Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold888

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: 7169
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31


Found at i:2787 original size:18 final size:18

Alignment explanation


    Indices: 2758--2810  Score: 88
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       2748 GAGCTTCACT

                               
       2758 ACTAGCCATCAATATCGTC
          1 ACTAG-CATCAATATCGTC

                              
       2777 ACTAGCATCAATATCGTC
          1 ACTAGCATCAATATCGTC

                *           
       2795 ACTATCATCAATATCG
          1 ACTAGCATCAATATCG

       2811 ATATCATCAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  18   28  0.85
  19    5  0.15

ACGTcount: A:0.34, C:0.28, G:0.09, T:0.28


Consensus pattern (18 bp):   
ACTAGCATCAATATCGTC

Found at i:2815 original size:15 final size:17

Alignment explanation


    Indices: 2764--2822  Score: 77
    Period size: 18  Copynumber: 3.5  Consensus size: 17

       2754 CACTACTAGC

                             *
       2764 CATCAATATCGTCACTAG
          1 CATCAATATCG-CACTAT

                              
       2782 CATCAATATCGTCACTAT
          1 CATCAATATCG-CACTAT

                             
       2800 CATCAATATCG-A-TAT
          1 CATCAATATCGCACTAT

                    
       2815 CATCAATA
          1 CATCAATA

       2823 AGAAAAACCT


Statistics
Matches: 40,  Mismatches: 1, Indels: 3
        0.91            0.02        0.07

Matches are distributed among these distances:
  15   11  0.28
  16    1  0.03
  18   28  0.70

ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31


Consensus pattern (17 bp):   
CATCAATATCGCACTAT

Found at i:5219 original size:21 final size:21

Alignment explanation


    Indices: 5189--5277  Score: 90
    Period size: 21  Copynumber: 4.1  Consensus size: 21

       5179 CTCACAAAGA

                        * *      
       5189 AAAAAG-GAAGTGAGTTAGAC
          1 AAAAAGAGAAGTAACTTAGAC

                       *     *   
       5209 AAAAAGAGAAGCAACTTGGAC
          1 AAAAAGAGAAGTAACTTAGAC

                             *   
       5230 AAAAAGAGAAGTAACTTGGAC
          1 AAAAAGAGAAGTAACTTAGAC

                           *        
       5251 AAAAAGAAACGAAGTGACTTAGAC
          1 AAAAAG--A-GAAGTAACTTAGAC

               
       5275 AAA
          1 AAA

       5278 TCTTTTTTGT


Statistics
Matches: 58,  Mismatches: 7, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  20    6  0.10
  21   36  0.62
  23    1  0.02
  24   15  0.26

ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12


Consensus pattern (21 bp):   
AAAAAGAGAAGTAACTTAGAC

Found at i:5270 original size:24 final size:21

Alignment explanation


    Indices: 5189--5257  Score: 95
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       5179 CTCACAAAGA

                        * *  *   
       5189 AAAAAG-GAAGTGAGTTAGAC
          1 AAAAAGAGAAGTAACTTGGAC

                       *         
       5209 AAAAAGAGAAGCAACTTGGAC
          1 AAAAAGAGAAGTAACTTGGAC

                                 
       5230 AAAAAGAGAAGTAACTTGGAC
          1 AAAAAGAGAAGTAACTTGGAC

                   
       5251 AAAAAGA
          1 AAAAAGA

       5258 AACGAAGTGA


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    6  0.14
  21   37  0.86

ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12


Consensus pattern (21 bp):   
AAAAAGAGAAGTAACTTGGAC
Done.