Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020289.1 Corchorus olitorius cultivar O-4 contig20322, 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: 7314
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:272 original size:22 final size:22
Alignment explanation
Indices: 191--345 Score: 97
Period size: 22 Copynumber: 7.0 Consensus size: 22
181 TCTTGTCTCT
*
191 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTACCAAAATTTCAT-A
* * * * *
214 G-ATGATTACTATAATTTGAT-
1 GTGTGGTTACCAAAATTTCATA
* *
234 GATGAGGTTATCC-AAATTCCATA
1 G-TGTGGTTA-CCAAAATTTCATA
257 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
* *
279 -TG-GAAGTTATCAAAATATCAT-
1 GTGTG--GTTACCAAAATTTCATA
* * *
300 GGGTAGGTTATCAAAATTTCATT
1 GTGT-GGTTACCAAAATTTCATA
323 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTACCAAAATTTCATA
345 G
1 G
346 GATCAGGTTA
Statistics
Matches: 99, Mismatches: 22, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.02
21 4 0.04
22 86 0.87
23 6 0.06
24 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGTGGTTACCAAAATTTCATA
Found at i:337 original size:44 final size:46
Alignment explanation
Indices: 261--373 Score: 117
Period size: 44 Copynumber: 2.5 Consensus size: 46
251 TCCATAGTGT
* * *
261 GGTTACCAAAATTTCATATGGAAGTTATCAAAATATCAT-GGGT-A
1 GGTTATCAAAATTTCATATGGAAGTTACCAAAATATCATAGGATCA
** *
305 GGTTATCAAAATTTCAT-TGTGTGGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATATG-GAAGTTACCAAAATATCATAGGATCA
* *
351 GGTTATTAAAATTTCTTA-GGAAG
1 GGTTATCAAAATTTCATATGGAAG
374 GTTATTGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
43 2 0.04
44 31 0.56
45 5 0.09
46 17 0.31
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (46 bp):
GGTTATCAAAATTTCATATGGAAGTTACCAAAATATCATAGGATCA
Found at i:361 original size:24 final size:22
Alignment explanation
Indices: 268--379 Score: 84
Period size: 22 Copynumber: 5.0 Consensus size: 22
258 TGTGGTTACC
*
268 AAAATTTCATATGGAA-GTTATC
1 AAAATTTCATA-GGAAGGTTATT
* * * *
290 AAAATATCATGGGTAGGTTATC
1 AAAATTTCATAGGAAGGTTATT
* * **
312 AAAATTTCATTGTG-TGGTTACC
1 AAAATTTCATAG-GAAGGTTATT
334 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGA--AGGTTATT
*
358 AAAATTTCTTAGGAAGGTTATT
1 AAAATTTCATAGGAAGGTTATT
380 GCAATTTTAT
Statistics
Matches: 73, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
21 4 0.05
22 50 0.68
23 1 0.01
24 18 0.25
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATT
Found at i:386 original size:22 final size:23
Alignment explanation
Indices: 334--379 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
324 TGTGGTTACC
334 AAAATTTCATAGGATCAGGTTATT
1 AAAATTTCATAGGA-CAGGTTATT
*
358 AAAATTTCTTAGGA-AGGTTATT
1 AAAATTTCATAGGACAGGTTATT
380 GCAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
24 13 0.62
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (23 bp):
AAAATTTCATAGGACAGGTTATT
Found at i:386 original size:68 final size:65
Alignment explanation
Indices: 238--772 Score: 198
Period size: 66 Copynumber: 7.8 Consensus size: 65
228 TTTGATGATG
* * *
238 AGGTTATCCAAATTCCATAGTGTGGTTACCAAAATTTCATATGGAAGTTATCAAAATATCATGGG
1 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGAAGTTATCAAAATATCATAGG
*
303 T
65 A
* * * *
304 AGGTTATCAAAATTTCATTGTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTA
1 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA--A-GTTATCAAAATATCATA
369 GGA
63 GGA
*** * * * * *
372 AGGTTATTGCAATTTTATAGTGTGGTTATCACAATTTTATAGAAAGGTTATCAAAGAGATTATCA
1 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAA-GTTATC-AA-A-A-TATC-
*
437 AAATGTCGTA
60 ATA-G--G-A
* * *
447 GCGAGGTTAT-AAGAATTCCATAGTGTGGTTAACAAAATTTCATAAGG-AGCTTA-CAAATATTT
1 ---AGGTTATCAA-AATTTCATAGTGTGGTTACCAAAATTTCAT-AGGAAG-TTATCAAA-ATAT
* *
509 CATGGGG
59 CATAGGA
* ** ** *
516 AGGTTATCAAAATTTCATA-TGAAGGTTATTAAACTCTCAATTTCATAAGG-AG-TCCCAAAATT
1 AGGTTATCAAAATTTCATAGTG-TGG---TT--AC-CAAAATTTCAT-AGGAAGTTATCAAAATA
*
578 TGATA-GA
58 TCATAGGA
* * * * * * *
585 AGGTTATC-AAATCTCATTGAGTGTTTATCGAAAA-TTCATAGAGATCGGATTATCAAAAT-TTA
1 AGGTTATCAAAATTTCATAGTGTGGTTA-CCAAAATTTCATAG-GA--AG-TTATCAAAATATCA
647 TAGGA
61 TAGGA
* * * * *
652 AGATTATCAAAATTTCATAGTGTTGTTATCAAAAATTTCAAAGCGAGGTTATCAAAAT-T-ATA-
1 AGGTTATCAAAATTTCATAGTGTGGTTA-CCAAAATTTCATAG-GAAGTTATCAAAATATCATAG
714 GA
64 GA
* * * * *
716 ATGTGATTATCAAAATTTCATAGAG-GGTCAACAAAATTTTATAGAGAGGTTATCAAA
1 A-G-G-TTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG-GAAGTTATCAAA
773 TTTTCAAAAT
Statistics
Matches: 355, Mismatches: 73, Indels: 83
0.69 0.14 0.16
Matches are distributed among these distances:
61 2 0.01
62 6 0.02
63 3 0.01
64 4 0.01
65 34 0.10
66 80 0.23
67 41 0.12
68 80 0.23
69 21 0.06
70 11 0.03
71 6 0.02
72 17 0.05
73 1 0.00
74 4 0.01
75 3 0.01
76 2 0.01
77 2 0.01
78 36 0.10
79 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (65 bp):
AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGAAGTTATCAAAATATCATAGGA
Found at i:420 original size:22 final size:22
Alignment explanation
Indices: 371--424 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
361 ATTTCTTAGG
** *
371 AAGGTTATTGCAATTTTATAGT
1 AAGGTTATCACAATTTTATAGA
**
393 GTGGTTATCACAATTTTATAGA
1 AAGGTTATCACAATTTTATAGA
415 AAGGTTATCA
1 AAGGTTATCA
425 AAGAGATTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (22 bp):
AAGGTTATCACAATTTTATAGA
Found at i:508 original size:22 final size:21
Alignment explanation
Indices: 478--534 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
468 AGTGTGGTTA
478 ACAAAATTTCATAAGGAGCTT
1 ACAAAATTTCATAAGGAGCTT
** *
499 ACAAATATTTCATGGGGAGGTT
1 ACAAA-ATTTCATAAGGAGCTT
521 ATCAAAATTTCATA
1 A-CAAAATTTCATA
535 TGAAGGTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 5 0.17
22 21 0.70
23 4 0.13
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (21 bp):
ACAAAATTTCATAAGGAGCTT
Found at i:541 original size:22 final size:21
Alignment explanation
Indices: 473--544 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
463 TCCATAGTGT
* *
473 GGTTAACAAAATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGAA
* * *
495 GCTTA-CAAATATTTCATGGGGA
1 GGTTATCAAA-ATTTCAT-AGAA
517 GGTTATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATA-GAA
539 GGTTAT
1 GGTTAT
545 TAAACTCTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.10
22 33 0.80
23 4 0.10
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGAA
Found at i:680 original size:22 final size:21
Alignment explanation
Indices: 634--806 Score: 93
Period size: 22 Copynumber: 8.0 Consensus size: 21
624 AGAGATCGGA
*
634 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG--GG
*
655 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTG-GG
* *
677 TTATCAAAAATTTCAAAGCGAGG
1 TTATC-AAAATTTCATAGTG-GG
*
700 TTATCAAAA-TT-ATAGAATGTGA
1 TTATCAAAATTTCATAG--TG-GG
*
722 TTATCAAAATTTCATAGAGGG
1 TTATCAAAATTTCATAGTGGG
* * * *
743 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTG-GG
* * * *
765 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTG-GG
*
787 TTACCAAAATTTCATAGTGG
1 TTATCAAAATTTCATAGTGG
807 TATTTCTGGG
Statistics
Matches: 115, Mismatches: 29, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.03
21 32 0.28
22 55 0.48
23 21 0.18
24 4 0.03
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGTGGG
Found at i:766 original size:65 final size:67
Alignment explanation
Indices: 653--803 Score: 182
Period size: 65 Copynumber: 2.3 Consensus size: 67
643 TTTATAGGAA
* * * * * *
653 GATTATCAAAATTTCATAGTGTTGTTATCAAAAATTTCAAAGCGAGGTTATCAAAATTAT-AGAA
1 GATTATCAAAATTTCATAGAGTGGTCAACAAAAATTTCAAAGAGAGGTTATC-AAATTATCAAAA
717 TGT
65 TGT
* * *
720 GATTATCAAAATTTCATAGAG-GGTCAAC-AAAATTTTATAGAGAGGTTATCAAATTTTCAAAAT
1 GATTATCAAAATTTCATAGAGTGGTCAACAAAAATTTCAAAGAGAGGTTATCAAATTATCAAAAT
783 GT
66 GT
*
785 GATTACCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
804 TGGTATTTCT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 6 0.08
65 43 0.59
66 4 0.05
67 20 0.27
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (67 bp):
GATTATCAAAATTTCATAGAGTGGTCAACAAAAATTTCAAAGAGAGGTTATCAAATTATCAAAAT
GT
Found at i:768 original size:88 final size:90
Alignment explanation
Indices: 609--780 Score: 201
Period size: 88 Copynumber: 1.9 Consensus size: 90
599 CATTGAGTGT
* * *
609 TTATCGAAAATTCATAGAGATCGGATTATCAAAATTTATAGGAAGATTATCAAAATTTCATAGTG
1 TTATCGAAAATTCATAGAGATCGGATTATCAAAATTTATAGGAAGATCAACAAAATTTCATAGAG
**
674 TTGTTATCAAAAATTTCAAAGCGAGG
66 AGGTTATC-AAAATTTCAAAGCGAGG
* * *
700 TTATC-AAAATT-ATAGA-AT-GTGATTATCAAAATTTCATA-GAGGGTCAACAAAATTTTATAG
1 TTATCGAAAATTCATAGAGATCG-GATTATCAAAATTT-ATAGGAAGATCAACAAAATTTCATAG
*
760 AGAGGTTATCAAATTTTCAAA
64 AGAGGTTATCAAAATTTCAAA
781 ATGTGATTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
87 11 0.16
88 40 0.57
89 8 0.11
90 6 0.09
91 5 0.07
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (90 bp):
TTATCGAAAATTCATAGAGATCGGATTATCAAAATTTATAGGAAGATCAACAAAATTTCATAGAG
AGGTTATCAAAATTTCAAAGCGAGG
Found at i:1686 original size:21 final size:20
Alignment explanation
Indices: 1662--1704 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
1652 CCTTAGGCAA
1662 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAA-CTT
1683 CTCCAATGAGCTTGAAACTT
1 CTCCAATGAGCTTGAAACTT
1703 CT
1 CT
1705 TTGTGAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (20 bp):
CTCCAATGAGCTTGAAACTT
Found at i:3596 original size:33 final size:33
Alignment explanation
Indices: 3559--3663 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
3549 ATTAGCATCC
3559 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTTTCATCACAAACAACACCT
* * * *
3592 AAAACAGATTTACTGTCATCACAAACAATACTT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
** * * * *
3625 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAGATTTAGTTTCATCACAAACAACACCT
3658 AAAACA
1 AAAACA
3664 ATCTTTGCAA
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
32 4 0.07
33 52 0.93
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.27
Consensus pattern (33 bp):
AAAACAGATTTAGTTTCATCACAAACAACACCT
Found at i:4623 original size:38 final size:38
Alignment explanation
Indices: 4572--4688 Score: 234
Period size: 38 Copynumber: 3.1 Consensus size: 38
4562 TTTCTTCTCG
4572 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
1 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
4610 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
1 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
4648 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
1 TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
4686 TGA
1 TGA
4689 GTGAATCAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 79 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (38 bp):
TGACCTACTTGAGGAACAAACAATTAAGAGCAATAACT
Done.