Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013779.1 Corchorus olitorius cultivar O-4 contig13812, 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: 9814
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:347 original size:25 final size:24

Alignment explanation


    Indices: 313--359  Score: 85
    Period size: 25  Copynumber: 1.9  Consensus size: 24

        303 CGATTTGCAC

                                     
        313 AAATACCTAAGAATTTGAATTAAAA
          1 AAATACCTAAGAATTT-AATTAAAA

                                  
        338 AAATACCTAAGAATTTAATTAA
          1 AAATACCTAAGAATTTAATTAA

        360 TGTAAGTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30


Consensus pattern (24 bp):   
AAATACCTAAGAATTTAATTAAAA

Found at i:404 original size:39 final size:40

Alignment explanation


    Indices: 350--430  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

        340 ATACCTAAGA

                                             *      
        350 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
        389 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
        429 AT
          1 AT

        431 AGGAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:657 original size:2 final size:2

Alignment explanation


    Indices: 646--695  Score: 84
    Period size: 2  Copynumber: 25.5  Consensus size: 2

        636 AGTTTAGACT

                                 *                                        
        646 TA TA TA -A TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                         
        687 TA TA TA TA T
          1 TA TA TA TA T

        696 TGACATATAG


Statistics
Matches: 45,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   44  0.98

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:5453 original size:110 final size:110

Alignment explanation


    Indices: 5255--5581  Score: 579
    Period size: 110  Copynumber: 3.0  Consensus size: 110

       5245 TAGTCATTTT

                                                   *                         
       5255 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTT-TATTGTTTGGTATGTGTGCT
          1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCAATTTTGTATTGTTTGGTATGTGTGCT

                                                         
       5319 TATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
         66 TATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

                                                             *               
       5364 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCAATTTTGTATTATTTGGTATGTGTGCT
          1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCAATTTTGTATTGTTTGGTATGTGTGCT

                 *                                       
       5429 TATTTTATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
         66 TATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

                        *     *                                              
       5474 GGTGCTTGTATTGTTCTTCAAATCC-ATAGTTCATTGC-ATTTTGTATTGTTTGGTATGTGTGCT
          1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCAATTTTGTATTGTTTGGTATGTGTGCT

                                      *                  
       5537 TATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATAATA
         66 TATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

       5582 TATATATAAT


Statistics
Matches: 209,  Mismatches: 8, Indels: 3
        0.95            0.04        0.01

Matches are distributed among these distances:
 108   68  0.33
 109   55  0.26
 110   86  0.41

ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44


Consensus pattern (110 bp):   
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCAATTTTGTATTGTTTGGTATGTGTGCT
TATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

Found at i:9630 original size:2 final size:2

Alignment explanation


    Indices: 9623--9650  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       9613 ACCATGAAGG

                                                     
       9623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       9651 CAATCAATTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Done.