Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.009G066800.2-JGI_221_v2.1
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: 8496
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Found at i:5305 original size:411 final size:411
Alignment explanation
Indices: 4543--5372 Score: 1414
Period size: 411 Copynumber: 2.0 Consensus size: 411
4533 AAATATGAGG
* *
4543 ACCTTCAGGGTAAGTTTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
1 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
* *
4608 AGGAACCACTTGTTGCAAAAATGGGAGGAGCTTTTGGATGGAATCAACATGCCCTCACAAATGCA
66 AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
*
4673 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGTTTACAGAGGCTAATCATGAAA
131 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
*
4738 CAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
196 CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
* **
4803 GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGATCTTCAATCAGTTATGCTTGAGAGGGA
261 GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGGA
* * *
4868 TCAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAATC-TTTCGGCGAAGGCAGCT
326 TAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAA-CGTTTCAGCAAAGGCAGCT
4932 CGA-TTTGAAGTTGAGAATGAAA
390 C-ATTTTGAAGTTGAGAATGAAA
* *
4954 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAACTGTTGGAACAATCCTTAATGGAA
1 ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
* * * *
5019 AGGAGCCACTTGGTGCAAAAATGGGTGGAACTTTTGGATGGAATCGACATGCCTTCACAAATGCA
66 AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
* *
5084 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTCGGGAGGGCGATTACAGAGGCTAATCATGAAA
131 ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
*
5149 GAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
196 CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
*
5214 GAGGAGT-CAGAAAAGAGAGTAGCTGATCTTGGGGCAGACCTTCAATCAGTTACACTTGAGAGGG
261 GAGG-GTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGG
5278 ATAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCT
325 ATAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCT
5343 CATTTTGAAGTTGAGAATGAAA
390 CATTTTGAAGTTGAGAATGAAA
5365 ACCTTCAG
1 ACCTTCAG
5373 ATTAGAGTCA
Statistics
Matches: 394, Mismatches: 22, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
410 2 0.01
411 390 0.99
412 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (411 bp):
ACCTTCAGGGCAAGATTTATAGGTTGGCAGAACGAAATGAAATGCTGGAACAATCCTTAATGGAA
AGGAACCACTTGGTGCAAAAATGGGAGGAACTTTTGGATGGAATCAACATGCCCTCACAAATGCA
ATCCATGGAACCTGAAGAAAAGATTGAATGGTTAGGAAGGGCGATTACAGAGGCTAATCATGAAA
CAAACTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTATGGGTCACTAGCTGCTGATTTG
GAGGGTCCAGAAAAGAGAGTAGCTGATCTTGAGGCAGACCTTCAATCAGTTACACTTGAGAGGGA
TAAACTTTCTGAAAAATTGGAGACTATGACTTCTAATCATCATAACGTTTCAGCAAAGGCAGCTC
ATTTTGAAGTTGAGAATGAAA
Done.