Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012305.1 Corchorus olitorius cultivar O-4 contig12338, whole genome shotgun sequence
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: 5625
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--164 Score: 155
Period size: 31 Copynumber: 5.4 Consensus size: 31
*
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAAAGTTAGGC
** *
32 CCTTATTTG-GCCAAATT---AAAAGATCAGGC
1 CCTTATTTGAG-CATTTTGGCAAAAG-TTAGGC
*
61 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAAAGTTAGGC
** *
92 CCTTATTTG-GTCAAATT---AAAAGATCAGGC
1 CCTTATTTGAG-CATTTTGGCAAAAG-TTAGGC
*
121 CCTTATTTGAGCATTTTGGCAAACGTTAGGC
1 CCTTATTTGAGCATTTTGGCAAAAGTTAGGC
152 CCTTATTTGAGCA
1 CCTTATTTGAGCA
165 ATTAGCCTAA
Statistics
Matches: 105, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
28 8 0.08
29 36 0.34
30 4 0.04
31 49 0.47
32 8 0.08
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
CCTTATTTGAGCATTTTGGCAAAAGTTAGGC
Found at i:65 original size:29 final size:28
Alignment explanation
Indices: 28--129 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 28
18 GGCAAATGTT
28 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
** * *
57 AGGCCCTTATTTGAGCATTTTGGCAAACG-TT
1 AGGCCCTTATTTG-GCAAATT---AAAAGATC
88 AGGCCCTTATTTGGTCAAATTAAAAGATC
1 AGGCCCTTATTTGG-CAAATTAAAAGATC
117 AGGCCCTTATTTG
1 AGGCCCTTATTTG
130 AGCATTTTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.07
29 31 0.53
30 2 0.03
31 18 0.31
32 4 0.07
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (28 bp):
AGGCCCTTATTTGGCAAATTAAAAGATC
Found at i:94 original size:60 final size:60
Alignment explanation
Indices: 1--160 Score: 302
Period size: 60 Copynumber: 2.7 Consensus size: 60
*
1 CCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
*
61 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCAGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
121 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
161 AGCAATTAGC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAGGC
Found at i:476 original size:35 final size:35
Alignment explanation
Indices: 437--506 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
427 GTAATTGTAT
437 TTATGTAAAAGGGTCTAAAGAAGCACAAAACGAAA
1 TTATGTAAAAGGGTCTAAAGAAGCACAAAACGAAA
* * *
472 TTATGTAAAAGGGTGTCAAGAAGCACAAAATGAAA
1 TTATGTAAAAGGGTCTAAAGAAGCACAAAACGAAA
507 GCAATACTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (35 bp):
TTATGTAAAAGGGTCTAAAGAAGCACAAAACGAAA
Found at i:3192 original size:27 final size:27
Alignment explanation
Indices: 3154--3217 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
3144 TATTTCTTAG
*
3154 TTGGTCATTTGCACTCTT-AAGGGCATT
1 TTGGTCATTTGCA-TATTCAAGGGCATT
*
3181 TTGGTCATTTGCATATTCAGGGGCATT
1 TTGGTCATTTGCATATTCAAGGGCATT
3208 TTGGTCATTT
1 TTGGTCATTT
3218 TGACATACTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (27 bp):
TTGGTCATTTGCATATTCAAGGGCATT
Found at i:4156 original size:27 final size:27
Alignment explanation
Indices: 4126--4203 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 27
4116 TTAGGATCAT
*
4126 CTAGGGGGATTTTGGTCATTTTTACAC
1 CTAGGGGGATTTTGGTCATTTGTACAC
* * **
4153 CTAGGGGGCATTTTGCTTATTTGTACTT
1 CTAGGGGG-ATTTTGGTCATTTGTACAC
*
4181 C-AGGGGTATTTTGGTCATTTGTA
1 CTAGGGGGATTTTGGTCATTTGTA
4204 GTTCAGGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.33
27 13 0.31
28 15 0.36
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.44
Consensus pattern (27 bp):
CTAGGGGGATTTTGGTCATTTGTACAC
Found at i:4232 original size:26 final size:26
Alignment explanation
Indices: 4157--4226 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
4147 TTACACCTAG
* * *
4157 GGGGCATTTTGCTTATTTGTACTTCA
1 GGGGCATTTTGATCATTTGTAGTTCA
* *
4183 GGGGTATTTTGGTCATTTGTAGTTCA
1 GGGGCATTTTGATCATTTGTAGTTCA
4209 GGGGCATTTTGATCATTT
1 GGGGCATTTTGATCATTT
4227 TAAGTTGACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.16, C:0.11, G:0.27, T:0.46
Consensus pattern (26 bp):
GGGGCATTTTGATCATTTGTAGTTCA
Done.