Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016354.1 Corchorus olitorius cultivar O-4 contig16387, 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: 42469
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:167 original size:13 final size:14
Alignment explanation
Indices: 143--185 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
133 GGAAATCTTT
*
143 GTCCAAAATCCAAA
1 GTCCAAACTCCAAA
157 GTCC-AACTCCAAA
1 GTCCAAACTCCAAA
170 GTCCAAACTCCAAA
1 GTCCAAACTCCAAA
184 GT
1 GT
186 ACTTGTTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.42, C:0.33, G:0.09, T:0.16
Consensus pattern (14 bp):
GTCCAAACTCCAAA
Found at i:169 original size:20 final size:20
Alignment explanation
Indices: 144--182 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
134 GAAATCTTTG
*
144 TCCAAAATCCAAAGTCCAAC
1 TCCAAAATCCAAACTCCAAC
*
164 TCCAAAGTCCAAACTCCAA
1 TCCAAAATCCAAACTCCAA
183 AGTACTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.36, G:0.05, T:0.15
Consensus pattern (20 bp):
TCCAAAATCCAAACTCCAAC
Found at i:12109 original size:1 final size:1
Alignment explanation
Indices: 12105--12138 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
12095 AAATATGGAG
12105 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12139 AGTAAAGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13961 original size:45 final size:45
Alignment explanation
Indices: 13897--14020 Score: 230
Period size: 45 Copynumber: 2.8 Consensus size: 45
13887 CCTATGCCTG
13897 TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAAAGAGGGTTTAA
1 TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAAAGAGGGTTTAA
13942 TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAAAGAGGGTTTAA
1 TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAAAGAGGGTTTAA
* *
13987 TCACAGGCCCAAAGAGTTCTCTGCTGGCAAGAAA
1 TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAA
14021 CAAGGGGTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (45 bp):
TCACAGGCCCAGAGAGTTCTCTGCTGTCAAGAAAAGAGGGTTTAA
Found at i:15704 original size:15 final size:15
Alignment explanation
Indices: 15677--15745 Score: 75
Period size: 15 Copynumber: 4.4 Consensus size: 15
15667 CCCACCCCCG
*
15677 CCACAACCTCCACCT
1 CCACAACCACCACCT
*
15692 CCGCAACCACCACCT
1 CCACAACCACCACCT
**
15707 CCACAACCACAACCACAA
1 CCACAA-C-C-ACCACCT
15725 CCACAACCACCACCT
1 CCACAACCACCACCT
15740 CCACAA
1 CCACAA
15746 TTACAACCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 29 0.66
16 2 0.05
17 2 0.05
18 11 0.25
ACGTcount: A:0.36, C:0.57, G:0.01, T:0.06
Consensus pattern (15 bp):
CCACAACCACCACCT
Found at i:15716 original size:6 final size:6
Alignment explanation
Indices: 15707--15734 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
15697 ACCACCACCT
15707 CCACAA CCACAA CCACAA CCACAA CCAC
1 CCACAA CCACAA CCACAA CCACAA CCAC
15735 CACCTCCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.54, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACAA
Found at i:15719 original size:21 final size:21
Alignment explanation
Indices: 15677--15726 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
15667 CCCACCCCCG
** *
15677 CCACAACCTCCACCTCCGCAA
1 CCACAACCTCCACAACCACAA
*
15698 CCACCACCTCCACAACCACAA
1 CCACAACCTCCACAACCACAA
15719 CCACAACC
1 CCACAACC
15727 ACAACCACCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.58, G:0.02, T:0.06
Consensus pattern (21 bp):
CCACAACCTCCACAACCACAA
Found at i:15736 original size:21 final size:21
Alignment explanation
Indices: 15712--15758 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
15702 CACCTCCACA
15712 ACCACAACCACAACCACAACC
1 ACCACAACCACAACCACAACC
** **
15733 ACCACCTCCACAATTACAACC
1 ACCACAACCACAACCACAACC
15754 ACCAC
1 ACCAC
15759 CTATAATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.51, G:0.00, T:0.06
Consensus pattern (21 bp):
ACCACAACCACAACCACAACC
Found at i:41992 original size:341 final size:331
Alignment explanation
Indices: 41341--42469 Score: 1561
Period size: 340 Copynumber: 3.4 Consensus size: 331
41331 AAAAAACATG
*
41341 GAAATAAATTCAGAAAAAATGGAAAAACGATATTAAAAGCGTGAAAAACCCTAAAATAGTTTTGG
1 GAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGG
* * *
41406 AGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGT
66 CGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAATTTTCGGGTCAGT
* * *
41471 TTTGTGCAAAATTTTAGCCAAAATCGTGTACTAACCATTACGGTTTTTGGCTAAAAACGCGTTTC
131 TTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCGTTTC
* * *
41536 GGGGGCC-TGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTATCGAAATATCTATATTCATC
194 -GGGGCCATGACTCAGTTTTACATGATTTTTGGCAGAAACACTTCTCGAAATATCTATATTCATC
* * *
41600 TAATCAAATCTCTCAGCCACAATGCATTTACGAATTTATTTTTATGAGTATCTGAATCTTATTTC
258 TAATCAAA-CTCTCAGCCACAATGCATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTC
41665 GATTTAATTA
322 GATTTAATTA
* ** * *
41675 GAAATAAATTCAGAAAAAAATGGAAAAACGATATTTGAAGCGTGAAAAATTCTGAAATATTTTTG
1 GAAATAAATTCAG-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTG
* * *
41740 GCGTTGAATTATATTATTTTTCTGAGTATTGTGGCAAAAAATTGTGGAAAAAATTTTCGGATCAG
65 GCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAATTTTCGGGTCAG
* *
41805 TTTTTTTTCCTTCAAAATTTTAGCCGAAATCGTGTACT-CATCACGGTTTTTTTGGCTAAAAAAA
130 ---TTTTT--TGCAAAATTTTAGCCGAAATCGTGTACTACATCACGG--TTTTTGGCT-AAAAAC
* * *
41869 GCGTTTCGGGGCCAAGGTCTCAGTTTTACATGATTTTTGGCAGAAATACTTCTCGAAATATCTAT
187 GCGTTTCGGGGCC-ATGACTCAGTTTTACATGATTTTTGGCAGAAACACTTCTCGAAATATCTAT
* *
41934 ATTCATCTAATCAATACTCTCAGCCACAATGCATTTACGGATTTATTTTAACGAGTATCTTAATC
251 ATTCATCTAATCAA-ACTCTCAGCCACAATGCATTTACGGATTTATTTTTACGAGTATCTGAATC
41999 TTGTTTCGATTTAATTA
315 TTGTTTCGATTTAATTA
*
42016 GAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGA
1 GAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGG
* * * *
42081 CGTTGAATTATATGATTTTTCTGAATATTGTGGCAAGAAATTGGGGAGAAACTTTTCGGGTCAGT
66 CGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAATTTTCGGGTCAGT
** *
42146 TTTTTGCAAAATTTTAGCCGAAATCGTAAACTAACCATCAC-GTTTTTGGCTAAAAACGTGTTTC
131 TTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCACGGTTTTTGGCTAAAAACGCGTTTC
* * ** *
42210 GGGGCCATGACTCAGTTTTCCATGATTTTTGGCAGGAACACACCTCGAAATATTTATATTCATCT
194 GGGGCCATGACTCAGTTTTACATGATTTTTGGCAGAAACACTTCTCGAAATATCTATATTCATCT
* * * * * * **
42275 AACCAAA-TCCCAGCCACATTGGATTTACGGATTTGTTTTTACGAGCATCTGAATCTTGTTAAGA
259 AATCAAACTCTCAGCCACAATGCATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGA
42339 TTTAATTA
324 TTTAATTA
* * *
42347 GAAATAAATTCAGAAAAAATGAAAAAAGGATATTAGAAGCGTG-AAAACCCTAAAATATTTTTGG
1 GAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGG
*
42411 CGTTGAATTATATGATTTTTCTAAGTATTGTGGC-AAAAATT-GGGACAAAAACTTTTCGG
66 CGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGA-AAAAA-TTTTCGG
Statistics
Matches: 706, Mismatches: 72, Indels: 38
0.87 0.09 0.05
Matches are distributed among these distances:
328 4 0.01
329 9 0.01
330 58 0.08
331 97 0.14
332 1 0.00
333 56 0.08
334 30 0.04
335 138 0.20
337 13 0.02
338 10 0.01
339 15 0.02
340 141 0.20
341 133 0.19
342 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (331 bp):
GAAATAAATTCAGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGG
CGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAAATTTTCGGGTCAGT
TTTTTGCAAAATTTTAGCCGAAATCGTGTACTACATCACGGTTTTTGGCTAAAAACGCGTTTCGG
GGCCATGACTCAGTTTTACATGATTTTTGGCAGAAACACTTCTCGAAATATCTATATTCATCTAA
TCAAACTCTCAGCCACAATGCATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATT
TAATTA
Done.