Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021850.1 Corchorus olitorius cultivar O-4 contig21883, 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: 26773
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:3507 original size:11 final size:12

Alignment explanation


    Indices: 3480--3507  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

       3470 ACCCTTGCCT

                        
       3480 AAAAACTAGAAG
          1 AAAAACTAGAAG

                        
       3492 AAAAACTAGAAG
          1 AAAAACTAGAAG

                
       3504 AAAA
          1 AAAA

       3508 GATCTAAAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.71, C:0.07, G:0.14, T:0.07


Consensus pattern (12 bp):   
AAAAACTAGAAG

Found at i:4137 original size:19 final size:18

Alignment explanation


    Indices: 4104--4139  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4094 TTGAAATAAT

                              
       4104 TCTTCAATAGTCTTCAAG
          1 TCTTCAATAGTCTTCAAG

                     *        
       4122 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATAGTCTTCAA

       4140 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATAGTCTTCAAG

Found at i:25558 original size:27 final size:27

Alignment explanation


    Indices: 25528--25627  Score: 155
    Period size: 27  Copynumber: 3.7  Consensus size: 27

      25518 AGTGGAATTA

                   *    *          *   
      25528 AAATGACTAAAAAGCCCCTGAGTATGC
          1 AAATGACCAAAATGCCCCTGAGTGTGC

                                      *
      25555 AAATGACCAAAATGCCCCTGAGTGTGT
          1 AAATGACCAAAATGCCCCTGAGTGTGC

                             *         
      25582 AAATGACCAAAATGCCCATGAGTGTGC
          1 AAATGACCAAAATGCCCCTGAGTGTGC

                               
      25609 AAATGACCAAAATGCCCCT
          1 AAATGACCAAAATGCCCCT

      25628 AGGTGACCCT


Statistics
Matches: 66,  Mismatches: 7, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   66  1.00

ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAGTGTGC
Done.