Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: evm.model.Scaffold78.109

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: 2208
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27


Found at i:198 original size:6 final size:6

Alignment explanation


    Indices: 189--213  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

        179 CCTCCTGCGA

                                         
        189 CGCCTC CGCCTC CGCCTC CGCCTC C
          1 CGCCTC CGCCTC CGCCTC CGCCTC C

        214 AAAAAACCGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.00, C:0.68, G:0.16, T:0.16


Consensus pattern (6 bp):   
CGCCTC

Found at i:1681 original size:39 final size:40

Alignment explanation


    Indices: 1622--1752  Score: 117
    Period size: 39  Copynumber: 3.4  Consensus size: 40

       1612 TCTTATGATA

                          **            *   *       
       1622 TCTCAGGGGCAAAGCCAAAATTA-GAAGTTTCTTGCAATG
          1 TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG

             *                                 *   *
       1661 TGTCAGGGGCAAAGAGAAAA-TATGAAGATTCCTGTAATT
          1 TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG

                    *                           *   *
       1700 TCTCAGGGCCAAAGAGAAAATCTA--AAGATTCCTGTAATT
          1 TCTCAGGGGCAAAGAGAAAAT-TATGAAGATTCCTGCAATG

             *      *     
       1739 TATCAGGGCCAAAG
          1 TCTCAGGGGCAAAG

       1753 GGAATATCAG


Statistics
Matches: 79,  Mismatches: 10, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  38    2  0.03
  39   75  0.95
  41    2  0.03

ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24


Consensus pattern (40 bp):   
TCTCAGGGGCAAAGAGAAAATTATGAAGATTCCTGCAATG

Found at i:1769 original size:39 final size:39

Alignment explanation


    Indices: 1663--1752  Score: 144
    Period size: 39  Copynumber: 2.3  Consensus size: 39

       1653 TTGCAATGTG

                  *            * *                *
       1663 TCAGGGGCAAAGAGAAAATATGAAGATTCCTGTAATTTC
          1 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA

                                                   
       1702 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA
          1 TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA

                        
       1741 TCAGGGCCAAAG
          1 TCAGGGCCAAAG

       1753 GGAATATCAG


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  39   47  1.00

ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23


Consensus pattern (39 bp):   
TCAGGGCCAAAGAGAAAATCTAAAGATTCCTGTAATTTA

Found at i:1783 original size:78 final size:78

Alignment explanation


    Indices: 1588--1783  Score: 198
    Period size: 78  Copynumber: 2.5  Consensus size: 78

       1578 TGAGACTTCT

                    *                   *             *     *            *   
       1588 GGGCCAAAAGGAAAATCAGAAGATTCTTATGATATCTCAGGGGCAAAGCCAAAATTAGAAGTTTC
          1 GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAATTAGAAGATTC

            *        *   
       1653 TTGCAATGTGTCA
         66 CTGCAATGTATCA

               *     *                 *   *  *               *              
       1666 GGGGCAAAGAGAAAAT-ATGAAGATTCCTGTAATTTCTCAGGGCCAAAGAGAAAATCTA-AAGAT
          1 GGGCCAAAGGGAAAATCA-GAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAAT-TAGAAGAT

                 *   *     
       1729 TCCTGTAATTTATCA
         64 TCCTGCAATGTATCA

                         *      *             *     
       1744 GGGCCAAAGGGAATATCAGAGGATTCTTGTGATAACTCAG
          1 GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAG

       1784 TTCTGATAAC


Statistics
Matches: 92,  Mismatches: 23, Indels: 6
        0.76            0.19        0.05

Matches are distributed among these distances:
  77    1  0.01
  78   88  0.96
  79    3  0.03

ACGTcount: A:0.37, C:0.15, G:0.23, T:0.24


Consensus pattern (78 bp):   
GGGCCAAAGGGAAAATCAGAAGATTCTTGTGATATCTCAGGGCCAAAGACAAAATTAGAAGATTC
CTGCAATGTATCA
Done.