Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016865.1 Corchorus olitorius cultivar O-4 contig16898, 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: 17626
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34


Found at i:9493 original size:22 final size:22

Alignment explanation


    Indices: 9465--9512  Score: 96
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       9455 AGGAGTTGAA

                                  
       9465 GAAAATAATGCTCTGCAAAGTG
          1 GAAAATAATGCTCTGCAAAGTG

                                  
       9487 GAAAATAATGCTCTGCAAAGTG
          1 GAAAATAATGCTCTGCAAAGTG

                
       9509 GAAA
          1 GAAA

       9513 GAATGAAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   26  1.00

ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21


Consensus pattern (22 bp):   
GAAAATAATGCTCTGCAAAGTG

Found at i:9545 original size:55 final size:55

Alignment explanation


    Indices: 9461--9571  Score: 204
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       9451 TACAAGGAGT

                                                           *       
       9461 TGAAGAAAATAATGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGTGGAAAGAA
          1 TGAAGAAAATAATGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGTAGAAAGAA

                            *                                      
       9516 TGAAGAAAATAATGCTTTGCAAAGTGGAAAATAATGCTCTGCAAAGTAGAAAGAA
          1 TGAAGAAAATAATGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGTAGAAAGAA

             
       9571 T
          1 T

       9572 CTCTGCAAAG


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  55   54  1.00

ACGTcount: A:0.46, C:0.10, G:0.23, T:0.22


Consensus pattern (55 bp):   
TGAAGAAAATAATGCTCTGCAAAGTGGAAAATAATGCTCTGCAAAGTAGAAAGAA

Found at i:9548 original size:22 final size:22

Alignment explanation


    Indices: 9519--9581  Score: 85
    Period size: 22  Copynumber: 3.0  Consensus size: 22

       9509 GAAAGAATGA

                         *        
       9519 AGAAAATAATGCTTTGCAAAGT
          1 AGAAAATAATGCTCTGCAAAGT

            *                     
       9541 GGAAAATAATGCTCTGCAAAGT
          1 AGAAAATAATGCTCTGCAAAGT

                  *              
       9563 AG-AAAGAAT-CTCTGCAAAG
          1 AGAAAATAATGCTCTGCAAAG

       9582 ATGTTTCCAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   10  0.27
  21    6  0.16
  22   21  0.57

ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22


Consensus pattern (22 bp):   
AGAAAATAATGCTCTGCAAAGT

Found at i:11392 original size:21 final size:21

Alignment explanation


    Indices: 11368--11438  Score: 124
    Period size: 21  Copynumber: 3.4  Consensus size: 21

      11358 CTTAGGCAAT

                         *       
      11368 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                *                
      11389 TCCATTGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
      11410 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                    
      11431 TCCAATGA
          1 TCCAATGA

      11439 TCTCCTAGCA


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   47  1.00

ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Found at i:17413 original size:16 final size:17

Alignment explanation


    Indices: 17392--17435  Score: 63
    Period size: 16  Copynumber: 2.6  Consensus size: 17

      17382 TCTTTTAATA

                             
      17392 ATAAAAAATTAAA-ATT
          1 ATAAAAAATTAAATATT

                             
      17408 ATAAAAAATTAAATATT
          1 ATAAAAAATTAAATATT

            *          
      17425 TTAAAATAATT
          1 ATAAAA-AATT

      17436 TTAATTTTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  16   13  0.52
  17    8  0.32
  18    4  0.16

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (17 bp):   
ATAAAAAATTAAATATT

Done.