Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00948.P1

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: 4503
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32


Found at i:993 original size:19 final size:20

Alignment explanation


    Indices: 957--994  Score: 51
    Period size: 19  Copynumber: 1.9  Consensus size: 20

        947 TTAGATTGTT

                       * *      
        957 AAAATAATAATTATATAAAA
          1 AAAATAATAATCAGATAAAA

                               
        977 AAAATAA-AATCAGATAAA
          1 AAAATAATAATCAGATAAA

        995 GTACAATGAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  19    9  0.56
  20    7  0.44

ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24


Consensus pattern (20 bp):   
AAAATAATAATCAGATAAAA

Found at i:1666 original size:18 final size:17

Alignment explanation


    Indices: 1611--1667  Score: 51
    Period size: 18  Copynumber: 3.2  Consensus size: 17

       1601 AAAAAATTGT

                *    *       
       1611 AAATCATAATAATATAA
          1 AAATAATAAAAATATAA

                   *        *  
       1628 AAATAGAGAAAAATAGAAA
          1 AAATA-ATAAAAATA-TAA

                           * 
       1647 AAATAATAAAAATATTA
          1 AAATAATAAAAATATAA

                
       1664 AAAT
          1 AAAT

       1668 TAAAATATTT


Statistics
Matches: 31,  Mismatches: 7, Indels: 4
        0.74            0.17        0.10

Matches are distributed among these distances:
  17    9  0.29
  18   15  0.48
  19    7  0.23

ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23


Consensus pattern (17 bp):   
AAATAATAAAAATATAA

Found at i:1934 original size:22 final size:21

Alignment explanation


    Indices: 1907--1974  Score: 82
    Period size: 22  Copynumber: 3.1  Consensus size: 21

       1897 AATTGATATT

                      *           
       1907 AACTTATAAAAATTATAATAAA
          1 AACTTATAAATATTATAA-AAA

                   *             
       1929 AACTTATGAATATTATAAAAA
          1 AACTTATAAATATTATAAAAA

                 *                 
       1950 AATCTAATAAATTATTATAAAAA
          1 AA-CTTATAAA-TATTATAAAAA

              
       1973 AA
          1 AA

       1975 TTAGAACATT


Statistics
Matches: 40,  Mismatches: 4, Indels: 3
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    5  0.12
  22   22  0.55
  23   13  0.32

ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32


Consensus pattern (21 bp):   
AACTTATAAATATTATAAAAA

Found at i:1963 original size:20 final size:21

Alignment explanation


    Indices: 1916--1972  Score: 64
    Period size: 21  Copynumber: 2.7  Consensus size: 21

       1906 TAACTTATAA

                             *   
       1916 AAATTATAATAAAAACTTATG
          1 AAATTATAATAAAAACTAATG

                                   
       1937 AATATTATAA-AAAAATCTAAT-
          1 AA-ATTATAATAAAAA-CTAATG

                   *       
       1958 AAATTATTATAAAAA
          1 AAATTATAATAAAAA

       1973 AATTAGAACA


Statistics
Matches: 31,  Mismatches: 2, Indels: 6
        0.79            0.05        0.15

Matches are distributed among these distances:
  20    6  0.19
  21   14  0.45
  22   11  0.35

ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33


Consensus pattern (21 bp):   
AAATTATAATAAAAACTAATG

Done.