Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08999

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: 2601
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28


Found at i:1373 original size:51 final size:51

Alignment explanation


    Indices: 1292--1390  Score: 162
    Period size: 51  Copynumber: 1.9  Consensus size: 51

       1282 GATGCTAGGT

                *                                 *            
       1292 TGGATCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATATCTGGGAGAAGTG
          1 TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAAGTG

                            *        *                      
       1343 TGGAGCAGGCTGCTGATTCAAGAAACGAAGTTGGAATAACTGGGAGAA
          1 TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAA

       1391 ATTTAGAGCC


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  51   44  1.00

ACGTcount: A:0.35, C:0.11, G:0.33, T:0.20


Consensus pattern (51 bp):   
TGGAGCAGGCTGCTGAATCAAGAAAAGAAGTTGGAATAACTGGGAGAAGTG

Found at i:1446 original size:60 final size:60

Alignment explanation


    Indices: 1350--1519  Score: 216
    Period size: 60  Copynumber: 2.8  Consensus size: 60

       1340 GTGTGGAGCA

                     *  *     *            *                      *    *
       1350 GGCTGCTGATTCAAGAAACGAAGTTGGAATAACTGGGAGAAATTTAGAGCCAAGTCAACT
          1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGAAATTTAGAGCCAAGGCAACC

            *                                         *                  
       1410 TGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGA-AGAGTTTAGAGCCAAGGCAACC
          1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGA-AATTTAGAGCCAAGGCAACC

                                   *        *        *   *    
       1470 GGCTGCTGAATCTAGAAAAGAAGCTGGAATAGTTGGGAGAACTTTGGAGC
          1 GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGAAATTTAGAGC

       1520 AGGGAGCTGA


Statistics
Matches: 95,  Mismatches: 13, Indels: 4
        0.85            0.12        0.04

Matches are distributed among these distances:
  59    1  0.01
  60   93  0.98
  61    1  0.01

ACGTcount: A:0.35, C:0.14, G:0.30, T:0.21


Consensus pattern (60 bp):   
GGCTGCTGAATCTAGAAAAGAAGTTGGAATAGCTGGGAGAAATTTAGAGCCAAGGCAACC
Done.