Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002319.1 Corchorus olitorius cultivar O-4 contig02319, 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, 604

Length: 1008
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:335 original size:18 final size:18

Alignment explanation


    Indices: 308--342  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

        298 TGATAGGGAA

                              
        308 TTGTTCATGAACAATTTT
          1 TTGTTCATGAACAATTTT

                 *           
        326 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

        343 CAGTTTTTGT


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

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51


Consensus pattern (18 bp):   
TTGTTCATGAACAATTTT

Found at i:619 original size:22 final size:22

Alignment explanation


    Indices: 589--649  Score: 63
    Period size: 21  Copynumber: 2.8  Consensus size: 22

        579 AGCCCTAGTC

                *                  
        589 GTTAACAAAATTTTATACG-AAG
          1 GTTATCAAAATTTTATA-GTAAG

                               ** 
        611 GTTATC-AAATTTTATAGTGTG
          1 GTTATCAAAATTTTATAGTAAG

                         *    
        632 GTTATCAAAATTTCATAG
          1 GTTATCAAAATTTTATAG

        650 GGAGGGAGGT


Statistics
Matches: 33,  Mismatches: 4, Indels: 4
        0.80            0.10        0.10

Matches are distributed among these distances:
  20    1  0.03
  21   17  0.52
  22   15  0.45

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39


Consensus pattern (22 bp):   
GTTATCAAAATTTTATAGTAAG

Found at i:671 original size:26 final size:26

Alignment explanation


    Indices: 631--680  Score: 82
    Period size: 26  Copynumber: 1.9  Consensus size: 26

        621 TTTATAGTGT

                                      
        631 GGTTATCAAAATTTCATAGGGAGGGA
          1 GGTTATCAAAATTTCATAGGGAGGGA

                      *    *        
        657 GGTTATCAAAGTTTCCTAGGGAGG
          1 GGTTATCAAAATTTCATAGGGAGG

        681 TTAACAAAAT


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

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.30, C:0.10, G:0.32, T:0.28


Consensus pattern (26 bp):   
GGTTATCAAAATTTCATAGGGAGGGA

Found at i:680 original size:22 final size:22

Alignment explanation


    Indices: 652--710  Score: 66
    Period size: 22  Copynumber: 2.7  Consensus size: 22

        642 TTTCATAGGG

                      *    *      
        652 AGGGAGGTTATCAAAGTTTCCT
          1 AGGGAGGTTAACAAAATTTCCT

                                * 
        674 AGGGAGGTTAACAAAATTTCAT
          1 AGGGAGGTTAACAAAATTTCCT

            *  *            
        696 TGGAAGGTT-ACAAAA
          1 AGGGAGGTTAACAAAA

        711 ATTTTATGGA


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  21    6  0.19
  22   26  0.81

ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27


Consensus pattern (22 bp):   
AGGGAGGTTAACAAAATTTCCT

Found at i:879 original size:22 final size:22

Alignment explanation


    Indices: 830--924  Score: 77
    Period size: 22  Copynumber: 4.4  Consensus size: 22

        820 TATCCAAAGT

                      *        *  
        830 TTTCATAGTGCGATTA-C-CAA
          1 TTTCATAGTGTGATTATCAAAA

               *                  
        850 TTTTATAGTGTGATTATCAAAA
          1 TTTCATAGTGTGATTATCAAAA

                    * *      *    
        872 TTTCATAGGGAGATTATGAAAA
          1 TTTCATAGTGTGATTATCAAAA

                 *   *  *         *
        894 TTTCACAGTATGGTTATCAAATT
          1 TTTCATAGTGTGATTATCAAA-A

                    
        917 TTTCATAG
          1 TTTCATAG

        925 GTTATCGAAA


Statistics
Matches: 57,  Mismatches: 15, Indels: 3
        0.76            0.20        0.04

Matches are distributed among these distances:
  20   14  0.25
  21    1  0.02
  22   35  0.61
  23    7  0.12

ACGTcount: A:0.34, C:0.11, G:0.16, T:0.40


Consensus pattern (22 bp):   
TTTCATAGTGTGATTATCAAAA
Done.