Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold856
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: 172397
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6492 original size:23 final size:22
Alignment explanation
Indices: 6440--6492 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
6430 TCCACGTCTT
*
6440 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
6462 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
6485 TTTCTTTT
1 TTTCTTTT
6493 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:7707 original size:22 final size:22
Alignment explanation
Indices: 7677--7718 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
7667 TTTGGTATTT
7677 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
7699 GGGATTTGGTACGAAATGGT
1 GGGAATTGGTACGAAATGGT
7719 GATGGTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.26
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:12644 original size:22 final size:22
Alignment explanation
Indices: 12614--12657 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12604 TTTGGTATTT
12614 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
12636 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
12658 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:19951 original size:13 final size:12
Alignment explanation
Indices: 19931--19977 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
19921 ATGGAAACCA
19931 AATTTTTTTTTG
1 AATTTTTTTTTG
19943 AATTTTTTTTTG
1 AATTTTTTTTTG
*
19955 AATTTTTTTTTC
1 AATTTTTTTTTG
19967 AAGTTTTTTTT
1 AA-TTTTTTTT
19978 CGAGAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 25 0.76
13 8 0.24
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:23307 original size:10 final size:10
Alignment explanation
Indices: 23291--23348 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
23281 CAACTCCGAC
23291 CAGCTCAATT
1 CAGCTCAATT
* *
23301 GAGCTCATTT
1 CAGCTCAATT
23311 CAGCTCAA-T
1 CAGCTCAATT
23320 CGAGCTCAATT
1 C-AGCTCAATT
*
23331 TAGCTACAATT
1 CAGCT-CAATT
23342 CAGCTCA
1 CAGCTCA
23349 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:23314 original size:20 final size:20
Alignment explanation
Indices: 23291--23351 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
23281 CAACTCCGAC
23291 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
23311 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
23332 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
23352 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:25421 original size:20 final size:19
Alignment explanation
Indices: 25398--25462 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
25388 AAGCTCAAAC
25398 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
25418 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
25438 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
25458 GAGCT
1 GAGCT
25463 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:31325 original size:18 final size:18
Alignment explanation
Indices: 31304--31338 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31294 TTTTTCTTTT
31304 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31322 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31339 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:33695 original size:23 final size:22
Alignment explanation
Indices: 33643--33695 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
33633 TCCACGTCTT
*
33643 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
33665 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
33688 TTTCTTTT
1 TTTCTTTT
33696 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:37198 original size:12 final size:14
Alignment explanation
Indices: 37181--37213 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
37171 AACTCAAAAA
37181 TTTTTTTGA-TT-T
1 TTTTTTTGACTTCT
37193 TTTTTTTGACTTCT
1 TTTTTTTGACTTCT
37207 TTTTTTT
1 TTTTTTT
37214 TGTTACGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 2 0.11
14 8 0.42
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTTTGACTTCT
Found at i:47216 original size:11 final size:11
Alignment explanation
Indices: 47196--47230 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
47186 AAAAGAGAAG
47196 AAATTCAAAAA
1 AAATTCAAAAA
*
47207 AAATTTAAAAA
1 AAATTCAAAAA
47218 AAA-TCAAAAA
1 AAATTCAAAAA
47228 AAA
1 AAA
47231 AGGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:47237 original size:21 final size:20
Alignment explanation
Indices: 47182--47241 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
47172 TATTGGATTT
* *
47182 AAAAAAAAGAGAAGAAATTCA
1 AAAAAAAAGA-AAAAAAATCA
**
47203 AAAAAAATTTAAAAAAAATCA
1 AAAAAAA-AGAAAAAAAATCA
47224 AAAAAAAAGGAAAAAAAA
1 AAAAAAAA-GAAAAAAAA
47242 AGGTGAGCCA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAATCA
Found at i:48319 original size:6 final size:6
Alignment explanation
Indices: 48287--48394 Score: 76
Period size: 6 Copynumber: 17.7 Consensus size: 6
48277 AAAGAAATTG
* * ** *
48287 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** * *
48334 AAAGAA ATCA-AA AAAGTG AAAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
48385 AAAGAA AAAG
1 AAAGAA AAAG
48395 CGAAAAAAGA
Statistics
Matches: 77, Mismatches: 20, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
5 4 0.05
6 61 0.79
7 8 0.10
8 4 0.05
ACGTcount: A:0.73, C:0.04, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:48374 original size:14 final size:13
Alignment explanation
Indices: 48355--48392 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
48345 AAAAGTGAAA
48355 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
48367 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
48382 GAAAAAGAAAA
1 GAAAAAGAAAA
48393 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:48429 original size:12 final size:12
Alignment explanation
Indices: 48398--48429 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
48388 GAAAAAGCGA
*
48398 AAAAAGAATTTG
1 AAAAAGAGTTTG
48410 AAAAAGAGTTTG
1 AAAAAGAGTTTG
48422 AAAAAGAG
1 AAAAAGAG
48430 AAGAGTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (12 bp):
AAAAAGAGTTTG
Found at i:53611 original size:23 final size:23
Alignment explanation
Indices: 53585--53632 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
53575 AATCAGCTTC
53585 TTTAATAC-ACCTATTAAGACACA
1 TTTAA-ACGACCTATTAAGACACA
* *
53608 TTTAAACGACTTATTAGGACACA
1 TTTAAACGACCTATTAAGACACA
53631 TT
1 TT
53633 AATCATACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (23 bp):
TTTAAACGACCTATTAAGACACA
Found at i:57640 original size:19 final size:18
Alignment explanation
Indices: 57604--57643 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57594 TTTCCACTCG
*
57604 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
57622 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
57641 TTT
1 TTT
57644 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:58755 original size:12 final size:13
Alignment explanation
Indices: 58706--58754 Score: 73
Period size: 14 Copynumber: 3.7 Consensus size: 13
58696 TAGCTTCTTC
58706 TTTTTTTCACGAAT
1 TTTTTTTCAC-AAT
58720 TTTTTTTCACAATT
1 TTTTTTTCACAA-T
58734 TTTTTTTCA-AAT
1 TTTTTTTCACAAT
58746 TTTTTTTCA
1 TTTTTTTCA
58755 ACTTGATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.29
13 4 0.12
14 20 0.59
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.65
Consensus pattern (13 bp):
TTTTTTTCACAAT
Found at i:58808 original size:12 final size:12
Alignment explanation
Indices: 58791--58835 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
58781 AATGGAAACC
58791 AATTTTTTTTTG
1 AATTTTTTTTTG
58803 AATTTTTTTTTG
1 AATTTTTTTTTG
58815 AA-TTTTTTTTG
1 AATTTTTTTTTG
58826 AATTTTTTTT
1 AATTTTTTTT
58836 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.18, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:58810 original size:11 final size:11
Alignment explanation
Indices: 58794--58838 Score: 81
Period size: 11 Copynumber: 4.0 Consensus size: 11
58784 GGAAACCAAT
58794 TTTTTTTTGAA
1 TTTTTTTTGAA
58805 TTTTTTTTTGAA
1 -TTTTTTTTGAA
58817 TTTTTTTTGAA
1 TTTTTTTTGAA
58828 TTTTTTTTGAA
1 TTTTTTTTGAA
58839 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:70420 original size:22 final size:22
Alignment explanation
Indices: 70369--70434 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
70359 GGTATTTGGG
* *
70369 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
70390 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
70412 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
70435 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:76135 original size:21 final size:23
Alignment explanation
Indices: 76090--76136 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
76080 TCACCTGCAA
* *
76090 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
76113 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
76134 TAA
1 TAA
76137 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:81923 original size:4 final size:4
Alignment explanation
Indices: 81914--81947 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
81904 TTAAACTAAG
81914 TAAA TAAA TAAA TAAA TAAA T-AA -AAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
81948 ACTTTACAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.14
4 24 0.86
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:83345 original size:23 final size:22
Alignment explanation
Indices: 83293--83345 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
83283 TCCACGTCTT
*
83293 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
83315 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
83338 TTTCTTTT
1 TTTCTTTT
83346 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:87578 original size:16 final size:15
Alignment explanation
Indices: 87557--87593 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
87547 CTTCTTCTTC
87557 TTTTTTTCACGAAATT
1 TTTTTTTCACG-AATT
87573 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
87588 TTTTTT
1 TTTTTT
87594 CAACTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:87648 original size:12 final size:12
Alignment explanation
Indices: 87631--87690 Score: 79
Period size: 11 Copynumber: 4.9 Consensus size: 12
87621 GAATGGAAAC
87631 CAATTTTTTTTT
1 CAATTTTTTTTT
87643 CAA-TTTTTTTT
1 CAATTTTTTTTT
87654 CAATTTTTTTTTTT
1 CAA--TTTTTTTTT
87668 CAA-TTTTTTTT
1 CAATTTTTTTTT
87679 CGAATTTTTTTT
1 C-AATTTTTTTT
87691 GAAGAAACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
11 20 0.47
12 5 0.12
13 7 0.16
14 11 0.26
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:87653 original size:14 final size:14
Alignment explanation
Indices: 87634--87678 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
87624 TGGAAACCAA
87634 TTTTTTTTTCAA--
1 TTTTTTTTTCAATT
87646 -TTTTTTTTCAATT
1 TTTTTTTTTCAATT
87659 TTTTTTTTTCAATT
1 TTTTTTTTTCAATT
87673 TTTTTT
1 TTTTTT
87679 CGAATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.37
14 19 0.63
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTCAATT
Found at i:87668 original size:25 final size:26
Alignment explanation
Indices: 87634--87690 Score: 107
Period size: 25 Copynumber: 2.2 Consensus size: 26
87624 TGGAAACCAA
87634 TTTTTTTTTCAATTTTTTTTC-AATT
1 TTTTTTTTTCAATTTTTTTTCGAATT
87659 TTTTTTTTTCAATTTTTTTTCGAATT
1 TTTTTTTTTCAATTTTTTTTCGAATT
87685 TTTTTT
1 TTTTTT
87691 GAAGAAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTTTTTCAATTTTTTTTCGAATT
Found at i:91441 original size:11 final size:10
Alignment explanation
Indices: 91416--91496 Score: 69
Period size: 10 Copynumber: 8.1 Consensus size: 10
91406 ACCAATAAAA
91416 TAAA-TGAGC
1 TAAATTGAGC
*
91425 TGAATTGTAGC
1 TAAATTG-AGC
91436 TAAATTGAGC
1 TAAATTGAGC
**
91446 TCGATTGAGC
1 TAAATTGAGC
91456 TGAAA-TGAGC
1 T-AAATTGAGC
*
91466 TCAATTGAGC
1 TAAATTGAGC
91476 TGAAA-TGAGC
1 T-AAATTGAGC
*
91486 TCAATTGAGC
1 TAAATTGAGC
91496 T
1 T
91497 GGTCGGAGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 7 0.12
10 38 0.67
11 12 0.21
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:91456 original size:20 final size:20
Alignment explanation
Indices: 91417--91497 Score: 119
Period size: 20 Copynumber: 4.0 Consensus size: 20
91407 CCAATAAAAT
*
91417 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
91437 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
91458 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
91478 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
91498 GTCGGAGTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
20 43 0.77
21 13 0.23
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:91485 original size:30 final size:31
Alignment explanation
Indices: 91417--91496 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
91407 CCAATAAAAT
91417 AAATGAGCTGAATTGTAGCTAAATTGAGCTCG
1 AAATGAGCTGAATTG-AGCTAAATTGAGCTCG
* * *
91449 -ATTGAGCTGAAATGAGCTCAATTGAGCT-G
1 AAATGAGCTGAATTGAGCTAAATTGAGCTCG
*
91478 AAATGAGCTCAATTGAGCT
1 AAATGAGCTGAATTGAGCT
91497 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.02
30 28 0.68
31 12 0.29
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (31 bp):
AAATGAGCTGAATTGAGCTAAATTGAGCTCG
Found at i:93606 original size:12 final size:12
Alignment explanation
Indices: 93559--93631 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
93549 TCAACATCTT
93559 TTTCTTTTTCAA
1 TTTCTTTTTCAA
93571 TTT-TTTTCTCAA
1 TTTCTTTT-TCAA
* ** *
93583 TCTCAATCTCAA
1 TTTCTTTTTCAA
93595 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
93607 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
93622 TTTCTTTTTC
1 TTTCTTTTTC
93632 TCTCACTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
11 4 0.09
12 24 0.51
13 8 0.17
14 7 0.15
15 4 0.09
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:102262 original size:20 final size:20
Alignment explanation
Indices: 102239--102292 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
102229 AGTTTTTCCC
*
102239 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
102259 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
102279 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
102293 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:102274 original size:30 final size:30
Alignment explanation
Indices: 102239--102312 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
102229 AGTTTTTCCC
102239 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
102269 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
102299 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
102313 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:102302 original size:20 final size:20
Alignment explanation
Indices: 102239--102303 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
102229 AGTTTTTCCC
* * * *
102239 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
102259 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
102278 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
102299 AGCTC
1 AGCTC
102304 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:108346 original size:12 final size:12
Alignment explanation
Indices: 108329--108366 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
108319 TTCAAAAATT
108329 TTTTTTTTTGAA
1 TTTTTTTTTGAA
108341 TTTTTTTTTGAA
1 TTTTTTTTTGAA
*
108353 TTTTTTTTTCAA
1 TTTTTTTTTGAA
108365 TT
1 TT
108367 ACAATATGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:112149 original size:45 final size:45
Alignment explanation
Indices: 111911--112146 Score: 364
Period size: 45 Copynumber: 5.2 Consensus size: 45
111901 TCGGCCATGG
* * * * *
111911 TGCTTCCTTAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
111956 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
112001 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
112046 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * **
112091 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
112136 TGCTTCCTTAA
1 TGCTTCCTTAA
112147 TTTCATGCCG
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 178 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:112331 original size:16 final size:16
Alignment explanation
Indices: 112310--112341 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
112300 CATTCTGCAT
112310 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
112326 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
112342 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:113729 original size:11 final size:10
Alignment explanation
Indices: 113704--113764 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
113694 ACCAATAAAA
113704 TAAA-TGAGC
1 TAAATTGAGC
*
113713 TGAATTGTAGC
1 TAAATTG-AGC
113724 TAAATTGAGC
1 TAAATTGAGC
**
113734 TCGATTGAGC
1 TAAATTGAGC
113744 TGAAA-TGAGC
1 T-AAATTGAGC
*
113754 TCAATTGAGC
1 TAAATTGAGC
113764 T
1 T
113765 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:113765 original size:20 final size:20
Alignment explanation
Indices: 113705--113765 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
113695 CCAATAAAAT
*
113705 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
113725 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
113746 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
113766 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:120578 original size:21 final size:23
Alignment explanation
Indices: 120533--120579 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
120523 TCACCTGCAA
* *
120533 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
120556 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
120577 TAA
1 TAA
120580 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:121932 original size:22 final size:22
Alignment explanation
Indices: 121881--121946 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
121871 GGTATTTGGG
* *
121881 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
121902 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
121924 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
121947 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:129837 original size:4 final size:4
Alignment explanation
Indices: 129828--129855 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
129818 AAGTTTTATT
129828 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
129856 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:130925 original size:11 final size:11
Alignment explanation
Indices: 130909--130952 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
130899 AACCGTATGT
130909 AATTTTTTTTC
1 AATTTTTTTTC
130920 AATTTTTTTTTC
1 AA-TTTTTTTTC
130932 AATTTTTTTTC
1 AATTTTTTTTC
*
130943 -TTTTTTTTTC
1 AATTTTTTTTC
130953 GAACTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 9 0.29
11 11 0.35
12 11 0.35
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (11 bp):
AATTTTTTTTC
Found at i:130928 original size:12 final size:12
Alignment explanation
Indices: 130911--130966 Score: 64
Period size: 12 Copynumber: 4.7 Consensus size: 12
130901 CCGTATGTAA
130911 TTTTTTTTCAAT
1 TTTTTTTTCAAT
130923 TTTTTTTTCAA-
1 TTTTTTTTCAAT
130934 TTTTTTTTC--T
1 TTTTTTTTCAAT
130944 TTTTTTTTCGAACT
1 TTTTTTTTC-AA-T
130958 CTTTTTTTT
1 -TTTTTTTT
130967 ACGTACCTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.24
11 9 0.24
12 11 0.29
14 1 0.03
15 8 0.21
ACGTcount: A:0.11, C:0.11, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:130939 original size:23 final size:21
Alignment explanation
Indices: 130909--130952 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 21
130899 AACCGTATGT
130909 AATTTTTTTTCAATTTTTTTTTC
1 AATTTTTTTTC--TTTTTTTTTC
130932 AATTTTTTTTCTTTTTTTTTC
1 AATTTTTTTTCTTTTTTTTTC
130953 GAACTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.48
23 11 0.52
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (21 bp):
AATTTTTTTTCTTTTTTTTTC
Found at i:130962 original size:22 final size:21
Alignment explanation
Indices: 130922--130963 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
130912 TTTTTTTCAA
* *
130922 TTTTTTTTTCAATTTTTTTTC
1 TTTTTTTTTCAACTCTTTTTC
130943 TTTTTTTTTCGAACTCTTTTT
1 TTTTTTTTTC-AACTCTTTTT
130964 TTTACGTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTCAACTCTTTTTC
Found at i:130962 original size:23 final size:22
Alignment explanation
Indices: 130913--130964 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
130903 GTATGTAATT
*
130913 TTTTTTCAATTTTTTTTTCAATT
1 TTTTTTC-ATTTTTTTTTCAATC
130936 TTTTTTC-TTTTTTTTTCGAACTC
1 TTTTTTCATTTTTTTTTC-AA-TC
130959 TTTTTT
1 TTTTTT
130965 TTACGTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.38
22 2 0.08
23 14 0.54
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTTCATTTTTTTTTCAATC
Found at i:131318 original size:22 final size:22
Alignment explanation
Indices: 131267--131332 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
131257 GGTATTTGGG
* *
131267 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
131288 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
131310 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
131333 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:136052 original size:13 final size:12
Alignment explanation
Indices: 136032--136076 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
136022 AACCGTATGT
136032 AATTTTTTTTTC
1 AATTTTTTTTTC
136044 AATTTTTTTTTC
1 AATTTTTTTTTC
136056 AAATTTTTTTTTC
1 -AATTTTTTTTTC
136069 --TTTTTTTT
1 AATTTTTTTT
136077 CGAACTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.25
12 12 0.38
13 12 0.38
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:136444 original size:22 final size:22
Alignment explanation
Indices: 136393--136458 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
136383 GGTATTTGGG
* *
136393 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
136414 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
136436 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
136459 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:141359 original size:16 final size:15
Alignment explanation
Indices: 141340--141376 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
141330 AAAAAAATAT
141340 AAAAAAAAATTCGAAA
1 AAAAAAAAATTC-AAA
141356 AAAAAAAAATTCAAA
1 AAAAAAAAATTCAAA
141371 AAAAAA
1 AAAAAA
141377 TAAAAGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.81, C:0.05, G:0.03, T:0.11
Consensus pattern (15 bp):
AAAAAAAAATTCAAA
Found at i:141440 original size:13 final size:13
Alignment explanation
Indices: 141422--141447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
141412 ATTTAGTATT
141422 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
141435 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
141448 TTCGGAATTA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:141502 original size:34 final size:34
Alignment explanation
Indices: 141426--141501 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 34
141416 AGTATTGAAG
**
141426 AAAAAAAAAGAAGAAAAAAAAATTCGGAATTAAA
1 AAAAAAAAAGAAGAAAAAAAAATTCAAAATTAAA
*
141460 ACAAAAAAAGAAG-AAAAAAAA-TCAAAATTGAAA
1 AAAAAAAAAGAAGAAAAAAAAATTCAAAATT-AAA
141493 AAAAAAAAA
1 AAAAAAAAA
141502 AAGTGATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.16
33 19 0.51
34 12 0.32
ACGTcount: A:0.78, C:0.04, G:0.09, T:0.09
Consensus pattern (34 bp):
AAAAAAAAAGAAGAAAAAAAAATTCAAAATTAAA
Found at i:142419 original size:21 final size:20
Alignment explanation
Indices: 142390--142435 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
142380 AATCTTGAAT
*
142390 GAAATTGAGAGAAGAAAAAAA
1 GAAAATGAGAG-AGAAAAAAA
* *
142411 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAAAAAAA
142431 GAAAA
1 GAAAA
142436 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAAAAAAA
Found at i:142462 original size:12 final size:12
Alignment explanation
Indices: 142442--142477 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
142432 AAAAAAGAAT
*
142442 TTGAGATTGAGA
1 TTGATATTGAGA
*
142454 TTGATATTGATA
1 TTGATATTGAGA
142466 TTGATATTGAGA
1 TTGATATTGAGA
142478 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:147135 original size:13 final size:12
Alignment explanation
Indices: 147115--147159 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
147105 AACCGTATGT
147115 AATTTTTTTTTC
1 AATTTTTTTTTC
147127 AATTTTTTTTTC
1 AATTTTTTTTTC
147139 AAATTTTTTTTTC
1 -AATTTTTTTTTC
147152 --TTTTTTTT
1 AATTTTTTTT
147160 CGAACTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.25
12 12 0.38
13 12 0.38
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (12 bp):
AATTTTTTTTTC
Found at i:147526 original size:22 final size:22
Alignment explanation
Indices: 147475--147540 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
147465 GGTATTTGGG
* *
147475 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
147496 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
147518 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
147541 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:154944 original size:4 final size:4
Alignment explanation
Indices: 154935--154962 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
154925 AAGTTTTATT
154935 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
154963 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:156515 original size:10 final size:10
Alignment explanation
Indices: 156500--156561 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
156490 TTTGAACCAT
*
156500 TACCAATTCG
1 TACCAATTCA
*
156510 TACCAAATACCA
1 TACC-AAT-TCA
*
156522 TACCATTTCA
1 TACCAATTCA
156532 TACCAATTCCA
1 TACCAATT-CA
* *
156543 TACCATTTCG
1 TACCAATTCA
156553 TACCAATTC
1 TACCAATTC
156562 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:156545 original size:21 final size:21
Alignment explanation
Indices: 156500--156562 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
156490 TTTGAACCAT
* *
156500 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
156522 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
156543 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
156563 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:157881 original size:11 final size:11
Alignment explanation
Indices: 157865--157907 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
157855 CCGTATACAA
157865 TTTTTTTTC-T
1 TTTTTTTTCAT
157875 TTTTTTTTCAAT
1 TTTTTTTTC-AT
*
157887 TTTTTTTTGAT
1 TTTTTTTTCAT
157898 TTTTTTTTCA
1 TTTTTTTTCA
157908 CGAGTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.31
11 11 0.38
12 9 0.31
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTTCAT
Found at i:157900 original size:23 final size:22
Alignment explanation
Indices: 157865--157907 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
157855 CCGTATACAA
*
157865 TTTTTTTTCTTTTTTTTTCAAT
1 TTTTTTTTATTTTTTTTTCAAT
157887 TTTTTTTTGATTTTTTTTTCA
1 TTTTTTTT-ATTTTTTTTTCA
157908 CGAGTTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTTTTATTTTTTTTTCAAT
Found at i:159691 original size:12 final size:11
Alignment explanation
Indices: 159649--159690 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
159639 TAGTTTCTCG
*
159649 AAAAAAAACTC
1 AAAAAAAATTC
159660 TAAAAAAAATTC
1 -AAAAAAAATTC
159672 AAAAAAAATTC
1 AAAAAAAATTC
159683 AAAAAAAA
1 AAAAAAAA
159691 ACTAGTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:159752 original size:14 final size:14
Alignment explanation
Indices: 159729--159769 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
159719 GGATATCAAG
159729 TTGT-AAAAAAAAA
1 TTGTGAAAAAAAAA
159742 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
159756 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
159770 GAGAGCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:167184 original size:14 final size:14
Alignment explanation
Indices: 167165--167212 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
167155 CTAGCTCTTC
167165 TTTTTTCACAATTT
1 TTTTTTCACAATTT
167179 TTTTTTCACAA--T
1 TTTTTTCACAATTT
167191 TTTTTTCA-AATTT
1 TTTTTTCACAATTT
167204 TTTTTTCAC
1 TTTTTTCAC
167213 TTGATATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 9 0.29
14 11 0.35
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTCACAATTT
Found at i:167208 original size:12 final size:13
Alignment explanation
Indices: 167165--167208 Score: 65
Period size: 12 Copynumber: 3.5 Consensus size: 13
167155 CTAGCTCTTC
167165 TTTTTTCACAATTT
1 TTTTTTCACAA-TT
167179 TTTTTTCACAA-T
1 TTTTTTCACAATT
167191 TTTTTTCA-AATT
1 TTTTTTCACAATT
167203 TTTTTT
1 TTTTTT
167209 TCACTTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.07
12 16 0.55
14 11 0.38
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTTCACAATT
Found at i:167265 original size:11 final size:11
Alignment explanation
Indices: 167249--167281 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
167239 GGAAACAATT
167249 TTTTTTTTGAA
1 TTTTTTTTGAA
167260 TTTTTTTTGAA
1 TTTTTTTTGAA
167271 TTTTTTTTGAA
1 TTTTTTTTGAA
167282 GAAACTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:170093 original size:15 final size:15
Alignment explanation
Indices: 170070--170099 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
170060 AAAACAGCAA
*
170070 CTATTATAGCTTAAT
1 CTATAATAGCTTAAT
170085 CTATAATAGCTTAAT
1 CTATAATAGCTTAAT
170100 GGACAAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (15 bp):
CTATAATAGCTTAAT
Done.