Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020530.1 Corchorus olitorius cultivar O-4 contig20563, 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: 23589
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3008 original size:137 final size:140
Alignment explanation
Indices: 2762--3039 Score: 517
Period size: 137 Copynumber: 2.0 Consensus size: 140
2752 ACTAGACAAT
2762 TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAGAAAAAAGATGTTACTATTATATCCAT
1 TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAGAAAAAAGATGTTACTATTATATCCAT
*
2827 AATAATATATATAAATCTTGAATGAATAATTTAATTGTTCTGACTTATATTAATTTAAGAAATAA
66 AATAATATATATAAATCTTGAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAGAAATAA
2892 AGTATATTAA
131 AGTATATTAA
*
2902 TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAG-AAGAAGATGTTACTATTATATCCAT
1 TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAGAAAAAAGATGTTACTATTATATCCAT
2966 -A-AATATATATAAATCTTGAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAGAAATAA
66 AATAATATATATAAATCTTGAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAGAAATAA
3029 AGTATATTAA
131 AGTATATTAA
3039 T
1 T
3040 TAGTGCAATG
Statistics
Matches: 136, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
137 72 0.53
138 1 0.01
139 24 0.18
140 39 0.29
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (140 bp):
TATGTTTTAAAGAATGTAGCTAAATATACTTCTTACTAGAAAAAAGATGTTACTATTATATCCAT
AATAATATATATAAATCTTGAATAAATAATTTAATTGTTCTGACTTATATTAATTTAAGAAATAA
AGTATATTAA
Found at i:3285 original size:60 final size:61
Alignment explanation
Indices: 3166--3293 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
3156 AAAATGTTTG
* * * *
3166 AATAAGGGCCCAAAGAAAAAAAAATGCTAAAATCAGGACCCAACATTTGCGAAAGTGCTCA
1 AATAAGTGCCCAAAGAAAAAAAAATACTAAAATAAGGACCCAACATTTGCAAAAGTGCTCA
* * ** *
3227 AATAAGTGTCCAAAGAAAAAAAAA-ACTCAAATAAGGGTCCAACATTTAG-AAAATTGCTCA
1 AATAAGTGCCCAAAGAAAAAAAAATACTAAAATAAGGACCCAACATTT-GCAAAAGTGCTCA
3287 AATAAGT
1 AATAAGT
3294 TTCTGCGGTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 34 0.60
61 23 0.40
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (61 bp):
AATAAGTGCCCAAAGAAAAAAAAATACTAAAATAAGGACCCAACATTTGCAAAAGTGCTCA
Found at i:8180 original size:11 final size:11
Alignment explanation
Indices: 8166--8202 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8156 TGGAATGGTG
8166 ATGGCACGGGC
1 ATGGCACGGGC
8177 ATGGC-CGGTG-
1 ATGGCACGG-GC
8187 ATGGCACGGGC
1 ATGGCACGGGC
8198 ATGGC
1 ATGGC
8203 TGGTGGTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.16, C:0.24, G:0.46, T:0.14
Consensus pattern (11 bp):
ATGGCACGGGC
Found at i:8186 original size:21 final size:21
Alignment explanation
Indices: 8162--8218 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
8152 GGCATGGAAT
8162 GGTGATGGCACGGGCATGGCC
1 GGTGATGGCACGGGCATGGCC
*
8183 GGTGATGGCACGGGCATGGCT
1 GGTGATGGCACGGGCATGGCC
* *
8204 GGTGGTGACACGGGC
1 GGTGATGGCACGGGC
8219 TTAACCGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.14, C:0.21, G:0.49, T:0.16
Consensus pattern (21 bp):
GGTGATGGCACGGGCATGGCC
Found at i:11424 original size:26 final size:25
Alignment explanation
Indices: 11386--11459 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
11376 GGAAAACGCA
* *
11386 GAAAAAATATTTTTTTT-AAAAAAC
1 GAAAAACTTTTTTTTTTCAAAAAAC
* * *
11410 GTAAAACATTTTTTTTTTCGCAAAACC
1 GAAAAAC-TTTTTTTTTTC-AAAAAAC
11437 GAAAAACTTTTTTTTTTCAAAAA
1 GAAAAACTTTTTTTTTTCAAAAA
11460 CGCAAACACA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
24 5 0.12
25 13 0.32
26 11 0.28
27 11 0.28
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (25 bp):
GAAAAACTTTTTTTTTTCAAAAAAC
Found at i:13967 original size:101 final size:101
Alignment explanation
Indices: 13854--14058 Score: 410
Period size: 101 Copynumber: 2.0 Consensus size: 101
13844 AACTTGTGTT
13854 CAAACTTAAAGTGAAGTGAAGATATATATGTGAGACCAAAAGCATCCCATCAACACAGCTAAGAG
1 CAAACTTAAAGTGAAGTGAAGATATATATGTGAGACCAAAAGCATCCCATCAACACAGCTAAGAG
13919 CATGGTTAGGCATGCAAAAATTAAATGCTATAGCGA
66 CATGGTTAGGCATGCAAAAATTAAATGCTATAGCGA
13955 CAAACTTAAAGTGAAGTGAAGATATATATGTGAGACCAAAAGCATCCCATCAACACAGCTAAGAG
1 CAAACTTAAAGTGAAGTGAAGATATATATGTGAGACCAAAAGCATCCCATCAACACAGCTAAGAG
14020 CATGGTTAGGCATGCAAAAATTAAATGCTATAGCGA
66 CATGGTTAGGCATGCAAAAATTAAATGCTATAGCGA
14056 CAA
1 CAA
14059 GGACAAACGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (101 bp):
CAAACTTAAAGTGAAGTGAAGATATATATGTGAGACCAAAAGCATCCCATCAACACAGCTAAGAG
CATGGTTAGGCATGCAAAAATTAAATGCTATAGCGA
Found at i:22560 original size:18 final size:19
Alignment explanation
Indices: 22532--22568 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
22522 CTCTTCTTCT
22532 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
22551 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
22569 GGCTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:23311 original size:28 final size:28
Alignment explanation
Indices: 23252--23325 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
23242 GGTCATCTAG
* *
23252 GGGCATTTTGGATCA-TTTGCACGTCCAG
1 GGGCATTTTGG-TCATTTTGCACATCCAA
* *
23280 GGGCATTTTGGTCATTTTGCATATTCAA
1 GGGCATTTTGGTCATTTTGCACATCCAA
* *
23308 GGGCATCTCGGTCATTTT
1 GGGCATTTTGGTCATTTT
23326 AAGCTCACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.38
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTTGCACATCCAA
Done.