Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008243.1 Corchorus olitorius cultivar O-4 contig08270, 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, 621

Length: 1035
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43


Found at i:329 original size:2 final size:2

Alignment explanation


    Indices: 322--379  Score: 62
    Period size: 2  Copynumber: 28.5  Consensus size: 2

        312 ATTGTTAGGA

                                          *        *        *        *    
        322 AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT AT CT AT AT CT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

               *                   
        364 AT CT AT AT ACT AT AT A
          1 AT AT AT AT A-T AT AT A

        380 AGTCTAAACT


Statistics
Matches: 45,  Mismatches: 10, Indels: 2
        0.79            0.18        0.04

Matches are distributed among these distances:
   2   43  0.96
   3    2  0.04

ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:339 original size:12 final size:12

Alignment explanation


    Indices: 322--378  Score: 78
    Period size: 12  Copynumber: 4.7  Consensus size: 12

        312 ATTGTTAGGA

                    *   
        322 ATATATATATAT
          1 ATATATATCTAT

                        
        334 ATATATATCTAT
          1 ATATATATCTAT

              *         
        346 ATCTATATCTAT
          1 ATATATATCTAT

              *         
        358 ATCTATATCTAT
          1 ATATATATCTAT

                     
        370 ATACTATAT
          1 ATA-TATAT

        379 AAGTCTAAAC


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  12   36  0.88
  13    5  0.12

ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49


Consensus pattern (12 bp):   
ATATATATCTAT

Found at i:352 original size:18 final size:18

Alignment explanation


    Indices: 325--378  Score: 81
    Period size: 18  Copynumber: 2.9  Consensus size: 18

        315 GTTAGGAATA

                 *            
        325 TATATATATATATATATC
          1 TATATCTATATATATATC

                       *      
        343 TATATCTATATCTATATC
          1 TATATCTATATATATATC

                              
        361 TATATCTATATACTATAT
          1 TATATCTATATA-TATAT

        379 AAGTCTAAAC


Statistics
Matches: 32,  Mismatches: 3, Indels: 1
        0.89            0.08        0.03

Matches are distributed among these distances:
  18   27  0.84
  19    5  0.16

ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50


Consensus pattern (18 bp):   
TATATCTATATATATATC
Done.