Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2883
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: 40620
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Found at i:4934 original size:40 final size:40
Alignment explanation
Indices: 4860--5082 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
4850 GCTCCTCGTT
*
4860 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
4899 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
4939 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
4979 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
5018 CAAAT-CCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
5058 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5083 CATCATTCAA
Statistics
Matches: 162, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
37 2 0.01
38 5 0.03
39 51 0.31
40 99 0.61
41 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:5016 original size:79 final size:79
Alignment explanation
Indices: 4860--5082 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 79
4850 GCTCCTCGTT
* * *
4860 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
*
4924 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
*
4939 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGG
*
5003 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* * * * * *
5018 CAAAT-CCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACCAATGCCTTCGGGACTTAGCCCG
5081 GA
64 GA
5083 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
77 3 0.02
78 32 0.25
79 53 0.42
80 36 0.29
81 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:13031 original size:78 final size:80
Alignment explanation
Indices: 12867--13037 Score: 265
Period size: 78 Copynumber: 2.2 Consensus size: 80
12857 GCTCCTCGTT
* *
12867 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
12932 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* * *
12947 CAAATGCCTTCGGGACTTAACCCGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
13010 AATTAGTATCTCGCA
66 AATTAGTAACTCGCA
13025 CAAATGCCTTCGG
1 CAAATGCCTTCGG
13038 ATTTAGTCCG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 35 0.42
79 25 0.30
80 24 0.29
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAACCCGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:13073 original size:78 final size:78
Alignment explanation
Indices: 12867--13089 Score: 252
Period size: 78 Copynumber: 2.8 Consensus size: 78
12857 GCTCCTCGTT
* * * * *
12867 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCC-GATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
*
12932 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* * *
12947 CAAATGCCTTCGGGACTTAACCCGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGGA
*
13011 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
13025 CAAATGCCTTC-GGATTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTA-ACCCGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCGG
13089 A
64 A
13090 CATCATTCAA
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
77 6 0.05
78 55 0.45
79 38 0.31
80 24 0.20
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAACCCGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:13089 original size:40 final size:40
Alignment explanation
Indices: 12867--13089 Score: 276
Period size: 40 Copynumber: 5.7 Consensus size: 40
12857 GCTCCTCGTT
* *
12867 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
12907 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
12947 CAAATGCCTTCGGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
12986 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
13025 CAAATGCCTTC-GGATTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC-TCGCA
13065 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
13090 CATCATTCAA
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 9 0.06
39 71 0.44
40 80 0.50
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:17293 original size:19 final size:19
Alignment explanation
Indices: 17271--17311 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17261 ATTTCATTTC
17271 ATTCATTT-CATTTAGATTA
1 ATTCATTTGCATTTAG-TTA
*
17290 ATTCATTTGTATTTAGTTA
1 ATTCATTTGCATTTAGTTA
17309 ATT
1 ATT
17312 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTCATTTGCATTTAGTTA
Found at i:18685 original size:314 final size:314
Alignment explanation
Indices: 18116--18746 Score: 1172
Period size: 314 Copynumber: 2.0 Consensus size: 314
18106 AAAGTCTAGA
* ** * *
18116 ACCATAAAATCTGTTGGGATGATAAAGTGATGCACTTTGGCTAACATATCTTCCAATACTCCTTT
1 ACCATAAAATCTATTGGGATGATAAAACGACGCACTTTGGCTAACACATCTTCCAATACTCCTTT
*
18181 CGGATGCACTGAGGATCTTTCGACCAACTGTAGTGTTATCTAGGTATTTTTGAGGTCCCCTAACC
66 CGGATGCACTGAGGATCTTTCGACCAACTGTAGTGTTATCTAAGTATTTTTGAGGTCCCCTAACC
18246 CAAGTTATTCAAAAATGGATAAAGGCAATAAATTAAGACTAGCTTCTACATCACATAGAGCTTTA
131 CAAGTTATTCAAAAATGGATAAAGGCAATAAATTAAGACTAGCTTCTACATCACATAGAGCTTTA
18311 TTAAAGTGAATGCTCTCTATCTCTATGGGAATAGTAAAACTTCATGGTCTTTCAATTTCTGAGGA
196 TTAAAGTGAATGCTCTCTATCTCTATGGGAATAGTAAAACTTCATGGTCTTTCAATTTCTGAGGA
18376 ACTTGTCTCAAAATAATAACACTATAGGAAGCACTTATATTAACTTGTTTGCCT
261 ACTTGTCTCAAAATAATAACACTATAGGAAGCACTTATATTAACTTGTTTGCCT
18430 ACCATAAAATCTATTGGGATGATAAAACGACGCACTTTGGCTAACACATCTTCCAATACTCCTTT
1 ACCATAAAATCTATTGGGATGATAAAACGACGCACTTTGGCTAACACATCTTCCAATACTCCTTT
*
18495 CGGATGCACTGAGGATCTTTCGACCAACTGTAGTGTTATCTAAGTATTTTTTAGGTCCCCTAACC
66 CGGATGCACTGAGGATCTTTCGACCAACTGTAGTGTTATCTAAGTATTTTTGAGGTCCCCTAACC
* * *
18560 CAAGTTATTCAAAAATGGGTAAAGGCGATAAATTAATACTAGCTTCTACATCACATAGAGCTTTA
131 CAAGTTATTCAAAAATGGATAAAGGCAATAAATTAAGACTAGCTTCTACATCACATAGAGCTTTA
18625 TTAAAGTGAATGCTCTCTATCTCTATGGGAATAGTAAAACTTCATGGTCTTTCAATTTCTGAGGA
196 TTAAAGTGAATGCTCTCTATCTCTATGGGAATAGTAAAACTTCATGGTCTTTCAATTTCTGAGGA
18690 ACTTGTCTCAAAATAATAACACTATAGGAAGCACTTATATTAACTTGTTTGCCT
261 ACTTGTCTCAAAATAATAACACTATAGGAAGCACTTATATTAACTTGTTTGCCT
18744 ACC
1 ACC
18747 TTAATTTTCC
Statistics
Matches: 307, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
314 307 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (314 bp):
ACCATAAAATCTATTGGGATGATAAAACGACGCACTTTGGCTAACACATCTTCCAATACTCCTTT
CGGATGCACTGAGGATCTTTCGACCAACTGTAGTGTTATCTAAGTATTTTTGAGGTCCCCTAACC
CAAGTTATTCAAAAATGGATAAAGGCAATAAATTAAGACTAGCTTCTACATCACATAGAGCTTTA
TTAAAGTGAATGCTCTCTATCTCTATGGGAATAGTAAAACTTCATGGTCTTTCAATTTCTGAGGA
ACTTGTCTCAAAATAATAACACTATAGGAAGCACTTATATTAACTTGTTTGCCT
Found at i:24469 original size:20 final size:19
Alignment explanation
Indices: 24417--24474 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
24407 TCATTTTTCC
*
24417 AAGTGGTATCGATACCAGTTA
1 AAGTAGTATCGATACC--TTA
*
24438 AAGTAATATCGATACCTTA
1 AAGTAGTATCGATACCTTA
*
24457 ATGTCAGTATCGATACCT
1 AAGT-AGTATCGATACCT
24475 ACGGACATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.19
20 12 0.38
21 14 0.44
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (19 bp):
AAGTAGTATCGATACCTTA
Found at i:32928 original size:27 final size:26
Alignment explanation
Indices: 32911--32980 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
32901 ATATTAAGTC
32911 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
32938 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
32966 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
32981 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:32974 original size:28 final size:28
Alignment explanation
Indices: 32911--33008 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
32901 ATATTAAGTC
*
32911 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
32938 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
32966 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
32995 CGCACACTTAGTGC
1 CGCACACTTAGTGC
33009 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33472 original size:12 final size:12
Alignment explanation
Indices: 33455--33481 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33445 TGGGCATACT
33455 TATGTATATATA
1 TATGTATATATA
33467 TATGTATATATA
1 TATGTATATATA
33479 TAT
1 TAT
33482 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Done.