Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007040.1 Corchorus olitorius cultivar O-4 contig07065, 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, 795

Length: 1325
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30


Found at i:786 original size:28 final size:27

Alignment explanation


    Indices: 753--905  Score: 186
    Period size: 28  Copynumber: 5.7  Consensus size: 27

        743 AAAAATCAAG

                                       
        753 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCATTTTTCACATTCA

                    *               * * 
        780 GTGGCATTATGGTCATTTTT-ACACTAA
          1 G-GGCATTTTGGTCATTTTTCACATTCA

                                       
        807 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCATTTTTCACATTCA

                    *               * * 
        834 GTGGCATTATGGTCATTTTT-ACACTAA
          1 G-GGCATTTTGGTCATTTTTCACATTCA

                                 *     
        861 GGGCATTTTGGTCA-TTTTCATATTCA
          1 GGGCATTTTGGTCATTTTTCACATTCA

                   *           
        887 GGGGCATGTTGGTCATTTT
          1 -GGGCATTTTGGTCATTTT

        906 GAGTCCACTT


Statistics
Matches: 106,  Mismatches: 14, Indels: 11
        0.81            0.11        0.08

Matches are distributed among these distances:
  25    4  0.04
  26   33  0.31
  27   32  0.30
  28   37  0.35

ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43


Consensus pattern (27 bp):   
GGGCATTTTGGTCATTTTTCACATTCA

Found at i:816 original size:54 final size:54

Alignment explanation


    Indices: 753--905  Score: 265
    Period size: 54  Copynumber: 2.9  Consensus size: 54

        743 AAAAATCAAG

                                                                  
        753 GGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTACACTAA
          1 GGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTACACTAA

                                                                  
        807 GGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTACACTAA
          1 GGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTACACTAA

                                 *      *                  
        861 GGGCATTTTGGTCA-TTTTCATATTCAGGGGCATGT-TGGTCATTTT
          1 GGGCATTTTGGTCATTTTTCACATTCAGTGGCAT-TATGGTCATTTT

        906 GAGTCCACTT


Statistics
Matches: 96,  Mismatches: 2, Indels: 3
        0.95            0.02        0.03

Matches are distributed among these distances:
  53   27  0.28
  54   69  0.72

ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43


Consensus pattern (54 bp):   
GGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTACACTAA

Found at i:818 original size:26 final size:26

Alignment explanation


    Indices: 753--905  Score: 171
    Period size: 27  Copynumber: 5.7  Consensus size: 26

        743 AAAAATCAAG

                                     * 
        753 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCATTTTT-ACATTAA

                    *              *   
        780 GTGGCATTATGGTCATTTTTACACTAA
          1 G-GGCATTTTGGTCATTTTTACATTAA

                                     * 
        807 GGGCATTTTGGTCATTTTTCACATTCA
          1 GGGCATTTTGGTCATTTTT-ACATTAA

                    *              *   
        834 GTGGCATTATGGTCATTTTTACACTAA
          1 G-GGCATTTTGGTCATTTTTACATTAA

                              * *     *
        861 GGGCATTTTGGTCATTTTCATATTCAG
          1 GGGCATTTTGGTCATTTTTACATT-AA

                  *           
        888 GGGCATGTTGGTCATTTT
          1 GGGCATTTTGGTCATTTT

        906 GAGTCCACTT


Statistics
Matches: 107,  Mismatches: 15, Indels: 8
        0.82            0.12        0.06

Matches are distributed among these distances:
  26   36  0.34
  27   37  0.35
  28   34  0.32

ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43


Consensus pattern (26 bp):   
GGGCATTTTGGTCATTTTTACATTAA
Done.