Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3022

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: 34553
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30


Found at i:704 original size:40 final size:40

Alignment explanation


    Indices: 660--855  Score: 313
    Period size: 40  Copynumber: 4.9  Consensus size: 40

        650 GGATATAGCT

                  *               *                 
        660 ACTCGCTCAAATGCCTTCGGGATTTAGCCCGGTTATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

                                         *  *       
        700 ACTCGCACAAATGCCTTCGGGACTTAGCCTGGATATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

                                             *       
        740 ACTCGCACAAATGCCTTCGGGACTTAAGCCCGGATATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTT-AGCCCGGTTATAGTA

                                       *   *        
        781 ACTCGCACAAATGCCTTC-GGACTTAGTCCGATTATAGTA
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

                                                
        820 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
          1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

        856 CATCCGAATA


Statistics
Matches: 144,  Mismatches: 10, Indels: 4
        0.91            0.06        0.03

Matches are distributed among these distances:
  39   30  0.21
  40   82  0.57
  41   32  0.22

ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26


Consensus pattern (40 bp):   
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA

Found at i:803 original size:80 final size:78

Alignment explanation


    Indices: 636--851  Score: 321
    Period size: 80  Copynumber: 2.7  Consensus size: 78

        626 AAACCAAGTA

                     *                      *               *         *      
        636 CCTTCGGA-ATAGCCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGATTTAGCCCGGTTATAGT
          1 CCTTCGGACTTAGCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT

                          
        699 AACTCGCACAAATG
         65 AACTCGCACAAATG

                                                                             
        713 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAAGCCCGGATATA
          1 CCTTC-GGACTTAGCC-GGATATAGTAACTCGCACAAATGCCTTCGGGACTT-AGCCCGGATATA

                            
        778 GTAACTCGCACAAATG
         63 GTAACTCGCACAAATG

                                                                       
        794 CCTTCGGACTTAGTCC-GATTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
          1 CCTTCGGACTTAG-CCGGA-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG

        852 TTATCATCCG


Statistics
Matches: 128,  Mismatches: 4, Indels: 12
        0.89            0.03        0.08

Matches are distributed among these distances:
  77    5  0.04
  78    3  0.02
  79   15  0.12
  80   71  0.55
  81   34  0.27

ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25


Consensus pattern (78 bp):   
CCTTCGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTCGCACAAATG

Found at i:8838 original size:40 final size:40

Alignment explanation


    Indices: 8767--8982  Score: 328
    Period size: 40  Copynumber: 5.4  Consensus size: 40

       8757 AAACCAAGTA

                 *   *                        *      
       8767 CCTTCAGGAATTAG-CCGGATATAGCT-ACTCGCTCAAATG
          1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG

                     *         *                    
       8806 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                            *                       
       8846 CCTTCGGGACTTAGCCTGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                           *                        
       8886 CCTTCGGGACTTAGCTCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                          *    *                    
       8926 CCTTCGGGACTTAGTCCGGTTATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                             
       8966 CCTTCGGGACTTAGCCC
          1 CCTTCGGGACTTAGCCC

       8983 AGTTATCATC


Statistics
Matches: 162,  Mismatches: 13, Indels: 3
        0.91            0.07        0.02

Matches are distributed among these distances:
  39   13  0.08
  40  149  0.92

ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:15662 original size:28 final size:28

Alignment explanation


    Indices: 15622--15700  Score: 95
    Period size: 28  Copynumber: 2.8  Consensus size: 28

      15612 GCAATCAAAT

                *   *     *             
      15622 ATGGTACTCAGTGTACGAAATATTGAGA
          1 ATGGCACTTAGTGTGCGAAATATTGAGA

                              *   *     
      15650 ATGGCACTTAGTGTGCGAGATAATGAGA
          1 ATGGCACTTAGTGTGCGAAATATTGAGA

               *            *      
      15678 ATGACACTTAGTGTGCAAAATAT
          1 ATGGCACTTAGTGTGCGAAATAT

      15701 CGAATGATTC


Statistics
Matches: 42,  Mismatches: 9, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  28   42  1.00

ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28


Consensus pattern (28 bp):   
ATGGCACTTAGTGTGCGAAATATTGAGA
Done.