Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006255.1 Corchorus capsularis cultivar CVL-1 contig06274, 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: 57241
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4772 original size:11 final size:11
Alignment explanation
Indices: 4758--4782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4748 TATATATTTT
4758 TATTTTTTTGA
1 TATTTTTTTGA
4769 TATTTTTTTGA
1 TATTTTTTTGA
4780 TAT
1 TAT
4783 AACTACAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (11 bp):
TATTTTTTTGA
Found at i:6433 original size:33 final size:33
Alignment explanation
Indices: 6315--6421 Score: 178
Period size: 33 Copynumber: 3.2 Consensus size: 33
6305 CTAATTGTGA
* *
6315 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
6348 TGAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
*
6381 TGAAAATAATTCTGTTTTGGTTGATCATAACAT
1 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
6414 TGAAAATA
1 TGAAAATA
6422 GGACTGTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (33 bp):
TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
Found at i:6848 original size:30 final size:30
Alignment explanation
Indices: 6812--6870 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
6802 CAAGGGGGAG
6812 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATGCG-CCAAGGACTTATCATGGAA
*
6842 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATGATGCGCCAAGGACTTATCATGGA
6871 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAA
Found at i:17176 original size:21 final size:21
Alignment explanation
Indices: 17138--17179 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17128 CCTTGGTTTA
*
17138 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
17159 TGATCTTCAATGGACTTCAAT
1 TGATCTTCAATACACTTCAAT
17180 CCTTCAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:25505 original size:22 final size:21
Alignment explanation
Indices: 25473--25520 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
25463 TAAATATTAG
25473 AAGA-TTTTTCGGAGAA-AGAGA
1 AAGAGTTTTTCGG-GAAGAG-GA
25494 AAGAGTTTTTCGGGAAGAGGA
1 AAGAGTTTTTCGGGAAGAGGA
25515 AAGAGT
1 AAGAGT
25521 AATGGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.40, C:0.04, G:0.33, T:0.23
Consensus pattern (21 bp):
AAGAGTTTTTCGGGAAGAGGA
Found at i:27473 original size:30 final size:30
Alignment explanation
Indices: 27433--27490 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27423 AGCTTCTCCT
* *
27433 TGCTATTTGAAGTAGGATTTGCGATTCCCA
1 TGCTACTTGAAGTAGGATTTACGATTCCCA
* *
27463 TGCTACTTGAATTAGGGTTTACGATTCC
1 TGCTACTTGAAGTAGGATTTACGATTCC
27491 TCCTCCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (30 bp):
TGCTACTTGAAGTAGGATTTACGATTCCCA
Found at i:33932 original size:30 final size:30
Alignment explanation
Indices: 33892--33949 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
33882 AGCTTCTCCT
*
33892 TGCTATTTGAAGTAGGATTTACGATTCCCA
1 TGCTACTTGAAGTAGGATTTACGATTCCCA
* * *
33922 TGCTACTTGAATTAGGGTTTGCGATTCC
1 TGCTACTTGAAGTAGGATTTACGATTCC
33950 TCCTCCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (30 bp):
TGCTACTTGAAGTAGGATTTACGATTCCCA
Found at i:40366 original size:21 final size:20
Alignment explanation
Indices: 40342--40381 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
40332 TAGCATCTCA
40342 ACCTGGGTGCCTGGAGTACTT
1 ACCTGGGTGCCTGG-GTACTT
40363 ACCTGGGTGCCTGGGTACT
1 ACCTGGGTGCCTGGGTACT
40382 ATCAGGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.12, C:0.25, G:0.35, T:0.28
Consensus pattern (20 bp):
ACCTGGGTGCCTGGGTACTT
Found at i:42164 original size:19 final size:18
Alignment explanation
Indices: 42140--42175 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42130 TGAAGATTTC
42140 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
42159 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
42176 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:47165 original size:17 final size:17
Alignment explanation
Indices: 47143--47177 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
47133 CGATACCCTT
*
47143 AACCTAAAACTAGAGAA
1 AACCTAAAACTAAAGAA
47160 AACCTAAAACTAAAGAA
1 AACCTAAAACTAAAGAA
47177 A
1 A
47178 GGTAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.09, T:0.11
Consensus pattern (17 bp):
AACCTAAAACTAAAGAA
Found at i:49547 original size:21 final size:21
Alignment explanation
Indices: 49534--49573 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49524 AGAAACTTTC
49534 AAATATAAATAAGAAACCTCT
1 AAATATAAATAAGAAACCTCT
*
49555 AAATATAAATAAGAGACCT
1 AAATATAAATAAGAAACCT
49574 GCAGCATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (21 bp):
AAATATAAATAAGAAACCTCT
Found at i:54491 original size:19 final size:18
Alignment explanation
Indices: 54458--54493 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54448 TTGAAATAAT
54458 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
54476 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
54494 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.