Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2449
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: 18354
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Found at i:4480 original size:27 final size:26
Alignment explanation
Indices: 4432--4485 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
4422 TAACACAAGT
*
4432 TAGTCATTTACACACGAGGGGCAAAA
1 TAGTCATTTACACACGAAGGGCAAAA
* *
4458 TAGTCATTTAACACCCTAAGGGCAAAA
1 TAGTCATTT-ACACACGAAGGGCAAAA
4485 T
1 T
4486 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (26 bp):
TAGTCATTTACACACGAAGGGCAAAA
Found at i:4493 original size:27 final size:27
Alignment explanation
Indices: 4450--4506 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
4440 TACACACGAG
*
4450 GGGCAAAATAGTCATTTAACACCC-TAA
1 GGGCAAAATAGTAATTTAAC-CCCATAA
* *
4477 GGGCAAAATGGTAATTTTACCCCATAA
1 GGGCAAAATAGTAATTTAACCCCATAA
4504 GGG
1 GGG
4507 TATCTCGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
GGGCAAAATAGTAATTTAACCCCATAA
Found at i:4536 original size:27 final size:27
Alignment explanation
Indices: 4486--4763 Score: 269
Period size: 27 Copynumber: 10.4 Consensus size: 27
4476 AGGGCAAAAT
* * * * *
4486 GGTAATTTTACCCCATAAGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
4513 GGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
4540 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * **
4567 GATAATTCTATCCTACAAGCTTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
4594 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
4621 AATAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
4648 GG-AA-T-T--CCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
4670 AGTATTTCTACCCTACAAGGGCATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
4697 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
4724 AATAATTCTACCTACTACAGGGGTATTTC
1 GGTAATTCTACC--CTACAGGGGTATTTC
4753 GGTAATTCTAC
1 GGTAATTCTAC
4764 AACTTATCCA
Statistics
Matches: 201, Mismatches: 43, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
22 14 0.07
23 1 0.00
24 2 0.01
25 2 0.01
26 2 0.01
27 157 0.78
29 23 0.11
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:4576 original size:54 final size:54
Alignment explanation
Indices: 4486--4763 Score: 296
Period size: 54 Copynumber: 5.2 Consensus size: 54
4476 AGGGCAAAAT
* * * * ** * *
4486 GGTAATTTTACCCCATAAGGGTATCTCGGTAATTCTACCTTACAGGAGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTC
* * * * **
4540 GGTATTTCTACCCTACAAGGGTATTTCGATAATTCTATCCTACAAGCTTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTC
* * *
4594 GGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTC
* * * *
4648 GG-AA-T-T--CCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGCATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTC
* *
4697 GGTAATTCTACCCTATAGGGGTATTTCAATAATTCTACCTACTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACC--CTACAGGGGTATTTC
4753 GGTAATTCTAC
1 GGTAATTCTAC
4764 AACTTATCCA
Statistics
Matches: 184, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
49 38 0.21
50 2 0.01
51 2 0.01
52 2 0.01
53 2 0.01
54 114 0.62
56 24 0.13
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (54 bp):
GGTAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTACAGGGGTATTTC
Found at i:4696 original size:76 final size:76
Alignment explanation
Indices: 4577--4722 Score: 220
Period size: 76 Copynumber: 1.9 Consensus size: 76
4567 GATAATTCTA
* * * *
4577 TCCTACAAGCTTATTTCGGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTATAGGGG
1 TCCTACAAGCGTATTTCAGTAATTCTACCCTACAAGGGCATTTCAATAATTCTACCCTATAGGGG
4642 TATTTTGGAAT
66 TATTTTGGAAT
* * **
4653 TCCTACAAGGGTATTTCAGTATTTCTACCCTACAAGGGCATTTCGGTAATTCTACCCTATAGGGG
1 TCCTACAAGCGTATTTCAGTAATTCTACCCTACAAGGGCATTTCAATAATTCTACCCTATAGGGG
4718 TATTT
66 TATTT
4723 CAATAATTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (76 bp):
TCCTACAAGCGTATTTCAGTAATTCTACCCTACAAGGGCATTTCAATAATTCTACCCTATAGGGG
TATTTTGGAAT
Found at i:4696 original size:103 final size:105
Alignment explanation
Indices: 4551--4765 Score: 312
Period size: 103 Copynumber: 2.1 Consensus size: 105
4541 GTATTTCTAC
* **
4551 CCTACAAGGGTATTTCGATAATTCTATCCTACAAGCTTATTTCGGTAATTCTACCCTACAGGGGT
1 CCTACAAGGGTATTTCGATAATTCTACCCTACAAGCGCATTTCGGTAATTCTACCCTACAGGGGT
* *
4616 ATTTCAATAATTCTACC-CTATAGGGGTATTTTGG-AATT
66 ATTTCAATAATTCTACCACTACAGGGGTATTTCGGTAATT
* * *
4654 CCTACAAGGGTATTTC-AGTATTTCTACCCTACAAGGGCATTTCGGTAATTCTACCCTATAGGGG
1 CCTACAAGGGTATTTCGA-TAATTCTACCCTACAAGCGCATTTCGGTAATTCTACCCTACAGGGG
4718 TATTTCAATAATTCTACCTACTACAGGGGTATTTCGGTAATT
65 TATTTCAATAATTCTACC-ACTACAGGGGTATTTCGGTAATT
4760 -CTACAA
1 CCTACAA
4766 CTTATCCACT
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
102 1 0.01
103 74 0.74
105 21 0.21
106 4 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (105 bp):
CCTACAAGGGTATTTCGATAATTCTACCCTACAAGCGCATTTCGGTAATTCTACCCTACAGGGGT
ATTTCAATAATTCTACCACTACAGGGGTATTTCGGTAATT
Found at i:6564 original size:40 final size:40
Alignment explanation
Indices: 6466--6634 Score: 225
Period size: 39 Copynumber: 4.3 Consensus size: 40
6456 TCCTCGTTCA
* * * *
6466 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
6505 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
6545 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
* * * *
6584 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
*
6624 AAGGCCTTCGG
1 AATGCCTTCGG
6635 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
39 72 0.62
40 45 0.38
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCACG
Found at i:6567 original size:79 final size:79
Alignment explanation
Indices: 6464--6634 Score: 227
Period size: 79 Copynumber: 2.2 Consensus size: 79
6454 GCTCCTCGTT
* * *
6464 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGG
1 CAAATGCCTTCGGGACATAACCCGGATTTAAT-ACTCACACGAATGCCTTCGGGACATAACCCGG
6528 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * * *
6543 CGAATGCCTTCGGGACTTAACCCGGATTTAATACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATACTCACACGAATGCCTTCGGGACATAACCCGGA
** *
6608 TTTAGTATCTCGCA
66 TTTAACAACTCGCA
*
6622 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
6635 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
78 7 0.09
79 72 0.91
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATACTCACACGAATGCCTTCGGGACATAACCCGGA
TTTAACAACTCGCA
Found at i:6647 original size:40 final size:39
Alignment explanation
Indices: 6466--6687 Score: 216
Period size: 39 Copynumber: 5.6 Consensus size: 39
6456 TCCTCGTTCA
* * * * *
6466 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCACG
* *
6505 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAA-TACTCGCACG
6545 AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCACG
* *
6584 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATA-CTCGCACG
* ** * * *
6624 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAAT-AC-TCGCACG
* *
6664 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
6688 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 75 0.47
40 75 0.47
41 9 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATACTCGCACG
Found at i:6647 original size:79 final size:79
Alignment explanation
Indices: 6464--6687 Score: 218
Period size: 79 Copynumber: 2.8 Consensus size: 79
6454 GCTCCTCGTT
* * * * * * * * *
6464 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAAGGCCTTCGGGACTTAACCCGGATATAATCACTCGCACAATGCCTTCGGGACTTAACCCGGA
6529 TTTAACAACTCGCA
66 TTTAACAACTCGCA
* * *
6543 CGAATGCCTTCGGGACTTAACCCGGATTTAAT-ACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAAGGCCTTCGGGACTTAACCCGGATATAATCACTCGCAC-AATGCCTTCGGGACTTAACCCGG
** *
6607 ATTTAGTATCTCGCA
65 ATTTAACAACTCGCA
** * * * *
6622 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAAGGCCTTCGGGA-CTTAACCCGGATATAATCAC-TCGCACAATGCCTTCGGGACTTAACCCG
6686 GA
64 GA
6688 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 10 0.08
79 83 0.68
80 24 0.20
81 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAAGGCCTTCGGGACTTAACCCGGATATAATCACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAACTCGCA
Found at i:6696 original size:41 final size:41
Alignment explanation
Indices: 6619--6696 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
6609 TTAGTATCTC
* * *
6619 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
6660 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
6697 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:14432 original size:40 final size:40
Alignment explanation
Indices: 14247--14418 Score: 231
Period size: 39 Copynumber: 4.3 Consensus size: 40
14237 GCTCCTCGTT
* * * * *
14247 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
14287 C-AATGCCTTCGGGACATAACCCGGATTTAA-AACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
14325 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* *
14365 CGAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 C-AAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
14406 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
14419 ATCTTAGTCC
Statistics
Matches: 120, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
38 8 0.07
39 54 0.45
40 21 0.17
41 37 0.31
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Done.