Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00179.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: 1895
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26


Found at i:795 original size:66 final size:66

Alignment explanation


    Indices: 689--1065  Score: 601
    Period size: 66  Copynumber: 5.7  Consensus size: 66

        679 CAAAAGGAAA

                                    *                        *               
        689 AAAGAGAAAATAACCTCATTGATGTTGGTGTGGCTGCAAATAACCCAGTCTGCATCGACAAAGAG
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG

             
        754 G
         66 G

                          *                                  *         *     
        755 AAAGAGAAAATAACGTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTCTGCATCGACGAAGAG
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG

             
        820 G
         66 G

                    *                 *                            *         
        821 AAAGAGAATATAACCTCATTGATGGTTGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAG
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG

             
        886 G
         66 G

            *                                                      *         
        887 CAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAG
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG

             
        952 G
         66 G

            *               *                     *                   *      
        953 CAAGAGAAAATAACCTAATTGATGGTGGTGTGGCTGCATATAACCCAGTATGCATCGAAAAAGAG
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG

             
       1018 G
         66 G

                    *       *     *                        
       1019 AAAGAGAATATAACCTAATTGACGGTGGTGTGGCTGCAAATAACCCA
          1 AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCA

       1066 ACTTTACTGG


Statistics
Matches: 291,  Mismatches: 20, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  66  291  1.00

ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21


Consensus pattern (66 bp):   
AAAGAGAAAATAACCTCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAG
G

Found at i:1106 original size:132 final size:128

Alignment explanation


    Indices: 706--1106  Score: 387
    Period size: 132  Copynumber: 3.0  Consensus size: 128

        696 AAATAACCTC

                   *                        *                              * 
        706 ATTGATGTTGGTGTGGCTGCAAATAACCCAGTCTGCATCGACAAAGAGGAAAGAGAAAATAACGT
          1 ATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAGGAAAGAGAAAATAACCT

                                            *        * **                    
        771 CATTGATGGTGGTGTGGCTGCAAATAACCCA-GTCT-GCATCGACGAAGAG-GAAAGAGAATATA
         66 CATTGATGGTGGTGTGGCTGCAAATAACCCATATCTGGCATGGGGGAAGAGAG-AAG-GAATAT-

                
        833 ACCT
        128 ---T

                      *                            *          *              
        837 CATTGATGGTTGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAGGCAAGAGAAAATAACC
          1 -ATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAGGAAAGAGAAAATAACC

                                                          * *  *         **  
        902 TCATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATGGACAAAGAGGCAAGAGA-AAATAA
         65 TCATTGATGGTGGTGTGGCTGCAAATAACCCA-TAT-C-TGG-C-ATGGGGGAAGAGAGAAGGAA

            ** *
        966 CCTA
        125 TATT

                                 *                   *               *       
        970 ATTGATGGTGGTGTGGCTGCATATAACCCAGTATGCATCGAAAAAGAGGAAAGAGAATATAACCT
          1 ATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAGGAAAGAGAAAATAACCT

            *     *                           *                  *   *   *   
       1035 AATTGACGGTGGTGTGGCTGCAAATAACCCAACTTTACTGGCTATGGGGGAAGTGAGCAGGGATA
         66 CATTGATGGTGGTGTGGCTGCAAATAACCC-A-TAT-CTGGC-ATGGGGGAAGAGAGAAGGAATA

              
       1100 TT
        127 TT

                 
       1102 ATTGA
          1 ATTGA

       1107 CAAAAACGTT


Statistics
Matches: 218,  Mismatches: 41, Indels: 20
        0.78            0.15        0.07

Matches are distributed among these distances:
 131   10  0.05
 132  188  0.86
 133    4  0.02
 134    1  0.00
 135    1  0.00
 136    1  0.00
 137    4  0.02
 138    3  0.01
 139    6  0.03

ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22


Consensus pattern (128 bp):   
ATTGATGGTGGTGTGGCTGCAAATAACCCAGTATGCATCGACAAAGAGGAAAGAGAAAATAACCT
CATTGATGGTGGTGTGGCTGCAAATAACCCATATCTGGCATGGGGGAAGAGAGAAGGAATATT
Done.