Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024467.1 Corchorus olitorius cultivar O-4 contig24500, 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: 12939
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:3699 original size:22 final size:21

Alignment explanation


    Indices: 3663--3704  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3653 ATTTTTTTCC

                           *     
       3663 TTTTTTTTTATGACGGAAAAT
          1 TTTTTTTTTATGACGCAAAAT

                     *           
       3684 TTTTTTTTTTTCGACGCAAAA
          1 TTTTTTTTTAT-GACGCAAAA

       3705 CACAAAACAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21   10  0.56
  22    8  0.44

ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52


Consensus pattern (21 bp):   
TTTTTTTTTATGACGCAAAAT

Found at i:4083 original size:16 final size:15

Alignment explanation


    Indices: 4045--4086  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4035 ATAGAGATTG

                   *       
       4045 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       4060 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       4075 ACTAGAAAACAA
          1 AC-AGAAAACAA

       4087 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:4850 original size:11 final size:11

Alignment explanation


    Indices: 4834--4866  Score: 66
    Period size: 11  Copynumber: 3.0  Consensus size: 11

       4824 CCTTTGCCTA

                       
       4834 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       4845 AAAACTAGAAG
          1 AAAACTAGAAG

                       
       4856 AAAACTAGAAG
          1 AAAACTAGAAG

       4867 TAAAGAAATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   22  1.00

ACGTcount: A:0.64, C:0.09, G:0.18, T:0.09


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:6725 original size:18 final size:18

Alignment explanation


    Indices: 6701--6765  Score: 85
    Period size: 18  Copynumber: 3.6  Consensus size: 18

       6691 CCTCCCTTGG

                              
       6701 GCGCTTCTGGCCATTGTA
          1 GCGCTTCTGGCCATTGTA

            *          *      
       6719 ACGCTTCTGGCAATTGTA
          1 GCGCTTCTGGCCATTGTA

             **               
       6737 GTACTTCTGGCCATTGTA
          1 GCGCTTCTGGCCATTGTA

             *         
       6755 GTGCTTCTGGC
          1 GCGCTTCTGGC

       6766 TAGCCTCCGC


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  18   40  1.00

ACGTcount: A:0.14, C:0.25, G:0.26, T:0.35


Consensus pattern (18 bp):   
GCGCTTCTGGCCATTGTA
Done.