Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013118.1 Corchorus capsularis cultivar CVL-1 contig13139, 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: 10060
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:4742 original size:94 final size:95

Alignment explanation


    Indices: 4563--4848  Score: 481
    Period size: 94  Copynumber: 3.0  Consensus size: 95

       4553 GAGATATTTA

                                     *                                       
       4563 ATAATCTTTAGGAAGAGAAAAAAAATTCTTTAGGAAG-ACAAATTGTA-TTTTTAAATAATTTCT
          1 ATAATCTTTAGGAAGA-AAAAAAAAATCTTTAGGAAGCA-AAATTGTATTTTTTAAATAATTTCT

                                            
       4626 ATTGATTATAATATCTTTAGCAAAATTATACT
         64 ATTGATTATAATATCTTTAGCAAAATTATACT

                                           *                                 
       4658 ATAATCTTTAGGAAGAAAAAAAAAATCTTTATGAAGCAAAATTGTATTTTTTAAATAATTTCTAT
          1 ATAATCTTTAGGAAGAAAAAAAAAATCTTTAGGAAGCAAAATTGTATTTTTTAAATAATTTCTAT

                                          
       4723 TGATTATAATA-CTTTAGCAAAATTATACT
         66 TGATTATAATATCTTTAGCAAAATTATACT

                     **                                                    * 
       4752 ATAATCTTTTCGAAGAAAAAAAAAA-CTTTAGGAAGCAAAATTGTATTTTTTAAATAATTTCTGT
          1 ATAATCTTTAGGAAGAAAAAAAAAATCTTTAGGAAGCAAAATTGTATTTTTTAAATAATTTCTAT

                                          
       4816 TGATTATAATATCTTTAGCAAAATTATACT
         66 TGATTATAATATCTTTAGCAAAATTATACT

               
       4846 ATA
          1 ATA

       4849 TATACTGTTA


Statistics
Matches: 182,  Mismatches: 6, Indels: 7
        0.93            0.03        0.04

Matches are distributed among these distances:
  93   48  0.26
  94   88  0.48
  95   46  0.25

ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39


Consensus pattern (95 bp):   
ATAATCTTTAGGAAGAAAAAAAAAATCTTTAGGAAGCAAAATTGTATTTTTTAAATAATTTCTAT
TGATTATAATATCTTTAGCAAAATTATACT

Found at i:9548 original size:22 final size:22

Alignment explanation


    Indices: 9522--9637  Score: 83
    Period size: 22  Copynumber: 5.3  Consensus size: 22

       9512 CCATATGATA

                                  
       9522 AAATTTTGATAATCACACTATG
          1 AAATTTTGATAATCACACTATG

                 *        * * *   
       9544 AAATTCTGATAATCTCCCAATG
          1 AAATTTTGATAATCACACTATG

                * **    * *       *
       9566 AAATCTCAATAACCTCTA-TATA
          1 AAATTTTGATAATCAC-ACTATG

                    *        *     
       9588 AAATTTTGTTAA-CATCTCTATG
          1 AAATTTTGATAATCA-CACTATG

                         *        
       9610 AAATTTTGATAATTACACTATG
          1 AAATTTTGATAATCACACTATG

                  
       9632 AAATTT
          1 AAATTT

       9638 AGGTAACCTA


Statistics
Matches: 68,  Mismatches: 22, Indels: 8
        0.69            0.22        0.08

Matches are distributed among these distances:
  21    1  0.01
  22   66  0.97
  23    1  0.01

ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38


Consensus pattern (22 bp):   
AAATTTTGATAATCACACTATG
Done.