Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011244.1 Corchorus olitorius cultivar O-4 contig11277, 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: 10142
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:528 original size:15 final size:18

Alignment explanation


    Indices: 489--529  Score: 54
    Period size: 15  Copynumber: 2.5  Consensus size: 18

        479 AGTTAATTTA

                              
        489 ATTAAATAAATATAAATT
          1 ATTAAATAAATATAAATT

                              
        507 ATT-AATAAA-A-AAATT
          1 ATTAAATAAATATAAATT

                     
        522 -TTAAATAA
          1 ATTAAATAA

        530 TTTTGGGAAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  14    2  0.09
  15   10  0.45
  16    1  0.05
  17    6  0.27
  18    3  0.14

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (18 bp):   
ATTAAATAAATATAAATT

Found at i:9111 original size:24 final size:26

Alignment explanation


    Indices: 9066--9114  Score: 75
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       9056 ACAATTTTTT

                *                     
       9066 TTTGTTATAATTATTTTAAAAATTTC
          1 TTTGATATAATTATTTTAAAAATTTC

                                     
       9092 TTTGATAT-ATTA-TTTAAAAATTT
          1 TTTGATATAATTATTTTAAAAATTT

       9115 TCTAACCAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   11  0.50
  25    4  0.18
  26    7  0.32

ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57


Consensus pattern (26 bp):   
TTTGATATAATTATTTTAAAAATTTC

Found at i:9111 original size:25 final size:26

Alignment explanation


    Indices: 9066--9117  Score: 70
    Period size: 25  Copynumber: 2.0  Consensus size: 26

       9056 ACAATTTTTT

                *           *         
       9066 TTTGTTATAATTATTTTAAAAATTTC
          1 TTTGATATAATTATTTAAAAAATTTC

                                 *    
       9092 TTTGATAT-ATTATTTAAAAATTTTC
          1 TTTGATATAATTATTTAAAAAATTTC

             
       9117 T
          1 T

       9118 AACCAAAATT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  25   16  0.70
  26    7  0.30

ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58


Consensus pattern (26 bp):   
TTTGATATAATTATTTAAAAAATTTC
Done.