Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001932.1 Corchorus olitorius cultivar O-4 contig01932, 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: 3845
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32


Found at i:487 original size:48 final size:48

Alignment explanation


    Indices: 1--523  Score: 483
    Period size: 48  Copynumber: 10.9  Consensus size: 48

                           *           *                    
          1 CCCACCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

                          **                              *  
         49 CCCACCACCACC-TGTCCACTCTCCTCCACCACCATACTACTACAAGTC
          1 CCCACCACCACCATCACCA-TCTCCTCCACCACCATACTACTACAAATC

                           *                                
         97 CCCACCACCACCATCCCCATCTCCTCCACCACCATACTACTACAAATC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

                            *                              *  
        145 CCCACCACCACC--CGTCCACTCTCCTCCACCACCATACTACTACAAGTC
          1 CCCACCACCACCATC-ACCA-TCTCCTCCACCACCATACTACTACAAATC

                           *           *                    
        193 CCCACCACCACCATCGCCATCTCCTCCTCCACCATACTACTACAAATC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

                                   *                          
        241 CCCACCACCACCAGT--CCATTCCCCTCCACCACCATACTACTACAAATC
          1 CCCACCACCACCA-TCACCA-TCTCCTCCACCACCATACTACTACAAATC

            *     *  *        *  *    **            * *     *  
        289 ACCACCTCCTCCAGT-A-GAGGCTCCAGCACCCACC-TACCAGTACAAGTC
          1 CCCACCACCACCA-TCACCA-TCTCCTCCA-CCACCATACTACTACAAATC

                     *           *  *                       
        337 CCCACCACCTCCATCACCATCACCACCACCACCATACTACTACAAATC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

                                       *     *  *           *  
        385 TCCC-CCACCACCAGTTCA-C-TCTCCACCACCCCCCTACTACTACAAGTC
          1 -CCCACCACCACCA--TCACCATCTCCTCCACCACCATACTACTACAAATC

                  *     *        *  *     *        *     *  
        433 CCCACCTCCACCTTCACCATCACCACCACCTCCATACTATTACAAGTC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

                  *  *  *     *  *  *  *  *            
        481 CCCACCTCCTCCCTCACCCTCACCCCCTCCCCCATACTACTAC
          1 CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTAC

        524 CACTCACCTC


Statistics
Matches: 403,  Mismatches: 53, Indels: 38
        0.82            0.11        0.08

Matches are distributed among these distances:
  46    4  0.01
  47   20  0.05
  48  357  0.89
  49   18  0.04
  50    4  0.01

ACGTcount: A:0.26, C:0.53, G:0.03, T:0.18


Consensus pattern (48 bp):   
CCCACCACCACCATCACCATCTCCTCCACCACCATACTACTACAAATC

Found at i:3152 original size:22 final size:22

Alignment explanation


    Indices: 3104--3165  Score: 81
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       3094 ATTAAATATT

                               *  
       3104 TTTATGAAATTTTGATAACTAC
          1 TTTATGAAATTTTGATAACCAC

                 *                
       3126 TTTATTAAATTTTGATAACCA-
          1 TTTATGAAATTTTGATAACCAC

                   *           
       3147 TCTTATGGAATTTTGATAA
          1 T-TTATGAAATTTTGATAA

       3166 TTTACCTATG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    1  0.03
  22   34  0.97

ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47


Consensus pattern (22 bp):   
TTTATGAAATTTTGATAACCAC

Found at i:3271 original size:24 final size:23

Alignment explanation


    Indices: 3200--3273  Score: 114
    Period size: 23  Copynumber: 3.2  Consensus size: 23

       3190 GATAACCTAA

                *                  
       3200 CTATGAAATTTTAATAAACCTTC
          1 CTATAAAATTTTAATAAACCTTC

                                   
       3223 CTATAAAATTTTAATAAACCTTC
          1 CTATAAAATTTTAATAAACCTTC

                                     
       3246 CTATAAAATTTTGTAAT-AACCTTC
          1 CTATAAAA-TTT-TAATAAACCTTC

                
       3270 CTAT
          1 CTAT

       3274 GATTTTTGAT


Statistics
Matches: 48,  Mismatches: 1, Indels: 3
        0.92            0.02        0.06

Matches are distributed among these distances:
  23   30  0.62
  24   14  0.29
  25    4  0.08

ACGTcount: A:0.39, C:0.18, G:0.03, T:0.41


Consensus pattern (23 bp):   
CTATAAAATTTTAATAAACCTTC
Done.