Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020197.1 Corchorus olitorius cultivar O-4 contig20230, 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: 20899
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35


Found at i:45 original size:31 final size:31

Alignment explanation


    Indices: 4--65  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

          1 GAA

                 *           * *           
          4 CTCTTGATTCATAAATATTTACAATATTCAT
          1 CTCTTCATTCATAAATAATCACAATATTCAT

                        *                  
         35 CTCTTCATTCATGAATAATCACAATATTCAT
          1 CTCTTCATTCATAAATAATCACAATATTCAT

         66 TAATAACTTT


Statistics
Matches: 27,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  31   27  1.00

ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42


Consensus pattern (31 bp):   
CTCTTCATTCATAAATAATCACAATATTCAT

Found at i:6780 original size:8 final size:7

Alignment explanation


    Indices: 6754--6778  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       6744 CTAAAAAGTT

                   
       6754 AAAATAA
          1 AAAATAA

                   
       6761 AAAATAA
          1 AAAATAA

                   
       6768 AAAATAA
          1 AAAATAA

                
       6775 AAAA
          1 AAAA

       6779 ATCTGTATGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12


Consensus pattern (7 bp):   
AAAATAA

Found at i:10384 original size:25 final size:25

Alignment explanation


    Indices: 10352--10402  Score: 77
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      10342 GCTCCAATTA

                 *                   
      10352 ATTAATTTTTAATAAT-ACAATTTT
          1 ATTAAATTTTAATAATGACAATTTT

                             *       
      10376 ATTAAATTTTAATAATGGCAATTTT
          1 ATTAAATTTTAATAATGACAATTTT

              
      10401 AT
          1 AT

      10403 ACCCTAAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  24   15  0.62
  25    9  0.38

ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51


Consensus pattern (25 bp):   
ATTAAATTTTAATAATGACAATTTT

Found at i:13783 original size:6 final size:6

Alignment explanation


    Indices: 13772--13796  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      13762 TACCACATCA

                                         
      13772 AATCTC AATCTC AATCTC AATCTC A
          1 AATCTC AATCTC AATCTC AATCTC A

      13797 TGATATTTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32


Consensus pattern (6 bp):   
AATCTC

Found at i:20869 original size:2 final size:2

Alignment explanation


    Indices: 20862--20899  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

      20852 TTAGTATCTA

                                                                    
      20862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT


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):   
AT

Done.