Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3888

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, 379

Length: 633
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29


Found at i:360 original size:20 final size:20

Alignment explanation


    Indices: 332--425  Score: 107
    Period size: 20  Copynumber: 4.7  Consensus size: 20

        322 AGGTCTTGTA

                *     *         
        332 AGGTGAAGTTGGGTAAGGTT
          1 AGGTTAAGTTAGGTAAGGTT

                *     *         
        352 AGGTAAAGTTGGGTAAGGTT
          1 AGGTTAAGTTAGGTAAGGTT

                  *       *     
        372 AGGTTAGGTTAGGTTAGGTT
          1 AGGTTAAGTTAGGTAAGGTT

                  *       *     
        392 AGGTTAGGTTAGGTTAGGTT
          1 AGGTTAAGTTAGGTAAGGTT

                  *       
        412 AGGTTAGGTTAGGT
          1 AGGTTAAGTTAGGT

        426 TAAATAACAC


Statistics
Matches: 69,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  20   69  1.00

ACGTcount: A:0.23, C:0.00, G:0.41, T:0.35


Consensus pattern (20 bp):   
AGGTTAAGTTAGGTAAGGTT

Found at i:377 original size:5 final size:5

Alignment explanation


    Indices: 347--427  Score: 126
    Period size: 5  Copynumber: 16.2  Consensus size: 5

        337 AAGTTGGGTA

                      *  *    *   *                                    
        347 AGGTT AGGTA AAGTT GGGTA AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT
          1 AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT

                                                 
        397 AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT A
          1 AGGTT AGGTT AGGTT AGGTT AGGTT AGGTT A

        428 AATAACACAA


Statistics
Matches: 68,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   5   68  1.00

ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37


Consensus pattern (5 bp):   
AGGTT

Done.