Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01031.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: 3996
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31


Found at i:3222 original size:28 final size:25

Alignment explanation


    Indices: 3164--3222  Score: 64
    Period size: 28  Copynumber: 2.2  Consensus size: 25

       3154 GTTTTTTATA

                                     
       3164 AAAAAATAATATAAAAAAATTAAAT
          1 AAAAAATAATATAAAAAAATTAAAT

             *     *                  * 
       3189 ACAAAATGATATAATATACAAATTAATT
          1 AAAAAATAATATAA-A-A-AAATTAAAT

                  
       3217 AAAAAA
          1 AAAAAA

       3223 AGTTGATTTT


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  25   12  0.44
  26    1  0.04
  27    1  0.04
  28   13  0.48

ACGTcount: A:0.69, C:0.03, G:0.02, T:0.25


Consensus pattern (25 bp):   
AAAAAATAATATAAAAAAATTAAAT

Found at i:3532 original size:128 final size:131

Alignment explanation


    Indices: 3367--3624  Score: 396
    Period size: 128  Copynumber: 1.9  Consensus size: 131

       3357 TATATATATA

                *                                                            
       3367 TTTGGAAATTATACACAACCATAAATACACAACGAAAAAAAATATTTTCTTTTGTGGTGTCAAG-
          1 TTTGAAAATTATACACAACCATAAATACACAACGAAAAAAAATATTTTCTTTTGTGGTGTCAAGC

                                                                             
       3431 T-C-TCGGTGGCACCTAAGGGTGTTCAAATGGTTAACCGTTTAGTTGATCGAACCGAACTAGTAT
         66 TACATCGGTGGCACCTAAGGGTGTTCAAATGGTTAACCGTTTAGTTGATCGAACCGAACTAGTAT

             
       3494 T
        131 T

                                       *    *                                
       3495 TTTGAAAATTATACACAACCATAAATATACAATGAAAAAAAATATTTTCTTTTGTGGTGTCAAGT
          1 TTTGAAAATTATACACAACCATAAATACACAACGAAAAAAAATATTTTCTTTTGTGGTGTCAAG-

                                                                        *    
       3560 CACTTGACACATCGGTGGCACCTAAGGGTGTTCAAATGGTTAACCGTTTAGTTGATCGAATCGAA
         65 --C-T---ACATCGGTGGCACCTAAGGGTGTTCAAATGGTTAACCGTTTAGTTGATCGAACCGAA

       3625 TTAATATTAA


Statistics
Matches: 116,  Mismatches: 4, Indels: 10
        0.89            0.03        0.08

Matches are distributed among these distances:
 128   61  0.53
 133    1  0.01
 137    1  0.01
 138   53  0.46

ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31


Consensus pattern (131 bp):   
TTTGAAAATTATACACAACCATAAATACACAACGAAAAAAAATATTTTCTTTTGTGGTGTCAAGC
TACATCGGTGGCACCTAAGGGTGTTCAAATGGTTAACCGTTTAGTTGATCGAACCGAACTAGTAT
T
Done.