Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g01393.N4

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: 2485
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25


Found at i:1993 original size:64 final size:64

Alignment explanation


    Indices: 1914--2038  Score: 178
    Period size: 64  Copynumber: 2.0  Consensus size: 64

       1904 TCATTCATAA

                                                             *              
       1914 CACATATAGTTAGGAGCATTGGATTCATGTCGATCATAGCATCCTAACTCTTTGACATAAGCAT
          1 CACATATAGTTAGGAGCATTGGATTCATGTCGATCATAGCATCCTAACTATTTGACATAAGCAT

                 *              *       *         **       *      *      
       1978 CACATCTAGTTAGGAGCATTTGATTCATTTCGATCATATTATCCTAATTATTTGGCATAAG
          1 CACATATAGTTAGGAGCATTGGATTCATGTCGATCATAGCATCCTAACTATTTGACATAAG

       2039 TATAGATACA


Statistics
Matches: 53,  Mismatches: 8, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  64   53  1.00

ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35


Consensus pattern (64 bp):   
CACATATAGTTAGGAGCATTGGATTCATGTCGATCATAGCATCCTAACTATTTGACATAAGCAT

Found at i:2193 original size:44 final size:43

Alignment explanation


    Indices: 2145--2278  Score: 121
    Period size: 44  Copynumber: 3.0  Consensus size: 43

       2135 AAACAGGCTA

                                                        
       2145 AAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
          1 AAAATTGCAG-TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG

                        *    * *       *          *    *   
       2189 AAAATGGTG-AGCCTTAACCCCCTAAGTAGTAG-GGAAACAG-GCTG
          1 AAAAT--TGCAGTCTTATCTCCCTAAGCAGTAGTGG-AGCAGATC-G

                             *                    *     
       2233 AAAATTGCAGGTCTTATATCCCTAAGCAGTAGTGGAGCGGATCG
          1 AAAATTGCA-GTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG

              
       2277 AA
          1 AA

       2279 GACGGTGAGC


Statistics
Matches: 68,  Mismatches: 14, Indels: 16
        0.69            0.14        0.16

Matches are distributed among these distances:
  42    2  0.03
  43    4  0.06
  44   55  0.81
  45    5  0.07
  46    2  0.03

ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22


Consensus pattern (43 bp):   
AAAATTGCAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG

Found at i:2259 original size:88 final size:88

Alignment explanation


    Indices: 2110--2485  Score: 486
    Period size: 88  Copynumber: 4.3  Consensus size: 88

       2100 TGAATTCACT

                       *            *         *                              
       2110 AGCCTTAACCCTCTAAGCAGTAGGAAAACAGGCTAAAAATTGCAGATCTTATCTCCCTAAGCAGT
          1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTGCAGATCTTATCTCCCTAAGCAGT

                              *    
       2175 AGTGGAGCAGATCGAAAATGGTG
         66 AGTGGAGCAGATCGAAAACGGTG

                             *                           *      *            
       2198 AGCCTTAACCCCCTAAGTAGTAGGGAAACAGGCTGAAAATTGCAGGTCTTATATCCCTAAGCAGT
          1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTGCAGATCTTATCTCCCTAAGCAGT

                    *       *      
       2263 AGTGGAGCGGATCGAAGACGGTG
         66 AGTGGAGCAGATCGAAAACGGTG

               *     **      *            * *  *     *     *                 
       2286 AGCTTTAACATCCTAAGTAGTAGGGAAACAAGTTGGAAATTACAGATTTTATCTCCCTAAGCAGT
          1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTGCAGATCTTATCTCCCTAAGCAGT

             *      *       *      
       2351 AATGGAGCGGATCGAAGACGGTG
         66 AGTGGAGCAGATCGAAAACGGTG

               *       *                       *     *                  *    
       2374 AGCTTTAACCCTCTAAGCAGTAGGGAAACAGGCTGGAAATTCCAGATCTTATCTCCCTAAACAGT
          1 AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTGCAGATCTTATCTCCCTAAGCAGT

                     *              
       2439 AGTGGAGCAAATC-AAAGACGGTG
         66 AGTGGAGCAGATCGAAA-ACGGTG

                                     
       2462 AGCCTTAA-CCCCTAAGCAGTAGGG
          1 AGCCTTAACCCCCTAAGCAGTAGGG


Statistics
Matches: 252,  Mismatches: 35, Indels: 3
        0.87            0.12        0.01

Matches are distributed among these distances:
  87   17  0.07
  88  235  0.93

ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22


Consensus pattern (88 bp):   
AGCCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAAATTGCAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAAACGGTG

Done.