Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009212.1 Corchorus olitorius cultivar O-4 contig09240, 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, 637

Length: 1063
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36


Found at i:331 original size:19 final size:18

Alignment explanation


    Indices: 293--328  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

        283 ATAAGCCCTT

                              
        293 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

                              
        311 TTTTATAGATTCATAAAA
          1 TTTTATAGATTCATAAAA

        329 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:336 original size:19 final size:18

Alignment explanation


    Indices: 296--336  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        286 AGCCCTTTTT

                             *
        296 TATAGATTCATAAAATTT
          1 TATAGATTCATAAAATTA

                               
        314 TATAGATTCATAAAAATTA
          1 TATAGATTCAT-AAAATTA

                
        333 TATA
          1 TATA

        337 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:529 original size:22 final size:21

Alignment explanation


    Indices: 494--545  Score: 70
    Period size: 22  Copynumber: 2.5  Consensus size: 21

        484 TCCGTTGACG

                             *   
        494 AAATAAT-AAAATAAAAGGAT
          1 AAATAATAAAAATAAAACGAT

              *                   
        514 AATTAAATAAAAATAAAACGAT
          1 AAAT-AATAAAAATAAAACGAT

                      
        536 AAATAATAAA
          1 AAATAATAAA

        546 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.