Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023015.1 Corchorus olitorius cultivar O-4 contig23048, 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: 24576
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:2493 original size:21 final size:21
Alignment explanation
Indices: 2460--2513 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2450 CTCCACCTGG
*
2460 GCACCCACATGG-TTGCCTTGA
1 GCACCCACGTGGTTTG-CTTGA
*
2481 GCACCCATGTGGTTTGCTTGA
1 GCACCCACGTGGTTTGCTTGA
* *
2502 GAACCCAGGTGG
1 GCACCCACGTGG
2514 GCAGTGTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.19, C:0.28, G:0.30, T:0.24
Consensus pattern (21 bp):
GCACCCACGTGGTTTGCTTGA
Found at i:2584 original size:76 final size:76
Alignment explanation
Indices: 2447--2598 Score: 173
Period size: 76 Copynumber: 2.0 Consensus size: 76
2437 ACAAGGACCC
* * *
2447 CGACTCCACCTGGGCACCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCACCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
2512 GGGCAGTGTCA
66 GGGCAGTGTCA
* ** * * **
2523 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TAAGGACCCATGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGGCACCCACATGG-TTGCCTTAAGCACCCATGTGGTTT-GCCTGAGAACCCAG
*
2586 ATGGGCTGTGTCA
64 ATGGGCAGTGTCA
2599 TAGCTCATCA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
75 4 0.06
76 55 0.87
77 4 0.06
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCACCCACATGGTTGCCTTAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:3112 original size:21 final size:23
Alignment explanation
Indices: 3088--3133 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 23
3078 CTCTCATCTC
*
3088 TTTTCTTG-TGAATATTT-T-AT
1 TTTTCTTGTTGAAAATTTCTAAT
3108 TTTT-TTGTTGAAAATTTCTAAT
1 TTTTCTTGTTGAAAATTTCTAAT
3130 TTTT
1 TTTT
3134 TCTTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 3 0.14
20 12 0.55
21 1 0.05
22 6 0.27
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTCTTGTTGAAAATTTCTAAT
Found at i:3381 original size:15 final size:15
Alignment explanation
Indices: 3357--3387 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3347 AACTTCCCTC
*
3357 TCCTTGCCTTTCCTT
1 TCCTTCCCTTTCCTT
3372 TCCTTCCCTTTCCTT
1 TCCTTCCCTTTCCTT
3387 T
1 T
3388 AATTACTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (15 bp):
TCCTTCCCTTTCCTT
Found at i:11539 original size:16 final size:16
Alignment explanation
Indices: 11518--11550 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11508 GAAAAAATTA
11518 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
11534 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
11550 T
1 T
11551 ATGATGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TGGCATATATTAAGAT
Found at i:12165 original size:21 final size:21
Alignment explanation
Indices: 12141--12189 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
12131 GGAATGGCGA
**
12141 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
12162 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
12183 TGGCACG
1 TGGCACG
12190 ATGAATGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:19564 original size:3 final size:3
Alignment explanation
Indices: 19556--19585 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19546 TCAAAACAGC
*
19556 AGA AGA AGA AGA AGA AGA ACA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
19586 GGCCAACGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20908 original size:63 final size:63
Alignment explanation
Indices: 20802--20939 Score: 213
Period size: 63 Copynumber: 2.2 Consensus size: 63
20792 TGATGAATTC
* *
20802 TGATGATAATGATAATGTTCAAAGTGGTGAATAATGATTTTTCTATGAACTGTAACTAGATAT
1 TGATGATAATGATAATATTCAAAGTGGTGAATAATGATGTTTCTATGAACTGTAACTAGATAT
** * * *
20865 TGATGATAATGATAATATTCATTGTGGTGAATATTGATGTTTCTATGTACTGTAATTAGATAT
1 TGATGATAATGATAATATTCAAAGTGGTGAATAATGATGTTTCTATGAACTGTAACTAGATAT
20928 TGATGATAATGA
1 TGATGATAATGA
20940 AAAAGGAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.41
Consensus pattern (63 bp):
TGATGATAATGATAATATTCAAAGTGGTGAATAATGATGTTTCTATGAACTGTAACTAGATAT
Found at i:21806 original size:33 final size:33
Alignment explanation
Indices: 21757--21822 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
21747 TACGAGCTGA
*
21757 ATTGAACTCGAGTGTTCATACTATGTTTGAGAT
1 ATTGAACTCAAGTGTTCATACTATGTTTGAGAT
*
21790 ATTGAACTCAATTGTTCATACTATGTTTGAGAT
1 ATTGAACTCAAGTGTTCATACTATGTTTGAGAT
21823 TACTTTGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (33 bp):
ATTGAACTCAAGTGTTCATACTATGTTTGAGAT
Done.