Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013097.1 Corchorus olitorius cultivar O-4 contig13130, 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: 2521
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37


Found at i:874 original size:30 final size:29

Alignment explanation


    Indices: 831--887  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

        821 TTAGGATTAG

                                         
        831 TTATTTATGCTTTAATTTTCAA-TTTCTT
          1 TTATTTATGCTTTAATTTTCAAGTTTCTT

                                         
        859 TTATCTTATGTCTTTAATTTTCAAGTTTC
          1 TTAT-TTATG-CTTTAATTTTCAAGTTTC

        888 ATTAATAAAC


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61


Consensus pattern (29 bp):   
TTATTTATGCTTTAATTTTCAAGTTTCTT

Found at i:2431 original size:21 final size:18

Alignment explanation


    Indices: 2407--2452  Score: 56
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       2397 AAGTTCGTGT

                                 
       2407 TTGAAGACATTTGAAGACAAA
          1 TTGAAGAC--TTGAAGAC-AA

                            * 
       2428 TTGAAGACTTGAAGACCA
          1 TTGAAGACTTGAAGACAA

                   
       2446 TTGAAGA
          1 TTGAAGA

       2453 ATAATTTCAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  18    8  0.33
  19    8  0.33
  21    8  0.33

ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24


Consensus pattern (18 bp):   
TTGAAGACTTGAAGACAA

Found at i:2433 original size:11 final size:10

Alignment explanation


    Indices: 2407--2452  Score: 51
    Period size: 10  Copynumber: 4.7  Consensus size: 10

       2397 AAGTTCGTGT

                     *
       2407 TTGAAGACAT
          1 TTGAAGACAA

                       
       2417 TTGAAGACAAA
          1 TTGAAGAC-AA

                      
       2428 TTGAAGAC--
          1 TTGAAGACAA

                    * 
       2436 TTGAAGACCA
          1 TTGAAGACAA

                   
       2446 TTGAAGA
          1 TTGAAGA

       2453 ATAATTTCAA


Statistics
Matches: 32,  Mismatches: 1, Indels: 6
        0.82            0.03        0.15

Matches are distributed among these distances:
   8    8  0.25
  10   15  0.47
  11    9  0.28

ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24


Consensus pattern (10 bp):   
TTGAAGACAA
Done.