Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023489.1 Corchorus olitorius cultivar O-4 contig23522, 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: 16461
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1734 original size:31 final size:31
Alignment explanation
Indices: 1699--1774 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
1689 TTTGAAAACA
1699 AAGGGATTTATTTGTCCCAAAAAAAAAAGAT
1 AAGGGATTTATTTGTCCCAAAAAAAAAAGAT
** *
1730 AAGGGATTTATTTGTCCCAAATGAAAAAGCT
1 AAGGGATTTATTTGTCCCAAAAAAAAAAGAT
*
1761 AAGGGATTTTTTTG
1 AAGGGATTTATTTG
1775 GTATTTAAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (31 bp):
AAGGGATTTATTTGTCCCAAAAAAAAAAGAT
Found at i:2169 original size:42 final size:44
Alignment explanation
Indices: 2118--2211 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
2108 AGTGCATTAC
* *
2118 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAACATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
2159 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
2204 CTAATATT
1 CTAATATT
2212 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:5332 original size:18 final size:18
Alignment explanation
Indices: 5311--5376 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
5301 AGGCGCAGCC
* *
5311 TCCACCATACCCTCCACG
1 TCCACCGTACCCACCACG
*
5329 TCCACCGTACCCACCGCG
1 TCCACCGTACCCACCACG
* *
5347 CCCTCCGTACCCACCACG
1 TCCACCGTACCCACCACG
*
5365 GCCACCGTACCC
1 TCCACCGTACCC
5377 TCCATAACCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.18, C:0.58, G:0.12, T:0.12
Consensus pattern (18 bp):
TCCACCGTACCCACCACG
Found at i:5369 original size:27 final size:27
Alignment explanation
Indices: 5339--5412 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
5329 TCCACCGTAC
* * *
5339 CCACCGCGCCCTCCGTACCCACCACGG
1 CCACCGCACCCTCCATAACCACCACGG
* * *
5366 CCACCGTACCCTCCATAACCGCCACGT
1 CCACCGCACCCTCCATAACCACCACGG
*
5393 CCACCGTACCCTCCATAACC
1 CCACCGCACCCTCCATAACC
5413 CCCTTGGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.20, C:0.55, G:0.12, T:0.12
Consensus pattern (27 bp):
CCACCGCACCCTCCATAACCACCACGG
Found at i:7510 original size:70 final size:70
Alignment explanation
Indices: 7397--7628 Score: 385
Period size: 70 Copynumber: 3.3 Consensus size: 70
7387 AATTTCCCGC
* *
7397 CACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTC
1 CACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTC
7462 AACAG
66 AACAG
* *
7467 CACAAGTCCGGGACAGGACTTGGGTAACTCCTGTCCAGTTCTTGTCCTGTATTTCTGCGCTCCTC
1 CACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTC
7532 AACAG
66 AACAG
* *
7537 CACAAGTCCGGGACAGGACTTGGGTAACTCATGCCCAGGTCTTGTCCTGTATTTCTGCGTTCCT-
1 CACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTC
7601 AACAG
66 AACAG
* *
7606 CCCAAGTCCTGGACAGGACTTGG
1 CACAAGTCCGGGACAGGACTTGG
7629 CCAAGATCTG
Statistics
Matches: 152, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 26 0.17
70 126 0.83
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (70 bp):
CACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTCTGCGCTCCTC
AACAG
Done.