Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17787

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, 370

Length: 618
ACGTcount: A:0.36, C:0.14, G:0.35, T:0.15


Found at i:175 original size:3 final size:3

Alignment explanation


    Indices: 169--193  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

        159 AGGCGAAGAT

                                             
        169 GAC GAC GAC GAC GAC GAC GAC GAC G
          1 GAC GAC GAC GAC GAC GAC GAC GAC G

        194 GAGAGGAGGA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.32, G:0.36, T:0.00


Consensus pattern (3 bp):   
GAC

Found at i:318 original size:21 final size:21

Alignment explanation


    Indices: 278--341  Score: 74
    Period size: 21  Copynumber: 3.0  Consensus size: 21

        268 GAGGATGTTA

                   *  *          
        278 AAGACGATGATGACGACGATG
          1 AAGACGACGACGACGACGATG

               *     *   *       
        299 AAGGCGACGGCGATGACGATG
          1 AAGACGACGACGACGACGATG

             *                   
        320 ACGACGACGACGACGACGATG
          1 AAGACGACGACGACGACGATG

             
        341 A
          1 A

        342 TGACAGTGAT


Statistics
Matches: 34,  Mismatches: 9, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   34  1.00

ACGTcount: A:0.34, C:0.20, G:0.36, T:0.09


Consensus pattern (21 bp):   
AAGACGACGACGACGACGATG

Found at i:338 original size:15 final size:15

Alignment explanation


    Indices: 289--345  Score: 60
    Period size: 15  Copynumber: 3.8  Consensus size: 15

        279 AGACGATGAT

                       * * 
        289 GACGACGATGAAGGC
          1 GACGACGATGACGAC

                *         *
        304 GACGGCGATGACGAT
          1 GACGACGATGACGAC

                    *      
        319 GACGACGACGACGAC
          1 GACGACGATGACGAC

                 *      
        334 GACGATGATGAC
          1 GACGACGATGAC

        346 AGTGATGACG


Statistics
Matches: 33,  Mismatches: 9, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  15   33  1.00

ACGTcount: A:0.32, C:0.23, G:0.37, T:0.09


Consensus pattern (15 bp):   
GACGACGATGACGAC

Found at i:496 original size:12 final size:12

Alignment explanation


    Indices: 465--508  Score: 52
    Period size: 12  Copynumber: 3.7  Consensus size: 12

        455 AAGAAAATGG

                  *     
        465 TGAAGAGGAAGA
          1 TGAAGAAGAAGA

            *           
        477 AGAAGAAGAAGA
          1 TGAAGAAGAAGA

               *     *  
        489 TGATGAAGACGA
          1 TGAAGAAGAAGA

                    
        501 TGAAGAAG
          1 TGAAGAAG

        509 GTAGTGGAAA


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.52, C:0.02, G:0.36, T:0.09


Consensus pattern (12 bp):   
TGAAGAAGAAGA
Done.