Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38957

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: 1845
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29


Found at i:1357 original size:15 final size:15

Alignment explanation


    Indices: 1333--1419  Score: 54
    Period size: 15  Copynumber: 5.8  Consensus size: 15

       1323 GGAGGTATCC

                 *         
       1333 CATCATGAAGTAGCT
          1 CATCAAGAAGTAGCT

                           *
       1348 CATCAAGAAGATA-CC
          1 CATCAAGAAG-TAGCT

                 *  *  *   
       1363 CATCACGATGTTGCT
          1 CATCAAGAAGTAGCT

                *       *  
       1378 CATCGAGAAGTATC-
          1 CATCAAGAAGTAGCT

                            
       1392 CGATCAAGAAGTAG-T
          1 C-ATCAAGAAGTAGCT

                    *    
       1407 CAGTCAAGGAGTA
          1 CA-TCAAGAAGTA

       1420 ACCCATCAGG


Statistics
Matches: 53,  Mismatches: 14, Indels: 10
        0.69            0.18        0.13

Matches are distributed among these distances:
  14    3  0.06
  15   48  0.91
  16    2  0.04

ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22


Consensus pattern (15 bp):   
CATCAAGAAGTAGCT

Found at i:1365 original size:30 final size:30

Alignment explanation


    Indices: 1305--1445  Score: 108
    Period size: 30  Copynumber: 4.7  Consensus size: 30

       1295 AGGAACAAAC

                    *     *   *  *        
       1305 TCATGAAGCAGCTCCTCAGGAGGTATCCCA
          1 TCATGAAGTAGCTCATCAAGAAGTATCCCA

                                           
       1335 TCATGAAGTAGCTCATCAAGAAG-ATACCCA
          1 TCATGAAGTAGCTCATCAAGAAGTAT-CCCA

               *  *  *       *          * 
       1365 TCACGATGTTGCTCATCGAGAAGTATCCGA
          1 TCATGAAGTAGCTCATCAAGAAGTATCCCA

               *                 *    *    
       1395 TCAAGAAGTAG-TCAGTCAAGGAGTAACCCA
          1 TCATGAAGTAGCTCA-TCAAGAAGTATCCCA

               *    *             
       1425 TCAGGAAGAAGCCTC-TCAAGA
          1 TCATGAAGTAG-CTCATCAAGA

       1446 GGTACCTTCT


Statistics
Matches: 87,  Mismatches: 19, Indels: 10
        0.75            0.16        0.09

Matches are distributed among these distances:
  29    5  0.06
  30   78  0.90
  31    2  0.02
  32    2  0.02

ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20


Consensus pattern (30 bp):   
TCATGAAGTAGCTCATCAAGAAGTATCCCA
Done.