Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3571
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: 28668
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:8791 original size:40 final size:40
Alignment explanation
Indices: 8690--9034 Score: 457
Period size: 40 Copynumber: 8.6 Consensus size: 40
8680 GCCCTCGTCA
* * * * *
8690 AATG-CTTCGGGACATAGCCCGG-TTTAGTAACTCACACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
8728 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
8767 ACTGCCTTCGGGACTTAACACCGGATTTAATAACTCGCACAG
1 AATGCCTTCGGGACTTAAC-CCGGATTTAATAACTCGCAC-G
*
8809 AATGCCTTCGGATACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGG-GACTTAACCCGGATTTAATAACTCGCACG
8850 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
8890 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCG-CACG
8931 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
8971 AATGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
9011 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9035 CAGCATTCAA
Statistics
Matches: 279, Mismatches: 18, Indels: 18
0.89 0.06 0.06
Matches are distributed among these distances:
38 4 0.01
39 37 0.13
40 141 0.51
41 60 0.22
42 30 0.11
43 7 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:8817 original size:81 final size:80
Alignment explanation
Indices: 8690--9034 Score: 457
Period size: 81 Copynumber: 4.3 Consensus size: 80
8680 GCCCTCGTCA
* * * * * *
8690 AATG-CTTCGGGACATAGCCCGG-TTTAGTAACTCACACAAATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
*
8753 TTAACAACTCGCAC-
66 TTAATAACTCGCACG
* *
8767 ACTGCCTTCGGGACTTAACACCGGATTTAATAACTCGCACAGAATGCCTTCGGATACTTAACCCG
1 AATGCCTTCGGGACTTAAC-CCGGATTTAATAACTCGCAC-GAATGCCTTCGG-GACTTAACCCG
8832 GATTTAATAACTCGCACG
63 GATTTAATAACTCGCACG
8850 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
8915 TTAATAACTCGCCACG
66 TTAATAACTCG-CACG
*
8931 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA
* * * *
8995 TATATTCACTTAGCAC-
65 TTTAATAAC-TCGCACG
* *
9011 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
9035 CAGCATTCAA
Statistics
Matches: 241, Mismatches: 18, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
77 3 0.01
78 12 0.05
79 4 0.02
80 62 0.26
81 95 0.39
82 47 0.20
83 18 0.07
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAATAACTCGCACG
Found at i:8869 original size:122 final size:121
Alignment explanation
Indices: 8690--9034 Score: 452
Period size: 122 Copynumber: 2.9 Consensus size: 121
8680 GCCCTCGTCA
* * * * * *
8690 AATG-CTTCGGGACATAGCCCGG-TTTAGTAACTCACACAAATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
*
8753 TTAACAACTCGCAC-ACTGCCTTCGGGACTTAACACCGGATTTAATAACTCG-CACAG
66 TTAACAACTCGCACGAATGCCTTCGGGACTTAAC-CCGGATTTAATAACTCGCCAC-G
*
8809 AATGCCTTCGGATACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGG-GACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
*
8874 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCCACG
65 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCCACG
*
8931 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA
* * * * *
8995 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
65 TTTA-ACAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
9035 CAGCATTCAA
Statistics
Matches: 201, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
119 4 0.02
120 9 0.04
121 83 0.41
122 84 0.42
123 21 0.10
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (121 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCCACG
Found at i:9018 original size:121 final size:122
Alignment explanation
Indices: 8690--9034 Score: 427
Period size: 121 Copynumber: 2.9 Consensus size: 122
8680 GCCCTCGTCA
* * * * * *
8690 AATG-CTTCGG-GACATAGCCCGG-TTTAGTAACTCACACAAATGCCTTCGGGACATAACCCGGA
1 AATGCCTTCGGAGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
* * * **
8752 TTTAACAACTCGCAC-ACTGCCTTCGGGACTTAACACCGGATTTAATAACTCGCACAG
66 TATAATAACTAGCACGAAAGCCTTCGGGACTTAAC-CCGGATTTAATAACTCGCACAG
*
8809 AATGCCTTCGGATACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGAGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
* * *
8874 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGC-CACG
66 TATAATAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACA-G
*
8931 AATGCCTTCGG-GACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGATCTTAATCCGG
1 AATGCCTTCGGAGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGG
* * *
8994 ATATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
65 ATATAATAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
9035 CAGCATTCAA
Statistics
Matches: 202, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
119 4 0.02
120 9 0.04
121 86 0.43
122 85 0.42
123 18 0.09
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (122 bp):
AATGCCTTCGGAGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
TATAATAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACAG
Found at i:16944 original size:40 final size:40
Alignment explanation
Indices: 16859--17200 Score: 455
Period size: 40 Copynumber: 8.6 Consensus size: 40
16849 TCCTCGTTCA
* * * *
16859 AATGCCTTC-GGACATTAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGAC-TTAACCCGGATTTAATAACTCGCACG
* *
16898 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
16938 ACTGCCTTCGGGACTTAACCCGGATTTAAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTT-AATAACTCGCACG
*
16979 AATGCCTTCGGGACTTAACCCGAATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
17019 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
17059 AATGCCTTCGGGACCTTAACCC-GATTT-A-AACTCGCACG
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCGCACG
17097 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
17137 AATGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
17177 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
17201 CAGCATTCAA
Statistics
Matches: 273, Mismatches: 20, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
37 8 0.03
38 28 0.10
39 33 0.12
40 151 0.55
41 53 0.19
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:16999 original size:81 final size:80
Alignment explanation
Indices: 16859--17161 Score: 440
Period size: 81 Copynumber: 3.8 Consensus size: 80
16849 TCCTCGTTCA
* * * * *
16859 AATGCCTTC-GGACATTAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGA-CATAACCCGG
1 AATGCCTTCGGGAC-TTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACCTTAACCCGG
16921 ATTTAACAACTCGCACG
65 ATTTAA-AACTCGCACG
* *
16938 ACTGCCTTCGGGACTTAACCCGGATTTAAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGA
1 AATGCCTTCGGGACTTAACCCGGATTT-AATAACTCGCACGAATGCCTTCGGGACCTTAACCCGG
17002 ATTTAATAACTCGCACG
65 ATTTAA-AACTCGCACG
17019 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACCTTAACCC-GA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACCTTAACCCGGA
17083 TTT-AAACTCGCACG
66 TTTAAAACTCGCACG
* *
17097 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACCTTAACCCGGA
17161 T
66 T
17162 ATATTCACTT
Statistics
Matches: 207, Mismatches: 12, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
77 10 0.05
78 62 0.30
79 20 0.10
80 44 0.21
81 71 0.34
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACCTTAACCCGGA
TTTAAAACTCGCACG
Found at i:17146 original size:118 final size:120
Alignment explanation
Indices: 16859--17200 Score: 448
Period size: 118 Copynumber: 2.9 Consensus size: 120
16849 TCCTCGTTCA
* * * * *
16859 AATGCCTTC-GGACATTAGCCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGA
1 AATGCCTTCGGGAC-TTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
*
16922 TTTAACAACTCGCACGACTGCCTTCGGGACTTAACCCGGATTTAAATAACTCGCACG
65 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT-AATAACTCGCACG
*
16979 AATGCCTTCGGGACTTAACCCGAATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
*
17044 TTAATAACTCGCACGAATGCCTTCGGGACCTTAACCC-GATTT-A-AACTCGCACG
66 TTAACAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTAATAACTCGCACG
*
17097 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA
* * * * *
17161 TATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
65 TTTA-ACAAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
17201 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
117 10 0.05
118 87 0.44
119 6 0.03
120 29 0.15
121 59 0.30
122 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:19689 original size:44 final size:45
Alignment explanation
Indices: 19559--19691 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
19549 AGTGGGCTCT
19559 CTGATA-GAAA-GTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGA-CATGGTTGAAAGATACCATGGCAAC
19603 CTGATATGAAATGTGTAAGACATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACATGGTTGAAAGATACCATGGCAAC
*
19648 CTGATATGAAATGTTTAAGACA-GGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACATGGTTGAAAGATACCATGGCAAC
19692 GTGACGGGGA
Statistics
Matches: 86, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
44 28 0.33
45 50 0.58
46 8 0.09
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (45 bp):
CTGATATGAAATGTGTAAGACATGGTTGAAAGATACCATGGCAAC
Found at i:20563 original size:16 final size:16
Alignment explanation
Indices: 20542--20583 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
20532 TCTTCCGCCA
20542 AGCTTCCAATCCAACG
1 AGCTTCCAATCCAACG
*
20558 AGCTTCTAATCCAACG
1 AGCTTCCAATCCAACG
20574 AGCTTCCAAT
1 AGCTTCCAAT
20584 TTACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.33, G:0.12, T:0.24
Consensus pattern (16 bp):
AGCTTCCAATCCAACG
Found at i:22037 original size:38 final size:38
Alignment explanation
Indices: 21967--22043 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
21957 CATTCAAAGT
21967 GGACCCAATTTACAACCTAGGCCAAAATTACCATTTTGC
1 GGACCCAATTTACAACCTAGG-CAAAATTACCATTTTGC
*
22006 GGACTCAATTTAACAACCTAGG-AAAATTACCATTTTGC
1 GGACCCAATTT-ACAACCTAGGCAAAATTACCATTTTGC
22044 CCTAACTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 16 0.44
39 10 0.28
40 10 0.28
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (38 bp):
GGACCCAATTTACAACCTAGGCAAAATTACCATTTTGC
Found at i:27377 original size:12 final size:12
Alignment explanation
Indices: 27360--27385 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27350 CATAACAATG
27360 ATATTATTGCAT
1 ATATTATTGCAT
27372 ATATTATTGCAT
1 ATATTATTGCAT
27384 AT
1 AT
27386 TGAAACTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATTATTGCAT
Done.