Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023340.1 Corchorus olitorius cultivar O-4 contig23373, 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: 6764
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:3592 original size:27 final size:27

Alignment explanation


    Indices: 3554--3611  Score: 73
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       3544 TTTGCTAAAC

                             *   **    
       3554 AACTTTTCCTACTCCTTTACATTACCA
          1 AACTTTTCCTACTCCTTAACAACACCA

                                        
       3581 AACTGTTT-CTACTCCTTAACAACACCA
          1 AACT-TTTCCTACTCCTTAACAACACCA

                
       3608 AACT
          1 AACT

       3612 AAAGGCAATT


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  27   24  0.89
  28    3  0.11

ACGTcount: A:0.31, C:0.33, G:0.02, T:0.34


Consensus pattern (27 bp):   
AACTTTTCCTACTCCTTAACAACACCA

Found at i:4170 original size:5 final size:5

Alignment explanation


    Indices: 4150--4200  Score: 77
    Period size: 5  Copynumber: 10.0  Consensus size: 5

       4140 ATAATCATTA

                                                                         
       4150 AAAAG -AAAG AAAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAAG AAAAG
          1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG

       4201 GAGGTTTGGT


Statistics
Matches: 43,  Mismatches: 0, Indels: 6
        0.88            0.00        0.12

Matches are distributed among these distances:
   4    4  0.09
   5   30  0.70
   6    9  0.21

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:6543 original size:35 final size:35

Alignment explanation


    Indices: 6503--6578  Score: 125
    Period size: 35  Copynumber: 2.2  Consensus size: 35

       6493 TAGTTTGTTT

                         *     *               
       6503 ATGTTCACGAACAGGCTCGTTTATTGTTCATTTAA
          1 ATGTTCACGAACAAGCTCGCTTATTGTTCATTTAA

            *                                  
       6538 GTGTTCACGAACAAGCTCGCTTATTGTTCATTTAA
          1 ATGTTCACGAACAAGCTCGCTTATTGTTCATTTAA

                  
       6573 ATGTTC
          1 ATGTTC

       6579 GTTTATATAA


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  35   37  1.00

ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39


Consensus pattern (35 bp):   
ATGTTCACGAACAAGCTCGCTTATTGTTCATTTAA
Done.