Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga04g01939.M1

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: 4551
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31


Found at i:2797 original size:29 final size:29

Alignment explanation


    Indices: 2739--2800  Score: 72
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       2729 AATTTTTAGA

                                 * * *   
       2739 AAAAATTATGGAAATGGGCCGTTTTGTTT
          1 AAAAATTATGGAAATGGGCCGATCTCTTT

                               *          
       2768 AAAAATTATTGGAAAT-GGTCGATCTCTTT
          1 AAAAATTA-TGGAAATGGGCCGATCTCTTT

                
       2797 AAAA
          1 AAAA

       2801 TGCATTGAGT


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

Matches are distributed among these distances:
  29   21  0.75
  30    7  0.25

ACGTcount: A:0.37, C:0.08, G:0.19, T:0.35


Consensus pattern (29 bp):   
AAAAATTATGGAAATGGGCCGATCTCTTT

Found at i:3133 original size:29 final size:29

Alignment explanation


    Indices: 3099--3159  Score: 95
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       3089 AAAAAAATTA

                                 * *     
       3099 GTTCTGAAAAAATAATTTTGAGGGGATGG
          1 GTTCTGAAAAAATAATTTTGACGAGATGG

                    *                    
       3128 GTTCTGAAGAAATAATTTTGACGAGATGG
          1 GTTCTGAAAAAATAATTTTGACGAGATGG

               
       3157 GTT
          1 GTT

       3160 GAGTTTTGTA


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.33, C:0.05, G:0.30, T:0.33


Consensus pattern (29 bp):   
GTTCTGAAAAAATAATTTTGACGAGATGG
Done.