Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008999.1 Corchorus capsularis cultivar CVL-1 contig09020, 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: 10295
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3445 original size:45 final size:45
Alignment explanation
Indices: 3327--3560 Score: 346
Period size: 45 Copynumber: 5.2 Consensus size: 45
3317 ACCAGTCCAT
* * * *
3327 GGTCAACTTTTATAGCCGCTG-AAACTGAAAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
*
3371 GGTCAAC-TTGATAACTGCTGAAAAATGAGAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
* * *
3415 GGTCGACTCTAATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
* *
3460 GCTCAACTTTGATAACTGCTGAAAACTGAGAAAGTCCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
*
3505 GGTCAACTTTGATAACTGCTGAAAACTGAAAAAGACCTGTTCTGA
1 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
*
3550 GGTCGACTTTG
1 GGTCAACTTTG
3561 GTGATCTTAT
Statistics
Matches: 170, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
43 10 0.06
44 34 0.20
45 126 0.74
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (45 bp):
GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTCTGA
Found at i:4883 original size:28 final size:24
Alignment explanation
Indices: 4859--4907 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4849 ACCTTTCGTC
*
4859 TTCTTTCTCT-T-TTTTCTTTTTT
1 TTCTTTCTCTCTCTCTTCTTTTTT
4881 TTCTTTCTCTCTCTCTTCTTTTTT
1 TTCTTTCTCTCTCTCTTCTTTTTT
4905 TTC
1 TTC
4908 ATGCACTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 13 0.54
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTTTCTCTCTCTCTTCTTTTTT
Found at i:5536 original size:13 final size:14
Alignment explanation
Indices: 5497--5540 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
5487 TTTTTTTTTT
* *
5497 TTTTTCATCTTTTC
1 TTTTTCTTCTCTTC
5511 TTTTTCTTCTCTTC
1 TTTTTCTTCTCTTC
5525 TTTTTCTT-TCTTC
1 TTTTTCTTCTCTTC
5538 TTT
1 TTT
5541 GAATTGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCTTCTCTTC
Found at i:6206 original size:14 final size:13
Alignment explanation
Indices: 6167--6222 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
6157 TAAAAACACG
6167 AAATCTTTTTTGA
1 AAATCTTTTTTGA
*
6180 CAA-CTCTTTTTGA
1 AAATCT-TTTTTGA
6193 AAATCTTTTCTTGA
1 AAATCTTTT-TTGA
*
6207 AAA-CAATTTTTGA
1 AAATC-TTTTTTGA
6220 AAA
1 AAA
6223 ACGTTCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.06
13 22 0.61
14 12 0.33
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (13 bp):
AAATCTTTTTTGA
Found at i:6216 original size:27 final size:26
Alignment explanation
Indices: 6167--6222 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
6157 TAAAAACACG
* **
6167 AAATCTTTTTTGACAACTCTTTTTGA
1 AAATCTTTTTTGAAAACAATTTTTGA
6193 AAATCTTTTCTTGAAAACAATTTTTGA
1 AAATCTTTT-TTGAAAACAATTTTTGA
6220 AAA
1 AAA
6223 ACGTTCCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (26 bp):
AAATCTTTTTTGAAAACAATTTTTGA
Found at i:9053 original size:20 final size:20
Alignment explanation
Indices: 9028--9176 Score: 119
Period size: 22 Copynumber: 7.3 Consensus size: 20
9018 TCTTTGAATC
*
9028 ACTGATCACCTTTTACTCTT
1 ACTGATTACCTTTTACTCTT
*
9048 ACTGATTACTATTTTACTCTT
1 ACTGATTAC-CTTTTACTCTT
*
9069 ACTGATTACCTTTTA--CTG
1 ACTGATTACCTTTTACTCTT
*
9087 A-TTATTA--TTTTACTCGTT
1 ACTGATTACCTTTTACTC-TT
*
9105 ACTGATTACCTTCTTACTTTTT
1 ACTGATTACCTT-TTAC-TCTT
**
9127 ACTGATTAATATTTTACTCTTT
1 ACTGATT-ACCTTTTACTC-TT
*
9149 ACTGATTACCATTTTGCTCTTT
1 ACTGATTACC-TTTTACTC-TT
9171 ACTGAT
1 ACTGAT
9177 CTCTCTTTAC
Statistics
Matches: 103, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
15 5 0.05
17 6 0.06
18 5 0.05
19 5 0.05
20 13 0.13
21 23 0.22
22 42 0.41
23 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (20 bp):
ACTGATTACCTTTTACTCTT
Found at i:9085 original size:35 final size:37
Alignment explanation
Indices: 9044--9122 Score: 135
Period size: 35 Copynumber: 2.2 Consensus size: 37
9034 CACCTTTTAC
9044 TCTTACTGATTACTATTTTACTC-TTACTGATTACCT
1 TCTTACTGATTACTATTTTACTCGTTACTGATTACCT
*
9080 T-TTACTGATTATTATTTTACTCGTTACTGATTACCT
1 TCTTACTGATTACTATTTTACTCGTTACTGATTACCT
9116 TCTTACT
1 TCTTACT
9123 TTTTACTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 20 0.50
36 15 0.38
37 5 0.12
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (37 bp):
TCTTACTGATTACTATTTTACTCGTTACTGATTACCT
Found at i:9132 original size:44 final size:44
Alignment explanation
Indices: 9074--9176 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 44
9064 CTCTTACTGA
* *
9074 TTACCTTTTACTGATTATTATTTTACTCGTTACTGATTACC-TT
1 TTACTTTTTACTGATTAATATTTTACTCGTTACTGATTACCATT
*
9117 CTTACTTTTTACTGATTAATATTTTACTCTTTACTGATTACCATT
1 -TTACTTTTTACTGATTAATATTTTACTCGTTACTGATTACCATT
* *
9162 TTGCTCTTTACTGAT
1 TTACTTTTTACTGAT
9177 CTCTCTTTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
44 51 0.96
45 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.53
Consensus pattern (44 bp):
TTACTTTTTACTGATTAATATTTTACTCGTTACTGATTACCATT
Found at i:9272 original size:15 final size:15
Alignment explanation
Indices: 9216--9273 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
9206 ACTGATTACT
9216 CTTTACTTTTTACCA
1 CTTTACTTTTTACCA
*
9231 TTTTACTTTTTACCGA
1 CTTTACTTTTTACC-A
9247 TCTCTCTTTACTTTTTACCA
1 -----CTTTACTTTTTACCA
9267 CTTTACT
1 CTTTACT
9274 GATTACTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
15 20 0.57
16 1 0.03
20 1 0.03
21 13 0.37
ACGTcount: A:0.17, C:0.26, G:0.02, T:0.55
Consensus pattern (15 bp):
CTTTACTTTTTACCA
Found at i:9272 original size:36 final size:36
Alignment explanation
Indices: 9143--9273 Score: 169
Period size: 36 Copynumber: 3.7 Consensus size: 36
9133 TAATATTTTA
** * *
9143 CTCTTTACTGATTACCATTTTGCTCTTTACTGATCT
1 CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
9179 CTCTTTACTTTTTACCATTCTT-C-TTTTACTGAT-T
1 CTCTTTACTTTTTACCATT-TTACTTTTTACTGATCT
*
9213 ACTCTTTACTTTTTACCATTTTACTTTTTACCGATCT
1 -CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
*
9250 CTCTTTACTTTTTACCACTTTACT
1 CTCTTTACTTTTTACCATTTTACT
9274 GATTACTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
34 3 0.04
35 29 0.34
36 50 0.59
37 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (36 bp):
CTCTTTACTTTTTACCATTTTACTTTTTACTGATCT
Found at i:9305 original size:25 final size:26
Alignment explanation
Indices: 9275--9336 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
9265 CACTTTACTG
*
9275 ATTACTATTTGCTCTC-TTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
*
9300 ATTACTATTTTCACTCTTTGAATTTA
1 ATTACTATTTGCACTCTTTGAATTTA
* *
9326 ATCACCATTTG
1 ATTACTATTTG
9337 TCATTTTACT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (26 bp):
ATTACTATTTGCACTCTTTGAATTTA
Found at i:9375 original size:33 final size:33
Alignment explanation
Indices: 9301--9383 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
9291 TTGAATTTAA
*
9301 TTACTATTTTCACTCTTTGAATTTAATCACCATT
1 TTACCATTTT-ACTCTTTGAATTTAATCACCATT
* *
9335 TGT--CATTTTACTCTTTGAATTTGATTACCATT
1 T-TACCATTTTACTCTTTGAATTTAATCACCATT
9367 TTACCATTTTACTCTTT
1 TTACCATTTTACTCTTT
9384 ACCGATTACT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.02
32 22 0.51
33 18 0.42
34 1 0.02
35 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (33 bp):
TTACCATTTTACTCTTTGAATTTAATCACCATT
Found at i:9533 original size:41 final size:41
Alignment explanation
Indices: 9419--9536 Score: 143
Period size: 40 Copynumber: 2.9 Consensus size: 41
9409 TTTTTATTCT
* *
9419 TTACTGATTTGCTGATTACTTCTTTTACTTTTACTC-TTAA
1 TTACTGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
*
9459 TTAC-CATTTTACTGATTACTTCTTTTACTTTGACTCTTTAA
1 TTACTGA-TTTACTGATTACTTCTTTTACTTTGACTCTTTAA
* * *
9500 TTACTGATTTCACTGATTA-ATCTCTTACCTTGACTCT
1 TTACTGATTT-ACTGATTACTTCTTTTACTTTGACTCT
9537 GGATTATCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 31 0.46
41 26 0.39
42 9 0.13
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (41 bp):
TTACTGATTTACTGATTACTTCTTTTACTTTGACTCTTTAA
Done.