Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018036.1 Corchorus olitorius cultivar O-4 contig18069, 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: 58595
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:447 original size:20 final size:20
Alignment explanation
Indices: 412--449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
402 AGTCCAATAG
*
412 GGGGGCGGTGTCTAGTAAAA
1 GGGGGCGGTATCTAGTAAAA
*
432 GGGGGCGGTATTTAGTAA
1 GGGGGCGGTATCTAGTAA
450 TACCCAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.45, T:0.24
Consensus pattern (20 bp):
GGGGGCGGTATCTAGTAAAA
Found at i:4337 original size:193 final size:195
Alignment explanation
Indices: 4000--4390 Score: 635
Period size: 193 Copynumber: 2.0 Consensus size: 195
3990 ACATAATGAG
* *
4000 TTATTTATGAAATAGTCCTAAGATATTTCTACATTATGCTATTTAGTCCCTTGCTATTTTTTTTA
1 TTATTTATGAAATAGTCCCAAGATATTTCTACATTATGCTATTTAGACCCTTGCTA-TTTTTTTA
* *
4065 TTTTACTCGATTTAGCCCTTAATCATATTTCTTTTACATCAAAACCCCCAGACATTCTATTCGAT
65 TTTTACTCGATTTAGCCCTTAATCATATTTCTTTTACATCAAAACCCCCAAACATTCTATTCCAT
* *
4130 ACGATTTTGTCCTTCAAACATTCTATTCTATACGATTTGATCTTTCAACTTTATTTCTTTTATCT
130 ACGATTTAGTCCTTCAAACATTCTATTCTATACGATCTGATCTTTCAACTTTATTTCTTTTATCT
4195 T
195 T
* *
4196 TTATTTATGAAATAGTCCCCATATATTTCTACA-T-TGCTATTTAGACCCTTTGCTA-TTTTTTA
1 TTATTTATGAAATAGTCCCAAGATATTTCTACATTATGCTATTTAGACCC-TTGCTATTTTTTTA
* * *
4258 TTTTACTCGATTTAGCCCTTAATTATATTTCTTTTACATCACAACCCTCAAACATTCTATTCCAT
65 TTTTACTCGATTTAGCCCTTAATCATATTTCTTTTACATCAAAACCCCCAAACATTCTATTCCAT
*
4323 ACGATTTAGTCCTTCAAACATTCTATTCTATATGATCTGATCTTTCAACTTTATTTCTTTTATCT
130 ACGATTTAGTCCTTCAAACATTCTATTCTATACGATCTGATCTTTCAACTTTATTTCTTTTATCT
4388 T
195 T
4389 TT
1 TT
4391 GTTATATTCT
Statistics
Matches: 182, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
193 132 0.73
194 13 0.07
195 7 0.04
196 30 0.16
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (195 bp):
TTATTTATGAAATAGTCCCAAGATATTTCTACATTATGCTATTTAGACCCTTGCTATTTTTTTAT
TTTACTCGATTTAGCCCTTAATCATATTTCTTTTACATCAAAACCCCCAAACATTCTATTCCATA
CGATTTAGTCCTTCAAACATTCTATTCTATACGATCTGATCTTTCAACTTTATTTCTTTTATCTT
Found at i:13707 original size:4 final size:4
Alignment explanation
Indices: 13698--13724 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13688 TTGAAGCGAT
13698 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
13725 AACACGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:24683 original size:31 final size:31
Alignment explanation
Indices: 24648--24712 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
24638 AGTAACATTA
*
24648 GTTAATTCATGCGTCTGTTGCTTGACAAGTT
1 GTTAATTCATGCGTCTATTGCTTGACAAGTT
24679 GTTAATTCATGCGTCTATTGCTTGACAAGTT
1 GTTAATTCATGCGTCTATTGCTTGACAAGTT
24710 GTT
1 GTT
24713 GATAAGCAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (31 bp):
GTTAATTCATGCGTCTATTGCTTGACAAGTT
Found at i:28276 original size:9 final size:10
Alignment explanation
Indices: 28262--28311 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
28252 GTATAACTAA
28262 TTCTT-TTCT
1 TTCTTCTTCT
28271 TTCTTTCTTACT
1 TTC-TTCTT-CT
28283 TTCTTCTTC-
1 TTCTTCTTCT
28292 TTCTTCTTC-
1 TTCTTCTTCT
28301 TTCTT-TTCT
1 TTCTTCTTCT
28310 TT
1 TT
28312 TCCTTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.08
9 19 0.51
10 3 0.08
11 7 0.19
12 5 0.14
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:28763 original size:57 final size:55
Alignment explanation
Indices: 28702--28863 Score: 146
Period size: 57 Copynumber: 2.8 Consensus size: 55
28692 GATGCAAACA
* *
28702 TTTTGCACGATTATGTGACCATTGCTGAAGCTCCAAAAGAGGTGGAGAACACCAACT-
1 TTTTGCACGATTAT-TG-CCATTCCTGAAGCTCCAAAAGAGGTGGACAA-ACCAACTC
* * * * ** *
28759 TTTTGCATGGCAATATCGCCATTCCTGAAGCTCCAAAGGAGGTGGACAATGCAATTC
1 TTTTGCA-CG-ATTATTGCCATTCCTGAAGCTCCAAAAGAGGTGGACAAACCAACTC
* * *
28816 TTTTGAATGATAATTTGGCCATTCCTGAAGCTCCAAAAGAGGTGGACA
1 TTTTGCACGATTA-TT-GCCATTCCTGAAGCTCCAAAAGAGGTGGACA
28864 CCGTTTCCAA
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
55 2 0.02
56 6 0.07
57 71 0.84
58 2 0.02
59 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (55 bp):
TTTTGCACGATTATTGCCATTCCTGAAGCTCCAAAAGAGGTGGACAAACCAACTC
Found at i:29020 original size:90 final size:90
Alignment explanation
Indices: 28867--29034 Score: 255
Period size: 90 Copynumber: 1.9 Consensus size: 90
28857 GTGGACACCG
* * * *
28867 TTTCCAACAGTCTTGAGAAGAAGACAACTGTTTCCAACAGTCATGAGAAGAATACAACTATTTCC
1 TTTCCAACAGTCATGAGAAGAACACAACGGTTTCCAACAGTCATGAGAAGAAGACAACTATTTCC
*
28932 AACAGTCATGAGAAGAACACAACTA
66 AACAGTCACGAGAAGAACACAACTA
** * *
28957 TTTCCAACAGTCATGAGAAGAACACGGCGGTTTCCAACAGTTATGAGAGGAAGACAACTATTTCC
1 TTTCCAACAGTCATGAGAAGAACACAACGGTTTCCAACAGTCATGAGAAGAAGACAACTATTTCC
29022 AACAGTCACGAGA
66 AACAGTCACGAGA
29035 GGAAGGTTGT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (90 bp):
TTTCCAACAGTCATGAGAAGAACACAACGGTTTCCAACAGTCATGAGAAGAAGACAACTATTTCC
AACAGTCACGAGAAGAACACAACTA
Found at i:29035 original size:30 final size:30
Alignment explanation
Indices: 28867--29039 Score: 229
Period size: 30 Copynumber: 5.8 Consensus size: 30
28857 GTGGACACCG
* *
28867 TTTCCAACAGTCTTGAGAAGAAGACAACTG
1 TTTCCAACAGTCATGAGAAGAAGACAACTA
*
28897 TTTCCAACAGTCATGAGAAGAATACAACTA
1 TTTCCAACAGTCATGAGAAGAAGACAACTA
*
28927 TTTCCAACAGTCATGAGAAGAACACAACTA
1 TTTCCAACAGTCATGAGAAGAAGACAACTA
* ** **
28957 TTTCCAACAGTCATGAGAAGAACACGGCGG
1 TTTCCAACAGTCATGAGAAGAAGACAACTA
* *
28987 TTTCCAACAGTTATGAGAGGAAGACAACTA
1 TTTCCAACAGTCATGAGAAGAAGACAACTA
* *
29017 TTTCCAACAGTCACGAGAGGAAG
1 TTTCCAACAGTCATGAGAAGAAG
29040 GTTGTAAAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 126 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (30 bp):
TTTCCAACAGTCATGAGAAGAAGACAACTA
Found at i:29552 original size:21 final size:21
Alignment explanation
Indices: 29526--29566 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
29516 GAAGAAGGAT
29526 AAGAAAGACAAGGAAAAGAAG
1 AAGAAAGACAAGGAAAAGAAG
29547 AAGAAAGACAAGGAAAAGAA
1 AAGAAAGACAAGGAAAAGAA
29567 ACGAAAGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.68, C:0.05, G:0.27, T:0.00
Consensus pattern (21 bp):
AAGAAAGACAAGGAAAAGAAG
Found at i:32659 original size:9 final size:9
Alignment explanation
Indices: 32625--32662 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
32615 TCTTTCTCCC
32625 CTTTTGTTT
1 CTTTTGTTT
32634 CTGTTTGTTT
1 CT-TTTGTTT
32644 CTTTT-TTT
1 CTTTTGTTT
*
32652 CTTTTTTTT
1 CTTTTGTTT
32661 CT
1 CT
32663 CACTAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.30
9 10 0.37
10 9 0.33
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (9 bp):
CTTTTGTTT
Found at i:34767 original size:5 final size:5
Alignment explanation
Indices: 34757--34783 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
34747 TTACTCTATT
34757 ATTAG ATTAG ATTAG ATTAG ATTAG AT
1 ATTAG ATTAG ATTAG ATTAG ATTAG AT
34784 ATAATTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTAG
Found at i:39780 original size:12 final size:13
Alignment explanation
Indices: 39762--39791 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
39752 ATAGAGTATG
39762 TATATTAATATTA
1 TATATTAATATTA
39775 -ATATTAATATTA
1 TATATTAATATTA
39787 TATAT
1 TATAT
39792 AAAGAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTAATATTA
Found at i:40606 original size:7 final size:7
Alignment explanation
Indices: 40594--40624 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40584 ACAAGTATAC
40594 TATCTGA
1 TATCTGA
40601 TATCTGA
1 TATCTGA
40608 TATCTGA
1 TATCTGA
40615 TATCTGA
1 TATCTGA
40622 TAT
1 TAT
40625 ATATTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (7 bp):
TATCTGA
Found at i:42877 original size:2 final size:2
Alignment explanation
Indices: 42870--42895 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42860 TTTCATGTTA
42870 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
42896 CTTCAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43335 original size:15 final size:15
Alignment explanation
Indices: 43315--43344 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43305 ATCTTCTGTT
43315 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
*
43330 TTCTTTTTTTTTTTC
1 TTCTTTTTCTTTTTC
43345 CATGGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:45221 original size:21 final size:22
Alignment explanation
Indices: 45195--45235 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
45185 GATAGACTTT
45195 GAAAAACATGACTT-GAAAGTG
1 GAAAAACATGACTTGGAAAGTG
*
45216 GAAAAACATTACTTGGAAAG
1 GAAAAACATGACTTGGAAAG
45236 GGATAGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.49, C:0.10, G:0.22, T:0.20
Consensus pattern (22 bp):
GAAAAACATGACTTGGAAAGTG
Found at i:50417 original size:42 final size:43
Alignment explanation
Indices: 50366--50459 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 43
50356 AGTGCATTAC
* * *
50366 CTAA-ATTCTA-CTCTATCTCTAGGTAATTCATCAAAATAAAT
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
50407 CTAATATTCTAGTCCTCCATCTCTAGATAATTCATCAAAATCAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
50452 CTAATATT
1 CTAATATT
50460 AATTGTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 35 0.78
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.36
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:54556 original size:17 final size:18
Alignment explanation
Indices: 54522--54559 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
54512 CCAAACCCAA
54522 TGAGGAACAACATTAATGTT
1 TGAGGAACAAC--TAATGTT
54542 TGAGGAACAAC-AATGTT
1 TGAGGAACAACTAATGTT
54559 T
1 T
54560 CACGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (18 bp):
TGAGGAACAACTAATGTT
Found at i:55686 original size:22 final size:22
Alignment explanation
Indices: 55657--55842 Score: 110
Period size: 22 Copynumber: 8.5 Consensus size: 22
55647 TGAATATTTT
* *
55657 TATGAAATTTTGATATCTACCC
1 TATGAAATTTTGATAACCACCC
* *
55679 TATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACCACCC
**
55701 TATGAAATTTTGATAATTA-CC
1 TATGAAATTTTGATAACCACCC
* * * * *
55722 AATGAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAACCACCC
* **
55744 TATGAAACTTTGATAACCTA-AA
1 TATGAAATTTTGATAACC-ACCC
* **
55766 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCACCC
* ** *
55789 TATGAAATTTT-CTAACCTTCT
1 TATGAAATTTTGATAACCACCC
* *
55810 TATG-ATTTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACCC
*
55831 TATGAGATTTTG
1 TATGAAATTTTG
55843 TTAATCTCCC
Statistics
Matches: 125, Mismatches: 33, Indels: 12
0.74 0.19 0.07
Matches are distributed among these distances:
20 5 0.04
21 37 0.30
22 68 0.54
23 15 0.12
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACCC
Found at i:55748 original size:43 final size:45
Alignment explanation
Indices: 55657--55759 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 45
55647 TGAATATTTT
* * * *
55657 TATGAAATTTTGAT-ATCTACCCTATTAAATTTTGATAACCACGC
1 TATGAAATTTTGATAATCTACCCAATGAAATTGTGATAAACACGC
*
55701 TATGAAATTTTGATAAT-TA-CCAATGAAATTGTGATAAACTC-C
1 TATGAAATTTTGATAATCTACCCAATGAAATTGTGATAAACACGC
*
55743 ATATGAAACTTTGATAA
1 -TATGAAATTTTGATAA
55760 CCTAAATATG
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 32 0.63
44 16 0.31
45 2 0.04
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (45 bp):
TATGAAATTTTGATAATCTACCCAATGAAATTGTGATAAACACGC
Found at i:55851 original size:22 final size:22
Alignment explanation
Indices: 55816--55867 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
55806 TTCTTATGAT
*
55816 TTTTGATAACCTCCCTATGAGA
1 TTTTGATAACCTCCCTATAAGA
* * *
55838 TTTTGTTAATCTCCCTATAAGT
1 TTTTGATAACCTCCCTATAAGA
55860 TTTTGATA
1 TTTTGATA
55868 TTATGGTATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCCCTATAAGA
Done.