Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013508.1 Corchorus capsularis cultivar CVL-1 contig13529, 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: 39469
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:3543 original size:19 final size:20
Alignment explanation
Indices: 3505--3543 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3495 GCTTGGTCCC
* *
3505 TTTGCTTCCAAATTTCAATT
1 TTTGCTGCCAAATCTCAATT
3525 TTTGCTGCCAAA-CTCAATT
1 TTTGCTGCCAAATCTCAATT
3544 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (20 bp):
TTTGCTGCCAAATCTCAATT
Found at i:8107 original size:17 final size:17
Alignment explanation
Indices: 8087--8119 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8077 GCAGCCTATC
*
8087 ACCTCATACTACCTAGT
1 ACCTCATACTAACTAGT
8104 ACCTCATACTAACTAG
1 ACCTCATACTAACTAG
8120 GTACTATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTAACTAGT
Found at i:8291 original size:21 final size:21
Alignment explanation
Indices: 8267--8309 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
8257 CAGAAGAGTT
8267 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
8288 CGCCTTCCTCAGCAAGTAAAA
1 CGCCTTCCTCAGCAAGTAAAA
8309 C
1 C
8310 CCGCCAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.35, G:0.14, T:0.19
Consensus pattern (21 bp):
CGCCTTCCTCAGCAAGTAAAA
Found at i:38118 original size:51 final size:52
Alignment explanation
Indices: 38058--38155 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
38048 CGTTAGCTGC
*
38058 AAAAGGGATGAAAGTCAGAAATAGATCAGAATTGAAGAAA-GTTTAAGCTAA
1 AAAAGGGATGAAAGTCAGAAATAGATCAGAATTAAAGAAATGTTTAAGCTAA
*
38109 AAAAGGGATGAAAGTCAGAAATATATCAGAATTAAAGAAATGTTTAA
1 AAAAGGGATGAAAGTCAGAAATAGATCAGAATTAAAGAAATGTTTAA
38156 TCAAACAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 38 0.86
52 6 0.14
ACGTcount: A:0.52, C:0.05, G:0.21, T:0.21
Consensus pattern (52 bp):
AAAAGGGATGAAAGTCAGAAATAGATCAGAATTAAAGAAATGTTTAAGCTAA
Found at i:38273 original size:19 final size:18
Alignment explanation
Indices: 38249--38309 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
38239 CTAGCAATCT
38249 TCTTTCTTTCTTCCTTCTC
1 TCTTTCTTTCTT-CTTCTC
*
38268 TCTTTCTCTCTT-TTCTC
1 TCTTTCTTTCTTCTTCTC
*
38285 TTCTTTTCTTCTTTTCTTCTC
1 -TC-TTTCTT-TCTTCTTCTC
38306 TCTT
1 TCTT
38310 CACTCCTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.14
18 2 0.06
19 18 0.51
20 5 0.14
21 5 0.14
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTCTTTCTTCTTCTC
Found at i:39282 original size:49 final size:49
Alignment explanation
Indices: 39164--39469 Score: 266
Period size: 49 Copynumber: 6.2 Consensus size: 49
39154 TTCCATCCGT
* * * *
39164 GAAGGGCGTTTTAGGG-AAAA-CA-AGTAAAAATTAGTGCCTTCCGTCCGG
1 GAAGGGCATTTT-GGGAAAAAGCAGA-TAAAAATAAGTGACTTCCGTCTGG
* * * * * *
39212 GAAGGGCATTTTGAGACAAAGCAGGTAAAGATTAGTGATTTCCGTCTGG
1 GAAGGGCATTTTGGGAAAAAGCAGATAAAAATAAGTGACTTCCGTCTGG
* ** * *
39261 GAAGGGCATTTTAGGAAAAAGCA-AGCGAAAATAAGTGGCTTCCGTCTAG
1 GAAGGGCATTTTGGGAAAAAGCAGA-TAAAAATAAGTGACTTCCGTCTGG
* *
39310 GAAGGGCATTTTGGGAAATAA-CAGATAAAAACAAGT-ACCTTCCGTCCGG
1 GAAGGGCATTTTGGGAAA-AAGCAGATAAAAATAAGTGA-CTTCCGTCTGG
* * * *
39359 GAAGGGCATTCTGGGAAATACCAGATAAAAACAAGT-ACCTTCCGTCTGG
1 GAAGGGCATTTTGGGAAAAAGCAGATAAAAATAAGTGA-CTTCCGTCTGG
* * * * *
39408 GAAGGGCATTTTGGGAAATAGCAGATAAAAACAGGATGCCTTCCGTCCGG
1 GAAGGGCATTTTGGGAAAAAGCAGATAAAAATAAG-TGACTTCCGTCTGG
39458 GAAGGGCATTTT
1 GAAGGGCATTTT
Statistics
Matches: 214, Mismatches: 34, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.01
48 15 0.07
49 171 0.80
50 26 0.12
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.22
Consensus pattern (49 bp):
GAAGGGCATTTTGGGAAAAAGCAGATAAAAATAAGTGACTTCCGTCTGG
Found at i:39353 original size:98 final size:97
Alignment explanation
Indices: 39152--39469 Score: 343
Period size: 98 Copynumber: 3.2 Consensus size: 97
39142 GAGAATGGTG
* * * * * *
39152 CCTTCCATCCGTGAAGGGCGTTTTAGGGAAAACAAGTAAAAATTAGTGCCTTCCGTCCGGGAAGG
1 CCTTCCGTCCGGGAAGGGCATTTTAGGAAAAACAAGTAAAAATAAGTGCCTTCCGTCTGGGAAGG
* * * **
39217 GCATTTTGAGACAA-AGCAGGTAAAGATTAGTGA
66 GCATTTTGGGA-AATAGCAGATAAAAACAAGT-A
* * ** * *
39250 -TTTCCGTCTGGGAAGGGCATTTTAGGAAAAAGCAAGCGAAAATAAGTGGCTTCCGTCTAGGAAG
1 CCTTCCGTCCGGGAAGGGCATTTTAGGAAAAA-CAAGTAAAAATAAGTGCCTTCCGTCTGGGAAG
*
39314 GGCATTTTGGGAAATAACAGATAAAAACAAGTA
65 GGCATTTTGGGAAATAGCAGATAAAAACAAGTA
* * * * * *
39347 CCTTCCGTCCGGGAAGGGCATTCTGGGAAATACCAGATAAAAACAAGTACCTTCCGTCTGGGAAG
1 CCTTCCGTCCGGGAAGGGCATTTTAGGAAAAACAAG-TAAAAATAAGTGCCTTCCGTCTGGGAAG
* *
39412 GGCATTTTGGGAAATAGCAGATAAAAACAGGATG
65 GGCATTTTGGGAAATAGCAGATAAAAACAAG-TA
39446 CCTTCCGTCCGGGAAGGGCATTTT
1 CCTTCCGTCCGGGAAGGGCATTTT
Statistics
Matches: 181, Mismatches: 34, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
97 31 0.17
98 126 0.70
99 24 0.13
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (97 bp):
CCTTCCGTCCGGGAAGGGCATTTTAGGAAAAACAAGTAAAAATAAGTGCCTTCCGTCTGGGAAGG
GCATTTTGGGAAATAGCAGATAAAAACAAGTA
Done.