Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019365.1 Corchorus olitorius cultivar O-4 contig19398, 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: 31682
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3686 original size:25 final size:25
Alignment explanation
Indices: 3639--3699 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
3629 ACATTATTAA
* * *
3639 ATTAAAATAT-ATAAAATTTCCATT
1 ATTAAAATTTAATAAAAGTGCCATT
3663 ATTAAAATTTAATAAAAGTGCCATT
1 ATTAAAATTTAATAAAAGTGCCATT
3688 ATTAAAATTTAA
1 ATTAAAATTTAA
3700 ATTTCAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 9 0.27
25 24 0.73
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.39
Consensus pattern (25 bp):
ATTAAAATTTAATAAAAGTGCCATT
Found at i:5260 original size:13 final size:13
Alignment explanation
Indices: 5242--5266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5232 TTCAATATTC
5242 TAAATATTATTTA
1 TAAATATTATTTA
5255 TAAATATTATTT
1 TAAATATTATTT
5267 GGAATTCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAATATTATTTA
Found at i:6399 original size:20 final size:20
Alignment explanation
Indices: 6374--6411 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6364 ACCTTGTCTC
* *
6374 AATAAAATATCCTTAATACT
1 AATAAAAAACCCTTAATACT
6394 AATAAAAAACCCTTAATA
1 AATAAAAAACCCTTAATA
6412 TTATTATAAT
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:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAAAAACCCTTAATACT
Found at i:6673 original size:29 final size:30
Alignment explanation
Indices: 6630--6691 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
6620 TAAAACGTTT
*
6630 AAAATTGAGAGTTTATGGGGCAAAATGTCC
1 AAAATTGAGAGTTTATGGGACAAAATGTCC
*
6660 AAAATTTA-AGTTTATGGGACAAAATGTCC
1 AAAATTGAGAGTTTATGGGACAAAATGTCC
6689 AAA
1 AAA
6692 CCGTACATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (30 bp):
AAAATTGAGAGTTTATGGGACAAAATGTCC
Found at i:7464 original size:187 final size:186
Alignment explanation
Indices: 7114--7489 Score: 675
Period size: 187 Copynumber: 2.0 Consensus size: 186
7104 CGCCAGGGAC
7114 TTAATTAACTAAATTAAATGGTTAGCTTATTTCAACATTTTTGCAAACATTAGGACCGACTTGAA
1 TTAATTAACTAAATTAAATGGTTAGCTTATTTCAACATTTTTGCAAACATTAGGACCGACTTGAA
* *
7179 TATTTATCTAAAAAACCATAAAATTTAAAAAAGAAAAAGAAAAAGAAAAAACCAATCCATTAAGA
66 TATTTATCCAAAAAACCATAAAATTTAAAAAAGAAAAAAAAAAAGAAAAAACCAATCCATTAAGA
7244 ATGGCCATTTGTCTAGTCCCTCATGAAAAGTAATAATGAGGGATTACTTTTAGGGT
131 ATGGCCATTTGTCTAGTCCCTCATGAAAAGTAATAATGAGGGATTACTTTTAGGGT
7300 TTAATTAACTAAATTAAATGGTTAGCTTATTTCAACATTTTTGCAAACATTAGGGACCGACTTGA
1 TTAATTAACTAAATTAAATGGTTAGCTTATTTCAACATTTTTGCAAACATTA-GGACCGACTTGA
7365 ATATTTATCCAAAAAACCATAAAATTTAAAAAAAGAAAAAAAAAGAAGAAAAAACCAATCCATTA
65 ATATTTATCCAAAAAACCATAAAATTT-AAAAAAGAAAAAAAAA-AAGAAAAAACCAATCCATTA
* *
7430 AGAATGGCCATTTGTC-A-TCCCTCATGAAAAGTAATAATGAGTGATTACTTTTATGGT
128 AGAATGGCCATTTGTCTAGTCCCTCATGAAAAGTAATAATGAGGGATTACTTTTAGGGT
7487 TTA
1 TTA
7490 TATATAATAC
Statistics
Matches: 183, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
186 52 0.28
187 79 0.43
188 16 0.09
189 36 0.20
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (186 bp):
TTAATTAACTAAATTAAATGGTTAGCTTATTTCAACATTTTTGCAAACATTAGGACCGACTTGAA
TATTTATCCAAAAAACCATAAAATTTAAAAAAGAAAAAAAAAAAGAAAAAACCAATCCATTAAGA
ATGGCCATTTGTCTAGTCCCTCATGAAAAGTAATAATGAGGGATTACTTTTAGGGT
Found at i:8485 original size:26 final size:26
Alignment explanation
Indices: 8456--8505 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
8446 GCACAAATGA
8456 ATTTAATTAGTGCAA-GATTTTGTACT
1 ATTTAATTAGTG-AAGGATTTTGTACT
8482 ATTTAATTAGTGAAGGATTTTGTA
1 ATTTAATTAGTGAAGGATTTTGTA
8506 GTAATGACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (26 bp):
ATTTAATTAGTGAAGGATTTTGTACT
Found at i:12214 original size:5 final size:5
Alignment explanation
Indices: 12204--12235 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12194 TAGGCAAATT
12204 TTATC TTATC TTATC TTATC TTA-C -TATC TTAT
1 TTATC TTATC TTATC TTATC TTATC TTATC TTAT
12236 TTTACTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 2 0.08
4 2 0.08
5 21 0.84
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATC
Found at i:12233 original size:8 final size:8
Alignment explanation
Indices: 12210--12259 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
12200 AATTTTATCT
12210 TATCTTATC
1 TATCTTA-C
12219 TTATCTTAC
1 -TATCTTAC
12228 TATCTTA-
1 TATCTTAC
12235 T-T-TTAC
1 TATCTTAC
*
12241 TATTTTAC
1 TATCTTAC
12249 TATCTTAC
1 TATCTTAC
12257 TAT
1 TAT
12260 ACTATACACT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
5 3 0.08
6 2 0.06
7 2 0.06
8 21 0.58
9 1 0.03
10 7 0.19
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (8 bp):
TATCTTAC
Found at i:12233 original size:13 final size:13
Alignment explanation
Indices: 12204--12243 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
12194 TAGGCAAATT
12204 TTATCTTATCTTATC
1 TTATCTTA-C-TATC
12219 TTATCTTACTATC
1 TTATCTTACTATC
*
12232 TTATTTTACTAT
1 TTATCTTACTAT
12244 TTTACTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 15 0.62
14 1 0.04
15 8 0.33
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATCTTACTATC
Found at i:12291 original size:22 final size:22
Alignment explanation
Indices: 12258--12317 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 22
12248 CTATCTTACT
12258 ATACTATACACTATACACTATAC
1 ATAC-ATACACTATACACTATAC
12281 ATACATACACTATACACTATAC
1 ATACATACACTATACACTATAC
*
12303 ATACACTATACTATA
1 ATACA-TACACTATA
12318 AAATCATGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 23 0.66
23 12 0.34
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (22 bp):
ATACATACACTATACACTATAC
Found at i:12295 original size:11 final size:11
Alignment explanation
Indices: 12270--12313 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
12260 ACTATACACT
12270 ATACACTATAC
1 ATACACTATAC
*
12281 ATACA-TACAC
1 ATACACTATAC
12291 TATACACTATAC
1 -ATACACTATAC
12303 ATACACTATAC
1 ATACACTATAC
12314 TATAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 4 0.14
11 21 0.72
12 4 0.14
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (11 bp):
ATACACTATAC
Found at i:12313 original size:7 final size:7
Alignment explanation
Indices: 12260--12303 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
12250 ATCTTACTAT
12260 ACTATAC
1 ACTATAC
12267 ACTATAC
1 ACTATAC
12274 ACTATAC
1 ACTATAC
12281 A-TACATAC
1 ACT--ATAC
12289 ACTATAC
1 ACTATAC
12296 ACTATAC
1 ACTATAC
12303 A
1 A
12304 TACACTATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 27 0.79
8 5 0.15
9 1 0.03
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
ACTATAC
Found at i:12584 original size:20 final size:19
Alignment explanation
Indices: 12551--12598 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
12541 TTTACTTCTA
*
12551 ATAATTATTT--TTAGATT
1 ATAATTATTTAATTAGAAT
12568 ATAATATATTTAATTAGAAT
1 ATAAT-TATTTAATTAGAAT
*
12588 ATTATTATTTA
1 ATAATTATTTA
12599 TAGTCATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
19 6 0.23
20 10 0.38
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
ATAATTATTTAATTAGAAT
Found at i:14883 original size:16 final size:16
Alignment explanation
Indices: 14864--14918 Score: 52
Period size: 17 Copynumber: 3.8 Consensus size: 16
14854 AACCCAAAAA
14864 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
14880 ACCC-AAA----AA--
1 ACCCAAAACCCGAATG
14889 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
14905 ACCCAAAAACCCGA
1 ACCC-AAAACCCGA
14919 GTGGCCTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 15
0.67 0.00 0.33
Matches are distributed among these distances:
9 4 0.13
10 3 0.10
11 2 0.06
14 2 0.06
15 3 0.10
16 8 0.26
17 9 0.29
ACGTcount: A:0.49, C:0.38, G:0.09, T:0.04
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:14889 original size:25 final size:25
Alignment explanation
Indices: 14855--14913 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
14845 CGAGTCTTAA
14855 ACCCAAAAAACCCAAAACCCGAATG
1 ACCCAAAAAACCCAAAACCCGAATG
14880 ACCCAAAAAACCCAAAACCCGAATG
1 ACCCAAAAAACCCAAAACCCGAATG
14905 ACCCAAAAA
1 ACCCAAAAA
14914 CCCGAGTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.54, C:0.36, G:0.07, T:0.03
Consensus pattern (25 bp):
ACCCAAAAAACCCAAAACCCGAATG
Found at i:15446 original size:49 final size:47
Alignment explanation
Indices: 15373--15497 Score: 182
Period size: 49 Copynumber: 2.7 Consensus size: 47
15363 CTAAATTCTA
*
15373 CTCTATCTCTAGGTTATTCATCAAAATAAAGCTGATATTCTACTCCT
1 CTCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
*
15420 CCATCTATCTCTAGGTAATTCATCAAAATAAAGTTGATATTCTACTCCT
1 -C-TCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
**
15469 C-C-ATCTCTAAATAATTCATCAAAATAAAG
1 CTCTATCTCTAGGTAATTCATCAAAATAAAG
15498 AATATATTAA
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
45 25 0.35
46 1 0.01
48 2 0.03
49 44 0.61
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (47 bp):
CTCTATCTCTAGGTAATTCATCAAAATAAAGCTGATATTCTACTCCT
Found at i:18931 original size:13 final size:13
Alignment explanation
Indices: 18913--18940 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18903 GTGTATCATT
18913 TTTTGTTTTCGTA
1 TTTTGTTTTCGTA
18926 TTTTGTTTTCGTA
1 TTTTGTTTTCGTA
18939 TT
1 TT
18941 GTGGGTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (13 bp):
TTTTGTTTTCGTA
Found at i:21080 original size:49 final size:49
Alignment explanation
Indices: 21008--21103 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
20998 TGAGTAATTA
* *
21008 TAATTTTAAGTAAAATTTTATCTTAAGTACTAGCTATAAAGTTAAATGG
1 TAATTTTAAGTAAAATTTTATCTTAAGTAATAGCCATAAAGTTAAATGG
* *
21057 TAATTTTAAGTAAAATTTTATCTTACGTAATAGCCATTAAGTTAAAT
1 TAATTTTAAGTAAAATTTTATCTTAAGTAATAGCCATAAAGTTAAAT
21104 TGAAGGAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (49 bp):
TAATTTTAAGTAAAATTTTATCTTAAGTAATAGCCATAAAGTTAAATGG
Found at i:21493 original size:29 final size:29
Alignment explanation
Indices: 21459--21538 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
21449 ACACAAAACG
21459 GCCAAATAAGCTCATGAACTCTAATTGCA
1 GCCAAATAAGCTCATGAACTCTAATTGCA
21488 GCCAAATAAGCCTC-TGAACTCTAATTGCA
1 GCCAAATAAG-CTCATGAACTCTAATTGCA
*
21517 GCCAAATAAGCCCATGAACTCT
1 GCCAAATAAGCTCATGAACTCT
21539 TAAAAAAACA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
28 2 0.04
29 43 0.90
30 3 0.06
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.23
Consensus pattern (29 bp):
GCCAAATAAGCTCATGAACTCTAATTGCA
Found at i:21802 original size:18 final size:18
Alignment explanation
Indices: 21779--21815 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
21769 CATTAATCTA
*
21779 TACAAAATTATATTTTAC
1 TACAAAATGATATTTTAC
21797 TACAAAATGATATTTTAC
1 TACAAAATGATATTTTAC
21815 T
1 T
21816 TCTGGAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (18 bp):
TACAAAATGATATTTTAC
Done.