Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00709.N4

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, 440

Length: 734
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:143 original size:24 final size:24

Alignment explanation


    Indices: 116--172  Score: 80
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        106 TGTTCTTCCC

                                     
        116 CCCACCTTT-ATATATAAAACCAAA
          1 CCCA-CTTTCATATATAAAACCAAA

                     *              
        140 CCCACTTTCCTATATAAAACCAAA
          1 CCCACTTTCATATATAAAACCAAA

              *      
        164 CCAACTTTC
          1 CCCACTTTC

        173 CTTTCACCAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  23    4  0.13
  24   26  0.87

ACGTcount: A:0.40, C:0.33, G:0.00, T:0.26


Consensus pattern (24 bp):   
CCCACTTTCATATATAAAACCAAA

Found at i:173 original size:24 final size:24

Alignment explanation


    Indices: 126--174  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        116 CCCACCTTTA

                            *       
        126 TATATAAAACCAAACCCACTTTCC
          1 TATATAAAACCAAACCAACTTTCC

                                    
        150 TATATAAAACCAAACCAACTTTCC
          1 TATATAAAACCAAACCAACTTTCC

             
        174 T
          1 T

        175 TTCACCAACC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.43, C:0.31, G:0.00, T:0.27


Consensus pattern (24 bp):   
TATATAAAACCAAACCAACTTTCC

Found at i:393 original size:3 final size:3

Alignment explanation


    Indices: 385--426  Score: 59
    Period size: 3  Copynumber: 14.0  Consensus size: 3

        375 CAATATCAGA

                                                       *            
        385 TCT TCT TCTT TCT T-T TCT TCT TCT TCT TCT TCA TCT TCT TCT
          1 TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT

        427 GCTGCTGCTG


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   2    2  0.06
   3   30  0.86
   4    3  0.09

ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67


Consensus pattern (3 bp):   
TCT

Done.