Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1169

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: 45538
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:7137 original size:27 final size:27

Alignment explanation


    Indices: 7092--7222  Score: 128
    Period size: 27  Copynumber: 4.9  Consensus size: 27

       7082 CACTAGATAT

                        *  *           
       7092 AGATAT-TGTGGTAGAGCCACCAGAAC
          1 AGATATATGTGGCAGTGCCACCAGAAC

                                     * 
       7118 AGATATATGTGGCAGTGCCACCAGATC
          1 AGATATATGTGGCAGTGCCACCAGAAC

                                      *  
       7145 AGATA-ATTGTGGCA-TAGCCACCAGGAC
          1 AGATATA-TGTGGCAGT-GCCACCAGAAC

                        *  *         * 
       7172 AGATATATGTGGTAGAGCCACCAGATC
          1 AGATATATGTGGCAGTGCCACCAGAAC

                                      
       7199 AGATA-ATTGTGGCA-TAGCCACCAG
          1 AGATATA-TGTGGCAGT-GCCACCAG

       7223 GACGCTTCCT


Statistics
Matches: 87,  Mismatches: 11, Indels: 13
        0.78            0.10        0.12

Matches are distributed among these distances:
  26    9  0.10
  27   77  0.89
  28    1  0.01

ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21


Consensus pattern (27 bp):   
AGATATATGTGGCAGTGCCACCAGAAC

Found at i:7223 original size:54 final size:54

Alignment explanation


    Indices: 7092--7225  Score: 216
    Period size: 54  Copynumber: 2.5  Consensus size: 54

       7082 CACTAGATAT

                        * *         *                 *           
       7092 AGAT-ATTGTGGTAGAGCCACCAGAACAGATATATGTGGCAGTGCCACCAGATC
          1 AGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATC

                                                   *              
       7145 AGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGTAGAGCCACCAGATC
          1 AGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATC

                                       
       7199 AGATAATTGTGGCATAGCCACCAGGAC
          1 AGATAATTGTGGCATAGCCACCAGGAC

       7226 GCTTCCTCCA


Statistics
Matches: 75,  Mismatches: 5, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  53    4  0.05
  54   71  0.95

ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20


Consensus pattern (54 bp):   
AGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGCCACCAGATC

Found at i:8852 original size:26 final size:26

Alignment explanation


    Indices: 8821--8928  Score: 173
    Period size: 26  Copynumber: 4.2  Consensus size: 26

       8811 TGAAATGCCC

                                      
       8821 ATCATGGAACATTTACCTAAACCATT
          1 ATCATGGAACATTTACCTAAACCATT

                                       
       8847 ATCATGGAACATTTACCT-AACTCATT
          1 ATCATGGAACATTTACCTAAAC-CATT

                     *          *     
       8873 ATCATGGAATATTTACCTAATCCATT
          1 ATCATGGAACATTTACCTAAACCATT

                                *     
       8899 ATCATGGAACATTTACCTAACCCATT
          1 ATCATGGAACATTTACCTAAACCATT

                
       8925 ATCA
          1 ATCA

       8929 ATTTGTACCA


Statistics
Matches: 76,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  25    3  0.04
  26   71  0.93
  27    2  0.03

ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33


Consensus pattern (26 bp):   
ATCATGGAACATTTACCTAAACCATT

Found at i:15859 original size:40 final size:40

Alignment explanation


    Indices: 15797--16041  Score: 336
    Period size: 40  Copynumber: 6.2  Consensus size: 40

      15787 AAACCAAGTA

                     *    *                   *      
      15797 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
          1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG

                                       *       *    
      15836 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACCAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                                    
      15876 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                                    
      15916 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

                                *      *   *         
      15956 CCTTCGGGACTTAGCCC-GAAATTAGTCACTAGCACAAATG
          1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG

                                       *   *  *      
      15996 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCCCAAATG
          1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG

                  
      16036 CCTTCG
          1 CCTTCG

      16042 TTATCATCCG


Statistics
Matches: 191,  Mismatches: 11, Indels: 7
        0.91            0.05        0.03

Matches are distributed among these distances:
  39   16  0.08
  40  173  0.91
  41    2  0.01

ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24


Consensus pattern (40 bp):   
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG

Found at i:42546 original size:25 final size:25

Alignment explanation


    Indices: 42499--42584  Score: 102
    Period size: 25  Copynumber: 3.3  Consensus size: 25

      42489 ATATTGAGTC

                                       
      42499 CGCACACTCAGTGCTACATAATCAACT
          1 CGCACACT-A-TGCTACATAATCAACT

                                    * 
      42526 CGCACACTATGCTACGA-AATCAAAT
          1 CGCACACTATGCTAC-ATAATCAACT

                      *        *      
      42551 CGCACACTTAGGCTACATAGTCAACT
          1 CGCACAC-TATGCTACATAATCAACT

                    
      42577 CGCACACT
          1 CGCACACT

      42585 TAGTGCCGCT


Statistics
Matches: 52,  Mismatches: 4, Indels: 8
        0.81            0.06        0.12

Matches are distributed among these distances:
  25   22  0.42
  26   22  0.42
  27    8  0.15

ACGTcount: A:0.34, C:0.33, G:0.13, T:0.21


Consensus pattern (25 bp):   
CGCACACTATGCTACATAATCAACT
Done.