Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_540 ID=scaffold_540-JGI_221_v2.0
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: 6274
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.30
Warning! 357 characters in sequence are not A, C, G, or T
Found at i:1733 original size:132 final size:131
Alignment explanation
Indices: 1395--2225 Score: 1213
Period size: 132 Copynumber: 6.3 Consensus size: 131
1385 NNNNNNNNNN
*
1395 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
* *
1460 GAATTACTGGCGTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCGTCATCTTTGACCTG
66 GAATTACTGGCTTCAATGTACTCCACTGCAAC-TCAGGGAGGTAAAATCCGCCATCTTTGACCTG
1525 CT
130 CT
* *
1527 CCACTACTGCTTA-GGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
* *
1591 GAATTACTGGCTTCAATGTACTCCACTGTAAC-CACGAGGAGGTAAAATCCGTCATCTTTGACCT
66 GAATTACTGGCTTCAATGTACTCCACTGCAACTCA-G-GGAGGTAAAATCCGCCATCTTTGACCT
1655 GCT
129 GCT
*
1658 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGTCCAGGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
* * *
1723 GAATTACTGGCTTCAATGTACTCCACTGTAAC-CACGAGGAGGTAAAATCTGCCATCTTTGATCT
66 GAATTACTGGCTTCAATGTACTCCACTGCAACTCA-G-GGAGGTAAAATCCGCCATCTTTGACCT
1787 GCT
129 GCT
* **
1790 CCACTACTGCTTAGGGAGACAAGATCCAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
* * * *
1855 GAATTATTGGCTTCAATGTACTCCACTGTAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCTG
66 GAATTACTGGCTTCAATGTACTCCACTGCAAC-TCAGGGAGGTAAAATCCGCCATCTTTGACCTG
1920 CT
130 CT
*
1922 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
* ** *
1987 GAATTACTGGCGTCAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCTTCATCTTTGACTTG
66 GAATTACTGGCTTCAATGTACTCCACTGCAAC-TCAGGGAGGTAAAATCCGCCATCTTTGACCTG
2052 CT
130 CT
* * * *
2054 CCATTACTGCTTAGGGAGGCAATATCTGAAATCTTTAATCTATTCCACTGCTGCCCAAGGAAGTA
1 CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
** * * *
2119 GAATTTTTTGGCTTTAATGTACTCCACTGCAACTTCAGGGAGGTAAAATCCACCATCTTTGATCT
66 GAA-TTACTGGCTTCAATGTACTCCACTGCAAC-TCAGGGAGGTAAAATCCGCCATCTTTGACCT
2184 GCT
129 GCT
* *
2187 CCACT-GT-CTATGCAGGAAGGCAAGATCTGAAATCTTCAA
1 CCACTACTGCT-T--AGGGAGGCAAGATCTGAAATCTTCAA
2226 CCTGCTCCAC
Statistics
Matches: 644, Mismatches: 46, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
129 2 0.00
130 1 0.00
131 123 0.19
132 432 0.67
133 61 0.09
134 25 0.04
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (131 bp):
CCACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
GAATTACTGGCTTCAATGTACTCCACTGCAACTCAGGGAGGTAAAATCCGCCATCTTTGACCTGC
T
Done.