Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00387.F1

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: 1688
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26


Found at i:335 original size:6 final size:6

Alignment explanation


    Indices: 328--388  Score: 74
    Period size: 6  Copynumber: 10.7  Consensus size: 6

        318 CAAACCACAA

                 *          *                              *       
        328 CAACAA CAACAG CATCAG C-A--G CAACAG CAACAG CAACAA CAACAG
          1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG

                              
        373 CAACAG CAACAG CAAC
          1 CAACAG CAACAG CAAC

        389 GGGAACATGT


Statistics
Matches: 47,  Mismatches: 5, Indels: 6
        0.81            0.09        0.10

Matches are distributed among these distances:
   3    2  0.04
   4    1  0.02
   6   44  0.94

ACGTcount: A:0.51, C:0.34, G:0.13, T:0.02


Consensus pattern (6 bp):   
CAACAG

Found at i:354 original size:15 final size:15

Alignment explanation


    Indices: 334--388  Score: 65
    Period size: 15  Copynumber: 3.7  Consensus size: 15

        324 ACAACAACAA

                    *      
        334 CAACAGCATCAGCAG
          1 CAACAGCAACAGCAG

                          *
        349 CAACAGCAACAGCAA
          1 CAACAGCAACAGCAG

                 *  *  *   
        364 CAACAACAGCAACAG
          1 CAACAGCAACAGCAG

                      
        379 CAACAGCAAC
          1 CAACAGCAAC

        389 GGGAACATGT


Statistics
Matches: 32,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  15   32  1.00

ACGTcount: A:0.49, C:0.35, G:0.15, T:0.02


Consensus pattern (15 bp):   
CAACAGCAACAGCAG

Found at i:1568 original size:3 final size:3

Alignment explanation


    Indices: 1560--1585  Score: 52
    Period size: 3  Copynumber: 8.7  Consensus size: 3

       1550 TCACTGTGGC

                                              
       1560 TGA TGA TGA TGA TGA TGA TGA TGA TG
          1 TGA TGA TGA TGA TGA TGA TGA TGA TG

       1586 TTGGGGGGTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   23  1.00

ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35


Consensus pattern (3 bp):   
TGA

Done.