Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010216.1 Corchorus olitorius cultivar O-4 contig10248, 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: 2969
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37


Found at i:1973 original size:21 final size:21

Alignment explanation


    Indices: 1947--1993  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1937 TCTCACAGGG

                                  
       1947 AGGTTATCAAAA-ATCATAGAA
          1 AGGTTA-CAAAATATCATAGAA

                        *      * 
       1968 AGGTTACAAAATTTCATAGGA
          1 AGGTTACAAAATATCATAGAA

                 
       1989 AGGTT
          1 AGGTT

       1994 TATTAAAATC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20    5  0.22
  21   18  0.78

ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28


Consensus pattern (21 bp):   
AGGTTACAAAATATCATAGAA

Found at i:2064 original size:43 final size:44

Alignment explanation


    Indices: 2015--2117  Score: 129
    Period size: 43  Copynumber: 2.4  Consensus size: 44

       2005 TATAGTTAGG

                    *                    *     *   *     
       2015 TTATCAAAGTTTCATACGG-AGTTTATCACAATTTCATACG-TAA
          1 TTATCAAAATTTCATACGGTAG-TTATCAAAATTTAATAAGATAA

                       *    *                           
       2058 TTATCAAAATTCCATAGGGTAGTTATCAAAATTTAATAAGATAA
          1 TTATCAAAATTTCATACGGTAGTTATCAAAATTTAATAAGATAA

                            
       2102 TTATCAAAATTTCATA
          1 TTATCAAAATTTCATA

       2118 AAAATATTCA


Statistics
Matches: 51,  Mismatches: 7, Indels: 3
        0.84            0.11        0.05

Matches are distributed among these distances:
  43   31  0.61
  44   20  0.39

ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37


Consensus pattern (44 bp):   
TTATCAAAATTTCATACGGTAGTTATCAAAATTTAATAAGATAA

Found at i:2086 original size:22 final size:21

Alignment explanation


    Indices: 1970--2117  Score: 104
    Period size: 22  Copynumber: 6.8  Consensus size: 21

       1960 TCATAGAAAG

                               * 
       1970 GTTA-CAAAATTTCATAGGAA
          1 GTTATCAAAATTTCATAGGTA

                   *             *  
       1990 GGTTTATTAAAATCTT-ATAGTTA
          1 -G-TTATCAAAAT-TTCATAGGTA

                      *            
       2013 GGTTATCAAAGTTTCATACGG-A
          1 -GTTATCAAAATTTCATA-GGTA

                    *         *   
       2035 GTTTATCACAATTTCATACGTA
          1 G-TTATCAAAATTTCATAGGTA

            *           *         
       2057 ATTATCAAAATTCCATAGGGTA
          1 GTTATCAAAATTTCATA-GGTA

                         *     *  
       2079 GTTATCAAAATTTAATAAGATA
          1 GTTATCAAAATTTCAT-AGGTA

            *                
       2101 ATTATCAAAATTTCATA
          1 GTTATCAAAATTTCATA

       2118 AAAATATTCA


Statistics
Matches: 99,  Mismatches: 19, Indels: 18
        0.73            0.14        0.13

Matches are distributed among these distances:
  21   20  0.20
  22   63  0.64
  23   14  0.14
  24    2  0.02

ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37


Consensus pattern (21 bp):   
GTTATCAAAATTTCATAGGTA

Done.