Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1010

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: 3377
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31


Found at i:2892 original size:17 final size:17

Alignment explanation


    Indices: 2867--2921  Score: 56
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       2857 CTCCTTTTCA

                *            
       2867 TTCTCTTTTTTTGAATT
          1 TTCTTTTTTTTTGAATT

                         * *  
       2884 TTCTTTTTTTTTTCATTT
          1 TTC-TTTTTTTTTGAATT

                   *     *   
       2902 TTCTTTTCTTTTGTATT
          1 TTCTTTTTTTTTGAATT

               
       2919 TTC
          1 TTC

       2922 GCCCTTTTCT


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  17   16  0.53
  18   14  0.47

ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76


Consensus pattern (17 bp):   
TTCTTTTTTTTTGAATT

Found at i:2895 original size:18 final size:18

Alignment explanation


    Indices: 2872--2913  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       2862 TTTCATTCTC

                   *          
       2872 TTTTTTTGAATTTTCTTT
          1 TTTTTTTCAATTTTCTTT

                     *        
       2890 TTTTTTTCATTTTTCTTT
          1 TTTTTTTCAATTTTCTTT

                  
       2908 TCTTTT
          1 T-TTTT

       2914 GTATTTTCGC


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  18   17  0.81
  19    4  0.19

ACGTcount: A:0.07, C:0.10, G:0.02, T:0.81


Consensus pattern (18 bp):   
TTTTTTTCAATTTTCTTT

Found at i:2919 original size:18 final size:18

Alignment explanation


    Indices: 2882--2920  Score: 53
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       2872 TTTTTTTGAA

                         *    
       2882 TTTTCTTTTTTTTTTCAT
          1 TTTTCTTTTTTTTGTCAT

                               
       2900 TTTTCTTTTCTTTTGT-AT
          1 TTTTCTTTT-TTTTGTCAT

               
       2918 TTT
          1 TTT

       2921 CGCCCTTTTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  18   14  0.74
  19    5  0.26

ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82


Consensus pattern (18 bp):   
TTTTCTTTTTTTTGTCAT
Done.