Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_41065

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, 855

Length: 1425
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28


Found at i:1344 original size:21 final size:21

Alignment explanation


    Indices: 1319--1358  Score: 80
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       1309 TTGGAGTTAA

                                 
       1319 AGAATGAGAAGCTGAGATTGG
          1 AGAATGAGAAGCTGAGATTGG

                               
       1340 AGAATGAGAAGCTGAGATT
          1 AGAATGAGAAGCTGAGATT

       1359 AGAATTAGAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.40, C:0.05, G:0.35, T:0.20


Consensus pattern (21 bp):   
AGAATGAGAAGCTGAGATTGG

Found at i:1369 original size:21 final size:20

Alignment explanation


    Indices: 1319--1373  Score: 76
    Period size: 21  Copynumber: 2.6  Consensus size: 20

       1309 TTGGAGTTAA

                                 
       1319 AGAATGAGAAGCTGAGATTGG
          1 AGAATGAGAAGCTGAGATT-G

                                
       1340 AGAATGAGAAGCTGAGATT-
          1 AGAATGAGAAGCTGAGATTG

                           
       1359 AGAATTAGAGAAGCT
          1 AGAA-T-GAGAAGCT

       1374 CAAAATGCAT


Statistics
Matches: 32,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  19    4  0.12
  20    1  0.03
  21   27  0.84

ACGTcount: A:0.42, C:0.05, G:0.33, T:0.20


Consensus pattern (20 bp):   
AGAATGAGAAGCTGAGATTG

Found at i:1369 original size:27 final size:25

Alignment explanation


    Indices: 1292--1370  Score: 76
    Period size: 27  Copynumber: 3.2  Consensus size: 25

       1282 TTGTTGCACC

                     *                *
       1292 AGAATGAGAGGCTGAGATTGGAGTTAA
          1 AGAATGAGAAGCTGAGATT-GA-TTAG

                                     
       1319 AGAATGAGAAGCTGAGATTG----G
          1 AGAATGAGAAGCTGAGATTGATTAG

                                       
       1340 AGAATGAGAAGCTGAGATTAGAATTAG
          1 AGAATGAGAAGCTGAGATT-G-ATTAG

                
       1367 AGAA
          1 AGAA

       1371 GCTCAAAATG


Statistics
Matches: 44,  Mismatches: 2, Indels: 12
        0.76            0.03        0.21

Matches are distributed among these distances:
  21   19  0.43
  22    1  0.02
  26    1  0.02
  27   23  0.52

ACGTcount: A:0.42, C:0.04, G:0.34, T:0.20


Consensus pattern (25 bp):   
AGAATGAGAAGCTGAGATTGATTAG
Done.