Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020761.1 Corchorus olitorius cultivar O-4 contig20794, 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: 17739
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:100 original size:60 final size:59
Alignment explanation
Indices: 1--163 Score: 256
Period size: 60 Copynumber: 2.7 Consensus size: 59
1 GCCCTTATTTGAGCATTTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCA-TTTT-GCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
*
62 GCTCTTATTTGAGCATTTT-CAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 GCCCTTATTTGAGCATTTTGC-A-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
*
122 GCCCTTATTTGAGCATTTTGCCAAACGTTAAGCCCTTATTTG
1 GCCCTTATTTGAGCATTTTG-CAAACGTTAGGCCCTTATTTG
164 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 77 0.81
61 15 0.16
62 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (59 bp):
GCCCTTATTTGAGCATTTTGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:103 original size:31 final size:30
Alignment explanation
Indices: 1--167 Score: 105
Period size: 31 Copynumber: 5.5 Consensus size: 30
1 GCCCTTATTTGAGCATTTTTGGC-AAACGTTAG
1 GCCCTTATTTGAGCA-TTTT--CAAAACGTTAG
** **
33 GCCCTTATTTG-GCCAAATT-AAAA-GATCGG
1 GCCCTTATTTGAG-CATTTTCAAAACG-TTAG
*
62 GCTCTTATTTGAGCATTTTCAATAACGTTAG
1 GCCCTTATTTGAGCATTTTCAA-AACGTTAG
** **
93 GCCCTTATTTG-GCCAAATT-AAAA-GATCGG
1 GCCCTTATTTGAG-CATTTTCAAAACG-TTAG
* *
122 GCCCTTATTTGAGCATTTTGCCAAACGTTAA
1 GCCCTTATTTGAGCATTTT-CAAAACGTTAG
153 GCCCTTATTTGAGCA
1 GCCCTTATTTGAGCA
168 ATTAGCCCAG
Statistics
Matches: 102, Mismatches: 20, Indels: 27
0.68 0.13 0.18
Matches are distributed among these distances:
28 2 0.02
29 38 0.37
30 7 0.07
31 40 0.39
32 15 0.15
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
GCCCTTATTTGAGCATTTTCAAAACGTTAG
Found at i:128 original size:29 final size:29
Alignment explanation
Indices: 32--132 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
22 GCAAACGTTA
32 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
* ** **
61 GGCTCTTATTTGAG-CATTTTCAATAACG-TTA
1 GGCCCTTATTTG-GCCAAATT-AA-AA-GATCG
92 GGCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGGCCAAATTAAAAGATCG
121 GGCCCTTATTTG
1 GGCCCTTATTTG
133 AGCATTTTGC
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.54
30 6 0.11
31 18 0.32
32 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (29 bp):
GGCCCTTATTTGGCCAAATTAAAAGATCG
Found at i:3356 original size:29 final size:30
Alignment explanation
Indices: 3314--3373 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
3304 TATAAACCCA
3314 TATATATATTACCTAGTTATTTTGACCCGC
1 TATATATATTACCTAGTTATTTTGACCCGC
3344 TATATATA-TACCTAGTTATTTTGACCCGC
1 TATATATATTACCTAGTTATTTTGACCCGC
3373 T
1 T
3374 GCTAAGGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (30 bp):
TATATATATTACCTAGTTATTTTGACCCGC
Found at i:5902 original size:4 final size:4
Alignment explanation
Indices: 5893--5920 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5883 TCGTTTACAC
5893 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5921 GGTAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:8451 original size:5 final size:5
Alignment explanation
Indices: 8414--8450 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
8404 CTAATGTTGC
8414 GAAAA GAAAA GAAAA GAAAA GAAAA -AAAA -AAAA -AAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
8451 ATCATAAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:8514 original size:22 final size:21
Alignment explanation
Indices: 8489--8627 Score: 120
Period size: 22 Copynumber: 6.3 Consensus size: 21
8479 ACATTAAAGT
*
8489 AAAATTTCGTAGGAAGGTTATC
1 AAAATTTCATA-GAAGGTTATC
*
8511 AAAATTTCATAG-TGTAGTTATC
1 AAAATTTCATAGAAG--GTTATC
* *
8533 AAAATTTCATACAGAGGTTATT
1 AAAATTTCATAGA-AGGTTATC
*
8555 AAAATTTCATACAAAGGTTATC
1 AAAATTTCATA-GAAGGTTATC
* *
8577 AAAATTTCTTAGAGAGGTTAAC
1 AAAATTTCATAGA-AGGTTATC
8599 AAAATTTCATACTG-AGGTTATC
1 AAAATTTCATA--GAAGGTTATC
*
8621 GAAATTT
1 AAAATTT
8628 TCACTACAAC
Statistics
Matches: 96, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 90 0.94
23 1 0.01
24 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
AAAATTTCATAGAAGGTTATC
Found at i:8552 original size:44 final size:43
Alignment explanation
Indices: 8503--8627 Score: 144
Period size: 44 Copynumber: 2.8 Consensus size: 43
8493 TTTCGTAGGA
8503 AGGTTATCAAAATTTCATAGTGTA-GTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATA-TG-AGGTTATCAAAATTTCATACAG
* ** * *
8547 AGGTTATTAAAATTTCATACAAAGGTTATCAAAATTTCTTAGAG
1 AGGTTATCAAAATTTCATA-TGAGGTTATCAAAATTTCATACAG
* *
8591 AGGTTAACAAAATTTCATACTGAGGTTATCGAAATTT
1 AGGTTATCAAAATTTCATA-TGAGGTTATCAAAATTT
8628 TCACTACAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
43 1 0.01
44 68 0.99
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (43 bp):
AGGTTATCAAAATTTCATATGAGGTTATCAAAATTTCATACAG
Found at i:8572 original size:66 final size:66
Alignment explanation
Indices: 8488--8619 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
8478 CACATTAAAG
* ** * *
8488 TAAAATTTCGTAGGAAGGTTATCAAAATTTCATAGTGTA-GTTATCAAAATTTCATACAGAGGTT
1 TAAAATTTCATACAAAGGTTATCAAAATTTCATAGAG-AGGTTAACAAAATTTCATACAGAGGTT
8552 AT
65 AT
* *
8554 TAAAATTTCATACAAAGGTTATCAAAATTTCTTAGAGAGGTTAACAAAATTTCATACTGAGGTTA
1 TAAAATTTCATACAAAGGTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCATACAGAGGTTA
8619 T
66 T
8620 CGAAATTTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.02
66 57 0.98
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (66 bp):
TAAAATTTCATACAAAGGTTATCAAAATTTCATAGAGAGGTTAACAAAATTTCATACAGAGGTTA
T
Found at i:8626 original size:66 final size:68
Alignment explanation
Indices: 8502--8636 Score: 186
Period size: 66 Copynumber: 2.0 Consensus size: 68
8492 ATTTCGTAGG
* * *
8502 AAGGTTATCAAAATTTCATAGTGTAGTTATCAAAATTTCATACAGAGGTTATTAAAA-TTTCA-T
1 AAGGTTATCAAAATTTCATAGAGTAGTTAACAAAATTTCATACAGAGGTTATCAAAATTTTCACT
8565 ACA
66 ACA
* * *
8568 AAGGTTATCAAAATTTCTTAGAG-AGGTTAACAAAATTTCATACTGAGGTTATCGAAATTTTCAC
1 AAGGTTATCAAAATTTCATAGAGTA-GTTAACAAAATTTCATACAGAGGTTATCAAAATTTTCAC
8632 TACA
65 TACA
8636 A
1 A
8637 CAAAATCAGT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
65 1 0.02
66 49 0.82
67 5 0.08
68 5 0.08
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (68 bp):
AAGGTTATCAAAATTTCATAGAGTAGTTAACAAAATTTCATACAGAGGTTATCAAAATTTTCACT
ACA
Found at i:10827 original size:22 final size:22
Alignment explanation
Indices: 10749--10829 Score: 56
Period size: 22 Copynumber: 3.5 Consensus size: 22
10739 AAATCAAAAT
* * * *
10749 TTTCATAAGAAGGTTAACAAAA
1 TTTCATAGGGAGGCTAACAAAC
*
10771 TTTCATAGGGAGTGAACTTATCAAAAC
1 TTTCATAGGGAG-G--C-TAAC-AAAC
*
10798 -TTCCTAGGGAGGCTAACAAAC
1 TTTCATAGGGAGGCTAACAAAC
10819 TTTCATAGGGA
1 TTTCATAGGGA
10830 ATTTTATGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
21 4 0.09
22 22 0.49
23 2 0.04
25 1 0.02
26 13 0.29
27 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TTTCATAGGGAGGCTAACAAAC
Found at i:11309 original size:21 final size:22
Alignment explanation
Indices: 11285--11326 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
11275 TGCTTTAGAC
11285 AGTTGTTGAG-TTTTTTTTTAA
1 AGTTGTTGAGATTTTTTTTTAA
11306 AGTTGTTGAGCATTTTTTTTT
1 AGTTGTTGAG-ATTTTTTTTT
11327 TTCGAGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.17, C:0.02, G:0.19, T:0.62
Consensus pattern (22 bp):
AGTTGTTGAGATTTTTTTTTAA
Found at i:11802 original size:13 final size:12
Alignment explanation
Indices: 11784--11813 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
11774 TTAGAATTCC
11784 AAATAATATTTA
1 AAATAATATTTA
11796 TAAATAATATTTA
1 -AAATAATATTTA
11809 AAATA
1 AAATA
11814 TTGAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATATTTA
Found at i:13447 original size:13 final size:14
Alignment explanation
Indices: 13421--13453 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13411 GTCATCGTAA
13421 TTTATGCTTAATTT
1 TTTATGCTTAATTT
13435 TTTATGC-TAATTT
1 TTTATGCTTAATTT
*
13448 GTTATG
1 TTTATG
13454 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.61
Consensus pattern (14 bp):
TTTATGCTTAATTT
Found at i:16238 original size:40 final size:40
Alignment explanation
Indices: 16156--16352 Score: 279
Period size: 40 Copynumber: 4.8 Consensus size: 40
16146 CAATACCCTA
* **
16156 CTGCCACGTCATCATGTTGACCGAGTCAACCCGCCACCTCAT
1 CTGCCACGTCATC-TGTTGACC-AGTCAACCTGCCATGTCAT
*
16198 CAGCCACGTCAT-TCGTTGACCAGTCAACCTGCCATGTCAT
1 CTGCCACGTCATCT-GTTGACCAGTCAACCTGCCATGTCAT
16238 CTGCCACGTCATCTGTTGACCAGTCAACCTGCCATGTCAT
1 CTGCCACGTCATCTGTTGACCAGTCAACCTGCCATGTCAT
*
16278 CTGCCACGTCATCTGTTGACCAGTCAACCTACCATGTCAT
1 CTGCCACGTCATCTGTTGACCAGTCAACCTGCCATGTCAT
* * *
16318 CTGCCACGTCATCCGCTGACCGAGTCAACCCGCCA
1 CTGCCACGTCATCTGTTGACC-AGTCAACCTGCCA
16353 CATTATTTAG
Statistics
Matches: 142, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
40 112 0.79
41 19 0.13
42 11 0.08
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (40 bp):
CTGCCACGTCATCTGTTGACCAGTCAACCTGCCATGTCAT
Found at i:16243 original size:12 final size:12
Alignment explanation
Indices: 16226--16292 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
16216 ACCAGTCAAC
*
16226 CTGCCATGTCAT
1 CTGCCACGTCAT
16238 CTGCCACGTCAT
1 CTGCCACGTCAT
*
16250 CTGTTGACCA-GTCAAC
1 C---TG-CCACGTC-AT
*
16266 CTGCCATGTCAT
1 CTGCCACGTCAT
16278 CTGCCACGTCAT
1 CTGCCACGTCAT
16290 CTG
1 CTG
16293 TTGACCAGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 30 0.67
13 5 0.11
15 5 0.11
16 5 0.11
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.28
Consensus pattern (12 bp):
CTGCCACGTCAT
Found at i:16568 original size:18 final size:18
Alignment explanation
Indices: 16545--16605 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
16535 CTGTTTTCTG
16545 CCTGTTTGACCTCTCGGT
1 CCTGTTTGACCTCTCGGT
*
16563 CCTGTTTGACCTCTCGAT
1 CCTGTTTGACCTCTCGGT
16581 CCTGTTTGACCTCTCGGT
1 CCTGTTTGACCTCTCGGT
16599 CCTGTTT
1 CCTGTTT
16606 TTAGCACTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.07, C:0.33, G:0.20, T:0.41
Consensus pattern (18 bp):
CCTGTTTGACCTCTCGGT
Done.