Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3638

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: 15946
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27


Found at i:430 original size:32 final size:30

Alignment explanation


    Indices: 394--496  Score: 82
    Period size: 32  Copynumber: 3.3  Consensus size: 30

        384 ATAGGATGGT

                                          * 
        394 ACAAAGCCATTAGTAGCTATAGTATGATCGGC
          1 ACAAAGCCATTAGTAGCTA-A-TATGATCGAC

                      * * * *            *
        426 ACAAAGCCATCAATCGGTAATATGATCGAT
          1 ACAAAGCCATTAGTAGCTAATATGATCGAC

                              *           * 
        456 ACAAAGCCATTAGTAATGGTAATAT-ATCGGC
          1 ACAAAGCCATTAGT-A-GCTAATATGATCGAC

               *      
        487 ACAGAGCCAT
          1 ACAAAGCCAT

        497 GGTCAGATGG


Statistics
Matches: 57,  Mismatches: 12, Indels: 5
        0.77            0.16        0.07

Matches are distributed among these distances:
  30   20  0.35
  31   14  0.25
  32   23  0.40

ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23


Consensus pattern (30 bp):   
ACAAAGCCATTAGTAGCTAATATGATCGAC

Found at i:452 original size:30 final size:30

Alignment explanation


    Indices: 416--496  Score: 85
    Period size: 30  Copynumber: 2.7  Consensus size: 30

        406 GTAGCTATAG

                                           
        416 TATGATCGGCACAAAGCCAT-CAATCGGTAA
          1 TATGATCGGCACAAAGCCATACAAT-GGTAA

                    **             *        
        446 TATGATCGATACAAAGCCATTAGTAATGGTAA
          1 TATGATCGGCACAAAGCCA-TA-CAATGGTAA

                         *      
        478 TAT-ATCGGCACAGAGCCAT
          1 TATGATCGGCACAAAGCCAT

        497 GGTCAGATGG


Statistics
Matches: 42,  Mismatches: 6, Indels: 6
        0.78            0.11        0.11

Matches are distributed among these distances:
  30   18  0.43
  31   13  0.31
  32    8  0.19
  33    3  0.07

ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23


Consensus pattern (30 bp):   
TATGATCGGCACAAAGCCATACAATGGTAA

Found at i:567 original size:22 final size:22

Alignment explanation


    Indices: 484--568  Score: 82
    Period size: 22  Copynumber: 3.9  Consensus size: 22

        474 GTAATATATC

                         **       
        484 GGCACAGAGCCATGGTCAG-AT
          1 GGCACAGAGCCATAATCAGAAT

                **       *   * *  
        505 GGCATGGAGCCATTATCGGGAT
          1 GGCACAGAGCCATAATCAGAAT

                         **       
        527 GGCACAGAGCCATCTTCAGAAT
          1 GGCACAGAGCCATAATCAGAAT

                                
        549 GGCACAGAGCCATAATCAGA
          1 GGCACAGAGCCATAATCAGA

        569 TCAAGTGGCT


Statistics
Matches: 50,  Mismatches: 13, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  21   14  0.28
  22   36  0.72

ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16


Consensus pattern (22 bp):   
GGCACAGAGCCATAATCAGAAT

Found at i:645 original size:43 final size:41

Alignment explanation


    Indices: 597--718  Score: 147
    Period size: 43  Copynumber: 2.9  Consensus size: 41

        587 TCGGTAGGTG

                                     *       *         
        597 CACAGTCGTCTCGCTCGACCCGTGCGACCTTAATAGAATAGTC
          1 CACAGTCGTCTCG-T-GACCCGTGCAACCTTAACAGAATAGTC

                               *                       
        640 CACAGTCGTCTCATGTGACTCGTGCAACCTTAACAGAATAGTC
          1 CACAGTCGTCTC--GTGACCCGTGCAACCTTAACAGAATAGTC

                                *                
        683 CACAGTCGTCTCGTGTGA-CTGTGCAACCTTAACAGA
          1 CACAGTCGTCTC--GTGACCCGTGCAACCTTAACAGA

        719 TCAATACTAG


Statistics
Matches: 71,  Mismatches: 6, Indels: 5
        0.87            0.07        0.06

Matches are distributed among these distances:
  42   16  0.23
  43   53  0.75
  44    1  0.01
  45    1  0.01

ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25


Consensus pattern (41 bp):   
CACAGTCGTCTCGTGACCCGTGCAACCTTAACAGAATAGTC
Done.