Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11488.1

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: 2794
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:340 original size:27 final size:27

Alignment explanation


    Indices: 218--340  Score: 140
    Period size: 27  Copynumber: 4.6  Consensus size: 27

        208 CCTTAATCGA

                      *             *  
        218 TAAAATGACTATTTTGCCCTTATGAGG
          1 TAAAATGACTGTTTTGCCCTTATGTGG

                    *        *         
        245 TAAAATGATTGTTTTGCTCTTATGTGG
          1 TAAAATGACTGTTTTGCCCTTATGTGG

                  *           *        
        272 TAAAATAACTGTTTTGCCTTTATGTGG
          1 TAAAATGACTGTTTTGCCCTTATGTGG

                  *   *            *    
        299 TAAAATAACTATTTTGCCCTT-TCTGGG
          1 TAAAATGACTGTTTTGCCCTTATGT-GG

               *           
        326 TAAGATGACTGTTTT
          1 TAAAATGACTGTTTT

        341 ACCACTATGT


Statistics
Matches: 81,  Mismatches: 14, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  26    2  0.02
  27   79  0.98

ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43


Consensus pattern (27 bp):   
TAAAATGACTGTTTTGCCCTTATGTGG

Found at i:685 original size:18 final size:18

Alignment explanation


    Indices: 662--712  Score: 68
    Period size: 17  Copynumber: 2.9  Consensus size: 18

        652 GGACTTGCAT

                              
        662 ACTGTTTACTGTTACTAC
          1 ACTGTTTACTGTTACTAC

                    *         
        680 ACTG-TTAGTGTTACTAC
          1 ACTGTTTACTGTTACTAC

               *      *     
        697 ACTATTTACTATTACT
          1 ACTGTTTACTGTTACT

        713 GTAATGGGCC


Statistics
Matches: 28,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  17   15  0.54
  18   13  0.46

ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45


Consensus pattern (18 bp):   
ACTGTTTACTGTTACTAC

Found at i:2633 original size:27 final size:27

Alignment explanation


    Indices: 2500--2622  Score: 147
    Period size: 27  Copynumber: 4.6  Consensus size: 27

       2490 AGATAGGGGT

                       *      * *      
       2500 AAAACAGTCATCTTACCATAAAAGGGC
          1 AAAACAGTCATTTTACCACATAAGGGC

                *   *              *   
       2527 AAAATAGTTATTTTACCACATAAAGGC
          1 AAAACAGTCATTTTACCACATAAGGGC

                    *                  
       2554 AAAACAGTTATTTTACCACATAAGGGC
          1 AAAACAGTCATTTTACCACATAAGGGC

                  *          **        
       2581 AAAACAATCATTTTACCTTATAAGGGC
          1 AAAACAGTCATTTTACCACATAAGGGC

                *          
       2608 AAAATAGTCATTTTA
          1 AAAACAGTCATTTTA

       2623 TCGATTAAGG


Statistics
Matches: 82,  Mismatches: 14, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  27   82  1.00

ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28


Consensus pattern (27 bp):   
AAAACAGTCATTTTACCACATAAGGGC

Done.