Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3452

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: 18581
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29


Found at i:6675 original size:40 final size:39

Alignment explanation


    Indices: 6584--6846  Score: 278
    Period size: 40  Copynumber: 6.6  Consensus size: 39

       6574 TCCTCGTTCA

                          *  *     *           *   
       6584 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

                                        *          
       6623 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
          1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

                                 *       *          
       6662 GAATGCCTTCGGGACTTAACCTGGATTTAATAACTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

                                            *       
       6702 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

               *         *                   *       
       6742 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
          1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC

                               **      *  * *    *    
       6782 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
          1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC

              *              *      
       6823 AAAGCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

       6847 CAGCATTCAA


Statistics
Matches: 195,  Mismatches: 23, Indels: 11
        0.85            0.10        0.05

Matches are distributed among these distances:
  39   39  0.20
  40  144  0.74
  41   12  0.06

ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26


Consensus pattern (39 bp):   
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC

Found at i:6855 original size:41 final size:41

Alignment explanation


    Indices: 6778--6855  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

       6768 TTTGTATCTC

                                   *     * *         
       6778 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
       6819 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

       6856 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

Found at i:14629 original size:40 final size:40

Alignment explanation


    Indices: 14583--14670  Score: 124
    Period size: 40  Copynumber: 2.2  Consensus size: 40

      14573 TCGTACGAAT

                                                     
      14583 GCCTTCGGGACATAACCCGG-ATTTAGTATCTAGCACAAAG
          1 GCCTTCGGGACATAACCCGGAATTT-GTATCTAGCACAAAG

                     * *                   *       *
      14623 GCCTTCGGGGCTTAACCCGGAATTTGTATCTCGCACAAAT
          1 GCCTTCGGGACATAACCCGGAATTTGTATCTAGCACAAAG

                    
      14663 GCCTTCGG
          1 GCCTTCGG

      14671 ATCTTAGTCC


Statistics
Matches: 43,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
  40   39  0.91
  41    4  0.09

ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25


Consensus pattern (40 bp):   
GCCTTCGGGACATAACCCGGAATTTGTATCTAGCACAAAG

Found at i:14732 original size:41 final size:41

Alignment explanation


    Indices: 14655--14732  Score: 97
    Period size: 40  Copynumber: 1.9  Consensus size: 41

      14645 TTTGTATCTC

                                   *     * *         
      14655 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
          1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA

                                                   
      14696 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
          1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA

      14733 ATTAATCATG


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  40   17  0.53
  41   15  0.47

ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24


Consensus pattern (41 bp):   
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.