Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024169.1 Corchorus olitorius cultivar O-4 contig24202, 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: 5934
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37


Found at i:1003 original size:23 final size:23

Alignment explanation


    Indices: 959--1009  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

        949 ACTTTTTTAG

                                  *
        959 TTTATTTAACTAACAACTCTATT
          1 TTTATTTAACTAACAACTCTATC

                     *     *        
        982 TTTATTTAATTAA-ATCTACTATC
          1 TTTATTTAACTAACAACT-CTATC

                 
       1005 TTTAT
          1 TTTAT

       1010 AACTATTTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22    3  0.12
  23   21  0.88

ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53


Consensus pattern (23 bp):   
TTTATTTAACTAACAACTCTATC

Found at i:3391 original size:21 final size:20

Alignment explanation


    Indices: 3366--3418  Score: 54
    Period size: 21  Copynumber: 2.5  Consensus size: 20

       3356 GGGATTGGAG

                          *     
       3366 TATTTATTTATCTTGTTGTT
          1 TATTTATTTATCTTCTTGTT

                         *        
       3386 TAATTT-TATTATTTTCTTGTT
          1 T-ATTTAT-TTATCTTCTTGTT

                        
       3407 TATTTACTTTAT
          1 TATTTA-TTTAT

       3419 TGTTCACATA


Statistics
Matches: 27,  Mismatches: 2, Indels: 7
        0.75            0.06        0.19

Matches are distributed among these distances:
  20    6  0.22
  21   20  0.74
  22    1  0.04

ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70


Consensus pattern (20 bp):   
TATTTATTTATCTTCTTGTT

Found at i:3638 original size:14 final size:13

Alignment explanation


    Indices: 3617--3650  Score: 50
    Period size: 14  Copynumber: 2.5  Consensus size: 13

       3607 ACTACTTTAC

                         
       3617 TTTTTTTTTGTGT
          1 TTTTTTTTTGTGT

                          
       3630 TTTTGTTTTTGTGT
          1 TTTT-TTTTTGTGT

                   
       3644 TCTTTTT
          1 T-TTTTT

       3651 GGAACTTTGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  13    4  0.21
  14   12  0.63
  15    3  0.16

ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82


Consensus pattern (13 bp):   
TTTTTTTTTGTGT
Done.