Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013689.1 Corchorus olitorius cultivar O-4 contig13722, 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: 10747
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1002 original size:40 final size:40
Alignment explanation
Indices: 947--1028 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
937 GGGAAGCTGG
947 GAATGGTTGTGCCAAAGTGTCTGTAGTGTGTGGGTGTGTT
1 GAATGGTTGTGCCAAAGTGTCTGTAGTGTGTGGGTGTGTT
987 GAATGGTTGTGCCAAAGTGTCTGTAGTGTGTGGGTGTGTT
1 GAATGGTTGTGCCAAAGTGTCTGTAGTGTGTGGGTGTGTT
1027 GA
1 GA
1029 GTGCTTGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.16, C:0.07, G:0.40, T:0.37
Consensus pattern (40 bp):
GAATGGTTGTGCCAAAGTGTCTGTAGTGTGTGGGTGTGTT
Found at i:2070 original size:28 final size:28
Alignment explanation
Indices: 2030--2091 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
2020 CAAATGTAAT
* * *
2030 ATGGAATGTGCAAATGTGATTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
2058 ATGGAATATGCAAATGTAACTTCTTAAA
1 ATGGAATATGCAAATGTAACTTCTTAAA
2086 ATGGAA
1 ATGGAA
2092 CTTAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (28 bp):
ATGGAATATGCAAATGTAACTTCTTAAA
Found at i:2404 original size:29 final size:29
Alignment explanation
Indices: 2336--2528 Score: 203
Period size: 29 Copynumber: 6.7 Consensus size: 29
2326 ATATGAACTT
*
2336 AAAATGACCAAAATGCCCCTGAACGT--A
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* **
2363 AAAATGACCAAAATGCCCCTGCATGTAAA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
2392 AAAATGACCAAAATGCCCTTGAATATGCG
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
2421 AAAATGACCACAATGTCCCTGAGTGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* **
2450 GAAATGACCAAAATGCCATTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGAATGTGCA
* * *
2479 GAAATGACCAAAATGCCCCCTGAATAT-AA
1 AAAATGACCAAAATG-CCCCTGAATGTGCA
*
2508 AAAATGACCAAAATACCCCTG
1 AAAATGACCAAAATGCCCCTG
2529 GATTTTTTTT
Statistics
Matches: 137, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
27 24 0.18
28 6 0.04
29 99 0.72
30 8 0.06
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.18
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATGTGCA
Found at i:5304 original size:30 final size:30
Alignment explanation
Indices: 5265--5324 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
5255 CAATTCTTGC
* *
5265 TCTTGAAATTACTCTTCAATGA-TCTTCAAA
1 TCTTCAAATT-CTCTTCAATAAGTCTTCAAA
*
5295 TCTTCAAATTGTCTTCAATAAGTCTTCAAA
1 TCTTCAAATTCTCTTCAATAAGTCTTCAAA
5325 CACGAACTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (30 bp):
TCTTCAAATTCTCTTCAATAAGTCTTCAAA
Found at i:5796 original size:45 final size:45
Alignment explanation
Indices: 5739--5824 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
5729 ACAATATTAC
*
5739 ATATGAAAATATATAACATATTACATATA-TA-ATATATATGAAA
1 ATATGAAAATATATAACATATTACATAAATTACATATATATGAAA
5782 ATATGAAAATATATATAACATATTACATAAATTACATATATAT
1 ATATG-AAA-ATATATAACATATTACATAAATTACATATATAT
5825 ATATATATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
43 5 0.13
44 3 0.08
45 20 0.53
46 2 0.05
47 8 0.21
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (45 bp):
ATATGAAAATATATAACATATTACATAAATTACATATATATGAAA
Done.