Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02404.M1

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: 5432
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:1999 original size:210 final size:210

Alignment explanation


    Indices: 1635--2474  Score: 1240
    Period size: 210  Copynumber: 4.0  Consensus size: 210

       1625 CAATCTATAA

                                                            *                
       1635 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA

               *                       *                *                    
       1700 GTTCCCTCAGC-GAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCTG
         66 GTTTCCTCA-CAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                                *                                         *  
       1764 ACAATTTATCCCAT-T-CTGGTTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGTAT
        130 ACAATTTA-CCC-TGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAAT

                       *      
       1827 CTGTCATCAGTAATCCAT
        193 CTGTCATCAGTGATCCAT

                                *         *    *                             
       1845 TTGAATCCTCTGCCTCATCCGATATCATTTTAAGTGAA-GAGATCTCCACGAGTTTACCTGATCC
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAG-CAATGAGATCTCCACGAGTTTACCTGATCC

                     *                    *                              *   
       1909 AGTTTCCTCGCAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTG
         65 AGTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                                                       *        *            
       1974 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCTCAAGTGGAATCT
        130 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT

                   *        
       2039 GTCATCAATGATCCAT
        195 GTCATCAGTGATCCAT

                                         *         *         *               
       2055 TTGAATCCTCTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA

            *                         *                 *                   *
       2120 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCTGGGAAATCTTCTGATCCTGT
         66 GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA

                                            *                                
       2185 CAATTTACCCTGTACTGATTTATACATGAGTGGTGAAATTCATAAAAATTCACAAGTGGAATCTG
        131 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG

                *          
       2250 TCATTAGTGATCCAT
        196 TCATCAGTGATCCAT

               *                        *           *        *               
       2265 TTGTATCCTCTGCCTCATCCAATATCATCTCTAA-CAATGGGATCTCCATGAGTTTACCTGATCC
          1 TTGAATCCTCTGCCTCATCCAATATCATTTC-AAGCAATGAGATCTCCACGAGTTTACCTGATCC

                                  *       *          *   *   *               
       2329 AGTTTCCTCACAGAATTTTGCCGGTGAACATATGTTGCAAAACTCGGGGGAATCTTCTGATCCTG
         65 AGTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                      *             *  **                   *                
       2394 ACAATTTACCATGTACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCT
        130 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT

                     *      
       2459 GTCATCAGTCATCCAT
        195 GTCATCAGTGATCCAT

       2475 CATCATCCTC


Statistics
Matches: 569,  Mismatches: 55, Indels: 12
        0.89            0.09        0.02

Matches are distributed among these distances:
 208    1  0.00
 209    7  0.01
 210  557  0.98
 211    4  0.01

ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33


Consensus pattern (210 bp):   
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT

Found at i:4553 original size:55 final size:55

Alignment explanation


    Indices: 4470--4602  Score: 225
    Period size: 55  Copynumber: 2.4  Consensus size: 55

       4460 CCAGTCTATA

                      *                    *                       
       4470 ACATA-TTTTGTCCATTACTTTTCATTTGTTTCAATACACCCATCATTATCATTT
          1 ACATATTTTTTTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT

                                                                   
       4524 ACATATTTTTTTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
          1 ACATATTTTTTTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT

                                     
       4579 ACAT-TTTTTTGTCCATTACTTTTC
          1 ACATATTTTTT-TCCATTACTTTTC

       4603 TTGCAATTGT


Statistics
Matches: 75,  Mismatches: 2, Indels: 3
        0.94            0.03        0.04

Matches are distributed among these distances:
  54   11  0.15
  55   64  0.85

ACGTcount: A:0.24, C:0.23, G:0.03, T:0.50


Consensus pattern (55 bp):   
ACATATTTTTTTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
Done.