Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008094.1 Corchorus capsularis cultivar CVL-1 contig08115, 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: 76872
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:31 original size:15 final size:15
Alignment explanation
Indices: 11--52 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1 TACTTAGTTT
11 ATTAGTTTATGATTA
1 ATTAGTTTATGATTA
26 ATTAG--TAT--TTA
1 ATTAGTTTATGATTA
37 ATTAGTTTATGATTA
1 ATTAGTTTATGATTA
52 A
1 A
53 AATGAAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
11 8 0.35
13 6 0.26
15 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (15 bp):
ATTAGTTTATGATTA
Found at i:231 original size:21 final size:21
Alignment explanation
Indices: 191--231 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
181 GAACAAAGTG
**
191 TAAAAGGGGGGTGGTATTTAA
1 TAAAAGGGGGACGGTATTTAA
*
212 TAAAAGGGGGACGGTGTTTA
1 TAAAAGGGGGACGGTATTTA
232 GCAATCCAGT
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:0.32, C:0.02, G:0.39, T:0.27
Consensus pattern (21 bp):
TAAAAGGGGGACGGTATTTAA
Found at i:16544 original size:65 final size:65
Alignment explanation
Indices: 16440--16571 Score: 264
Period size: 65 Copynumber: 2.0 Consensus size: 65
16430 AAAAGGGAGA
16440 TTAATTATACCAAAATGATTATCAATTTCATAGAGATGAACAATCTCATGACCTAATGAACCATG
1 TTAATTATACCAAAATGATTATCAATTTCATAGAGATGAACAATCTCATGACCTAATGAACCATG
16505 TTAATTATACCAAAATGATTATCAATTTCATAGAGATGAACAATCTCATGACCTAATGAACCATG
1 TTAATTATACCAAAATGATTATCAATTTCATAGAGATGAACAATCTCATGACCTAATGAACCATG
16570 TT
1 TT
16572 GAGAAAATGT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.32
Consensus pattern (65 bp):
TTAATTATACCAAAATGATTATCAATTTCATAGAGATGAACAATCTCATGACCTAATGAACCATG
Found at i:25803 original size:15 final size:15
Alignment explanation
Indices: 25783--25821 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
25773 CAAGGAAGAG
25783 AGTCAAGTAATTACT
1 AGTCAAGTAATTACT
* *
25798 AGTCAACTACTTACT
1 AGTCAAGTAATTACT
25813 AGTCAAGTA
1 AGTCAAGTA
25822 GTACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (15 bp):
AGTCAAGTAATTACT
Found at i:33615 original size:2 final size:2
Alignment explanation
Indices: 33608--33647 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
33598 CGAAGTCATC
33608 TA TA TA TA TA TA -A TA -A TA TA TA CTA TA TA TA TA 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
33648 CTTCTTTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:56032 original size:3 final size:3
Alignment explanation
Indices: 56026--56061 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
56016 CTATACCTAT
56026 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TATA TAA T
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA T
56062 TTCTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:62610 original size:31 final size:32
Alignment explanation
Indices: 62551--62625 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 32
62541 GCATAAATGC
*
62551 CATTTTGCACCCCTTAAATTTGTACGGACCGT
1 CATTTTGCACCCCTTAAATTCGTACGGACCGT
* * *
62583 CATTTTGCA-CCTTTAAGTTCGTACGGACTGT
1 CATTTTGCACCCCTTAAATTCGTACGGACCGT
* *
62614 CACTTTGTACCC
1 CATTTTGCACCC
62626 AACTTTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
31 25 0.69
32 11 0.31
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (32 bp):
CATTTTGCACCCCTTAAATTCGTACGGACCGT
Found at i:62799 original size:30 final size:30
Alignment explanation
Indices: 62735--62829 Score: 127
Period size: 31 Copynumber: 3.1 Consensus size: 30
62725 ACGTGGCATA
*
62735 CCACGTGTACCAAAAAGTGACAAGTGACATG
1 CCACGTGTACCAAAAAGTGACACGTGA-ATG
62766 CCACGTGTACCAAAAAGTGACACGTGAATG
1 CCACGTGTACCAAAAAGTGACACGTGAATG
* ** *
62796 CCACATGTTTCAAAAAGTGACACGTAGCATG
1 CCACGTGTACCAAAAAGTGACACGT-GAATG
62827 CCA
1 CCA
62830 TGTGCACAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 25 0.43
31 33 0.57
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (30 bp):
CCACGTGTACCAAAAAGTGACACGTGAATG
Found at i:62840 original size:30 final size:29
Alignment explanation
Indices: 62725--62840 Score: 99
Period size: 31 Copynumber: 3.8 Consensus size: 29
62715 ACGGTGTCCA
* *
62725 ACGTGGCATACCACGTGTACCAAAAAGTGAC
1 ACGT-GCATGCCATGTGTA-CAAAAAGTGAC
* *
62756 AAGTGACATGCCACGTGTACCAAAAAGTGAC
1 ACGTG-CATGCCATGTGTA-CAAAAAGTGAC
* *
62787 ACGTGAATGCCACATGT-TTCAAAAAGTGAC
1 ACGTGCATG-C-CATGTGTACAAAAAGTGAC
*
62817 ACGTAGCATGCCATGTGCACAAAA
1 ACGT-GCATGCCATGTGTACAAAA
62841 TGATACATGC
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.07
30 25 0.35
31 37 0.52
32 4 0.06
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (29 bp):
ACGTGCATGCCATGTGTACAAAAAGTGAC
Found at i:63438 original size:2 final size:2
Alignment explanation
Indices: 63431--63459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
63421 CCATTATAAT
63431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63460 TTTCAGAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65145 original size:1 final size:1
Alignment explanation
Indices: 65106--65134 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
65096 GAGCTTCATG
65106 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
65135 GATGATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:65473 original size:2 final size:2
Alignment explanation
Indices: 65466--65490 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65456 AACTATATGT
65466 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
65491 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74336 original size:45 final size:45
Alignment explanation
Indices: 74285--74375 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
74275 TGGTTGGAGC
*
74285 TTCTTCCTTTGGTAAGAAGTTCTTGAGCTCTTTGATCTGATAGTT
1 TTCTTCCTTTGGTAAGAAGTTCTTAAGCTCTTTGATCTGATAGTT
74330 TTCTTCCTTTGGTAAGAAGTTCTTAAGCTCTTTGATCTGATAGTT
1 TTCTTCCTTTGGTAAGAAGTTCTTAAGCTCTTTGATCTGATAGTT
74375 T
1 T
74376 CCTTATTTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (45 bp):
TTCTTCCTTTGGTAAGAAGTTCTTAAGCTCTTTGATCTGATAGTT
Found at i:74362 original size:23 final size:23
Alignment explanation
Indices: 74291--74363 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
74281 GAGCTTCTTC
*
74291 CTTTGGTAAGAAGTTCTTGAGCT
1 CTTTGGTAAGAAGTTCTTAAGCT
* ** ***
74314 CTTTGATCTGATAGTT-TTCTTC-
1 CTTTGGTAAGA-AGTTCTTAAGCT
74336 CTTTGGTAAGAAGTTCTTAAGCT
1 CTTTGGTAAGAAGTTCTTAAGCT
74359 CTTTG
1 CTTTG
74364 ATCTGATAGT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 4 0.11
22 11 0.31
23 16 0.46
24 4 0.11
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (23 bp):
CTTTGGTAAGAAGTTCTTAAGCT
Found at i:76850 original size:2 final size:2
Alignment explanation
Indices: 76843--76872 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
76833 TGAGTACTAG
76843 TA 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 TA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.