Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g01612.F1

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, 575

Length: 959
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34


Found at i:268 original size:141 final size:141

Alignment explanation


    Indices: 14--270  Score: 370
    Period size: 141  Copynumber: 1.8  Consensus size: 141

          4 TTTATCATTT

                      * *       *        *                        *          
         14 TGAAACCTTCTTTACTCAACTCGACAACCGTGCTCACCCAGCCTCCATTGCTTGTTTCACCTCCG
          1 TGAAACCTTCCTCACTCAACCCGACAACCCTGCTCACCCAGCCTCCATTGCTTGCTTCACCTCCG

                       *            *          *                             
         79 GCCACTAGCCCTAAACTCTTCTCGGGCATGCCATATAGAAAGGCAAGAAGAGACTCACCTTTGTT
         66 GCCACTAGCCCCAAACTCTTCTCGAGCATGCCATAGAGAAAGGCAAGAAGAGACTCACCTTTGTT

                       
        144 TTTCTCCGTTC
        131 TTTCTCCGTTC

                                      *    *            **            **  *  
        155 TGAAACCTTCCTCACTCAACCCGACAGCCCTTCTCACCCAGCCTTTATTGCTTGCTTCGTCTTCG
          1 TGAAACCTTCCTCACTCAACCCGACAACCCTGCTCACCCAGCCTCCATTGCTTGCTTCACCTCCG

                           *                                   
        220 GCCACTAGCCCCAAATTCTTCTCGAGCATGCCATAGAGAAAGGCAAGAAGA
         66 GCCACTAGCCCCAAACTCTTCTCGAGCATGCCATAGAGAAAGGCAAGAAGA

        271 AAGCTACTTC


Statistics
Matches: 100,  Mismatches: 16, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
 141  100  1.00

ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26


Consensus pattern (141 bp):   
TGAAACCTTCCTCACTCAACCCGACAACCCTGCTCACCCAGCCTCCATTGCTTGCTTCACCTCCG
GCCACTAGCCCCAAACTCTTCTCGAGCATGCCATAGAGAAAGGCAAGAAGAGACTCACCTTTGTT
TTTCTCCGTTC

Found at i:610 original size:41 final size:37

Alignment explanation


    Indices: 565--651  Score: 93
    Period size: 37  Copynumber: 2.2  Consensus size: 37

        555 TGTTATACAA

                                              **     
        565 GCGTGTTATGGGGGCGGATGTATAGCTCTTCAGAGTATTTG
          1 GCGTGTTAT-GGGGCGGA--T-TAGCTCTTCAGAACATTTG

                     *  **                       
        606 GCGTGTTATTGGTTGGATTAGCTCTTCAGAACATTTG
          1 GCGTGTTATGGGGCGGATTAGCTCTTCAGAACATTTG

                     
        643 GCGTGTTAT
          1 GCGTGTTAT

        652 CGGTTAGATT


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  37   26  0.63
  38    1  0.02
  40    5  0.12
  41    9  0.22

ACGTcount: A:0.17, C:0.13, G:0.32, T:0.38


Consensus pattern (37 bp):   
GCGTGTTATGGGGCGGATTAGCTCTTCAGAACATTTG

Found at i:686 original size:37 final size:37

Alignment explanation


    Indices: 587--668  Score: 128
    Period size: 37  Copynumber: 2.2  Consensus size: 37

        577 GGCGGATGTA

                        **              *    *   
        587 TAGCTCTTCAGAGTATTTGGCGTGTTATTGGTTGGAT
          1 TAGCTCTTCAGAACATTTGGCGTGTTATCGGTTAGAT

                                                 
        624 TAGCTCTTCAGAACATTTGGCGTGTTATCGGTTAGAT
          1 TAGCTCTTCAGAACATTTGGCGTGTTATCGGTTAGAT

                    
        661 TAGCTCTT
          1 TAGCTCTT

        669 ATGAGCGTTT


Statistics
Matches: 41,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  37   41  1.00

ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41


Consensus pattern (37 bp):   
TAGCTCTTCAGAACATTTGGCGTGTTATCGGTTAGAT

Found at i:692 original size:37 final size:37

Alignment explanation


    Indices: 587--693  Score: 119
    Period size: 37  Copynumber: 2.9  Consensus size: 37

        577 GGCGGATGTA

                        **                    *   
        587 TAGCTCTTCAGAGTATTTGGCGTGTTATT-GGTTGGAT
          1 TAGCTCTTCAGAACATTTGGCGTGTT-TTCGGTTAGAT

                                      *          
        624 TAGCTCTTCAGAACATTTGGCGTGTTATCGGTTAGAT
          1 TAGCTCTTCAGAACATTTGGCGTGTTTTCGGTTAGAT

                         * *    *             
        661 TAGCTCTT-ATGAGCGTTTGACGTGTTTTCGGTT
          1 TAGCTCTTCA-GAACATTTGGCGTGTTTTCGGTT

        694 GGACTACTTG


Statistics
Matches: 60,  Mismatches: 8, Indels: 4
        0.83            0.11        0.06

Matches are distributed among these distances:
  36    2  0.03
  37   58  0.97

ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42


Consensus pattern (37 bp):   
TAGCTCTTCAGAACATTTGGCGTGTTTTCGGTTAGAT
Done.