Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020718.1 Corchorus olitorius cultivar O-4 contig20751, 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: 16421
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:10236 original size:331 final size:323
Alignment explanation
Indices: 9511--10279 Score: 818
Period size: 324 Copynumber: 2.3 Consensus size: 323
9501 TTTGAACCAT
* * * * * * * * * * *
9511 GCTTTTAATATCATTTTTTATGTTTTTCTGAATTAATTTCTAATTAAATCAAAATAAGATTCAAA
1 GCTTCTAATATCGTTTTTCATATTATTCCGAATTAATTTCTAATTAAATCGAAACAACATTTAGA
* * *
9576 TGCTCGTAAAAACAAATCCATAAATGCAATGTGGCTGAGATTTGATTAGATGAATATGTATATTT
66 TGCTCGTAAAAA-AAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCT
* * * * *
9641 CAAGGAGTCTCGATGCCAAAAATCATGCAAAACTGAGCTGAGGTCCCGAAACACGTTTTTAACAA
130 CAAGGAATCTAGACGCCAAAAATCATGCAAAACTGAGCTGAGGGCCCGAAACACATTTTTAACAA
* * * **
9706 AAAACTGTGATACATGGTTTCGGCTAAAATTTTGCAAAAAATGACCAGAAAAATTTTTCCTCAAT
195 AAAACTGTGATACACGATTTCGGCTAAAATTTTACAAAAAATGACCAGAAAAACATTTCCTCAA-
* * * * * *
9771 TTTTTGGCTTAAATATTCATGAAATATATATAATTTAACGCCAAAAATATTGGAAGACTTTTCAC
259 TTTTTGGCTAAAATACTCATAAAAAACATATAATTCAACGCCAAAAATATTGGAAGACTTTTCAC
* * *
9836 GCTTCTCATATCGTTTTTCATATTATTCTGAATTAA-ATCTTAATTAAATCGAAAC-ACGATTTA
1 GCTTCTAATATCGTTTTTCATATTATTCCGAATTAATTTC-TAATTAAATCGAAACAAC-ATTTA
* *
9899 GATGCTCGTAAAAAAAATTCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATTTGGATATC
64 GATGCTCGTAAAAAAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATGGATATC
* * * **
9964 TCAAGTAATCTTAG-CGCCAAAAATCATGCAAAACTGA-CTCG-GGGCCATGGAATGCATTTTTA
129 TCAAGGAATC-TAGACGCCAAAAATCATGCAAAACTGAGCT-GAGGGCC-CGAAACACATTTTTA
* * *
10026 GCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTACAAAAATTGACC-GAAAACA
191 -ACAAAAAAC-TG-TG---A-TACACGATTTCGGCTAAAATTTTACAAAAAATGACCAGAAAA-A
*
10090 CATTTCCTCAA-TTTTGGCTAAAATACTCAATAAAAAACATATAATTCAATGCCAAAAATATT-G
248 CATTTCCTCAATTTTTGGCTAAAATACTC-ATAAAAAACATATAATTCAACGCCAAAAATATTGG
** *
10153 AAGGGTATTTTAC
312 AAGACT-TTTCAC
* * *
10166 GCTTTTAATATCGTTTTTCCTACTT-TTCCCGAATTAATTTCTAATTAAATTGAAACAACATTTA
1 GCTTCTAATATCGTTTTTCATA-TTATT-CCGAATTAATTTCTAATTAAATCGAAACAACATTTA
** *
10230 GATGCTCGTAAGAACCAATCCTTAAATCCAATGTGGCTGAGATTTGATTA
64 GATGCTCGTAA-AAAAAATCCTTAAATGCAATGTGGCTGAGATTTGATTA
10280 AAAAAAATAA
Statistics
Matches: 369, Mismatches: 55, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
323 6 0.02
324 90 0.24
325 69 0.19
326 2 0.01
327 2 0.01
329 20 0.05
330 60 0.16
331 82 0.22
332 38 0.10
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (323 bp):
GCTTCTAATATCGTTTTTCATATTATTCCGAATTAATTTCTAATTAAATCGAAACAACATTTAGA
TGCTCGTAAAAAAAATCCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAATATGGATATCTC
AAGGAATCTAGACGCCAAAAATCATGCAAAACTGAGCTGAGGGCCCGAAACACATTTTTAACAAA
AAACTGTGATACACGATTTCGGCTAAAATTTTACAAAAAATGACCAGAAAAACATTTCCTCAATT
TTTGGCTAAAATACTCATAAAAAACATATAATTCAACGCCAAAAATATTGGAAGACTTTTCAC
Found at i:11478 original size:12 final size:12
Alignment explanation
Indices: 11463--11487 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11453 CAATCTTGAA
11463 GAAAATCATGTC
1 GAAAATCATGTC
11475 GAAAATCATGTC
1 GAAAATCATGTC
11487 G
1 G
11488 GATTTTGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATCATGTC
Found at i:11510 original size:13 final size:13
Alignment explanation
Indices: 11492--11516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11482 ATGTCGGATT
11492 TTGTAGATCTAAG
1 TTGTAGATCTAAG
11505 TTGTAGATCTAA
1 TTGTAGATCTAA
11517 AATTCTGTCA
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:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:11653 original size:22 final size:21
Alignment explanation
Indices: 11595--11653 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
11585 TATTTTTTTA
*
11595 ATTATTATTAATTATTTAATT
1 ATTATTATTAATAATTTAATT
* *
11616 ATTAATTAATATTAATTTAAATT
1 ATT-ATTATTAATAATTT-AATT
*
11639 GTTATTATTAATAAT
1 ATTATTATTAATAAT
11654 AATTAATAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 21 0.70
23 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTAATAATTTAATT
Found at i:11856 original size:21 final size:21
Alignment explanation
Indices: 11814--11858 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11804 GCAAAATTGT
* ***
11814 CAAAAGGGGGGCGGTGTTTAG
1 CAAAAAGGGGGCGGTAAATAG
11835 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGGTAAATAG
11856 CAA
1 CAA
11859 CTCCCATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.40, T:0.13
Consensus pattern (21 bp):
CAAAAAGGGGGCGGTAAATAG
Found at i:14733 original size:36 final size:36
Alignment explanation
Indices: 14686--14755 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
14676 TTCAATAACC
* *
14686 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
14722 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
14756 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:15053 original size:36 final size:36
Alignment explanation
Indices: 15006--15075 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
14996 TTCAATAACC
* *
15006 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
15042 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
15076 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:15060 original size:320 final size:320
Alignment explanation
Indices: 14478--15812 Score: 1444
Period size: 320 Copynumber: 4.0 Consensus size: 320
14468 AACCTTTTAT
* * *
14478 CATCAATAAAGTGTTACAAATTTTATTACTTAAATTTACTAAAACTGCTGTAAAAGTTATTAAAA
1 CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAA
14543 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
66 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
14608 CATTTTTTTCTCAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATAGCACTATCCAC
131 CATTTTTTTCTCAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATAGCACTATCCAC
14673 TAATTCAATAACCTTACATCTTTTGTGATTTTGGTTATCATATTTCTTATTACATTTTTTGTAAT
196 TAATTCAATAACCTTACATCTTTTGTGATTTTGGTTATCATATTTCTTATTACATTTTTTGTAAT
14738 TTTGATTATCATATTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
261 TTTGATTATCATATTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
*
14798 CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTGTAAAAGTTATTAAAA
1 CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAA
14863 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
66 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
* *
14928 CATTTTTTTCTAAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATAACACTATCCAC
131 CATTTTTTTCTCAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATAGCACTATCCAC
14993 TAATTCAATAACCTTACATCTTTTGTGATTTTGGTTATCATATTTCTTATTACATTTTTTGTAAT
196 TAATTCAATAACCTTACATCTTTTGTGATTTTGGTTATCATATTTCTTATTACATTTTTTGTAAT
15058 TTTGATTATCATATTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
261 TTTGATTATCATATTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
* * * *
15118 TCAAATTTCCATATAAG-GTTATAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAAT
1 -C--A--TCAATA-AAGTGTTACAA--T-T---T----TT-AT------T-----ACT-TAAATT
* * * * ** *
15182 TAGGTGTACAAAA-ACTATAAAAGTTTTTAAAATTGTATTTACCAATCCTTACATTCTTAATAAC
37 TA---CTA-AAAATGCTATAAAAGTTATTAAAATTGTAATTACCAATCCTTATTTTTTTAATAAC
* * * * * *
15246 ATTAGTAAACTTTCATCAATGGTGAAGATTTACCATTTTTTTCCTCAAAAGTTACCGAAAAAGCT
98 ATTAGTAAACTTTCATCAACGGTGAATATTTGCCATTTTTTT-CTCAAAAATTACTGAAAAACCT
* * * * * * * * * * * ***
15311 ATAATAATCATAAAAAATGTTTTGTACTATCAACTAATTTAATGACCTTACA-CTATAAAGATAC
162 ATAATGATCACAAAAGAGGTATAGCACTATCCACTAATTCAATAACCTTACATCTTTTGTGAT--
* **** * * ** * * * *
15375 GTACAATACTGAT-TTTCTTATCTAAGATTAATTACTTAAAAGGTTATGGA-AAACATTATAGTA
225 TTTGGTTA-TCATATTTCTTAT-T-ACATT--TT--TTGTAA--TT-TTGATTATCA-TAT--TT
* * * * * * ** **** * * * *
15438 CTATCTAGAT-TGAAAGAACCTTACATCCTTATTA-ATTTTAGTAACCTTTTAT
277 CT-CCAAAATCT--CACAA--TT-CA-AC--AAAACATACCCG-GACCTGTAAG
15490 CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAA
1 CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAA
15555 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
66 TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
*
15620 CATTTTTTTCTCAAAAGTTACTGAAAAACCTATAATGATCACAAAAGAGGTATAGGCACTATCCA
131 CATTTTTTTCTCAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATA-GCACTATCCA
15685 CTAATTCAATAACCTTACATCTTTTGTGTATTTTGGTTATCATATTTCTTATTACA-TTTTTGTA
195 CTAATTCAATAACCTTACATCTTTTGTG-ATTTTGGTTATCATATTTCTTATTACATTTTTTGTA
15749 ATTTTGGATTATCATAGTTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
259 ATTTT-GATTATCATA-TTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
15813 TCAAATTTTC
Statistics
Matches: 819, Mismatches: 126, Indels: 137
0.76 0.12 0.13
Matches are distributed among these distances:
320 316 0.39
321 1 0.00
323 9 0.01
324 3 0.00
325 12 0.01
326 5 0.01
327 3 0.00
328 1 0.00
329 3 0.00
330 4 0.00
331 6 0.01
332 6 0.01
333 4 0.00
334 4 0.00
335 2 0.00
336 4 0.00
338 1 0.00
339 2 0.00
340 45 0.05
341 122 0.15
342 5 0.01
343 2 0.00
344 7 0.01
345 2 0.00
347 2 0.00
348 7 0.01
350 1 0.00
351 91 0.11
352 63 0.08
353 11 0.01
354 4 0.00
355 4 0.00
356 2 0.00
357 4 0.00
359 4 0.00
361 6 0.01
362 6 0.01
364 5 0.01
365 5 0.01
366 6 0.01
367 11 0.01
368 2 0.00
369 3 0.00
370 1 0.00
371 4 0.00
372 8 0.01
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (320 bp):
CATCAATAAAGTGTTACAATTTTTATTACTTAAATTTACTAAAAATGCTATAAAAGTTATTAAAA
TTGTAATTACCAATCCTTATTTTTTTAATAACATTAGTAAACTTTCATCAACGGTGAATATTTGC
CATTTTTTTCTCAAAAATTACTGAAAAACCTATAATGATCACAAAAGAGGTATAGCACTATCCAC
TAATTCAATAACCTTACATCTTTTGTGATTTTGGTTATCATATTTCTTATTACATTTTTTGTAAT
TTTGATTATCATATTTCTCCAAAATCTCACAATTCAACAAAACATACCCGGACCTGTAAG
Found at i:15747 original size:36 final size:38
Alignment explanation
Indices: 15699--15770 Score: 105
Period size: 36 Copynumber: 1.9 Consensus size: 38
15689 TTCAATAACC
*
15699 TTACATCTTTTGTGTATTTTGG-TTATCATA-TTTCTTA
1 TTACATCTTTTGT-AATTTTGGATTATCATAGTTTCTTA
15736 TTACAT-TTTTGTAATTTTGGATTATCATAGTTTCT
1 TTACATCTTTTGTAATTTTGGATTATCATAGTTTCT
15771 CCAAAATCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 7 0.22
36 14 0.44
37 11 0.34
ACGTcount: A:0.21, C:0.10, G:0.11, T:0.58
Consensus pattern (38 bp):
TTACATCTTTTGTAATTTTGGATTATCATAGTTTCTTA
Done.