Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1746

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: 12138
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27


Found at i:968 original size:27 final size:25

Alignment explanation


    Indices: 867--972  Score: 90
    Period size: 25  Copynumber: 4.2  Consensus size: 25

        857 AGCATGGCTG

                                    *  
        867 CCAGATACAGA-AATGTGACAGAGTCA
          1 CCAGA-ACAGATAATGTG-CAGAGCCA

                 *      * *  *  *    
        893 CCA-ATCAGATATTTTGTAGTGCCA
          1 CCAGAACAGATAATGTGCAGAGCCA

                                *    
        917 CCAGAACAGATAATGTGCAGGGCCA
          1 CCAGAACAGATAATGTGCAGAGCCA

                                 *     
        942 CCAGAACAGATAATTTGTGCATAGCCA
          1 CCAGAACAGATAA--TGTGCAGAGCCA

                
        969 CCAG
          1 CCAG

        973 GACGCTTCCT


Statistics
Matches: 63,  Mismatches: 13, Indels: 7
        0.76            0.16        0.08

Matches are distributed among these distances:
  24   12  0.19
  25   34  0.54
  26    3  0.05
  27   14  0.22

ACGTcount: A:0.36, C:0.23, G:0.22, T:0.20


Consensus pattern (25 bp):   
CCAGAACAGATAATGTGCAGAGCCA

Found at i:1121 original size:26 final size:27

Alignment explanation


    Indices: 1077--1134  Score: 82
    Period size: 26  Copynumber: 2.2  Consensus size: 27

       1067 AAATTAACCC

                          *            
       1077 TAGGGTATAAAGGTCA-TTTACATACA
          1 TAGGGTATAAAGGTAATTTTACATACA

                      *         *      
       1103 TAGGGTATAATGGTAATTTTGCATACA
          1 TAGGGTATAAAGGTAATTTTACATACA

                 
       1130 TAGGG
          1 TAGGG

       1135 GTATTCTAGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  26   14  0.50
  27   14  0.50

ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33


Consensus pattern (27 bp):   
TAGGGTATAAAGGTAATTTTACATACA

Found at i:2196 original size:12 final size:13

Alignment explanation


    Indices: 2177--2209  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       2167 GGGTTCGGCT

                         
       2177 ATGGAGAAGGAAG
          1 ATGGAGAAGGAAG

                      *  
       2190 A-GGAGAAGGTAG
          1 ATGGAGAAGGAAG

                    
       2202 ATGGAGAA
          1 ATGGAGAA

       2210 AAGAATAAAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  12   11  0.61
  13    7  0.39

ACGTcount: A:0.45, C:0.00, G:0.45, T:0.09


Consensus pattern (13 bp):   
ATGGAGAAGGAAG

Found at i:2810 original size:31 final size:33

Alignment explanation


    Indices: 2755--2819  Score: 116
    Period size: 31  Copynumber: 2.0  Consensus size: 33

       2745 CAACTTTTAC

                                             
       2755 AGAATTCCCAAAAATTGGGGCGTTACACACATT
          1 AGAATTCCCAAAAATTGGGGCGTTACACACATT

                                             
       2788 AGAATTCCC-AAAATT-GGGCGTTACACACATT
          1 AGAATTCCCAAAAATTGGGGCGTTACACACATT

             
       2819 A
          1 A

       2820 TCAAAATGTA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  31   17  0.53
  32    6  0.19
  33    9  0.28

ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25


Consensus pattern (33 bp):   
AGAATTCCCAAAAATTGGGGCGTTACACACATT

Found at i:10194 original size:25 final size:27

Alignment explanation


    Indices: 10125--10232  Score: 102
    Period size: 27  Copynumber: 4.1  Consensus size: 27

      10115 AGCATGGCTG

                              *     *  
      10125 CCAGAACAGATAA---TGACAGAGTCA
          1 CCAGAACAGATAATTGTGGCAGAGCCA

                   *       *            
      10149 CCAGATATAGATAATCGTGGCAGAG-CA
          1 CCAGA-ACAGATAATTGTGGCAGAGCCA

                                        
      10176 CCA-AACAGA-AATATGTGGCAGAGCCA
          1 CCAGAACAGATAAT-TGTGGCAGAGCCA

                 *               *     
      10202 CCAGATCAGATAATTGTGGCATAGCCA
          1 CCAGAACAGATAATTGTGGCAGAGCCA

                
      10229 CCAG
          1 CCAG

      10233 GACGCTTCCT


Statistics
Matches: 70,  Mismatches: 6, Indels: 13
        0.79            0.07        0.15

Matches are distributed among these distances:
  24    8  0.11
  25   20  0.29
  26    6  0.09
  27   26  0.37
  28   10  0.14

ACGTcount: A:0.39, C:0.22, G:0.23, T:0.16


Consensus pattern (27 bp):   
CCAGAACAGATAATTGTGGCAGAGCCA

Done.