Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00343.F2

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, 604

Length: 1007
ACGTcount: A:0.20, C:0.13, G:0.37, T:0.30


Found at i:383 original size:30 final size:30

Alignment explanation


    Indices: 343--403  Score: 88
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        333 TTACAAAGGC

                 *                         
        343 ATTGGTGGTCTAGG-GGGTTTAGGCGGTGGA
          1 ATTGGAGGTCTAGGTGGG-TTAGGCGGTGGA

                                   *      
        373 ATTGGAGGTCTAGGTGGGTTAGGGGGTGGA
          1 ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA

             
        403 A
          1 A

        404 CTGGTGGCGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30   25  0.89
  31    3  0.11

ACGTcount: A:0.16, C:0.05, G:0.51, T:0.28


Consensus pattern (30 bp):   
ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA

Found at i:429 original size:42 final size:42

Alignment explanation


    Indices: 375--470  Score: 165
    Period size: 42  Copynumber: 2.3  Consensus size: 42

        365 GCGGTGGAAT

                                          *           
        375 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACTGGTGGCGGAGG
          1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

                           *                         *
        417 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGCGGAGT
          1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

                        
        459 TGGAGGTCTAGG
          1 TGGAGGTCTAGG

        471 CAGTGGGACC


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42   51  1.00

ACGTcount: A:0.15, C:0.08, G:0.54, T:0.23


Consensus pattern (42 bp):   
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

Found at i:482 original size:33 final size:33

Alignment explanation


    Indices: 440--503  Score: 110
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        430 GGTTTAGGGG

                      *                      
        440 GTGGAACCGGTGGCGGAGTTGGAGGTCTAGGCA
          1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA

                *                          
        473 GTGGGACCGGGGGCGGAGTTGGAGGTCTAGG
          1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGG

        504 TGGTGGTGGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.16, C:0.14, G:0.53, T:0.17


Consensus pattern (33 bp):   
GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA

Found at i:587 original size:57 final size:57

Alignment explanation


    Indices: 502--623  Score: 190
    Period size: 57  Copynumber: 2.1  Consensus size: 57

        492 TGGAGGTCTA

                               *                       *       *     
        502 GGTGGTGGTGGTTGTCCAGGTACAGGTGGTGTAGGCAGTGAAGGTGGAGGTCTAGGT
          1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT

                                   *            *   *                
        559 GGTGGTGGTGGTTGTCCAGATACCGGTGGTGTAGGCGGTGGAGCTGGAGGTATAGGT
          1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT

                    
        616 GGTGGTGG
          1 GGTGGTGG

        624 CAGCGGCGGA


Statistics
Matches: 59,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  57   59  1.00

ACGTcount: A:0.14, C:0.09, G:0.51, T:0.26


Consensus pattern (57 bp):   
GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT
Done.