Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15907

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: 2109
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26


Found at i:1500 original size:17 final size:17

Alignment explanation


    Indices: 1458--1500  Score: 63
    Period size: 15  Copynumber: 2.6  Consensus size: 17

       1448 TCATATCCCT

                             
       1458 TTGTCCTCTTGGAATTA
          1 TTGTCCTCTTGGAATTA

                             
       1475 -T-TCCTCTTGGAATTA
          1 TTGTCCTCTTGGAATTA

                *      
       1490 TTGTACTCTTG
          1 TTGTCCTCTTG

       1501 CAGAAAGAGC


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  15   14  0.61
  16    2  0.09
  17    7  0.30

ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49


Consensus pattern (17 bp):   
TTGTCCTCTTGGAATTA

Found at i:1921 original size:36 final size:36

Alignment explanation


    Indices: 1881--1958  Score: 120
    Period size: 36  Copynumber: 2.2  Consensus size: 36

       1871 CTCTGGAATC

                 *        *                     
       1881 AACACTACCTAAACTTGATACAAAAGAGAATCCCAA
          1 AACACAACCTAAACCTGATACAAAAGAGAATCCCAA

                                             ** 
       1917 AACACAACCTAAACCTGATACAAAAGAGAATCCTGA
          1 AACACAACCTAAACCTGATACAAAAGAGAATCCCAA

                  
       1953 AACACA
          1 AACACA

       1959 GCCGGTGCTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  36   38  1.00

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


Consensus pattern (36 bp):   
AACACAACCTAAACCTGATACAAAAGAGAATCCCAA
Done.