Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024634.1 Corchorus olitorius cultivar O-4 contig24667, 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: 14951
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:3128 original size:42 final size:44
Alignment explanation
Indices: 3077--3170 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
3067 AGTGCATTAT
* *
3077 CTAA-ATTCTACT-T-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAACTCATCAAAATAAAG
3118 CTAATATTCTACTCCTCCATCTCTAGATAACTCATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAACTCATCAAAATAAAG
3163 CTAATATT
1 CTAATATT
3171 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 1 0.02
45 34 0.72
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAACTCATCAAAATAAAG
Found at i:6542 original size:46 final size:45
Alignment explanation
Indices: 6477--6565 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 45
6467 TATTATTACT
6477 TTTTACTTTTTAGCTTAATTAACTCT-A-CTACTGATTACTCTTGC
1 TTTTACTTTTTAGCTTAATT-ACTCTAATCTACTGATTACTCTTGC
*
6521 TTTTACTTCTTTTAGCTTAATTACTCTAATCTTCTGATTACTCTT
1 TTTTAC-T-TTTTAGCTTAATTACTCTAATCTACTGATTACTCTT
6566 TCTTCTGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
44 6 0.15
45 6 0.15
46 14 0.35
47 14 0.35
ACGTcount: A:0.21, C:0.20, G:0.06, T:0.53
Consensus pattern (45 bp):
TTTTACTTTTTAGCTTAATTACTCTAATCTACTGATTACTCTTGC
Found at i:6577 original size:47 final size:46
Alignment explanation
Indices: 6484--6577 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 46
6474 ACTTTTTACT
*
6484 TTTTAGCTTAATTAACTCTACTACTGATTACTCTTGCTTTTACTTC
1 TTTTAGCTTAATTAACTCTACTACTGATTACTCTTGCTTCTACTTC
* * *
6530 TTTTAGCTTAATT-ACTCTAATCTTCTGATTACTCTTTCTTCTGCTTC
1 TTTTAGCTTAATTAACTCT-A-CTACTGATTACTCTTGCTTCTACTTC
6577 T
1 T
6578 GATTACTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 5 0.12
46 14 0.33
47 23 0.55
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.52
Consensus pattern (46 bp):
TTTTAGCTTAATTAACTCTACTACTGATTACTCTTGCTTCTACTTC
Found at i:6760 original size:28 final size:22
Alignment explanation
Indices: 6551--6740 Score: 192
Period size: 22 Copynumber: 8.8 Consensus size: 22
6541 TTACTCTAAT
6551 CTTCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTCTG
6573 CTTCTGATTACTCTTTC-TC--
1 CTTCTGATTACTCTTTCTTCTG
* *
6592 CTTCTAATTACTTTTTCTT-TG
1 CTTCTGATTACTCTTTCTTCTG
* * * * *
6613 ACTTTTGATTATTCTTCCTTTTA
1 -CTTCTGATTACTCTTTCTTCTG
* * *
6636 C-TCTGATTACCCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTCTG
*
6657 CTTCTGATTACCCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTCTG
* * * *
6679 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTCTG
*
6701 CTCCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTCTG
6723 CTTCTGATTACTCTTTCT
1 CTTCTGATTACTCTTTCT
6741 CTTACTGCTT
Statistics
Matches: 137, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
19 15 0.11
20 1 0.01
21 19 0.14
22 101 0.74
23 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.55
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTCTG
Found at i:6828 original size:47 final size:46
Alignment explanation
Indices: 6779--7562 Score: 880
Period size: 47 Copynumber: 16.7 Consensus size: 46
6769 CAAATTGTTT
* * * * ** *
6779 TCTTCTTCTCTTGCTCTTTAGTTTAATTACCTGGAATTAAGCTCTTT
1 TCTTCTTCTTTTACTC-TTAGTTTAATTACCTAGAATTAAACTAATC
* * **
6826 TCTTCTTCTTTTACTTTTTAGTTTAATCACCCGGAATTAAACTAACCTC
1 TCTTCTTCTTTTAC-TCTTAGTTTAATTACCTAGAATTAAACTAA--TC
* ** *
6875 TGTTTACTTCTTCTTTTACTCTTTAGTTTAATTACCCAGAATTAAACTCCTT
1 ----T-CTTCTTCTTTTACTC-TTAGTTTAATTACCTAGAATTAAACTAATC
* * * * * ** *
6927 TCTTCTTCAATTAATTTTTAGTTTAATTACCCAGAATTAAACTGCTT
1 TCTTCTTC-TTTTACTCTTAGTTTAATTACCTAGAATTAAACTAATC
* * *
6974 TCTTCTTCTCTTGCTCTTTAGTTTAATTACCTAGAATTAAACTAACC
1 TCTTCTTCTTTTACTC-TTAGTTTAATTACCTAGAATTAAACTAATC
*
7021 TCTTCTTCTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* * *
7068 TCTTCTTCTTCTACTACTTAGTTTAATTACCTAGAATCAGACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* *
7115 T-TTCCTTCTTCTACTACTTAGTTTAATTACCTAGAATTAACCTAATC
1 TCTT-CTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* * * *
7162 TCTCCTTCTTTTGCTACTTAGTTTAATTACCTAGAATCAGACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
*
7209 T-TTCCTTCTTCTACTACTTAGTTTAATTACCTAGAATTAAACTAATC
1 TCTT-CTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
*
7256 TCTTCTTCTTTTA--CTTAGTTTAATTACCTGGAATTAAACTAATC
1 TCTTCTTCTTTTACTCTTAGTTTAATTACCTAGAATTAAACTAATC
7300 TCTTCTTCTTTTACTACTTAGTTTAATTACCTAGAATTAAACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* * *
7347 TCTTCTTCTTCTACTACTTAGTTTAATTACCTAGAATCAGACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
*
7394 T-TTCCTTCTTCTACTACTTAGTTTAATTACCTAGAATTAAACTAATC
1 TCTT-CTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* *
7441 TCTTCTTCTTTTGCTACTTAGTTTACTTACCTAGAATTAAACTAATC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACCTAGAATTAAACTAATC
* *
7488 TCTTCTTCTTTTA--CTTAATTTAATTACCTGGAATTAAACTAATC
1 TCTTCTTCTTTTACTCTTAGTTTAATTACCTAGAATTAAACTAATC
7532 TCTTCTTCTTTTACTACTTAGTTTAATTACC
1 TCTTCTTCTTTTACT-CTTAGTTTAATTACC
7563 CTTCTAATTA
Statistics
Matches: 644, Mismatches: 69, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
44 84 0.13
46 7 0.01
47 501 0.78
48 11 0.02
49 1 0.00
52 1 0.00
53 2 0.00
54 37 0.06
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (46 bp):
TCTTCTTCTTTTACTCTTAGTTTAATTACCTAGAATTAAACTAATC
Found at i:7588 original size:22 final size:22
Alignment explanation
Indices: 7563--7632 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
7553 TTTAATTACC
* *
7563 CTTCTAATTACAT-TTTCTTTTA
1 CTTCTGATTAC-TCTTTCTTCTA
* *
7585 CTTCTGATTGCTCTTCCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
7607 CTTCTGATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
7629 CTTC
1 CTTC
7633 CTAGCTTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 1 0.02
22 40 0.98
ACGTcount: A:0.14, C:0.27, G:0.04, T:0.54
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTCTA
Found at i:9185 original size:11 final size:10
Alignment explanation
Indices: 9160--9184 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9150 ATCTGTAAGC
9160 TTTTTCTTTT
1 TTTTTCTTTT
9170 TTTTTCTTTT
1 TTTTTCTTTT
9180 TTTTT
1 TTTTT
9185 TTAAGGGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:11334 original size:23 final size:23
Alignment explanation
Indices: 11308--11356 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
11298 ATTAATATGC
11308 TACAAGAATGAGATAATGAATTA
1 TACAAGAATGAGATAATGAATTA
*
11331 TACAAGAATGAGGTAATGAATTA
1 TACAAGAATGAGATAATGAATTA
11354 TAC
1 TAC
11357 TAAATGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (23 bp):
TACAAGAATGAGATAATGAATTA
Found at i:14475 original size:26 final size:25
Alignment explanation
Indices: 14433--14481 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
14423 TGTCCCCCTG
*
14433 AAAAAAAAAGAGCGTTAGTAACCTC
1 AAAAAAAAAGAGAGTTAGTAACCTC
*
14458 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAA-AAAAAGAGAGTTAGTAACC
14482 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.12, G:0.20, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAGAGAGTTAGTAACCTC
Done.