Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016725.1 Corchorus olitorius cultivar O-4 contig16758, 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: 8674
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:3437 original size:41 final size:41

Alignment explanation


    Indices: 3387--3569  Score: 240
    Period size: 41  Copynumber: 4.4  Consensus size: 41

       3377 CAAGAGTCAA

                    *           *   *              * 
       3387 ATGACTTGGTCTTGAATTGACAATCTAATTCAAGGGTCTTG
          1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG

             **     *                    *              
       3428 ACAACTTGGTCTTGAATTGATAATAATTCGATTCAAGGGTCTCG
          1 ATGACTTGATCTTGAATTGATAAT--TT-AATTCAAGGGTCTCG

                    *                                
       3472 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCG
          1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG

                  **                                 
       3513 ATGACTCAATCTTGAATTGATAATTTAATTCAAGGGTCTCG
          1 ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG

                            
       3554 ATGACTTGATCTTGAA
          1 ATGACTTGATCTTGAA

       3570 CAAACGAAAA


Statistics
Matches: 124,  Mismatches: 15, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
  41   87  0.70
  42    2  0.02
  43    1  0.01
  44   34  0.27

ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37


Consensus pattern (41 bp):   
ATGACTTGATCTTGAATTGATAATTTAATTCAAGGGTCTCG

Found at i:3485 original size:85 final size:82

Alignment explanation


    Indices: 3387--3569  Score: 240
    Period size: 85  Copynumber: 2.2  Consensus size: 82

       3377 CAAGAGTCAA

                    *                              *       ***               
       3387 ATGACTTGGTCTTGAATTGACAATCTAATTCAAGGGTCTTGACAACTTGGTCTTGAATTGATAAT
          1 ATGACTTGATCTTGAATTGACAATCTAATTCAAGGGTCTCGACAACTCAATCTTGAATTGATAAT

                 *              
       3452 AATTCGATTCAAGGGTCTCG
         66 --TT-AATTCAAGGGTCTCG

                    *           *   *                 **                     
       3472 ATGACTTGTTCTTGAATTGATAATTTAATTCAAGGGTCTCGATGACTCAATCTTGAATTGATAAT
          1 ATGACTTGATCTTGAATTGACAATCTAATTCAAGGGTCTCGACAACTCAATCTTGAATTGATAAT

                             
       3537 TTAATTCAAGGGTCTCG
         66 TTAATTCAAGGGTCTCG

                            
       3554 ATGACTTGATCTTGAA
          1 ATGACTTGATCTTGAA

       3570 CAAACGAAAA


Statistics
Matches: 87,  Mismatches: 11, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
  82   29  0.33
  83    2  0.02
  85   56  0.64

ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37


Consensus pattern (82 bp):   
ATGACTTGATCTTGAATTGACAATCTAATTCAAGGGTCTCGACAACTCAATCTTGAATTGATAAT
TTAATTCAAGGGTCTCG

Found at i:3682 original size:16 final size:16

Alignment explanation


    Indices: 3663--3695  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3653 CATCTGAAAA

                            
       3663 TACTTCAGAGCTTTTC
          1 TACTTCAGAGCTTTTC

                            
       3679 TACTTCAGAGCTTTTC
          1 TACTTCAGAGCTTTTC

             
       3695 T
          1 T

       3696 GCTTTCTGAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45


Consensus pattern (16 bp):   
TACTTCAGAGCTTTTC

Found at i:7017 original size:8 final size:8

Alignment explanation


    Indices: 7013--7052  Score: 55
    Period size: 9  Copynumber: 4.9  Consensus size: 8

       7003 AGATTTTTTA

                    
       7013 TTTTTATT
          1 TTTTTATT

                     
       7021 TTTTTATTT
          1 TTTTTA-TT

                     
       7030 TTTTTAGTT
          1 TTTTTA-TT

                    
       7039 TTTTT-TT
          1 TTTTTATT

                   
       7046 TTTTTAT
          1 TTTTTAT

       7053 AGAAAGCAAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
   7    7  0.24
   8    7  0.24
   9   15  0.52

ACGTcount: A:0.10, C:0.00, G:0.03, T:0.88


Consensus pattern (8 bp):   
TTTTTATT
Done.