Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013061.1 Corchorus olitorius cultivar O-4 contig13094, 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: 8072
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30


Found at i:2299 original size:5 final size:5

Alignment explanation


    Indices: 2289--2313  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

       2279 AATTCATTCT

                                         
       2289 TTTTA TTTTA TTTTA TTTTA TTTTA
          1 TTTTA TTTTA TTTTA TTTTA TTTTA

       2314 ATTTCTTTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80


Consensus pattern (5 bp):   
TTTTA

Found at i:3540 original size:35 final size:35

Alignment explanation


    Indices: 3493--3805  Score: 473
    Period size: 35  Copynumber: 8.9  Consensus size: 35

       3483 AAATTCTCAG

                                               
       3493 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

            *                                  
       3528 AAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

            *                                  
       3563 AAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

                                               
       3598 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

                    *  *                       
       3633 GAATCCAGGTGGCTCGGTGTAGCATCTTCAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

                    *                   *      
       3668 GAATCCAGGTGACTCGGTGTAGCATCTTTAAAGAT
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

                           *                  * *
       3703 GAATCCAGATGACTCAGTGTAGCATCTTCAAAAAAAC
          1 GAATCCAGATGACTCGGTGTAGCATCTTC--AAAGAT

                *   *                       * *
       3740 GAATTCAGGTGACTCGGTGTAGCATCTTCAAAAAC
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

                *         *                
       3775 GAATTCAGATGACTTGGTGTAGCATCTTCAA
          1 GAATCCAGATGACTCGGTGTAGCATCTTCAA

       3806 CATGAACTCA


Statistics
Matches: 260,  Mismatches: 16, Indels: 4
        0.93            0.06        0.01

Matches are distributed among these distances:
  35  230  0.88
  37   30  0.12

ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26


Consensus pattern (35 bp):   
GAATCCAGATGACTCGGTGTAGCATCTTCAAAGAT

Found at i:4102 original size:28 final size:28

Alignment explanation


    Indices: 4062--4166  Score: 192
    Period size: 28  Copynumber: 3.8  Consensus size: 28

       4052 GGTCACTTAA

                                        
       4062 AGGGGCATTTTGGTCATTTTGCATATCC
          1 AGGGGCATTTTGGTCATTTTGCATATCC

                                        
       4090 AGGGGCATTTTGGTCATTTTGCATATCC
          1 AGGGGCATTTTGGTCATTTTGCATATCC

                                *  *    
       4118 AGGGGCATTTTGGTCATTTTACACATCC
          1 AGGGGCATTTTGGTCATTTTGCATATCC

                                 
       4146 AGGGGCATTTTGGTCATTTTG
          1 AGGGGCATTTTGGTCATTTTG

       4167 AGTGCACATT


Statistics
Matches: 74,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   74  1.00

ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39


Consensus pattern (28 bp):   
AGGGGCATTTTGGTCATTTTGCATATCC

Found at i:4569 original size:14 final size:14

Alignment explanation


    Indices: 4524--4561  Score: 76
    Period size: 14  Copynumber: 2.7  Consensus size: 14

       4514 TAGTTGCATT

                          
       4524 TTTTGCATGGCACC
          1 TTTTGCATGGCACC

                          
       4538 TTTTGCATGGCACC
          1 TTTTGCATGGCACC

                      
       4552 TTTTGCATGG
          1 TTTTGCATGG

       4562 TATCTTTTAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   24  1.00

ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39


Consensus pattern (14 bp):   
TTTTGCATGGCACC
Done.