Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1314

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: 36072
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:2641 original size:23 final size:23

Alignment explanation


    Indices: 2615--2659  Score: 74
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2605 AGTGGAAGGA

                                    
       2615 GCCAATTGGGAGACAA-ACTATTT
          1 GCCAATTGGG-GACAAGACTATTT

                                  
       2638 GCCAATTGGGGACAAGACTATT
          1 GCCAATTGGGGACAAGACTATT

       2660 GGTATAGAGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  22    5  0.24
  23   16  0.76

ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24


Consensus pattern (23 bp):   
GCCAATTGGGGACAAGACTATTT

Found at i:17225 original size:21 final size:21

Alignment explanation


    Indices: 17199--17239  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      17189 TCAGACGCAA

                   * *           
      17199 TACTCCACAGCAGGTGGAGTG
          1 TACTCCAAAACAGGTGGAGTG

                                
      17220 TACTCCAAAACAGGTGGAGT
          1 TACTCCAAAACAGGTGGAGT

      17240 TTGAGCAGAT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20


Consensus pattern (21 bp):   
TACTCCAAAACAGGTGGAGTG

Found at i:19175 original size:16 final size:16

Alignment explanation


    Indices: 19142--19175  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      19132 GGAGATTGTT

                       * *  
      19142 AACATTAATGGGAGAC
          1 AACATTAATGGCAAAC

                            
      19158 AACATTAATGGCAAAC
          1 AACATTAATGGCAAAC

              
      19174 AA
          1 AA

      19176 TACAAAGTGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18


Consensus pattern (16 bp):   
AACATTAATGGCAAAC

Found at i:32558 original size:21 final size:21

Alignment explanation


    Indices: 32532--32577  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      32522 TCGATCCTGT

                      *          
      32532 TCCTCATAAATAAAGTTTAAA
          1 TCCTCATAAACAAAGTTTAAA

                                 
      32553 TCCTCATAAACAAAGTTTAAA
          1 TCCTCATAAACAAAGTTTAAA

                
      32574 TCCT
          1 TCCT

      32578 TATAGATGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33


Consensus pattern (21 bp):   
TCCTCATAAACAAAGTTTAAA
Done.