Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012451.1 Corchorus capsularis cultivar CVL-1 contig12472, 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: 38179
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:11488 original size:5 final size:5
Alignment explanation
Indices: 11481--11514 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
11471 TTTTTTTTTA
* *
11481 AAAAA AAAAG AAAAG AAAAG AAAAG AGAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
11515 AGAAGTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:12921 original size:108 final size:109
Alignment explanation
Indices: 12754--13048 Score: 432
Period size: 108 Copynumber: 2.7 Consensus size: 109
12744 ACTATTATAG
* *
12754 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
12819 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
12868 TTTTATTCTACTAAAAACTCTA-TTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* * *
12932 TTACCAAAAATTTTGGATANATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* **
12976 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
13040 TTTTTACCA
63 TTTTTACCA
13049 TTTTAATTTA
Statistics
Matches: 169, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
108 101 0.60
109 26 0.15
110 6 0.04
111 15 0.09
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:14911 original size:2 final size:2
Alignment explanation
Indices: 14904--14931 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14894 TGATAGTATG
14904 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14932 ATAGATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19674 original size:7 final size:7
Alignment explanation
Indices: 19664--19697 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
19654 TCTAAACCGA
19664 CCCAAAG
1 CCCAAAG
19671 CCCAAAG
1 CCCAAAG
19678 CCCAAAG
1 CCCAAAG
*
19685 CTCAAAG
1 CCCAAAG
19692 CCCAAA
1 CCCAAA
19698 ACTCAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.41, G:0.12, T:0.03
Consensus pattern (7 bp):
CCCAAAG
Found at i:19702 original size:14 final size:14
Alignment explanation
Indices: 19673--19703 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19663 ACCCAAAGCC
*
19673 CAAAGCCCAAAGCT
1 CAAAGCCCAAAACT
19687 CAAAGCCCAAAACT
1 CAAAGCCCAAAACT
19701 CAA
1 CAA
19704 TATTTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.35, G:0.10, T:0.06
Consensus pattern (14 bp):
CAAAGCCCAAAACT
Found at i:24294 original size:23 final size:24
Alignment explanation
Indices: 24249--24295 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
24239 GTTATATGAA
*
24249 GAAACTATAATTCTTTTTTTAAAT
1 GAAACTATAATTCTCTTTTTAAAT
24273 GAAACTATAATTC-CTTTTTAAAT
1 GAAACTATAATTCTCTTTTTAAAT
24296 CTTCTCTCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (24 bp):
GAAACTATAATTCTCTTTTTAAAT
Found at i:24563 original size:2 final size:2
Alignment explanation
Indices: 24558--24584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24548 GGTAAATTAC
24558 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
24585 CCGGTTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28888 original size:22 final size:22
Alignment explanation
Indices: 28856--28900 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
28846 TTTGTTTTTA
28856 TTTTTTTAATCTTA-TTTAATT
1 TTTTTTTAATCTTATTTTAATT
28877 TTTTTTTCAATCTTATTTTAATT
1 TTTTTTT-AATCTTATTTTAATT
28900 T
1 T
28901 ATCACCTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
23 8 0.36
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTAATCTTATTTTAATT
Found at i:31861 original size:28 final size:29
Alignment explanation
Indices: 31810--31868 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
31800 ATTGTTATCA
*
31810 CAAAAATCAAATTAGTCTGTATATTAAAC
1 CAAAAATCAAAATAGTCTGTATATTAAAC
31839 CAAAAATCAAAATAGTCT-TATATTAAAC
1 CAAAAATCAAAATAGTCTGTATATTAAAC
31867 CA
1 CA
31869 TACTAATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (29 bp):
CAAAAATCAAAATAGTCTGTATATTAAAC
Found at i:32226 original size:1 final size:1
Alignment explanation
Indices: 32222--32254 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
32212 TTGCTTTGGC
*
32222 TTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32255 AGTGCTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Done.