Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014611.1 Corchorus olitorius cultivar O-4 contig14644, 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: 8105
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:7616 original size:4 final size:4

Alignment explanation


    Indices: 7591--7644  Score: 65
    Period size: 4  Copynumber: 13.5  Consensus size: 4

       7581 CCGCCCGTAG

                   *                                    *    *          
       7591 TTAT TTTT TTAT TT-T GTTAT TTAT TTAT TTAT TTAC TTAC TTAT TTAT
          1 TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT

                   
       7639 TTAT TT
          1 TTAT TT

       7645 TATTATTATT


Statistics
Matches: 44,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
   3    1  0.02
   4   42  0.95
   5    1  0.02

ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74


Consensus pattern (4 bp):   
TTAT

Found at i:7652 original size:3 final size:3

Alignment explanation


    Indices: 7639--7699  Score: 108
    Period size: 3  Copynumber: 21.0  Consensus size: 3

       7629 ACTTATTTAT

                                                                           
       7639 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA

                               
       7686 TTA TTA TTA -TA TTA
          1 TTA TTA TTA TTA TTA

       7700 ATTTAAATTA


Statistics
Matches: 56,  Mismatches: 0, Indels: 4
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    4  0.07
   3   52  0.93

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
TTA

Found at i:7662 original size:24 final size:24

Alignment explanation


    Indices: 7631--7699  Score: 90
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       7621 ATTTACTTAC

                                     
       7631 TTATTTATTTATTTTATTATTATTA
          1 TTATTTA-TTATTTTATTATTATTA

                                     
       7656 TTA-TTATTATTATTATTATTATTA
          1 TTATTTATTATT-TTATTATTATTA

                                  
       7680 TTA-TTATTATTATTA-TATTA
          1 TTATTTATTATT-TTATTATTA

       7700 ATTTAAATTA


Statistics
Matches: 43,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
  23   10  0.23
  24   30  0.70
  25    3  0.07

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (24 bp):   
TTATTTATTATTTTATTATTATTA

Found at i:7999 original size:3 final size:3

Alignment explanation


    Indices: 7991--8098  Score: 216
    Period size: 3  Copynumber: 36.0  Consensus size: 3

       7981 CCTGTAAAAT

                                                                           
       7991 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                                                           
       8039 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                           
       8087 TAA TAA TAA TAA
          1 TAA TAA TAA TAA

       8099 NATAAAA


Statistics
Matches: 105,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3  105  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
TAA

Done.