Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1757

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: 5375
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40


Found at i:809 original size:22 final size:22

Alignment explanation


    Indices: 758--809  Score: 52
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        748 ATATATTAAG

                                  
        758 ATAAAATATATTAAATAAGTTA
          1 ATAAAATATATTAAATAAGTTA

            * **        *          
        780 TTTTAATATATTTAA-AAGATTA
          1 ATAAAATATATTAAATAAG-TTA

                    
        802 ATAAAATA
          1 ATAAAATA

        810 GTTTCATTTT


Statistics
Matches: 22,  Mismatches: 7, Indels: 2
        0.71            0.23        0.06

Matches are distributed among these distances:
  21    3  0.14
  22   19  0.86

ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40


Consensus pattern (22 bp):   
ATAAAATATATTAAATAAGTTA

Found at i:1584 original size:13 final size:13

Alignment explanation


    Indices: 1566--1596  Score: 62
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       1556 TTTTTCGTAA

                         
       1566 AATATTTATATTT
          1 AATATTTATATTT

                         
       1579 AATATTTATATTT
          1 AATATTTATATTT

                 
       1592 AATAT
          1 AATAT

       1597 AAATATAAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58


Consensus pattern (13 bp):   
AATATTTATATTT

Found at i:1627 original size:18 final size:17

Alignment explanation


    Indices: 1602--1641  Score: 53
    Period size: 18  Copynumber: 2.3  Consensus size: 17

       1592 AATATAAATA

                      **     
       1602 TAAAATATAATTTTTTT
          1 TAAAATATAAAATTTTT

                              
       1619 TAAATATATAAAATTTTT
          1 TAAA-ATATAAAATTTTT

                 
       1637 TAAAA
          1 TAAAA

       1642 AAATTAAAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  17    5  0.25
  18   15  0.75

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (17 bp):   
TAAAATATAAAATTTTT
Done.