Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021288.1 Corchorus olitorius cultivar O-4 contig21321, 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: 7078
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:3724 original size:42 final size:42

Alignment explanation


    Indices: 3665--3750  Score: 172
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       3655 TAATGCAGTG

                                                      
       3665 TATAACAAACGGTCTCACATCAAGTTCTAATCAATGGAGGAC
          1 TATAACAAACGGTCTCACATCAAGTTCTAATCAATGGAGGAC

                                                      
       3707 TATAACAAACGGTCTCACATCAAGTTCTAATCAATGGAGGAC
          1 TATAACAAACGGTCTCACATCAAGTTCTAATCAATGGAGGAC

              
       3749 TA
          1 TA

       3751 ACTAAGAGAC


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24


Consensus pattern (42 bp):   
TATAACAAACGGTCTCACATCAAGTTCTAATCAATGGAGGAC

Found at i:4752 original size:29 final size:29

Alignment explanation


    Indices: 4710--4781  Score: 76
    Period size: 30  Copynumber: 2.4  Consensus size: 29

       4700 ACGGTTTGCT

                   * *                     
       4710 CAAATTGAGTCTAAACCT-TTACTCA-GCAC
          1 CAAATTGGGCCTAAACCTATT-C-CAGGCAC

                                  *       
       4739 CAAATTGGGCCTAAACCTATTCGAGGGCAC
          1 CAAATTGGGCCTAAACCTATTCCA-GGCAC

                         
       4769 CAAATTGGGCCTA
          1 CAAATTGGGCCTA

       4782 TTTTTGACGG


Statistics
Matches: 37,  Mismatches: 3, Indels: 5
        0.82            0.07        0.11

Matches are distributed among these distances:
  28    1  0.03
  29   17  0.46
  30   19  0.51

ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24


Consensus pattern (29 bp):   
CAAATTGGGCCTAAACCTATTCCAGGCAC

Found at i:5116 original size:44 final size:44

Alignment explanation


    Indices: 5058--5152  Score: 154
    Period size: 44  Copynumber: 2.2  Consensus size: 44

       5048 TTTCCAACTG

                                              *         
       5058 CTTCAATTCATTCTTCTTTTTCTCCTTTTTGGTAGAAAAACTTC
          1 CTTCAATTCATTCTTCTTTTTCTCCTTTTTGGTAAAAAAACTTC

                     *     *        *                   
       5102 CTTCAATTCTTTCTTTTTTTTCTCTTTTTTGGTAAAAAAACTTC
          1 CTTCAATTCATTCTTCTTTTTCTCCTTTTTGGTAAAAAAACTTC

                   
       5146 CTTCAAT
          1 CTTCAAT

       5153 CCTCTGTATT


Statistics
Matches: 47,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  44   47  1.00

ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53


Consensus pattern (44 bp):   
CTTCAATTCATTCTTCTTTTTCTCCTTTTTGGTAAAAAAACTTC

Found at i:5859 original size:25 final size:27

Alignment explanation


    Indices: 5825--5886  Score: 83
    Period size: 29  Copynumber: 2.3  Consensus size: 27

       5815 TTTTCCCTTC

                           *           
       5825 TGAAATTTTTTTTT-CT-AAAATTTAA
          1 TGAAATTTTTTTTTAATCAAAATTTAA

                                         
       5850 TGAAATTTTTTTTTGAAATCAAAATTTAA
          1 TGAAATTTTTTTTT--AATCAAAATTTAA

                    
       5879 TGAAATTT
          1 TGAAATTT

       5887 AATAAAATTA


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  25   14  0.44
  28    1  0.03
  29   17  0.53

ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52


Consensus pattern (27 bp):   
TGAAATTTTTTTTTAATCAAAATTTAA
Done.