Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024062.1 Corchorus olitorius cultivar O-4 contig24095, 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: 18343
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:108 original size:54 final size:54
Alignment explanation
Indices: 1--353 Score: 311
Period size: 54 Copynumber: 6.6 Consensus size: 54
* * * *
1 ACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT-AGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGA-AGATCA
* *
54 ACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * *
108 ACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATCGGGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * * * * *
162 ACTTTGATCTTTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATG-ACCACACCGGATCATCTGAAGATCA
* * * * * *
216 ACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAGGATCA
1 ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
* * * * * * **
270 ACTCTGACCATT-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGGGATCA
1 ACTCTGATC-TTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
*
324 ACTCTGACCATT-GAAAACTTCTTGGAATGA
1 ACTCTGATC-TTCGAAAACTTCTTGGAATGA
354 GATCAACTCT
Statistics
Matches: 250, Mismatches: 45, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
53 22 0.09
54 225 0.90
55 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (54 bp):
ACTCTGATCTTCGAAAACTTCTTGGAATGACCACACCGGATCATCTGAAGATCA
Found at i:325 original size:162 final size:162
Alignment explanation
Indices: 47--350 Score: 378
Period size: 162 Copynumber: 1.9 Consensus size: 162
37 GGATCATCTA
* * * *
47 GAGATCAACTCTGATCTTCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCAACTC
1 GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
* * * * * *
112 TGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATCGGGAGATCAACTTTGATCTTTGAA
66 TGACCTTCGAAAACTTCTTGAAACGACAACACCGGACCATCGGGAGATCAACTCTGACCATTGAA
177 AACTTCTAGGAAGAACCGCACTGGACCTTTTG
131 AACTTCTAGGAAGAACCGCACTGGACCTTTTG
* * * *
209 GAGATCAACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAGGATCAACTC
1 GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
* * ** * * *
274 TGACCATT-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGG-GATCAACTCTGACCATTG
66 TGACC-TTCGAAAACTTCTTGAAACGACAACACCGGACC-ATCGGGAGATCAACTCTGACCATTG
*
337 AAAACTTCTTGGAA
129 AAAACTTCTAGGAA
351 TGAGATCAAC
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
162 112 0.95
163 6 0.05
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (162 bp):
GAGATCAACTCTGATCATCAAAAACCTCTTGAAATGACCACACCGGATCATCTGAAGATCAACTC
TGACCTTCGAAAACTTCTTGAAACGACAACACCGGACCATCGGGAGATCAACTCTGACCATTGAA
AACTTCTAGGAAGAACCGCACTGGACCTTTTG
Found at i:353 original size:108 final size:108
Alignment explanation
Indices: 1--350 Score: 395
Period size: 108 Copynumber: 3.2 Consensus size: 108
* *
1 ACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCT-AGAGATCAACTCTGATCT
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATCT
* ** * * * * *
64 TCGAAAACTTCTTGAAATGACCATACCGGATCATCTGAAGATCA
66 T-GAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
* * * * * *
108 ACTCTGATCTTCGAAAATTTCTTGAAACGACAACACCGGATCATC-GGGAGATCAACTTTGATCT
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATC-
*
172 TTGAAAACTTCTAGGAA-GAACCGCACTGGACCTTTTGGAGATCA
65 TTGAAAACTTCTTGGAATG-ACCGCACTGGACCTTTTGGAGATCA
* * * * * *
216 ACTCTGATCATCAAAAACCTCTTGGAATGACCGCACGGGATCATCTGAG-GATCAACTCTGACCA
1 ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATC-
*
280 TTGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGGGATCA
65 TTGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
* *
324 ACTCTGACCATTGAAAACTTCTTGGAA
1 ACTCTGATCATCGAAAACTTCTTGGAA
351 TGAGATCAAC
Statistics
Matches: 201, Mismatches: 36, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
107 21 0.10
108 175 0.87
109 5 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (108 bp):
ACTCTGATCATCGAAAACTTCTTGGAACGACCACACCGGATCATCTGAGAGATCAACTCTGATCT
TGAAAACTTCTTGGAATGACCGCACTGGACCTTTTGGAGATCA
Found at i:358 original size:35 final size:35
Alignment explanation
Indices: 319--582 Score: 348
Period size: 35 Copynumber: 7.4 Consensus size: 35
309 ACCTTTTGGG
* ** *
319 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
354 GATCAACTCTGATCATAAAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
391 GATCAACTCTGATCATAAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
*
428 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
463 GATCAACTCTGATAATAAAAACCTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
498 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
533 GATCAACTCTGATAATAAAAAAACTTCTTGAGAGGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
*
569 GATCAACTCAGATC
1 GATCAACTCTGATC
583 TCAGAAAGCT
Statistics
Matches: 208, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
35 110 0.53
36 29 0.14
37 69 0.33
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Found at i:2009 original size:26 final size:25
Alignment explanation
Indices: 1979--2033 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1969 ATCTTTAGCA
* *
1979 TTTTCAACTTCTTTCTTTTCTTTTCT
1 TTTTCAACTTCTTTATCTT-TTTTCT
* *
2005 TTTTCAATTTTTTTATCTTTTTTCT
1 TTTTCAACTTCTTTATCTTTTTTCT
2030 TTTT
1 TTTT
2034 TCTTTCCCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTCAACTTCTTTATCTTTTTTCT
Found at i:10291 original size:16 final size:15
Alignment explanation
Indices: 10270--10309 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
10260 TTGCTTTGCT
10270 TTGTTTTCTAGTATAA
1 TTGTTTTCT-GTATAA
* *
10286 TTGTTTTCTTTTTAA
1 TTGTTTTCTGTATAA
10301 TTGTTTTCT
1 TTGTTTTCT
10310 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.15, C:0.07, G:0.10, T:0.68
Consensus pattern (15 bp):
TTGTTTTCTGTATAA
Found at i:10303 original size:15 final size:15
Alignment explanation
Indices: 10283--10311 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10273 TTTTCTAGTA
10283 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
10298 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
10312 CAACCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:11136 original size:183 final size:182
Alignment explanation
Indices: 10829--11183 Score: 656
Period size: 183 Copynumber: 1.9 Consensus size: 182
10819 GTCATATTTA
10829 GCTCATCAAATTATAAAAACAATACTTAGTCAAAAAATGGCTTAAACCGGGGTGTAAAAGCCACA
1 GCTCATCAAATTATAAAAACAATACTTAGTCAAAAAATGGCTTAAACCGGGGTGTAAAAGCCACA
* **
10894 TGTCCTTAATTGAAAAACTTGCAAAAGTTGCAACCGAAGTCGGAATAAGCCTTAATTTCACCAAC
66 TGTCCTTAATTGAAAAACTTGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAAATTTCACCAAC
*
10959 ATGGTTCAATCAACCTAATATGATATTAGGGAAAGACTTAGTCAAAAATGTG
131 AGGGTTCAATCAACCTAATATGATATTAGGGAAAGACTTAGTCAAAAATGTG
11011 GCTCATCAAATTATAAAAACAATACTTAGTCAAGAAAATGGCTTAAACCGGGGTGTAAAAGCCAC
1 GCTCATCAAATTATAAAAACAATACTTAGTCAA-AAAATGGCTTAAACCGGGGTGTAAAAGCCAC
*
11076 ATGTCCTTAATTGAAAAATTTGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAAATTTCACCAA
65 ATGTCCTTAATTGAAAAACTTGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAAATTTCACCAA
11141 CAGGGTTCAATCAACCTAATATGATATTAGGGAAAGACTTAGT
130 CAGGGTTCAATCAACCTAATATGATATTAGGGAAAGACTTAGT
11184 TGAAAATCCC
Statistics
Matches: 167, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
182 33 0.20
183 134 0.80
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (182 bp):
GCTCATCAAATTATAAAAACAATACTTAGTCAAAAAATGGCTTAAACCGGGGTGTAAAAGCCACA
TGTCCTTAATTGAAAAACTTGCAAAAGTTGCAAACGAAGTCGGAATAAGCCAAAATTTCACCAAC
AGGGTTCAATCAACCTAATATGATATTAGGGAAAGACTTAGTCAAAAATGTG
Found at i:13278 original size:9 final size:9
Alignment explanation
Indices: 13264--13296 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
13254 AGAATTATGT
*
13264 GTATGTGAA
1 GTATGTGAG
13273 GTATGTGAG
1 GTATGTGAG
13282 GTATGTGAG
1 GTATGTGAG
13291 GTATGT
1 GTATGT
13297 TACAGGAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.36
Consensus pattern (9 bp):
GTATGTGAG
Found at i:15422 original size:42 final size:42
Alignment explanation
Indices: 15368--15453 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
15358 TTAATTGGCC
15368 AAATTCCAAATCCAATTTGGCTTAGGATTTCAATTTAGCCAA
1 AAATTCCAAATCCAATTTGGCTTAGGATTTCAATTTAGCCAA
*
15410 AAATTCCAAATCCAATTTGGCTTAGGATTTTAATTTAGCCAA
1 AAATTCCAAATCCAATTTGGCTTAGGATTTCAATTTAGCCAA
15452 AA
1 AA
15454 TTGATTAGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (42 bp):
AAATTCCAAATCCAATTTGGCTTAGGATTTCAATTTAGCCAA
Done.