Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35695

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: 2694
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26


Found at i:97 original size:6 final size:6

Alignment explanation


    Indices: 86--145  Score: 50
    Period size: 6  Copynumber: 10.0  Consensus size: 6

         76 TTCATCCCCA

                                     *          *      *      *     
         86 AAAATC AAAATC AAAATTC AAATTC -AAATC CAAATC GAAATC GAAATC
          1 AAAATC AAAATC AAAA-TC AAAATC AAAATC AAAATC AAAATC AAAATC

            *      *     
        134 GAAATC GAAATC
          1 AAAATC AAAATC

        146 CAAACCCAAA


Statistics
Matches: 49,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
   5    4  0.08
   6   40  0.82
   7    5  0.10

ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20


Consensus pattern (6 bp):   
AAAATC

Found at i:126 original size:18 final size:18

Alignment explanation


    Indices: 105--155  Score: 59
    Period size: 18  Copynumber: 2.8  Consensus size: 18

         95 ATCAAAATTC

                              
        105 AAATTCAAATCCAAATCG
          1 AAATTCAAATCCAAATCG

                        *      
        123 AAA-TCGAAATCGAAATCG
          1 AAATTC-AAATCCAAATCG

                *    *     
        141 AAATCCAAACCCAAA
          1 AAATTCAAATCCAAA

        156 CCCTAATCCC


Statistics
Matches: 27,  Mismatches: 4, Indels: 4
        0.77            0.11        0.11

Matches are distributed among these distances:
  17    2  0.07
  18   24  0.89
  19    1  0.04

ACGTcount: A:0.53, C:0.24, G:0.08, T:0.16


Consensus pattern (18 bp):   
AAATTCAAATCCAAATCG

Found at i:1869 original size:30 final size:30

Alignment explanation


    Indices: 1833--1889  Score: 105
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       1823 TGAGCAGGAA

                                          
       1833 TGATAAAGGGAAAGGGAAAATGGTTGATGC
          1 TGATAAAGGGAAAGGGAAAATGGTTGATGC

                               *       
       1863 TGATAAAGGGAAAGGGAAACTGGTTGA
          1 TGATAAAGGGAAAGGGAAAATGGTTGA

       1890 CACCATAGCG


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.40, C:0.04, G:0.37, T:0.19


Consensus pattern (30 bp):   
TGATAAAGGGAAAGGGAAAATGGTTGATGC
Done.