Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013523.1 Corchorus capsularis cultivar CVL-1 contig13544, 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: 27758
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:3339 original size:30 final size:29
Alignment explanation
Indices: 3276--3345 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
3266 ACCGAACCGT
* ****
3276 CAAATAAGCCCCTGAACTTTTATTTCAGC
1 CAAATAAGCCCCTGAACTCTTAAAAAAGC
3305 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTCTTAAAAAA-GC
3335 CAAATAAGCCC
1 CAAATAAGCCC
3346 TATTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTCTTAAAAAAGC
Found at i:6874 original size:13 final size:13
Alignment explanation
Indices: 6856--6881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6846 TAAGTGTTTG
6856 GTTTGACTTACAA
1 GTTTGACTTACAA
6869 GTTTGACTTACAA
1 GTTTGACTTACAA
6882 ATACCTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
GTTTGACTTACAA
Found at i:9522 original size:10 final size:11
Alignment explanation
Indices: 9496--9534 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
9486 GACCAAGATT
9496 TCTATTTCTCA
1 TCTATTTCTCA
9507 TCTATTTCTC-
1 TCTATTTCTCA
9517 TCTATTTCTCA
1 TCTATTTCTCA
*
9528 TCCATTT
1 TCTATTT
9535 TTATCATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.15, C:0.28, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTATTTCTCA
Found at i:11333 original size:2 final size:2
Alignment explanation
Indices: 11323--11398 Score: 60
Period size: 2 Copynumber: 41.5 Consensus size: 2
11313 ATAAAAAATT
11323 TA TA T- TA TA TA TA TA TA TA TA -A TA -A TA -A TA -A TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * *
11361 TG T- TA TA TA TA TA -A TA TA TA TA AA TA TT TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11399 TAAAATTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
1 8 0.13
2 50 0.83
3 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:11392 original size:17 final size:18
Alignment explanation
Indices: 11367--11408 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
11357 CATATGTTAT
*
11367 ATATATAATATATA-TAA
1 ATATTTAATATATATTAA
11384 ATATTTAATATATATTAA
1 ATATTTAATATATATTAA
11402 A-ATTTAA
1 ATATTTAA
11409 CCTGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTTAATATATATTAA
Found at i:11398 original size:11 final size:12
Alignment explanation
Indices: 11320--11399 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 12
11310 TGAATAAAAA
11320 ATTTATATTATAT
1 ATTTATA-TATAT
*
11333 ATATATATATAAT
1 ATTTATATAT-AT
* *
11346 AATAATAATATCAT
1 ATTTAT-ATAT-AT
11360 ATGTTATATATAT
1 AT-TTATATATAT
* *
11373 AATATATATAAAT
1 -ATTTATATATAT
11386 ATTTA-ATATAT
1 ATTTATATATAT
11397 ATT
1 ATT
11400 AAAATTTAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
11 8 0.15
12 7 0.13
13 21 0.40
14 13 0.25
15 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:17701 original size:26 final size:25
Alignment explanation
Indices: 17662--17711 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
17652 AATATCAATT
17662 ATAAAGAAAACAATTAAA-CTAAAA
1 ATAAAGAAAACAATTAAATCTAAAA
17686 ATAAAGCAAAACCAATTAAATCTAAA
1 ATAAAG-AAAA-CAATTAAATCTAAA
17712 TCTAAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 4 0.17
26 8 0.35
27 5 0.22
ACGTcount: A:0.66, C:0.12, G:0.04, T:0.18
Consensus pattern (25 bp):
ATAAAGAAAACAATTAAATCTAAAA
Found at i:26877 original size:13 final size:13
Alignment explanation
Indices: 26861--26887 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26851 TTTAATAATA
26861 TTATTTCTTATTT
1 TTATTTCTTATTT
26874 TTATTTCTTATTT
1 TTATTTCTTATTT
26887 T
1 T
26888 CGTATATATT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATTTCTTATTT
Done.