Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014866.1 Corchorus olitorius cultivar O-4 contig14899, 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: 11563
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--38  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

                                                                    
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         39 AATACCTAAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:6908 original size:13 final size:13

Alignment explanation


    Indices: 6891--6920  Score: 51
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       6881 TAAAAAAATA

                          
       6891 AAAAACTAAAAACT
          1 AAAAA-TAAAAACT

                         
       6905 AAAAATAAAAACT
          1 AAAAATAAAAACT

               
       6918 AAA
          1 AAA

       6921 GTTTAAAAGG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   11  0.69
  14    5  0.31

ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13


Consensus pattern (13 bp):   
AAAAATAAAAACT

Found at i:6909 original size:8 final size:7

Alignment explanation


    Indices: 6891--6920  Score: 53
    Period size: 7  Copynumber: 4.4  Consensus size: 7

       6881 TAAAAAAATA

                   
       6891 AAAAACT
          1 AAAAACT

                   
       6898 AAAAACT
          1 AAAAACT

                   
       6905 AAAAA-T
          1 AAAAACT

                   
       6911 AAAAACT
          1 AAAAACT

               
       6918 AAA
          1 AAA

       6921 GTTTAAAAGG


Statistics
Matches: 22,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   6    6  0.27
   7   16  0.73

ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13


Consensus pattern (7 bp):   
AAAAACT

Found at i:7919 original size:16 final size:17

Alignment explanation


    Indices: 7890--7924  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       7880 GTTAAAACAT

                             
       7890 ATATATTAAAAATTAAA
          1 ATATATTAAAAATTAAA

                     *       
       7907 ATAT-TTAATAATTAAA
          1 ATATATTAAAAATTAAA

              
       7923 AT
          1 AT

       7925 TCCACGTCAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   13  0.76
  17    4  0.24

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (17 bp):   
ATATATTAAAAATTAAA
Done.