Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17971

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: 2423
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28


Found at i:1370 original size:9 final size:9

Alignment explanation


    Indices: 1356--1414  Score: 52
    Period size: 9  Copynumber: 6.9  Consensus size: 9

       1346 GATGGAGCCC

                     
       1356 CCTCCTCCA
          1 CCTCCTCCA

                    *
       1365 CCTCCTCCT
          1 CCTCCTCCA

              *     *
       1374 CCGCCTCCG
          1 CCTCCTCCA

                 *   
       1383 CCTCCCCCA
          1 CCTCCTCCA

                  *  
       1392 CCTCC-GC-
          1 CCTCCTCCA

                     
       1399 CC-CCTCCA
          1 CCTCCTCCA

                    
       1407 CCTCCTCC
          1 CCTCCTCC

       1415 GGCACTTGCT


Statistics
Matches: 39,  Mismatches: 8, Indels: 6
        0.74            0.15        0.11

Matches are distributed among these distances:
   6    2  0.05
   7    3  0.08
   8    3  0.08
   9   31  0.79

ACGTcount: A:0.05, C:0.71, G:0.05, T:0.19


Consensus pattern (9 bp):   
CCTCCTCCA

Found at i:1386 original size:15 final size:15

Alignment explanation


    Indices: 1356--1411  Score: 64
    Period size: 15  Copynumber: 3.9  Consensus size: 15

       1346 GATGGAGCCC

                           
       1356 CCTCCTCCACCT---
          1 CCTCCTCCACCTCCG

                    *      
       1368 CCTCCTCCGCCTCCG
          1 CCTCCTCCACCTCCG

                 *         
       1383 CCTCCCCCACCTCCG
          1 CCTCCTCCACCTCCG

              *           
       1398 CCCCCTCCACCTCC
          1 CCTCCTCCACCTCC

       1412 TCCGGCACTT


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  12   11  0.31
  15   25  0.69

ACGTcount: A:0.05, C:0.71, G:0.05, T:0.18


Consensus pattern (15 bp):   
CCTCCTCCACCTCCG
Done.