Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010311.1 Corchorus olitorius cultivar O-4 contig10343, 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: 12382
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:201 original size:3 final size:3

Alignment explanation


    Indices: 181--246  Score: 114
    Period size: 3  Copynumber: 22.0  Consensus size: 3

        171 CAAGTTAATA

                  *       *                                                
        181 CAT CAA CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT

                                   
        229 CAT CAT CAT CAT CAT CAT
          1 CAT CAT CAT CAT CAT CAT

        247 TATTATTATT


Statistics
Matches: 59,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   59  1.00

ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30


Consensus pattern (3 bp):   
CAT

Found at i:251 original size:3 final size:3

Alignment explanation


    Indices: 245--274  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

        235 CATCATCATC

                                                     
        245 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT A
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A

        275 GTAGTAGTTG


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   24  0.92

ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63


Consensus pattern (3 bp):   
ATT

Found at i:264 original size:14 final size:14

Alignment explanation


    Indices: 245--272  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

        235 CATCATCATC

                          
        245 ATTATTATTATTAT
          1 ATTATTATTATTAT

                          
        259 ATTATTATTATTAT
          1 ATTATTATTATTAT

        273 TAGTAGTAGT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (14 bp):   
ATTATTATTATTAT

Found at i:3150 original size:27 final size:26

Alignment explanation


    Indices: 3096--3156  Score: 72
    Period size: 27  Copynumber: 2.3  Consensus size: 26

       3086 CTAAATTTCC

                                        
       3096 ATTATTTTAATAATGGAATAATTAAAAT
          1 ATTA-TTTAATAATGGAAT-ATTAAAAT

                                        
       3124 ATTATTTAATAATGGCAAT-TTAGAAAT
          1 ATTATTTAATAATGG-AATATTA-AAAT

                   
       3151 A-TATTT
          1 ATTATTT

       3157 GAAAAAAAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
  26    8  0.26
  27   16  0.52
  28    7  0.23

ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44


Consensus pattern (26 bp):   
ATTATTTAATAATGGAATATTAAAAT
Done.