Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23818

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, 549

Length: 915
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22


Found at i:242 original size:18 final size:18

Alignment explanation


    Indices: 172--230  Score: 64
    Period size: 18  Copynumber: 3.1  Consensus size: 18

        162 TGGTGATAAC

                     * *    * 
        172 GAAGACGAACAGGAAGTG
          1 GAAGACGAAGAAGAAGAG

                                 
        190 GAAGAGCAGAACGAAGAAGAG
          1 GAAGA-C-GAA-GAAGAAGAG

                              
        211 GAAGACGAAGAAGAAGAG
          1 GAAGACGAAGAAGAAGAG

              
        229 GA
          1 GA

        231 GGAGGAGGAA


Statistics
Matches: 35,  Mismatches: 3, Indels: 6
        0.80            0.07        0.14

Matches are distributed among these distances:
  18   16  0.46
  19    4  0.11
  20    4  0.11
  21   11  0.31

ACGTcount: A:0.51, C:0.08, G:0.39, T:0.02


Consensus pattern (18 bp):   
GAAGACGAAGAAGAAGAG

Found at i:656 original size:15 final size:15

Alignment explanation


    Indices: 636--665  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        626 TAAGCCATCA

                           
        636 TTCCTCCTCTTCTTC
          1 TTCCTCCTCTTCTTC

                  *        
        651 TTCCTCTTCTTCTTC
          1 TTCCTCCTCTTCTTC

        666 GTCGGTAAAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (15 bp):   
TTCCTCCTCTTCTTC

Found at i:657 original size:12 final size:12

Alignment explanation


    Indices: 640--665  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

        630 CCATCATTCC

                        
        640 TCCTCTTCTTCT
          1 TCCTCTTCTTCT

                        
        652 TCCTCTTCTTCT
          1 TCCTCTTCTTCT

              
        664 TC
          1 TC

        666 GTCGGTAAAA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58


Consensus pattern (12 bp):   
TCCTCTTCTTCT
Done.