Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012645.1 Corchorus olitorius cultivar O-4 contig12678, 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: 3928
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26


Found at i:627 original size:26 final size:26

Alignment explanation


    Indices: 598--655  Score: 71
    Period size: 26  Copynumber: 2.2  Consensus size: 26

        588 GCTAATTAAC

                        *   *    *    
        598 AATACAAAAATATAAATAATAGTAAA
          1 AATACAAAAATAAAAAAAATAATAAA

                *                    *
        624 AATAAAAAAATAAAAAAAATAATAAT
          1 AATACAAAAATAAAAAAAATAATAAA

                  
        650 AATACA
          1 AATACA

        656 TCGTTTGTTT


Statistics
Matches: 26,  Mismatches: 6, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21


Consensus pattern (26 bp):   
AATACAAAAATAAAAAAAATAATAAA

Found at i:653 original size:9 final size:9

Alignment explanation


    Indices: 603--653  Score: 52
    Period size: 9  Copynumber: 5.8  Consensus size: 9

        593 TTAACAATAC

                     
        603 AAAAAT-AT
          1 AAAAATAAT

                    * 
        611 AAATAATAGT
          1 AAA-AATAAT

                     
        621 AAAAATAA-
          1 AAAAATAAT

                    *
        629 AAAAATAAA
          1 AAAAATAAT

                     
        638 AAAAATAAT
          1 AAAAATAAT

              *    
        647 AATAATA
          1 AAAAATA

        654 CATCGTTTGT


Statistics
Matches: 36,  Mismatches: 4, Indels: 5
        0.80            0.09        0.11

Matches are distributed among these distances:
   8   11  0.31
   9   21  0.58
  10    4  0.11

ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22


Consensus pattern (9 bp):   
AAAAATAAT

Found at i:932 original size:17 final size:18

Alignment explanation


    Indices: 905--938  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

        895 CAAACAAATA

                        *     
        905 AAAGAAAACATGCAAGAC
          1 AAAGAAAACATGAAAGAC

                             
        923 AAAG-AAACATGAAAGA
          1 AAAGAAAACATGAAAGA

        939 AATGGAACCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06


Consensus pattern (18 bp):   
AAAGAAAACATGAAAGAC
Done.