Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga09g00857.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: 3346
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:1154 original size:159 final size:158

Alignment explanation


    Indices: 865--1340  Score: 612
    Period size: 159  Copynumber: 3.0  Consensus size: 158

        855 TTACTCCTAG

                            * *   *                                          
        865 CAGTGGCCTTCACAGAGTACTTCCTTCAGAAATCTTTGAACAACGCAGCGTTGAGAGATCTGGAT
          1 CAGTGGCCTTCACAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCGTTGAGAGATCTGGAT

              **      *                      *                               
        930 TTTCTGGAAGAAGTGATGAAAGAGATTCAGGAAGCAGTTATGGGAAAAGAAGAAATAATGGAAAT
         66 TTAGTGGAAGCAGTGATGAAAGAGATTCAGGAAACAGTTATGGG-AAAGAAGAAATAATGGAAAT

                        *            *   
        995 GGTAAAGAATCTGAAAAACATGGTGGTCA
        130 GGTAAAGAATCTCAAAAACATGGTGATCA

                                       *                    *       *        
       1024 CAGTGGCCTTCACAGAATGCTTTCTTCTGAAATCTTTGAACAACGCAGTGTTGAGAAATCTGGAT
          1 CAGTGGCCTTCACAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCGTTGAGAGATCTGGAT

                                              **             *       *       
       1089 TTAGTGGAAGCAGTGATGAAAGAGATTCAGGAAATGGTTATGGTGAAAGGAGAAATATTGGAAAT
         66 TTAGTGGAAGCAGTGATGAAAGAGATTCAGGAAACAGTTATGG-GAAAGAAGAAATAATGGAAAT

             *            *             *
       1154 GTTAAAGAATCTCAGAAACATGGTGATCG
        130 GGTAAAGAATCTCAAAAACATGGTGATCA

                 *      * *               * *  *    *        **              
       1183 CAGTGTCCTTCATAAAATGCTTTCTTCAGATACCTATGAAAAACGCAGCACTGAGAGATCTGGAT
          1 CAGTGGCCTTCACAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCGTTGAGAGATCTGGAT

                                   *             *                  *        
       1248 TTAGTGG-AGCAAGTGATGAAAGGGATTCAGGAAACAATTATGGGGAAAGAAGAAAAAATGGAAA
         66 TTAGTGGAAGC-AGTGATGAAAGAGATTCAGGAAACAGTTAT-GGGAAAGAAGAAATAATGGAAA

                              *    *     
       1312 TGGTAAAGAATCTCAAAAGCATGTTGATC
        129 TGGTAAAGAATCTCAAAAACATGGTGATC

       1341 GCAAGAGAAT


Statistics
Matches: 272,  Mismatches: 42, Indels: 6
        0.85            0.13        0.02

Matches are distributed among these distances:
 158    3  0.01
 159  266  0.98
 160    3  0.01

ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25


Consensus pattern (158 bp):   
CAGTGGCCTTCACAGAATGCTTTCTTCAGAAATCTTTGAACAACGCAGCGTTGAGAGATCTGGAT
TTAGTGGAAGCAGTGATGAAAGAGATTCAGGAAACAGTTATGGGAAAGAAGAAATAATGGAAATG
GTAAAGAATCTCAAAAACATGGTGATCA

Found at i:2583 original size:72 final size:72

Alignment explanation


    Indices: 2401--2586  Score: 246
    Period size: 72  Copynumber: 2.6  Consensus size: 72

       2391 CAGCTCCTGC

                     *                 *          *     **                ** 
       2401 ACAATCCCCGGGGTGGCAAGCACTTCATGCCCATGTCACGGGGCCTGGCTTGCAGTATTCACTGG
          1 ACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGGCAAGGCTTGCAGTATTCACCAG

                *  
       2466 CACCTGT
         66 CACCAGT

                                  *   *                          *           
       2473 ACAATCCCCTGGGTGGCAAGCAGTTCGAGCCCATGTCATGGGGCAAGGCTTGCGGTATTCACCAG
          1 ACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGGCAAGGCTTGCAGTATTCACCAG

             **    
       2538 CTTCAGT
         66 CACCAGT

                                *                     
       2545 ACAATCCCCTGGGTGGCAAGTACTTCAAGCCCATGTCATGGG
          1 ACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGG

       2587 TTATGCAGTG


Statistics
Matches: 98,  Mismatches: 16, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  72   98  1.00

ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22


Consensus pattern (72 bp):   
ACAATCCCCTGGGTGGCAAGCACTTCAAGCCCATGTCATGGGGCAAGGCTTGCAGTATTCACCAG
CACCAGT
Done.