Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3243
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: 38404
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5988 original size:20 final size:20
Alignment explanation
Indices: 5942--5988 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
5932 AGCTCGTTTC
*
5942 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
5962 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
5982 CAGCTCA
1 CAGCTCA
5989 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:7532 original size:11 final size:10
Alignment explanation
Indices: 7511--7544 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
7501 AGAAGTGAGC
7511 AAAAAAGAAA
1 AAAAAAGAAA
7521 AAAAAAGTAAA
1 AAAAAAG-AAA
7532 AAAAAA-AAA
1 AAAAAAGAAA
7541 AAAA
1 AAAA
7545 GTGAAAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 7 0.30
11 9 0.39
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:7532 original size:18 final size:18
Alignment explanation
Indices: 7479--7551 Score: 65
Period size: 18 Copynumber: 4.0 Consensus size: 18
7469 TTGGAGTATC
*
7479 AAAAAAAAAAATTCAAAAA
1 AAAAAAAAAAAGT-AAAAA
* *** *
7498 AAAAGAAGTGAGCAAAAA
1 AAAAAAAAAAAGTAAAAA
*
7516 AGAAAAAAAAAGTAAAAA
1 AAAAAAAAAAAGTAAAAA
*
7534 AAAAAAAAAAAGTGAAAA
1 AAAAAAAAAAAGTAAAAA
7552 GTCTTGCGAG
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
18 33 0.82
19 7 0.17
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.07
Consensus pattern (18 bp):
AAAAAAAAAAAGTAAAAA
Found at i:10377 original size:20 final size:20
Alignment explanation
Indices: 10331--10377 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10321 AGCTCGTTTC
*
10331 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10351 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
10371 CAGCTCA
1 CAGCTCA
10378 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14949 original size:30 final size:30
Alignment explanation
Indices: 14915--15011 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
14905 TAAACTAAAA
14915 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
14945 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
14975 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
15005 TGAGCTA
1 TGAGCTA
15012 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:15210 original size:155 final size:155
Alignment explanation
Indices: 15024--15333 Score: 514
Period size: 155 Copynumber: 2.0 Consensus size: 155
15014 AGTGAGCTCG
15024 GTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGA
1 GTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGA
* * *
15089 GCTGGAAATGAGCTTGGATCAGCTTGCCAACATGTCATTGCTCGGCTTGACAGACTTGCTT-GAT
66 GCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTGACAGACTTG-TTCGAT
**
15153 AAAGTTTGCGGGGCGTGCTCGTATCA
130 AAAGTTCACGGGGCGTGCTCGTATCA
* * *
15179 GTTTAGCTCAGGCAAGTTGGATTGAGCTCGAATAAGTTGGATTTGAGCTGGACGGAGCTCGTGGA
1 GTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGA
*
15244 GCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTGACAGACTTGTTCGATG
66 GCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTGACAGACTTGTTCGATA
*
15309 AAGTTCATGGGGCGTGCTCGTATCA
131 AAGTTCACGGGGCGTGCTCGTATCA
15334 TAAGTCCAAC
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
154 2 0.01
155 142 0.99
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (155 bp):
GTTTAGCTCAGGCAAGATGGATTGAGCTCGAATAAGCTGGATTTGAGCTAGACGGAGCTCGTGGA
GCTGGAAACGAGCTGGGATCAGCTTGCCAACATGTCAATGCTCGGCTTGACAGACTTGTTCGATA
AAGTTCACGGGGCGTGCTCGTATCA
Found at i:19032 original size:18 final size:18
Alignment explanation
Indices: 19000--19057 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
18990 AAATGAGATT
**
19000 GAAAAAGAGAATGAAAAA
1 GAAAAAGAGGTTGAAAAA
19018 GAAAAAGAGGTTGAACAAA
1 GAAAAAGAGGTTGAA-AAA
*
19037 -AGAAAAGA-GTGGAAAAA
1 GA-AAAAGAGGTTGAAAAA
19054 GAAA
1 GAAA
19058 TTGAGGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 5 0.15
18 20 0.59
19 9 0.26
ACGTcount: A:0.66, C:0.02, G:0.26, T:0.07
Consensus pattern (18 bp):
GAAAAAGAGGTTGAAAAA
Found at i:19738 original size:14 final size:14
Alignment explanation
Indices: 19715--19758 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
19705 GTAGAAAGAG
* *
19715 GGGTACGAACGGAA
1 GGGTAGGAACGAAA
*
19729 TGGTAGGAACGAAA
1 GGGTAGGAACGAAA
19743 GGGTAGGAAC-AAA
1 GGGTAGGAACGAAA
19756 GGG
1 GGG
19759 ATATGAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.39, C:0.09, G:0.43, T:0.09
Consensus pattern (14 bp):
GGGTAGGAACGAAA
Found at i:19766 original size:14 final size:13
Alignment explanation
Indices: 19730--19769 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
19720 CGAACGGAAT
19730 GGTAGGAACGAAAG
1 GGTAGGAAC-AAAG
19744 GGTAGGAACAAAG
1 GGTAGGAACAAAG
*
19757 GGATATGAACAAA
1 GG-TAGGAACAAA
19770 TTGGTCGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.47, C:0.07, G:0.35, T:0.10
Consensus pattern (13 bp):
GGTAGGAACAAAG
Found at i:22298 original size:13 final size:12
Alignment explanation
Indices: 22260--22313 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
22250 TTTCTTTTGT
22260 TTCTTTTTCTAAC
1 TTCTTTTTC-AAC
* *
22273 -TCATTTTC-TC
1 TTCTTTTTCAAC
22283 TTCTTTCTTCAAC
1 TTCTTT-TTCAAC
22296 TTCTTTTTCAA-
1 TTCTTTTTCAAC
22307 TTCTTTT
1 TTCTTTT
22314 CTGTTTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 1 0.03
11 11 0.32
12 15 0.44
13 7 0.21
ACGTcount: A:0.13, C:0.24, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTTTTCAAC
Found at i:22302 original size:23 final size:22
Alignment explanation
Indices: 22251--22302 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
22241 CCTCGTCTTT
*
22251 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
22273 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
22296 TTCTTTT
1 TTCTTTT
22303 TCAATTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:23627 original size:6 final size:6
Alignment explanation
Indices: 23616--23641 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23606 ATAAATAAAT
23616 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
23642 CTTTACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:27914 original size:30 final size:30
Alignment explanation
Indices: 27880--27981 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 30
27870 CACGAGCTCG
*
27880 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * * *
27910 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* *
27940 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
*
27970 TGAGCTAGGCTT
1 TGAGCTAAGCTT
27982 GACAGACTTG
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
30 50 0.94
31 3 0.06
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:27915 original size:19 final size:19
Alignment explanation
Indices: 27873--27915 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27863 CCAGCTCCAC
27873 GAGCTCGTGAGCTAAGCTT
1 GAGCTCGTGAGCTAAGCTT
* *
27892 TAGCTTGTGAGCTAAAG-TT
1 GAGCTCGTGAGCT-AAGCTT
27911 GAGCT
1 GAGCT
27916 GAGATTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
GAGCTCGTGAGCTAAGCTT
Done.