Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020700.1 Corchorus olitorius cultivar O-4 contig20733, 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: 39896
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2367 original size:25 final size:25
Alignment explanation
Indices: 2326--2375 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2316 CTGGTATTTT
* *
2326 GGTTCAATTATCAGTTTAATCGGTC
1 GGTTCAATCATCAGTTTAACCGGTC
*
2351 GGTTCAATCATCGGTTTAACCGGTC
1 GGTTCAATCATCAGTTTAACCGGTC
2376 AAATGACAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (25 bp):
GGTTCAATCATCAGTTTAACCGGTC
Found at i:6208 original size:49 final size:50
Alignment explanation
Indices: 6138--6238 Score: 159
Period size: 49 Copynumber: 2.0 Consensus size: 50
6128 CTGCAGATGC
6138 GTTATGATTCTCTTTCAAAGAGAGGAT-CGAAGATCCTCGTGTGCTGCAA
1 GTTATGATTCTCTTTCAAAGAGAGGATGCGAAGATCCTCGTGTGCTGCAA
* *
6187 GTTATGATTCTCTTTCGAAGAGAGGATCGGCGAAGATCCTCTTGTGCTGCAA
1 GTTATGATTCTCTTTCAAAGAGAGGAT--GCGAAGATCCTCGTGTGCTGCAA
6239 CAGCCGGTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 26 0.55
52 21 0.45
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
GTTATGATTCTCTTTCAAAGAGAGGATGCGAAGATCCTCGTGTGCTGCAA
Found at i:7183 original size:1 final size:1
Alignment explanation
Indices: 7177--7206 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
7167 GGATATTAGG
7177 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
7207 TCAAGTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8553 original size:1 final size:1
Alignment explanation
Indices: 8547--8575 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
8537 TTTTAAAATT
8547 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8576 CTCTAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12159 original size:18 final size:18
Alignment explanation
Indices: 12136--12179 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
12126 AACTGGTTCG
*
12136 GGCTCAACTTCTTTTGCA
1 GGCTCAACTTCTTTTGAA
12154 GGCTCAACTTCTTTTGAA
1 GGCTCAACTTCTTTTGAA
12172 GGCTCAAC
1 GGCTCAAC
12180 ATTTGTTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (18 bp):
GGCTCAACTTCTTTTGAA
Found at i:14286 original size:9 final size:9
Alignment explanation
Indices: 14272--14314 Score: 68
Period size: 9 Copynumber: 4.7 Consensus size: 9
14262 GTTTCAAATA
14272 ATATGTAGT
1 ATATGTAGT
14281 ATATGTAGT
1 ATATGTAGT
14290 ATATGTAGT
1 ATATGTAGT
*
14299 ATATATAGT
1 ATATGTAGT
14308 ACTATGT
1 A-TATGT
14315 TTTAGATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
9 27 0.87
10 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (9 bp):
ATATGTAGT
Found at i:25548 original size:6 final size:6
Alignment explanation
Indices: 25537--25575 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
25527 TTAGATCCTC
25537 CAGGAA CAGGAA CAGGAA CAGGAA CAGGAA CAGGAA CAG
1 CAGGAA CAGGAA CAGGAA CAGGAA CAGGAA CAGGAA CAG
25576 AGCTGGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.33, T:0.00
Consensus pattern (6 bp):
CAGGAA
Found at i:26891 original size:71 final size:72
Alignment explanation
Indices: 26736--26892 Score: 167
Period size: 71 Copynumber: 2.2 Consensus size: 72
26726 ACCACTCTCA
* ** * * *
26736 GTTAGGGGTTTGAATTTATGTTCTTTCATTTTTCTCGATTTAATGATCTCAGCACTAATCTCACT
1 GTTAGGGGTTTGAAATTATGTTCTCCCATTTTTCTCGATCTAATGATCTCAGCACCAATATCACT
* *
26801 GAGACAT
66 AAGACAC
* * * *
26808 GTT-GAAGATTTGAAATTATGTTCTCCCA-TTTTCTCGATCTAATGAT-TAGAGCACCAATATCT
1 GTTAG-GGGTTTGAAATTATGTTCTCCCATTTTTCTCGATCTAATGATCT-CAGCACCAATATCA
26870 CTAAGACAC
64 CTAAGACAC
26879 GTTAGGGGTTTGAA
1 GTTAGGGGTTTGAA
26893 CTTTTATCTT
Statistics
Matches: 68, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
70 1 0.01
71 45 0.66
72 22 0.32
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (72 bp):
GTTAGGGGTTTGAAATTATGTTCTCCCATTTTTCTCGATCTAATGATCTCAGCACCAATATCACT
AAGACAC
Found at i:26906 original size:71 final size:71
Alignment explanation
Indices: 26831--27045 Score: 179
Period size: 71 Copynumber: 3.2 Consensus size: 71
26821 AATTATGTTC
26831 TCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCTAAGACACGTTAGGGGTTTGAACTT
1 TCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCTAAGACACGTTAGGGGTTTGAACTT
26896 TTATCT
66 TTATCT
* * * ** * * * **
26902 TCCCATCTTCTCG--C--ACG-TTACAATACC-AT-T-T-TGACATACAC---A-TGATTTGGGC
1 TCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCT-A-AGACACGTTAGGGGTTTGAAC
26954 TTTTAT-T
64 TTTTATCT
* *
26961 CTCCCATTTTCTCGATCTAATGATCAGAGCACCAATATCACTAAGACACGTTAGGGGTTTGAACT
1 -TCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCTAAGACACGTTAGGGGTTTGAACT
*
27026 TTTGTCT
65 TTTATCT
*
27033 TCCCATATTCTCG
1 TCCCATTTTCTCG
27046 CACGTTATAA
Statistics
Matches: 103, Mismatches: 24, Indels: 34
0.64 0.15 0.21
Matches are distributed among these distances:
59 1 0.01
60 24 0.23
61 1 0.01
62 2 0.02
63 2 0.02
64 8 0.08
65 8 0.08
66 9 0.09
67 8 0.08
68 1 0.01
69 2 0.02
70 1 0.01
71 35 0.34
72 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (71 bp):
TCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCTAAGACACGTTAGGGGTTTGAACTT
TTATCT
Found at i:27037 original size:131 final size:131
Alignment explanation
Indices: 26828--27075 Score: 433
Period size: 131 Copynumber: 1.9 Consensus size: 131
26818 TGAAATTATG
* *
26828 TTCTCCCATTTTCTCGATCTAATGATTAGAGCACCAATATCTCTAAGACACGTTAGGGGTTTGAA
1 TTCTCCCATTTTCTCGATCTAATGATCAGAGCACCAATATCACTAAGACACGTTAGGGGTTTGAA
*
26893 CTTTTATCTTCCCATCTTCTCGCACGTTACAATACCATTTTGACATACACATGATTTGGGCTTTT
66 CTTTTATCTTCCCATATTCTCGCACGTTACAATACCATTTTGACATACACATGATTTGGGCTTTT
26958 A
131 A
26959 TTCTCCCATTTTCTCGATCTAATGATCAGAGCACCAATATCACTAAGACACGTTAGGGGTTTGAA
1 TTCTCCCATTTTCTCGATCTAATGATCAGAGCACCAATATCACTAAGACACGTTAGGGGTTTGAA
* * * *
27024 CTTTTGTCTTCCCATATTCTCGCACGTTATAATACCGTTTTGACATGCACAT
66 CTTTTATCTTCCCATATTCTCGCACGTTACAATACCATTTTGACATACACAT
27076 CAAGGGGTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 110 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.36
Consensus pattern (131 bp):
TTCTCCCATTTTCTCGATCTAATGATCAGAGCACCAATATCACTAAGACACGTTAGGGGTTTGAA
CTTTTATCTTCCCATATTCTCGCACGTTACAATACCATTTTGACATACACATGATTTGGGCTTTT
A
Found at i:28907 original size:7 final size:7
Alignment explanation
Indices: 28897--28938 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
28887 TTTCTTTTTC
28897 TTTTATT
1 TTTTATT
28904 TTTTATT
1 TTTTATT
28911 TTTTATT
1 TTTTATT
28918 TTTTATT
1 TTTTATT
28925 TTTTATT
1 TTTTATT
28932 TTTTATT
1 TTTTATT
28939 CCTCCACCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTATT
Found at i:30310 original size:439 final size:438
Alignment explanation
Indices: 29484--30610 Score: 1203
Period size: 439 Copynumber: 2.6 Consensus size: 438
29474 AAAATTTTAA
* * *
29484 AAGC-TTTTTTTAGAATTGAAACATAAAAATTAGCTTTTGAGTCTTTCATGAAAGTTGCAGATCA
1 AAGCATTTTTTTAGAATTGAAACATAATAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCA
* * * * * * *
29548 TAAAATTACCTTTTCATAGACACCTGAATTACCTTAATTGGACACATAAAACAAAGAAAATAAAA
66 TAAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAGAACAAAG--AATAAAA
* ** * *
29613 AAA-AAA-CTGAAGTGTTAAATCGAGTAAGATATAATTTGTAAAGGACTAAGTAGCATAAAATAA
129 AAATAAAGCTTAAACGTT--A--GATTAAGATATAATTTGTAAAGGACTAAGTAGCATAAAGTAA
* * *
29676 AAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGTTAATGGAGATCTTAAA
190 AAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTAAA
* * * * *
29741 ACATAAAAATTCTCTTTTGAACTCTTCATGAAACTCGTGGATCAAATTAACTTTCGGGTTATTCA
255 ACATAAAAATTCTCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGATCATTCA
* * * * * *
29806 TGAAAGTCATAGATCATACAGTAACATTTTAATCGACAGTTGAATAACTTTAATTGGACATGTGG
320 TGAAAGTCATAAATCATACAGTAACATTTTAACCGACACTTCAATAACTTCAATCGGACATGTGG
* *** *
29871 ATC-GAAAATTATATGGTACTAAA-TAGACCAACAATCAAAACGACCAAA-TTTAGG
385 A-CAAAAAATTATACAATACTAAATTA-ACCAACAATCAAAACCA-CAAACTTTAGG
* * *
29925 AAGCATTTTTTTTTGAATTGAAACATAATAATTTGCTTTTGAGTCCTTCATGAAAGTTATAGATC
1 AAGCA-TTTTTTTAGAATTGAAACATAATAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATC
* *
29990 ATAAAATTACCTTTTGATAGACACATGAATCAATTTAATCGGACAAATAGAACAAAGAATAAAAA
65 ATAAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAGAACAAAGAATAAAAA
* * * *
30055 AATAAAGCTTAAACATTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAG
130 AATAAAGCTTAAACGTTAGATTAAGATATAATTTGTAAAGGACTAAGTAGCATAAAGTAAAAAAG
* *
30120 TATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAACATA
195 TATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTAAAACATA
* * *
30185 AAAATTC-CTTTCTGAACCCTTCACGAAACTCGTAGATCAACTTTAGCTTTCGGATCCTT-ATGA
260 AAAATTCTCTTT-TGAACCCTTCACGAAACTCGTAGATCAA-ATTAACTTTCGGATCATTCATGA
* *
30248 AAGTCGTAAATCATGCCA-TAACCA-TTTAACCGACACTTCAATAACTTCAATCGGACATGTGGA
323 AAGTCATAAATCAT-ACAGTAA-CATTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGA
* ** *
30311 CAAAAAATTATACAATATTAAATTAACCGGCAATCAAAACCACAAACTTTCGG
386 CAAAAAATTATACAATACTAAATTAACCAACAATCAAAACCACAAACTTTAGG
* ** * * * * *
30364 AAGCA-ATTTTTAGAATCAAAACATTATAATTGGC-TTTGAAGTTCTTAATGAAAATTGTAGATC
1 AAGCATTTTTTTAGAATTGAAACATAATAATTAGCTTTTG-AGTCCTTCATGAAAGTTGTAGATC
* * * * * *
30427 ATGAAATAACCTTTTAATAGACACTTGAATCACCTTATAATCAGATAAATAGAA-AAA-AAAAAC
65 ATAAAATTACCTTTTAATAGACACATGAATCA-CTT-TAATCGGACAAATAGAACAAAGAATAA-
* * *
30490 AAAAATAAAAGC-TAACACGTTAAATCGTCAA-ACCTATAA-TGGTAAAGGACTAAATAGCATAA
127 AAAAAT-AAAGCTTAA-ACGTTAGAT--T-AAGA--TATAATTTGTAAAGGACTAAGTAGCATAA
* * * * * *
30552 AGCATAAAAGTATGAGGGTCATTAGATAAATAATCC-AACAA-AAAATATTAGTTTATGGA
185 AGTAAAAAAGTATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGA
30611 CAATGGGATC
Statistics
Matches: 580, Mismatches: 84, Indels: 45
0.82 0.12 0.06
Matches are distributed among these distances:
436 4 0.01
437 75 0.13
438 23 0.04
439 253 0.44
440 34 0.06
441 21 0.04
442 58 0.10
443 112 0.19
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (438 bp):
AAGCATTTTTTTAGAATTGAAACATAATAATTAGCTTTTGAGTCCTTCATGAAAGTTGTAGATCA
TAAAATTACCTTTTAATAGACACATGAATCACTTTAATCGGACAAATAGAACAAAGAATAAAAAA
ATAAAGCTTAAACGTTAGATTAAGATATAATTTGTAAAGGACTAAGTAGCATAAAGTAAAAAAGT
ATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGAGATCTTAAAACATAA
AAATTCTCTTTTGAACCCTTCACGAAACTCGTAGATCAAATTAACTTTCGGATCATTCATGAAAG
TCATAAATCATACAGTAACATTTTAACCGACACTTCAATAACTTCAATCGGACATGTGGACAAAA
AATTATACAATACTAAATTAACCAACAATCAAAACCACAAACTTTAGG
Found at i:31505 original size:2 final size:2
Alignment explanation
Indices: 31498--31532 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31488 TTTCTTATAA
*
31498 CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
31533 AAATTATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:32170 original size:2 final size:2
Alignment explanation
Indices: 32163--32195 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32153 TGTACTCATG
32163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32196 CAAATGAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34461 original size:44 final size:47
Alignment explanation
Indices: 34398--34491 Score: 158
Period size: 44 Copynumber: 2.1 Consensus size: 47
34388 GTTTTGATTT
34398 GTATTTTTATTTTTATTTAAA-T-TATA-TATATTATATATTATAAA
1 GTATTTTTATTTTTATTTAAATTATATATTATATTATATATTATAAA
*
34442 GTATTTTTATTTTTATTTAAATTATATATTATATTATTTATTATAAA
1 GTATTTTTATTTTTATTTAAATTATATATTATATTATATATTATAAA
34489 GTA
1 GTA
34492 ATATATGATA
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 21 0.46
45 1 0.02
46 4 0.09
47 20 0.43
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (47 bp):
GTATTTTTATTTTTATTTAAATTATATATTATATTATATATTATAAA
Found at i:37730 original size:15 final size:15
Alignment explanation
Indices: 37710--37741 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
37700 TAAATGTATC
37710 TCGTGTCGTGGTGTG
1 TCGTGTCGTGGTGTG
*
37725 TCGTGTCGTGTTGTG
1 TCGTGTCGTGGTGTG
37740 TC
1 TC
37742 ATGACCCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.41, T:0.44
Consensus pattern (15 bp):
TCGTGTCGTGGTGTG
Found at i:39043 original size:24 final size:24
Alignment explanation
Indices: 39016--39066 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
39006 ATTCATTCTC
*
39016 TTTTGAAATTTCTTTATGAATGAA
1 TTTTGAAATTTCTTTATAAATGAA
39040 TTTTGAAATTTCTTTATAAATGAA
1 TTTTGAAATTTCTTTATAAATGAA
39064 TTT
1 TTT
39067 CGAATTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (24 bp):
TTTTGAAATTTCTTTATAAATGAA
Found at i:39675 original size:2 final size:2
Alignment explanation
Indices: 39670--39704 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39660 GGGGGGCCTT
39670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39705 GAGTAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.