Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008250.1 Corchorus capsularis cultivar CVL-1 contig08271, 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: 35631
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:2330 original size:38 final size:38
Alignment explanation
Indices: 2277--2396 Score: 208
Period size: 38 Copynumber: 3.2 Consensus size: 38
2267 TCATATTCAG
*
2277 GTCAACACGAA-GATGGTCAAATATTTACGAATACAAAT
1 GTCAACAC-AACGATGGTCAAATATTTATGAATACAAAT
2315 GTCAACACAACGATGGTCAAATATTTATGAATACAAAT
1 GTCAACACAACGATGGTCAAATATTTATGAATACAAAT
2353 GTCAACACAACGATGGTCAAATATTTATGAATACAAAT
1 GTCAACACAACGATGGTCAAATATTTATGAATACAAAT
2391 GT-AACA
1 GTCAACA
2397 TTTTATATAA
Statistics
Matches: 80, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
37 6 0.08
38 74 0.93
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (38 bp):
GTCAACACAACGATGGTCAAATATTTATGAATACAAAT
Found at i:2452 original size:32 final size:32
Alignment explanation
Indices: 2416--2479 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2406 AATTTGTTTC
2416 GATGTATTTAAGTATTTAAAAATTAATTTTGT
1 GATGTATTTAAGTATTTAAAAATTAATTTTGT
2448 GATGTATTTAAGTATTTAAAAATTAATTTTGT
1 GATGTATTTAAGTATTTAAAAATTAATTTTGT
2480 CCACACGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (32 bp):
GATGTATTTAAGTATTTAAAAATTAATTTTGT
Found at i:10965 original size:14 final size:14
Alignment explanation
Indices: 10946--10974 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10936 TGGAAAAGCA
10946 GTGGTATTTTTCCT
1 GTGGTATTTTTCCT
10960 GTGGTATTTTTCCT
1 GTGGTATTTTTCCT
10974 G
1 G
10975 ATTATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.24, T:0.55
Consensus pattern (14 bp):
GTGGTATTTTTCCT
Found at i:11901 original size:31 final size:29
Alignment explanation
Indices: 11858--11924 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
11848 CAACCCATTT
*
11858 TCCTGAATTGACACAAATTGATAACGTTTGA
1 TCCTGAAATGACA-AAATTG-TAACGTTTGA
***
11889 TCCTGAAATGACAGTTTTGTAACGTTTGA
1 TCCTGAAATGACAAAATTGTAACGTTTGA
11918 TCCTGAA
1 TCCTGAA
11925 TTGCTCATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.53
30 3 0.09
31 12 0.38
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (29 bp):
TCCTGAAATGACAAAATTGTAACGTTTGA
Found at i:16892 original size:75 final size:75
Alignment explanation
Indices: 16767--17179 Score: 560
Period size: 75 Copynumber: 5.5 Consensus size: 75
16757 TCATGAAAAA
* * *
16767 TCTAAACGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCGGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
16832 CCCGTATAAC
66 CCCGTATAAC
* *
16842 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACTCGCAGACGGCCGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
16907 CCCGTATAAC
66 CCCGTATAAC
* *
16917 TCTAAGCGAGGTCGAACGTCCAAGCAAACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
16982 CCCGGTATAAC
66 CCC-GTATAAC
* * * * * * * *
16993 TCTAAGCGACGCCGAACGTCCAAGCAGATGCCACCCG-AGGACGGCTGAGTGCCTAGATTGGTGT
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCA-GACGGCTGAGCGCCTAGACTGGCGC
17057 CCCCGTATAAC
65 CCCCGTATAAC
* * * *
17068 TCTAAGCGAGGTCGATCGTCCAAGCAGGCGTCACCCGCAGACGACTGAGCACCTAGACTGGCGCT
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGC-
*
17133 ACCCGTATAAC
65 CCCCGTATAAC
* * * *
17144 TCCAAGCTGA-GTCAAACATCCAAACAGACGTCACCC
1 TCTAAGC-GAGGTCGAACGTCCAAGCAGACGTCACCC
17180 ACAGGAGTCC
Statistics
Matches: 296, Mismatches: 37, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
75 192 0.65
76 102 0.34
77 2 0.01
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.14
Consensus pattern (75 bp):
TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCAGACGGCTGAGCGCCTAGACTGGCGCC
CCCGTATAAC
Found at i:17166 original size:151 final size:150
Alignment explanation
Indices: 16767--17179 Score: 560
Period size: 151 Copynumber: 2.7 Consensus size: 150
16757 TCATGAAAAA
* *
16767 TCTAAACGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCGGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGCC
* * *
16832 CCCGTATAACTCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACTCGCAGACGGCCGAGCGCCTA
66 CCCGTATAACTCTAAGCGACGTCGAACGTCCAAGCAGACGCCACCCGCAGACGGCCGAGCGCCTA
16897 GACTGGCGCCCCCGTATAAC
131 GACTGGCGCCCCCGTATAAC
*
16917 TCTAAGCGAGGTCGAACGTCCAAGCAAACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGCC
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGCC
* * * *
16982 CCCGGTATAACTCTAAGCGACGCCGAACGTCCAAGCAGATGCCACCCG-AGGACGGCTGAGTGCC
66 CCC-GTATAACTCTAAGCGACGTCGAACGTCCAAGCAGACGCCACCCGCA-GACGGCCGAGCGCC
* * *
17046 TAGATTGGTGTCCCCGTATAAC
129 TAGACTGGCGCCCCCGTATAAC
* * * * *
17068 TCTAAGCGAGGTCGATCGTCCAAGCAGGCGTCACCCGCAGACGACTGAGCACCTAGACTGGCGCT
1 TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGC-
* * * * * *
17133 ACCCGTATAACTCCAAGCTGA-GTCAAACATCCAAACAGACGTCACCC
65 CCCCGTATAACTCTAAGC-GACGTCGAACGTCCAAGCAGACGCCACCC
17180 ACAGGAGTCC
Statistics
Matches: 232, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
150 66 0.28
151 161 0.69
152 5 0.02
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.14
Consensus pattern (150 bp):
TCTAAGCGAGGTCGAACGTCCAAGCAGACGTCACCCGCGGACGGCTGAGCGCCTAGACTGGCGCC
CCCGTATAACTCTAAGCGACGTCGAACGTCCAAGCAGACGCCACCCGCAGACGGCCGAGCGCCTA
GACTGGCGCCCCCGTATAAC
Found at i:17770 original size:19 final size:18
Alignment explanation
Indices: 17746--17782 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17736 TTGAAGATTT
17746 CTTGAAGACAATTTGAAGA
1 CTTGAAGACAA-TTGAAGA
*
17765 CTTGAAGACCATTGAAGA
1 CTTGAAGACAATTGAAGA
17783 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (18 bp):
CTTGAAGACAATTGAAGA
Found at i:22706 original size:21 final size:21
Alignment explanation
Indices: 22660--22700 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
22650 GTCAGCCCGC
*
22660 CAAAATTCGAAATTTGAATTT
1 CAAAATTCGAAATTCGAATTT
22681 CAAAATTCGAAATTCGAATT
1 CAAAATTCGAAATTCGAATT
22701 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
CAAAATTCGAAATTCGAATTT
Found at i:23568 original size:15 final size:15
Alignment explanation
Indices: 23548--23578 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
23538 CATTAAACCA
23548 ACCAATTAATATGTC
1 ACCAATTAATATGTC
23563 ACCAATTAATATGTC
1 ACCAATTAATATGTC
23578 A
1 A
23579 GGTATATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (15 bp):
ACCAATTAATATGTC
Found at i:25838 original size:3 final size:3
Alignment explanation
Indices: 25832--25863 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
25822 ATAAATAAAG
25832 ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A
25864 AGAAGATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:32182 original size:12 final size:12
Alignment explanation
Indices: 32165--32189 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32155 CTCCATAGAA
32165 AAAAAAAAAAAT
1 AAAAAAAAAAAT
32177 AAAAAAAAAAAT
1 AAAAAAAAAAAT
32189 A
1 A
32190 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAAAT
Done.