Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021658.1 Corchorus olitorius cultivar O-4 contig21691, 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: 6782
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:106 original size:15 final size:16

Alignment explanation


    Indices: 76--115  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

         66 TTACTCTGCT

                            
         76 TTGTTTTCTAGTTTAA
          1 TTGTTTTCTAGTTTAA

                     *      
         92 TTGTTTT-TTGTTTAA
          1 TTGTTTTCTAGTTTAA

               *     
        107 TTGCTTTCT
          1 TTGTTTTCT

        116 GTCAATCTCT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:622 original size:29 final size:29

Alignment explanation


    Indices: 586--672  Score: 104
    Period size: 29  Copynumber: 2.9  Consensus size: 29

        576 TAATTTATTA

                                          
        586 GTTTTGCGTTTTTGGAAAAAAAAAATT-TT
          1 GTTTTGCGTTTTT-GAAAAAAAAAATTCTT

                          *                
        615 GTTTTGCGTTTTCTAAAAAAAAAAATTTCTT
          1 GTTTTGCGTTTT-TGAAAAAAAAAA-TTCTT

                *                      
        646 GTTCCTGCGTTTTTAGAAAAAAAAAAT
          1 GTT-TTGCGTTTTT-GAAAAAAAAAAT

        673 ATTTTCTTTA


Statistics
Matches: 50,  Mismatches: 3, Indels: 8
        0.82            0.05        0.13

Matches are distributed among these distances:
  29   22  0.44
  30    3  0.06
  31    7  0.14
  32   18  0.36

ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41


Consensus pattern (29 bp):   
GTTTTGCGTTTTTGAAAAAAAAAATTCTT

Found at i:637 original size:32 final size:30

Alignment explanation


    Indices: 590--677  Score: 97
    Period size: 32  Copynumber: 2.8  Consensus size: 30

        580 TTATTAGTTT

                     **                  *
        590 TGCGTTTTTGGAAAAAAAAAATTTTGTT-T
          1 TGCGTTTTTAAAAAAAAAAAATTTTGTTCC

                                 *          
        619 TGCGTTTTCTAAAAAAAAAAATTTCTTGTTCC
          1 TGCGTTTT-TAAAAAAAAAAAATT-TTGTTCC

                                       
        651 TGCGTTTTTAGAAAAAAAAAATATTTT
          1 TGCGTTTTTA-AAAAAAAAAA-ATTTT

        678 CTTTATTTTC


Statistics
Matches: 49,  Mismatches: 5, Indels: 7
        0.80            0.08        0.11

Matches are distributed among these distances:
  29    8  0.16
  30   12  0.24
  31    7  0.14
  32   20  0.41
  33    2  0.04

ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42


Consensus pattern (30 bp):   
TGCGTTTTTAAAAAAAAAAAATTTTGTTCC

Found at i:4613 original size:21 final size:21

Alignment explanation


    Indices: 4589--4643  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       4579 CGCCCATTCA

                           **    
       4589 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       4610 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       4631 CCGTGCCATCACC
          1 CCGTGCCACCACC

       4644 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC
Done.