Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2584

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: 12387
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28


Found at i:3578 original size:27 final size:27

Alignment explanation


    Indices: 3548--3746  Score: 220
    Period size: 27  Copynumber: 7.4  Consensus size: 27

       3538 ACGGAAAAAT

                   *     *          *  
       3548 GGTAATTATACCCAACAAGGGTATCTC
          1 GGTAATTCTACCCTACAAGGGTATTTC

                             *         
       3575 GGTAATTCTACCCTACATGGGTATTTC
          1 GGTAATTCTACCCTACAAGGGTATTTC

                *                     *
       3602 GGTATTTCTACCCTACAAGGGTATTTT
          1 GGTAATTCTACCCTACAAGGGTATTTC

                      *   ** *         
       3629 GGTAATTCTATCCTGTAGGGGTATTTC
          1 GGTAATTCTACCCTACAAGGGTATTTC

                             *        *
       3656 -GTAATTCTACCCTACAGGGGTATTTT
          1 GGTAATTCTACCCTACAAGGGTATTTC

            **               *         
       3682 AATAATTCTACCCTACAGGGGTATTTC
          1 GGTAATTCTACCCTACAAGGGTATTTC

             *          *    *         
       3709 GATAATTCTACCATACAGGGGTATTTC
          1 GGTAATTCTACCCTACAAGGGTATTTC

             *         
       3736 GATAATTCTAC
          1 GGTAATTCTAC

       3747 AACTTATCCA


Statistics
Matches: 150,  Mismatches: 21, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  26   22  0.15
  27  128  0.85

ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36


Consensus pattern (27 bp):   
GGTAATTCTACCCTACAAGGGTATTTC

Found at i:3669 original size:80 final size:80

Alignment explanation


    Indices: 3566--3746  Score: 229
    Period size: 80  Copynumber: 2.2  Consensus size: 80

       3556 TACCCAACAA

                  *                   *         **  *                     * *
       3566 GGGTATCTCGGTAATTCTACCCTACATGGGTATTTCGGTATTTCTACCCTACAAGGGTATTTTGG
          1 GGGTATTTC-GTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGA

                         **  
       3631 TAATTCTATCC-TGTAG
         65 TAATTCTA-CCATACAG

                                              *                 *            
       3647 GGGTATTTCGTAATTCTACCCTACAGGGGTATTTTAATAATTCTACCCTACAGGGGTATTTCGAT
          1 GGGTATTTCGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGAT

                           
       3712 AATTCTACCATACAG
         66 AATTCTACCATACAG

                                
       3727 GGGTATTTCGATAATTCTAC
          1 GGGTATTTCG-TAATTCTAC

       3747 AACTTATCCA


Statistics
Matches: 87,  Mismatches: 11, Indels: 4
        0.85            0.11        0.04

Matches are distributed among these distances:
  79    2  0.02
  80   68  0.78
  81   17  0.20

ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37


Consensus pattern (80 bp):   
GGGTATTTCGTAATTCTACCCTACAGGGGTATTTCAATAATTCTACCCTACAAGGGTATTTCGAT
AATTCTACCATACAG

Found at i:9796 original size:27 final size:26

Alignment explanation


    Indices: 9748--9799  Score: 68
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       9738 GCGAGGCTGC

                             *        
       9748 CAGATATTGTGACGAAGTCACCAGAA
          1 CAGATATTGTGACGAAGCCACCAGAA

                        *   *         
       9774 CAGATATATGTGGCGAGGCCACCAGA
          1 CAGATAT-TGTGACGAAGCCACCAGA

       9800 TTACAGCGAG


Statistics
Matches: 22,  Mismatches: 3, Indels: 1
        0.85            0.12        0.04

Matches are distributed among these distances:
  26    7  0.32
  27   15  0.68

ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17


Consensus pattern (26 bp):   
CAGATATTGTGACGAAGCCACCAGAA

Found at i:10467 original size:27 final size:27

Alignment explanation


    Indices: 10411--10468  Score: 64
    Period size: 27  Copynumber: 2.1  Consensus size: 27

      10401 TTTATGCAAG

                         *           * 
      10411 AGGGCAAAATAGTCATTTAACACCCTA
          1 AGGGCAAAATAGTAATTTAACACCCCA

                      *       *         
      10438 AGGGCAAAATGGTAATTTTAC-CCCACA
          1 AGGGCAAAATAGTAATTTAACACCC-CA

                
      10465 AGGG
          1 AGGG

      10469 TATCTCGGTA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  26    3  0.12
  27   23  0.88

ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21


Consensus pattern (27 bp):   
AGGGCAAAATAGTAATTTAACACCCCA

Found at i:10478 original size:27 final size:27

Alignment explanation


    Indices: 10449--10645  Score: 245
    Period size: 27  Copynumber: 7.3  Consensus size: 27

      10439 GGGCAAAATG

                  *     *   *      *  *
      10449 GTAATTTTACCCCACAAGGGTATCTCG
          1 GTAATTCTACCCTACAGGGGTATTTCA

                         *             
      10476 GTAATTCTA-CCTGCAGGGGTATTTCA
          1 GTAATTCTACCCTACAGGGGTATTTCA

               *      *     *          
      10502 GTATTTCTACTCTACAAGGGTATTTCA
          1 GTAATTCTACCCTACAGGGGTATTTCA

                     *                 
      10529 GTAATTCTATCCTACAGGGGTATTTCA
          1 GTAATTCTACCCTACAGGGGTATTTCA

                          *            
      10556 GTAATTCTACCCTATAGGGGTATTTCA
          1 GTAATTCTACCCTACAGGGGTATTTCA

            *                         *
      10583 ATAATTCTACCCTACAGGGGTATTTCG
          1 GTAATTCTACCCTACAGGGGTATTTCA

                       *               
      10610 GTAATTCTACCTTACAGGGGTATTTC-
          1 GTAATTCTACCCTACAGGGGTATTTCA

                      
      10636 GATAATTCTA
          1 G-TAATTCTA

      10646 GAACTTATTC


Statistics
Matches: 147,  Mismatches: 21, Indels: 4
        0.85            0.12        0.02

Matches are distributed among these distances:
  26   21  0.14
  27  126  0.86

ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36


Consensus pattern (27 bp):   
GTAATTCTACCCTACAGGGGTATTTCA

Done.