Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013488.1 Corchorus olitorius cultivar O-4 contig13521, 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: 15633
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:15 original size:6 final size:6
Alignment explanation
Indices: 3--142 Score: 199
Period size: 6 Copynumber: 23.3 Consensus size: 6
1 CT
* * * * * * *
3 TCTCTC TGTCTC TTTCTC TCTCTG TCGCTA TCTCTT TCTCTC TCTGTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* *
51 TCTATC TCTGTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
99 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TC
143 ACGTTTTCTT
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 121 1.00
ACGTcount: A:0.01, C:0.44, G:0.04, T:0.51
Consensus pattern (6 bp):
TCTCTC
Found at i:24 original size:16 final size:16
Alignment explanation
Indices: 3--142 Score: 199
Period size: 16 Copynumber: 8.8 Consensus size: 16
1 CT
* *
3 TCTCTCTGTCTCTTTC
1 TCTCTCTCTCTCTCTC
* * *
19 TCTCTCTGTCGCTATC
1 TCTCTCTCTCTCTCTC
* *
35 TCTTTCTCTCTCTGTC
1 TCTCTCTCTCTCTCTC
* *
51 TCTATCTCTGTCTCTC
1 TCTCTCTCTCTCTCTC
67 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTC
83 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTC
99 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTC
115 TCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTC
131 TCTCTCTCTCTC
1 TCTCTCTCTCTC
143 ACGTTTTCTT
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 113 1.00
ACGTcount: A:0.01, C:0.44, G:0.04, T:0.51
Consensus pattern (16 bp):
TCTCTCTCTCTCTCTC
Found at i:39 original size:22 final size:22
Alignment explanation
Indices: 3--142 Score: 199
Period size: 22 Copynumber: 6.4 Consensus size: 22
1 CT
* *
3 TCTCTCTGTCTCTTTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
* * * *
25 TGTCGCTATCTCTTTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
* * *
47 TGTCTCTATCTCTGTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
69 TCTCTCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
91 TCTCTCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
113 TCTCTCTCTCTCTCTCTCTCTC
1 TCTCTCTCTCTCTCTCTCTCTC
135 TCTCTCTC
1 TCTCTCTC
143 ACGTTTTCTT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 110 1.00
ACGTcount: A:0.01, C:0.44, G:0.04, T:0.51
Consensus pattern (22 bp):
TCTCTCTCTCTCTCTCTCTCTC
Found at i:232 original size:65 final size:65
Alignment explanation
Indices: 128--253 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 65
118 CTCTCTCTCT
* *
128 CTCTCTCTCTCTCTCACGTTTTCTTTAATGTGTGTGGTATGTATATAAATCTATATGTTTTGCGC
1 CTCTCTCTCTCTCTCACGTCTTCTTCAATGTGTGTGGTATGTATATAAATCTATATGTTTTGCGC
* ** *
193 CTCTCTCTCTCTTTCTTGTCTTCTTCAGTGTGTGTGGTATGTATATAAATCTATATGTTTT
1 CTCTCTCTCTCTCTCACGTCTTCTTCAATGTGTGTGGTATGTATATAAATCTATATGTTTT
254 TGCTTTACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.16, C:0.19, G:0.15, T:0.50
Consensus pattern (65 bp):
CTCTCTCTCTCTCTCACGTCTTCTTCAATGTGTGTGGTATGTATATAAATCTATATGTTTTGCGC
Found at i:2564 original size:55 final size:55
Alignment explanation
Indices: 2480--2638 Score: 291
Period size: 55 Copynumber: 2.9 Consensus size: 55
2470 TTATAAATCT
*
2480 CTTTATCAAACCCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTTGGTTCC
1 CTTTATCAAACTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTTGGTTCC
* *
2535 CTTTATTAAATTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTTGGTTCC
1 CTTTATCAAACTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTTGGTTCC
2590 CTTTATCAAACTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTT
1 CTTTATCAAACTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTT
2639 AGTGATTAAG
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 99 1.00
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (55 bp):
CTTTATCAAACTCAATGCTTATTTATTAGCTATTTCCAAAACTATCCTTGGTTCC
Found at i:12399 original size:2 final size:2
Alignment explanation
Indices: 12392--12425 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12382 AAAAAGGAAA
12392 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12426 TGAAGAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12854 original size:26 final size:26
Alignment explanation
Indices: 12823--12882 Score: 113
Period size: 25 Copynumber: 2.3 Consensus size: 26
12813 TATATTTTAT
12823 TTTTATTTTTTTTGTTCAAACCTATA
1 TTTTATTTTTTTTGTTCAAACCTATA
12849 TTTTA-TTTTTTTGTTCAAACCTATA
1 TTTTATTTTTTTTGTTCAAACCTATA
12874 TTTTATTTT
1 TTTTATTTT
12883 ATAGTCCTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.76
26 8 0.24
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.65
Consensus pattern (26 bp):
TTTTATTTTTTTTGTTCAAACCTATA
Found at i:15613 original size:3 final size:3
Alignment explanation
Indices: 15605--15633 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15595 TATATTATAT
15605 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.