Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_11143

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: 2222
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28


Found at i:1478 original size:15 final size:15

Alignment explanation


    Indices: 1458--1510  Score: 52
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       1448 CTCTCCACCT

                           
       1458 CCTCCACCACCATCA
          1 CCTCCACCACCATCA

                    *  *   
       1473 CCTCCACCGCCCTCA
          1 CCTCCACCACCATCA

              *     *  *   
       1488 CCACCACCTCCTTCA
          1 CCTCCACCACCATCA

              *     
       1503 CCCCCACC
          1 CCTCCACC

       1511 CCCTACATAT


Statistics
Matches: 32,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  15   32  1.00

ACGTcount: A:0.19, C:0.66, G:0.02, T:0.13


Consensus pattern (15 bp):   
CCTCCACCACCATCA

Found at i:1490 original size:54 final size:54

Alignment explanation


    Indices: 1432--1549  Score: 123
    Period size: 54  Copynumber: 2.2  Consensus size: 54

       1422 CCTCCGCCAC

                           *    *     *   *                         
       1432 CACCACCGCCT-ATTTACTCTCCACCTCCTCCACCA-CCATCACCTCCACCGCCCT
          1 CACCACCGCCTCATTCAC-CCCCACCCCCTACA-CATCCATCACCTCCACCGCCCT

                   *    *                   *                   * 
       1486 CACCACCACCTCCTTCACCCCCACCCCCTACATATCCATCACCTCCACCGCCTT
          1 CACCACCGCCTCATTCACCCCCACCCCCTACACATCCATCACCTCCACCGCCCT

                *     
       1540 CACCCCCGCC
          1 CACCACCGCC

       1550 ACCTACTTAT


Statistics
Matches: 52,  Mismatches: 10, Indels: 4
        0.79            0.15        0.06

Matches are distributed among these distances:
  53    1  0.02
  54   47  0.90
  55    4  0.08

ACGTcount: A:0.19, C:0.60, G:0.03, T:0.18


Consensus pattern (54 bp):   
CACCACCGCCTCATTCACCCCCACCCCCTACACATCCATCACCTCCACCGCCCT

Found at i:1528 original size:39 final size:39

Alignment explanation


    Indices: 1485--1592  Score: 126
    Period size: 39  Copynumber: 2.8  Consensus size: 39

       1475 TCCACCGCCC

                       *              *            
       1485 TCACCACCACCTCCTTCACCCCCACCCCCTACATATCCA
          1 TCACCACCACCCCCTTCACCCCCACCACCTACATATCCA

                 *     *           *        *     *
       1524 TCACCTCCACCGCCTTCACCCCCGCCACCTACTTATCCG
          1 TCACCACCACCCCCTTCACCCCCACCACCTACATATCCA

             *      *            *        
       1563 TTACCACCGCCCCCTTCACCCTCACCACCT
          1 TCACCACCACCCCCTTCACCCCCACCACCT

       1593 GCGCCAATAT


Statistics
Matches: 57,  Mismatches: 12, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  39   57  1.00

ACGTcount: A:0.19, C:0.58, G:0.04, T:0.19


Consensus pattern (39 bp):   
TCACCACCACCCCCTTCACCCCCACCACCTACATATCCA

Found at i:2106 original size:69 final size:70

Alignment explanation


    Indices: 1974--2128  Score: 231
    Period size: 75  Copynumber: 2.2  Consensus size: 70

       1964 ATCACCTTCA

                 *                                            *              
       1974 CCACCGCCACCCGTTGTAACATATTCCTCACCACCACCACCACCGCCGCCGCCTCCAGTTATTTA
          1 CCACCACCACCCGTTGTAACATATTCCTCACCACCACCACCA----C-CCACCTCCAGTTATTTA

                      
       2039 CCATTCACCT
         61 CCATTCACCT

                                                             *               
       2049 CCACCACCACCCGTTGTAACATATTCCTCACCACCACCACCA-CCACCTTCAGTTATTTACCATT
          1 CCACCACCACCCGTTGTAACATATTCCTCACCACCACCACCACCCACCTCCAGTTATTTACCATT

                 
       2113 CACCT
         66 CACCT

                       
       2118 CCACCACCACC
          1 CCACCACCACC

       2129 ACTGTCACCC


Statistics
Matches: 77,  Mismatches: 3, Indels: 6
        0.90            0.03        0.07

Matches are distributed among these distances:
  69   36  0.47
  75   41  0.53

ACGTcount: A:0.24, C:0.48, G:0.06, T:0.21


Consensus pattern (70 bp):   
CCACCACCACCCGTTGTAACATATTCCTCACCACCACCACCACCCACCTCCAGTTATTTACCATT
CACCT

Found at i:2116 original size:36 final size:36

Alignment explanation


    Indices: 2008--2130  Score: 105
    Period size: 36  Copynumber: 3.5  Consensus size: 36

       1998 TCCTCACCAC

                      *  *  *   *               
       2008 CACCACCACCGCCGCCGCCTCCAGTTATTTACCATT
          1 CACCACCACCACCACCACCTTCAGTTATTTACCATT

                *             *        *           
       2044 CACCTCCACCACCACC-CGTT--GTAACATATT-CC--T
          1 CACCACCACCACCACCACCTTCAGT--TAT-TTACCATT

                                                
       2077 CACCACCACCACCACCACCTTCAGTTATTTACCATT
          1 CACCACCACCACCACCACCTTCAGTTATTTACCATT

                *             
       2113 CACCTCCACCACCACCAC
          1 CACCACCACCACCACCAC

       2131 TGTCACCCCC


Statistics
Matches: 68,  Mismatches: 10, Indels: 18
        0.71            0.10        0.19

Matches are distributed among these distances:
  33   20  0.29
  34    7  0.10
  35    6  0.09
  36   35  0.51

ACGTcount: A:0.24, C:0.49, G:0.06, T:0.21


Consensus pattern (36 bp):   
CACCACCACCACCACCACCTTCAGTTATTTACCATT

Done.