Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1996

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, 698

Length: 1164
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35


Found at i:728 original size:37 final size:37

Alignment explanation


    Indices: 647--729  Score: 89
    Period size: 38  Copynumber: 2.2  Consensus size: 37

        637 ATATGTGTGG

                           *                 *   
        647 AATTGAATCGAATATTGACTTGAAAATGGAAAAGTGA
          1 AATTGAATCGAATATCGACTTGAAAATGGAAAAATGA

              *                        *            
        684 ATTTTGAATCGAAT-TGCGA-TTGAAAGTGGAAAAAATGA
          1 A-ATTGAATCGAATAT-CGACTTGAAAATGG-AAAAATGA

                    
        722 AATTGAAT
          1 AATTGAAT

        730 TAAAATGTGA


Statistics
Matches: 38,  Mismatches: 5, Indels: 6
        0.78            0.10        0.12

Matches are distributed among these distances:
  37   17  0.45
  38   21  0.55

ACGTcount: A:0.45, C:0.05, G:0.22, T:0.29


Consensus pattern (37 bp):   
AATTGAATCGAATATCGACTTGAAAATGGAAAAATGA

Found at i:856 original size:21 final size:20

Alignment explanation


    Indices: 832--950  Score: 95
    Period size: 21  Copynumber: 6.0  Consensus size: 20

        822 GCTTTGCCGG

                                 
        832 TCAGGCACTTTATGTGTCGTA
          1 TCAGGCAC-TTATGTGTCGTA

                      **        *
        853 TCAGGCAACTCGTGTGTCGTT
          1 TCAGGC-ACTTATGTGTCGTA

                                
        874 TCAGGCACTTATGTGTCGTA
          1 TCAGGCACTTATGTGTCGTA

                     *  **      
        894 T-----ACTGATCAGTCGTA
          1 TCAGGCACTTATGTGTCGTA

                      **        *
        909 TCAGGCAACTCGTGTGTCGTT
          1 TCAGGC-ACTTATGTGTCGTA

                                
        930 TCAGGCACTTATGTGTCGTA
          1 TCAGGCACTTATGTGTCGTA

             
        950 T
          1 T

        951 ACTGATCAGG


Statistics
Matches: 74,  Mismatches: 17, Indels: 15
        0.70            0.16        0.14

Matches are distributed among these distances:
  15   12  0.16
  20   24  0.32
  21   36  0.49
  22    2  0.03

ACGTcount: A:0.18, C:0.21, G:0.25, T:0.35


Consensus pattern (20 bp):   
TCAGGCACTTATGTGTCGTA

Found at i:933 original size:56 final size:56

Alignment explanation


    Indices: 847--959  Score: 226
    Period size: 56  Copynumber: 2.0  Consensus size: 56

        837 CACTTTATGT

                                                                    
        847 GTCGTATCAGGCAACTCGTGTGTCGTTTCAGGCACTTATGTGTCGTATACTGATCA
          1 GTCGTATCAGGCAACTCGTGTGTCGTTTCAGGCACTTATGTGTCGTATACTGATCA

                                                                    
        903 GTCGTATCAGGCAACTCGTGTGTCGTTTCAGGCACTTATGTGTCGTATACTGATCA
          1 GTCGTATCAGGCAACTCGTGTGTCGTTTCAGGCACTTATGTGTCGTATACTGATCA

             
        959 G
          1 G

        960 GTACTATGTA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  56   57  1.00

ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34


Consensus pattern (56 bp):   
GTCGTATCAGGCAACTCGTGTGTCGTTTCAGGCACTTATGTGTCGTATACTGATCA
Done.