Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7499.1

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: 6755
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:567 original size:79 final size:79

Alignment explanation


    Indices: 436--593  Score: 271
    Period size: 79  Copynumber: 2.0  Consensus size: 79

        426 CTAGTAACAT

                       *              *             *                        
        436 CAGATTCGAGCTGTATGAAAAGCCTTCATGTTTATTCCGCTCTAGTGGTTTTATTCTTAACTTGC
          1 CAGATTCGAGCGGTATGAAAAGCCTTAATGTTTATTCCGCACTAGTGGTTTTATTCTTAACTTGC

                          
        501 GGGGCAGCAATGGC
         66 GGGGCAGCAATGGC

                             **                                              
        515 CAGATTCGAGCGGTATGGCAAGCCTTAATGTTTATTCCGCACTAGTGGTTTTATTCTTAACTTGC
          1 CAGATTCGAGCGGTATGAAAAGCCTTAATGTTTATTCCGCACTAGTGGTTTTATTCTTAACTTGC

                          
        580 GGGGCAGCAATGGC
         66 GGGGCAGCAATGGC

        594 TACGAAGCAG


Statistics
Matches: 74,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  79   74  1.00

ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33


Consensus pattern (79 bp):   
CAGATTCGAGCGGTATGAAAAGCCTTAATGTTTATTCCGCACTAGTGGTTTTATTCTTAACTTGC
GGGGCAGCAATGGC

Found at i:4586 original size:26 final size:26

Alignment explanation


    Indices: 4556--4607  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       4546 AAAATTAATG

                       *              
       4556 CTAATTAAACCGAAATATTGAATGTT
          1 CTAATTAAACCAAAATATTGAATGTT

                      *               
       4582 CTAATTAAACTAAAATATTGAATGTT
          1 CTAATTAAACCAAAATATTGAATGTT

       4608 TTCTTTTATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37


Consensus pattern (26 bp):   
CTAATTAAACCAAAATATTGAATGTT

Found at i:5645 original size:39 final size:38

Alignment explanation


    Indices: 5600--5678  Score: 149
    Period size: 39  Copynumber: 2.1  Consensus size: 38

       5590 ATAATTTGCA

                                                  
       5600 ATAGTTCATTGCCTATGGACACCTTTGTTTCATTTTCC
          1 ATAGTTCATTGCCTATGGACACCTTTGTTTCATTTTCC

                                                   
       5638 ATNAGTTCATTGCCTATGGACACCTTTGTTTCATTTTCC
          1 AT-AGTTCATTGCCTATGGACACCTTTGTTTCATTTTCC

              
       5677 AT
          1 AT

       5679 TTTCACTCCT


Statistics
Matches: 40,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  38    2  0.05
  39   38  0.95

ACGTcount: A:0.19, C:0.23, G:0.13, T:0.44


Consensus pattern (38 bp):   
ATAGTTCATTGCCTATGGACACCTTTGTTTCATTTTCC
Done.