Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2319

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: 20392
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30


Found at i:950 original size:40 final size:40

Alignment explanation


    Indices: 849--993  Score: 184
    Period size: 40  Copynumber: 3.6  Consensus size: 40

        839 TACTCGAATG

                                    *            *   
        849 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCAACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT

             *      *                                
        890 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT

                                        *      *   *
        930 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

                     *    *         
        970 ATATCCGGGTTAAGACCCGAAGGC
          1 ATATCCGGGCTAAGTCCCGAAGGC

        994 CTTGTGTGAG


Statistics
Matches: 91,  Mismatches: 11, Indels: 5
        0.85            0.10        0.05

Matches are distributed among these distances:
  39    1  0.01
  40   61  0.67
  41   28  0.31
  42    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

Found at i:8118 original size:40 final size:40

Alignment explanation


    Indices: 8024--8167  Score: 184
    Period size: 40  Copynumber: 3.6  Consensus size: 40

       8014 TACTCGAATG

                                    *                
       8024 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT

             *      *                                
       8065 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
          1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT

                                        *      *   *
       8105 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

                     *    *         
       8145 ATATCCGGGTTAAGACCC-AAGGC
          1 ATATCCGGGCTAAGTCCCGAAGGC

       8168 CTTGTGCGAG


Statistics
Matches: 91,  Mismatches: 10, Indels: 6
        0.85            0.09        0.06

Matches are distributed among these distances:
  39    6  0.07
  40   56  0.62
  41   28  0.31
  42    1  0.01

ACGTcount: A:0.26, C:0.25, G:0.26, T:0.24


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT

Found at i:10333 original size:27 final size:27

Alignment explanation


    Indices: 10303--10480  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

      10293 ATATTGAGTC

                    *       *   *    * 
      10303 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
      10330 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
      10357 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
      10385 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
      10412 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
      10439 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
      10466 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

      10481 GTACAATTTA


Statistics
Matches: 130,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   24  0.18

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:10442 original size:82 final size:81

Alignment explanation


    Indices: 10324--10479  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

      10314 TGCTATATAA

                                   *                       *                 
      10324 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
      10389 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
      10406 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
      10470 CACTTAGTGC
         65 CACTTAGTGC

      10480 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   16  0.24
  82   51  0.76

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


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG

Found at i:18449 original size:27 final size:27

Alignment explanation


    Indices: 18419--18596  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

      18409 ATATTGAGTC

                    *       *   *    * 
      18419 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                             *  *      
      18446 CGCACACTTAGTGCTACGTAATCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                        
      18473 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAAA-T

                          **   *     * 
      18501 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                                 *   ** 
      18528 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAAAT

                          *            
      18555 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAAAT

                           
      18582 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

      18597 GTACAATTTA


Statistics
Matches: 130,  Mismatches: 18, Indels: 6
        0.84            0.12        0.04

Matches are distributed among these distances:
  27  106  0.82
  28   24  0.18

ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAAAT

Found at i:18558 original size:82 final size:81

Alignment explanation


    Indices: 18440--18595  Score: 233
    Period size: 82  Copynumber: 1.9  Consensus size: 81

      18430 TGCTATATAA

                                   *                       *                 
      18440 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
          1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA

                             
      18505 CACTTAGTGCCGCATGG
         65 CACTTAGTGCCGCATGG

                *                      *   **                                
      18522 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
          1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA

                      
      18586 CACTTAGTGC
         65 CACTTAGTGC

      18596 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   16  0.24
  82   51  0.76

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


Consensus pattern (81 bp):   
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG

Done.