Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023734.1 Corchorus olitorius cultivar O-4 contig23767, 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: 1769
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30


Found at i:906 original size:31 final size:27

Alignment explanation


    Indices: 871--937  Score: 73
    Period size: 27  Copynumber: 2.4  Consensus size: 27

        861 AATATAAAAA

                                   *       
        871 ACGCAGACAAAAAATTTTCTTTTTTTTTATG
          1 ACGCAGA-AAAAAA--TT-TTTTATTTTATG

                     *                 
        902 ACGCAGAAACAAATTTTTTATTTTATG
          1 ACGCAGAAAAAAATTTTTTATTTTATG

                      
        929 ACGCA-AAAA
          1 ACGCAGAAAA

        938 TTTTTTTTTT


Statistics
Matches: 33,  Mismatches: 3, Indels: 5
        0.80            0.07        0.12

Matches are distributed among these distances:
  26    3  0.09
  27   16  0.48
  28    2  0.06
  30    5  0.15
  31    7  0.21

ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37


Consensus pattern (27 bp):   
ACGCAGAAAAAAATTTTTTATTTTATG

Found at i:938 original size:23 final size:22

Alignment explanation


    Indices: 890--959  Score: 77
    Period size: 23  Copynumber: 2.9  Consensus size: 22

        880 AAAAATTTTC

                                      
        890 TTTTTTTTTATGACGCAGAAACAAAT
          1 TTTTTTTTTATGACGC---AA-AAAT

                                   
        916 TTTTTATTTTATGACGCAAAAAT
          1 TTTTT-TTTTATGACGCAAAAAT

                     *           
        939 TTTTTTTTTTTCGACGCAAAA
          1 TTTTTTTTTAT-GACGCAAAA

        960 CACAAAACAA


Statistics
Matches: 41,  Mismatches: 1, Indels: 7
        0.84            0.02        0.14

Matches are distributed among these distances:
  22    5  0.12
  23   18  0.44
  24    2  0.05
  26    5  0.12
  27   11  0.27

ACGTcount: A:0.31, C:0.11, G:0.10, T:0.47


Consensus pattern (22 bp):   
TTTTTTTTTATGACGCAAAAAT

Found at i:945 original size:27 final size:26

Alignment explanation


    Indices: 880--949  Score: 79
    Period size: 27  Copynumber: 2.7  Consensus size: 26

        870 AACGCAGACA

                     *                
        880 AAAAATTTTCTTTTTTTTTATGACGC
          1 AAAAATTTTTTTTTTTTTTATGACGC

                    **      *           
        906 AGAAACA-AATTTTTTATTTTATGACGC
          1 A-AAA-ATTTTTTTTTTTTTTATGACGC

                             
        933 AAAAATTTTTTTTTTTT
          1 AAAAATTTTTTTTTTTT

        950 CGACGCAAAA


Statistics
Matches: 34,  Mismatches: 7, Indels: 6
        0.72            0.15        0.13

Matches are distributed among these distances:
  25    1  0.03
  26   12  0.35
  27   20  0.59
  28    1  0.03

ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53


Consensus pattern (26 bp):   
AAAAATTTTTTTTTTTTTTATGACGC

Found at i:1406 original size:16 final size:15

Alignment explanation


    Indices: 1352--1411  Score: 50
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       1342 AAAACAAAAC

                              
       1352 ACAGAAAACAGAGGTTAA
          1 ACAGAAAACA-A--TTAA

                            
       1370 A-AGAAAAACAATTAA
          1 ACAG-AAAACAATTAA

                         **
       1385 ACAGAAAACAATTTT
          1 ACAGAAAACAATTAA

                        
       1400 ACTAGAAAACAA
          1 AC-AGAAAACAA

       1412 AACAAACAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
  15   16  0.43
  16   11  0.30
  17    3  0.08
  18    7  0.19

ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.