTTTTCAATTAGA-TACATGAGTTT
339545 GATTTCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.57
Consensus pattern (26 bp):
TTTTTTCAATTAGATACATGAGTTTT
Found at i:339718 original size:30 final size:30
Alignment explanation
Indices: 339662--339719 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
339652 ATTAAATTGA
* *
339662 ACATTGAAACCAAACTCATATACTAAATTC
1 ACATTAAAACCAAACTCAGATACTAAATTC
339692 ACATTAAAACCAAACTCAAGAT-CTAAAT
1 ACATTAAAACCAAACTC-AGATACTAAAT
339720 AGTATATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.50, C:0.22, G:0.03, T:0.24
Consensus pattern (30 bp):
ACATTAAAACCAAACTCAGATACTAAATTC
Found at i:341810 original size:52 final size:53
Alignment explanation
Indices: 341731--341835 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 53
341721 CATCCTATTC
341731 TCATAAAATCCTTCCATGAAATCCGTACAATCACGTCGGATTATAACAGTTTG
1 TCATAAAATCCTTCCATGAAATCCGTACAATCACGTCGGATTATAACAGTTTG
*
341784 TCATAAAA-GCTTCCATGAAATCCGTACAATCACGTCGGATTATAACAGTTTG
1 TCATAAAATCCTTCCATGAAATCCGTACAATCACGTCGGATTATAACAGTTTG
341836 ATTGGTAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 43 0.84
53 8 0.16
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (53 bp):
TCATAAAATCCTTCCATGAAATCCGTACAATCACGTCGGATTATAACAGTTTG
Found at i:351132 original size:132 final size:131
Alignment explanation
Indices: 350843--351235 Score: 361
Period size: 132 Copynumber: 3.0 Consensus size: 131
350833 TTTCTGTTTA
* ** *
350843 AGCACTTGTTCATGCTTGTATACACTTGTAATCAATATGTTAGCTTAGAATA-GGCATAGATGAG
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGGCATAGATGAG
* * * *** ** * ** ***
350907 CTTAGATGCAAATTGTAGCATAGGTTCGCTG-TTGATGTAA-CATACATACTTCCCAGTTTTTG-
66 C-TAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGAT--GTAACA-TAAATGC
***
350969 T-GTA
127 TCCCC
*
350973 AGCACTTGTTCATGCTTGTATATACTTGTATTCAATATGTTAATTTATAATA-GGCATAGATGAG
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGGCATAGATGAG
351037 CTAGATACAAATTGTAACATAGTGTTT-CTGATTCAGC-TGTAACCATGGATGTAACATAAATGC
66 CTAGATACAAATTGTAACATAG-GTTTGCTGA-TC--CTTGTAACCATGGATGTAACATAAATGC
351100 TCCCC
127 TCCCC
* * *
351105 AGCACTTGTTCATGCTTGTATATACTTGTAATCGATATGTTAGTTTGTAATAGGGGCATAGATGA
1 AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATA-GGGCATAGATGA
* *** * * *
351170 GCTTGATGTGAATTGTAACATAGGTTTGCTGATCCTTGTAACCGTTGATGTAACATACATGCTCC
65 GCTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCC
351235 C
130 C
351236 TTTTTCTGTA
Statistics
Matches: 219, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
129 22 0.10
130 66 0.30
131 6 0.03
132 80 0.37
133 11 0.05
134 34 0.16
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (131 bp):
AGCACTTGTTCATGCTTGTATATACTTGTAATCAATATGTTAATTTATAATAGGGCATAGATGAG
CTAGATACAAATTGTAACATAGGTTTGCTGATCCTTGTAACCATGGATGTAACATAAATGCTCCC
C
Found at i:351632 original size:135 final size:133
Alignment explanation
Indices: 351438--351679 Score: 387
Period size: 135 Copynumber: 1.8 Consensus size: 133
351428 TCGAAGTAAT
* * *
351438 ATACATGCTCTCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATATTTGTAATATATATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
* *
351503 TTAGCATAGTAATCATAGATGAGCTATCTGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
66 TTAGCATAG---TCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
351568 CCATTG
128 CCATTG
*
351574 ATACATGCGCCCCAGTTTCTGTGTAAGCAC-TGTTCATGCTTTGTATATACTTGTAATATGTATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
*
351638 TTAGCATAGTCATTGATAAGCTATATGCAAATTGTAACATAG
66 TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAG
351680 GATTGCCGAT
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
132 30 0.30
135 41 0.41
136 28 0.28
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (133 bp):
ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAACCA
TTG
Found at i:353323 original size:135 final size:133
Alignment explanation
Indices: 353129--353370 Score: 387
Period size: 135 Copynumber: 1.8 Consensus size: 133
353119 TCGAAGTAAT
* * *
353129 ATACATGCTCTCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATATTTGTAATATATATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
* *
353194 TTAGCATAGTAATCATAGATGAGCTATCTGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
66 TTAGCATAG---TCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAA
353259 CCATTG
128 CCATTG
*
353265 ATACATGCGCCCCAGTTTCTGTGTAAGCAC-TGTTCATGCTTTGTATATACTTGTAATATGTATG
1 ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
*
353329 TTAGCATAGTCATTGATAAGCTATATGCAAATTGTAACATAG
66 TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAG
353371 GATTGCCGAT
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
132 30 0.30
135 41 0.41
136 28 0.28
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (133 bp):
ATACATGCGCCCCAGTTTCTGTGTAAGCACTTGTTCATGCTTTGTATATACTTGTAATATATATG
TTAGCATAGTCATAGATAAGCTATATGCAAATTGTAACATAGTGCCACTGATCCAGCTGTAACCA
TTG
Found at i:362151 original size:42 final size:42
Alignment explanation
Indices: 362105--362185 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
362095 TAGAAAAGTT
*
362105 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
*
362147 ACAGAGAGCAAACGTGAGAAAGAAAGAAGGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGA
362186 AAGAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.05
Consensus pattern (42 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:363009 original size:47 final size:47
Alignment explanation
Indices: 362945--363055 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
362935 GACATTGAGT
*
362945 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
362992 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
363039 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
363056 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Done.