Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024380.1 Corchorus olitorius cultivar O-4 contig24413, 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: 23466
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30


Found at i:3865 original size:3 final size:3

Alignment explanation


    Indices: 3857--3883  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       3847 ACATATATGG

                                               
       3857 ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA

       3884 TCGAAAATTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:15790 original size:15 final size:16

Alignment explanation


    Indices: 15766--15805  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      15756 AGAGGTTGAA

                 *          
      15766 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
      15781 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
      15797 AGAAAACAA
          1 AGAAAACAA

      15806 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:17362 original size:31 final size:30

Alignment explanation


    Indices: 17327--17386  Score: 77
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      17317 CCAATTAGAG

                                            
      17327 CAATTATA-CATAATCAGGCCTCAAATTGCAA
          1 CAATTA-AGCATAAT-AGGCCTCAAATTGCAA

                           * *           
      17358 CAATTAAGCATAATATGTCTCAAATTGCA
          1 CAATTAAGCATAATAGGCCTCAAATTGCA

      17387 GTAATTGAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  30   14  0.54
  31   12  0.46

ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28


Consensus pattern (30 bp):   
CAATTAAGCATAATAGGCCTCAAATTGCAA

Found at i:18129 original size:15 final size:16

Alignment explanation


    Indices: 18105--18144  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      18095 AGAGGTTGAA

                 *          
      18105 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
      18120 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
      18136 AGAAAACAA
          1 AGAAAACAA

      18145 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.