Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010863.1 Corchorus olitorius cultivar O-4 contig10895, 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: 26631
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32


Found at i:2417 original size:27 final size:27

Alignment explanation


    Indices: 2369--2429  Score: 68
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       2359 ATTACCAAAA

                 *           *    *    
       2369 TACCCGTGATGGACAAATTTACTATAT
          1 TACCCCTGATGGACAAAATTACGATAT

                      *  *           * 
       2396 TACCCCTGATTGATAAAATTACGATTT
          1 TACCCCTGATGGACAAAATTACGATAT

                   
       2423 TACCCCT
          1 TACCCCT

       2430 ATAATGAGGA


Statistics
Matches: 28,  Mismatches: 6, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34


Consensus pattern (27 bp):   
TACCCCTGATGGACAAAATTACGATAT

Found at i:11008 original size:15 final size:17

Alignment explanation


    Indices: 10983--11022  Score: 57
    Period size: 15  Copynumber: 2.5  Consensus size: 17

      10973 TTATTGACCT

                  *          
      10983 AATAATAATTATT-TTC
          1 AATAATTATTATTATTC

                             
      10999 -ATAATTATTATTATTC
          1 AATAATTATTATTATTC

                    
      11015 AATAATTA
          1 AATAATTA

      11023 CTTAATAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  15   11  0.52
  16    3  0.14
  17    7  0.33

ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50


Consensus pattern (17 bp):   
AATAATTATTATTATTC

Found at i:12691 original size:17 final size:17

Alignment explanation


    Indices: 12669--12701  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      12659 TTTTATCAGA

                             
      12669 AAAATGAAAAATAAAAT
          1 AAAATGAAAAATAAAAT

                            
      12686 AAAATGAAAAATAAAA
          1 AAAATGAAAAATAAAA

      12702 AATAAAAAAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15


Consensus pattern (17 bp):   
AAAATGAAAAATAAAAT

Found at i:15680 original size:29 final size:31

Alignment explanation


    Indices: 15638--15706  Score: 97
    Period size: 31  Copynumber: 2.3  Consensus size: 31

      15628 AATTCAGAAA

                                 *   *     
      15638 CTTATTTGACCTTTTC-C-AAGGGTTAGACC
          1 CTTATTTGACCTTTTCACTAAAGGTCAGACC

                *                          
      15667 CTTACTTGACCTTTTCACTAAAGGTCAGACC
          1 CTTATTTGACCTTTTCACTAAAGGTCAGACC

                     
      15698 CTTATTTGA
          1 CTTATTTGA

      15707 ATTTTTAGCT


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  29   15  0.44
  30    1  0.03
  31   18  0.53

ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38


Consensus pattern (31 bp):   
CTTATTTGACCTTTTCACTAAAGGTCAGACC

Done.