Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013806.1 Corchorus olitorius cultivar O-4 contig13839, 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: 7025
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Found at i:4026 original size:4 final size:4
Alignment explanation
Indices: 4017--4046 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
4007 ATTTAAGACG
4017 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
4047 TTTGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:6182 original size:43 final size:43
Alignment explanation
Indices: 6115--6435 Score: 317
Period size: 41 Copynumber: 7.6 Consensus size: 43
6105 TAAAGAGAAA
*
6115 TGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAGATAGAGG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG
* * *
6158 TGCC-CTTGTGTCATAAATGTGTTTGGGGACTTT-AG-TATG-GA
1 TGCCTC-TGTGTTATAAATGTGTTTGAGGACTTTGAGATA-GAGG
*
6199 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG--AGAGG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG
* *
6240 ATGGCC-CATGTGTTATAAATGTGTTTGGGGACTTTGATATAGA--
1 -T-GCCTC-TGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG
*
6283 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTG-GAATAGAGA
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAG-ATAGAGG
* * * *
6326 TGCCCCTGTGATATAAATGTGTTTGGGGACTTT-A-ATATAGG
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG
* * **
6367 TGCCTCTGTGTTATGAATGTGTTTGAGGACTTT-AGAAAGAAAAT
1 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAG--AGG
* *
6411 TGCCCCTGTGTTATAATTGTGTTTG
1 TGCCTCTGTGTTATAAATGTGTTTG
6436 GGGGCTTTTG
Statistics
Matches: 232, Mismatches: 28, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.00
41 104 0.45
42 13 0.06
43 88 0.38
44 23 0.10
45 3 0.01
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (43 bp):
TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG
Found at i:6213 original size:84 final size:83
Alignment explanation
Indices: 6114--6443 Score: 393
Period size: 84 Copynumber: 3.9 Consensus size: 83
6104 ATAAAGAGAA
* *
6114 ATGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAGATAGAGGTGCCCTTGTGTCATAAATGTG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGGTGCCCATGTGT-ATAAATGTG
6179 TTTGGGGACTTTAGTATGG
65 TTTGGGGACTTTAGTATGG
*
6198 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG--AGAGGATGGCCCATGTGTTATAAATG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGG-T-GCCCATGTG-TATAAATG
*
6261 TGTTTGGGGACTTT-GATATAG
63 TGTTTGGGGACTTTAG-TATGG
* *
6282 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTG-GAATAGAGATGCCCCTGTGATATAAATGT
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAG-ATAGAGGTGCCCATGTG-TATAAATGT
*
6346 GTTTGGGGACTTTAATATAGG
64 GTTTGGGGACTTTAGTAT-GG
* * ** * *
6367 -TGCCTCTGTGTTATGAATGTGTTTGAGGACTTT-AGAAAGAAAATTGCCCCTGTGTTATAATTG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAG--AGGTGCCCATGTG-TATAAATG
*
6430 TGTTTGGGGGCTTT
63 TGTTTGGGGACTTT
6444 TGGTTATTGG
Statistics
Matches: 217, Mismatches: 17, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
82 5 0.02
83 6 0.03
84 168 0.77
85 34 0.16
86 4 0.02
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (83 bp):
ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTGAGATAGAGGTGCCCATGTGTATAAATGTGT
TTGGGGACTTTAGTATGG
Found at i:6392 original size:168 final size:168
Alignment explanation
Indices: 6114--6443 Score: 488
Period size: 168 Copynumber: 2.0 Consensus size: 168
6104 ATAAAGAGAA
* *
6114 ATGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAGATAGAGGTGCCCTTGTGTCATAAATGTG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAGATAGAGATGCCCCTGTGTCATAAATGTG
* **
6179 TTTGGGGACTTTAGTATGGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAG-AGAGGATG
66 TTTGGGGACTTTAATATGGATGCCTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGAAGAAAATG
6243 GCCCATGTGTTATAAATGTGTTTGGGGACTTTGATATAG
130 GCCCATGTGTTATAAATGTGTTTGGGGACTTTGATATAG
*
6282 ATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTG-GAATAGAGATGCCCCTGTGAT-ATAAATG
1 ATGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAG-ATAGAGATGCCCCTGTG-TCATAAATG
*
6345 TGTTTGGGGACTTTAATATAGG-TGCCTCTGTGTTATGAATGTGTTTGAGGACTTTAGAAAGAAA
64 TGTTTGGGGACTTTAATAT-GGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-AAGAAA
* * * *
6409 ATTGCCCCTGTGTTATAATTGTGTTTGGGGGCTTT
127 ATGGCCCATGTGTTATAAATGTGTTTGGGGACTTT
6444 TGGTTATTGG
Statistics
Matches: 146, Mismatches: 11, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
167 6 0.04
168 103 0.71
169 37 0.25
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.38
Consensus pattern (168 bp):
ATGCCTCTGTGTTATAAATGTGTTTGAGGAATTTGAGATAGAGATGCCCCTGTGTCATAAATGTG
TTTGGGGACTTTAATATGGATGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGAAGAAAATGG
CCCATGTGTTATAAATGTGTTTGGGGACTTTGATATAG
Done.