Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3749

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, 401

Length: 669
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31


Found at i:446 original size:27 final size:27

Alignment explanation


    Indices: 387--545  Score: 128
    Period size: 27  Copynumber: 5.9  Consensus size: 27

        377 CGGAAAGGTT

                *                **  * 
        387 GTAAGATGACCGT-ATACCCCCATAAG
          1 GTAAAATGACCGTAATACCCCTGTAGG

              *                        
        413 GTTAAATGACCGTAATACCCCTGTAGG
          1 GTAAAATGACCGTAATACCCCTGTAGG

                      **     *    *     
        440 GTAAAATGACTATAAT-GCCCTTTAAGG
          1 GTAAAATGACCGTAATACCCCTGT-AGG

                                   *  * 
        467 GTAAAATGACCGTAATA-CCCTCATAAG
          1 GTAAAATGACCGTAATACCCCT-GTAGG

              *        *        *      
        494 GTTAAATGACCATAATACCCTTGTAGG
          1 GTAAAATGACCGTAATACCCCTGTAGG

                     *                
        521 GTAAAATGATCGTAA-AGCCCCTGTA
          1 GTAAAATGACCGTAATA-CCCCTGTA

        546 TGATCGATTT


Statistics
Matches: 104,  Mismatches: 23, Indels: 11
        0.75            0.17        0.08

Matches are distributed among these distances:
  26   17  0.16
  27   83  0.80
  28    4  0.04

ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25


Consensus pattern (27 bp):   
GTAAAATGACCGTAATACCCCTGTAGG

Found at i:479 original size:54 final size:54

Alignment explanation


    Indices: 416--545  Score: 158
    Period size: 54  Copynumber: 2.4  Consensus size: 54

        406 CCATAAGGTT

                                  *           *     *              
        416 AAATGACCGTAATACCCCTGTAGGGTAAAATGACTATAATGCCCTT-TAAGGGTA
          1 AAATGACCGTAATACCCCTGTAAGGTAAAATGACCATAATACCCTTGT-AGGGTA

                                *      *                           
        470 AAATGACCGTAATA-CCCTCATAAGGTTAAATGACCATAATACCCTTGTAGGGTA
          1 AAATGACCGTAATACCCCT-GTAAGGTAAAATGACCATAATACCCTTGTAGGGTA

                  *                
        524 AAATGATCGTAA-AGCCCCTGTA
          1 AAATGACCGTAATA-CCCCTGTA

        546 TGATCGATTT


Statistics
Matches: 65,  Mismatches: 7, Indels: 8
        0.81            0.09        0.10

Matches are distributed among these distances:
  53    5  0.08
  54   55  0.85
  55    5  0.08

ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25


Consensus pattern (54 bp):   
AAATGACCGTAATACCCCTGTAAGGTAAAATGACCATAATACCCTTGTAGGGTA
Done.