Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_28130

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, 979

Length: 1632
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23


Found at i:409 original size:24 final size:24

Alignment explanation


    Indices: 358--409  Score: 61
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        348 GGAAAATAAT

                          *      *  
        358 AAGAATAGTAAGAAGAAGAAGGCA
          1 AAGAATAGTAAGAAAAAGAAGCCA

                                    *
        382 AAGAATAAG-AAGAAAAAGAAGCCG
          1 AAGAAT-AGTAAGAAAAAGAAGCCA

                
        406 AAGA
          1 AAGA

        410 TTGTGAGTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  24   22  0.92
  25    2  0.08

ACGTcount: A:0.62, C:0.06, G:0.27, T:0.06


Consensus pattern (24 bp):   
AAGAATAGTAAGAAAAAGAAGCCA

Found at i:1411 original size:18 final size:18

Alignment explanation


    Indices: 1397--1431  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1387 CCAAAAGGAT

                              
       1397 CTGCGAGTGTCAAAGCAA
          1 CTGCGAGTGTCAAAGCAA

               *             
       1415 CTGTGAGTGTCAAAGCA
          1 CTGCGAGTGTCAAAGCA

       1432 CCTACAGTTA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20


Consensus pattern (18 bp):   
CTGCGAGTGTCAAAGCAA

Found at i:1559 original size:201 final size:195

Alignment explanation


    Indices: 1220--1592  Score: 494
    Period size: 201  Copynumber: 1.9  Consensus size: 195

       1210 CCAAAAGGAT

                      **                               * *                   
       1220 CTGTGAGTGTTGAAGCACATACAGTTAATGAAGTTGGTGGTTCGATGGTTAATGAAGCACCTACG
          1 CTGTGAGTGTCAAAGCACATACAGTTAATGAAGTTGGTGGTTCAACGGTTAATGAAGCACCTACG

                 *  *          *        *         *  *  *                    
       1285 GTTAATGAGGTTGATAACGGTGGCTCAAGCATTACCAGTGGTAAGTTGAGGAGAAGGACATGCTA
         66 GTTAACGAAGTTGATAACGATGGCTCAACCATTACCAGCGGGAAATTGAGGAGAAGGACATGCTA

            *                       *           *                            
       1350 TGAGTGCGGACAAAAGGGCCATATTTCTTCTGCTTGTCCAAAAGGATCTGCGAGTGTCAAAGCAA
        131 CGAGTGCGGACAAAAGGGCCATATCTCTTCTGCTTGCCCAAAAGGATCTGCGAGTGTCAAAGCAA

                              *                                              
       1415 CTGTGAGTGTCAAAGCACCTACAGTTAATGAAGTTGGCAACGGTGGTTCAACGGTTAATGAAGCA
          1 CTGTGAGTGTCAAAGCACATACAGTTAATGAAGTT------GGTGGTTCAACGGTTAATGAAGCA

                               *   *       **   *   *                        
       1480 CCTACGGTTAACGAAGTTGCTAATGATGGCTTGACCGTTAGCAGCGGGAAATTGAGGAGAAGGAC
         60 CCTACGGTTAACGAAGTTGATAACGATGGCTCAACCATTACCAGCGGGAAATTGAGGAGAAGGAC

                                    *                       
       1545 ATGCTACGAGTGCGGACAAAAGGGTCATATCTCTTCTGCTTGCCCAAA
        125 ATGCTACGAGTGCGGACAAAAGGGCCATATCTCTTCTGCTTGCCCAAA

       1593 TAAGAAATCT


Statistics
Matches: 150,  Mismatches: 22, Indels: 6
        0.84            0.12        0.03

Matches are distributed among these distances:
 195   32  0.21
 201  118  0.79

ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25


Consensus pattern (195 bp):   
CTGTGAGTGTCAAAGCACATACAGTTAATGAAGTTGGTGGTTCAACGGTTAATGAAGCACCTACG
GTTAACGAAGTTGATAACGATGGCTCAACCATTACCAGCGGGAAATTGAGGAGAAGGACATGCTA
CGAGTGCGGACAAAAGGGCCATATCTCTTCTGCTTGCCCAAAAGGATCTGCGAGTGTCAAAGCAA
Done.