Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024117.1 Corchorus olitorius cultivar O-4 contig24150, 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: 10747
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:355 original size:2 final size:2

Alignment explanation


    Indices: 310--339  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

        300 AGTCCTAAAG

                                                        
        310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        340 TAGAAATATG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1741 original size:17 final size:17

Alignment explanation


    Indices: 1716--1756  Score: 64
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1706 GGATCACCCC

                             
       1716 TGATCTTAGATTACTGG
          1 TGATCTTAGATTACTGG

                *        *   
       1733 TGATTTTAGATTATTGG
          1 TGATCTTAGATTACTGG

                   
       1750 TGATCTT
          1 TGATCTT

       1757 TGAGGGTTTA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   21  1.00

ACGTcount: A:0.22, C:0.07, G:0.22, T:0.49


Consensus pattern (17 bp):   
TGATCTTAGATTACTGG

Found at i:4167 original size:27 final size:27

Alignment explanation


    Indices: 4137--4209  Score: 110
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       4127 AGGGTCACCT

                       *          **   
       4137 AGGGGCATTTTAGTCATTTGCATGTCC
          1 AGGGGCATTTTGGTCATTTGCACATCC

                                     * 
       4164 AGGGGCATTTTGGTCATTTGCACATTC
          1 AGGGGCATTTTGGTCATTTGCACATCC

                               
       4191 AGGGGCATTTTGGTCATTT
          1 AGGGGCATTTTGGTCATTT

       4210 TAAGTTCACA


Statistics
Matches: 42,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   42  1.00

ACGTcount: A:0.18, C:0.16, G:0.27, T:0.38


Consensus pattern (27 bp):   
AGGGGCATTTTGGTCATTTGCACATCC

Found at i:6516 original size:41 final size:41

Alignment explanation


    Indices: 6459--6563  Score: 138
    Period size: 41  Copynumber: 2.6  Consensus size: 41

       6449 TTTTTCCGTT

                  *                     *   *        
       6459 TTCAATATAGTCCCTGATTTAGGGTAATGTTTGTTAATTGA
          1 TTCAATTTAGTCCCTGATTTAGGGTAATATTTATTAATTGA

                    *             *            *     
       6500 TTCAATTTTGTCCCTGATTTAGAGTAATATTTATTTATTGA
          1 TTCAATTTAGTCCCTGATTTAGGGTAATATTTATTAATTGA

                    * *            
       6541 TTCAATTTCGCCCCTGATTTAGG
          1 TTCAATTTAGTCCCTGATTTAGG

       6564 ATTTTATTTT


Statistics
Matches: 55,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  41   55  1.00

ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46


Consensus pattern (41 bp):   
TTCAATTTAGTCCCTGATTTAGGGTAATATTTATTAATTGA

Done.