Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08295

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, 441

Length: 735
ACGTcount: A:0.19, C:0.13, G:0.42, T:0.27


Found at i:362 original size:30 final size:30

Alignment explanation


    Indices: 322--382  Score: 88
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        312 TTACAAAGGC

                 *                         
        322 ATTGGTGGTCTAGG-GGGTTTAGGCGGTGGA
          1 ATTGGAGGTCTAGGTGGG-TTAGGCGGTGGA

                                   *      
        352 ATTGGAGGTCTAGGTGGGTTAGGGGGTGGA
          1 ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA

             
        382 A
          1 A

        383 CTGGTGGCGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30   25  0.89
  31    3  0.11

ACGTcount: A:0.16, C:0.05, G:0.51, T:0.28


Consensus pattern (30 bp):   
ATTGGAGGTCTAGGTGGGTTAGGCGGTGGA

Found at i:408 original size:42 final size:42

Alignment explanation


    Indices: 354--449  Score: 165
    Period size: 42  Copynumber: 2.3  Consensus size: 42

        344 GCGGTGGAAT

                                          *           
        354 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACTGGTGGCGGAGG
          1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

                           *                         *
        396 TGGAGGTCTAGGTGGTTTAGGGGGTGGAACCGGTGGCGGAGT
          1 TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

                        
        438 TGGAGGTCTAGG
          1 TGGAGGTCTAGG

        450 CAGTGGGACC


Statistics
Matches: 51,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  42   51  1.00

ACGTcount: A:0.15, C:0.08, G:0.54, T:0.23


Consensus pattern (42 bp):   
TGGAGGTCTAGGTGGGTTAGGGGGTGGAACCGGTGGCGGAGG

Found at i:461 original size:33 final size:33

Alignment explanation


    Indices: 419--482  Score: 110
    Period size: 33  Copynumber: 1.9  Consensus size: 33

        409 GGTTTAGGGG

                      *                      
        419 GTGGAACCGGTGGCGGAGTTGGAGGTCTAGGCA
          1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA

                *                          
        452 GTGGGACCGGGGGCGGAGTTGGAGGTCTAGG
          1 GTGGAACCGGGGGCGGAGTTGGAGGTCTAGG

        483 TGGTGGTGGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.16, C:0.14, G:0.53, T:0.17


Consensus pattern (33 bp):   
GTGGAACCGGGGGCGGAGTTGGAGGTCTAGGCA

Found at i:566 original size:57 final size:57

Alignment explanation


    Indices: 481--602  Score: 190
    Period size: 57  Copynumber: 2.1  Consensus size: 57

        471 TGGAGGTCTA

                               *                       *       *     
        481 GGTGGTGGTGGTTGTCCAGGTACAGGTGGTGTAGGCAGTGAAGGTGGAGGTCTAGGT
          1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT

                                   *            *   *                
        538 GGTGGTGGTGGTTGTCCAGATACCGGTGGTGTAGGCGGTGGAGCTGGAGGTATAGGT
          1 GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT

                    
        595 GGTGGTGG
          1 GGTGGTGG

        603 CAGCGGCGGA


Statistics
Matches: 59,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  57   59  1.00

ACGTcount: A:0.14, C:0.09, G:0.51, T:0.26


Consensus pattern (57 bp):   
GGTGGTGGTGGTTGTCCAGATACAGGTGGTGTAGGCAGTGAAGCTGGAGGTATAGGT
Done.