Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023416.1 Corchorus olitorius cultivar O-4 contig23449, 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: 8912
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:482 original size:13 final size:12

Alignment explanation


    Indices: 464--508  Score: 54
    Period size: 14  Copynumber: 3.5  Consensus size: 12

        454 ATTTTATTAC

                         
        464 TGTTTTATTAAAT
          1 TGTTTTA-TAAAT

                        
        477 TGTTTTATAAAT
          1 TGTTTTATAAAT

            *             
        489 GGTTTTAAATAAAT
          1 TGTTTT--ATAAAT

                  
        503 TGTTTT
          1 TGTTTT

        509 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    7  0.25
  14   11  0.39

ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58


Consensus pattern (12 bp):   
TGTTTTATAAAT

Found at i:3299 original size:26 final size:27

Alignment explanation


    Indices: 3243--3314  Score: 92
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       3233 AGGGTCACCC

                                       
       3243 AGGGGCATTTTGGTCATTTGCACACTA
          1 AGGGGCATTTTGGTCATTTGCACACTA

                     *            * * *
       3270 A-GGGCATTCTGGTCATTTGCATATTC
          1 AGGGGCATTTTGGTCATTTGCACACTA

                        *      
       3296 AGGGGCATTTTGATCATTT
          1 AGGGGCATTTTGGTCATTT

       3315 TTTAGATTAG


Statistics
Matches: 38,  Mismatches: 6, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  26   22  0.58
  27   16  0.42

ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGCACACTA

Found at i:3825 original size:20 final size:20

Alignment explanation


    Indices: 3800--3840  Score: 73
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3790 GAAAATACAA

                                
       3800 GGCATTTGATTTACAAATTG
          1 GGCATTTGATTTACAAATTG

                        *       
       3820 GGCATTTGATTTGCAAATTG
          1 GGCATTTGATTTACAAATTG

             
       3840 G
          1 G

       3841 TGCTCTTTTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.27, C:0.10, G:0.24, T:0.39


Consensus pattern (20 bp):   
GGCATTTGATTTACAAATTG

Found at i:5981 original size:21 final size:21

Alignment explanation


    Indices: 5957--6048  Score: 150
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       5947 CTTAGGCAAT

                                 
       5957 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                                 
       5978 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                         *       
       5999 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                         *        
       6020 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGAAACCTT-C

                    
       6041 TCCAATGA
          1 TCCAATGA

       6049 TCTCCTAGCA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   66  0.96

ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACCTTC

Done.