Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024500.1 Corchorus olitorius cultivar O-4 contig24533, 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: 2794
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:887 original size:11 final size:11

Alignment explanation


    Indices: 871--896  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        861 AGATAATTTC

                       
        871 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
        882 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
        893 TTTT
          1 TTTT

        897 TTAGGCAAAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG

Found at i:1688 original size:14 final size:14

Alignment explanation


    Indices: 1657--1697  Score: 55
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       1647 TTACTCTGCT

                            
       1657 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-G-TTAA

                          
       1673 TTGTTTTCTGTTAA
          1 TTGTTTTCTGTTAA

               *       
       1687 TTGCTTTCTGT
          1 TTGTTTTCTGT

       1698 CAATCTGATA


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

Matches are distributed among these distances:
  14   14  0.58
  15    1  0.04
  16    9  0.38

ACGTcount: A:0.12, C:0.10, G:0.15, T:0.63


Consensus pattern (14 bp):   
TTGTTTTCTGTTAA

Found at i:2527 original size:21 final size:21

Alignment explanation


    Indices: 2503--2615  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

       2493 TCTTAGGATT

                         *       
       2503 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2524 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *          * 
       2545 TCCAATGAACTTGGAACCTGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2566 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                                  
       2587 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2608 TCCAATGA
          1 TCCAATGA

       2616 ACTTCTAGCA


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.