Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1384

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: 13021
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29


Found at i:2934 original size:39 final size:39

Alignment explanation


    Indices: 2832--3059  Score: 354
    Period size: 39  Copynumber: 5.9  Consensus size: 39

       2822 GATATAGCTT

                 *                                 
       2832 CTCGCTCAAATGCCTTCGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTAA

                                                   
       2871 CTCGCAC-AATGCCTTCGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTAA

              *      *                             
       2909 CTAGCACAATTGCCTTCGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTAA

                     *                *             
       2948 CTCGCACAATTGCCTTCGGGACTT-GGCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTC-GGACTTAGCCCGGTTATAGTAA

                                            *       
       2987 CTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATAGTAA
          1 CTCGCACAAATGCCTTC-GGACTTAGCCCGGTTATAGTAA

                               *              
       3026 CTCGCACAAATGCCTTCGGGCTTAGCCCGGTTAT
          1 CTCGCACAAATGCCTTCGGACTTAGCCCGGTTAT

       3060 CATCCGAATA


Statistics
Matches: 175,  Mismatches: 10, Indels: 8
        0.91            0.05        0.04

Matches are distributed among these distances:
  38   49  0.28
  39  115  0.66
  40   11  0.06

ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26


Consensus pattern (39 bp):   
CTCGCACAAATGCCTTCGGACTTAGCCCGGTTATAGTAA

Found at i:10814 original size:39 final size:40

Alignment explanation


    Indices: 10787--10976  Score: 318
    Period size: 40  Copynumber: 4.9  Consensus size: 40

      10777 GATATAGCTT

                 *                                  
      10787 CTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA

                     *                              
      10827 CTCGCACAATTGCCTTCGGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA

              *                                     
      10867 CTAGCAC-AATGCCTTC-GGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA

                                                    
      10905 CTCGCAC-AATGCCTTCGGGACTTAGCCCGGTTATAGTAA
          1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA

                                               
      10944 CTCGCACAAATGCCTTCGGG-CTTAG-CCGGTTAT
          1 CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT

      10977 CAATCCGAAT


Statistics
Matches: 143,  Mismatches: 5, Indels: 6
        0.93            0.03        0.04

Matches are distributed among these distances:
  38   45  0.31
  39   42  0.29
  40   56  0.39

ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27


Consensus pattern (40 bp):   
CTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAA

Found at i:10907 original size:78 final size:78

Alignment explanation


    Indices: 10793--10976  Score: 318
    Period size: 78  Copynumber: 2.4  Consensus size: 78

      10783 GCTTCTCGCT

                                                                             
      10793 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCGCACAA-TGCCTTCGGGACTTAGCCCGG

                           
      10858 TTATAGTAACTAGCA
         64 TTATAGTAACTAGCA

                                                                             
      10873 C-AATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGTT
          1 CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGTT

                     *   
      10937 ATAGTAACTCGCA
         66 ATAGTAACTAGCA

                         *              
      10950 CAAATGCCTTCGGGCTTAG-CCGGTTAT
          1 CAAATGCCTTCGGACTTAGCCCGGTTAT

      10977 CAATCCGAAT


Statistics
Matches: 101,  Mismatches: 2, Indels: 5
        0.94            0.02        0.05

Matches are distributed among these distances:
  77   44  0.44
  78   47  0.47
  79    9  0.09
  80    1  0.01

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


Consensus pattern (78 bp):   
CAAATGCCTTCGGACTTAGCCCGGTTATAGTAACTCGCACAATGCCTTCGGGACTTAGCCCGGTT
ATAGTAACTAGCA
Done.