Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold337
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: 28880
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:6862 original size:40 final size:40
Alignment explanation
Indices: 6788--7023 Score: 406
Period size: 40 Copynumber: 6.0 Consensus size: 40
6778 AACCCAAGTA
* * *
6788 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
6827 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCAC-AATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
6866 CCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
6905 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
6945 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
*
6985 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAAT
7024 CTTCGGATCT
Statistics
Matches: 188, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
38 19 0.10
39 49 0.26
40 120 0.64
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATG
Found at i:7006 original size:80 final size:79
Alignment explanation
Indices: 6788--7023 Score: 411
Period size: 78 Copynumber: 3.0 Consensus size: 79
6778 AACCCAAGTA
* * *
6788 CCTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
6853 AACTAGCAC-AATG
66 AACTAGCACAAATG
*
6866 CCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
6931 AACTAGCACAAATG
66 AACTAGCACAAATG
6945 CCTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
7010 TCACTAGCACAAAT
65 TAACTAGCACAAAT
7024 CTTCGGATCT
Statistics
Matches: 150, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
78 70 0.47
79 18 0.12
80 62 0.41
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
AACTAGCACAAATG
Found at i:7036 original size:118 final size:117
Alignment explanation
Indices: 6788--7041 Score: 417
Period size: 118 Copynumber: 2.2 Consensus size: 117
6778 AACCCAAGTA
*
6788 CCTTCGGGAT-TTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
1 CCTTCGGGATCTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
6852 TAACTAGCACAATGCCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAT
66 TAACTAGCACAATGCCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAT
*
6904 GCCTTCGGGA-CTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 -CCTTCGGGATCTTAG-CCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
6968 AGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
64 AGTAACTAGCAC-AATGCCTTCGGGACTTAG-CCGGATATAGTCACTAGCACAAAT
7024 -CTTC-GGATCTTAGTCCGG
1 CCTTCGGGATCTTAG-CCGG
7042 TTATCATCGA
Statistics
Matches: 129, Mismatches: 3, Indels: 9
0.91 0.02 0.06
Matches are distributed among these distances:
117 16 0.12
118 71 0.55
119 18 0.14
120 24 0.19
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.24
Consensus pattern (117 bp):
CCTTCGGGATCTTAGCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTAGCACAATGCCTTCGGGACTTAGCCGGATATAGTCACTAGCACAAAT
Found at i:10683 original size:29 final size:28
Alignment explanation
Indices: 10626--10724 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 28
10616 TACCTGTATC
*
10626 TGGCCCATTAAGCCC-AATCA-TATTCATA
1 TGGCCCATTAGGCCCAAATCACT-TT-ATA
10654 TGGCCCATTAGGCCCAAATCACTTGTATA
1 TGGCCCATTAGGCCCAAATCACTT-TATA
* *
10683 TGGCCCATTAGGCTCAAATCTCATTTATA
1 TGGCCCATTAGGCCCAAATCAC-TTTATA
*
10712 TGGCCCGTTAGGC
1 TGGCCCATTAGGC
10725 ACAGTCACAT
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
28 14 0.22
29 45 0.71
30 4 0.06
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAAATCACTTTATA
Found at i:10973 original size:16 final size:16
Alignment explanation
Indices: 10952--10986 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
10942 TAGCCAAACA
10952 TTCAGCTTTTCGGCAT
1 TTCAGCTTTTCGGCAT
10968 TTCAGCTTTTCGGCAT
1 TTCAGCTTTTCGGCAT
10984 TTC
1 TTC
10987 GACATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
TTCAGCTTTTCGGCAT
Found at i:15720 original size:27 final size:27
Alignment explanation
Indices: 15689--15866 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
15679 TAAATTGTAC
15689 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
15716 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
15742 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
15770 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
15798 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
15825 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
15852 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
15867 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:15803 original size:82 final size:81
Alignment explanation
Indices: 15690--15845 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
15680 AAATTGTACA
* *
15690 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
15754 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
15771 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
15836 TGCGAGTTGA
65 TGCGAATTGA
15846 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:15857 original size:82 final size:81
Alignment explanation
Indices: 15686--15866 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
15676 GATTAAATTG
* *
15686 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
15751 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
15767 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
15831 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
15849 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
15867 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Done.