Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold603

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: 6849
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29


Found at i:1548 original size:77 final size:81

Alignment explanation


    Indices: 1406--1586  Score: 212
    Period size: 77  Copynumber: 2.3  Consensus size: 81

       1396 GCTACTCGTT

                            *       **                                       
       1406 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG

              *         *   
       1471 ATTTAGTAAC-TCGCA
         66 ATATAGTAACTTAGCA

                                             *    *                     **   
       1486 CAAATGCCTTC-GG-CTTAGCCCGAAT-TAGTATCTCGTACAAATGCCTTC-GGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG

                 *  *        
       1547 GATATGGTCACTTAGCA
         65 GATATAGTAACTTAGCA

                                    
       1564 CAAA-GCCTTCGGGACTTAGCCCG
          1 CAAATGCCTTCGGGACTTAGCCCG

       1587 GACATCATTC


Statistics
Matches: 86,  Mismatches: 11, Indels: 9
        0.81            0.10        0.08

Matches are distributed among these distances:
  76    3  0.03
  77   42  0.49
  78   19  0.22
  79   11  0.13
  80   11  0.13

ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25


Consensus pattern (81 bp):   
CAAATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA

Found at i:1588 original size:40 final size:40

Alignment explanation


    Indices: 1387--1588  Score: 218
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       1377 CGGAATTTAA

                              **                *    
       1387 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                                 * 
       1427 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *                                 
       1467 CCGGATTTAGTAACTCGCACAAATGCCTTC-GG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

               *        *    *                      *
       1505 CCGAAT-TAGTATCTCGTACAAATGCCTTC-GGATCTTAGT
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
       1544 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
       1584 CCGGA
          1 CCGGA

       1589 CATCATTCAA


Statistics
Matches: 137,  Mismatches: 19, Indels: 12
        0.82            0.11        0.07

Matches are distributed among these distances:
  37   23  0.17
  38   10  0.07
  39   13  0.09
  40   81  0.59
  41   10  0.07

ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.