Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015089.1 Corchorus olitorius cultivar O-4 contig15122, 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: 19355
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:488 original size:19 final size:21

Alignment explanation


    Indices: 466--505  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        456 CCTTATACTA

                                 
        466 TATAA-ATTTTT-ATAACCTT
          1 TATAACATTTTTAATAACCTT

                  *              
        485 TATAACTTTTTTAATAACCTT
          1 TATAACATTTTTAATAACCTT

        506 AAAGAAGAAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19    5  0.28
  20    5  0.28
  21    8  0.44

ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53


Consensus pattern (21 bp):   
TATAACATTTTTAATAACCTT

Found at i:15585 original size:147 final size:147

Alignment explanation


    Indices: 15355--15652  Score: 416
    Period size: 147  Copynumber: 2.0  Consensus size: 147

      15345 ATTTCCATCA

                                       *  *                      * * *    *  
      15355 ATTCCTCCTACAAAATCCAATGGATTCGATCATCTTACTTGCCTAAAGCTTGAGAGTGTTACTTT
          1 ATTCCTCCTACAAAATCCAATGGATTCAATAATCTTACTTGCCTAAAGCTTGAAAATCTTACCTT

                                               *           *  *              
      15420 CAATAATGAAGGATTTGAGAATCTCATTGCAAAGTGCCCCCAACTTAGTAGATTGCACTTGAATC
         66 CAATAATGAAGGATTTGAGAATCTCATTGCAAAGTCCCCCCAACTTAATACATTGCACTTGAATC

            ***              
      15485 TTGTTGATGGATTGAAC
        131 GCCTTGATGGATTGAAC

                *           *     *                  *                       
      15502 ATTCGTCCTACAAAATTCAATGTATTCAATAATCTTACTTGGCTAAAGCTTGAAAATCTTACCTT
          1 ATTCCTCCTACAAAATCCAATGGATTCAATAATCTTACTTGCCTAAAGCTTGAAAATCTTACCTT

                                  *  *    *                                 *
      15567 CAATAATGAAGGATTTGAGAATTTCGTTGCCAAGTCCCCCCAACTTAATACATTGCACTTGAATG
         66 CAATAATGAAGGATTTGAGAATCTCATTGCAAAGTCCCCCCAACTTAATACATTGCACTTGAATC

                             
      15632 GCCTTGATGGATTGAAC
        131 GCCTTGATGGATTGAAC

                
      15649 ATTC
          1 ATTC

      15653 ATCATGCTCC


Statistics
Matches: 131,  Mismatches: 20, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
 147  131  1.00

ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33


Consensus pattern (147 bp):   
ATTCCTCCTACAAAATCCAATGGATTCAATAATCTTACTTGCCTAAAGCTTGAAAATCTTACCTT
CAATAATGAAGGATTTGAGAATCTCATTGCAAAGTCCCCCCAACTTAATACATTGCACTTGAATC
GCCTTGATGGATTGAAC

Found at i:16808 original size:2 final size:2

Alignment explanation


    Indices: 16801--16835  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      16791 CTTGAATACT

                                                         *      
      16801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      16836 TTATCGGTTG


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.