Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011908.1 Corchorus capsularis cultivar CVL-1 contig11929, whole genome shotgun sequence

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: 16725
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:4912 original size:23 final size:24

Alignment explanation


    Indices: 4871--4923  Score: 74
    Period size: 23  Copynumber: 2.3  Consensus size: 24

       4861 CCAAATATGA

                          *         
       4871 TACAAAGAATGACTTAAACCAAGT
          1 TACAAAGAATGACTCAAACCAAGT

                        *           
       4895 TACAAAG-ATGAGTCAAACCAAGT
          1 TACAAAGAATGACTCAAACCAAGT

                   
       4918 TA-AAAG
          1 TACAAAG

       4924 GGACAAATAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  22    4  0.15
  23   16  0.59
  24    7  0.26

ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19


Consensus pattern (24 bp):   
TACAAAGAATGACTCAAACCAAGT

Found at i:10883 original size:39 final size:38

Alignment explanation


    Indices: 10827--10909  Score: 112
    Period size: 39  Copynumber: 2.2  Consensus size: 38

      10817 TGATTCTATG

                        *            *            
      10827 AAAAAATAGAGAGAAATATTTGGAATAATTAGCAGCAA
          1 AAAAAATAGAGAAAAATATTTGGAAAAATTAGCAGCAA

                   *                         *  *  
      10865 AAAAAATGGAAGAAAAATATTTGGAAAAATTAGTAGGAA
          1 AAAAAATAG-AGAAAAATATTTGGAAAAATTAGCAGCAA

                  
      10904 AAAAAA
          1 AAAAAA

      10910 AGTGTGTTAA


Statistics
Matches: 39,  Mismatches: 5, Indels: 1
        0.87            0.11        0.02

Matches are distributed among these distances:
  38    8  0.21
  39   31  0.79

ACGTcount: A:0.60, C:0.02, G:0.18, T:0.19


Consensus pattern (38 bp):   
AAAAAATAGAGAAAAATATTTGGAAAAATTAGCAGCAA

Found at i:15454 original size:24 final size:24

Alignment explanation


    Indices: 15420--15474  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      15410 TTAATCAGAG

                  *             *    
      15420 TTGACACTTTG-ATGAGTTTTTTGC
          1 TTGACATTTTGCATG-GTTTATTGC

                        *           
      15444 TTGACATTTTGCTTGGTTTATTGC
          1 TTGACATTTTGCATGGTTTATTGC

                   
      15468 TTGACAT
          1 TTGACAT

      15475 GTGGAGTGGG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  24   25  0.93
  25    2  0.07

ACGTcount: A:0.16, C:0.13, G:0.20, T:0.51


Consensus pattern (24 bp):   
TTGACATTTTGCATGGTTTATTGC
Done.