Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014878.1 Corchorus capsularis cultivar CVL-1 contig14899, 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: 11664
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:64 original size:10 final size:9
Alignment explanation
Indices: 35--145 Score: 67
Period size: 11 Copynumber: 12.3 Consensus size: 9
25 TTTTTTAATA
35 TTAATTAGT
1 TTAATTAGT
44 TTATGATTAGT
1 TTA--ATTAGT
55 CTTAATTAG-
1 -TTAATTAGT
**
64 TTAATTAAAA
1 TTAATT-AGT
*
74 TTACTTAGT
1 TTAATTAGT
83 TT-ATTAGT
1 TTAATTAGT
91 TT-A-T-GT
1 TTAATTAGT
97 TTAATTAGT
1 TTAATTAGT
106 ATCTAATTAGT
1 -T-TAATTAGT
117 TT-ATTA--
1 TTAATTAGT
123 TTAATTAGTTT
1 TTAATTAG--T
134 TTAATTAGT
1 TTAATTAGT
143 TTA
1 TTA
146 TGATTAAAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 30
0.70 0.04 0.26
Matches are distributed among these distances:
6 6 0.07
7 6 0.07
8 19 0.23
9 14 0.17
10 12 0.15
11 22 0.27
12 3 0.04
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (9 bp):
TTAATTAGT
Found at i:114 original size:26 final size:26
Alignment explanation
Indices: 85--152 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
75 TACTTAGTTT
85 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
* *
111 ATTAGTTTAT-TATTAATTAGTTTTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
137 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
153 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 36 0.97
ACGTcount: A:0.32, C:0.01, G:0.10, T:0.56
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:196 original size:24 final size:25
Alignment explanation
Indices: 162--220 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
152 AAATGAAGGA
*
162 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
185 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
210 AAATGAAGTTT
1 AAATGAAGTTT
221 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:321 original size:21 final size:21
Alignment explanation
Indices: 291--334 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
281 CAAAAGTGTA
291 AAAAGAGGGGCGGTATTTAGC
1 AAAAGAGGGGCGGTATTTAGC
* *
312 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGAGGGGCGGTATTTAGC
333 AA
1 AA
335 TCCAGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.41, T:0.18
Consensus pattern (21 bp):
AAAAGAGGGGCGGTATTTAGC
Found at i:570 original size:21 final size:21
Alignment explanation
Indices: 531--571 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
521 TTTGTAAGGG
* *
531 TTACAATAAAATCTCATCTCA
1 TTACAATAAAATATAATCTCA
*
552 TTACAATCAAATATAATCTC
1 TTACAATAAAATATAATCTC
572 TTATATGCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (21 bp):
TTACAATAAAATATAATCTCA
Found at i:5568 original size:17 final size:17
Alignment explanation
Indices: 5546--5586 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5536 ATAAAGCCAT
*
5546 GTGATCTT-GCATCACTG
1 GTGATCTTAG-ATCACTA
5563 GTGATCTTAGATCACTA
1 GTGATCTTAGATCACTA
5580 GTGATCT
1 GTGATCT
5587 GGGGGCGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 21 0.95
18 1 0.05
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (17 bp):
GTGATCTTAGATCACTA
Found at i:8783 original size:74 final size:74
Alignment explanation
Indices: 8657--8804 Score: 242
Period size: 74 Copynumber: 2.0 Consensus size: 74
8647 AGTTGTTCTC
* * * *
8657 GTACAAATCCCAGTATCTGGTACCCACATTGTATCTTGATTAACCCAGAGTCGAGTCTTTTAAAT
1 GTACAAATCCCAGTATCGGGTACCCACATTATATCTTGATTAACCCAAAGTCGAGCCTTTTAAAT
*
8722 TAATTTGAA
66 TAATCTGAA
*
8731 GTACAAATCCCAGTATCGGGTACCCACATTATATCTTGATTAACCTAAAGTCGAGCCTTTTAAAT
1 GTACAAATCCCAGTATCGGGTACCCACATTATATCTTGATTAACCCAAAGTCGAGCCTTTTAAAT
8796 TAATCTGAA
66 TAATCTGAA
8805 ATTGAGCTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (74 bp):
GTACAAATCCCAGTATCGGGTACCCACATTATATCTTGATTAACCCAAAGTCGAGCCTTTTAAAT
TAATCTGAA
Done.