Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001241.1 Corchorus capsularis cultivar CVL-1 contig01241, 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: 11376
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:532 original size:19 final size:20

Alignment explanation


    Indices: 508--547  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

        498 AAGGCAGCAA

                                
        508 CAGCAAAACA-GGGAAAGAG
          1 CAGCAAAACAGGGGAAAGAG

                                
        527 CAGCAAAACAGGGGAAAGAG
          1 CAGCAAAACAGGGGAAAGAG

             
        547 C
          1 C

        548 GCTAGTTGGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   10  0.50
  20   10  0.50

ACGTcount: A:0.50, C:0.17, G:0.33, T:0.00


Consensus pattern (20 bp):   
CAGCAAAACAGGGGAAAGAG

Found at i:684 original size:9 final size:9

Alignment explanation


    Indices: 670--712  Score: 54
    Period size: 9  Copynumber: 4.9  Consensus size: 9

        660 TAATATTAAT

                     
        670 ATATATATA
          1 ATATATATA

                     
        679 ATATATATA
          1 ATATATATA

                      
        688 ACTA-AT-TA
          1 A-TATATATA

             *       
        696 AAATATATA
          1 ATATATATA

                    
        705 ATATATAT
          1 ATATATAT

        713 GATTTGTCGG


Statistics
Matches: 29,  Mismatches: 2, Indels: 6
        0.78            0.05        0.16

Matches are distributed among these distances:
   7    1  0.03
   8    5  0.17
   9   21  0.72
  10    2  0.07

ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42


Consensus pattern (9 bp):   
ATATATATA

Found at i:4744 original size:48 final size:49

Alignment explanation


    Indices: 4665--4808  Score: 138
    Period size: 48  Copynumber: 3.0  Consensus size: 49

       4655 CTAAAAATGA

                                                    *          
       4665 TCTAAAATCTAAAGGCTAATC-TC-CATGACTTCC-GGAGGCCAAAATTGG
          1 TCTAAAATCTAAAGGCTAATCATCACA-GACTTCCGGGA-ACCAAAATTGG

                    *                                   *    
       4713 TCTAAAATTTAAAGGCTAATCATCACA-ACTTCCGGGAACCAAATTTGG
          1 TCTAAAATCTAAAGGCTAATCATCACAGACTTCCGGGAACCAAAATTGG

            *        *                    *  *  *  *          
       4761 CCTAAAATCCAAAGGCT-ATCCATCAC-GATTTTCGAGACCCAAAATTGG
          1 TCTAAAATCTAAAGGCTAAT-CATCACAGACTTCCGGGAACCAAAATTGG

       4809 CTACAAAGGC


Statistics
Matches: 80,  Mismatches: 11, Indels: 10
        0.79            0.11        0.10

Matches are distributed among these distances:
  47    2  0.03
  48   71  0.89
  49    5  0.06
  50    2  0.03

ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25


Consensus pattern (49 bp):   
TCTAAAATCTAAAGGCTAATCATCACAGACTTCCGGGAACCAAAATTGG

Done.