Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3538

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: 8726
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33


Found at i:1839 original size:23 final size:23

Alignment explanation


    Indices: 1813--1908  Score: 162
    Period size: 23  Copynumber: 4.3  Consensus size: 23

       1803 ATAAGTGCCA

                                   
       1813 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                                   
       1836 CACTGATATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                                   
       1859 CACTG--ATGTAGCC-AAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                  *                
       1879 CACTGAAATGTAGCCGAAGCTAC
          1 CACTGATATGTAGCCGAAGCTAC

                   
       1902 CACTGAT
          1 CACTGAT

       1909 CAATAACACT


Statistics
Matches: 69,  Mismatches: 1, Indels: 6
        0.91            0.01        0.08

Matches are distributed among these distances:
  20   12  0.17
  21    8  0.12
  22    8  0.12
  23   41  0.59

ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21


Consensus pattern (23 bp):   
CACTGATATGTAGCCGAAGCTAC

Found at i:1879 original size:43 final size:44

Alignment explanation


    Indices: 1820--1908  Score: 162
    Period size: 43  Copynumber: 2.0  Consensus size: 44

       1810 CCACACTGAT

                                  *                     
       1820 ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

                                                        
       1864 ATGTAGCC-AAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
          1 ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG

              
       1907 AT
          1 AT

       1909 CAATAACACT


Statistics
Matches: 44,  Mismatches: 1, Indels: 1
        0.96            0.02        0.02

Matches are distributed among these distances:
  43   36  0.82
  44    8  0.18

ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20


Consensus pattern (44 bp):   
ATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTACCACTG
Done.