Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015338.1 Corchorus olitorius cultivar O-4 contig15371, 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: 3695
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:24 original size:2 final size:2
Alignment explanation
Indices: 17--44 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7 CTACTTGTAA
17 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45 TCATCTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1213 original size:320 final size:322
Alignment explanation
Indices: 280--3022 Score: 2510
Period size: 320 Copynumber: 8.5 Consensus size: 322
270 CGAAATCCTG
* * * * *
280 TTGTTTCGATTTAATAAGAAATTAATTCAGAAAAGAAATGAAAAAAAGATATTAGAAGTGTG-AA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGTGTGAAA
* * * *
344 AACCCTTCAATCTTTTTTGCGTTGAATTATATTTTTTTTATTCTGAGTATTGTGGCAAAAAATTG
65 AACCCTTCAATCTTTTTGGCGTTGAATTATA--TATTTT-TTCTGAATATTTTGGCAAAAAATTG
* * * *
409 AGAAAAAAATTTTCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAA
127 AGGAAAAACTTTTCGGGTCAG-TTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAA
* *
474 AAACGCGTTTCGGA-TCTCC-GCTCAGTTTTAAATTATTTTTGGCAGAAAGACTCCTTGAAATAT
191 AAACGCGTTTCGGAGTC-CCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATAT
* * * * *
537 CTATATTCATCTAACAAAATCTTAGCCACAATGGATTTAAGAATTTGTTTTTATGAGCATCTC-A
255 CTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGA
601 ATC
320 ATC
* **
604 TTTGTTTCGATTTAATTTGAAATAAATTCGGAAAAAAA-GGAAAAACGATATTAGAAACGTGAAA
1 -TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAA
* ** * *
668 AACCCTTCAATATTTTTGGCGTCAAATTATATATTTTTTCTGACTATTATGGCAAAAAATTGAGG
65 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAGG
*
733 AAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTTGCCGAAATCGTGTACT-AACTATCACGATT
130 -AAAAACTTTTCGGGTCAG-TTTT-----A-----GCCGAAATCGTGTACTAAAC-ATCACGATT
* * * ** *
797 TTTGGCAAAAAATGCGTTTCAGAGTCCCGGCTCAATTTTGCATAATTTTTGGC-GTAAAGACTCC
182 TTTGGCTAAAAACGCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAG-AAAGACTCC
* * * *
861 TTGAAATATCTATATTCATCGAACGAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACGA
246 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGA
926 GCATC-CGAATC
311 GCATCTCGAATC
* * * *
937 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATTGAAAAAACAATATTAGAAGTGCGAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAA-TGGAAAAACGATATTAGAAGTGTGAAA
* * * *
1002 AGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAAT-TTTTGGCAAAAACTTGA-T
65 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAGG
* *
1065 AAAGACTTTTCGGGTTAGTTATTAGCCGAAATCGTGTA-TAAAACATCACGATTTTTGGCTAAAA
130 AAAAACTTTTCGGGTCAGTT-TTAGCCGAAATCGTGTACT-AAACATCACGATTTTTGGCTAAAA
* * * * *
1129 ACGCGTTTCGGA-TCCCTGCTTAGTTTTAAATGATTTTGGGCAGAAAGACTCCTTCAAATATCTA
193 ACGCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
** * * * *
1193 TATTCATCTAATTAAATCTCAACCACATTGGATTTAAGAATTTGTTTGTACGAGCATCT-GAATA
258 TATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATC
* * *
1257 TTGTTTCTATTTAATTAGAAATAAATTCGGGGAAAAAAAAGGAAAAACGATATTTGAA-TCGTGA
1 TTGTTTCGATTTAATTAGAAATAAATTC--GGAAAAAAATGGAAAAACGATATTAGAAGT-GTGA
* **
1321 AAAACGCCTTCAAT-TTTTTGGCGTTTAATTATATATTTTTT-TGTGTATTTTGGCAAAAAATTG
63 AAAAC-CCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTG
* * * * * *
1384 AGGAAAAACTTTTCAGGTCAATTTGT-G-CAAAAT--TTTAGGCGAAATCATATATCACGGTTTT
127 AGGAAAAACTTTTCGGGTCAGTTT-TAGCCGAAATCGTGTA--CTAAA-C----ATCACGATTTT
* * * ** * * *
1445 TGGCTTAAAACGCGTTCCGGAGTGCCGGCTCAATTTTGCAGGATTTTTGGCACAAAGATTCCTTG
184 TGGCTAAAAACGCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTG
* * * * **
1510 AAATATCTATATTCATCGAACCAAATGTCAACCACATTGGATATAAGGATTTGTTTTTATTAGCA
249 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCA
1575 TCTCG-ATC
314 TCTCGAATC
* ** * ** * *
1583 TGGTTTTAATTTAATTAGAAATTAATTTTGAAACAAATGGAAAAACGATATTAGAAGGGTGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAA
* * * * * **
1648 ACCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTAAATA-TTTCGTAAAAAATTGATAA
66 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAGGA
* *
1712 AAAACTTTTCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAAC
131 AAAACTTTTCGGGTCAG-TTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAAC
* * *
1777 GCGTTTCGGA-TCCTGACTCAGTTTTAAATGATTTTTGGCAGAAAGACTCCTTG----ATC--TA
195 GCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATA
* * * *
1835 ---A-C--A--AAATCTTAGCCACAATGGATTTAAGAATTTATTTTTACGAGCATCTC-AATC
260 TTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATC
* *
1889 TTTGTTTCGATTTAATTAGAAAGAAATTCGGAAAAAAA-GG-AAAACGATATTAGAAATGTGAAA
1 -TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAA
* * * * * * *
1952 AACCCTTCTATATTTTTGGCGTTAAATTATATATTTTTTCTTAGA-ATTATGGTAAAATATTGAG
65 AACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGA-ATATTTTGGCAAAAAATTGAG
*
2016 GAAAAACTTTTCGTGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTGCTTTTTTTTGCCAACG
129 GAAAAACTTTTCG-G---G----T-C--AGTTTTAGCCGAAATC--GTG--------T-------
* * * * * *
2081 AAATCGTGTACTAACTATCACGGTTTTTGGCAAAAAACGCGCTCCGGACTCCCGGCTCAATTTTG
166 --A-C---TA--AAC-ATCACGATTTTTGGCTAAAAACGCGTTTCGGAGTCCCGGCTCAATTTTA
* * * * *
2146 CATGATTTTTGGCATAAAGACTCCTTGAAATGTCTATATTCTTCGAACCAAATCTCAGCCACATT
222 AATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT
*
2211 GTATATAA-AGATTTGTTTTTACGAGCATC-CGAATC
287 GGATATAAGA-ATTTGTTTTTACGAGCATCTCGAATC
* * * * *
2246 TTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAAATGATATTAGAAGCGCGAAAA
1 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAA
* *
2311 GCCCGTCAATCTTTTTGGCGTTG-A--AT-TA-------T--ATATTTT-GCAAAAAATTGA-GA
66 ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAGGA
* * * * * *
2361 AAAACTTTTCGGGTTAGTTTATACCCGAAATCGTGTTCTAAGCATTACGATTTTTGGCTAAAAAA
131 AAAACTTTTCGGGTCAGTTT-TAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAAC
* * *
2426 GCGTTTCGGA-TCCCCGCTCAGTTTTAAATGATTTTTGGTAGAAAGACTCCTTGAAATATCTATA
195 GCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATA
** * * * *
2490 TTCATCTAATTAAATCTCAGCCACATTGGATTTAAGAAATTATTTTTACGAGCATCT-GAATA
260 TTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATC
** *
2552 TTGTTTTAATTTAATTAGAAATAAATTCGGGAAAAAAAAGGAAAAACGATATTAGGAA-TGTGAA
1 TTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAAATGGAAAAACGATATTA-GAAGTGTGAA
* * * * *
2616 AAACCCTTCAATTTTTTTGGCGTTGAATTATATA-CTTTTCTGAGTATTCTGGCAAAATATTGAG
64 AAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAG
* *** * *
2680 GAAATTTA-TTTT--GCAAAGTTTTAGCCGAAATCGTGTACTAACCAACACGATTTTTGGCTAAA
129 GAAA--AACTTTTCGGGTCAGTTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAA
* * * * ** *
2742 AACGCGTTTTGGAGTGCCGACTCAAATTTGCATGATTTTTGGCCACAAAGACTCCTTGAAATATC
192 AACGCGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGG-CAGAAAGACTCCTTGAAATATC
* * * **
2807 TATATTCATCTAACCAAATGTCAACCACATTGGATATAAGGA-TT-TTTTTATTAGCATCTC-AA
256 TATATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAA
2869 TC
321 TC
* * * **
2871 TTTGTTTCGATTTAATTAGAAATAAATTCGGGGAAAAAA-GGAAAAACAATATTACAAACGTGAA
1 -TTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAAATGGAAAAACGATATTAGAAGTGTGAA
* * * * *
2935 AAACCCTTCAATATTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTATGGAAAAAAATTGAG
64 AAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAG
* *
3000 GAAAAACGTTTCGTGTCAGTTTT
129 GAAAAACTTTTCGGGTCAGTTTT
3023 GGCAAAATTT
Statistics
Matches: 1969, Mismatches: 309, Indels: 284
0.77 0.12 0.11
Matches are distributed among these distances:
305 59 0.03
306 191 0.10
307 104 0.05
308 7 0.00
310 6 0.00
311 3 0.00
313 1 0.00
314 3 0.00
315 1 0.00
316 17 0.01
317 2 0.00
318 9 0.00
319 122 0.06
320 274 0.14
321 231 0.12
322 67 0.03
323 28 0.01
324 120 0.06
325 67 0.03
326 126 0.06
327 2 0.00
328 3 0.00
330 2 0.00
331 22 0.01
332 88 0.04
333 122 0.06
334 60 0.03
335 2 0.00
336 1 0.00
339 3 0.00
341 2 0.00
342 29 0.01
343 50 0.03
344 11 0.01
345 4 0.00
347 3 0.00
349 2 0.00
353 1 0.00
354 2 0.00
355 3 0.00
356 36 0.02
357 45 0.02
358 38 0.02
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (322 bp):
TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAA
ACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGGCAAAAAATTGAGGA
AAAACTTTTCGGGTCAGTTTTAGCCGAAATCGTGTACTAAACATCACGATTTTTGGCTAAAAACG
CGTTTCGGAGTCCCGGCTCAATTTTAAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATAT
TCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTTGTTTTTACGAGCATCTCGAATC
Found at i:2260 original size:663 final size:656
Alignment explanation
Indices: 1433--2683 Score: 1696
Period size: 663 Copynumber: 1.9 Consensus size: 656
1423 CGAAATCATA
** * * *
1433 TATCACGGTTTTTGGCTTAAAACGCGTTCCGGAGTGCCGGCTCAATTTTGCAGGATTTTTGGCAC
1 TATCACGGTTTTTGGCAAAAAACGCGCTCCGGACTCCCGGCTCAATTTTGCAGGATTTTTGGCAC
* * *
1498 AAAGATTCCTTGAAATATCTATATTCATCGAACCAAATGTCAACCACATTGGATATAAGGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACATTGGATATAAAGATTTG
** * * *
1563 TTTTTATTAGCATCTCGATCTGGTTTTAATTTAATTAGAAATTAATTTTGAAACAAATGGAAAAA
131 TTTTTACGAGCATCTCGATCTGGTTTCAATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAAA
* *
1628 CGATATTAGAAGGGTGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATATTTTTTCTAAATA
196 CGATATTAGAAGCGCGAAAAACCCGTCAATCTTTTTGGCATTGAA-T-TATA-------T--AT-
* * * *
1693 TTTCGTAAAAAATTGATAAAAAACTTTTCGTGTCAGTTTTTAGCCGAAATCGTGTACTAACCATC
249 TTT-GCAAAAAATTGA-AAAAAACTTTTCGGGTCAGTTTATACCCGAAATCGTGTACTAACCATC
* *
1758 ACGATTTTTGGCTAAAAACGCGTTTCGGAT-CCTGACTCAGTTTTAAATGATTTTTGGCAGAAAG
312 ACGATTTTTGGCTAAAAAAGCGTTTCGGATCCCCG-CTCAGTTTTAAATGATTTTTGGCAGAAAG
* *
1822 ACTCCTTG-ATC-TA-A-C-A-AAATCTTAGCCACAATGGATTTAAGAATTTATTTTTACGAGCA
376 ACTCCTTGAATCATATATCAATAAATCTCAGCCACAATGGATTTAAGAAATTATTTTTACGAGCA
* *
1881 TCTCAATCTTTGTTTCGATTTAATTAGAAAGAAATTC-GG-AAAAAAAGG-AAAACGATATTAGA
441 TCTCAAT-ATTGTTTCAATTTAATTAGAAAGAAATTCGGGAAAAAAAAGGAAAAACGATATTAGA
* * * *
1943 AATGTGAAAAACCCTTCTATATTTTTGGCGTTAAATTATATATTTTTTCTTAGAATTATGGTAAA
505 AATGTGAAAAACCCTTCAATATTTTTGGCGTTAAATTATATA-CTTTTCTGAGAATTATGGCAAA
2008 ATATTGAGGAAAAACTTTTCGTGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTGCTTTTTTT
569 ATATTGAGGAAAAACTTTTCGTGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTGCTTTTTTT
2073 TGCCAACGAAATCGTGTACTAAC
634 TGCCAACGAAATCGTGTACTAAC
* *
2096 TATCACGGTTTTTGGCAAAAAACGCGCTCCGGACTCCCGGCTCAATTTTGCATGATTTTTGGCAT
1 TATCACGGTTTTTGGCAAAAAACGCGCTCCGGACTCCCGGCTCAATTTTGCAGGATTTTTGGCAC
* * * *
2161 AAAGACTCCTTGAAATGTCTATATTCTTCGAACCAAATCTCAGCCACATTGTATATAAAGATTTG
66 AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACATTGGATATAAAGATTTG
* *
2226 TTTTTACGAGCATC-CGAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAA
131 TTTTTACGAGCATCTCG-ATCTGGTTTCAATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAA
* * *
2290 ATGATATTAGAAGCGCGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATATATTTTGCAAAAAA
195 ACGATATTAGAAGCGCGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATATTTTGCAAAAAA
* * * * *
2355 TTGAGAAAAACTTTTCGGGTTAGTTTATACCCGAAATCGTGTTCTAAGCATTACGATTTTTGGCT
260 TTGAAAAAAACTTTTCGGGTCAGTTTATACCCGAAATCGTGTACTAACCATCACGATTTTTGGCT
*
2420 AAAAAAGCGTTTCGGATCCCCGCTCAGTTTTAAATGATTTTTGGTAGAAAGACTCCTTGAAATAT
325 AAAAAAGCGTTTCGGATCCCCGCTCAGTTTTAAATGATTTTTGGCAGAAAGACTCCTTG--A-AT
* *
2485 CTATATTCATCTAATTAAATCTCAGCCACATTGGATTTAAGAAATTATTTTTACGAGCATCTGAA
387 C-ATA-T-ATC-AA-TAAATCTCAGCCACAATGGATTTAAGAAATTATTTTTACGAGCATCTCAA
* * *
2550 TATTGTTTTAATTTAATTAGAAATAAATTCGGGAAAAAAAAGGAAAAACGATATTAGGAATGTGA
447 TATTGTTTCAATTTAATTAGAAAGAAATTCGGGAAAAAAAAGGAAAAACGATATTAGAAATGTGA
* * * *
2615 AAAACCCTTCAATTTTTTTGGCGTTGAATTATATACTTTTCTGAGTATTCTGGCAAAATATTGAG
512 AAAACCCTTCAATATTTTTGGCGTTAAATTATATACTTTTCTGAGAATTATGGCAAAATATTGAG
2680 GAAA
577 GAAA
2684 TTTATTTTGC
Statistics
Matches: 514, Mismatches: 55, Indels: 37
0.85 0.09 0.06
Matches are distributed among these distances:
649 105 0.20
650 14 0.03
651 3 0.01
652 2 0.00
653 3 0.01
654 1 0.00
655 2 0.00
658 1 0.00
659 1 0.00
661 5 0.01
662 28 0.05
663 259 0.50
664 38 0.07
665 52 0.10
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (656 bp):
TATCACGGTTTTTGGCAAAAAACGCGCTCCGGACTCCCGGCTCAATTTTGCAGGATTTTTGGCAC
AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACATTGGATATAAAGATTTG
TTTTTACGAGCATCTCGATCTGGTTTCAATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAAA
CGATATTAGAAGCGCGAAAAACCCGTCAATCTTTTTGGCATTGAATTATATATTTTGCAAAAAAT
TGAAAAAAACTTTTCGGGTCAGTTTATACCCGAAATCGTGTACTAACCATCACGATTTTTGGCTA
AAAAAGCGTTTCGGATCCCCGCTCAGTTTTAAATGATTTTTGGCAGAAAGACTCCTTGAATCATA
TATCAATAAATCTCAGCCACAATGGATTTAAGAAATTATTTTTACGAGCATCTCAATATTGTTTC
AATTTAATTAGAAAGAAATTCGGGAAAAAAAAGGAAAAACGATATTAGAAATGTGAAAAACCCTT
CAATATTTTTGGCGTTAAATTATATACTTTTCTGAGAATTATGGCAAAATATTGAGGAAAAACTT
TTCGTGTTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTGCTTTTTTTTGCCAACGAAATCGTGT
ACTAAC
Done.