Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23702

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: 1800
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25


Found at i:1088 original size:27 final size:27

Alignment explanation


    Indices: 1057--1112  Score: 76
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       1047 CCCTACTACC

                       *               
       1057 CCAACATCACCGGACACAAATCCGACT
          1 CCAACATCACCAGACACAAATCCGACT

                   *         *      *  
       1084 CCAACATTACCAGACACTAATCCGGCT
          1 CCAACATCACCAGACACAAATCCGACT

              
       1111 CC
          1 CC

       1113 CACCGGCCCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.34, C:0.41, G:0.11, T:0.14


Consensus pattern (27 bp):   
CCAACATCACCAGACACAAATCCGACT

Found at i:1136 original size:24 final size:24

Alignment explanation


    Indices: 1109--1160  Score: 77
    Period size: 24  Copynumber: 2.2  Consensus size: 24

       1099 ACTAATCCGG

                                    
       1109 CTCCCACCGGCCCTACCACGACTC
          1 CTCCCACCGGCCCTACCACGACTC

                *  *          *     
       1133 CTCCGACTGGCCCTACCATGACTC
          1 CTCCCACCGGCCCTACCACGACTC

                
       1157 CTCC
          1 CTCC

       1161 GACTGGGACA


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   25  1.00

ACGTcount: A:0.15, C:0.54, G:0.13, T:0.17


Consensus pattern (24 bp):   
CTCCCACCGGCCCTACCACGACTC

Found at i:1161 original size:24 final size:24

Alignment explanation


    Indices: 1117--1232  Score: 97
    Period size: 24  Copynumber: 4.8  Consensus size: 24

       1107 GGCTCCCACC

                                    
       1117 GGCCCTACCACGACTCCTCCGACT
          1 GGCCCTACCACGACTCCTCCGACT

                      *             
       1141 GGCCCTACCATGACTCCTCCGACT
          1 GGCCCTACCACGACTCCTCCGACT

              ** *     *        *   
       1165 GGGACAACCACAACTCCTCCAACT
          1 GGCCCTACCACGACTCCTCCGACT

              ** *     *        *   
       1189 GGGACAACCACAACTCCTCCAACT
          1 GGCCCTACCACGACTCCTCCGACT

              ** *     *        
       1213 GGGACAACCACAACTCCTCC
          1 GGCCCTACCACGACTCCTCC

       1233 AACAGGGACA


Statistics
Matches: 85,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   85  1.00

ACGTcount: A:0.26, C:0.45, G:0.15, T:0.15


Consensus pattern (24 bp):   
GGCCCTACCACGACTCCTCCGACT

Found at i:1233 original size:24 final size:24

Alignment explanation


    Indices: 1153--1271  Score: 211
    Period size: 24  Copynumber: 5.0  Consensus size: 24

       1143 CCCTACCATG

                    *               
       1153 ACTCCTCCGACTGGGACAACCACA
          1 ACTCCTCCAACTGGGACAACCACA

                                    
       1177 ACTCCTCCAACTGGGACAACCACA
          1 ACTCCTCCAACTGGGACAACCACA

                                    
       1201 ACTCCTCCAACTGGGACAACCACA
          1 ACTCCTCCAACTGGGACAACCACA

                       *            
       1225 ACTCCTCCAACAGGGACAACCACA
          1 ACTCCTCCAACTGGGACAACCACA

                       *           
       1249 ACTCCTCCAACAGGGACAACCAC
          1 ACTCCTCCAACTGGGACAACCAC

       1272 GAGTCCAGGA


Statistics
Matches: 93,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   93  1.00

ACGTcount: A:0.34, C:0.42, G:0.13, T:0.11


Consensus pattern (24 bp):   
ACTCCTCCAACTGGGACAACCACA

Done.