Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00281.F2

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: 4760
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35


Found at i:2820 original size:110 final size:110

Alignment explanation


    Indices: 2627--2848  Score: 426
    Period size: 110  Copynumber: 2.0  Consensus size: 110

       2617 TTCATACTCT

                       *                                                     
       2627 CTATAAGTTGATGACTTGATGGTATCATCTGTTTTCATGAATGTGTCATGCTTTTCTGCATGGCA
          1 CTATAAGTTGAAGACTTGATGGTATCATCTGTTTTCATGAATGTGTCATGCTTTTCTGCATGGCA

                                                         
       2692 TTCTCTTTTTATTTCATGGTCCTTAAGGTGATTTTGCTAGTATCA
         66 TTCTCTTTTTATTTCATGGTCCTTAAGGTGATTTTGCTAGTATCA

                                 *                                           
       2737 CTATAAGTTGAAGACTTGATGTTATCATCTGTTTTCATGAATGTGTCATGCTTTTCTGCATGGCA
          1 CTATAAGTTGAAGACTTGATGGTATCATCTGTTTTCATGAATGTGTCATGCTTTTCTGCATGGCA

                                                         
       2802 TTCTCTTTTTATTTCATGGTCCTTAAGGTGATTTTGCTAGTATCA
         66 TTCTCTTTTTATTTCATGGTCCTTAAGGTGATTTTGCTAGTATCA

              
       2847 CT
          1 CT

       2849 TGTTAAAAAT


Statistics
Matches: 110,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
 110  110  1.00

ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45


Consensus pattern (110 bp):   
CTATAAGTTGAAGACTTGATGGTATCATCTGTTTTCATGAATGTGTCATGCTTTTCTGCATGGCA
TTCTCTTTTTATTTCATGGTCCTTAAGGTGATTTTGCTAGTATCA

Found at i:4132 original size:39 final size:39

Alignment explanation


    Indices: 4075--4239  Score: 215
    Period size: 39  Copynumber: 4.2  Consensus size: 39

       4065 CATGCTTCCA

                       * *          *    *         
       4075 CAGCAAATGCCTGTGGGCCAGATGAGTTCCATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

              *         *                          
       4114 CATCAAATGCCAACGGGCCAGATGGGTTCAATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

                  *    * *                          
       4153 CAGCAAGTG-CTGGGGGCCCAGATGGGTTCAATGTATCCT
          1 CAGCAAATGCCAGCGGG-CCAGATGGGTTCAATGTATCCT

                          *              *         
       4192 CAGCAAATGCCAGCTGGCCAGATGGGTTCGATGTATCCT
          1 CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

                     
       4231 CAGCAAATG
          1 CAGCAAATG

       4240 TATGGCAACC


Statistics
Matches: 108,  Mismatches: 16, Indels: 4
        0.84            0.12        0.03

Matches are distributed among these distances:
  38    4  0.04
  39  100  0.93
  40    4  0.04

ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Consensus pattern (39 bp):   
CAGCAAATGCCAGCGGGCCAGATGGGTTCAATGTATCCT

Found at i:4211 original size:78 final size:78

Alignment explanation


    Indices: 4075--4239  Score: 242
    Period size: 78  Copynumber: 2.1  Consensus size: 78

       4065 CATGCTTCCA

                         *               *           *                       
       4075 CAGCAAATGCCTGTGGGCCAGATGAGTTCCATGTATCCTCATCAAATGCCAACGGGCCAGATGGG
          1 CAGCAAATGCCTGGGGGCCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGGG

                         
       4140 TTCAATGTATCCT
         66 TTCAATGTATCCT

                  *                  *                          * *          
       4153 CAGCAAGTG-CTGGGGGCCCAGATGGGTTCAATGTATCCTCAGCAAATGCCAGCTGGCCAGATGG
          1 CAGCAAATGCCTGGGGG-CCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGG

                *         
       4217 GTTCGATGTATCCT
         65 GTTCAATGTATCCT

                     
       4231 CAGCAAATG
          1 CAGCAAATG

       4240 TATGGCAACC


Statistics
Matches: 77,  Mismatches: 9, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
  77    6  0.08
  78   71  0.92

ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23


Consensus pattern (78 bp):   
CAGCAAATGCCTGGGGGCCAGATGAGTTCAATGTATCCTCAGCAAATGCCAACGGGCCAGATGGG
TTCAATGTATCCT

Done.