Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007805.1 Corchorus olitorius cultivar O-4 contig07832, 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, 684

Length: 1141
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36


Found at i:70 original size:22 final size:22

Alignment explanation


    Indices: 45--264  Score: 92
    Period size: 22  Copynumber: 10.0  Consensus size: 22

         35 TATCAGTATA

                              *  *
         45 TCATATGGAGGTTATCAACATC
          1 TCATATGGAGGTTATCAAAATT

                    **             
         67 TCATAGTGTTGGTTATCAAAATT
          1 TCATA-TGGAGGTTATCAAAATT

                      *            
         90 TCAT-TGGGAAGTTATCAAAATT
          1 TCATAT-GGAGGTTATCAAAATT

                                    
        112 TCATA-GTGAGGTCT-TCAAAATT
          1 TCATATG-GAGGT-TATCAAAATT

            * *  *        *        
        134 CCTTAGGGAGGTTAACAAAATTT
          1 TCATATGGAGGTTATCAAAA-TT

                 * *   *  **      
        157 TCATAAGAAGGCTAAAAAAATT
          1 TCATATGGAGGTTATCAAAATT

                 ***     *  *     
        179 T-ATAAAAAGGTTCTCGAAATT
          1 TCATATGGAGGTTATCAAAATT

            *      *  *     *      
        200 GCATA-GTATCGTTATTAAAATT
          1 TCATATGGA-GGTTATCAAAATT

                                   
        222 TCATA-GGAAGGTTATCAAAATT
          1 TCATATGG-AGGTTATCAAAATT

             * * *      *        
        244 TTACAAGGAGGTCATCAAAAT
          1 TCATATGGAGGTTATCAAAAT

        265 CAGTGTAATT


Statistics
Matches: 149,  Mismatches: 37, Indels: 24
        0.71            0.18        0.11

Matches are distributed among these distances:
  21   18  0.12
  22   93  0.62
  23   38  0.26

ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33


Consensus pattern (22 bp):   
TCATATGGAGGTTATCAAAATT

Found at i:80 original size:45 final size:45

Alignment explanation


    Indices: 31--119  Score: 108
    Period size: 45  Copynumber: 2.0  Consensus size: 45

         21 TTCCATAACG

                     **             *        *            
         31 TGGTTATCAGTATATCATAT-GGAGGTTATCAACATCTCATAGTGT
          1 TGGTTATCAAAATATCAT-TGGGAAGTTATCAAAATCTCATAGTGT

                         *                     *        
         76 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTG
          1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTG

        120 AGGTCTTCAA


Statistics
Matches: 37,  Mismatches: 6, Indels: 2
        0.82            0.13        0.04

Matches are distributed among these distances:
  44    1  0.03
  45   36  0.97

ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38


Consensus pattern (45 bp):   
TGGTTATCAAAATATCATTGGGAAGTTATCAAAATCTCATAGTGT

Found at i:93 original size:23 final size:23

Alignment explanation


    Indices: 45--161  Score: 100
    Period size: 22  Copynumber: 5.2  Consensus size: 23

         35 TATCAGTATA

                               *  *
         45 TCATA-TGGAGGTTATCAACATC
          1 TCATAGTGGAGGTTATCAAAATT

                    **             
         67 TCATAGTGTTGGTTATCAAAATT
          1 TCATAGTGGAGGTTATCAAAATT

                *     *            
         90 TCATTG-GGAAGTTATCAAAATT
          1 TCATAGTGGAGGTTATCAAAATT

                                    
        112 TCATAGT-GAGGTCT-TCAAAATT
          1 TCATAGTGGAGGT-TATCAAAATT

            * *            *        
        134 CCTTAG-GGAGGTTAACAAAATTT
          1 TCATAGTGGAGGTTATCAAAA-TT

                 
        157 TCATA
          1 TCATA

        162 AGAAGGCTAA


Statistics
Matches: 74,  Mismatches: 15, Indels: 11
        0.74            0.15        0.11

Matches are distributed among these distances:
  21    1  0.01
  22   49  0.66
  23   24  0.32

ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36


Consensus pattern (23 bp):   
TCATAGTGGAGGTTATCAAAATT

Found at i:153 original size:44 final size:45

Alignment explanation


    Indices: 51--161  Score: 120
    Period size: 45  Copynumber: 2.5  Consensus size: 45

         41 TATATCATAT

                        *  *         *                   
         51 GGAGGTTATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTG
          1 GGAGGTTATCAAAATTTCATAGTGTAGGTTATCAAAATTTCATTG

               *                                      *    
         96 GGAAGTTATCAAAATTTCATAGTG-AGGTCT-TCAAAA-TTCCTTAG
          1 GGAGGTTATCAAAATTTCATAGTGTAGGT-TATCAAAATTTCATT-G

                    *             
        140 GGAGGTTAACAAAATTTTCATA
          1 GGAGGTTATCAAAA-TTTCATA

        162 AGAAGGCTAA


Statistics
Matches: 56,  Mismatches: 7, Indels: 6
        0.81            0.10        0.09

Matches are distributed among these distances:
  43    5  0.09
  44   22  0.39
  45   29  0.52

ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35


Consensus pattern (45 bp):   
GGAGGTTATCAAAATTTCATAGTGTAGGTTATCAAAATTTCATTG
Done.