Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018842.1 Corchorus olitorius cultivar O-4 contig18875, 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: 27251
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:325 original size:46 final size:46
Alignment explanation
Indices: 269--385 Score: 139
Period size: 45 Copynumber: 2.5 Consensus size: 46
259 TCCATTTTAA
*
269 TAAAGCCCATTTCCTCATTAGTTTCATTCAAAGTCCATTACCATTT
1 TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
* * * * **
315 TAGAGCCCATTCCCTTATTTAG--TAATTCAAAGTCCATTTCTTTTT
1 TAAAGCCCATTTCCTTA-TTAGTTTCATTCAAAGTCCATTACCATTT
360 TAAAGACCCATTTCCTTATTAGTTTC
1 TAAAG-CCCATTTCCTTATTAGTTTC
386 TCAAAATGTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
45 27 0.47
46 25 0.44
47 5 0.09
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (46 bp):
TAAAGCCCATTTCCTTATTAGTTTCATTCAAAGTCCATTACCATTT
Found at i:4162 original size:34 final size:34
Alignment explanation
Indices: 4124--4219 Score: 129
Period size: 34 Copynumber: 2.8 Consensus size: 34
4114 GAGAATATCA
* * *
4124 TTAAGTTTTTTTATTGGAAAAGTTCCCACCAGTT
1 TTAAGTTTTCTAATTGGGAAAGTTCCCACCAGTT
* * *
4158 TTAAGTTTTGTAATCGGGAAAGTTCCCACCGGTT
1 TTAAGTTTTCTAATTGGGAAAGTTCCCACCAGTT
*
4192 TTAAGTTTTCAAATTGGGAAAGTTCCCA
1 TTAAGTTTTCTAATTGGGAAAGTTCCCA
4220 TTCAATTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (34 bp):
TTAAGTTTTCTAATTGGGAAAGTTCCCACCAGTT
Found at i:7318 original size:28 final size:28
Alignment explanation
Indices: 7286--7358 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
7276 GACATCAACT
* *
7286 AAACCCAAAACACTAGAAAAGAATAAAC
1 AAACCCAAAACACCACAAAAGAATAAAC
* *
7314 AAACCCACAACACCACAAAAGAGTAAAC
1 AAACCCAAAACACCACAAAAGAATAAAC
*
7342 AAATCCAATAGACACCA
1 AAACCCAA-A-ACACCA
7359 GAAATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
28 30 0.81
29 1 0.03
30 6 0.16
ACGTcount: A:0.59, C:0.27, G:0.07, T:0.07
Consensus pattern (28 bp):
AAACCCAAAACACCACAAAAGAATAAAC
Found at i:10555 original size:52 final size:52
Alignment explanation
Indices: 10415--10778 Score: 527
Period size: 52 Copynumber: 7.0 Consensus size: 52
10405 GGGATCTTTC
* * *
10415 CCTAAATTGAACGCTTTGAAAACTTGATGGGAACTTTCCCGCTTTGAAAAGA
1 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
10467 CCTAAATTTC-AACACTTTAAAAACTTGACGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAA--TCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
*
10520 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCGCACTTTGAAAAGA
1 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
*
10572 CCTAAATTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
1 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* *
10624 CCTAAATCGAACACTTTGAAAACTTGATCGGAACTTTCCCACTTTGAAAAAA
1 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* * *
10676 CCTAACTCGAACACTTTAAAAACTTGATGGGAACTTTCCCACTTTG--AAGG
1 CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
* * *
10726 CTTAAATTGAACACTTTGAAAACGTGATGATGGGAACTTTCACACTTTGAAAA
1 CCTAAATCGAACACTTTGAAAAC-T--TGATGGGAACTTTCCCACTTTGAAAA
10779 CTTTGAAGGA
Statistics
Matches: 281, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
50 21 0.07
51 3 0.01
52 188 0.67
53 66 0.23
54 1 0.00
55 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (52 bp):
CCTAAATCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
Found at i:12752 original size:26 final size:26
Alignment explanation
Indices: 12715--12764 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
12705 AAAAGTTTGC
*
12715 GGTTTTGGAGGTTATTTGGGGATTAA
1 GGTTTTGCAGGTTATTTGGGGATTAA
*
12741 GGTTTTGCAGGTTTTTTGGGGATT
1 GGTTTTGCAGGTTATTTGGGGATT
12765 TCTTGATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.38, T:0.46
Consensus pattern (26 bp):
GGTTTTGCAGGTTATTTGGGGATTAA
Found at i:12932 original size:20 final size:20
Alignment explanation
Indices: 12881--12945 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
12871 TTAGAGCTCA
*
12881 TTGAATTCAAAATAGGGTTC
1 TTGAGTTCAAAATAGGGTTC
*
12901 TTGAGTTTCAAACTAGGGTTC
1 TTGAG-TTCAAAATAGGGTTC
* *
12922 TTGAGTTCAAATTAGGGTTT
1 TTGAGTTCAAAATAGGGTTC
12942 TTGA
1 TTGA
12946 TTTATTGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 21 0.52
21 19 0.47
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGAGTTCAAAATAGGGTTC
Found at i:13459 original size:2 final size:2
Alignment explanation
Indices: 13452--13488 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13442 TGGTAAACAA
*
13452 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT TT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
13489 AGAATTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
GT
Found at i:15067 original size:27 final size:21
Alignment explanation
Indices: 15010--15053 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
15000 AATATTTATT
15010 TTACTTGTTTAGCAATTTCAA
1 TTACTTGTTTAGCAATTTCAA
15031 TTACTTGTTTAGCAATTTCAA
1 TTACTTGTTTAGCAATTTCAA
15052 TT
1 TT
15054 TAGCTGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (21 bp):
TTACTTGTTTAGCAATTTCAA
Found at i:21291 original size:437 final size:438
Alignment explanation
Indices: 20334--21368 Score: 1280
Period size: 437 Copynumber: 2.4 Consensus size: 438
20324 AATAGATTAT
* ** * * * * *
20334 CAATCGAAATCACAAAATTTCAAAAGTATTTTTTAGAATTGAAACGTAAAAATTAACTTTTGAG-
1 CAATCGAAACCACAAAATTTCGGAAGCATTTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGT
* * *
20398 TCTTTCATGAAAGTTGTAGATCATAAAATTACTTTTTAATAGACACATGAATTACCTTAATTGGA
66 TC-TTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGA
20463 CAAATAGAACAAAGAAAATAAAAAAAAAATGAAGCGTTAAATCGAGTAAGATAAAATTTGTAAAG
130 CAAATAGAACAAAG--AAT---AAAAAAATGAAGCGTTAAATCGAGTAAGATAAAATTTGTAAAG
* * * *
20528 GACTAAGTAGCATAAAATATAAAATAGAAAAGTATGGGGGTCATTTGATAATTAATTCAAATAAA
190 GACTAAG-AG-AT-AAATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAA
* * *
20593 AAAATATTTCTTAATGGATATCTTGAAACATAAAAATTCCCTTTTGGACCCTTCATGAAACTCGT
252 AAAATATTTCTTAATGGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGT
* * * *
20658 AGATCAAATTAACTTTCGGATTATTCATGAAAGTCGTACATCATACAGTTCCTTTTAACCGACAC
317 AGATCAAATTAACTTTCGGATCATTCATGAAAGTCGTAAATCATACAATACCTTTTAACCGACAC
* * * *** * *
20723 TTGAATAAATTTAATCGGACATGTGGATCGAAAATTATATGGTATTAAATAAACCAA
382 TTCAATAAATTCAATCGGACATGTGAAAAAAAAATTATACGATATTAAATAAACCAA
* ** * *
20780 CAATCGAAACGACCTAATTTAGGAAGCATTTTTTTGAATTAAAACATAAAAATTTGCTTTTGAGT
1 CAATCGAAACCACAAAATTTCGGAAGCATTTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGT
* *
20845 CCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGAC
66 TCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGAC
* *
20910 AAATAGAACAAAGAATAAAAAAATGAATC-TTAAA-CGTTAGATTAAGATAGAATTTGTAAAGGA
131 AAATAGAACAAAGAATAAAAAAATGAAGCGTTAAATCG--AG--TAAGATAAAATTTGTAAAGGA
*
20973 CT-A-AG-T-AATATAAAATAGAAAAATATGAGGGTCATTTGATAAAT-ATCCAAATAAGAAAAT
192 CTAAGAGATAAATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAAAAAAT
* * * *
21033 GTTTGTTAATGGAGATCTTGAAGCATAAAAACTCTCTTTTGAACCCTTCATGAAACTCGTAGATC
257 ATTTCTTAATGGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTAGATC
* * * * *
21098 AAATTTAGCTTTTGGGTCCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTC
322 AAA-TTAACTTTCGGATCATTCATGAAAGTCGTAAATCATACAAT-ACCTTTTAACCGACACTTC
* ** *
21163 AATAACTTCAATCGGACATGTGAAAAAAAAATTATACGATATTAAATTGACCGA
385 AATAAATTCAATCGGACATGTGAAAAAAAAATTATACGATATTAAATAAACCAA
* ** * * *
21217 CAATCAAAACCACAAAATTTCGGAAGCATTTTTTTGAATCCAAACATCAAAATTGGCTCTTGAGT
1 CAATCGAAACCACAAAATTTCGGAAGCATTTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGT
* * * *
21282 TCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGAT
66 TCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGAC
* *
21347 AAATAGGA-AAA-AATACAAAAAT
131 AAATAGAACAAAGAATAAAAAAAT
21369 AAATGTGAAC
Statistics
Matches: 511, Mismatches: 71, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
435 85 0.17
436 71 0.14
437 181 0.35
438 1 0.00
439 2 0.00
440 7 0.01
441 14 0.03
442 1 0.00
443 22 0.04
444 3 0.01
446 123 0.24
447 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (438 bp):
CAATCGAAACCACAAAATTTCGGAAGCATTTTTTTGAATTAAAACATAAAAATTAGCTTTTGAGT
TCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCACCTTAATTGGAC
AAATAGAACAAAGAATAAAAAAATGAAGCGTTAAATCGAGTAAGATAAAATTTGTAAAGGACTAA
GAGATAAATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAAAAAATATTT
CTTAATGGAGATCTTGAAACATAAAAACTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAAT
TAACTTTCGGATCATTCATGAAAGTCGTAAATCATACAATACCTTTTAACCGACACTTCAATAAA
TTCAATCGGACATGTGAAAAAAAAATTATACGATATTAAATAAACCAA
Done.