Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011226.1 Corchorus capsularis cultivar CVL-1 contig11247, 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: 12062
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:147 original size:24 final size:25
Alignment explanation
Indices: 115--163 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
105 TTCAATGATT
*
115 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
* *
139 GAGAATTGAAAATTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
164 AGGAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.35
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:1148 original size:78 final size:80
Alignment explanation
Indices: 969--1159 Score: 271
Period size: 84 Copynumber: 2.4 Consensus size: 80
959 TGAACAAATT
* *
969 AATCGAAAAGCTTTTTCAAACCTTTCAATTCCATTAACTCAACAAGTAATTAACCAAAATTTCAT
1 AATCGAAAAGCTTTTTCAAACCTTCCAATTCCATTAAATCAACAAGTAATTAACCAAAATTTCAT
*
1034 GTCCAAAAAAAATGGCATC
66 GT----AAAAAATGGCAGC
*
1053 AATGGAAAAGCTTTTTCAAACCTTCCAATTCCATTAAAT-AAGCAAGTAATTAACCAAAATTTCA
1 AATCGAAAAGCTTTTTCAAACCTTCCAATTCCATTAAATCAA-CAAGTAATTAACCAAAATTTCA
1117 T-T-AAAAATGGCAGC
65 TGTAAAAAATGGCAGC
*
1131 AATCGAAAAGTTTTTTCAAACCTTCCAAT
1 AATCGAAAAGCTTTTTCAAACCTTCCAAT
1160 ACTAAATAAG
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
78 38 0.38
83 3 0.03
84 59 0.59
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (80 bp):
AATCGAAAAGCTTTTTCAAACCTTCCAATTCCATTAAATCAACAAGTAATTAACCAAAATTTCAT
GTAAAAAATGGCAGC
Found at i:1200 original size:53 final size:54
Alignment explanation
Indices: 1142--1246 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
1132 ATCGAAAAGT
* * *
1142 TTTTTCAAACCTTCCAATACT-AAATAAGTAATTAACCAAAATTTCCTTACCGC
1 TTTTTCAAACCTTCCAATACTCAAACAAATAATAAACCAAAATTTCCTTACCGC
1195 TTTTTCAAACCTTCCAATACTCAAACAAATAATAAACCAAAATTTCCTTACC
1 TTTTTCAAACCTTCCAATACTCAAACAAATAATAAACCAAAATTTCCTTACC
1247 TCAACAAACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 21 0.44
54 27 0.56
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.32
Consensus pattern (54 bp):
TTTTTCAAACCTTCCAATACTCAAACAAATAATAAACCAAAATTTCCTTACCGC
Found at i:5534 original size:11 final size:11
Alignment explanation
Indices: 5518--5549 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
5508 GAAGTTCGTG
5518 TTTGAAGATTA
1 TTTGAAGATTA
*
5529 TTTGAAGATAA
1 TTTGAAGATTA
5540 TTTGAAGATT
1 TTTGAAGATT
5550 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:5546 original size:22 final size:22
Alignment explanation
Indices: 5518--5577 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
5508 GAAGTTCGTG
*
5518 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
5540 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
5559 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
5578 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:5552 original size:19 final size:18
Alignment explanation
Indices: 5528--5565 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5518 TTTGAAGATT
*
5528 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
5547 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
5565 A
1 A
5566 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:6947 original size:15 final size:14
Alignment explanation
Indices: 6913--6943 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6903 TAGTTTTTAG
*
6913 TTTAATTGTTTTCT
1 TTTAATTGATTTCT
6927 TTTAATTGATTTCT
1 TTTAATTGATTTCT
6941 TTT
1 TTT
6944 TAATCCCCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (14 bp):
TTTAATTGATTTCT
Found at i:9662 original size:12 final size:13
Alignment explanation
Indices: 9645--9673 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
9635 TTTTCCTTGC
9645 ATTGCTTTGATT-
1 ATTGCTTTGATTG
9657 ATTGCTTTGATTG
1 ATTGCTTTGATTG
9670 ATTG
1 ATTG
9674 TCTATTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (13 bp):
ATTGCTTTGATTG
Found at i:11182 original size:11 final size:11
Alignment explanation
Indices: 11166--11197 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
11156 GAAGTTCGTG
11166 TTTGAAGATTA
1 TTTGAAGATTA
*
11177 TTTGAAGATAA
1 TTTGAAGATTA
11188 TTTGAAGATT
1 TTTGAAGATT
11198 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Done.