Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_1468

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: 30945
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:3637 original size:57 final size:57

Alignment explanation


    Indices: 3575--3689  Score: 176
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       3565 ATCACGGGTA

                      *                               * *    *       
       3575 CATTTTCTATGTATAATACTAATGTCATTGCCTTAATTGATCTAGGGTCTACCCATT
          1 CATTTTCTATCTATAATACTAATGTCATTGCCTTAATTGATCCACGGTCAACCCATT

                                **                                   
       3632 CATTTTCTATCTATAATACTTGTGTCATTGCCTTAATTGATCCACGGTCAACCCATT
          1 CATTTTCTATCTATAATACTAATGTCATTGCCTTAATTGATCCACGGTCAACCCATT

             
       3689 C
          1 C

       3690 GTACATTTGC


Statistics
Matches: 52,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  57   52  1.00

ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41


Consensus pattern (57 bp):   
CATTTTCTATCTATAATACTAATGTCATTGCCTTAATTGATCCACGGTCAACCCATT

Found at i:13606 original size:20 final size:20

Alignment explanation


    Indices: 13581--13631  Score: 84
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      13571 GGAAGAGGGG

                                
      13581 CACGGGCGTGTCCCCAAGCA
          1 CACGGGCGTGTCCCCAAGCA

                                
      13601 CACGGGCGTGTCCCCAAGCA
          1 CACGGGCGTGTCCCCAAGCA

            *     *    
      13621 TACGGGTGTGT
          1 CACGGGCGTGT

      13632 GCTTTTCCTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   29  1.00

ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16


Consensus pattern (20 bp):   
CACGGGCGTGTCCCCAAGCA

Found at i:29555 original size:26 final size:24

Alignment explanation


    Indices: 29521--29608  Score: 99
    Period size: 25  Copynumber: 3.5  Consensus size: 24

      29511 CAGCACGGCT

                                      
      29521 CCAGAACAGATAAT-TGACAGAGTCA
          1 CCAGAACAGATAATGTG-CAGAG-CA

                                      
      29546 CCAGATACAGATAATCGTGCAGAGCA
          1 CCAGA-ACAGATAAT-GTGCAGAGCA

                                      
      29572 CCAGAACA-ATATATGTGGCAGAGCA
          1 CCAGAACAGATA-ATGT-GCAGAGCA

                 *      
      29597 CCAGATCAGATA
          1 CCAGAACAGATA

      29609 TTTATGGCAT


Statistics
Matches: 56,  Mismatches: 1, Indels: 11
        0.82            0.01        0.16

Matches are distributed among these distances:
  24    5  0.09
  25   25  0.45
  26   19  0.34
  27    5  0.09
  28    2  0.04

ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16


Consensus pattern (24 bp):   
CCAGAACAGATAATGTGCAGAGCA

Found at i:29616 original size:26 final size:27

Alignment explanation


    Indices: 29538--29627  Score: 80
    Period size: 26  Copynumber: 3.4  Consensus size: 27

      29528 AGATAATTGA

                 *               * *    
      29538 CAGAGTCACCAGATACAGATAATCGT-G
          1 CAGAGCCACCAGAT-CAGATATTTGTGG

                         *       *     
      29565 CAGAG-CACCAGAACA-ATATATGTGG
          1 CAGAGCCACCAGATCAGATATTTGTGG

                                   *   
      29590 CAGAG-CACCAGATCAGATATTTATGG
          1 CAGAGCCACCAGATCAGATATTTGTGG

              *         
      29616 CATAGCCACCAG
          1 CAGAGCCACCAG

      29628 GACGCCTCCT


Statistics
Matches: 52,  Mismatches: 8, Indels: 6
        0.79            0.12        0.09

Matches are distributed among these distances:
  24    5  0.10
  25   17  0.33
  26   19  0.37
  27   11  0.21

ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18


Consensus pattern (27 bp):   
CAGAGCCACCAGATCAGATATTTGTGG
Done.