Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008017.1 Corchorus capsularis cultivar CVL-1 contig08038, 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: 16253
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2218 original size:32 final size:32

Alignment explanation


    Indices: 2152--2233  Score: 155
    Period size: 33  Copynumber: 2.5  Consensus size: 32

       2142 ACTCGTGTAT

                                            
       2152 AAAACAACTTAAAAACGTTTCCTCAAAAAAAA
          1 AAAACAACTTAAAAACGTTTCCTCAAAAAAAA

                                             
       2184 AAAATCAACTTAAAAACGTTTCCTCAAAAAAAA
          1 AAAA-CAACTTAAAAACGTTTCCTCAAAAAAAA

                             
       2217 AAAACAACTTAAAAACG
          1 AAAACAACTTAAAAACG

       2234 AAAAATGAAT


Statistics
Matches: 49,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  32   17  0.35
  33   32  0.65

ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18


Consensus pattern (32 bp):   
AAAACAACTTAAAAACGTTTCCTCAAAAAAAA

Found at i:2816 original size:81 final size:81

Alignment explanation


    Indices: 2681--2843  Score: 317
    Period size: 81  Copynumber: 2.0  Consensus size: 81

       2671 TAGTATTTAT

                                                                             
       2681 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
          1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA

                   *        
       2746 ACAATTAGGGAGAAAA
         66 ACAATTAAGGAGAAAA

                                                                             
       2762 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
          1 TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA

                            
       2827 ACAATTAAGGAGAAAA
         66 ACAATTAAGGAGAAAA

             
       2843 T
          1 T

       2844 TTTGGATCTA


Statistics
Matches: 81,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  81   81  1.00

ACGTcount: A:0.42, C:0.09, G:0.18, T:0.31


Consensus pattern (81 bp):   
TATGAAACTACAATTTTGGAGTTAATTTTGGATCTAAAATGAGATGTACAATTAGGTTTAACACA
ACAATTAAGGAGAAAA

Found at i:11289 original size:2 final size:2

Alignment explanation


    Indices: 11282--11308  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      11272 GATTCAAAAT

                                                    
      11282 AG AG AG AG AG AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG A

      11309 CCTTGACAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00


Consensus pattern (2 bp):   
AG

Done.