Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012637.1 Corchorus olitorius cultivar O-4 contig12670, 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: 21041
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:4425 original size:78 final size:79
Alignment explanation
Indices: 4317--4479 Score: 256
Period size: 78 Copynumber: 2.1 Consensus size: 79
4307 AAATTTATAG
* *
4317 TTTTACCCAACTAAAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTAT
1 TTTTACCCAACT-AAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAG
*
4382 TTTACCATTTTACTA
65 TTTACCATTTAACTA
* * *
4397 TTTTACTCAACT-AAAAATTCTATTTTTATTTAATTAAATTTAATATCTTTATAACTATTTCAGT
1 TTTTACCCAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGT
4461 TTACCATTTAACTA
66 TTACCATTTAACTA
4475 TTTTA
1 TTTTA
4480 ACTAGAAAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 66 0.86
80 11 0.14
ACGTcount: A:0.36, C:0.13, G:0.01, T:0.50
Consensus pattern (79 bp):
TTTTACCCAACTAAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGT
TTACCATTTAACTA
Found at i:4992 original size:16 final size:16
Alignment explanation
Indices: 4958--4993 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4948 ATCAGGGTTC
* *
4958 GGGTCTCGGGTCTGCT
1 GGGTCTCGGGTCAGAT
4974 GGGTCTCGGGTCAGAT
1 GGGTCTCGGGTCAGAT
4990 GGGT
1 GGGT
4994 TCATGTTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.47, T:0.28
Consensus pattern (16 bp):
GGGTCTCGGGTCAGAT
Found at i:13065 original size:3 final size:3
Alignment explanation
Indices: 13057--13096 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
13047 AGCATACTAT
13057 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13097 AGTACTGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16490 original size:61 final size:60
Alignment explanation
Indices: 16420--16577 Score: 169
Period size: 60 Copynumber: 2.6 Consensus size: 60
16410 CTAATTGCTT
* * *
16420 AAATAAGGGTCTAACGTT-TGTCAAAATATTCAAATAACGG-CTCGATATTTTTAATTTGGCC
1 AAATAAGGGTCTAACGTTAT-TCAAAATACTCAAATAAAGGTC-CGAT-CTTTTAATTTGGCC
** * *
16481 AAATAAGGGTCTAATATTATTGAAAATGCTCAAATAAAGGTCCGATCTTTTAATTTGGCC
1 AAATAAGGGTCTAACGTTATTCAAAATACTCAAATAAAGGTCCGATCTTTTAATTTGGCC
** *
16541 AAATAAGGACCTAACGTTA-TCGAAAATGCTCAAATAA
1 AAATAAGGGTCTAACGTTATTC-AAAATACTCAAATAA
16578 GAGACTAAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 43 0.52
61 36 0.44
62 2 0.02
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (60 bp):
AAATAAGGGTCTAACGTTATTCAAAATACTCAAATAAAGGTCCGATCTTTTAATTTGGCC
Found at i:17605 original size:178 final size:178
Alignment explanation
Indices: 17295--17627 Score: 422
Period size: 178 Copynumber: 1.9 Consensus size: 178
17285 AATCCGATCA
* * **
17295 AGGTGATTTAAGTGTCTATTAAAAGACTATTCCATGATCTACAACTTTCATGGAGGACTCAAAAA
1 AGGTGATTCAAGTGTCTACTAAAAGACTATTCCATGATCTACAACTTTCATAAAGGACTCAAAAA
* ** **
17360 CTAAATTGAATGTTTCAAGTATCAAAAATGCTTCCGAAATTTTTTTTGTTTCGGTTAACAGGAAT
66 CTAAATTGAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAACAGGAAT
17425 AGACAGTCCACTTAATATTATATAACTTTTGTTCTAGATGTCTGATTG
131 AGACAGTCCACTTAATATTATATAACTTTTGTTCTAGATGTCTGATTG
* ** * *
17473 AGGTGATTCAAGTGTCTCCTAAAAGGTTGTTCTATGATCTACAACTTTCATAAAGGACTCAAAAA
1 AGGTGATTCAAGTGTCTACTAAAAGACTATTCCATGATCTACAACTTTCATAAAGGACTCAAAAA
* * **
17538 CTAAATTTAATG-TTCAAGGTATAAAAAATGTTTCC-AAAGAATTAGTTGTTT-GGATTGGC-GA
66 CTAAATTGAATGTTTCAA-GTATAAAAAATGCTTCCGAAA-AATTAGTTGTTTCGG-TTAACAG-
* *
17599 GAATAGACGGTCTACTTAATATTATATAA
127 GAATAGACAGTCCACTTAATATTATATAA
17628 TATATGTGCT
Statistics
Matches: 131, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
177 11 0.08
178 120 0.92
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (178 bp):
AGGTGATTCAAGTGTCTACTAAAAGACTATTCCATGATCTACAACTTTCATAAAGGACTCAAAAA
CTAAATTGAATGTTTCAAGTATAAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAACAGGAAT
AGACAGTCCACTTAATATTATATAACTTTTGTTCTAGATGTCTGATTG
Found at i:18526 original size:178 final size:177
Alignment explanation
Indices: 18242--18572 Score: 463
Period size: 178 Copynumber: 1.9 Consensus size: 177
18232 AAGGTGATTT
* *
18242 AAGTGTCTATTAAAAGATTGTTTAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
* * * ** *
18307 ATGTTTTAAATATCAAAAATGCTTCCGAAAGATTTGTTGTTTCGGTTAACGGGAATAGATGGTCC
66 ATGTTTCAAATATCAAAAATGATTCCGAAAGATTAGTTGTTTCGGTTAACGAAAATAGACGG-CC
*
18372 ACTTAATATTATATAACTTT-TGCTCCAGATGTCTGATTGAGATGGTTC
130 ACTTAATATTACATAA-TTTATGCTCCAGATGTCTGATTGAGATGGTTC
* * * *
18420 AAGTGTCTCTTAAAAGGCTGTTCCATGATCTACAACTTTCATGAATGACTCGAAAACTAAATTTA
1 AAGTGTCTATTAAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
18485 ATG-TTCAAGATAT-AAACAATGATTCC-AAAGAATTAGTTGTTTCGGTTAACGAAAATAGACGG
66 ATGTTTCAA-ATATCAAA-AATGATTCCGAAAG-ATTAGTTGTTTCGGTTAACGAAAATAGACGG
*
18547 CTACTTAATATTACATAATTTATGCT
128 CCACTTAATATTACATAATTTATGCT
18573 TATGGTAGAA
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
176 3 0.02
177 31 0.23
178 101 0.75
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (177 bp):
AAGTGTCTATTAAAAGACTGTTCAATGATCTACAACTTTCATGAAGGACTCGAAAACTAAATTTA
ATGTTTCAAATATCAAAAATGATTCCGAAAGATTAGTTGTTTCGGTTAACGAAAATAGACGGCCA
CTTAATATTACATAATTTATGCTCCAGATGTCTGATTGAGATGGTTC
Found at i:20306 original size:21 final size:20
Alignment explanation
Indices: 20280--20329 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
20270 ACGACGGTCT
20280 TTAATTGAACAAATTTTATAC
1 TTAATTGAA-AAATTTTATAC
20301 TTAATTG-AAAATTTTATAC
1 TTAATTGAAAAATTTTATAC
20320 TTAATTGAAA
1 TTAATTGAAA
20330 GCTATGGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 18 0.64
20 3 0.11
21 7 0.25
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (20 bp):
TTAATTGAAAAATTTTATAC
Found at i:20576 original size:21 final size:22
Alignment explanation
Indices: 20552--20594 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
20542 TTATTTTTCA
*
20552 TTATTTTT-TTTTAAAAAAAAC
1 TTATTTTTCTTTGAAAAAAAAC
20573 TTATTTTTCTTTGAAAAAAAAC
1 TTATTTTTCTTTGAAAAAAAAC
20595 CTTAGACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATTTTTCTTTGAAAAAAAAC
Done.