Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1340

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: 1980
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26


Found at i:48 original size:14 final size:15

Alignment explanation


    Indices: 3--55  Score: 53
    Period size: 14  Copynumber: 3.7  Consensus size: 15

          1 GA

                           
          3 AATA-TCTAAGAGGG
          1 AATAGTCTAAGAGGG

                            
         17 AATAGTCT--G-GGTG
          1 AATAGTCTAAGAGG-G

                            
         30 AAATA-TCTAAGAGGG
          1 -AATAGTCTAAGAGGG

                       
         45 AATAGTCTAAG
          1 AATAGTCTAAG

         56 TTAAAGGCTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 13
        0.71            0.00        0.29

Matches are distributed among these distances:
  12    2  0.06
  13    5  0.16
  14   12  0.38
  15   11  0.34
  16    2  0.06

ACGTcount: A:0.40, C:0.08, G:0.28, T:0.25


Consensus pattern (15 bp):   
AATAGTCTAAGAGGG

Found at i:877 original size:87 final size:87

Alignment explanation


    Indices: 746--971  Score: 303
    Period size: 87  Copynumber: 2.6  Consensus size: 87

        736 CTTGACAGTG

                                  *                 *         *              
        746 AAGCAGATCGAAGATAC-AAGCTTTGTCTCCATCAGTTGTGGTGGAACTGGTTGAAGATAGCAGA
          1 AAGCAGATCGAA-A-ACAAAGCCTTGTCTCCATCAGTTGTAGTGGAACTGATTGAAGATAGCAGA

                          *         
        810 TCTGGCCTTCCTGCGTTAACAACA
         64 TCTGGCCTTCCTGCATTAACAACA

                    *                                   *                    
        834 AAGCAGATTGAAAACAAAGCCTTGTCTCCATCAGTTGTAGTGGAGCTGATTGAAGATAGCAGATC
          1 AAGCAGATCGAAAACAAAGCCTTGTCTCCATCAGTTGTAGTGGAACTGATTGAAGATAGCAGATC

             *                   *
        899 TTGCCTTCCTGCATTAACAACG
         66 TGGCCTTCCTGCATTAACAACA

                     *              *       *    *              
        921 AAGCAGATCAAAAACAAAGCCTTGCCTCCATCGGTTGCAGT-GAAGCTGATT
          1 AAGCAGATCGAAAACAAAGCCTTGTCTCCATCAGTTGTAGTGGAA-CTGATT

        972 AAAATAAAAG


Statistics
Matches: 122,  Mismatches: 14, Indels: 5
        0.87            0.10        0.04

Matches are distributed among these distances:
  86    4  0.03
  87  107  0.88
  88   11  0.09

ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25


Consensus pattern (87 bp):   
AAGCAGATCGAAAACAAAGCCTTGTCTCCATCAGTTGTAGTGGAACTGATTGAAGATAGCAGATC
TGGCCTTCCTGCATTAACAACA

Found at i:1088 original size:44 final size:44

Alignment explanation


    Indices: 1020--1113  Score: 125
    Period size: 44  Copynumber: 2.1  Consensus size: 44

       1010 TAGATCGCAT

                               *     *                  
       1020 CAGATTGAAGCCAGAAATCTTATCTTCCTAAGATTACAGCGGAG
          1 CAGATTGAAGCCAGAAATCCTATCTCCCTAAGATTACAGCGGAG

                       *  *              *         *    
       1064 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
          1 CAGATTGAAGCCAGAAATCCTATCTCCCTAAGATTACAGCGGAG

             *    
       1108 CGGATT
          1 CAGATT

       1114 AAAACAAAGG


Statistics
Matches: 43,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  44   43  1.00

ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27


Consensus pattern (44 bp):   
CAGATTGAAGCCAGAAATCCTATCTCCCTAAGATTACAGCGGAG
Done.