Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g02518.N2

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, 847

Length: 1412
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28


Found at i:574 original size:80 final size:80

Alignment explanation


    Indices: 434--603  Score: 225
    Period size: 80  Copynumber: 2.1  Consensus size: 80

        424 CGGAACACAA

                       *                        *                  *         
        434 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCAGATATAACGACTTGCACAAATG
          1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTCAGCCCAGATATAACGACTAGCACAAATG

                *        * 
        499 CCTTTGGGTATTAGC
         66 CCTTCGGGTATTAAC

                          **                              *   *            * 
        514 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTCAGCCCAGATGTAGTC-ACTAGCACAATT
          1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTCAGCCCAGATATA-ACGACTAGCACAAAT

                      *     
        578 GCCTTCGGGTCTTAAC
         65 GCCTTCGGGTATTAAC

                      
        594 CCGGATATAA
          1 CCGGATATAA

        604 ATACTAGCAT


Statistics
Matches: 78,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  80   77  0.99
  81    1  0.01

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


Consensus pattern (80 bp):   
CCGGATATAACAACACGCACGAATGCCTTCGGGTCTCAGCCCAGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC

Found at i:610 original size:40 final size:40

Alignment explanation


    Indices: 450--637  Score: 182
    Period size: 40  Copynumber: 4.7  Consensus size: 40

        440 ATAACCACAC

                *                     *       **   *
        450 GCACGAATGCCTTCGGGTCTTAGCCCAGATATAACGACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAATACTA

                         *    *                     *
        490 GCACAAATGCCTTTGGGTATTAGCCCGGATATAACA-ACTT
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAA-ATACTA

                *               *     *   *   *      
        530 GCACGAATGCCTTCGGGTCTCAGCCCAGATGT-AGTCACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAAT-ACTA

                  *               *                 
        570 GCACAATTGCCTTCGGGTCTTAACCCGGATATAAATACTA
          1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAATACTA

               *     *       *          
        610 GCATAAATGTCTTCGGGACTTAGCCCGG
          1 GCACAAATGCCTTCGGGTCTTAGCCCGG

        638 GTATCATTCA


Statistics
Matches: 119,  Mismatches: 25, Indels: 8
        0.78            0.16        0.05

Matches are distributed among these distances:
  39    1  0.01
  40  116  0.97
  41    2  0.02

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


Consensus pattern (40 bp):   
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAATACTA

Found at i:624 original size:80 final size:80

Alignment explanation


    Indices: 434--635  Score: 221
    Period size: 80  Copynumber: 2.5  Consensus size: 80

        424 CGGAACACAA

                       *         *                                  *        
        434 CCGGATATAACCAC-ACGCACGAATGCCTTCGGGTCTTAGCCCAGATATAACGACTTGCACAAAT
          1 CCGGATATAACAACTA-GCACAAATGCCTTCGGGTCTTAGCCCAGATATAACGACTAGCACAAAT

                 *        * 
        498 GCCTTTGGGTATTAGC
         65 GCCTTCGGGTATTAAC

                           *    *               *         *   *            * 
        514 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTCAGCCCAGATGTAGTC-ACTAGCACAATT
          1 CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCAGATATA-ACGACTAGCACAAAT

                      *     
        578 GCCTTCGGGTCTTAAC
         65 GCCTTCGGGTATTAAC

                                *     *       *        
        594 CCGGATATAA-ATACTAGCATAAATGTCTTCGGGACTTAGCCC
          1 CCGGATATAACA-ACTAGCACAAATGCCTTCGGGTCTTAGCCC

        636 GGGTATCATT


Statistics
Matches: 103,  Mismatches: 16, Indels: 6
        0.82            0.13        0.05

Matches are distributed among these distances:
  79    1  0.01
  80  101  0.98
  81    1  0.01

ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25


Consensus pattern (80 bp):   
CCGGATATAACAACTAGCACAAATGCCTTCGGGTCTTAGCCCAGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Done.