Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1669

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: 8522
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30


Found at i:637 original size:36 final size:37

Alignment explanation


    Indices: 526--738  Score: 213
    Period size: 39  Copynumber: 5.6  Consensus size: 37

        516 GCTCCTCGTT

                           *       *              
        526 CAAATGCCTTCGGACATACCCGGTTATAGTAACTCGCA
          1 CAAATGCCTTCGGACTTACCCGGAT-TAGTAACTCGCA

                                                   
        564 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGACTT-ACCCGGA-TTAGTAACTCGCA

                         *                *      
        603 CAAATGCCTTCGGGCTTA-CCGGATTAGTATCTCGCA
          1 CAAATGCCTTCGGACTTACCCGGATTAGTAACTCGCA

                                           *      
        639 C--ATGCCTTCGG-CTTAGCCCGGATTAGTATCTCGCA
          1 CAAATGCCTTCGGACTTA-CCCGGATTAGTAACTCGCA

                                *        *  *    *   
        674 C-AATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGA-CTTA-CCCGGAT-TAGTAAC-TCGCA

                                      
        714 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTC-GGACTTA-CCCGGA

        739 CATCATTCAA


Statistics
Matches: 154,  Mismatches: 10, Indels: 20
        0.84            0.05        0.11

Matches are distributed among these distances:
  33    4  0.03
  34   10  0.06
  35   19  0.12
  36   23  0.15
  37    5  0.03
  38   28  0.18
  39   38  0.25
  40   22  0.14
  41    5  0.03

ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26


Consensus pattern (37 bp):   
CAAATGCCTTCGGACTTACCCGGATTAGTAACTCGCA

Found at i:698 original size:110 final size:112

Alignment explanation


    Indices: 529--731  Score: 263
    Period size: 110  Copynumber: 1.8  Consensus size: 112

        519 CCTCGTTCAA

                                *                                        *   
        529 ATGCCTTCGGACATACCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATTTAG
          1 ATGCCTTCGGACATACCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATATAG

                  *                                         
        594 TAAC-TCGCACAAATGCCTTCGGG-CTTACCGGATTAGTATCTCGCAC
         66 TAACTTAGCACAAA-GCCTTCGGGACTTACCGGATTAGTATCTCGCAC

                        *                *                         **        
        640 ATGCCTTCGG-CTTAGCCCGGAT-TAGTATCTCGCAC-AATGCCTTCGGATCTTAGTCCGGATAT
          1 ATGCCTTCGGACATA-CCCGGATATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCGGATAT

            *  *                          
        702 GGTCACTTAGCACAAAGCCTTCGGGACTTA
         64 AGTAACTTAGCACAAAGCCTTCGGGACTTA

        732 GCCCGGACAT


Statistics
Matches: 79,  Mismatches: 9, Indels: 8
        0.82            0.09        0.08

Matches are distributed among these distances:
 109   12  0.15
 110   39  0.49
 111   28  0.35

ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27


Consensus pattern (112 bp):   
ATGCCTTCGGACATACCCGGATATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGGATATAG
TAACTTAGCACAAAGCCTTCGGGACTTACCGGATTAGTATCTCGCAC
Done.