Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01542.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, 327

Length: 546
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41


Found at i:346 original size:101 final size:100

Alignment explanation


    Indices: 1--518  Score: 398
    Period size: 101  Copynumber: 5.3  Consensus size: 100

                 *   *             *            *  **         *            * 
          1 AAATGCTCTATTAATTTTGCATTTAATAAAATCTTGGCAAAGTAGTTTGGTTGGGTAGTTTGGGA
          1 AAATGTTCTCTTAATTTTGCATTCAATAAAAT-TTGTCAGGGTAGTTTGGCTGGGTAGTTTGGCA

                   *      *   *                 
         66 TGACAGTTTATTTCGTCCTAATTTGAATGCTTATAA
         65 TGACAGTCTATTTCATCCCAATTTGAATGCTTATAA

                        *               *  *    *    *       **           *  
        102 AAATG-TCTTCTAAATTTTGCATTCAATCAATTTTGGCAGGATAGTTTGATTGGGTAGTTTGACA
          1 AAATGTTC-TCTTAATTTTGCATTCAATAAAATTTGTCAGGGTAGTTTGGCTGGGTAGTTTGGCA

                    *                           
        166 TGACAGTCCATTTCATCCCAA--TG--T--TTATAA
         65 TGACAGTCTATTTCATCCCAATTTGAATGCTTATAA

                          *             *             * * *      * *         
        196 AAAT-TTCCTCTTATTTTTGCATTCAATCAAATTCT-TCTAGAGCAATTTGGCAGAGTAGTTTGG
          1 AAATGTT-CTCTTAATTTTGCATTCAATAAAATT-TGTC-AGGGTAGTTTGGCTGGGTAGTTTGG

               *            *                      
        259 CATAACAGTCTATTTCGTCCCAATTTGAACT-CTTATAA
         63 CATGACAGTCTATTTCATCCCAATTTGAA-TGCTTATAA

                                *  *                  *         *            
        297 AAATGTTCTCTTAATTTTGCTTTTAATAAAAATTTGTCAGGGCAGTTTGGCTTGGTAGTTTGGCA
          1 AAATGTTCTCTTAATTTTGCATTCAAT-AAAATTTGTCAGGGTAGTTTGGCTGGGTAGTTTGGCA

                             *            *   **
        362 TGACAGTCTATTTCATCTCAATTTGAATGCCTATTG
         65 TGACAGTCTATTTCATCCCAATTTGAATGCTTATAA

                  *                     *                     *              
        398 AAATGTCCTCTTAATTTTGCATTCAAT-CAATTT-T-----T-G--T---AGGGTAGTTTGGCAT
          1 AAATGTTCTCTTAATTTTGCATTCAATAAAATTTGTCAGGGTAGTTTGGCTGGGTAGTTTGGCAT

                     *          *             *
        450 GACAGTCTACTTCATCCCAAATTGAATGCTTATAG
         66 GACAGTCTATTTCATCCCAATTTGAATGCTTATAA

                  *     *     *               
        485 AAATGTCCTCTTGATTTTTCATTCAATAAAATTT
          1 AAATGTTCTCTTAATTTTGCATTCAATAAAATTT

        519 TGGTAGGGCC


Statistics
Matches: 340,  Mismatches: 61, Indels: 45
        0.76            0.14        0.10

Matches are distributed among these distances:
  87   68  0.20
  88    5  0.01
  90    1  0.00
  92    1  0.00
  94   34  0.10
  95   38  0.11
  96    1  0.00
  97    2  0.01
  98    3  0.01
  99    5  0.01
 100   47  0.14
 101  126  0.37
 102    9  0.03

ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41


Consensus pattern (100 bp):   
AAATGTTCTCTTAATTTTGCATTCAATAAAATTTGTCAGGGTAGTTTGGCTGGGTAGTTTGGCAT
GACAGTCTATTTCATCCCAATTTGAATGCTTATAA

Found at i:496 original size:87 final size:88

Alignment explanation


    Indices: 350--526  Score: 266
    Period size: 87  Copynumber: 2.0  Consensus size: 88

        340 AGTTTGGCTT

                                  *      *   *            *                  
        350 GGTAGTTTGGCATGACAGTCTATTTCATCTCAATTTGAATGCCTATTGAAATGTCCTCTTAATTT
          1 GGTAGTTTGGCATGACAGTCTACTTCATCCCAAATTGAATGCCTATAGAAATGTCCTCTTAATTT

                       *      *    
        415 TGCATTCAAT-CAATTTTTGTAG
         66 TGCATTCAATAAAATTTTGGTAG

                                                      *                 *    
        437 GGTAGTTTGGCATGACAGTCTACTTCATCCCAAATTGAATGCTTATAGAAATGTCCTCTTGATTT
          1 GGTAGTTTGGCATGACAGTCTACTTCATCCCAAATTGAATGCCTATAGAAATGTCCTCTTAATTT

             *                     
        502 TTCATTCAATAAAATTTTGGTAG
         66 TGCATTCAATAAAATTTTGGTAG

              
        525 GG
          1 GG

        527 CCATTTGGTT


Statistics
Matches: 80,  Mismatches: 9, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  87   68  0.85
  88   12  0.15

ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40


Consensus pattern (88 bp):   
GGTAGTTTGGCATGACAGTCTACTTCATCCCAAATTGAATGCCTATAGAAATGTCCTCTTAATTT
TGCATTCAATAAAATTTTGGTAG
Done.