Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_01596

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, 977

Length: 1629
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27


Found at i:1475 original size:72 final size:71

Alignment explanation


    Indices: 1378--1617  Score: 318
    Period size: 72  Copynumber: 3.3  Consensus size: 71

       1368 GGATGAACTT

                             *                                               
       1378 GAGAAGGATGAGGCCTCAAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACACAA
          1 GAGAAGGATGA-GCCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACACAA

                   
       1443 GTATCTC
         65 GTATCTC

            *               *                                       *        
       1450 AAGAAGGATGAGCCCTTGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATTGAACACAA
          1 GAGAAGGATGAG-CCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACACAA

              *  * 
       1515 GTGTCCC
         65 GTATCTC

                    *    *                           * *    *                
       1522 GAGAAGGACGAAGTCTCGAAGAAAGCCGAGGTTAAAGAATCCCAAGAATTGAAAATCGAACACAA
          1 GAGAAGGATG-AGCCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACACAA

            *      
       1587 ATATCTC
         65 GTATCTC

                 *  *               
       1594 GAGAAAGAGGAAGCCTCGAAGAAA
          1 GAGAAGGATG-AGCCTCGAAGAAA

       1618 ACCAAATTTT


Statistics
Matches: 146,  Mismatches: 20, Indels: 4
        0.86            0.12        0.02

Matches are distributed among these distances:
  71    1  0.01
  72  143  0.98
  73    2  0.01

ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15


Consensus pattern (71 bp):   
GAGAAGGATGAGCCTCGAAGAAAGCCGAGGTTAAAGAATCTCGAGAACTGAAAATCGAACACAAG
TATCTC
Done.