Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4875

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: 13052
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31


Found at i:1950 original size:40 final size:40

Alignment explanation


    Indices: 1863--2044  Score: 203
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       1853 AATGATATCT

                                       *   *         *
       1863 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-ATATCT
          1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT-TCC

              *                                      
       1903 GGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATTCC
          1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATTCC

                                 *              *   
       1943 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC

               *                                  *  
       1982 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACC
          1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCC

                  *     *          
       2022 GGGCTATGTCCCAAAGGCATTTG
          1 GGGCTAAGTCCCGAAGGCATTTG

       2045 ACGAGTAGCT


Statistics
Matches: 122,  Mismatches: 14, Indels: 12
        0.82            0.09        0.08

Matches are distributed among these distances:
  39   36  0.30
  40   76  0.62
  41   10  0.08

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26


Consensus pattern (40 bp):   
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCC

Found at i:2050 original size:79 final size:77

Alignment explanation


    Indices: 1913--2076  Score: 199
    Period size: 79  Copynumber: 2.1  Consensus size: 77

       1903 GGACTAAGAT

                                       *             *                       
       1913 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTA
          1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATT-GTGCGAG-TAGCTA

                        *  
       1977 AATCCGGGTTAAGTC
         64 AATCC-GGTTAAATC

                                                 *                           
       1992 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCATT-TGACGAGTAGCT
          1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGTG-CGAGTAGCT

             *            *
       2055 ATATCCGGTTAAATT
         63 AAATCCGGTTAAATC

                   
       2070 CCGAAGG
          1 CCGAAGG

       2077 TATGTGATTC


Statistics
Matches: 75,  Mismatches: 6, Indels: 9
        0.83            0.07        0.10

Matches are distributed among these distances:
  78   20  0.27
  79   44  0.59
  80   11  0.15

ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26


Consensus pattern (77 bp):   
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATTGTGCGAGTAGCTAAA
TCCGGTTAAATC

Found at i:10016 original size:40 final size:40

Alignment explanation


    Indices: 9932--10123  Score: 207
    Period size: 40  Copynumber: 4.8  Consensus size: 40

       9922 TCGAATGATA

                                 *        *   *       
       9932 TCCGGGCTAAGT-CCG-AGGCTTTTGTGCTAAGTGACCT-AT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTA-CTAAT

                  *                                   
       9971 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
          1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT

                                    *              *
      10012 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT

                  *                                 
      10051 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT

             *        *                *      
      10090 AACCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT

      10124 AGCTATATCC


Statistics
Matches: 132,  Mismatches: 14, Indels: 12
        0.84            0.09        0.08

Matches are distributed among these distances:
  39   36  0.27
  40   75  0.57
  41   10  0.08
  42   11  0.08

ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT

Found at i:10074 original size:79 final size:79

Alignment explanation


    Indices: 9985--10149  Score: 219
    Period size: 79  Copynumber: 2.1  Consensus size: 79

       9975 GGACTAAGAT

                                        *                         *          
       9985 CCGAAGGCATTTGTGCGAGTTACTA-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-C
          1 CCGAAGGCATTTGTGCGAGTTACTATA-ACCGGGCTAAGTCCCGAAGGCATTGGAGCGAG-TAGC

                          *  
      10047 TAAATCCGGGTTAAGTC
         64 TAAATCC-GGTTAAATC

                                                *              *             
      10064 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAGCGAGTAGCTA
          1 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAGCTA

            *            *
      10129 TATCCGGTTAAATT
         66 AATCCGGTTAAATC

                   
      10143 CCGAAGG
          1 CCGAAGG

      10150 TATGTGATTC


Statistics
Matches: 76,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  79   50  0.66
  80   26  0.34

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25


Consensus pattern (79 bp):   
CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTGGAGCGAGTAGCTA
AATCCGGTTAAATC

Done.