Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013444.1 Corchorus olitorius cultivar O-4 contig13477, 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: 28614
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32


Found at i:2153 original size:21 final size:21

Alignment explanation


    Indices: 2120--2168  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       2110 AAGAATTGTA

                          **     
       2120 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       2140 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       2161 GCATTCCT
          1 GC-TTCCT

       2169 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:6192 original size:11 final size:11

Alignment explanation


    Indices: 6168--6202  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       6158 GTAAAACTGT

                     * 
       6168 AAAAGTAAATA
          1 AAAAGTAAAGA

                 *     
       6179 AAAAGAAAAGA
          1 AAAAGTAAAGA

                       
       6190 AAAAGTAAAGA
          1 AAAAGTAAAGA

              
       6201 AA
          1 AA

       6203 GCAAACACTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09


Consensus pattern (11 bp):   
AAAAGTAAAGA

Found at i:14130 original size:21 final size:21

Alignment explanation


    Indices: 14091--14130  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      14081 AGGAGTTGCC

                        *        
      14091 AAAGATGCCATTTGATCCATT
          1 AAAGATGCCATTAGATCCATT

                          *    
      14112 AAAGATGCCATTAGGTCCA
          1 AAAGATGCCATTAGATCCA

      14131 ATGACAAGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28


Consensus pattern (21 bp):   
AAAGATGCCATTAGATCCATT

Found at i:24515 original size:29 final size:29

Alignment explanation


    Indices: 24483--24588  Score: 149
    Period size: 29  Copynumber: 3.7  Consensus size: 29

      24473 AGGATCACCT

                    *               *    
      24483 AGGGGCATGTTGGTCATTTTTGCATATTC
          1 AGGGGCATTTTGGTCATTTTTGCACATTC

                           **            
      24512 AGGGGCATTTTGGTCGCTTTTGCACATTC
          1 AGGGGCATTTTGGTCATTTTTGCACATTC

                *    *                   
      24541 AGGGACATTATGGTCATTTTTGCACATTC
          1 AGGGGCATTTTGGTCATTTTTGCACATTC

                 *             
      24570 AGGGGTATTTTGGTCATTT
          1 AGGGGCATTTTGGTCATTT

      24589 GTACTCCAGG


Statistics
Matches: 66,  Mismatches: 11, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   66  1.00

ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41


Consensus pattern (29 bp):   
AGGGGCATTTTGGTCATTTTTGCACATTC
Done.