Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold936

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: 21407
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:845 original size:39 final size:39

Alignment explanation


    Indices: 750--932  Score: 198
    Period size: 39  Copynumber: 4.7  Consensus size: 39

        740 TTGAATGATG

                                         *          
        750 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACATA

                 *                                    
        789 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATAC-TAA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACAT-A

                                                   * 
        828 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACAAA
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACATA

                  *                         *       
        867 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTAC-ATA

            *        *                
        907 ACCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

        933 AACGAGGAGC


Statistics
Matches: 123,  Mismatches: 11, Indels: 19
        0.80            0.07        0.12

Matches are distributed among these distances:
  38   11  0.09
  39   67  0.54
  40   45  0.37

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


Consensus pattern (39 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACATA

Found at i:884 original size:78 final size:80

Alignment explanation


    Indices: 750--932  Score: 234
    Period size: 78  Copynumber: 2.3  Consensus size: 80

        740 TTGAATGATG

                                                  *                          
        750 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACATATCCGGACTAAGATCCGAAGGCATTT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAAATCCGGACTAAGATCCGAAGGCATTT

                            
        814 GTGCGAGA-TACTA-A
         66 GTGCGA-ATTACTATA

                                           *   *          **                 
        828 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACAAATCCGGGTTAAG-TCCCGAAGGCAT
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAAATCCGGACTAAGAT-CCGAAGGCAT

                             
        890 TTGTGCGAATTACTATA
         64 TTGTGCGAATTACTATA

            *        *                
        907 ACCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

        933 AACGAGGAGC


Statistics
Matches: 92,  Mismatches: 7, Indels: 10
        0.84            0.06        0.09

Matches are distributed among these distances:
  77    2  0.02
  78   57  0.62
  79   33  0.36

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


Consensus pattern (80 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAATTACTATA

Found at i:8105 original size:13 final size:13

Alignment explanation


    Indices: 8087--8115  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       8077 GGTTGTTTAT

                         
       8087 TAAACTAATTAAC
          1 TAAACTAATTAAC

                         
       8100 TAAACTAATTAAC
          1 TAAACTAATTAAC

               
       8113 TAA
          1 TAA

       8116 TTAAACTAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31


Consensus pattern (13 bp):   
TAAACTAATTAAC

Found at i:16512 original size:13 final size:13

Alignment explanation


    Indices: 16494--16522  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

      16484 GGTTGTTTAT

                         
      16494 TAAACTAATTAAC
          1 TAAACTAATTAAC

                         
      16507 TAAACTAATTAAC
          1 TAAACTAATTAAC

               
      16520 TAA
          1 TAA

      16523 TTAAACTAAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31


Consensus pattern (13 bp):   
TAAACTAATTAAC
Done.