Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1663

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: 25837
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Found at i:568 original size:18 final size:17

Alignment explanation


    Indices: 547--580  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        537 AAACATTATC

                              
        547 AGAACTAGAAATCAAAAG
          1 AGAACTAG-AATCAAAAG

                *           
        565 AGAATTAGAATCAAAA
          1 AGAACTAGAATCAAAA

        581 TTAGGTAACA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    8  0.53
  18    7  0.47

ACGTcount: A:0.62, C:0.09, G:0.15, T:0.15


Consensus pattern (17 bp):   
AGAACTAGAATCAAAAG

Found at i:622 original size:36 final size:37

Alignment explanation


    Indices: 565--639  Score: 91
    Period size: 36  Copynumber: 2.1  Consensus size: 37

        555 AAATCAAAAG

                 *                               
        565 AGAATTAGAATCAAAATTAGGTAACAAAATCAGAATC
          1 AGAATCAGAATCAAAATTAGGTAACAAAATCAGAATC

                                   * * *          
        602 AGAATCAGAAT-AAGAA-TAGGTGATAGAATCAGAATC
          1 AGAATCAGAATCAA-AATTAGGTAACAAAATCAGAATC

              
        638 AG
          1 AG

        640 TACCAGGTAA


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  36   21  0.64
  37   12  0.36

ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20


Consensus pattern (37 bp):   
AGAATCAGAATCAAAATTAGGTAACAAAATCAGAATC

Found at i:853 original size:27 final size:27

Alignment explanation


    Indices: 785--890  Score: 101
    Period size: 27  Copynumber: 4.0  Consensus size: 27

        775 AGCATGGCTG

                              *     *  
        785 CCAG-AATA-ATATTGTGACAGAGTCA
          1 CCAGAAATAGATATTGTGGCAGAGCCA

                ** *                   
        810 CCAGTTACAGATATTGTGGCAGAGCCA
          1 CCAGAAATAGATATTGTGGCAGAGCCA

                                  *     
        837 CCAG-AATAGATATTTGTGGCATAGCCA
          1 CCAGAAATAGATA-TTGTGGCAGAGCCA

                          *       *    
        864 CCAAGAAATAGATAATGTGGCAAAGCC
          1 CC-AGAAATAGATATTGTGGCAGAGCC

        891 CTTAACGAAT


Statistics
Matches: 67,  Mismatches: 9, Indels: 7
        0.81            0.11        0.08

Matches are distributed among these distances:
  25    4  0.06
  26    8  0.12
  27   34  0.51
  28   13  0.19
  29    8  0.12

ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22


Consensus pattern (27 bp):   
CCAGAAATAGATATTGTGGCAGAGCCA

Found at i:1721 original size:26 final size:27

Alignment explanation


    Indices: 1618--1758  Score: 128
    Period size: 26  Copynumber: 5.2  Consensus size: 27

       1608 GGGCAAAATG

                  *                *  *
       1618 GTAATTTTACCCTACAAGGGTATCTCG
          1 GTAATTCTACCCTACAAGGGTATTTCA

                             *          
       1645 GTAATTCTACCCTACAGGGGGTATTTC-
          1 GTAATTCTACCCTACA-AGGGTATTTCA

                *                       * 
       1672 GATATTTCTTAACCCTACAAGGGTATTTTA
          1 G-TAATTC-T-ACCCTACAAGGGTATTTCA

                            *          
       1702 GTAATTCTA-CCTACAGGGGTATTTCA
          1 GTAATTCTACCCTACAAGGGTATTTCA

                   *          *        
       1728 GTAATTCCACCC-ACAA-AGTATTTCA
          1 GTAATTCTACCCTACAAGGGTATTTCA

            *     
       1753 ATAATT
          1 GTAATT

       1759 GGAAATCGAG


Statistics
Matches: 95,  Mismatches: 13, Indels: 14
        0.78            0.11        0.11

Matches are distributed among these distances:
  25   13  0.14
  26   26  0.27
  27   19  0.20
  28   14  0.15
  29   14  0.15
  30    9  0.09

ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35


Consensus pattern (27 bp):   
GTAATTCTACCCTACAAGGGTATTTCA

Found at i:14746 original size:42 final size:42

Alignment explanation


    Indices: 14685--14780  Score: 149
    Period size: 42  Copynumber: 2.3  Consensus size: 42

      14675 TGAAATTATA

                                                       
      14685 TGTAAGACCATATAAGGGATATGGCATCAATATGAGACTAT-G
          1 TGTAAGACCATATAAGGGATATGGCATCAATATGAGACT-TCG

                         **             *             
      14727 TGTAAGACCATATCCGGGATATGGCATCGATATGAGACTTCG
          1 TGTAAGACCATATAAGGGATATGGCATCAATATGAGACTTCG

                        
      14769 TGTAAGACCATA
          1 TGTAAGACCATA

      14781 GTTGGGCTAT


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  41    1  0.02
  42   49  0.98

ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26


Consensus pattern (42 bp):   
TGTAAGACCATATAAGGGATATGGCATCAATATGAGACTTCG

Found at i:17097 original size:28 final size:29

Alignment explanation


    Indices: 17032--17130  Score: 125
    Period size: 28  Copynumber: 3.5  Consensus size: 29

      17022 CATGAGATTG

                                 *   *    
      17032 GCACTAAGTGTGCG-GGTTCAAATTGTATA
          1 GCACTAAGTGTGCGAGGTTC-GATTATATA

                                         
      17061 GCACTAAGTGTGCGAGGTT-GATTATATA
          1 GCACTAAGTGTGCGAGGTTCGATTATATA

                                  *       
      17089 GCACTAAGTGTGCGA-GTTCGACTAT-TAA
          1 GCACTAAGTGTGCGAGGTTCGATTATAT-A

                          
      17117 GCACTAAGTGTGCG
          1 GCACTAAGTGTGCG

      17131 GGCTTATTAT


Statistics
Matches: 64,  Mismatches: 3, Indels: 7
        0.86            0.04        0.09

Matches are distributed among these distances:
  27    4  0.06
  28   42  0.66
  29   14  0.22
  30    4  0.06

ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29


Consensus pattern (29 bp):   
GCACTAAGTGTGCGAGGTTCGATTATATA
Done.