Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold8.333

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: 1842
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22


Found at i:330 original size:3 final size:3

Alignment explanation


    Indices: 322--356  Score: 70
    Period size: 3  Copynumber: 11.7  Consensus size: 3

        312 AGCTATTCCC

                                                          
        322 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
          1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA

        357 GCAGCAGCAG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   32  1.00

ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00


Consensus pattern (3 bp):   
CAA

Found at i:662 original size:3 final size:3

Alignment explanation


    Indices: 654--678  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

        644 TGCTCAGTGG

                                             
        654 TGC TGC TGC TGC TGC TGC TGC TGC T
          1 TGC TGC TGC TGC TGC TGC TGC TGC T

        679 CAGTTTAGTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36


Consensus pattern (3 bp):   
TGC

Found at i:1180 original size:15 final size:15

Alignment explanation


    Indices: 1162--1205  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       1152 GCAGCAGCCA

                    *  *   
       1162 CAGCAACATCAGCAG
          1 CAGCAACAACAACAG

                           
       1177 CAGCAACAACAACAG
          1 CAGCAACAACAACAG

                *   *     
       1192 CAGCTACAGCAACA
          1 CAGCAACAACAACA

       1206 TTCTCAACAA


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  15   25  1.00

ACGTcount: A:0.45, C:0.34, G:0.16, T:0.05


Consensus pattern (15 bp):   
CAGCAACAACAACAG
Done.