Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020266.1 Corchorus olitorius cultivar O-4 contig20299, 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: 5015
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:721 original size:338 final size:330
Alignment explanation
Indices: 1--1403 Score: 1316
Period size: 330 Copynumber: 4.2 Consensus size: 330
* * *
1 AGATGCTCCTAAAAACAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATAGATA
1 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGACTTGATTAGATGAATATAGATA
* * * * * ***
66 TTTCAAGTAATCTCGGATCCCAAAATCAGGCAAAACTAAGCCAAAG-CCCCGAAACGCTTTTTTA
66 TTTCAAGTAATCTCAGAGCCAAAAATCATGCAAAACTGAGCCTGGGCCCCCG-AACGCTTTTTTA
* * *
130 GCCAAAAATCGTGA----TA-TACACGATTTTGACTAAAATTTTGCAAAAAATGATCCGAAAAAT
130 GCCAAAAATCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAAATGA-CCCAAAATT
* * * *
190 TTTTCATCAATTTTTTGGATAAAATACACATAATATATATTATATATATATATAGTTTAACACCA
194 TTTTCCTCAA-TTTTTGGATAAAAT--AC-TCATA-A-A--A-ATATATATA-A-TTCAACGCCA
* * *
255 AAAAAATTGGAGGACTTTCCATGCTTTAAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTA
248 AAAAGATTGGAGGACTTTCCACGCTTTTAATATCGTTTTTCATA--TTTTCTGAATTAATTTCTA
*
320 ATTAAATCGAAACGAGATTT
311 ATTAAATCGAAACAAGATTT
* *
340 AGATGCTCGTAAACACAAATCCTTAAATGCAATGTGGCTGAGACTTGATTAGATGAATATAGATA
1 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGACTTGATTAGATGAATATAGATA
* * *
405 TTTCAAGTAGTCTCAGAGCCAAAAATCATGCAAAACT-A-CGCTGGGCCCCCGAACGCGTTTTTC
66 TTTCAAGTAATCTCAGAGCCAAAAATCATGCAAAACTGAGC-CTGGGCCCCCGAACGCTTTTTTA
* *
468 GCCCAAAAAAACGTGATGGTTAGTACACGATTTTGACTAAAATTTTGCAACAAAAAAATGACCCA
130 G-CC-AAAAATCGTGATGGTTAGTACACGATTTCGACTAAAATTTTG---C-AAAAAATGACCCA
* *
533 ATAATTTGTTTCCTCAATTTTTGGATAAAATACCCATAAAAAATATATATAATTTAACGCCAAAA
189 A-AATTT-TTTCCTCAATTTTTGGATAAAATACTCAT-AAAAATATATATAATTCAACGCCAAAA
* * *
598 AGATTGGATGACTTTCCATGCTTTTAATATTGTTTTTCATATTTTCTGAATTAATTTCTAATTAA
251 AGATTGGAGGACTTTCCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAA
663 ATCGAAACAAGATTT
316 ATCGAAACAAGATTT
* * * * *
678 TGATGCTCGTTAAAGCAAATTCTTAAATCCAATGTGGCTGAGACTTGATTAGATGAATATGGATA
1 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGACTTGATTAGATGAATATAGATA
* * * ** * * * ** *
743 TCTCAAGGAGTCTTGGTGTC--AAATCATGCAAAACTGAGCCGGGGCCCTAGAATGCTTTTTTAG
66 TTTCAAGTAATCTCAGAGCCAAAAATCATGCAAAACTGAGCCTGGGCCCCCGAACGCTTTTTTAG
* * * * * * *
806 CCAAAAATTGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTAACCTGAAAGA-T
131 CCAAAAATCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAAATGACC-CAAA-ATT
* * * * * * *
870 ATTACCTCAATTTTTGGCTAAAATACTTATAAAAAT-CATATAATTCAACGTCAAAAAGATTGAA
194 TTTTCCTCAATTTTTGGATAAAATACTCATAAAAATATATATAATTCAACGCCAAAAAGATTGGA
* ** * * * * *
934 GGGCTTTTGACGCTTCTAATATCGTTTATCCTATTTTTTCCGAATTAATTTCTAATAAAATCGAA
259 GGACTTTCCACGCTTTTAATATCGTTT-TTC-ATATTTTCTGAATTAATTTCTAATTAAATCGAA
*
999 ACAAGATTC
322 ACAAGATTT
* * * *
1008 AGATACACATAAAAACAAATCCTTAAATCTAATGTGGCTGAG-CTTTGATTAGATTG-ATATAGA
1 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAC-TTGATTAGA-TGAATATAGA
* * * *
1071 TATTTCAAGTAATCTCAGAGCCAAAAATCATG-AAAATTTGAGTC-GGGTCCCCGGAACGCATTT
64 TATTTCAAGTAATCTCAGAGCCAAAAATCATGCAAAA-CTGAGCCTGGG-CCCCCGAACGCTTTT
** * * * *
1134 TT-GTTAAAAACCGTGATGGTTAGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACAC
127 TTAGCCAAAAATCGTGAT-G---GTTAGTACACGATTTCGACTAAAATTTTGCAAAAAATGACCC
* * * * *
1198 TAAATATTTTTCCTCAATTTTTTGCTAAAATACTCAT-GAAA-AGATATAATTCAACGCCAAAAA
188 AAAAT-TTTTTCCTCAATTTTTGGATAAAATACTCATAAAAATATATATAATTCAACGCCAAAAA
* * * * *
1261 TATTGGAGGGCTTTTCACGCTTTTAATATCGTATTTCTTATTTTTTCTGAATTAATTTCTAATTA
252 GATTGGAGGACTTTCCACGCTTTTAATATCGT-TTT-TCATATTTTCTGAATTAATTTCTAATTA
1326 AATCGAAACAAGATTCAAGATT
315 AATCGAAACAAGA-T-----TT
* * * * * *
1348 CAGATGCTCGTAAAAA-AAATTCTTAAATCCACTATTGCTGAGAATTGGTTAGATGA
1 -AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGACTTGATTAGATGA
1404 TGTAAAGTAT
Statistics
Matches: 886, Mismatches: 132, Indels: 91
0.80 0.12 0.08
Matches are distributed among these distances:
328 44 0.05
329 9 0.01
330 127 0.14
331 31 0.03
332 30 0.03
333 1 0.00
334 90 0.10
335 104 0.12
336 17 0.02
337 20 0.02
338 125 0.14
339 103 0.12
340 89 0.10
341 13 0.01
342 9 0.01
343 1 0.00
344 2 0.00
345 25 0.03
346 3 0.00
347 3 0.00
348 5 0.01
349 27 0.03
350 8 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGACTTGATTAGATGAATATAGATA
TTTCAAGTAATCTCAGAGCCAAAAATCATGCAAAACTGAGCCTGGGCCCCCGAACGCTTTTTTAG
CCAAAAATCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAAATGACCCAAAATTTT
TTCCTCAATTTTTGGATAAAATACTCATAAAAATATATATAATTCAACGCCAAAAAGATTGGAGG
ACTTTCCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAACAA
GATTT
Found at i:3755 original size:13 final size:13
Alignment explanation
Indices: 3739--3763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3729 AAAAAATAGA
3739 GGAAAAAGGAAAG
1 GGAAAAAGGAAAG
3752 GGAAAAAGGAAA
1 GGAAAAAGGAAA
3764 AAGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (13 bp):
GGAAAAAGGAAAG
Found at i:3802 original size:17 final size:18
Alignment explanation
Indices: 3782--3815 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3772 AAATGAATGG
3782 AAAAGAAAAAG-AGAAAA
1 AAAAGAAAAAGAAGAAAA
*
3799 AAAAGAAGAAGAAGAAA
1 AAAAGAAAAAGAAGAAA
3816 GGAAATAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAGAAAA
Found at i:3813 original size:26 final size:25
Alignment explanation
Indices: 3755--3815 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
3745 AGGAAAGGGA
*
3755 AAAAGGAAAAAGAAAAAAAATGAATGG
1 AAAA-GAAAAAGAAAAAAAAAGAA-GG
3782 AAAAGAAAAAGAGAAAAAAAAGAA-G
1 AAAAGAAAAAGA-AAAAAAAAGAAGG
3807 AAGAAGAAA
1 AA-AAGAAA
3816 GGAAATAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 14 0.45
27 14 0.45
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.03
Consensus pattern (25 bp):
AAAAGAAAAAGAAAAAAAAAGAAGG
Found at i:4643 original size:28 final size:27
Alignment explanation
Indices: 4611--4667 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4601 TATTTGCCCT
* *
4611 TTGGTCGGCTAAAATTACCATTTTACCC
1 TTGGTCGACT-AAATTACAATTTTACCC
* *
4639 TTGGTTGACTAAATTACAATTTTGCCC
1 TTGGTCGACTAAATTACAATTTTACCC
4666 TT
1 TT
4668 AAACGTCGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (27 bp):
TTGGTCGACTAAATTACAATTTTACCC
Done.