Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_5041

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: 12488
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32


Found at i:1719 original size:24 final size:26

Alignment explanation


    Indices: 1553--1745  Score: 191
    Period size: 27  Copynumber: 7.3  Consensus size: 26

       1543 CGGTTTAAAT

                             *          
       1553 TGTA-CACATAAGTGTGGAGCTTGATTA
          1 TGTAGCAC-TAAGTGTGCAG-TTGATTA

                              *         
       1580 TGTAGCACTAAGTGTGAGGAGTTGATTA
          1 TGTAGCACTAAGTGT--GCAGTTGATTA

                                 * *    
       1608 TGTATAGCACTAAGTGTGCAGCTAATTA
          1 TG--TAGCACTAAGTGTGCAGTTGATTA

                                        
       1636 TGTAGGCACTAAGTGTGCGAGTTGATTA
          1 TGTA-GCACTAAGTGTGC-AGTTGATTA

                                      
       1664 TGTAGCACTAAGTGTGCAGTTGATTA
          1 TGTAGCACTAAGTGTGCAGTTGATTA

                      *                
       1690 TGTAGCACTACGT-TGC-GTTTG-TTA
          1 TGTAGCACTAAGTGTGCAG-TTGATTA

             *                 *      
       1714 TATAGCACTAA-TGTGC-GATGATTA
          1 TGTAGCACTAAGTGTGCAGTTGATTA

             *      
       1738 TATAGCAC
          1 TGTAGCAC

       1746 GAGTGTGGGA


Statistics
Matches: 147,  Mismatches: 9, Indels: 23
        0.82            0.05        0.13

Matches are distributed among these distances:
  23    3  0.02
  24   28  0.19
  25    6  0.04
  26   23  0.16
  27   37  0.25
  28   33  0.22
  29    4  0.03
  30   13  0.09

ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34


Consensus pattern (26 bp):   
TGTAGCACTAAGTGTGCAGTTGATTA

Found at i:1752 original size:24 final size:24

Alignment explanation


    Indices: 1574--1752  Score: 101
    Period size: 24  Copynumber: 6.9  Consensus size: 24

       1564 GTGTGGAGCT

                   *               *  
       1574 TGATTATGTAGCACTAAGTGTGAGGA
          1 TGATTATATAGCACT-AGTGTG-CGA

                                         *
       1600 GTTGATTATGTATAGCACTAAGTGTGCAGC
          1 --TGATTA--TATAGCACT-AGTGTGC-GA

             *     *                  
       1630 TAATTATGTAGGCACTAAGTGTGCGA
          1 TGATTATATA-GCACT-AGTGTGCGA

                     *                 *
       1656 GTTGATTATGTAGCACTAAGTGTGCAGT
          1 --TGATTATATAGCACT-AGTGTGC-GA

                   *                 *
       1684 TGATTATGTAGCACTACGT-TGCGTT
          1 TGATTATATAGCACTA-GTGTGCG-A

                            *       
       1709 TG-TTATATAGCACTAATGTGCGA
          1 TGATTATATAGCACTAGTGTGCGA

                          *      
       1732 TGATTATATAGCACGAGTGTG
          1 TGATTATATAGCACTAGTGTG

       1753 GGACTTATAT


Statistics
Matches: 127,  Mismatches: 13, Indels: 26
        0.77            0.08        0.16

Matches are distributed among these distances:
  23    3  0.02
  24   33  0.26
  25    7  0.06
  26   21  0.17
  27   26  0.20
  28   21  0.17
  30   16  0.13

ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34


Consensus pattern (24 bp):   
TGATTATATAGCACTAGTGTGCGA

Found at i:9248 original size:18 final size:18

Alignment explanation


    Indices: 9206--9248  Score: 61
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       9196 GCCCATTCCG

                  *           
       9206 AAGTATATATATATACAT
          1 AAGTATGTATATATACAT

                               
       9224 ATA-TATGTATATATACAT
          1 A-AGTATGTATATATACAT

                   
       9242 AAGTATG
          1 AAGTATG

       9249 CCCATTCGTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  17    1  0.05
  18   20  0.91
  19    1  0.05

ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40


Consensus pattern (18 bp):   
AAGTATGTATATATACAT

Found at i:9734 original size:27 final size:28

Alignment explanation


    Indices: 9698--9819  Score: 196
    Period size: 28  Copynumber: 4.5  Consensus size: 28

       9688 TAATTGTACA

                                    *   
       9698 CACTAA-TGTGCGAG-TTGATTATGTAG
          1 CACTAAGTGTGCGAGTTTGATTATATAG

                                    *   
       9724 CACTAAGTGTGCGAGTTTGATTATGTAG
          1 CACTAAGTGTGCGAGTTTGATTATATAG

                                        
       9752 CACTAAGTGTGCGAGTTTGATTATATAG
          1 CACTAAGTGTGCGAGTTTGATTATATAG

                                        
       9780 CACTAAGTGTGCGAG-TTGATTATATAG
          1 CACTAAGTGTGCGAGTTTGATTATATAG

                *        
       9807 CACTGAGTGTGCG
          1 CACTAAGTGTGCG

       9820 GACTTAATAT


Statistics
Matches: 92,  Mismatches: 2, Indels: 3
        0.95            0.02        0.03

Matches are distributed among these distances:
  26    6  0.07
  27   32  0.35
  28   54  0.59

ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34


Consensus pattern (28 bp):   
CACTAAGTGTGCGAGTTTGATTATATAG

Done.