Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4821.1
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: 43367
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Warning! 581 characters in sequence are not A, C, G, or T
Found at i:5020 original size:17 final size:16
Alignment explanation
Indices: 4998--5042 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
4988 TTCAATCACT
4998 TTTTTTTTAATTTCGAA
1 TTTTTTTTAATTTC-AA
**
5015 TTTTTTTTGAATTTCTC
1 TTTTTTTT-AATTTCAA
5032 TTTTTTTTAAT
1 TTTTTTTTAAT
5043 ACCGAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.64
18 6 0.24
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTTTTAATTTCAA
Found at i:5036 original size:18 final size:17
Alignment explanation
Indices: 4996--5039 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4986 ATTTCAATCA
4996 CTTTTTTTTTAATTTCG
1 CTTTTTTTTTAATTTCG
* * *
5013 AATTTTTTTTGAATTTCT
1 -CTTTTTTTTTAATTTCG
5031 CTTTTTTTT
1 CTTTTTTTT
5040 AATACCGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (17 bp):
CTTTTTTTTTAATTTCG
Found at i:5468 original size:60 final size:60
Alignment explanation
Indices: 5386--5507 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
5376 GGAGTAAAGG
*
5386 ATAAAGAAAAACGAATAAAATGGATAGTTAATTTTGCGTTAATTTGTGGGAATGGAGAAT
1 ATAAAGAAAAACGAATAAAATGGATAGTTAATTTTGCGGTAATTTGTGGGAATGGAGAAT
5446 ATAAAGAAAAACGAATAAAATGGATAGTTAATTTTGCGGTAATTTGTGGGAATGGAGAAT
1 ATAAAGAAAAACGAATAAAATGGATAGTTAATTTTGCGGTAATTTGTGGGAATGGAGAAT
5506 AT
1 AT
5508 GGACTTAACT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.43, C:0.03, G:0.24, T:0.30
Consensus pattern (60 bp):
ATAAAGAAAAACGAATAAAATGGATAGTTAATTTTGCGGTAATTTGTGGGAATGGAGAAT
Found at i:5930 original size:45 final size:45
Alignment explanation
Indices: 5881--6293 Score: 763
Period size: 45 Copynumber: 9.2 Consensus size: 45
5871 TCGGCCATGG
* * * *
5881 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
5926 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
5971 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6016 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6061 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6106 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6151 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6196 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
6241 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATTTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
6286 TGCTTCCT
1 TGCTTCCT
6294 TAATTTCATG
Statistics
Matches: 360, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 360 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:10563 original size:11 final size:10
Alignment explanation
Indices: 10549--10582 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
10539 AAAAATTTTG
10549 AAAAACAAATC
1 AAAAA-AAATC
10560 AAAAAAAATC
1 AAAAAAAATC
10570 AAAGAAAAATC
1 AAA-AAAAATC
10581 AA
1 AA
10583 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.76, C:0.12, G:0.03, T:0.09
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:12844 original size:21 final size:21
Alignment explanation
Indices: 12791--12848 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 21
12781 AAGGCAAAGG
12791 AACAAAAAG-AAAAGATG-GAA
1 AACAAAAAGAAAAAG-TGAGAA
*
12811 AA-AGAAA-AAAAAGTGAGAA
1 AACAAAAAGAAAAAGTGAGAA
12830 AACAAAAAGAAAAAGTGAG
1 AACAAAAAGAAAAAGTGAG
12849 TTGAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 6 0.19
21 10 0.31
ACGTcount: A:0.71, C:0.03, G:0.21, T:0.05
Consensus pattern (21 bp):
AACAAAAAGAAAAAGTGAGAA
Found at i:18327 original size:23 final size:22
Alignment explanation
Indices: 18275--18327 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
18265 TCCACGTCTT
*
18275 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
18297 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
18320 TTTCTTTT
1 TTTCTTTT
18328 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:22831 original size:24 final size:25
Alignment explanation
Indices: 22790--22837 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
22780 TCAGATTTTT
22790 TTTTCTTTTCGAAATTTTTTTTGAA
1 TTTTCTTTTCGAAATTTTTTTTGAA
*
22815 TTTT-TTTTCGAATTTTTTTTTGA
1 TTTTCTTTTCGAAATTTTTTTTGA
22838 CTTGTATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTTCTTTTCGAAATTTTTTTTGAA
Found at i:22834 original size:12 final size:12
Alignment explanation
Indices: 22790--22834 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
22780 TCAGATTTTT
22790 TTTTCTTTTCGAAA
1 TTTT-TTTTCG-AA
22804 TTTTTTTT-GAA
1 TTTTTTTTCGAA
22815 TTTTTTTTCGAA
1 TTTTTTTTCGAA
22827 TTTTTTTT
1 TTTTTTTT
22835 TGACTTGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.33
12 12 0.40
13 4 0.13
14 4 0.13
ACGTcount: A:0.16, C:0.07, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:26596 original size:13 final size:13
Alignment explanation
Indices: 26580--26631 Score: 86
Period size: 13 Copynumber: 3.9 Consensus size: 13
26570 CAAATTTTGA
26580 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
26593 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
*
26606 GATTTTTTTCTTCT
1 -TTTTTTTTCTTCT
26620 TTTTTTTTCTTC
1 TTTTTTTTCTTC
26632 AATACTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 24 0.67
14 12 0.33
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:26701 original size:14 final size:13
Alignment explanation
Indices: 26667--26717 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
26657 AAATTGAATA
26667 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
*
26681 -GAA-TTTTTTTT
1 CAAATTTTTTTTT
26692 CAAAATTTTTTTTT
1 C-AAATTTTTTTTT
26706 CAAATTTTTTTT
1 CAAATTTTTTTT
26718 ATATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
11 8 0.25
13 15 0.47
14 9 0.28
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:26726 original size:13 final size:12
Alignment explanation
Indices: 26672--26728 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
26662 GAATACAAAC
*
26672 TTTTTTTTTGAA
1 TTTTTTTTTAAA
*
26684 TTTTTTTTCAAAA
1 TTTTTTTT-TAAA
26697 TTTTTTTTTCAAA
1 TTTTTTTTT-AAA
*
26710 -TTTTTTTTATA
1 TTTTTTTTTAAA
26721 TTTTTTTT
1 TTTTTTTT
26729 ACAATACCGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 2 0.05
12 23 0.61
13 13 0.34
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTTAAA
Found at i:26729 original size:11 final size:11
Alignment explanation
Indices: 26673--26729 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
26663 AATACAAACT
*
26673 TTTTTTTTGAA
1 TTTTTTTTAAA
26684 TTTTTTTTCAAAA
1 TTTTTTTT--AAA
26697 TTTTTTTTTCAAA
1 -TTTTTTTT-AAA
*
26710 TTTTTTTTATA
1 TTTTTTTTAAA
26721 TTTTTTTTA
1 TTTTTTTTA
26730 CAATACCGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 19 0.47
12 8 0.20
13 5 0.12
14 8 0.20
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:27052 original size:22 final size:22
Alignment explanation
Indices: 27022--27065 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27012 TTTGGTATTT
27022 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27044 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27066 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:34209 original size:22 final size:22
Alignment explanation
Indices: 34181--34224 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
34171 TTTTGAACCA
34181 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
34203 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
34225 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:39155 original size:10 final size:10
Alignment explanation
Indices: 39139--39207 Score: 77
Period size: 10 Copynumber: 6.8 Consensus size: 10
39129 ATCAGCTCAC
*
39139 TTGAGCTTGT
1 TTGAGCTCGT
*
39149 TTTAGCTCGT
1 TTGAGCTCGT
39159 TTGAGCTCGT
1 TTGAGCTCGT
*
39169 TTTAGCTCGT
1 TTGAGCTCGT
39179 TTGAGCTCGAAT
1 TTGAGCTCG--T
39191 TT-AGCTCGT
1 TTGAGCTCGT
*
39200 TTCAGCTC
1 TTGAGCTC
39208 ATTCCTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
9 3 0.06
10 39 0.76
11 6 0.12
12 3 0.06
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (10 bp):
TTGAGCTCGT
Found at i:39162 original size:20 final size:20
Alignment explanation
Indices: 39139--39207 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
39129 ATCAGCTCAC
*
39139 TTGAGCTTGTTTTAGCTCGT
1 TTGAGCTCGTTTTAGCTCGT
39159 TTGAGCTCGTTTTAGCTCGT
1 TTGAGCTCGTTTTAGCTCGT
*
39179 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-TTTTAGCTCGT
*
39200 TTCAGCTC
1 TTGAGCTC
39208 ATTCCTTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGAGCTCGTTTTAGCTCGT
Found at i:41362 original size:67 final size:66
Alignment explanation
Indices: 41238--41366 Score: 181
Period size: 67 Copynumber: 1.9 Consensus size: 66
41228 ACATGGTGAA
* * *
41238 CACTTAGTACCACCCATGTGACCTAGCCAGTTTATCTCGTAGCTCTCTTGTCTACATGGTGTCCT
1 CACTTAGAACCACCCATGCGACCTAGCCAGTATATCTCGTAGCTCTCTTGTCTACATGGTGTCCT
41303 T
66 T
*
41304 CACTTAGAACCACGCATGCGACCTAGCTACA-TATATC-CTGTAGCTCTCTTGTCTACATGGTGT
1 CACTTAGAACCACCCATGCGACCTAGC--CAGTATATCTC-GTAGCTCTCTTGTCTACATGGTGT
41367 ACACATAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
66 25 0.45
67 29 0.52
68 2 0.04
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (66 bp):
CACTTAGAACCACCCATGCGACCTAGCCAGTATATCTCGTAGCTCTCTTGTCTACATGGTGTCCT
T
Found at i:43025 original size:13 final size:13
Alignment explanation
Indices: 43007--43032 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42997 GGCTATTACA
43007 TATTTAATTATGT
1 TATTTAATTATGT
43020 TATTTAATTATGT
1 TATTTAATTATGT
43033 AGGTTAGCCA
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TATTTAATTATGT
Done.