Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2821
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: 7423
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Found at i:301 original size:25 final size:25
Alignment explanation
Indices: 262--341 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 25
252 TGGTACAAAT
262 TGATAATAGGTTAGGTAAAATGTTCA
1 TGATAATAGGTTAGGT-AAATGTTCA
288 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
313 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
339 TGA
1 TGA
342 AAGAATTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
24 7 0.14
25 17 0.33
26 25 0.49
27 2 0.04
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:2011 original size:26 final size:26
Alignment explanation
Indices: 1933--2040 Score: 121
Period size: 27 Copynumber: 4.1 Consensus size: 26
1923 TGGAGGAAGC
* *
1933 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
1960 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
1987 GTTCTGGT-GCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* *
2013 GTATCTGGTGAC-CTGTCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
2039 GT
1 GT
2041 CTTGGCAGCC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
26 27 0.38
27 43 0.61
28 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:2033 original size:53 final size:53
Alignment explanation
Indices: 1933--2040 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 53
1923 TGGAGGAAGC
*
1933 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACAT-TATCT
* * * *
1987 GTTCTGGT-GCTCTGCCACGATTATCTGTATCTGGTGAC-CTGTCACATTATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATTATCT
2039 GT
1 GT
2041 CTTGGCAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 7 0.15
53 24 0.50
54 17 0.35
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (53 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATTATCT
Found at i:3024 original size:85 final size:81
Alignment explanation
Indices: 2873--3029 Score: 226
Period size: 81 Copynumber: 1.9 Consensus size: 81
2863 TGTTTGAACG
* *
2873 TTTTCATGTGGCATGTCGGATCCGGCCATAACGTCTGGCTGGTTTGGGGTACATTTAGTGGTATC
1 TTTTCATGTGGCATGCCGGATCCGGCCATAACGTCTGGCGGGTTTGGGGTACATTTAGTGGTATC
2938 AGAGCCTTTTTTTAGT
66 AGAGCCTTTTTTTAGT
* *
2954 TTTTGATGTGGCATGCCGGATCC-GCCATAACTTCTGGGCCGGGTTTGGGGTGCTACATTTAGTG
1 TTTTCATGTGGCATGCCGGATCCGGCCATAACGTCT-GG-CGGGTTT-GGG-G-TACATTTAGTG
3018 GTATCAGAGCCT
61 GTATCAGAGCCT
3030 AAGTTGCAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
80 11 0.16
81 23 0.34
82 6 0.09
83 3 0.04
84 1 0.01
85 23 0.34
ACGTcount: A:0.16, C:0.19, G:0.30, T:0.35
Consensus pattern (81 bp):
TTTTCATGTGGCATGCCGGATCCGGCCATAACGTCTGGCGGGTTTGGGGTACATTTAGTGGTATC
AGAGCCTTTTTTTAGT
Found at i:6051 original size:26 final size:25
Alignment explanation
Indices: 5989--6096 Score: 180
Period size: 25 Copynumber: 4.2 Consensus size: 25
5979 TGATACAAAT
5989 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
6014 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
6040 TGATAATGGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCA
*
6065 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
6091 TGATAA
1 TGATAA
6097 GAATTTCATG
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
25 46 0.57
26 34 0.43
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:6052 original size:51 final size:51
Alignment explanation
Indices: 5989--6096 Score: 189
Period size: 51 Copynumber: 2.1 Consensus size: 51
5979 TGATACAAAT
5989 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
* * *
6040 TGATAATGGGTTAGGTAAATGTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
6091 TGATAA
1 TGATAA
6097 GAATTTCATG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATAGGTTAGGTAAATGTTCCA
Done.