Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_33738

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, 671

Length: 1119
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25


Found at i:688 original size:57 final size:56

Alignment explanation


    Indices: 625--838  Score: 162
    Period size: 57  Copynumber: 3.9  Consensus size: 56

        615 ACCACATCCA

                                                                 **  
        625 CCTCCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCT
          1 CCTCCAGTTCC-GTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAGCCT

                                      **      *            *        
        682 CCTCCAGTTCCG-------G-AACCACATCCTCCACCAGTTCCAGTCCATAAGCCT
          1 CCTCCAGTTCCGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAGCCT

                                     *          *  *      *    *     *
        730 CCTCCAGTTCCGGTATACAAGAAACGA-GTCCCTCCTCCGGTTCCAATCTACAAGCCC
          1 CCTCCAGTTCC-GTATACAAGAAACCATGT-CCTCCCCCAGTTCCAGTCTATAAGCCT

                                *         *                  *    
        787 CCTCCAGTTCCTGTATACAACAAACCACT-ACCT-CCCCAGGTTCCAGTGTATA
          1 CCTCCAGTTCC-GTATACAAGAAACCA-TGTCCTCCCCCA-GTTCCAGTCTATA

        839 CGAAGCCACT


Statistics
Matches: 121,  Mismatches: 23, Indels: 26
        0.71            0.14        0.15

Matches are distributed among these distances:
  48   40  0.33
  49    2  0.02
  56    6  0.05
  57   73  0.60

ACGTcount: A:0.26, C:0.38, G:0.13, T:0.23


Consensus pattern (56 bp):   
CCTCCAGTTCCGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAGCCT

Found at i:707 original size:24 final size:24

Alignment explanation


    Indices: 680--742  Score: 65
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        670 GTCTATAAAT

                                 * * 
        680 CTCCTCCAGTTCCGGAACCA-CATC
          1 CTCCTCCAGTTCCGG-ACCATAAGC

                *        * *        
        704 CTCCACCAGTTCCAGTCCATAAGC
          1 CTCCTCCAGTTCCGGACCATAAGC

                           
        728 CTCCTCCAGTTCCGG
          1 CTCCTCCAGTTCCGG

        743 TATACAAGAA


Statistics
Matches: 31,  Mismatches: 7, Indels: 2
        0.77            0.17        0.05

Matches are distributed among these distances:
  23    3  0.10
  24   28  0.90

ACGTcount: A:0.19, C:0.44, G:0.14, T:0.22


Consensus pattern (24 bp):   
CTCCTCCAGTTCCGGACCATAAGC

Found at i:931 original size:18 final size:18

Alignment explanation


    Indices: 908--943  Score: 56
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        898 TACAAGCCAC

                               
        908 TCCCTCCACTTCCC-AAGA
          1 TCCCTCCA-TTCCCTAAGA

                              
        926 TCCCTCCATTCCCTAAGA
          1 TCCCTCCATTCCCTAAGA

        944 AGCCATGCCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    5  0.29
  18   12  0.71

ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25


Consensus pattern (18 bp):   
TCCCTCCATTCCCTAAGA

Found at i:1015 original size:60 final size:60

Alignment explanation


    Indices: 951--1073  Score: 212
    Period size: 60  Copynumber: 2.0  Consensus size: 60

        941 AGAAGCCATG

                                                                         
        951 CCCTCCCCTTCCTAAGCTACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
          1 CCCTCCCCTTCCTAAGCTACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA

                  *           *                                         
       1011 CCCTCCTCTTCCTAAGCTGCCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
          1 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA

               
       1071 CCC
          1 CCC

       1074 CAAGTTCGGA


Statistics
Matches: 60,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  59    4  0.07
  60   56  0.93

ACGTcount: A:0.19, C:0.49, G:0.06, T:0.27


Consensus pattern (60 bp):   
CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA

Found at i:1051 original size:18 final size:18

Alignment explanation


    Indices: 1012--1052  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 18

       1002 CCACCACCAC

                    *      *  
       1012 CCTCCTCTTCCTAAGCTG
          1 CCTCCTCTCCCTAAGATG

                             *
       1030 CCTCCTCTCCCTAAGATT
          1 CCTCCTCTCCCTAAGATG

                 
       1048 CCTCC
          1 CCTCC

       1053 CAAGTATTTC


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.12, C:0.49, G:0.07, T:0.32


Consensus pattern (18 bp):   
CCTCCTCTCCCTAAGATG

Found at i:1093 original size:60 final size:60

Alignment explanation


    Indices: 970--1095  Score: 157
    Period size: 60  Copynumber: 2.1  Consensus size: 60

        960 TCCTAAGCTA

                                                          **     *  **  
        970 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCCTCTTCCTAAGCTG
          1 CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG

                                                             *   *        
       1030 CCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCACCC-CAAGTTCGGAAAATGG
          1 CCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAAT-G

                  
       1090 CCTCCT
          1 CCTCCT

       1096 TTGCCACCCT


Statistics
Matches: 57,  Mismatches: 7, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  59   11  0.19
  60   46  0.81

ACGTcount: A:0.21, C:0.44, G:0.09, T:0.26


Consensus pattern (60 bp):   
CCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAATG
Done.