Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010909.1 Corchorus olitorius cultivar O-4 contig10941, 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: 3276
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31


Found at i:2166 original size:21 final size:21

Alignment explanation


    Indices: 2142--2317  Score: 239
    Period size: 21  Copynumber: 8.4  Consensus size: 21

       2132 CTTAGGCAAT

                         *       
       2142 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2163 TCCAATGATCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *            
       2184 TCCAATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

               *    *            
       2205 TCCGATGAACTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    *        *   
       2226 TCCAATGAACTTGGAACTTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2247 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                             * * 
       2268 TCCAATGAGCTTGGAACATGC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       2289 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       2310 TCCAATGA
          1 TCCAATGA

       2318 ACTTCTAGCA


Statistics
Matches: 140,  Mismatches: 12, Indels: 6
        0.89            0.08        0.04

Matches are distributed among these distances:
  20    3  0.02
  21  136  0.97
  22    1  0.01

ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:2484 original size:123 final size:123

Alignment explanation


    Indices: 2323--2546  Score: 369
    Period size: 123  Copynumber: 1.8  Consensus size: 123

       2313 AATGAACTTC

                              *              *     *                         
       2323 TAGCATCTTCAAGCTTCTTCAAGCCTCCTTGCCGCATATGCACATTCCCT-CCATGATCTCCATT
          1 TAGCATCTTCAAGCTTCTCCAAGCCTCCTTGCCACATATACACA-TCCCTGCCATGATCTCCATT

                     * *    *                                          
       2387 GTGCTCTTCTAGACCATGATGAGTCCTTGGCGCATCAGATGAGCTTGAAACTTCTTCCT
         65 GTGCTCTTCAAAACCAGGATGAGTCCTTGGCGCATCAGATGAGCTTGAAACTTCTTCCT

                                                           *                 
       2446 TAGCATCTTCAAGCTTCTCCAAGCCTCCTTGCCACATATACACATCCTTGCCATGATCTCCATTG
          1 TAGCATCTTCAAGCTTCTCCAAGCCTCCTTGCCACATATACACATCCCTGCCATGATCTCCATTG

                                                
       2511 TGCTCTTCAAAACCAGGATGAGTCCTTGGCGCATCA
         66 TGCTCTTCAAAACCAGGATGAGTCCTTGGCGCATCA

       2547 TCCCCTCTCC


Statistics
Matches: 93,  Mismatches: 7, Indels: 2
        0.91            0.07        0.02

Matches are distributed among these distances:
 122    4  0.04
 123   89  0.96

ACGTcount: A:0.22, C:0.32, G:0.16, T:0.31


Consensus pattern (123 bp):   
TAGCATCTTCAAGCTTCTCCAAGCCTCCTTGCCACATATACACATCCCTGCCATGATCTCCATTG
TGCTCTTCAAAACCAGGATGAGTCCTTGGCGCATCAGATGAGCTTGAAACTTCTTCCT
Done.