Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6704.1
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: 10293
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:313 original size:115 final size:115
Alignment explanation
Indices: 111--339 Score: 449
Period size: 115 Copynumber: 2.0 Consensus size: 115
101 AGTTAACAAG
*
111 AATGGTTTCAGATAAATTTGTAATCCAAATGCAAGCAAAATAGAATAAGAAAATCCCATGGGAGT
1 AATGGTTTCAAATAAATTTGTAATCCAAATGCAAGCAAAATAGAATAAGAAAATCCCATGGGAGT
176 GGACGGATGCAAAACAACATGTTCACAACCATGCAAACAAACTAATGTAA
66 GGACGGATGCAAAACAACATGTTCACAACCATGCAAACAAACTAATGTAA
226 AATGGTTTCAAATAAATTTGTAATCCAAATGCAAGCAAAATAGAATAAGAAAATCCCATGGGAGT
1 AATGGTTTCAAATAAATTTGTAATCCAAATGCAAGCAAAATAGAATAAGAAAATCCCATGGGAGT
291 GGACGGATGCAAAACAACATGTTCACAACCATGCAAACAAACTAATGTA
66 GGACGGATGCAAAACAACATGTTCACAACCATGCAAACAAACTAATGTA
340 CTCGTTAATG
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 113 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (115 bp):
AATGGTTTCAAATAAATTTGTAATCCAAATGCAAGCAAAATAGAATAAGAAAATCCCATGGGAGT
GGACGGATGCAAAACAACATGTTCACAACCATGCAAACAAACTAATGTAA
Found at i:2563 original size:16 final size:15
Alignment explanation
Indices: 2544--2596 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
2534 TTTAACTTGA
2544 TTTTTTTTTGCTCACC
1 TTTTTTTTTGCTCA-C
2560 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
2575 TTTTTTTTT--TCAC
1 TTTTTTTTTGCTCAC
2588 TTTTTTTTT
1 TTTTTTTTT
2597 AAATTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 11 0.31
15 9 0.26
16 13 0.37
17 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:2567 original size:31 final size:29
Alignment explanation
Indices: 2521--2598 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 29
2511 CTCGCAAGAC
*
2521 TTTTCACTTTTTTTTTAACTTGATTTTTT
1 TTTTCACTTTTTTTTTAACTCGATTTTTT
*
2550 TTTGCTCACCTTTTTTTTT-GCTCGATTTTTT
1 TTT--TCA-CTTTTTTTTTAACTCGATTTTTT
2581 TTTTCACTTTTTTTTTAA
1 TTTTCACTTTTTTTTTAA
2599 ATTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
28 10 0.24
29 6 0.14
31 16 0.38
32 10 0.24
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.69
Consensus pattern (29 bp):
TTTTCACTTTTTTTTTAACTCGATTTTTT
Found at i:2578 original size:15 final size:15
Alignment explanation
Indices: 2528--2583 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
2518 GACTTTTCAC
* *
2528 TTTTTTTTTAACTTGA
1 TTTTTTTTT-GCTCGA
2544 TTTTTTTTTGCTC-A
1 TTTTTTTTTGCTCGA
2558 CCTTTTTTTTTGCTCGA
1 --TTTTTTTTTGCTCGA
2575 TTTTTTTTT
1 TTTTTTTTT
2584 TCACTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 11 0.31
16 22 0.63
17 1 0.03
ACGTcount: A:0.09, C:0.12, G:0.07, T:0.71
Consensus pattern (15 bp):
TTTTTTTTTGCTCGA
Found at i:2591 original size:13 final size:13
Alignment explanation
Indices: 2544--2611 Score: 50
Period size: 16 Copynumber: 4.9 Consensus size: 13
2534 TTTAACTTGA
2544 TTTTTTTTTGCTCACC
1 TTTTTTTTT--TCA-C
2560 TTTTTTTTTGCTCGA-
1 TTTTTTTTT--TC-AC
2575 TTTTTTTTTTCAC
1 TTTTTTTTTTCAC
* *
2588 -TTTTTTTTTAAA
1 TTTTTTTTTTCAC
2600 TTTTTTTTTTCA
1 TTTTTTTTTTCA
2612 ATCAATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
12 11 0.24
13 12 0.26
15 9 0.20
16 13 0.28
17 1 0.02
ACGTcount: A:0.10, C:0.13, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTTTTTTTTCAC
Found at i:2620 original size:25 final size:25
Alignment explanation
Indices: 2574--2621 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2564 TTTTTGCTCG
* ***
2574 ATTTTTTTTTTCACTTTTTTTTTAA
1 ATTTTTTTTTTCAATCAATTTTTAA
2599 ATTTTTTTTTTCAATCAATTTTT
1 ATTTTTTTTTTCAATCAATTTTT
2622 TTTTCGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (25 bp):
ATTTTTTTTTTCAATCAATTTTTAA
Found at i:2631 original size:13 final size:13
Alignment explanation
Indices: 2561--2648 Score: 51
Period size: 12 Copynumber: 6.7 Consensus size: 13
2551 TTGCTCACCT
*
2561 TTTTTTTTGCTCGAT
1 TTTTTTTT--TCGAA
*
2576 TTTTTTTTTC-AC
1 TTTTTTTTTCGAA
*
2588 TTTTTTTTT-AAA
1 TTTTTTTTTCGAA
*
2600 TTTTTTTTTTCAATCAA
1 -TTTTTTTTTC---GAA
2617 TTTTTTTTTCGAA
1 TTTTTTTTTCGAA
2630 -TTTTTTTT-G-A
1 TTTTTTTTTCGAA
2640 TTTTTTTTT
1 TTTTTTTTT
2649 GTTACTCCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
10 1 0.02
11 9 0.15
12 19 0.31
13 13 0.21
15 8 0.13
16 10 0.16
17 2 0.03
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.74
Consensus pattern (13 bp):
TTTTTTTTTCGAA
Found at i:2647 original size:11 final size:11
Alignment explanation
Indices: 2616--2649 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2606 TTTTCAATCA
2616 ATTTTTTTTTCG
1 ATTTTTTTTT-G
*
2628 AATTTTTTTTG
1 ATTTTTTTTTG
2639 ATTTTTTTTTG
1 ATTTTTTTTTG
2650 TTACTCCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:3905 original size:45 final size:45
Alignment explanation
Indices: 3841--3930 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
3831 GTCAGCCACC
* *
3841 GATGCATGTAGGTGGATATTCATGCACTCTTCCATTCATTGTATT
1 GATGCATGTAAGTGAATATTCATGCACTCTTCCATTCATTGTATT
*
3886 GATGCATGTAAGTGAATATTCATGCATTCTTCCATTCATTGTATT
1 GATGCATGTAAGTGAATATTCATGCACTCTTCCATTCATTGTATT
3931 AAATCATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (45 bp):
GATGCATGTAAGTGAATATTCATGCACTCTTCCATTCATTGTATT
Found at i:4329 original size:10 final size:10
Alignment explanation
Indices: 4316--4353 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
4306 AAGAAGCTAA
4316 ATTGAGCTCG
1 ATTGAGCTCG
4326 ATTGAGCT-G
1 ATTGAGCTCG
4335 ACTTGAGCTCG
1 A-TTGAGCTCG
*
4346 AGTGAGCT
1 ATTGAGCT
4354 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:4340 original size:20 final size:20
Alignment explanation
Indices: 4317--4354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4307 AGAAGCTAAA
*
4317 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
4337 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
4355 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:6410 original size:21 final size:22
Alignment explanation
Indices: 6374--6425 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
6364 TCACAACTCT
6374 TTTTCTTTTCTCTTTCATTTTC-
1 TTTTC-TTTCTCTTTCATTTTCA
*
6396 TTTTCTTTCTTTTTCATTTTCA
1 TTTTCTTTCTCTTTCATTTTCA
*
6418 CTTTCTTT
1 TTTTCTTT
6426 TTCCAATCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTCTTTCTCTTTCATTTTCA
Found at i:7553 original size:30 final size:30
Alignment explanation
Indices: 7517--7576 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
7507 TTCTCGAGCC
7517 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
7547 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
7577 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:7709 original size:20 final size:20
Alignment explanation
Indices: 7686--7733 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
7676 AGCTCCGTCC
7686 AGCTCAACTCAGCTCATTTA
1 AGCTCAACTCAGCTCATTTA
*** * *
7706 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTA
7726 AGCTCAAC
1 AGCTCAAC
7734 CGAGCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTA
Done.