Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold740

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: 7989
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30

Warning! 71 characters in sequence are not A, C, G, or T


Found at i:2334 original size:38 final size:40

Alignment explanation


    Indices: 2269--2343  Score: 102
    Period size: 38  Copynumber: 1.9  Consensus size: 40

       2259 TGAATCACAA

                                                    
       2269 CACTTTTTTTTAATTCACGAATTTTTTT-AA-TTTCTATT
          1 CACTTTTTTTTAATTCACGAATTTTTTTGAACTTTCTATT

                        *        *                
       2307 CACTTTTTTTTATTTCA-GATTTTTTTTTGAACTTTCT
          1 CACTTTTTTTTAATTCACGA-ATTTTTTTGAACTTTCT

       2344 TTTATTTCGG


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  37    2  0.06
  38   23  0.72
  39    2  0.06
  40    5  0.16

ACGTcount: A:0.20, C:0.13, G:0.04, T:0.63


Consensus pattern (40 bp):   
CACTTTTTTTTAATTCACGAATTTTTTTGAACTTTCTATT

Found at i:4992 original size:77 final size:76

Alignment explanation


    Indices: 4859--5006  Score: 203
    Period size: 77  Copynumber: 1.9  Consensus size: 76

       4849 AGATCTGATC

                                              *               *              
       4859 GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGGCAACTCGATCTTGGTTCGCGCGCAA-CCTT
          1 GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGACAACTCGATCTTGGTCCGCGCGCAATCC-T

                        
       4923 CTATCACCACGT
         65 CTATCACCACGT

                 *         *                                                 
       4935 GTCTATAGCTCTCGTTGGA-TTTTC-CTGTGACTTGACAAGCTCGATCTTGGTCCGCGCGCAATC
          1 GTCTAGAGCT-TCGTAGGAGTTTTCTC-GTGACTTGACAA-CTCGATCTTGGTCCGCGCGCAATC

                     
       4998 CTCTATCAC
         63 CTCTATCAC

       5007 TTCTCTTGGG


Statistics
Matches: 64,  Mismatches: 4, Indels: 7
        0.85            0.05        0.09

Matches are distributed among these distances:
  75    1  0.02
  76   25  0.39
  77   36  0.56
  78    2  0.03

ACGTcount: A:0.17, C:0.28, G:0.22, T:0.32


Consensus pattern (76 bp):   
GTCTAGAGCTTCGTAGGAGTTTTCTCGTGACTTGACAACTCGATCTTGGTCCGCGCGCAATCCTC
TATCACCACGT
Done.