Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_10458

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, 200

Length: 290
ACGTcount: A:0.17, C:0.16, G:0.35, T:0.32


Found at i:252 original size:21 final size:21

Alignment explanation


    Indices: 228--277  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

        218 TGCTTCTGAT

                                 
        228 GGTTGTGGTGGCAAAGGTGGA
          1 GGTTGTGGTGGCAAAGGTGGA

                       ****      
        249 GGTTGTGGTGGTGGGGGTGGA
          1 GGTTGTGGTGGCAAAGGTGGA

                    
        270 GGTTGTGG
          1 GGTTGTGG

        278 GGGTGGAGGT


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

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.10, C:0.02, G:0.60, T:0.28


Consensus pattern (21 bp):   
GGTTGTGGTGGCAAAGGTGGA

Found at i:277 original size:15 final size:15

Alignment explanation


    Indices: 259--289  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        249 GGTTGTGGTG

                           
        259 GTGGGGGTGGAGGTT
          1 GTGGGGGTGGAGGTT

                           
        274 GTGGGGGTGGAGGTT
          1 GTGGGGGTGGAGGTT

             
        289 G
          1 G

        290 A


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.06, C:0.00, G:0.68, T:0.26


Consensus pattern (15 bp):   
GTGGGGGTGGAGGTT

Found at i:282 original size:21 final size:21

Alignment explanation


    Indices: 243--283  Score: 73
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        233 TGGTGGCAAA

                          *      
        243 GGTGGAGGTTGTGGTGGTGGG
          1 GGTGGAGGTTGTGGGGGTGGG

                                
        264 GGTGGAGGTTGTGGGGGTGG
          1 GGTGGAGGTTGTGGGGGTGG

        284 AGGTTGA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.05, C:0.00, G:0.68, T:0.27


Consensus pattern (21 bp):   
GGTGGAGGTTGTGGGGGTGGG
Done.