Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016127.1 Corchorus olitorius cultivar O-4 contig16160, 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: 36310
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1177 original size:11 final size:11
Alignment explanation
Indices: 1161--1203 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1151 ATTAATGGTC
1161 TGGCCTAACTT
1 TGGCCTAACTT
*
1172 TGGCCTAACTC
1 TGGCCTAACTT
1183 TGGCCT-ACTTT
1 TGGCCTAAC-TT
*
1194 TTGCCTAACT
1 TGGCCTAACT
1204 CTAATATCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.37
Consensus pattern (11 bp):
TGGCCTAACTT
Found at i:1187 original size:22 final size:22
Alignment explanation
Indices: 1159--1205 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1149 TAATTAATGG
1159 TCTGGCCTAAC-TTTGGCCTAAC
1 TCTGGCCT-ACTTTTGGCCTAAC
*
1181 TCTGGCCTACTTTTTGCCTAAC
1 TCTGGCCTACTTTTGGCCTAAC
1203 TCT
1 TCT
1206 AATATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.15, C:0.32, G:0.15, T:0.38
Consensus pattern (22 bp):
TCTGGCCTACTTTTGGCCTAAC
Found at i:3002 original size:18 final size:18
Alignment explanation
Indices: 2979--3026 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
2969 GGTAATAAGA
*
2979 AATAAATATTAATTAGTT
1 AATAAATATTAATTAATT
2997 AATAAATATTTAATTAATT
1 AATAAATA-TTAATTAATT
3016 -ATAAAT-TTAAT
1 AATAAATATTAAT
3027 ATTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.18
18 14 0.50
19 9 0.32
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATATTAATTAATT
Found at i:4061 original size:11 final size:11
Alignment explanation
Indices: 4045--4090 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
4035 ACACGCGCTG
4045 ACGTGGATGAC
1 ACGTGGATGAC
*
4056 ACGTGGAAGAC
1 ACGTGGATGAC
*
4067 ACGTGTA-GAC
1 ACGTGGATGAC
4077 A--TGGATGAC
1 ACGTGGATGAC
4086 ACGTG
1 ACGTG
4091 TATGCCAGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
8 3 0.10
9 4 0.14
10 4 0.14
11 18 0.62
ACGTcount: A:0.30, C:0.17, G:0.35, T:0.17
Consensus pattern (11 bp):
ACGTGGATGAC
Found at i:7986 original size:29 final size:29
Alignment explanation
Indices: 7932--7989 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
7922 TTTGACCCAA
**
7932 ATCGAAAGGTTTAGCACTTATTTGACCTT
1 ATCGAAAGGTTTAGCACTTAAATGACCTT
*
7961 ATCGAAAGG-TTAGGCCCTTAAATGACCTT
1 ATCGAAAGGTTTA-GCACTTAAATGACCTT
7990 TTCTCTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (29 bp):
ATCGAAAGGTTTAGCACTTAAATGACCTT
Found at i:11212 original size:25 final size:25
Alignment explanation
Indices: 11184--11232 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
11174 TGTAATCCCT
11184 TAGAAAGACATCTTTTCATGTTTCA
1 TAGAAAGACATCTTTTCATGTTTCA
*
11209 TAGAAATACATCTTTTCATGTTTC
1 TAGAAAGACATCTTTTCATGTTTC
11233 TGCATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (25 bp):
TAGAAAGACATCTTTTCATGTTTCA
Found at i:11256 original size:19 final size:19
Alignment explanation
Indices: 11232--11270 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11222 TTTCATGTTT
11232 CTGCATATTTTGAATATGA
1 CTGCATATTTTGAATATGA
*
11251 CTGCATTTTTTGAATATGA
1 CTGCATATTTTGAATATGA
11270 C
1 C
11271 AGTTATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (19 bp):
CTGCATATTTTGAATATGA
Found at i:12103 original size:23 final size:22
Alignment explanation
Indices: 12053--12118 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
12043 AAATTCTACT
** *
12053 CCTTTTTATTTCTTTTAACTTT
1 CCTTTTTATTTCTTTTTTCTTC
*
12075 CATTTTTAATTTCTTTTTTCTTC
1 CCTTTTT-ATTTCTTTTTTCTTC
*
12098 CCTTTTT-TTTCTCTTTTCTTC
1 CCTTTTTATTTCTTTTTTCTTC
12119 TTCGATCCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.35
22 6 0.16
23 18 0.49
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (22 bp):
CCTTTTTATTTCTTTTTTCTTC
Found at i:13047 original size:25 final size:25
Alignment explanation
Indices: 13019--13067 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
13009 ATTTTTTATG
13019 TTTTTT-TTCTTGCGGAATTTTCCC
1 TTTTTTCTTCTTGCGGAATTTTCCC
*
13043 TTTTTTCTTCTTGTGGAATTTTCCC
1 TTTTTTCTTCTTGCGGAATTTTCCC
13068 CATTATGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.08, C:0.20, G:0.12, T:0.59
Consensus pattern (25 bp):
TTTTTTCTTCTTGCGGAATTTTCCC
Found at i:16203 original size:2 final size:2
Alignment explanation
Indices: 16196--16223 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16186 TAAATAATTG
16196 AT 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 AT
16224 GTTAGTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17020 original size:109 final size:109
Alignment explanation
Indices: 16829--17046 Score: 373
Period size: 109 Copynumber: 2.0 Consensus size: 109
16819 TAGTCATTTT
* *
16829 GGTGCTTATATTTTTCTTTAAATTCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTATATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
* *
16894 ATTTAATATGTTCAATTGAATAAACAACATAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
* *
16938 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTATATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
*
17003 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
17047 TATATAATAG
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (109 bp):
GGTGCTTATATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:17641 original size:21 final size:21
Alignment explanation
Indices: 17617--17661 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17607 GTAGTATCAA
17617 TTATATATAAAAAAATATAAT
1 TTATATATAAAAAAATATAAT
* * *
17638 TTATCTTTAAAAATATATAAT
1 TTATATATAAAAAAATATAAT
17659 TTA
1 TTA
17662 ATGAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
TTATATATAAAAAAATATAAT
Found at i:17901 original size:23 final size:23
Alignment explanation
Indices: 17856--17901 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
17846 AAAAACGAAA
*
17856 ACATAAGTTAAAACTCTTGAAAC
1 ACATAAGTTAAAACTCTTAAAAC
* *
17879 ACATAAGTTAGATCTCTTAAAAC
1 ACATAAGTTAAAACTCTTAAAAC
17902 GCATTTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (23 bp):
ACATAAGTTAAAACTCTTAAAAC
Found at i:20472 original size:17 final size:17
Alignment explanation
Indices: 20419--20473 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
20409 ATCACCCCCC
* * *
20419 AGATCACTACTGATCTA
1 AGATCACCAGTGATCAA
20436 AGATCACCAGTGAT-ACA
1 AGATCACCAGTGATCA-A
*
20453 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCAA
20470 AGAT
1 AGAT
20474 TACATGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 31 0.97
18 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (17 bp):
AGATCACCAGTGATCAA
Found at i:24540 original size:20 final size:20
Alignment explanation
Indices: 24515--24555 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
24505 ACATAAAAGC
24515 ATACTGCAAGAAGTTAATGG
1 ATACTGCAAGAAGTTAATGG
24535 ATACTGCAAGAAGTTAATGG
1 ATACTGCAAGAAGTTAATGG
24555 A
1 A
24556 AGATTTGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
ATACTGCAAGAAGTTAATGG
Found at i:30466 original size:51 final size:50
Alignment explanation
Indices: 30365--30466 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
30355 ATTCTTCATA
* **
30365 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
30415 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
30466 T
1 T
30467 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.42
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:31372 original size:34 final size:34
Alignment explanation
Indices: 31323--31394 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
31313 TGCATTACCT
* **
31323 AAATTCTAGTACTCCATCTATAGGTAATTCATCA
1 AAATTCTACTACTCCATCTATACATAATTCATCA
* * *
31357 AAATTCTACTCCTCCATCTCTACATAATTCATTA
1 AAATTCTACTACTCCATCTATACATAATTCATCA
31391 AAAT
1 AAAT
31395 AAAGCTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (34 bp):
AAATTCTACTACTCCATCTATACATAATTCATCA
Found at i:31618 original size:12 final size:12
Alignment explanation
Indices: 31601--31627 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31591 GAATTAGTTG
31601 AGAGCATTTGCA
1 AGAGCATTTGCA
31613 AGAGCATTTGCA
1 AGAGCATTTGCA
31625 AGA
1 AGA
31628 CTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (12 bp):
AGAGCATTTGCA
Found at i:35199 original size:11 final size:11
Alignment explanation
Indices: 35183--35223 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
35173 TTTAAAAAAT
*
35183 GAAAACGTAAC
1 GAAAACGAAAC
*
35194 GAAAACAAAAC
1 GAAAACGAAAC
35205 GAAAACGAAA-
1 GAAAACGAAAC
35215 GAAAA-GAAA
1 GAAAACGAAA
35224 AAACAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 18 0.67
ACGTcount: A:0.68, C:0.12, G:0.17, T:0.02
Consensus pattern (11 bp):
GAAAACGAAAC
Found at i:36218 original size:38 final size:37
Alignment explanation
Indices: 36119--36228 Score: 125
Period size: 38 Copynumber: 2.9 Consensus size: 37
36109 TCCCTAATTA
*
36119 AAAACTTTGAAAACTGAATGGGAACTTTCCCAA-TTTG
1 AAAA-TTTGAAAACTGGATGGGAACTTTCCCAATTTTG
* * * *
36156 AAAACTTAAAAATTTGG-TGGGAACTTCCCCAATTTTG
1 AAAATTTGAAAA-CTGGATGGGAACTTTCCCAATTTTG
*
36193 ACAATTTTGAAAACTGGATGGGAACTTTCCCAATTT
1 A-AAATTTGAAAACTGGATGGGAACTTTCCCAATTT
36229 GAAGACTGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
36 20 0.34
37 14 0.24
38 25 0.42
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (37 bp):
AAAATTTGAAAACTGGATGGGAACTTTCCCAATTTTG
Done.