Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold6344.1

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: 12251
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.30

Warning! 474 characters in sequence are not A, C, G, or T


Found at i:376 original size:21 final size:23

Alignment explanation


    Indices: 331--377  Score: 62
    Period size: 23  Copynumber: 2.1  Consensus size: 23

        321 TTCAGTGCAA

                           *  *    
        331 TAAACACATTAAAATGAGTTTAT
          1 TAAACACATTAAAATCAGCTTAT

                                   
        354 TAAACACATTAAAA-CA-CTTAT
          1 TAAACACATTAAAATCAGCTTAT

               
        375 TAA
          1 TAA

        378 TCATAACACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    7  0.32
  22    1  0.05
  23   14  0.64

ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32


Consensus pattern (23 bp):   
TAAACACATTAAAATCAGCTTAT

Found at i:1301 original size:19 final size:18

Alignment explanation


    Indices: 1277--1332  Score: 53
    Period size: 19  Copynumber: 3.0  Consensus size: 18

       1267 AAAATTCAGT

                               
       1277 TGAAAAAGTCAAAAAAAAG
          1 TGAAAAA-TCAAAAAAAAG

                                
       1296 TGAAAAATACAAAATAAAA-
          1 TGAAAAAT-CAAAA-AAAAG

                     *         
       1315 T-AAAAATTTAAAAAAAAG
          1 TGAAAAA-TCAAAAAAAAG

       1333 ATTCAGCAGG


Statistics
Matches: 32,  Mismatches: 1, Indels: 9
        0.76            0.02        0.21

Matches are distributed among these distances:
  17    4  0.12
  18   10  0.31
  19   14  0.44
  20    4  0.12

ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16


Consensus pattern (18 bp):   
TGAAAAATCAAAAAAAAG
Done.