Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012762.1 Corchorus capsularis cultivar CVL-1 contig12783, 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: 10708
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Found at i:2096 original size:13 final size:13
Alignment explanation
Indices: 2077--2112 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2067 AAAGATCGTC
2077 ATTATTATTTATT
1 ATTATTATTTATT
*
2090 GTTATTATTTATT
1 ATTATTATTTATT
*
2103 ATTATCATTT
1 ATTATTATTT
2113 TTAAATGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (13 bp):
ATTATTATTTATT
Found at i:6120 original size:21 final size:22
Alignment explanation
Indices: 6094--6137 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6084 ACTCTTGGAA
*
6094 TTACTGATCAC-CTTTTACTCT
1 TTACTGATCACTATTTTACTCT
*
6115 TTACTGATTACTATTTTACTCT
1 TTACTGATCACTATTTTACTCT
6137 T
1 T
6138 ACTAATTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.20, C:0.23, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTGATCACTATTTTACTCT
Found at i:6139 original size:21 final size:21
Alignment explanation
Indices: 6106--6231 Score: 97
Period size: 21 Copynumber: 6.3 Consensus size: 21
6096 ACTGATCACC
6106 TTTTACTCTTTACTGATTACTA
1 TTTTACTC-TTACTGATTACTA
* *
6128 TTTTACTCTTACTAATTACCA
1 TTTTACTCTTACTGATTACTA
* * ** *
6149 CTTTGCTCCCACTGATTACTG
1 TTTTACTCTTACTGATTACTA
6170 TTTTACTCTTACTGATTAC--
1 TTTTACTCTTACTGATTACTA
* *
6189 -CTTA----TATTGATTACTA
1 TTTTACTCTTACTGATTACTA
*
6205 TTTTACTCTTACTGATTAC-C
1 TTTTACTCTTACTGATTACTA
6225 TTTTACT
1 TTTTACT
6232 GATTACCTTC
Statistics
Matches: 79, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.11
17 3 0.04
18 3 0.04
20 7 0.09
21 49 0.62
22 8 0.10
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (21 bp):
TTTTACTCTTACTGATTACTA
Found at i:6200 original size:35 final size:34
Alignment explanation
Indices: 6159--6259 Score: 130
Period size: 35 Copynumber: 2.9 Consensus size: 34
6149 CTTTGCTCCC
6159 ACTGATTACTGTTTTACTCTTACTGATTACCTTAT
1 ACTGATTACT-TTTTACTCTTACTGATTACCTTAT
* *
6194 ATTGATTACTATTTTACTCTTACTGATTACCTTTT
1 ACTGATTACT-TTTTACTCTTACTGATTACCTTAT
* * *
6229 ACTGATTACCTTCTTACTCTCATTGATTACC
1 ACTGATTA-CTTTTTACTCTTACTGATTACC
6260 ATTTTGCTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 56 0.97
36 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.49
Consensus pattern (34 bp):
ACTGATTACTTTTTACTCTTACTGATTACCTTAT
Found at i:6202 original size:56 final size:55
Alignment explanation
Indices: 6142--6300 Score: 151
Period size: 56 Copynumber: 2.8 Consensus size: 55
6132 ACTCTTACTA
* ** * * *
6142 ATTACCACTTTGCTCCCACTGATTACTGTTTTACTCTTACTGATTAC-CTTATATTG
1 ATTACCATTTTGCTCTTACTGATTACTATTTTACTATTACTGATTACTC-T-CATTG
* * * **
6198 ATTACTATTTTACTCTTACTGATTAC-CTTTTACTGATTACCTTCTTACTCTCATTG
1 ATTACCATTTTGCTCTTACTGATTACTATTTTACT-ATTA-CTGATTACTCTCATTG
*
6254 ATTACCATTTTGCTCTTACTGATTACTATTTTACCTTTTACTGATTA
1 ATTACCATTTTGCTCTTACTGATTACTATTTTA-CTATTACTGATTA
6301 TCATTACTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
55 7 0.09
56 57 0.70
57 15 0.18
58 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.07, T:0.48
Consensus pattern (55 bp):
ATTACCATTTTGCTCTTACTGATTACTATTTTACTATTACTGATTACTCTCATTG
Found at i:6230 original size:14 final size:15
Alignment explanation
Indices: 6211--6246 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
6201 ACTATTTTAC
6211 TCTTACTGATTACCT
1 TCTTACTGATTACCT
6226 T-TTACTGATTACCT
1 TCTTACTGATTACCT
6240 TCTTACT
1 TCTTACT
6247 CTCATTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.50
Consensus pattern (15 bp):
TCTTACTGATTACCT
Found at i:6237 original size:21 final size:21
Alignment explanation
Indices: 6196--6237 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
6186 TACCTTATAT
*
6196 TGATTACTATTTTACTCTTAC
1 TGATTACTATTTTACTATTAC
*
6217 TGATTAC-CTTTTACTGATTAC
1 TGATTACTATTTTACT-ATTAC
6238 CTTCTTACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (21 bp):
TGATTACTATTTTACTATTAC
Found at i:6269 original size:21 final size:21
Alignment explanation
Indices: 6229--6305 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
6219 ATTACCTTTT
6229 ACTGATTACC-TTCTTACTCTC
1 ACTGATTACCATT-TTACTCTC
* * *
6250 ATTGATTACCATTTTGCTCTT
1 ACTGATTACCATTTTACTCTC
* * *
6271 ACTGATTACTATTTTACCTTTT
1 ACTGATTACCATTTTA-CTCTC
*
6293 ACTGATTATCATT
1 ACTGATTACCATT
6306 ACTTTTTTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 28 0.62
22 17 0.38
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.49
Consensus pattern (21 bp):
ACTGATTACCATTTTACTCTC
Found at i:6645 original size:16 final size:16
Alignment explanation
Indices: 6592--6647 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
6582 CTTAATCTCT
6592 TTTTACTGATTACTATC
1 TTTTACTGATTACTA-C
* *
6609 TTTTACTTAATTGCTGA-
1 TTTTAC-TGATTACT-AC
6626 -TTTACTGATTACTAC
1 TTTTACTGATTACTAC
6641 TTTTACT
1 TTTTACT
6648 CCCTTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 11 0.35
17 6 0.19
18 6 0.19
19 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (16 bp):
TTTTACTGATTACTAC
Found at i:7413 original size:41 final size:40
Alignment explanation
Indices: 7296--7415 Score: 138
Period size: 37 Copynumber: 3.0 Consensus size: 40
7286 AACTAAGAAA
7296 AAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
1 AAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
*** ** * **
7336 AA--AACCCAAAGGA-TAAGTGGAAAGCCCAATATCATTT
1 AAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
7373 CAAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
1 -AAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
7414 AA
1 AA
7416 ATCACTCTTT
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
37 21 0.35
38 8 0.13
40 10 0.17
41 21 0.35
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (40 bp):
AAGCAACCTTTATTACAAAGTTTAAAGCCCAATATCATTT
Found at i:7426 original size:41 final size:39
Alignment explanation
Indices: 7301--7428 Score: 125
Period size: 41 Copynumber: 3.2 Consensus size: 39
7291 AGAAAAAGCA
7301 ACCTTTATTACAAAGTTTAAAGCCCAATATCATTTAAA-
1 ACCTTTATTACAAAGTTTAAAGCCCAATATCATTTAAAC
*** ** * ** *
7339 ACCCAAAGGA-TAAGTGGAAAGCCCAATATCATTTCAAGC
1 ACCTTTATTACAAAGTTTAAAGCCCAATATCATTT-AAAC
7378 AACCTTTATTACAAAGTTTAAAGCCCAATATCATTTAAATC
1 -ACCTTTATTACAAAGTTTAAAGCCCAATATCATTTAAA-C
7419 ACTCTTTATT
1 AC-CTTTATT
7429 CCAATCCAAA
Statistics
Matches: 66, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
37 21 0.32
38 7 0.11
40 9 0.14
41 29 0.44
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (39 bp):
ACCTTTATTACAAAGTTTAAAGCCCAATATCATTTAAAC
Found at i:10505 original size:2 final size:2
Alignment explanation
Indices: 10488--10534 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
10478 CTTAGTTAAA
*
10488 AT AT CAT AT A- AT AT AT AT AT AT AT AT AT AT AT AT CT -T AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10529 AT AT AT
1 AT AT AT
10535 TTAAAACAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.