Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000858.1 Corchorus capsularis cultivar CVL-1 contig00858, 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, 749

Length: 1249
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36


Found at i:388 original size:20 final size:20

Alignment explanation


    Indices: 348--396  Score: 64
    Period size: 20  Copynumber: 2.4  Consensus size: 20

        338 AGAATGTAAG

                                 
        348 ATATTACTAAATTTATTAATA
          1 ATATTA-TAAATTTATTAATA

                                 
        369 ATATTATAACATTT-TTAATA
          1 ATATTATAA-ATTTATTAATA

              *     
        389 ATTTTATA
          1 ATATTATA

        397 CCTTTTGAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20   16  0.62
  21   10  0.38

ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51


Consensus pattern (20 bp):   
ATATTATAAATTTATTAATA

Found at i:547 original size:20 final size:21

Alignment explanation


    Indices: 502--583  Score: 72
    Period size: 21  Copynumber: 4.3  Consensus size: 21

        492 GATATAATAG

                  *    * *       
        502 TATAATGTTCTTGGTAACCTT
          1 TATAATTTTCTCGATAACCTT

                        *        
        523 TATAATTTTCTCAATAACC-T
          1 TATAATTTTCTCGATAACCTT

                                 
        543 TATAA-----T-GATAACCTT
          1 TATAATTTTCTCGATAACCTT

                                 
        558 TATAATTTTCTCGATAACC-T
          1 TATAATTTTCTCGATAACCTT

                  
        578 TATAAT
          1 TATAAT

        584 GAGAAAATTG


Statistics
Matches: 49,  Mismatches: 5, Indels: 15
        0.71            0.07        0.22

Matches are distributed among these distances:
  14    6  0.12
  15    7  0.14
  20   14  0.29
  21   22  0.45

ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45


Consensus pattern (21 bp):   
TATAATTTTCTCGATAACCTT

Found at i:562 original size:35 final size:35

Alignment explanation


    Indices: 516--585  Score: 131
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        506 ATGTTCTTGG

                                               
        516 TAACCTTTATAATTTTCTCAATAACCTTATAATGA
          1 TAACCTTTATAATTTTCTCAATAACCTTATAATGA

                               *               
        551 TAACCTTTATAATTTTCTCGATAACCTTATAATGA
          1 TAACCTTTATAATTTTCTCAATAACCTTATAATGA

        586 GAAAATTGGT


Statistics
Matches: 34,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  35   34  1.00

ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43


Consensus pattern (35 bp):   
TAACCTTTATAATTTTCTCAATAACCTTATAATGA
Done.