Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016053.1 Corchorus olitorius cultivar O-4 contig16086, 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: 14398
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Found at i:906 original size:68 final size:69
Alignment explanation
Indices: 781--916 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 69
771 TTGCTTGAAA
* * * *
781 TGCATTATCTTTATATGTAATTTTAGCATTTGCATGTAACTAATGGTGTTCCTACCA-TTTTTTC
1 TGCATTATCTTTATATGTAATTTTAACATTTGCATGTAACTAATAGTGCTCCCACCATTTTTTTC
845 TTAG
66 TTAG
* * *
849 TGCATTGTCTTTATATGTAATTTTAACA-TTGAGATGTAATTAATAGTGCTCCCACCATTTTTTT
1 TGCATTATCTTTATATGTAATTTTAACATTTG-CATGTAACTAATAGTGCTCCCACCATTTTTTT
913 CTTA
65 CTTA
917 ATTGTTTAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
67 3 0.05
68 46 0.78
69 10 0.17
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (69 bp):
TGCATTATCTTTATATGTAATTTTAACATTTGCATGTAACTAATAGTGCTCCCACCATTTTTTTC
TTAG
Found at i:1156 original size:18 final size:18
Alignment explanation
Indices: 1133--1168 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1123 CAGTCCTACA
1133 GCAAACCATATATTTGGC
1 GCAAACCATATATTTGGC
1151 GCAAACCATATATTTGGC
1 GCAAACCATATATTTGGC
1169 TTCGTGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
GCAAACCATATATTTGGC
Found at i:2027 original size:36 final size:36
Alignment explanation
Indices: 1980--2053 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1970 GTGACGATTC
1980 TGCAAAATTCAATTAAGATGATAAAGTAAGTTAAAA
1 TGCAAAATTCAATTAAGATGATAAAGTAAGTTAAAA
2016 TGCAAAATTCAATTAAGATGATAAAGTAAGTTAAAA
1 TGCAAAATTCAATTAAGATGATAAAGTAAGTTAAAA
2052 TG
1 TG
2054 TTAAATGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (36 bp):
TGCAAAATTCAATTAAGATGATAAAGTAAGTTAAAA
Found at i:2031 original size:18 final size:18
Alignment explanation
Indices: 1980--2031 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1970 GTGACGATTC
*
1980 TGCAAAATTCAATTAAGA
1 TGCAAAATTCAATTAAAA
*
1998 TG-ATAAAGT-AAGTTAAAA
1 TGCA-AAATTCAA-TTAAAA
2016 TGCAAAATTCAATTAA
1 TGCAAAATTCAATTAA
2032 GATGATAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29
Consensus pattern (18 bp):
TGCAAAATTCAATTAAAA
Found at i:2058 original size:18 final size:18
Alignment explanation
Indices: 1992--2058 Score: 66
Period size: 18 Copynumber: 3.7 Consensus size: 18
1982 CAAAATTCAA
*
1992 TTAAGATGATAAAGTAAG
1 TTAAAATGATAAAGTAAG
*
2010 TTAAAATGCA-AAATTCAA-
1 TTAAAATG-ATAAAGT-AAG
*
2028 TTAAGATGATAAAGTAAG
1 TTAAAATGATAAAGTAAG
*
2046 TTAAAATGTTAAA
1 TTAAAATGATAAA
2059 TGACAAACGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.08
18 33 0.85
19 3 0.08
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (18 bp):
TTAAAATGATAAAGTAAG
Found at i:2888 original size:14 final size:14
Alignment explanation
Indices: 2869--2898 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2859 GCTAATATCC
2869 AATGAAAAAAGGGA
1 AATGAAAAAAGGGA
*
2883 AATGAAAGAAGGGA
1 AATGAAAAAAGGGA
2897 AA
1 AA
2899 CTATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.30, T:0.07
Consensus pattern (14 bp):
AATGAAAAAAGGGA
Found at i:8582 original size:10 final size:10
Alignment explanation
Indices: 8567--8597 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
8557 TAGCTGTAAT
8567 TAAAAAAAAA
1 TAAAAAAAAA
8577 TAAAAAAAAAA
1 T-AAAAAAAAA
8588 TAAAAAAAAA
1 TAAAAAAAAA
8598 GGGAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
TAAAAAAAAA
Found at i:8584 original size:11 final size:11
Alignment explanation
Indices: 8568--8597 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
8558 AGCTGTAATT
8568 AAAAAAAAATA
1 AAAAAAAAATA
8579 AAAAAAAAATA
1 AAAAAAAAATA
8590 AAAAAAAA
1 AAAAAAAA
8598 GGGAAAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAAAAATA
Found at i:10711 original size:90 final size:92
Alignment explanation
Indices: 10543--10721 Score: 245
Period size: 92 Copynumber: 2.0 Consensus size: 92
10533 CTACCTAGAG
* * * * ** * *
10543 AAATTGAAGTTTATAACAAGATCAGTATTGTACACCAAATGATGGAACCATGATGGCAAACAACA
1 AAATAGAAGTTTATAACAAGATCAGGATTATACACCAAAGGATACAACCATAATAGCAAACAACA
10608 AGAAGCAAACAACAATAACACAAAGCA
66 AGAAGCAAACAACAATAACACAAAGCA
* *
10635 AAATAGAAGTTTATTACAATATCAGGATTATACACCAAAGGATACAA-C-TAATAGCAAACAACA
1 AAATAGAAGTTTATAACAAGATCAGGATTATACACCAAAGGATACAACCATAATAGCAAACAACA
*
10698 AGAAGCAAGCAACAATAACACAAA
66 AGAAGCAAACAACAATAACACAAA
10722 CCTCTCCTGG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 36 0.47
91 1 0.01
92 39 0.51
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.17
Consensus pattern (92 bp):
AAATAGAAGTTTATAACAAGATCAGGATTATACACCAAAGGATACAACCATAATAGCAAACAACA
AGAAGCAAACAACAATAACACAAAGCA
Found at i:12187 original size:14 final size:13
Alignment explanation
Indices: 12162--12197 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
12152 CAAAACATAA
12162 TTTTTTA-AAATT
1 TTTTTTATAAATT
12174 TTTTTTATATAATT
1 TTTTTTATA-AATT
12188 TTTTTTATAA
1 TTTTTTATAA
12198 TTAAAGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTATAAATT
Found at i:13582 original size:25 final size:26
Alignment explanation
Indices: 13554--13603 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
13544 TGTTTATGGT
*
13554 TTTTCCTAGTAGGATTAGG-TTTTAC
1 TTTTCCTAGTAGAATTAGGATTTTAC
*
13579 TTTTCCTATTAGAATTAGGATTTTA
1 TTTTCCTAGTAGAATTAGGATTTTA
13604 AGTTAAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.50
Consensus pattern (26 bp):
TTTTCCTAGTAGAATTAGGATTTTAC
Found at i:14360 original size:45 final size:45
Alignment explanation
Indices: 14311--14397 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
14301 AGATCTTTTC
14311 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
*
14356 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAA
1 TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAA
14398 T
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.25, C:0.05, G:0.26, T:0.44
Consensus pattern (45 bp):
TTTGTTTGTAAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGGA
Done.