Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018852.1 Corchorus olitorius cultivar O-4 contig18885, 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: 9270
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:485 original size:20 final size:20
Alignment explanation
Indices: 445--486 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
435 GGAAACAACT
*
445 CGTTGAAACCCGGTGTGACC
1 CGTTGAAACCCGGTGTAACC
465 CGTTGAAACCCGGAT-TAACC
1 CGTTGAAACCCGG-TGTAACC
485 CG
1 CG
487 GTGACCCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.24, C:0.31, G:0.26, T:0.19
Consensus pattern (20 bp):
CGTTGAAACCCGGTGTAACC
Found at i:4964 original size:122 final size:121
Alignment explanation
Indices: 4725--4966 Score: 256
Period size: 122 Copynumber: 2.0 Consensus size: 121
4715 AACTTTTTAA
* *
4725 ATTAAAATAGTAAAAATAAAATAATTATAAAATATTGAGTTTAATTAAATGAAAATAGAGTTTTT
1 ATTAAAATAGTAAAAATAAAATAATTATAAAATATTGAGTTTAATTAAATAAAAAAAGAGTTTTT
* * *** * * ** * *
4790 GATAGAATAATATTGTATATTAAAAAAATTAATATATCCAAATTTTTATTGAAAAT
66 AATAGAATAAAATACAATAATAAAAAAATGAATATATAAAAATATGTATTGAAAAT
* *
4846 ATTAAAATGGTAAAAATAAAGTAATTATAAAGATATT-AGATTTAATTAAATAAAAAAAGAGTTT
1 ATTAAAATAGTAAAAATAAAATAATTATAAA-ATATTGAG-TTTAATTAAATAAAAAAAGAGTTT
* ** *
4910 TTAATAGAATAAAACTACAATAATCAAGTAATGACATTTA-AAAAATATGT-TTGAAAA
64 TTAATAGAATAAAA-TACAATAATAAAAAAATGA-ATATATAAAAATATGTATTGAAAA
4967 ATAAGATTAG
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
121 31 0.32
122 46 0.47
123 17 0.17
124 4 0.04
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (121 bp):
ATTAAAATAGTAAAAATAAAATAATTATAAAATATTGAGTTTAATTAAATAAAAAAAGAGTTTTT
AATAGAATAAAATACAATAATAAAAAAATGAATATATAAAAATATGTATTGAAAAT
Found at i:5040 original size:27 final size:29
Alignment explanation
Indices: 4987--5057 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 29
4977 GCTTAAATAC
*
4987 CAAATAAATCCCTTATCTTTTTATTTTGGGA
1 CAAATAAATCCCTGA--TTTTTATTTTGGGA
*
5018 CAAATAAATCCCTGA-TTTT-TTTTGGGC
1 CAAATAAATCCCTGATTTTTATTTTGGGA
5045 CAAATAAATCCCT
1 CAAATAAATCCCT
5058 CAGCTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 20 0.53
28 4 0.11
31 14 0.37
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (29 bp):
CAAATAAATCCCTGATTTTTATTTTGGGA
Found at i:5749 original size:31 final size:32
Alignment explanation
Indices: 5694--5757 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
5684 TTGGAAAACA
5694 GGTGAATGGGTGTGGGTTTTTTTGAATGGTAT
1 GGTGAATGGGTGTGGGTTTTTTTGAATGGTAT
5726 GGTGAATGGGTGTGGG-TTTTTTGAATGGTAT
1 GGTGAATGGGTGTGGGTTTTTTTGAATGGTAT
5757 G
1 G
5758 ATTCTCGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 16 0.50
32 16 0.50
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (32 bp):
GGTGAATGGGTGTGGGTTTTTTTGAATGGTAT
Found at i:8994 original size:34 final size:30
Alignment explanation
Indices: 8904--9264 Score: 388
Period size: 34 Copynumber: 11.7 Consensus size: 30
8894 ATCTTCTGTT
8904 CAGAAGTTGTCAT-ATTAAATTATCTTGACAC
1 CAGAAGTTGTCATCA--AAATTATCTTGACAC
*
8935 CAGAAGTTGTCATGAAAATTA--TTGACAC
1 CAGAAGTTGTCATCAAAATTATCTTGACAC
8963 CAGAAGTTGTCATACCAAATTATTATCTTGACAC
1 CAGAAGTTGTCAT--CAAA--ATTATCTTGACAC
*
8997 CAGAAGTTGTCATGAAAATTA--TTGACAC
1 CAGAAGTTGTCATCAAAATTATCTTGACAC
9025 CAGAAGTTGTCATATCAAATTATTATCTTGACAC
1 CAGAAGTTGTC--ATCAAA--ATTATCTTGACAC
*
9059 CAGAAGTTGTCATGAAAATTA--TTGACAC
1 CAGAAGTTGTCATCAAAATTATCTTGACAC
9087 CAGAAGTTGTCATATCAAATTATTATCTTGACAC
1 CAGAAGTTGTC--ATCAAA--ATTATCTTGACAC
*
9121 CAGAAGTTGTCAT-GAAATTA--TTGACAC
1 CAGAAGTTGTCATCAAAATTATCTTGACAC
9148 CAGAAGTTGTCATATCAAATTATTATCTTGACAC
1 CAGAAGTTGTC--ATCAAA--ATTATCTTGACAC
9182 CAGAAGTTGTCAT-AAAATT-T-TTGACAC
1 CAGAAGTTGTCATCAAAATTATCTTGACAC
9209 CAGAAGTTGTCATATCAAATTATTATCTTGACAC
1 CAGAAGTTGTC--ATCAAA--ATTATCTTGACAC
*
9243 CAGAAGTTGTCATGAAAATTAT
1 CAGAAGTTGTCATCAAAATTAT
9265 TGACAC
Statistics
Matches: 289, Mismatches: 8, Indels: 67
0.79 0.02 0.18
Matches are distributed among these distances:
27 36 0.12
28 57 0.20
29 11 0.04
30 37 0.13
31 18 0.06
32 37 0.13
33 1 0.00
34 92 0.32
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (30 bp):
CAGAAGTTGTCATCAAAATTATCTTGACAC
Found at i:9148 original size:27 final size:27
Alignment explanation
Indices: 9114--9270 Score: 161
Period size: 27 Copynumber: 5.3 Consensus size: 27
9104 AATTATTATC
*
9114 TTGACACCAGAAGTTGTCATGAAATTA
1 TTGACACCAGAAGTTGTCATAAAATTA
9141 TTGACACCAGAAGTTGTCATATCAAATTATTA
1 TTGACACCAGAAGTTGTC--AT-AAA--ATTA
*
9173 TCTTGACACCAGAAGTTGTCATAAAATTT
1 --TTGACACCAGAAGTTGTCATAAAATTA
9202 TTGACACCAGAAGTTGTCATATCAAATTATTA
1 TTGACACCAGAAGTTGTC--AT-AAA--ATTA
9234 TCTTGACACCAGAAGTTGTCATGAAAATTA
1 --TTGACACCAGAAGTTGTCAT-AAAATTA
9264 TTGACAC
1 TTGACAC
Statistics
Matches: 112, Mismatches: 4, Indels: 27
0.78 0.03 0.19
Matches are distributed among these distances:
27 36 0.32
28 7 0.06
29 7 0.06
30 9 0.08
31 3 0.03
32 14 0.12
34 36 0.32
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (27 bp):
TTGACACCAGAAGTTGTCATAAAATTA
Found at i:9169 original size:61 final size:62
Alignment explanation
Indices: 8904--9270 Score: 672
Period size: 62 Copynumber: 6.0 Consensus size: 62
8894 ATCTTCTGTT
*
8904 CAGAAGTTGTCATAT-TAA--ATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
*
8963 CAGAAGTTGTCATACCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
9025 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
9087 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATG-AAATTATTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
*
9148 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCAT-AAAATTTTTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
9209 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
1 CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
Statistics
Matches: 298, Mismatches: 5, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
59 14 0.05
60 2 0.01
61 119 0.40
62 163 0.55
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (62 bp):
CAGAAGTTGTCATATCAAATTATTATCTTGACACCAGAAGTTGTCATGAAAATTATTGACAC
Done.