Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023810.1 Corchorus olitorius cultivar O-4 contig23843, 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: 2163
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:507 original size:30 final size:30

Alignment explanation


    Indices: 472--565  Score: 145
    Period size: 30  Copynumber: 3.1  Consensus size: 30

        462 TATAGGCCCA

                  *   *                   
        472 CCAACACACTCCACACACATTAAAAAGGGC
          1 CCAACATACTTCACACACATTAAAAAGGGC

                                          
        502 CCAACATACTTCACACACATTAAAAAGGGC
          1 CCAACATACTTCACACACATTAAAAAGGGC

                              *            
        532 CCAACATACTTCACACACTTTAAAATA-GGC
          1 CCAACATACTTCACACACATTAAAA-AGGGC

                
        562 CCAA
          1 CCAA

        566 TGAATTTAAC


Statistics
Matches: 60,  Mismatches: 3, Indels: 2
        0.92            0.05        0.03

Matches are distributed among these distances:
  30   59  0.98
  31    1  0.02

ACGTcount: A:0.43, C:0.33, G:0.09, T:0.16


Consensus pattern (30 bp):   
CCAACATACTTCACACACATTAAAAAGGGC

Found at i:1754 original size:23 final size:21

Alignment explanation


    Indices: 1735--1780  Score: 74
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1725 AGGTTATCAT

                                 
       1735 CTTCAATCGGTAAAATTTATC
          1 CTTCAATCGGTAAAATTTATC

                *  *             
       1756 CTTCTATTGGTAAAATTTATC
          1 CTTCAATCGGTAAAATTTATC

                
       1777 CTTC
          1 CTTC

       1781 TATTCATCAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43


Consensus pattern (21 bp):   
CTTCAATCGGTAAAATTTATC

Found at i:1767 original size:21 final size:21

Alignment explanation


    Indices: 1743--1784  Score: 84
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1733 ATCTTCAATC

                                 
       1743 GGTAAAATTTATCCTTCTATT
          1 GGTAAAATTTATCCTTCTATT

                                 
       1764 GGTAAAATTTATCCTTCTATT
          1 GGTAAAATTTATCCTTCTATT

       1785 CATCATTCAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48


Consensus pattern (21 bp):   
GGTAAAATTTATCCTTCTATT
Done.