Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008931.1 Corchorus olitorius cultivar O-4 contig08958, 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, 640

Length: 1067
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37


Found at i:413 original size:36 final size:36

Alignment explanation


    Indices: 366--434  Score: 138
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        356 CGTCTCTATC

                                                
        366 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT
          1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT

                                             
        402 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT
          1 GTTTTCTGTATTATTAGAAATTTGTGATTCTTT

        435 CTTTTTACTT


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   33  1.00

ACGTcount: A:0.20, C:0.06, G:0.14, T:0.59


Consensus pattern (36 bp):   
GTTTTCTGTATTATTAGAAATTTGTGATTCTTTTTT

Found at i:725 original size:21 final size:21

Alignment explanation


    Indices: 699--747  Score: 80
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        689 TGTCATCATC

                  *        *     
        699 ATTATCTTTAGGATTCTTGGT
          1 ATTATCATTAGGATTATTGGT

                                 
        720 ATTATCATTAGGATTATTGGT
          1 ATTATCATTAGGATTATTGGT

                   
        741 ATTATCA
          1 ATTATCA

        748 GTATCATCGG


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  21   26  1.00

ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49


Consensus pattern (21 bp):   
ATTATCATTAGGATTATTGGT

Found at i:726 original size:27 final size:27

Alignment explanation


    Indices: 667--729  Score: 92
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        657 TTCCTCTAGT

                                       
        667 TTATCATTATCATTAGGATTCTTGTCA
          1 TTATCATTATCATTAGGATTCTTGTCA

             *         *                
        694 TCATCATTATCTTTAGGATTCTTGGT-A
          1 TTATCATTATCATTAGGATTCTT-GTCA

                     
        721 TTATCATTA
          1 TTATCATTA

        730 GGATTATTGG


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  27   30  0.94
  28    2  0.06

ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49


Consensus pattern (27 bp):   
TTATCATTATCATTAGGATTCTTGTCA

Found at i:778 original size:27 final size:27

Alignment explanation


    Indices: 748--998  Score: 423
    Period size: 27  Copynumber: 9.3  Consensus size: 27

        738 GGTATTATCA

                           *           
        748 GTATCATCGGTATTAATAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                               *       
        775 GTATCATCGGTATTAGTAAGAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        802 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        829 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                                       
        856 GTATCATCGGTATTAGTAAAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                              *      * 
        883 GTATCATCGGTATTAGTATAAGTATCG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                              *      * 
        910 GTATCATCGGTATTAGTATAAGTATCG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                           *           
        937 GTATCATCGGTATTAAT-AAAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                               *       
        963 GTATCATCGGTATTAGTAAGAGTATTG
          1 GTATCATCGGTATTAGTAAAAGTATTG

                     
        990 GTATCATCG
          1 GTATCATCG

        999 CTTTTTTTAA


Statistics
Matches: 213,  Mismatches: 10, Indels: 2
        0.95            0.04        0.01

Matches are distributed among these distances:
  26   23  0.11
  27  190  0.89

ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37


Consensus pattern (27 bp):   
GTATCATCGGTATTAGTAAAAGTATTG

Done.