Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015886.1 Corchorus capsularis cultivar CVL-1 contig15907, 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: 31300
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2396 original size:16 final size:16
Alignment explanation
Indices: 2372--2437 Score: 80
Period size: 16 Copynumber: 4.2 Consensus size: 16
2362 ATTTTTGGGT
*
2372 ACCCAAACCCGAAATT
1 ACCCAAACCCGAAATG
* *
2388 ACCCGAACCC-AAACG
1 ACCCAAACCCGAAATG
*
2403 ACCCGAACCCGAAATG
1 ACCCAAACCCGAAATG
*
2419 ACCCAAACCCAAAATG
1 ACCCAAACCCGAAATG
2435 ACC
1 ACC
2438 TGAATCTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.30
16 30 0.70
ACGTcount: A:0.42, C:0.41, G:0.11, T:0.06
Consensus pattern (16 bp):
ACCCAAACCCGAAATG
Found at i:2408 original size:15 final size:15
Alignment explanation
Indices: 2388--2431 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2378 ACCCGAAATT
2388 ACCCGAACCCAAACG
1 ACCCGAACCCAAACG
*
2403 ACCCGAACCCGAAATG
1 ACCCGAACCC-AAACG
*
2419 ACCCAAACCCAAA
1 ACCCGAACCCAAA
2432 ATGACCTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.43, C:0.43, G:0.11, T:0.02
Consensus pattern (15 bp):
ACCCGAACCCAAACG
Found at i:2412 original size:31 final size:31
Alignment explanation
Indices: 2372--2431 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2362 ATTTTTGGGT
* *
2372 ACCCAAACCCGAAATTACCCGAACCCAAACG
1 ACCCAAACCCGAAATGACCCAAACCCAAACG
*
2403 ACCCGAACCCGAAATGACCCAAACCCAAA
1 ACCCAAACCCGAAATGACCCAAACCCAAA
2432 ATGACCTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.42, G:0.10, T:0.05
Consensus pattern (31 bp):
ACCCAAACCCGAAATGACCCAAACCCAAACG
Found at i:2832 original size:26 final size:24
Alignment explanation
Indices: 2803--2850 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
2793 TTGAAGAGGA
*
2803 AAATAAAATGGATTATAAGTTATAAT
1 AAATAAAATAGATTA-AA-TTATAAT
2829 AAATAAAATAGATTAAATTATA
1 AAATAAAATAGATTAAATTATA
2851 TTGTGCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 2 0.10
26 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATAAAATAGATTAAATTATAAT
Found at i:3408 original size:2 final size:2
Alignment explanation
Indices: 3396--3429 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
3386 GAAAGTCTAT
3396 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
3430 AATCAGAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3817 original size:15 final size:17
Alignment explanation
Indices: 3782--3819 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
3772 AACCGAAAAC
3782 GACCC-AACCCATAATT
1 GACCCGAACCCATAATT
3798 GACCCGAACCCA-AA-T
1 GACCCGAACCCATAATT
3813 GACCCGA
1 GACCCGA
3820 CATTTGAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.13, T:0.11
Consensus pattern (17 bp):
GACCCGAACCCATAATT
Found at i:5681 original size:21 final size:21
Alignment explanation
Indices: 5657--5697 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5647 TAACTGGATT
5657 GCTAAACACCGCCCCATTTTC
1 GCTAAACACCGCCCCATTTTC
** *
5678 GCTATTCACCGCCCTATTTT
1 GCTAAACACCGCCCCATTTT
5698 TTACACTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.39, G:0.10, T:0.32
Consensus pattern (21 bp):
GCTAAACACCGCCCCATTTTC
Found at i:15223 original size:29 final size:29
Alignment explanation
Indices: 15181--15240 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
15171 TTTTCCTTTT
15181 TACTTTTACACTTGATCATCTTTGATTTG
1 TACTTTTACACTTGATCATCTTTGATTTG
15210 TACTTTTACACTTGATCATCTTTGATTTG
1 TACTTTTACACTTGATCATCTTTGATTTG
15239 TA
1 TA
15241 GGAAAATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.52
Consensus pattern (29 bp):
TACTTTTACACTTGATCATCTTTGATTTG
Found at i:17425 original size:6 final size:6
Alignment explanation
Indices: 17416--17442 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17406 AAAGCAAAGC
17416 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
17443 GCAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:17457 original size:13 final size:13
Alignment explanation
Indices: 17439--17473 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
17429 AATCTAAATC
*
17439 TAAAGCAGATTAA
1 TAAAGCAAATTAA
17452 TAAAGCAAATTAA
1 TAAAGCAAATTAA
17465 TAAAGCAAA
1 TAAAGCAAA
17474 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:24500 original size:6 final size:6
Alignment explanation
Indices: 24491--24517 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24481 AAAGCAAAGC
24491 AAATCT AAATCT AAATCT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA
24518 GTAGATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATCT
Found at i:24538 original size:13 final size:13
Alignment explanation
Indices: 24522--24548 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
24512 TCTAAAGTAG
24522 ATTAATAAAGCAA
1 ATTAATAAAGCAA
24535 ATTAATAAAGCAA
1 ATTAATAAAGCAA
24548 A
1 A
24549 CAATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTAATAAAGCAA
Done.