Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004386.1 Corchorus olitorius cultivar O-4 contig04401, 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, 630

Length: 1051
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36


Found at i:408 original size:19 final size:18

Alignment explanation


    Indices: 370--405  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        360 ATAAGCCCTT

                              
        370 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

                              
        388 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

        406 ATTATATAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44


Consensus pattern (18 bp):   
TTTTATAGATTCATAAAA

Found at i:413 original size:19 final size:18

Alignment explanation


    Indices: 373--413  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        363 AGCCCTTTTT

                             *
        373 TATAGATTCATAAAATTT
          1 TATAGATTCATAAAATTA

                               
        391 TATAGATTCATAAAAATTA
          1 TATAGATTCAT-AAAATTA

                
        410 TATA
          1 TATA

        414 AAAAAATGAG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  18   11  0.52
  19   10  0.48

ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41


Consensus pattern (18 bp):   
TATAGATTCATAAAATTA

Found at i:607 original size:22 final size:21

Alignment explanation


    Indices: 572--623  Score: 70
    Period size: 22  Copynumber: 2.5  Consensus size: 21

        562 TCCGTTGACG

                             *   
        572 AAATAAT-AAAATAAAAGGAT
          1 AAATAATAAAAATAAAACGAT

              *                   
        592 AATTAAATAAAAATAAAACGAT
          1 AAAT-AATAAAAATAAAACGAT

                      
        614 AAATAATAAA
          1 AAATAATAAA

        624 GATTCTTTTT


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  20    3  0.11
  21    9  0.33
  22   15  0.56

ACGTcount: A:0.71, C:0.02, G:0.06, T:0.21


Consensus pattern (21 bp):   
AAATAATAAAAATAAAACGAT
Done.