Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11598.1

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: 2696
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.36


Found at i:2566 original size:23 final size:23

Alignment explanation


    Indices: 2540--2586  Score: 69
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       2530 TTTTCTCGTC

                 *                 
       2540 TTTTTGTC-ACTTTTTTTCGAAT
          1 TTTTTTTCAACTTTTTTTCGAAT

                      *            
       2562 TTTTTTTCAATTTTTTTTCGAAT
          1 TTTTTTTCAACTTTTTTTCGAAT

              
       2585 TT
          1 TT

       2587 CTTCTCTTTT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  22    7  0.32
  23   15  0.68

ACGTcount: A:0.15, C:0.11, G:0.06, T:0.68


Consensus pattern (23 bp):   
TTTTTTTCAACTTTTTTTCGAAT

Found at i:2579 original size:11 final size:12

Alignment explanation


    Indices: 2550--2586  Score: 67
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       2540 TTTTTGTCAC

                        
       2550 TTTTTTTCGAAT
          1 TTTTTTTCGAAT

                        
       2562 TTTTTTTC-AAT
          1 TTTTTTTCGAAT

                        
       2573 TTTTTTTCGAAT
          1 TTTTTTTCGAAT

              
       2585 TT
          1 TT

       2587 CTTCTCTTTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  11   11  0.46
  12   13  0.54

ACGTcount: A:0.16, C:0.08, G:0.05, T:0.70


Consensus pattern (12 bp):   
TTTTTTTCGAAT

Found at i:2598 original size:23 final size:23

Alignment explanation


    Indices: 2550--2600  Score: 70
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       2540 TTTTTGTCAC

                          *  *     
       2550 TTTTTTTCGAATTTTTTTTCAAT
          1 TTTTTTTCGAATTTCTTCTCAAT

                                   
       2573 TTTTTTTCGAATTTCTTCTC--T
          1 TTTTTTTCGAATTTCTTCTCAAT

                   
       2594 TTTTTTT
          1 TTTTTTT

       2601 GTTAATCCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 2
        0.87            0.07        0.07

Matches are distributed among these distances:
  21    8  0.31
  23   18  0.69

ACGTcount: A:0.12, C:0.12, G:0.04, T:0.73


Consensus pattern (23 bp):   
TTTTTTTCGAATTTCTTCTCAAT
Done.