Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1900
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, 729
Length: 1216
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Found at i:104 original size:21 final size:21
Alignment explanation
Indices: 80--122 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
70 ATAGTTACCT
80 ATCCATAACCCTTAACCCCTA
1 ATCCATAACCCTTAACCCCTA
* *
101 ATCCTTAACCTTTAACCCCTA
1 ATCCATAACCCTTAACCCCTA
122 A
1 A
123 CCCCTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (21 bp):
ATCCATAACCCTTAACCCCTA
Found at i:351 original size:82 final size:81
Alignment explanation
Indices: 256--413 Score: 221
Period size: 82 Copynumber: 1.9 Consensus size: 81
246 TAACCCCTAA
* *
256 CCCTAACTACTAACCCCTAAACCTTATTTAATATACAAATTAAAA-ATATTAATTAATCAAAACC
1 CCCTAACTACTAACCCCTAAACCTTATTTAATAT--AAATTAAAACACACTAATTAATCAAAACC
*
320 CTAAATCCTAACCCAAAT
64 CTAAAGCCTAACCCAAAT
* * *
338 CCCTAACCT-CTAACCCCTAAATCTTATTTAATATAAATTAAAACACACTGATTAATCTAAACCC
1 CCCTAA-CTACTAACCCCTAAACCTTATTTAATATAAATTAAAACACACTAATTAATCAAAACCC
402 TAAAGCCTAACC
65 TAAAGCCTAACC
414 TGACACTGAA
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
80 9 0.13
81 27 0.40
82 30 0.44
83 2 0.03
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (81 bp):
CCCTAACTACTAACCCCTAAACCTTATTTAATATAAATTAAAACACACTAATTAATCAAAACCCT
AAAGCCTAACCCAAAT
Found at i:434 original size:81 final size:81
Alignment explanation
Indices: 258--413 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
248 ACCCCTAACC
* * *
258 CTAA-CTACTAACCCCTAAACCTTATTTAATATACAAATTAAAAATATTAATTAATCAAAACCCT
1 CTAACCTA-TAACCCCTAAATCTTATTTAATATA-AAATTAAAAACACTAATTAATCAAAACCCT
* *
322 AAATCCTAACCCAAATCC
64 AAAGCCTAACCCAAATCA
* * *
340 CTAACCTCTAACCCCTAAATCTTATTTAATAT-AAATTAAAACACACTGATTAATCTAAACCCTA
1 CTAACCTATAACCCCTAAATCTTATTTAATATAAAATTAAAA-ACACTAATTAATCAAAACCCTA
404 AAGCCTAACC
65 AAGCCTAACC
414 TGACACTGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
80 9 0.14
81 27 0.42
82 27 0.42
83 2 0.03
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.28
Consensus pattern (81 bp):
CTAACCTATAACCCCTAAATCTTATTTAATATAAAATTAAAAACACTAATTAATCAAAACCCTAA
AGCCTAACCCAAATCA
Found at i:601 original size:26 final size:26
Alignment explanation
Indices: 580--629 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
570 AACAAATATT
580 TTTCTAAGT-T-ATTTATTTCAAATTA
1 TTTCTAAGTCTGA-TTATTTCAAATTA
*
605 TTTCTACGTCTGATTATTTCAAATT
1 TTTCTAAGTCTGATTATTTCAAATT
630 TATCCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 13 0.59
27 1 0.05
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTCTAAGTCTGATTATTTCAAATTA
Found at i:777 original size:41 final size:41
Alignment explanation
Indices: 720--980 Score: 328
Period size: 41 Copynumber: 6.4 Consensus size: 41
710 ATAAAATATT
720 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCTC-GAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCT-AAAGCTCTGAGCA
*
761 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCA
* * *
802 CTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGATCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCA
* * * * * *
843 TTAGCGTCGCTTCTCCAAAAATGCTGCTAAAGCTCTGAACA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCA
* * *
884 TTAGCGGTGATTTTTCAAAAACGCCGCTAAATCTCTGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCA
* * * *
925 TTAGCGGCGCTTATCCAAAAACGCCGCTAAAGACT-AGCGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG-CTCTGAGCA
*
966 TTAGCGGCGTTTTTT
1 TTAGCGGCGCTTTTT
981 ATTTAGCGGC
Statistics
Matches: 189, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
40 6 0.03
41 181 0.96
42 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGCTCTGAGCA
Found at i:942 original size:123 final size:123
Alignment explanation
Indices: 720--974 Score: 361
Period size: 123 Copynumber: 2.1 Consensus size: 123
710 ATAAAATATT
* * * *
720 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAAGCTCGAGCATTAGCGGCGCTTTTTCAAAAACGC
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAAGCTCGAACATTAGCGGCGATTTTTCAAAAACGC
*
785 CGCTAAAGATCTGAGCACTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGATCT-GAGCA
66 CGCTAAAGATCTGAGCACTAGCGGCGCTTATCCAAAAACGCCGCTAAAGA-CTAGAGCA
* * * *
843 TTAGCGTCGCTTCTCCAAAAATGCTGCT-AAAGCTCTGAACATTAGCGGTGATTTTTCAAAAACG
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAAGCTC-GAACATTAGCGGCGATTTTTCAAAAACG
** * *
907 CCGCTAAATCTCTGAGCATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGACTAGCGCA
65 CCGCTAAAGATCTGAGCACTAGCGGCGCTTATCCAAAAACGCCGCTAAAGACTAGAGCA
966 TTAGCGGCG
1 TTAGCGGCG
975 TTTTTTATTT
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
122 9 0.08
123 107 0.92
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (123 bp):
TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAAGCTCGAACATTAGCGGCGATTTTTCAAAAACGC
CGCTAAAGATCTGAGCACTAGCGGCGCTTATCCAAAAACGCCGCTAAAGACTAGAGCA
Found at i:1051 original size:41 final size:41
Alignment explanation
Indices: 982--1135 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
972 GCGTTTTTTA
* * * *
982 TTTAGCGGCATTTTTTGAGAAGCACCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* *
1023 TTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* * * * **
1064 TTTAGCAGCGTTTTTGAAAAAGAGACGCTAATGCTC-GGGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
1104 TTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1136 AACATTTTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.01
41 94 0.99
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
Done.