Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold207
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: 34533
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Found at i:1400 original size:23 final size:23
Alignment explanation
Indices: 1374--1418 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1364 AGTTACACTT
1374 TGGAAGTGGAGAGGGGTAACCCA
1 TGGAAGTGGAGAGGGGTAACCCA
** * *
1397 TGGATTTGTAGAGGGGTTACCC
1 TGGAAGTGGAGAGGGGTAACCC
1419 TTGACTCCGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.40, T:0.22
Consensus pattern (23 bp):
TGGAAGTGGAGAGGGGTAACCCA
Found at i:4661 original size:46 final size:44
Alignment explanation
Indices: 4611--4715 Score: 126
Period size: 46 Copynumber: 2.4 Consensus size: 44
4601 ATGTATAAGC
*
4611 GCCGAATG-GCTTAATGCGAAATG-GTATGAGATAGATATGAGGTAAA
1 GCCGAATGAGC-TAATGCGAAACGTGTAT-AGATAGATATG-GGT-AA
*
4657 GCCGAATGAGCTAATGCGAAACGTGTATAGATGGATATGGGTAA
1 GCCGAATGAGCTAATGCGAAACGTGTATAGATAGATATGGGTAA
*
4701 GCCAAATGA-CTAATG
1 GCCGAATGAGCTAATG
4716 TGAGATATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 6 0.11
44 10 0.19
45 3 0.06
46 29 0.54
47 6 0.11
ACGTcount: A:0.36, C:0.11, G:0.30, T:0.23
Consensus pattern (44 bp):
GCCGAATGAGCTAATGCGAAACGTGTATAGATAGATATGGGTAA
Found at i:4733 original size:44 final size:47
Alignment explanation
Indices: 4622--4733 Score: 119
Period size: 46 Copynumber: 2.5 Consensus size: 47
4612 CCGAATGGCT
* *
4622 TAATGCG-AA-ATGGTATGAGATAGATATGAGGTAAAGCCGAATGAGC
1 TAATGCGAAACAT-GTATGAGATGGATATGAGGTAAAGCCAAATGAGC
*
4668 TAATGCGAAACGTGTAT-AGATGGATATG-GGT-AAGCCAAATGA-C
1 TAATGCGAAACATGTATGAGATGGATATGAGGTAAAGCCAAATGAGC
* * *
4711 TAATGTGAGATATGTATGAGATG
1 TAATGCGAAACATGTATGAGATG
4734 TGTATATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
43 14 0.25
44 15 0.27
45 3 0.05
46 17 0.30
47 6 0.11
48 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.29, T:0.25
Consensus pattern (47 bp):
TAATGCGAAACATGTATGAGATGGATATGAGGTAAAGCCAAATGAGC
Found at i:12995 original size:43 final size:43
Alignment explanation
Indices: 12805--12981 Score: 300
Period size: 43 Copynumber: 4.1 Consensus size: 43
12795 GTTAAATCCC
*
12805 GCAGGCTTCGTGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
* *
12848 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
*
12891 GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCATGCCTA
1 GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
* *
12934 GTAGGCTTCATGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
12977 GCAGG
1 GCAGG
12982 TGTAATACCG
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 126 1.00
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (43 bp):
GCAGGCTTCATGCCGGTGATGTATATTCGGGCCTTCGTGCCTA
Found at i:29930 original size:46 final size:46
Alignment explanation
Indices: 29877--30147 Score: 288
Period size: 46 Copynumber: 5.9 Consensus size: 46
29867 TTAGGATTTT
** * *
29877 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGCAA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGCCA
* *
29923 ATGTGATGAATGTGAACCTGTATATATAGCAGGATAAGGCCGAATGACCA
1 ATGTGATGAATGTGAACATGCATATAT-G-A-GATAAGGCCGAATG-CCA
* * * * *
29973 ATGTGATGAATGTGAACATGCGTATGTGTGATAA-GTC--AT-TC-
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGCCA
* * *
30014 -TGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAAT-GCCA
30060 ATGTGATGAATGTGAACATGCATAT-TGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAAT-GCCA
* *
30106 ATGTGATGAATGTGAACATGTATATATGTG-TAAGGCCGAATG
1 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATG
30148 GCTAATGCGA
Statistics
Matches: 197, Mismatches: 16, Indels: 25
0.83 0.07 0.11
Matches are distributed among these distances:
40 33 0.17
41 2 0.01
42 1 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 82 0.42
47 32 0.16
48 1 0.01
49 15 0.08
50 25 0.13
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (46 bp):
ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGCCA
Found at i:30195 original size:92 final size:92
Alignment explanation
Indices: 29884--30163 Score: 247
Period size: 87 Copynumber: 3.1 Consensus size: 92
29874 TTTATGTGAT
** * * * * *
29884 GAATGTGAATGTGTATATATGAGATAAGGCCGAAT-GCAAATGTGATGAATGTGAACCTGTATAT
1 GAATGTGAACATGCATAT-TGAGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT
* * *
29948 ATAGCAGGATAAGGCCGAATGACCAATGTGA
65 AT-G--TGATAAGGCCGAATGGCCAATGCGA
* * * * *
29979 TGAATGTGAACATGCGTATGTGTGAT-AAGTC--AT--TC--TGTGATGAATGTGAACATGCGTA
1 -GAATGTGAACATGCATAT-TGAGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATA
* *
30037 TGTGTGATAAGGCCGAATGGCCAATGTGA
64 TATGTGATAAGGCCGAATGGCCAATGCGA
* *
30066 TGAATGTGAACATGCATATTGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTATAT
1 -GAATGTGAACATGCATATTGAGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATAT
*
30131 ATGTG-TAAGGCCGAATGGCTAATGCGA
65 ATGTGATAAGGCCGAATGGCCAATGCGA
30158 -AATGTG
1 GAATGTG
30164 TATGAGATAG
Statistics
Matches: 151, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
86 5 0.03
87 44 0.29
89 3 0.02
90 28 0.19
91 1 0.01
92 20 0.13
93 28 0.19
95 3 0.02
96 19 0.13
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (92 bp):
GAATGTGAACATGCATATTGAGATAAAGCCGAATGGCCAATGTGATGAATGTGAACATGCATATA
TGTGATAAGGCCGAATGGCCAATGCGA
Found at i:30264 original size:46 final size:46
Alignment explanation
Indices: 30129--30264 Score: 184
Period size: 46 Copynumber: 3.0 Consensus size: 46
30119 GAACATGTAT
* *
30129 ATATGT-GTAAGGCCGAATGGCTAATGCGAAATGTGTATGAGATAG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* *
30174 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
* * * * *
30220 ATATGTGGTAAAGCCAAATGACTAATGTGAGATATGTATGAGATG
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATG
30265 TGTATATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 5 0.06
46 74 0.94
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
Found at i:33794 original size:26 final size:27
Alignment explanation
Indices: 33765--33824 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
33755 CCACATATAT
*
33765 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
33791 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
33818 ATATCTG
1 ATATCTG
33825 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Done.