Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023951.1 Corchorus olitorius cultivar O-4 contig23984, 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: 11261
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:405 original size:16 final size:15
Alignment explanation
Indices: 387--422 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
377 CAAGACATGT
387 TTTTCAAGAAAATTG
1 TTTTCAAGAAAATTG
*
402 TTTTCAAGAAAA-AG
1 TTTTCAAGAAAATTG
416 TTTTCAA
1 TTTTCAA
423 AAATAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (15 bp):
TTTTCAAGAAAATTG
Found at i:420 original size:14 final size:13
Alignment explanation
Indices: 387--446 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 13
377 CAAGACATGT
*
387 TTTTCAAGAAAATTG
1 TTTTCAA-AAAA-GG
*
402 TTTTCAAGAAAAAG
1 TTTTCAA-AAAAGG
416 TTTTCAAAAATAGG
1 TTTTCAAAAA-AGG
430 TTTTCAAAAAAGG
1 TTTTCAAAAAAGG
443 TTTT
1 TTTT
447 GAGTCTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.24
14 20 0.48
15 12 0.29
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAAAGG
Found at i:2013 original size:67 final size:67
Alignment explanation
Indices: 1922--2050 Score: 195
Period size: 67 Copynumber: 1.9 Consensus size: 67
1912 GAATGCTTTG
** * * *
1922 GCTTTTCCACAAGCCAAATTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCAAGCCGC
1 GCTTTTCCACAAGCCAAACACGTTTCCATACGAGTCAATTCAAGCCTTGATTCCACCCAAGCCGC
1987 AT
66 AT
* *
1989 GCTTTTCCATAAGCCAAACACGTTTCCATACGAGTCAATTGAAGCCTTGATTCCACCCAAGC
1 GCTTTTCCACAAGCCAAACACGTTTCCATACGAGTCAATTCAAGCCTTGATTCCACCCAAGC
2051 AACAGGGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (67 bp):
GCTTTTCCACAAGCCAAACACGTTTCCATACGAGTCAATTCAAGCCTTGATTCCACCCAAGCCGC
AT
Found at i:2198 original size:69 final size:70
Alignment explanation
Indices: 2109--2261 Score: 184
Period size: 69 Copynumber: 2.2 Consensus size: 70
2099 TTCCAAGACT
* * * * * *
2109 AACTCGTTTCTATACGAGTCAGTTTAAGCCTTGGTTCCATCCAAGCAGCAT-GTGCTTTTCCATA
1 AACTCGTTTCCATACAAGTCAGTTCAAACCTCGGTTCCATCCAAGCAGCATAG-GCTTTTCCACA
2173 AGCCA-
65 AGCCAC
* * *
2178 AACTCGTTTCCATACAAGTCAGTTCAAACCTCGGTTTCGTCCAGGCAGCATAGGCTTTTCCACAA
1 AACTCGTTTCCATACAAGTCAGTTCAAACCTCGGTTCCATCCAAGCAGCATAGGCTTTTCCACAA
2243 GCCAC
66 GCCAC
**
2248 AGTTCGTTTCCATA
1 AACTCGTTTCCATA
2262 TGGTGCATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
69 58 0.82
70 13 0.18
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (70 bp):
AACTCGTTTCCATACAAGTCAGTTCAAACCTCGGTTCCATCCAAGCAGCATAGGCTTTTCCACAA
GCCAC
Found at i:2330 original size:35 final size:35
Alignment explanation
Indices: 2280--2397 Score: 193
Period size: 35 Copynumber: 3.4 Consensus size: 35
2270 TACCATCTTC
*
2280 TCAGATGACTTGGTGTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
* *
2315 TCAGATGACTCGGTGTAGCATCTTCAAAGATGACT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
2350 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
*
2385 TCAGGTGA-TCGGT
1 TCAGATGACTCGGT
2398 CGTTGAACAA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
34 5 0.06
35 72 0.94
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTGAAT
Found at i:4009 original size:76 final size:76
Alignment explanation
Indices: 3872--4023 Score: 182
Period size: 76 Copynumber: 2.0 Consensus size: 76
3862 ACAAGGATCC
* * *
3872 CGACTCCACCTGGGCGCCCACATGGTTGCCTGGAGCACCCATGTGATTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGATTTGCCTGAGAACCCAGAT
3937 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * * **
3948 CGACTCCAGCTGGGTGCCGACATGGTTTGTCTGAAG-ACCCATGT-ATTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTGAAGCACCCATGTGATTT-GCCTGAGAACCCAG
*
4011 ATGGGCTGTGTCA
64 ATGGGCAGTGTCA
4024 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
75 4 0.06
76 52 0.81
77 8 0.12
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTGAAGCACCCATGTGATTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:7877 original size:15 final size:16
Alignment explanation
Indices: 7846--7880 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7836 TTACTTTGCT
7846 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
7862 TTGTTTTCT-TTTTAA
1 TTGTTTTCTAGTTTAA
7877 TTGT
1 TTGT
7881 GATTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Done.