Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17152

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: 3873
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29


Found at i:2241 original size:30 final size:30

Alignment explanation


    Indices: 2207--2297  Score: 80
    Period size: 30  Copynumber: 3.0  Consensus size: 30

       2197 AGTGGGAGTA

                                          
       2207 GTGGTTATAACAGTGAAGAAGTGATGGAAG
          1 GTGGTTATAACAGTGAAGAAGTGATGGAAG

                  * *    *   *             * 
       2237 GTGGTTTTGA-AGGGAGTGATAGTG--GGAGTG
          1 GTGGTTATAACAGTGA-AGA-AGTGATGGA-AG

                            *             
       2267 GTGGTTATAACAGTGAGGAAGTGATGGAAG
          1 GTGGTTATAACAGTGAAGAAGTGATGGAAG

             
       2297 G
          1 G

       2298 CCTCCAACCA


Statistics
Matches: 45,  Mismatches: 10, Indels: 12
        0.67            0.15        0.18

Matches are distributed among these distances:
  29   11  0.24
  30   23  0.51
  31   11  0.24

ACGTcount: A:0.30, C:0.02, G:0.43, T:0.25


Consensus pattern (30 bp):   
GTGGTTATAACAGTGAAGAAGTGATGGAAG

Found at i:2274 original size:60 final size:60

Alignment explanation


    Indices: 2181--2297  Score: 189
    Period size: 60  Copynumber: 1.9  Consensus size: 60

       2171 TTATATTTGC

                      *                                                 
       2181 TTTTGAAAGGTGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG
          1 TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG

                   *       *         *                *              
       2241 TTTTGAAGGGAGTGATAGTGGGAGTGGTGGTTATAACAGTGAGGAAGTGATGGAAGG
          1 TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGG

       2298 CCTCCAACCA


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  60   52  1.00

ACGTcount: A:0.29, C:0.03, G:0.42, T:0.26


Consensus pattern (60 bp):   
TTTTGAAAGGAGTGACAGTGGGAGTAGTGGTTATAACAGTGAAGAAGTGATGGAAGGTGG
Done.