Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018446.1 Corchorus olitorius cultivar O-4 contig18479, 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: 26142
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:144 original size:2 final size:2
Alignment explanation
Indices: 137--175 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
127 AGACCTAAGC
137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
176 TAGTATAGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6929 original size:103 final size:103
Alignment explanation
Indices: 6789--7022 Score: 316
Period size: 103 Copynumber: 2.3 Consensus size: 103
6779 ATTTTAATTT
*
6789 TAATTTAGGCTAAACTTAGTG-AATTAGTTATATATTTTATTCCTAAAACCCTATAACAAT-ATT
1 TAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTCCTAAAACCCTATAACAATAATT
*
6852 ATTAATTATGGAATTTACCCTTAAA-ATAAAA-AAAA-G
66 ATTAATTATGAAATTTACCCTTAAATA-AAAATAAAATG
*
6888 TAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATATTTTATTTCTAAAACCCTATAACAATA
1 TAATTT-GGGCTAAACTTAGTGAAATTAG--TTATATATTTTATTCCTAAAACCCTATAACAAT-
* *
6953 AATTATTAATTTTGAAATTTACCCTTAAATAAAAATAAAATTT
62 AATTATTAATTATGAAATTTACCCTTAAATAAAAATAAAA-TG
* *
6996 TAATTTGAGTTAAACTTAGTGAAATTA
1 TAATTTGGGCTAAACTTAGTGAAATTA
7023 AGGCTAAACT
Statistics
Matches: 118, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
99 6 0.05
100 14 0.12
101 6 0.05
103 32 0.27
105 30 0.25
106 5 0.04
107 19 0.16
108 6 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (103 bp):
TAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTCCTAAAACCCTATAACAATAATT
ATTAATTATGAAATTTACCCTTAAATAAAAATAAAATG
Found at i:8573 original size:13 final size:12
Alignment explanation
Indices: 8551--8586 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
8541 ATTTAACCAA
8551 GAAAAAAAAATT
1 GAAAAAAAAATT
8563 GAAAAATAAAATT
1 GAAAAA-AAAATT
8576 GTAAAAAAAAA
1 G-AAAAAAAAA
8587 AAAAGGGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 11 0.50
14 5 0.23
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:14298 original size:102 final size:102
Alignment explanation
Indices: 14113--14318 Score: 385
Period size: 102 Copynumber: 2.0 Consensus size: 102
14103 TCCAAGACTT
*
14113 TGCCCTGATTAATCCGGATTCGACCCGCGTCGCACACCTAGTTATGGTGGGTGAGTCTCCCAACA
1 TGCCCTGACTAATCCGGATTCGACCCGCGTCGCACACCTAGTTATGGTGGGTGAGTCTCCCAACA
14178 GGGGCAGCTGCGTACGCAAGGTCTTGAACCTAAGACC
66 GGGGCAGCTGCGTACGCAAGGTCTTGAACCTAAGACC
* *
14215 TGCCTTGACTAATCCGGATTCGACCCGTGTCGCACACCTAGTTATGGTGGGTGAGTCTCCCAACA
1 TGCCCTGACTAATCCGGATTCGACCCGCGTCGCACACCTAGTTATGGTGGGTGAGTCTCCCAACA
14280 GGGGCAGCTGCGTACGCAAGGTCTTGAACCTAAGACC
66 GGGGCAGCTGCGTACGCAAGGTCTTGAACCTAAGACC
14317 TG
1 TG
14319 TTTAAGCTGG
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.21, C:0.29, G:0.28, T:0.22
Consensus pattern (102 bp):
TGCCCTGACTAATCCGGATTCGACCCGCGTCGCACACCTAGTTATGGTGGGTGAGTCTCCCAACA
GGGGCAGCTGCGTACGCAAGGTCTTGAACCTAAGACC
Found at i:16152 original size:12 final size:12
Alignment explanation
Indices: 16135--16163 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
16125 ATTAGATTGC
16135 AAAAAAAAACAA
1 AAAAAAAAACAA
16147 AAAAAAAAACAA
1 AAAAAAAAACAA
16159 AAAAA
1 AAAAA
16164 GTGTAACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:17592 original size:43 final size:44
Alignment explanation
Indices: 17553--17651 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 44
17543 CTTATGGAGT
* * *
17553 TTATCACAATTTTATA-GGTAATTATCAAAACTTAATATGGTGG
1 TTATCAAAATTTAATAGGGTAATTATCAAAACTTAATATGGTGA
** * *
17596 TTATCAAAATTTAATAGGGTGGTTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTAATAGGGTAATTATCAAAACTTAATATGGTGA
17640 TTATCAAAATTT
1 TTATCAAAATTT
17652 CATAAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 14 0.29
44 34 0.71
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTAATAGGGTAATTATCAAAACTTAATATGGTGA
Found at i:17602 original size:22 final size:22
Alignment explanation
Indices: 17574--17651 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
17564 TTATAGGTAA
* *
17574 TTATCAAAACTTAATATGGTGG
1 TTATCAAAATTTAATAGGGTGG
17596 TTATCAAAATTTAATAGGGTGG
1 TTATCAAAATTTAATAGGGTGG
*
17618 TTATCAAAATTTAATAGGGTGA
1 TTATCAAAATTTAATAGGGTGG
17640 TTATCAAAATTT
1 TTATCAAAATTT
17652 CATAAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGTGG
Found at i:25266 original size:22 final size:22
Alignment explanation
Indices: 25241--25308 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
25231 ATGTAGCTAA
25241 TCATGTAGCGGTGTACGGGTCT
1 TCATGTAGCGGTGTACGGGTCT
*
25263 TCATGTAGCGGTGTACGGATCT
1 TCATGTAGCGGTGTACGGGTCT
*
25285 TCATGTAGCGATGTACGGGTCT
1 TCATGTAGCGGTGTACGGGTCT
25307 TC
1 TC
25309 CTATGCGTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.16, C:0.19, G:0.32, T:0.32
Consensus pattern (22 bp):
TCATGTAGCGGTGTACGGGTCT
Found at i:25703 original size:23 final size:23
Alignment explanation
Indices: 25672--25730 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
25662 ATGAATGTTC
25672 AAGATTGCAAAGATTTATCAAAA
1 AAGATTGCAAAGATTTATCAAAA
*
25695 CAGATTGCAAAGATTTATCAAAA
1 AAGATTGCAAAGATTTATCAAAA
25718 AAGATTGCAAAGA
1 AAGATTGCAAAGA
25731 GCATAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (23 bp):
AAGATTGCAAAGATTTATCAAAA
Done.