Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold403

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: 8626
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Found at i:2007 original size:77 final size:81

Alignment explanation


    Indices: 1873--2055  Score: 218
    Period size: 77  Copynumber: 2.3  Consensus size: 81

       1863 TTGAATGATG

                                                   *                         
       1873 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCA-T
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT

                            
       1936 T-TGCGAGATACTA-A
         66 TGTGCGAGATACTATA

                                           *   *  *        **                
       1950 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA

                      *       
       2012 TTTGTGCGAGTTACTATA
         64 TTTGTGCGAGATACTATA

            *        *                
       2030 ACCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       2056 AACGAGTAGC


Statistics
Matches: 90,  Mismatches: 9, Indels: 10
        0.83            0.08        0.09

Matches are distributed among these distances:
  76    1  0.01
  77   34  0.38
  78   20  0.22
  79   20  0.22
  80   15  0.17

ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25


Consensus pattern (81 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA

Found at i:2017 original size:40 final size:40

Alignment explanation


    Indices: 1873--2055  Score: 216
    Period size: 40  Copynumber: 4.7  Consensus size: 40

       1863 TTGAATGATG

                                          *   *  * * 
       1873 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                           *      *
       1913 TCCGGACTAAGAT-CCGAAGGCA-TT-TGCGAGATACTAAT
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

                                                    
       1951 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                                  
       1990 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA

                     *                
       2031 -CCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       2056 AACGAGTAGC


Statistics
Matches: 123,  Mismatches: 13, Indels: 14
        0.82            0.09        0.09

Matches are distributed among these distances:
  37    9  0.07
  38   17  0.14
  39   25  0.20
  40   69  0.56
  41    3  0.02

ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

Found at i:2078 original size:79 final size:76

Alignment explanation


    Indices: 1924--2087  Score: 190
    Period size: 79  Copynumber: 2.1  Consensus size: 76

       1914 CCGGACTAAG

                                       *                        **           
       1924 ATCCGAAGGCATTTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
          1 ATCCGAAGGCATTTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA

                       
       1989 ATCCGGGTTAA
         66 ATCCGGGTTAA

            *                     *                 *                        
       2000 GTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-T
          1 AT-CCGAAGGCA-TT-TGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTT

                 *           
       2063 AGCTATATCC-GGTTAA
         61 A-CTAAATCCGGGTTAA

                     
       2079 ATCCGAAGG
          1 ATCCGAAGG

       2088 TACGTGATTT


Statistics
Matches: 74,  Mismatches: 8, Indels: 10
        0.80            0.09        0.11

Matches are distributed among these distances:
  76    1  0.01
  77    9  0.12
  78   11  0.15
  79   28  0.38
  80   25  0.34

ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25


Consensus pattern (76 bp):   
ATCCGAAGGCATTTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAA
Done.