Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01036.N1

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: 2569
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33


Found at i:1010 original size:41 final size:42

Alignment explanation


    Indices: 950--1115  Score: 173
    Period size: 41  Copynumber: 4.1  Consensus size: 42

        940 ATTCGCGGCG

                                                      
        950 TTTGGA-TAAAAACGCCACTATAGCTCAACCTTTT-GCTGCA
          1 TTTGGACTAAAAACGCCACTATAGCTCAACCTTTTAGCTGCA

                           *           ** *        *  *
        990 TTTGGACTAAAAACGTCACTATTA--TTTAGCTTTTAGCAGCG
          1 TTTGGACTAAAAACGCCACTA-TAGCTCAACCTTTTAGCTGCA

                                  *       *           
       1031 TTTGGACTAAAAACGCCACTATTGCTCAA-TTTTTAGCTGCA
          1 TTTGGACTAAAAACGCCACTATAGCTCAACCTTTTAGCTGCA

            *      *              *            *      
       1072 GTTGGACCAAAAACGCCACTATTGCTCAA-CTTTTTGCTGCA
          1 TTTGGACTAAAAACGCCACTATAGCTCAACCTTTTAGCTGCA

               
       1113 TTT
          1 TTT

       1116 TCCTACTAGC


Statistics
Matches: 103,  Mismatches: 18, Indels: 9
        0.79            0.14        0.07

Matches are distributed among these distances:
  40   14  0.14
  41   85  0.83
  42    4  0.04

ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34


Consensus pattern (42 bp):   
TTTGGACTAAAAACGCCACTATAGCTCAACCTTTTAGCTGCA

Found at i:1105 original size:82 final size:81

Alignment explanation


    Indices: 947--1105  Score: 212
    Period size: 82  Copynumber: 2.0  Consensus size: 81

        937 TATATTCGCG

                                                       *      *       *      
        947 GCGTTTGGATAAAAACGCCACTATAGCTCAACCTTTTGCTGCATTTGGACTAAAAACGTCACTAT
          1 GCGTTTGGATAAAAACGCCACTATAGCTCAACCTTTTGCTGCAGTTGGACCAAAAACGCCACTAT

              * * *         
       1012 TATTTAGCTTTTAGCA
         66 TACTCAACTTTTAGCA

                                     *       *                               
       1028 GCGTTTGGACTAAAAACGCCACTATTGCTCAA-TTTTTAGCTGCAGTTGGACCAAAAACGCCACT
          1 GCGTTTGGA-TAAAAACGCCACTATAGCTCAACCTTTT-GCTGCAGTTGGACCAAAAACGCCACT

               *          
       1092 ATTGCTCAACTTTT
         64 ATTACTCAACTTTT

       1106 TGCTGCATTT


Statistics
Matches: 67,  Mismatches: 9, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  81   13  0.19
  82   54  0.81

ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32


Consensus pattern (81 bp):   
GCGTTTGGATAAAAACGCCACTATAGCTCAACCTTTTGCTGCAGTTGGACCAAAAACGCCACTAT
TACTCAACTTTTAGCA

Found at i:1489 original size:17 final size:17

Alignment explanation


    Indices: 1457--1503  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

       1447 AAACAATATT

                   *         
       1457 TTAAAATGAT-AAAATC
          1 TTAAAATAATAAAAATC

                             
       1473 TTAAAATAATAAAAATC
          1 TTAAAATAATAAAAATC

            *        *    
       1490 GTAAAATAACAAAA
          1 TTAAAATAATAAAA

       1504 TCACCGAATA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  16    9  0.33
  17   18  0.67

ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26


Consensus pattern (17 bp):   
TTAAAATAATAAAAATC
Done.