Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009637.1 Corchorus capsularis cultivar CVL-1 contig09658, 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: 69227
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2439 original size:40 final size:38
Alignment explanation
Indices: 2381--2462 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
2371 TGTGACTATA
* * * *
2381 AGGTATTACTCCTGAAAATGTTTCTTGCTTGAAGATTTTG
1 AGGTATTACTCATAAAAAT-CTCCTT-CTTGAAGATTTTG
* *
2421 AGGTATTATTCATAAAAATCTCCTTTTTGAAGATTTTG
1 AGGTATTACTCATAAAAATCTCCTTCTTGAAGATTTTG
2459 AGGT
1 AGGT
2463 TCCTTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
38 16 0.44
39 4 0.11
40 16 0.44
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (38 bp):
AGGTATTACTCATAAAAATCTCCTTCTTGAAGATTTTG
Found at i:8872 original size:56 final size:55
Alignment explanation
Indices: 8805--8916 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 55
8795 GGAGTTATAC
8805 TAAGTCTGCTAGTTGAGAGCATATGTAAATTAAGGTCTGTTTTTCATTTCACCTAG
1 TAAGTCTGCTAGTTGAGAGCATATGTAAATTAA-GTCTGTTTTTCATTTCACCTAG
8861 TAAGTCTGCTAGTTGAGAGCATATGTAAATTAAGTCTGTTTTTCATTTCACCTAG
1 TAAGTCTGCTAGTTGAGAGCATATGTAAATTAAGTCTGTTTTTCATTTCACCTAG
8916 T
1 T
8917 CAGCAAGATG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 23 0.41
56 33 0.59
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (55 bp):
TAAGTCTGCTAGTTGAGAGCATATGTAAATTAAGTCTGTTTTTCATTTCACCTAG
Found at i:15336 original size:17 final size:17
Alignment explanation
Indices: 15294--15336 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
15284 TCAATGATAT
*
15294 TATTATATAGTACTACA
1 TATTATATACTACTACA
*
15311 TATTATATATACTAGTACA
1 TA-T-TATATACTACTACA
15330 TATTATA
1 TATTATA
15337 ATATTGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.27
18 2 0.09
19 14 0.64
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (17 bp):
TATTATATACTACTACA
Found at i:16914 original size:15 final size:15
Alignment explanation
Indices: 16891--16920 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16881 ATCGGTTGAA
*
16891 ATATTGTGTATCGTG
1 ATATCGTGTATCGTG
16906 ATATCGTGTATCGTG
1 ATATCGTGTATCGTG
16921 GCGGCCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (15 bp):
ATATCGTGTATCGTG
Found at i:27918 original size:19 final size:19
Alignment explanation
Indices: 27894--27935 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
27884 AGTTCAGTCT
27894 AAATCTTTTCCAATAATCA
1 AAATCTTTTCCAATAATCA
27913 AAATCTTTTCCAATAATCA
1 AAATCTTTTCCAATAATCA
27932 AAAT
1 AAAT
27936 TTTCTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATCTTTTCCAATAATCA
Found at i:51508 original size:2 final size:2
Alignment explanation
Indices: 51497--51535 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
51487 ACTATAAGTC
*
51497 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51536 ATAGTAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:55831 original size:22 final size:24
Alignment explanation
Indices: 55803--55851 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55793 CAATATGAAA
55803 AAGAGAGAAGATAAAACTGTTCGT
1 AAGAGAGAAGATAAAACTGTTCGT
55827 AAGAGAGAAGATAAAACTGTTCGT
1 AAGAGAGAAGATAAAACTGTTCGT
55851 A
1 A
55852 GAACCTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
AAGAGAGAAGATAAAACTGTTCGT
Found at i:56435 original size:132 final size:132
Alignment explanation
Indices: 56195--56458 Score: 501
Period size: 132 Copynumber: 2.0 Consensus size: 132
56185 AGTTTTCTAA
*
56195 AGCCAAGAGCCTCTCAGGGGCTGCTACACTGAAGCAGCAAGTGAATAAGAAATTCAATGAAGTCA
1 AGCCAAGAGCCTCTCAGGGGCTGCTACACTGAAGCAGCAACTGAATAAGAAATTCAATGAAGTCA
56260 TGGCACGGCCTGAGATAAATGAGAAGCTTGAAGCCTTAAAGGCTGAGGTTCAGAGTTCTGGTGCA
66 TGGCACGGCCTGAGATAAATGAGAAGCTTGAAGCCTTAAAGGCTGAGGTTCAGAGTTCTGGTGCA
56325 TC
131 TC
*
56327 AGCCAAGAGCCTCTCAGGGGCTGCTACACTGAAGCAGCAACTGAATGAGAAATTCAATGAAGTCA
1 AGCCAAGAGCCTCTCAGGGGCTGCTACACTGAAGCAGCAACTGAATAAGAAATTCAATGAAGTCA
*
56392 TGGCACGGCCTGAGATAAATGAGAAGCTTGAAGCCTTAGAGGCTGAGGTTCAGAGTTCTGGTGCA
66 TGGCACGGCCTGAGATAAATGAGAAGCTTGAAGCCTTAAAGGCTGAGGTTCAGAGTTCTGGTGCA
56457 TC
131 TC
56459 CAGCTTTGCT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (132 bp):
AGCCAAGAGCCTCTCAGGGGCTGCTACACTGAAGCAGCAACTGAATAAGAAATTCAATGAAGTCA
TGGCACGGCCTGAGATAAATGAGAAGCTTGAAGCCTTAAAGGCTGAGGTTCAGAGTTCTGGTGCA
TC
Found at i:65141 original size:10 final size:10
Alignment explanation
Indices: 65126--65153 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
65116 AAAAGAAAGC
65126 TTTCCACCCA
1 TTTCCACCCA
65136 TTTCCACCCA
1 TTTCCACCCA
65146 TTTCCACC
1 TTTCCACC
65154 AATTCATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (10 bp):
TTTCCACCCA
Found at i:66798 original size:27 final size:27
Alignment explanation
Indices: 66745--66798 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
66735 GCACGTGACA
*
66745 TTTTTGACACGTGGCGTGCCATGTGTCC
1 TTTTTGACACGTGGCATGCCA-GTGTCC
*
66773 TTTTTGTAGACGTGGCATGCCA-TGTC
1 TTTTTG-ACACGTGGCATGCCAGTGTC
66799 GGATGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 6 0.26
29 13 0.57
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (27 bp):
TTTTTGACACGTGGCATGCCAGTGTCC
Done.