Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002186.1 Corchorus olitorius cultivar O-4 contig02186, 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, 621

Length: 1036
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26


Found at i:310 original size:9 final size:9

Alignment explanation


    Indices: 297--340  Score: 52
    Period size: 9  Copynumber: 4.8  Consensus size: 9

        287 TTTACATTCA

                    *
        297 AATAAAAAA
          1 AATAAAAAT

                      
        306 AATAATAAAT
          1 AATAA-AAAT

                 *   
        316 AATAATAAT
          1 AATAAAAAT

                 *   
        325 AATAATAAT
          1 AATAAAAAT

                   
        334 AATAAAA
          1 AATAAAA

        341 TTTAATCTAA


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
   9   23  0.74
  10    8  0.26

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (9 bp):   
AATAAAAAT

Found at i:312 original size:3 final size:3

Alignment explanation


    Indices: 306--338  Score: 57
    Period size: 3  Copynumber: 10.7  Consensus size: 3

        296 AAATAAAAAA

                                                       
        306 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA

        339 AATTTAATCT


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3   26  0.90
   4    3  0.10

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (3 bp):   
AAT

Found at i:315 original size:16 final size:16

Alignment explanation


    Indices: 296--329  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        286 ATTTACATTC

                            
        296 AAATAAAAAAAATAAT
          1 AAATAAAAAAAATAAT

                  *  *      
        312 AAATAATAATAATAAT
          1 AAATAAAAAAAATAAT

              
        328 AA
          1 AA

        330 TAATAATAAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (16 bp):   
AAATAAAAAAAATAAT

Done.