Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018356.1 Corchorus olitorius cultivar O-4 contig18389, 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: 40350
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--31 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1 TTGAAT
7 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32 TGTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5414 original size:206 final size:206
Alignment explanation
Indices: 5060--5433 Score: 644
Period size: 206 Copynumber: 1.8 Consensus size: 206
5050 AAATTTAACG
*
5060 GACTACACAAGCGGGTTCTGAAGGGTGACATGTGTCTTCTAGGGACTAGATTGAAATATTTAAAA
1 GACTACACAAGCGGGTTCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAA
* * *
5125 TTTAATTAATTTAAAAAATAGACATGTGTCAACTTCACAACCCGCTTGTAGAGTCCAAAATTTAC
66 CTTAATTAATTCAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTTAC
*
5190 ATCGCCGGTGTATCAAATAATCACCCTATATATATATATGGCAAATTATACAATACACCGGCGGT
131 ACCGCCGGTGTATCAAATAATCACCCTATATATATATATGGCAAATTATACAATACACCGGCGGT
5255 GGAGTTTAGCA
196 GGAGTTTAGCA
5266 GACTACACAAGCGGG-TCTTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAA
1 GACTACACAAGCGGGTTC-TGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAA
* *
5330 ACTTAATTAATTCAAGAAAT-GAACATGTGTCAACTCCACAACCCGCTTGTGGAGTCCAAAATTT
65 ACTTAATTAATTCAAAAAATAG-ACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTT
*
5394 ACACCGCCGGTGTATCAAATAATTACCCTATATATATATA
129 ACACCGCCGGTGTATCAAATAATCACCCTATATATATATA
5434 CACTATGTAT
Statistics
Matches: 158, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
205 3 0.02
206 155 0.98
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (206 bp):
GACTACACAAGCGGGTTCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAA
CTTAATTAATTCAAAAAATAGACATGTGTCAACTCCACAACCCGCTTGTAGAGTCCAAAATTTAC
ACCGCCGGTGTATCAAATAATCACCCTATATATATATATGGCAAATTATACAATACACCGGCGGT
GGAGTTTAGCA
Found at i:13369 original size:47 final size:47
Alignment explanation
Indices: 13296--13389 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
13286 TTGTGAGACT
* * *
13296 CACCCACCACGAATTAATCTGGTTTTTCTTCTATCAAAACCCAAGCA
1 CACCCACCACGAATTAATCCGATTTTTCTTATATCAAAACCCAAGCA
*
13343 CACCCACCACGGATTAATCCGATTTTTCTTATATCAAAACCCAAGCA
1 CACCCACCACGAATTAATCCGATTTTTCTTATATCAAAACCCAAGCA
13390 TGAAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.33, C:0.32, G:0.09, T:0.27
Consensus pattern (47 bp):
CACCCACCACGAATTAATCCGATTTTTCTTATATCAAAACCCAAGCA
Found at i:29119 original size:2 final size:2
Alignment explanation
Indices: 29112--29141 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29102 CTCTTATACA
29112 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29142 TTCAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30003 original size:27 final size:22
Alignment explanation
Indices: 29950--30009 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
29940 AAAATGGCAT
*
29950 GGCACAACACGACCTACGTGCC
1 GGCACAACACGACCCACGTGCC
29972 GGCACAACACGACCCACGTGCC
1 GGCACAACACGACCCACGTGCC
* *
29994 GGCGCAGCACGACCCA
1 GGCACAACACGACCCA
30010 TTTTTAATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.43, G:0.25, T:0.05
Consensus pattern (22 bp):
GGCACAACACGACCCACGTGCC
Found at i:30729 original size:20 final size:20
Alignment explanation
Indices: 30704--30743 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
30694 ATGTACTAAT
30704 ATTTGTATTAGTTATTAAAA
1 ATTTGTATTAGTTATTAAAA
30724 ATTTGTATTAGTTATTAAAA
1 ATTTGTATTAGTTATTAAAA
30744 CGATAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
ATTTGTATTAGTTATTAAAA
Found at i:31090 original size:20 final size:20
Alignment explanation
Indices: 31065--31104 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
31055 TTAGGTTCAA
31065 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
31085 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
31105 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:34032 original size:2 final size:2
Alignment explanation
Indices: 34025--34066 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
34015 GAGAATATTT
34025 TA TA TA TA TA TA GTA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34067 ATGACAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:34236 original size:47 final size:47
Alignment explanation
Indices: 34137--34238 Score: 159
Period size: 47 Copynumber: 2.2 Consensus size: 47
34127 GTAATTAACC
* * *
34137 TCATGGGCCATCTCTCCTTTAAAAACATGAATGACAATGACAGAGAG
1 TCATGGGCAATCTCTCCTTGAAAAACATGAATGACAATGACAGAGAA
* *
34184 CCATGGGCAATCTCTCCTTGAAAAACATGAATGACAATGACAGTGAA
1 TCATGGGCAATCTCTCCTTGAAAAACATGAATGACAATGACAGAGAA
34231 TCATGGGC
1 TCATGGGC
34239 CAAGTTATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (47 bp):
TCATGGGCAATCTCTCCTTGAAAAACATGAATGACAATGACAGAGAA
Found at i:39843 original size:6 final size:6
Alignment explanation
Indices: 39832--39881 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
39822 ATTTGGAGCT
* * * * *
39832 AATGGC AATGGC AATTGC AATGGG AATGGG AATGGG AATGGG AATGGC
1 AATGGC AATGGC AATGGC AATGGC AATGGC AATGGC AATGGC AATGGC
39880 AA
1 AA
39882 AGCCAAGCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.36, C:0.08, G:0.38, T:0.18
Consensus pattern (6 bp):
AATGGC
Found at i:39859 original size:18 final size:18
Alignment explanation
Indices: 39832--39881 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
39822 ATTTGGAGCT
* *
39832 AATGGCAATGGCAATTGC
1 AATGGGAATGGCAATGGC
* *
39850 AATGGGAATGGGAATGGG
1 AATGGGAATGGCAATGGC
39868 AATGGGAATGGCAA
1 AATGGGAATGGCAA
39882 AGCCAAGCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.38, T:0.18
Consensus pattern (18 bp):
AATGGGAATGGCAATGGC
Done.