Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007331.1 Corchorus olitorius cultivar O-4 contig07356, 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: 1724
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34


Found at i:530 original size:19 final size:19

Alignment explanation


    Indices: 508--566  Score: 63
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        498 TATCAATTGT

                               
        508 TTTCTTAATTATTCACTGC
          1 TTTCTTAATTATTCACTGC

                   *       *  *
        527 TTTCTT-GTTA---ATTGT
          1 TTTCTTAATTATTCACTGC

                               
        542 TTTCTTAATTATTCACTGC
          1 TTTCTTAATTATTCACTGC

                  
        561 TTTCTT
          1 TTTCTT

        567 GTTAATTGTT


Statistics
Matches: 30,  Mismatches: 6, Indels: 8
        0.68            0.14        0.18

Matches are distributed among these distances:
  15    9  0.30
  16    3  0.10
  18    3  0.10
  19   15  0.50

ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59


Consensus pattern (19 bp):   
TTTCTTAATTATTCACTGC

Found at i:541 original size:34 final size:34

Alignment explanation


    Indices: 502--586  Score: 161
    Period size: 34  Copynumber: 2.5  Consensus size: 34

        492 GGTTTTTATC

                                              
        502 AATTGTTTTCTTAATTATTCACTGCTTTCTTGTT
          1 AATTGTTTTCTTAATTATTCACTGCTTTCTTGTT

                                              
        536 AATTGTTTTCTTAATTATTCACTGCTTTCTTGTT
          1 AATTGTTTTCTTAATTATTCACTGCTTTCTTGTT

                             
        570 AATTGTTTTCTTTAATT
          1 AATTGTTTTC-TTAATT

        587 TTCTTGATTA


Statistics
Matches: 50,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  34   44  0.88
  35    6  0.12

ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60


Consensus pattern (34 bp):   
AATTGTTTTCTTAATTATTCACTGCTTTCTTGTT

Found at i:601 original size:12 final size:13

Alignment explanation


    Indices: 584--613  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        574 GTTTTCTTTA

                         
        584 ATTTTCTTGATT-
          1 ATTTTCTTGATTG

                         
        596 ATTTTCTTGATTG
          1 ATTTTCTTGATTG

                 
        609 ATTTT
          1 ATTTT

        614 AATTACTAGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   12  0.71
  13    5  0.29

ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67


Consensus pattern (13 bp):   
ATTTTCTTGATTG
Done.