Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2045

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: 9326
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30


Found at i:7679 original size:38 final size:40

Alignment explanation


    Indices: 7516--7738  Score: 235
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       7506 GCTACTCGTT

                            *  *                     
       7516 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA

                                                    
       7556 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                                  *  
       7596 -ACAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACA
          1 CA-AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                               *      *      *      
       7636 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGT-TCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                                ** *    * *  *    *   
       7673 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
       7714 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

       7739 CATCATTCAA


Statistics
Matches: 158,  Mismatches: 16, Indels: 18
        0.82            0.08        0.09

Matches are distributed among these distances:
  37    8  0.05
  38   24  0.15
  39   25  0.16
  40   88  0.56
  41   13  0.08

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


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:7722 original size:117 final size:119

Alignment explanation


    Indices: 7518--7738  Score: 272
    Period size: 117  Copynumber: 1.9  Consensus size: 119

       7508 TACTCGTTCA

                                   *                                         
       7518 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
          1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT

            *        *       *                                    
       7583 TTAGTAACTCGCAACAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
         66 ATAGTAACTAGCAACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC

                          *                 *                          ** *  
       7637 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGT-TCTCGCACAAATGCCTTC-GGATCTTAGTCTGG
          1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG

                *  *                           *      
       7698 ATATGGTCACTTAGC-ACAAAGCCTTCGGGACTTAGCCCGGA
         64 ATATAGTAAC-TAGCAACAAAGCCTTCGGGACTTAACCCGGA

       7739 CATCATTCAA


Statistics
Matches: 87,  Mismatches: 12, Indels: 8
        0.81            0.11        0.07

Matches are distributed among these distances:
 116    3  0.03
 117   56  0.64
 118   16  0.18
 119   12  0.14

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


Consensus pattern (119 bp):   
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTAGCAACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
Done.