Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024215.1 Corchorus olitorius cultivar O-4 contig24248, 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: 10409
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34


Found at i:1723 original size:21 final size:23

Alignment explanation


    Indices: 1694--1747  Score: 76
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       1684 TCGACTAGGG

                                   
       1694 AATTGTCGAC-CAA-AGGAAGCA
          1 AATTGTCGACTCAAGAGGAAGCA

                *                  
       1715 AATTTTCGACTCAAGAGGAAGCA
          1 AATTGTCGACTCAAGAGGAAGCA

               *      
       1738 AATCGTCGAC
          1 AATTGTCGAC

       1748 AAGAAGGCAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  21    9  0.32
  22    3  0.11
  23   16  0.57

ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19


Consensus pattern (23 bp):   
AATTGTCGACTCAAGAGGAAGCA

Found at i:1737 original size:23 final size:21

Alignment explanation


    Indices: 1694--1761  Score: 73
    Period size: 23  Copynumber: 3.0  Consensus size: 21

       1684 TCGACTAGGG

                                 
       1694 AATTGTCGACCAAAGGAAGCA
          1 AATTGTCGACCAAAGGAAGCA

                *                  
       1715 AATTTTCGACTCAAGAGGAAGCA
          1 AATTGTCGAC-CAA-AGGAAGCA

               *      *            
       1738 AATCGTCGACAAGAAGGCAAGCA
          1 AATTGTCGACCA-AAGG-AAGCA

             
       1761 A
          1 A

       1762 GGAATTTCGG


Statistics
Matches: 39,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
  21    9  0.23
  22    7  0.18
  23   23  0.59

ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15


Consensus pattern (21 bp):   
AATTGTCGACCAAAGGAAGCA

Found at i:2664 original size:22 final size:22

Alignment explanation


    Indices: 2633--2676  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2623 CCAATTTAGG

                 *      *   *     
       2633 TTTAGTTTTAAGTTTTTTTTTT
          1 TTTAGATTTAAGATTTATTTTT

                                  
       2655 TTTAGATTTAAGATTTATTTTT
          1 TTTAGATTTAAGATTTATTTTT

       2677 ATGCATCTTA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.20, C:0.00, G:0.09, T:0.70


Consensus pattern (22 bp):   
TTTAGATTTAAGATTTATTTTT

Found at i:3427 original size:20 final size:19

Alignment explanation


    Indices: 3398--3437  Score: 53
    Period size: 20  Copynumber: 2.1  Consensus size: 19

       3388 AAAGGGTAAT

                      *   *    
       3398 TAAAAAAAAATTGTTTTCA
          1 TAAAAAAAAAGTGTATTCA

                                
       3417 TAAAAAGAAAAGTGTATTCA
          1 TAAAAA-AAAAGTGTATTCA

             
       3437 T
          1 T

       3438 GATAGAGGAG


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

Matches are distributed among these distances:
  19    6  0.33
  20   12  0.67

ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33


Consensus pattern (19 bp):   
TAAAAAAAAAGTGTATTCA

Found at i:6755 original size:13 final size:13

Alignment explanation


    Indices: 6720--6758  Score: 60
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       6710 TAGTATTAAC

                  *  *   
       6720 TTTAGGTTTAGTT
          1 TTTAGGATTGGTT

                         
       6733 TTTAGGATTGGTT
          1 TTTAGGATTGGTT

                         
       6746 TTTAGGATTGGTT
          1 TTTAGGATTGGTT

       6759 AGGTAGTTCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  13   24  1.00

ACGTcount: A:0.15, C:0.00, G:0.28, T:0.56


Consensus pattern (13 bp):   
TTTAGGATTGGTT

Found at i:7613 original size:21 final size:21

Alignment explanation


    Indices: 7587--7678  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       7577 TGCTAGGACA

                                  
       7587 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 
       7608 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                 
       7629 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
       7650 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
       7671 TCATTGGA
          1 TCATTGGA

       7679 ATTGCCTAAG


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    2  0.03
  21   67  0.97

ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:8597 original size:25 final size:24

Alignment explanation


    Indices: 8561--8607  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

       8551 TCCTTCTATT

                                    
       8561 CATCTATCATC-AAGTTTTTCATC
          1 CATCTATCATCAAAGTTTTTCATC

                                    
       8584 CATCTCATCCATCAAAGTTTTTCA
          1 CATCT-AT-CATCAAAGTTTTTCA

       8608 AATTTTCTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  23    5  0.24
  24    2  0.10
  25    4  0.19
  26   10  0.48

ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40


Consensus pattern (24 bp):   
CATCTATCATCAAAGTTTTTCATC

Done.