Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013247.1 Corchorus capsularis cultivar CVL-1 contig13268, 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: 12172
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Found at i:2267 original size:21 final size:21
Alignment explanation
Indices: 2243--2288 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
2233 TTTTCTATGC
*
2243 TTTTTA-CTATTTTTATGTGTA
1 TTTTTACCTA-TTTTATGAGTA
2264 TTTTTACCCTATTTTATGAGTA
1 TTTTTA-CCTATTTTATGAGTA
2286 TTT
1 TTT
2289 GTGTTTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 13 0.59
23 3 0.14
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (21 bp):
TTTTTACCTATTTTATGAGTA
Found at i:2438 original size:11 final size:10
Alignment explanation
Indices: 2422--2470 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
2412 AAGTTCGTGT
2422 TTGAAGACTTA
1 TTGAAGA-TTA
*
2433 TTGAAGATATT
1 TTGAAGAT-TA
2444 TTGAAGA-T-
1 TTGAAGATTA
2452 TTGAAGATTA
1 TTGAAGATTA
2462 TTGAAGATT
1 TTGAAGATT
2471 TATTTCAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 10 0.29
11 15 0.44
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:2467 original size:18 final size:19
Alignment explanation
Indices: 2433--2471 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
2423 TGAAGACTTA
*
2433 TTGAAGATATTTTGAAGAT
1 TTGAAGATATATTGAAGAT
2452 TTGAAGAT-TATTGAAGAT
1 TTGAAGATATATTGAAGAT
2470 TT
1 TT
2472 ATTTCAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.44
Consensus pattern (19 bp):
TTGAAGATATATTGAAGAT
Found at i:3856 original size:20 final size:21
Alignment explanation
Indices: 3812--3869 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
3802 TAGATTTAGA
*
3812 TTTAGTTTACTTTGCTTTATT
1 TTTAGTTTACATTGCTTTATT
* *
3833 TTTAGTTTA-ATTGTTTTCTT
1 TTTAGTTTACATTGCTTTATT
*
3853 TTTA-ATTA-ATTGCTTTA
1 TTTAGTTTACATTGCTTTA
3870 ATCCCCTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 10 0.32
20 12 0.39
21 9 0.29
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.66
Consensus pattern (21 bp):
TTTAGTTTACATTGCTTTATT
Found at i:4045 original size:12 final size:14
Alignment explanation
Indices: 4015--4064 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
4005 ACACGATCAA
4015 GTATCTATATATAT
1 GTATCTATATATAT
*
4029 CTATCTATAT-T-T
1 GTATCTATATATAT
*
4041 GTATCTATACTATCT
1 GTATCTATA-TATAT
*
4056 ATATCTATA
1 GTATCTATA
4065 CTACATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 9 0.30
13 2 0.07
14 10 0.33
15 9 0.30
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (14 bp):
GTATCTATATATAT
Found at i:4056 original size:9 final size:10
Alignment explanation
Indices: 4016--4063 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
4006 CACGATCAAG
*
4016 TATCTATATA
1 TATCTATCTA
4026 TATCTATCTA
1 TATCTATCTA
*
4036 TATTTGTATCTA
1 TA--TCTATCTA
4048 TA-CTATCTA
1 TATCTATCTA
4057 TATCTAT
1 TATCTAT
4064 ACTACATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
12 9 0.28
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (10 bp):
TATCTATCTA
Found at i:4415 original size:130 final size:130
Alignment explanation
Indices: 4157--4417 Score: 373
Period size: 130 Copynumber: 2.0 Consensus size: 130
4147 CATTGTTTAA
* * * * *
4157 ACTTTTATAGTTTTAGTCAGCTAGAAACTCTATTTTTATTTAATAAATATAATATCCTTATAATT
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATAAATATAATATCCTTATAACT
* *
4222 ATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTAAATAT
66 ATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAATAT
* * * * *
4287 ACTTTTATAATTTTACTCAATTAAAAACTCTA-TTTTGTTTAATGGAATCTAATATCCTTATACC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAAT-AAATATAATATCCTTATAAC
*
4351 TATTTTATTTTTACTATTTTACTAATTTAATTAAAAAAA-TTAGATATATTAGAATTTTTAAAAT
65 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTT-AAAT
4415 AT
129 AT
4417 A
1 A
4418 TTTCTTAAAT
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
129 29 0.25
130 87 0.75
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (130 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATAAATATAATATCCTTATAACT
ATTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAATAT
Found at i:6067 original size:12 final size:12
Alignment explanation
Indices: 6034--6067 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6024 CTTATAATTA
*
6034 ATTTTAATTATT
1 ATTTTAATTTTT
6046 ATTTTAATTTTT
1 ATTTTAATTTTT
*
6058 ATTTTCATTT
1 ATTTTAATTT
6068 AATTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTTTAATTTTT
Found at i:6067 original size:18 final size:17
Alignment explanation
Indices: 6031--6072 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
6021 CTACTTATAA
6031 TTAATTTTAATTATTATT
1 TTAATTTTAATTATTA-T
*
6049 TTAATTTTTATT-TTCAT
1 TTAATTTTAATTATT-AT
6066 TTAATTT
1 TTAATTT
6073 AAATACGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATTTTAATTATTAT
Found at i:11783 original size:141 final size:140
Alignment explanation
Indices: 11522--11854 Score: 506
Period size: 141 Copynumber: 2.4 Consensus size: 140
11512 TACAACTTTG
* * * *
11522 ATTAGATAATCATCAATCAATTACAACCTTGATTGGCAAAATTAACTAACAACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
* * *
11587 TTATTTTTTTGGTAACATAATTACTAATTGATTTATTTATTTATGGTAATCTTTTTGGTGGCGAT
66 TTATTTTTTTGATAACATAATTACTAATTGATTGATTTATTTATGGTAATCTTTTTGGTAGCGA-
11652 TTTATGGTAAA
130 TTTATGGTAAA
*
11663 ATTATATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
1 ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
* * * * *
11728 TTATTTTTTTGATAACATAATTACTAATTGATTGATTTATTTATGTTATTTTTTTTTGTAGTGAT
66 TTATTTTTTTGATAACATAATTACTAATTGATTGATTTATTTATGGTAATCTTTTTGGTAGCGAT
11793 TTATGGTAAA
131 TTATGGTAAA
* *
11803 ATTAAATAATTATCAATCAATTACAACTATGATTGGA-AAAATTAACTAACGA
1 ATTAAATAATCATCAATCAATTACAACTTTGATT-GACAAAATTAACTAACGA
11855 TCACTAACTT
Statistics
Matches: 176, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
140 57 0.32
141 119 0.68
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (140 bp):
ATTAAATAATCATCAATCAATTACAACTTTGATTGACAAAATTAACTAACGACATGTTCAATAAT
TTATTTTTTTGATAACATAATTACTAATTGATTGATTTATTTATGGTAATCTTTTTGGTAGCGAT
TTATGGTAAA
Done.