Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021519.1 Corchorus olitorius cultivar O-4 contig21552, 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: 59089
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5242 original size:32 final size:32
Alignment explanation
Indices: 5202--5307 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
5192 GGCAATTGGG
*
5202 CGGGCTCGGG-CAGGTTCGGGTTCGGGTATTTT
1 CGGGCTCGGGTCAAG-TCGGGTTCGGGTATTTT
* * *
5234 TGGGCTCGGGTTAAGTCGGGTTCGGTTATTTT
1 CGGGCTCGGGTCAAGTCGGGTTCGGGTATTTT
* *
5266 CGGGCTCGGGTTATGTCGGGTTCGGGTATTTT
1 CGGGCTCGGGTCAAGTCGGGTTCGGGTATTTT
*
5298 CGGGTTCGGG
1 CGGGCTCGGG
5308 CTCGGATAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
32 63 0.97
33 2 0.03
ACGTcount: A:0.07, C:0.16, G:0.42, T:0.35
Consensus pattern (32 bp):
CGGGCTCGGGTCAAGTCGGGTTCGGGTATTTT
Found at i:5258 original size:16 final size:16
Alignment explanation
Indices: 5217--5307 Score: 71
Period size: 16 Copynumber: 5.7 Consensus size: 16
5207 TCGGGCAGGT
*
5217 TCGGGTTCGGG-TATTT
1 TCGGGTTCGGGTTA-TG
* * *
5233 TTGGGCTCGGGTTAAG
1 TCGGGTTCGGGTTATG
*
5249 TCGGGTTC-GGTTATTT
1 TCGGGTTCGGGTTA-TG
*
5265 TCGGGCTCGGGTTATG
1 TCGGGTTCGGGTTATG
*
5281 TCGGGTTCGGG-TATTT
1 TCGGGTTCGGGTTA-TG
5297 TCGGGTTCGGG
1 TCGGGTTCGGG
5308 CTCGGATAGG
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
15 7 0.12
16 45 0.76
17 7 0.12
ACGTcount: A:0.07, C:0.14, G:0.41, T:0.38
Consensus pattern (16 bp):
TCGGGTTCGGGTTATG
Found at i:5658 original size:31 final size:31
Alignment explanation
Indices: 5623--5694 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
5613 TAAATTATTG
*
5623 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
5654 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
5685 CAAATTAAAA
1 CAAATTAAAA
5695 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:6169 original size:16 final size:16
Alignment explanation
Indices: 6150--6193 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
6140 TCGGACTGCC
*
6150 TCGGGTTCGGGTATTT
1 TCGGGTTCGGGTAATT
*
6166 TCGGGCTCGGGTAATT
1 TCGGGTTCGGGTAATT
6182 TCGGGTTCGGGT
1 TCGGGTTCGGGT
6194 TCGGGCGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.16, G:0.41, T:0.36
Consensus pattern (16 bp):
TCGGGTTCGGGTAATT
Found at i:6463 original size:29 final size:29
Alignment explanation
Indices: 6430--6487 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
6420 ACACATACCC
* *
6430 ATTTTTTGAATTAATTTTGTTTTTAAAAT
1 ATTTTCTGAATTAATTTCGTTTTTAAAAT
6459 ATTTTCTGAATTAATTTCGTTTTTAAAAT
1 ATTTTCTGAATTAATTTCGTTTTTAAAAT
6488 TTAAAACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.59
Consensus pattern (29 bp):
ATTTTCTGAATTAATTTCGTTTTTAAAAT
Found at i:11058 original size:20 final size:20
Alignment explanation
Indices: 11033--11082 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
11023 CTAAACTGGT
* *
11033 AAAAGAAGGAGGATAAGGAG
1 AAAAGAAGAAGGATAAGAAG
*
11053 AAAAGAAAAAGGATAAGAAG
1 AAAAGAAGAAGGATAAGAAG
*
11073 AGAAGAAGAA
1 AAAAGAAGAA
11083 ATCTGAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (20 bp):
AAAAGAAGAAGGATAAGAAG
Found at i:13936 original size:21 final size:21
Alignment explanation
Indices: 13910--14043 Score: 191
Period size: 21 Copynumber: 6.4 Consensus size: 21
13900 TGCTAGAAGT
13910 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
13931 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
13952 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
13973 TCATTGGAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
*
13994 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
* *
14015 TCATTAGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
14036 TCATTGGA
1 TCATTGGA
14044 ATTGCCTAAG
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
20 2 0.02
21 104 0.98
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:16079 original size:14 final size:15
Alignment explanation
Indices: 16053--16082 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
16043 CTAAGTCCAA
16053 TCCTTGTTTATTTAT
1 TCCTTGTTTATTTAT
16068 TCCTTG-TTATTTAT
1 TCCTTGTTTATTTAT
16082 T
1 T
16083 TTTCCTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TCCTTGTTTATTTAT
Found at i:17681 original size:21 final size:21
Alignment explanation
Indices: 17655--17696 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
17645 GCATCTTAGG
17655 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
17676 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
17697 TTCTTTGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:21919 original size:19 final size:17
Alignment explanation
Indices: 21882--21921 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
21872 CTTAAAAATT
*
21882 TGAAAAACTTTGATGGA
1 TGAAAAACTTTGATAGA
21899 TGAAAAACTTGATGATAGA
1 TGAAAAACTT--TGATAGA
21918 TGAA
1 TGAA
21922 TATAAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
19 10 0.50
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (17 bp):
TGAAAAACTTTGATAGA
Found at i:39421 original size:21 final size:21
Alignment explanation
Indices: 39395--39435 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39385 TTTAAACTCT
39395 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
39416 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
39436 GGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:42651 original size:20 final size:18
Alignment explanation
Indices: 42612--42651 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
42602 CTAGCCCAAA
*
42612 AACTAGAAGAAAAAATAG
1 AACTAGAAGAAAAAAAAG
42630 AACTAGAAGAGAAAAAGAAG
1 AACTAGAAGA-AAAAA-AAG
42650 AA
1 AA
42652 GAGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 5 0.26
20 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.20, T:0.07
Consensus pattern (18 bp):
AACTAGAAGAAAAAAAAG
Found at i:47477 original size:30 final size:30
Alignment explanation
Indices: 47441--47543 Score: 165
Period size: 31 Copynumber: 3.4 Consensus size: 30
47431 AAAAAAACCC
47441 TTTTTTTCAAAAAGACAAAAAACAAATTTTT
1 TTTTTTTCAAAAAGACAAAAAACAAA-TTTT
47472 TTTTTTTCAAAAAGACAAAAAACAAATTTT
1 TTTTTTTCAAAAAGACAAAAAACAAATTTT
47502 TTTTTTTCAAAAATG-CAAAAAA-AAATTTT
1 TTTTTTTCAAAAA-GACAAAAAACAAATTTT
*
47531 TTTTTTTGAAAAA
1 TTTTTTTCAAAAA
47544 AACGCAAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
29 19 0.27
30 24 0.34
31 27 0.39
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTTTTTCAAAAAGACAAAAAACAAATTTT
Found at i:47479 original size:31 final size:31
Alignment explanation
Indices: 47441--47537 Score: 164
Period size: 30 Copynumber: 3.2 Consensus size: 31
47431 AAAAAAACCC
47441 TTTTTTTCAAAAAGACAAAAAACAAATTTTT
1 TTTTTTTCAAAAAGACAAAAAACAAATTTTT
47472 TTTTTTTCAAAAAGACAAAAAACAAA-TTTT
1 TTTTTTTCAAAAAGACAAAAAACAAATTTTT
47502 TTTTTTTCAAAAATG-CAAAAAA-AAATTTTT
1 TTTTTTTCAAAAA-GACAAAAAACAAATTTTT
47532 TTTTTT
1 TTTTTT
47538 GAAAAAAACG
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
29 3 0.05
30 34 0.53
31 27 0.42
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (31 bp):
TTTTTTTCAAAAAGACAAAAAACAAATTTTT
Found at i:48226 original size:17 final size:17
Alignment explanation
Indices: 48194--48228 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48184 ATAATTATAT
* *
48194 TATTAATAATTTAGAAA
1 TATTAATAAATCAGAAA
48211 TATTAATAAATCAGAAA
1 TATTAATAAATCAGAAA
48228 T
1 T
48229 TATAAAAGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
TATTAATAAATCAGAAA
Found at i:49333 original size:9 final size:9
Alignment explanation
Indices: 49319--49354 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
49309 TAAGTAAATG
49319 ATTGATGAT
1 ATTGATGAT
*
49328 ATTGATGGT
1 ATTGATGAT
49337 GATTGATGAT
1 -ATTGATGAT
49347 ATTGATGA
1 ATTGATGA
49355 ATGAAATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.42
Consensus pattern (9 bp):
ATTGATGAT
Found at i:49341 original size:19 final size:19
Alignment explanation
Indices: 49317--49353 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
49307 GCTAAGTAAA
49317 TGATTGATGATATTGATGG
1 TGATTGATGATATTGATGG
49336 TGATTGATGATATTGATG
1 TGATTGATGATATTGATG
49354 AATGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (19 bp):
TGATTGATGATATTGATGG
Found at i:52568 original size:18 final size:18
Alignment explanation
Indices: 52530--52571 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
52520 TTGTTAATAC
* **
52530 AAACTGCCAAAACCGCTA
1 AAACCGCCAAAACCGAAA
52548 AAACCGCCAAAACCGAAA
1 AAACCGCCAAAACCGAAA
52566 AAACCG
1 AAACCG
52572 ACCGAACCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.33, G:0.12, T:0.05
Consensus pattern (18 bp):
AAACCGCCAAAACCGAAA
Found at i:56335 original size:22 final size:22
Alignment explanation
Indices: 56310--56351 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
56300 AAAATTCAGA
* *
56310 ACAAGTCCTGTCCAGAACTTCG
1 ACAACTCCTGCCCAGAACTTCG
*
56332 ACAACTCCTGCCCAGGACTT
1 ACAACTCCTGCCCAGAACTT
56352 GTTGTGTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (22 bp):
ACAACTCCTGCCCAGAACTTCG
Found at i:57425 original size:21 final size:21
Alignment explanation
Indices: 57399--57439 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57389 TTTAAACCCT
57399 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
57420 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
57440 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.