Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013478.1 Corchorus olitorius cultivar O-4 contig13511, 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: 12330
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34


Found at i:5018 original size:2 final size:2

Alignment explanation


    Indices: 5011--5038  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       5001 TTCCCTTGTT

                                                     
       5011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       5039 CACACAAAAG


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:6651 original size:13 final size:13

Alignment explanation


    Indices: 6633--6659  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       6623 CTCTATAGCC

                         
       6633 TCATAAATCATAT
          1 TCATAAATCATAT

                         
       6646 TCATAAATCATAT
          1 TCATAAATCATAT

             
       6659 T
          1 T

       6660 TATTATATTT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41


Consensus pattern (13 bp):   
TCATAAATCATAT

Found at i:9548 original size:16 final size:16

Alignment explanation


    Indices: 9527--9568  Score: 59
    Period size: 15  Copynumber: 2.7  Consensus size: 16

       9517 TTGCTTTGCT

                           *
       9527 TTGTTTTCTAGTTTAG
          1 TTGTTTTCTAGTTTAA

                            
       9543 TTGTTTTCT-GTTTAA
          1 TTGTTTTCTAGTTTAA

               *       
       9558 TTGCTTTCTAG
          1 TTGTTTTCTAG

       9569 CAATTTCTGT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  15   13  0.57
  16   10  0.43

ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62


Consensus pattern (16 bp):   
TTGTTTTCTAGTTTAA

Found at i:10012 original size:30 final size:29

Alignment explanation


    Indices: 9962--10045  Score: 109
    Period size: 30  Copynumber: 2.9  Consensus size: 29

       9952 TAATTTATTA

                          *              
       9962 GTTTTG-TGTTTTTGAAAAAAAAAATTTT
          1 GTTTTGCTGTTTTTAAAAAAAAAAATTTT

                                          
       9990 GTTTTGCTGTTTTCTAAAAAAAAAAATTTT
          1 GTTTTGCTGTTTT-TAAAAAAAAAAATTTT

                *         *            
      10020 GTTCCTGC-GTTTTAAAAAAAAAAAAT
          1 GTT-TTGCTGTTTTTAAAAAAAAAAAT

      10046 ATTTTCTTTA


Statistics
Matches: 50,  Mismatches: 3, Indels: 5
        0.86            0.05        0.09

Matches are distributed among these distances:
  28    6  0.12
  29   18  0.36
  30   23  0.46
  31    3  0.06

ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43


Consensus pattern (29 bp):   
GTTTTGCTGTTTTTAAAAAAAAAAATTTT

Done.