Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015288.1 Corchorus olitorius cultivar O-4 contig15321, 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: 38092
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:145 original size:32 final size:31
Alignment explanation
Indices: 99--175 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 31
89 CTCATTTTTG
*
99 AAACGTAAGGGATTAATTTGTCCCAAAAAAAA
1 AAACATAAGGGATTAATTTGTCCC-AAAAAAA
* **
131 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAAAAA
*
162 AAACCTAAGGGATT
1 AAACATAAGGGATT
176 TTTTTGGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 18 0.45
32 22 0.55
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (31 bp):
AAACATAAGGGATTAATTTGTCCCAAAAAAA
Found at i:266 original size:13 final size:13
Alignment explanation
Indices: 248--273 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
238 GTGGACTTTA
248 GTTAAATAATAAT
1 GTTAAATAATAAT
261 GTTAAATAATAAT
1 GTTAAATAATAAT
274 AATAGTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
GTTAAATAATAAT
Found at i:2024 original size:18 final size:18
Alignment explanation
Indices: 2003--2041 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1993 TGAAGGTGAT
2003 GGTGAAGGTCAAGTTAAA
1 GGTGAAGGTCAAGTTAAA
** *
2021 GGTGTTGGTCAAGTTGAA
1 GGTGAAGGTCAAGTTAAA
2039 GGT
1 GGT
2042 AATGTTGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.28
Consensus pattern (18 bp):
GGTGAAGGTCAAGTTAAA
Found at i:3508 original size:29 final size:29
Alignment explanation
Indices: 3474--3529 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3464 TTTTGTATAG
* *
3474 TATTTAACTAGTTTGATTGACTTGTTTAC
1 TATTTAACTAATTTAATTGACTTGTTTAC
3503 TATTTAACTAATTTAATTGACTTGTTT
1 TATTTAACTAATTTAATTGACTTGTTT
3530 TGTGCAGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.54
Consensus pattern (29 bp):
TATTTAACTAATTTAATTGACTTGTTTAC
Found at i:5550 original size:31 final size:31
Alignment explanation
Indices: 5506--5592 Score: 133
Period size: 31 Copynumber: 2.9 Consensus size: 31
5496 GTTTTGTGCT
* *
5506 TAAAAAT--AATTCAGGGTATAAGGTTTGCC
1 TAAAAATGCAATTCAGGATATGAGGTTTGCC
*
5535 TAAAAATGCAATTCAGGATATGCGGTTTGCC
1 TAAAAATGCAATTCAGGATATGAGGTTTGCC
5566 TAAAAATGCAATTCAGGATATGAGGTT
1 TAAAAATGCAATTCAGGATATGAGGTT
5593 ACAAAAAGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 7 0.13
31 45 0.87
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (31 bp):
TAAAAATGCAATTCAGGATATGAGGTTTGCC
Found at i:11333 original size:30 final size:30
Alignment explanation
Indices: 11264--11343 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
11254 TAAATACCCA
* **
11264 AAAAAAATCCCTTATGTTTTGCTTTTGGGAC
1 AAAATAATCCCTTATGTTTT-CTTTTAAGAC
11295 AAAATAATCCCTTATGTTTT-TTTTCAAGAC
1 AAAATAATCCCTTATGTTTTCTTTT-AAGAC
* *
11325 AAATTAATCCCTTACGTTT
1 AAAATAATCCCTTATGTTT
11344 CAAAAATGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 4 0.09
30 20 0.47
31 19 0.44
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (30 bp):
AAAATAATCCCTTATGTTTTCTTTTAAGAC
Found at i:11544 original size:31 final size:30
Alignment explanation
Indices: 11495--11560 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 30
11485 AAGGGACTAA
11495 TTTGT-CCAAAAAAAAACATAAGGGATTCT
1 TTTGTCCCAAAAAAAAACATAAGGGATTCT
*
11524 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAA-AAAAACATAAGGGATTCT
11555 TTTGTC
1 TTTGTC
11561 AACATAAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 5 0.15
30 6 0.18
31 23 0.68
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (30 bp):
TTTGTCCCAAAAAAAAACATAAGGGATTCT
Found at i:12038 original size:178 final size:180
Alignment explanation
Indices: 11830--12184 Score: 563
Period size: 179 Copynumber: 2.0 Consensus size: 180
11820 TAATGTCATT
11830 TAAGAAATATATTTTAAAATATTCTAATATATCTAA-TTTTTTAATTAAAATAGTAAAATGGTAA
1 TAAGAAATATATTTTAAAATATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAA
** *
11894 AAATAAAATAGTTATAAATATATTAGATTTGATTAAATAAAAATAGAGTTTTTAATTGAGTAAAA
66 AAATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTCTTTAATTGAGTAAAA
* * * * *
11959 TTGTAAAAGTTTAAACAATGGCATTTAAGAAATATATTTGAAAAATAAGAG
131 CTATAAAA-ATTAAACAATGACATTTAAGAAATATAATTGAAAAATAAGAG
* *
12010 TAAGAAATATA-TTTAAAA-ATTTTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTGA
1 TAAGAAATATATTTTAAAATATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAA
* **
12073 AAATAAAATATTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTCTTTCCTTGAGTAAAA
66 AAATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTCTTTAATTGAGTAAAA
12138 CTATAAAAATTAAACAATGACATTTAAGAAATATAATTGAAAAATAA
131 CTATAAAAATTAAACAATGACATTTAAGAAATATAATTGAAAAATAA
12185 AGGTATAATC
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
178 51 0.32
179 99 0.61
180 11 0.07
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.36
Consensus pattern (180 bp):
TAAGAAATATATTTTAAAATATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAA
AAATAAAATAGTTATAAATATATTAGATTAAATTAAATAAAAATAGAGTCTTTAATTGAGTAAAA
CTATAAAAATTAAACAATGACATTTAAGAAATATAATTGAAAAATAAGAG
Found at i:21734 original size:21 final size:21
Alignment explanation
Indices: 21708--21757 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
21698 GGAATGGCGA
**
21708 TGGCACGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
21729 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
21750 TGGCACGG
1 TGGCACGG
21758 TGAATGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:24396 original size:24 final size:25
Alignment explanation
Indices: 24345--24414 Score: 83
Period size: 24 Copynumber: 2.8 Consensus size: 25
24335 AACTTTTTGC
*
24345 TTTTTATATGACGCAGAAACAACTTT
1 TTTTTTTATGACGCA-AAACAACTTT
24371 TTTTTTTATGACGCAAAA-AA-TATT
1 TTTTTTTATGACGCAAAACAACT-TT
24395 TTTTTTT-TCGACGCAAAACA
1 TTTTTTTAT-GACGCAAAACA
24415 CAGAACAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.50
25 4 0.10
26 14 0.35
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (25 bp):
TTTTTTTATGACGCAAAACAACTTT
Found at i:24534 original size:47 final size:49
Alignment explanation
Indices: 24441--24531 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 49
24431 TTTCAAAAAA
24441 ACGCAAAACACAAAAAATAGAAAACGCAAAAATAACAAATTTTTTTATG
1 ACGCAAAACACAAAAAATAGAAAACGCAAAAATAACAAATTTTTTTATG
* *
24490 ACGC-AAACACAAAAATTA-AAAACG-GAAAA-AACAAATTTTTTT
1 ACGCAAAACACAAAAAATAGAAAACGCAAAAATAACAAATTTTTTT
24532 TTAGATTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 13 0.32
46 4 0.10
47 6 0.15
48 13 0.32
49 4 0.10
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.21
Consensus pattern (49 bp):
ACGCAAAACACAAAAAATAGAAAACGCAAAAATAACAAATTTTTTTATG
Found at i:27019 original size:29 final size:31
Alignment explanation
Indices: 26987--27046 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
26977 AAACGTAAAG
**
26987 GATTAATTTG-TCCCGAAA-AAAACATAAGA
1 GATTAATTTGTTCCAAAAACAAAACATAAGA
*
27016 GATTATTTTGTTCCAAAAACAAAACATAAGA
1 GATTAATTTGTTCCAAAAACAAAACATAAGA
27047 TTCTTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
30 6 0.23
31 11 0.42
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (31 bp):
GATTAATTTGTTCCAAAAACAAAACATAAGA
Found at i:29348 original size:27 final size:27
Alignment explanation
Indices: 29306--29383 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 27
29296 ACCCATTCAT
*
29306 GGTGCTCAA-CTCACTGCTCTTGATGAG
1 GGTGCTCAACCT-ACTGCTCTTGACGAG
*
29333 GGTGCTCAACCTACTGCTCCTCCCGACGAG
1 GGTGCTCAACCTACTGCT-CT--TGACGAG
* *
29363 GGTCCTCAACCCACTGCTCTT
1 GGTGCTCAACCTACTGCTCTT
29384 CCCGAGGAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 15 0.36
28 4 0.10
29 2 0.05
30 21 0.50
ACGTcount: A:0.17, C:0.36, G:0.22, T:0.26
Consensus pattern (27 bp):
GGTGCTCAACCTACTGCTCTTGACGAG
Found at i:29371 original size:30 final size:30
Alignment explanation
Indices: 29330--29414 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
29320 TGCTCTTGAT
* *
29330 GAGGGTGCTCAACCTACTGCTCCTCCCGAC
1 GAGGGTCCTCAACCCACTGCTCCTCCCGAC
* *
29360 GAGGGTCCTCAACCCACTGCTCTTCCCGAG
1 GAGGGTCCTCAACCCACTGCTCCTCCCGAC
* *
29390 GAGGATTCTCAACCCACTGCTCCTC
1 GAGGGTCCTCAACCCACTGCTCCTC
29415 TTGACAAGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.21
Consensus pattern (30 bp):
GAGGGTCCTCAACCCACTGCTCCTCCCGAC
Found at i:32799 original size:12 final size:12
Alignment explanation
Indices: 32774--32805 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
32764 GTCGTGTTTA
32774 AATTAAAA-AAT
1 AATTAAAATAAT
32785 AATTAAAATAAT
1 AATTAAAATAAT
32797 AATTAAAAT
1 AATTAAAAT
32806 TAATTATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTAAAATAAT
Found at i:33593 original size:45 final size:45
Alignment explanation
Indices: 33538--33664 Score: 227
Period size: 45 Copynumber: 2.8 Consensus size: 45
33528 AATTCTACTT
33538 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
* *
33583 CATCTATAGGTAATTCATCAAAATAAAGCTAATATTCTACTCCTC
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
*
33628 CATCTCTAGGTAATTCATCAAAATAAACCTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTA
33665 ATTGTTGCTT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAGCTAATATTATACTCCTC
Found at i:35516 original size:26 final size:27
Alignment explanation
Indices: 35463--35522 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
35453 AATTGTGAAA
* * *
35463 TTTAAAAAATTTCATTTATGAAATATT
1 TTTAAAAAATTTAATATATCAAATATT
35490 TTTAAAAAATTTAATATATCTAAAT-TT
1 TTTAAAAAATTTAATATATC-AAATATT
35517 GTTTAA
1 -TTTAA
35523 TTAAATTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTAAAAAATTTAATATATCAAATATT
Found at i:35646 original size:122 final size:127
Alignment explanation
Indices: 35490--35739 Score: 341
Period size: 132 Copynumber: 2.0 Consensus size: 127
35480 ATGAAATATT
* * * * *
35490 TTTAAAAAATTTAATATATCTAAATTTGTTTAATTAAATTAGTAAAATGGTAAAAA-T-GA-A-A
1 TTTAAAAAATTTAACATATATAAATTTGTTTAATTAAAATAGTAAAATGATAAAAATTAAATATA
35551 T-AGG-TTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTATA
66 TAAGGATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTATA
* *
35611 TTTAAAAAATTCTAACATATATAAGTTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAATAG
1 TTTAAAAAATT-TAACATATATAAATTTGTTTAATTAAAATAGTAAAATGATAAAAATTAAATA-
*
35676 TTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
64 -TATAAGG--ATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGT
35740 TTAAACAATG
Statistics
Matches: 110, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
121 11 0.10
122 39 0.35
123 1 0.01
124 1 0.01
125 1 0.01
128 2 0.02
129 3 0.03
132 52 0.47
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (127 bp):
TTTAAAAAATTTAACATATATAAATTTGTTTAATTAAAATAGTAAAATGATAAAAATTAAATATA
TAAGGATTAGATTTAATTAAATAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGTATA
Found at i:35686 original size:23 final size:23
Alignment explanation
Indices: 35643--35686 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
35633 AAGTTTTTTT
*
35643 AATTAAAATAGTAAAATGATAAA
1 AATTAAAATAGTAAAAGGATAAA
*
35666 AATT-AAATAGTTATAAGGATA
1 AATTAAAATAG-TAAAAGGATA
35687 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGATAAA
Found at i:36100 original size:31 final size:31
Alignment explanation
Indices: 36062--36120 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
36052 TATGTTAGAC
*
36062 AAATAAGGATATAATAGACGTTTCAAAAATT
1 AAATAAGGATACAATAGACGTTTCAAAAATT
* *
36093 AAATAAGGGTACAATAGGCGTTTCAAAA
1 AAATAAGGATACAATAGACGTTTCAAAA
36121 GTTTTACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (31 bp):
AAATAAGGATACAATAGACGTTTCAAAAATT
Found at i:36849 original size:42 final size:43
Alignment explanation
Indices: 36798--36891 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
36788 AGTGCATCAC
*
36798 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
36839 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
36884 CTAATATT
1 CTAATATT
36892 AAATATTTGC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:37811 original size:51 final size:51
Alignment explanation
Indices: 37735--37841 Score: 205
Period size: 51 Copynumber: 2.1 Consensus size: 51
37725 TTAATCCTCA
37735 ATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
*
37786 ATTTGGCCTTTAAGTAATTTCCATAGTCAGTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
37837 ATTTG
1 ATTTG
37842 AACATACACC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.40
Consensus pattern (51 bp):
ATTTGGCCTTTAAGTAATTTCCATAGTCACTAAAAATAATATATAGTATAT
Found at i:37996 original size:25 final size:24
Alignment explanation
Indices: 37968--38029 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 24
37958 GTGGATTGTA
*
37968 AAATAAATTGAATAATTAAGACATT
1 AAATAAATTCAATAATTAA-ACATT
* *
37993 AAATAAATTTAAGAATTAAACATT
1 AAATAAATTCAATAATTAAACATT
38017 AAA-AAATTCAATA
1 AAATAAATTCAATA
38030 CTGACCCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 8 0.24
24 8 0.24
25 17 0.52
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (24 bp):
AAATAAATTCAATAATTAAACATT
Done.