Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_781 ID=scaffold_781-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: 5665
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.22

Warning! 1871 characters in sequence are not A, C, G, or T


Found at i:869 original size:44 final size:44

Alignment explanation


    Indices: 819--965  Score: 161
    Period size: 44  Copynumber: 3.3  Consensus size: 44

        809 ATCTGCGATA

                               *               *   *    
        819 TTCGATCTACTTCACGCCAATACATGAAGACAAGACCTGCTTTC
          1 TTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTC

                          * *      ***                    
        863 TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-ATTATC
          1 TTCGATCTACTTC-ACGCCAGTACATGAAGACAAGATCTGATT-TC

              *                        *           *    
        908 TTTGATCTACTTCACGCCAGTACATGACGACAAGATCTGTTTTC
          1 TTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTC

               *          
        952 TTCAATCTACTTCA
          1 TTCGATCTACTTCA

        966 NNNNNNNNNN


Statistics
Matches: 82,  Mismatches: 18, Indels: 6
        0.77            0.17        0.06

Matches are distributed among these distances:
  44   48  0.59
  45   34  0.41

ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31


Consensus pattern (44 bp):   
TTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTGATTTC

Found at i:1428 original size:43 final size:45

Alignment explanation


    Indices: 1380--1475  Score: 133
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       1370 CTTAGGGAGG

                            *            **        *     
       1380 CAAGATCTG-TTTCTTTGATCTACTTCA-TGCCAGTACATGAAGA
          1 CAAGATCTGTTTTCTTGGATCTACTTCACCACCAGTACAGGAAGA

                                                 *       
       1423 CAAGATCTGTTTTCTTGGATCTACTTCACCACCAGTATAGGAAGA
          1 CAAGATCTGTTTTCTTGGATCTACTTCACCACCAGTACAGGAAGA

                    
       1468 CAAGATCT
          1 CAAGATCT

       1476 TTTGTATTCA


Statistics
Matches: 46,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  43    9  0.20
  44   17  0.37
  45   20  0.43

ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32


Consensus pattern (45 bp):   
CAAGATCTGTTTTCTTGGATCTACTTCACCACCAGTACAGGAAGA

Done.