Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3134

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: 18914
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36


Found at i:400 original size:41 final size:42

Alignment explanation


    Indices: 347--431  Score: 154
    Period size: 41  Copynumber: 2.0  Consensus size: 42

        337 GATACAGTTA

                                                      
        347 TTAATTTGAGCATCAATTTATCATTCATCACTC-ACAATTAT
          1 TTAATTTGAGCATCAATTTATCATTCATCACTCAACAATTAT

                                               *      
        388 TTAATTTGAGCATCAATTTATCATTCATCACTCAATAATTAT
          1 TTAATTTGAGCATCAATTTATCATTCATCACTCAACAATTAT

              
        430 TT
          1 TT

        432 TCCCACAATC


Statistics
Matches: 42,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  41   33  0.79
  42    9  0.21

ACGTcount: A:0.34, C:0.18, G:0.05, T:0.44


Consensus pattern (42 bp):   
TTAATTTGAGCATCAATTTATCATTCATCACTCAACAATTAT

Found at i:2247 original size:42 final size:41

Alignment explanation


    Indices: 2093--2248  Score: 158
    Period size: 42  Copynumber: 3.7  Consensus size: 41

       2083 TATGTTATCG

                                                     * 
       2093 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
          1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA

                        *         * *                   *
       2135 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
          1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA

                                                        
       2179 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
          1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA

                                        
       2221 TGTAAGACCACGTCTGGGACGTTGGCAT
          1 TGTAAGACCACGTCTGGGACGTTGGCAT

       2249 TGTCCGATTT


Statistics
Matches: 94,  Mismatches: 9, Indels: 22
        0.75            0.07        0.18

Matches are distributed among these distances:
  41    3  0.03
  42   53  0.56
  43    8  0.09
  44   28  0.30
  45    2  0.02

ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30


Consensus pattern (41 bp):   
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA

Found at i:9569 original size:42 final size:41

Alignment explanation


    Indices: 9415--9570  Score: 158
    Period size: 42  Copynumber: 3.7  Consensus size: 41

       9405 TATGTTATCG

                                                     * 
       9415 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
          1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA

                        *         * *                   *
       9457 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
          1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA

                                                        
       9501 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
          1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA

                                        
       9543 TGTAAGACCACGTCTGGGACGTTGGCAT
          1 TGTAAGACCACGTCTGGGACGTTGGCAT

       9571 TGTTTTTTTT


Statistics
Matches: 94,  Mismatches: 9, Indels: 22
        0.75            0.07        0.18

Matches are distributed among these distances:
  41    3  0.03
  42   53  0.56
  43    8  0.09
  44   28  0.30
  45    2  0.02

ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30


Consensus pattern (41 bp):   
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA

Found at i:16887 original size:42 final size:41

Alignment explanation


    Indices: 16733--16888  Score: 158
    Period size: 42  Copynumber: 3.7  Consensus size: 41

      16723 TATGTTATCG

                                                     * 
      16733 TGTAAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTA
          1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATT--GATTCA

                        *         * *                   *
      16775 TGTATAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTTCG
          1 TG--TAAGACCACGTCTGGGACGTTGGCATCGATA-TTGA-TTCA

                                                        
      16819 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTGATTACA
          1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTGATT-CA

                                        
      16861 TGTAAGACCACGTCTGGGACGTTGGCAT
          1 TGTAAGACCACGTCTGGGACGTTGGCAT

      16889 TGTCGATTTT


Statistics
Matches: 94,  Mismatches: 9, Indels: 22
        0.75            0.07        0.18

Matches are distributed among these distances:
  41    3  0.03
  42   53  0.56
  43    8  0.09
  44   28  0.30
  45    2  0.02

ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30


Consensus pattern (41 bp):   
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTGATTCA
Done.