Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009629.1 Corchorus olitorius cultivar O-4 contig09661, 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: 7628
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31


Found at i:17 original size:2 final size:2

Alignment explanation


    Indices: 11--39  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

          1 TGAGAAAGAG

                                                       
         11 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         40 GAAAAATAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:2773 original size:39 final size:39

Alignment explanation


    Indices: 2649--2780  Score: 123
    Period size: 39  Copynumber: 3.4  Consensus size: 39

       2639 TATAAAGAGG

                     *                               
       2649 GACCTAAGCGGGTTTGATTGAACGAAAC-TCT-AA-GAATA
          1 GACCTAAGCAGGTTTGATTGAACGAAACTTCTAAACG-A-A

                           *      *   *               
       2687 GACCTAAGCAGG-TTCACTTGAGCGGGAA-TTCTTAAAC-AA
          1 GACCTAAGCAGGTTTGA-TTGAAC-GAAACTTC-TAAACGAA

                                *                   
       2726 GAACCTAAGCAGGTTTGATTAAACGAAACTTCTAAACGAA
          1 G-ACCTAAGCAGGTTTGATTGAACGAAACTTCTAAACGAA

                           
       2766 GACCTAAGCAGGTTT
          1 GACCTAAGCAGGTTT

       2781 ACTCGAATGA


Statistics
Matches: 76,  Mismatches: 8, Indels: 19
        0.74            0.08        0.18

Matches are distributed among these distances:
  37    3  0.04
  38   16  0.21
  39   29  0.38
  40   23  0.30
  41    5  0.07

ACGTcount: A:0.36, C:0.18, G:0.22, T:0.23


Consensus pattern (39 bp):   
GACCTAAGCAGGTTTGATTGAACGAAACTTCTAAACGAA

Found at i:2879 original size:39 final size:38

Alignment explanation


    Indices: 2835--2983  Score: 133
    Period size: 38  Copynumber: 3.9  Consensus size: 38

       2825 ACAGAACAGA

                                              * ** 
       2835 GACCTAAGCAGGTTTGCTTAAACGGAAATTCTAAACAAG
          1 GACCTAAGCAGGTTT-CTTAAACGGAAATTCTAAGCGGG

                            * *    *  *  *         
       2874 GACCTAAGCAGGTTTAATCAAA-TGAGATACTAAGCGGG
          1 GACCTAAGCAGGTTT-CTTAAACGGAAATTCTAAGCGGG

                                  *    *            
       2912 GACCTAAGCAGGTTTC--AACAAGCGAGATTCTAAGCGGG
          1 GACCTAAGCAGGTTTCTTAA-ACG-GAAATTCTAAGCGGG

                                   *          
       2950 GACCTAAGCAGGTTTTCTTAAACAGAAATTCTAA
          1 GACCTAAGCAGG-TTTCTTAAACGGAAATTCTAA

       2984 TGAGATTCTA


Statistics
Matches: 89,  Mismatches: 15, Indels: 12
        0.77            0.13        0.10

Matches are distributed among these distances:
  35    2  0.02
  36    1  0.01
  38   51  0.57
  39   32  0.36
  40    1  0.01
  41    2  0.02

ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23


Consensus pattern (38 bp):   
GACCTAAGCAGGTTTCTTAAACGGAAATTCTAAGCGGG

Found at i:2924 original size:38 final size:38

Alignment explanation


    Indices: 2873--2964  Score: 141
    Period size: 38  Copynumber: 2.4  Consensus size: 38

       2863 TTCTAAACAA

                                    *              
       2873 GGACCTAAGCAGGTTT-AATCAAATGAGATACTAAGCGG
          1 GGACCTAAGCAGGTTTCAA-CAAACGAGATACTAAGCGG

                                  *      *        
       2911 GGACCTAAGCAGGTTTCAACAAGCGAGATTCTAAGCGG
          1 GGACCTAAGCAGGTTTCAACAAACGAGATACTAAGCGG

                            
       2949 GGACCTAAGCAGGTTT
          1 GGACCTAAGCAGGTTT

       2965 TCTTAAACAG


Statistics
Matches: 50,  Mismatches: 3, Indels: 2
        0.91            0.05        0.04

Matches are distributed among these distances:
  38   48  0.96
  39    2  0.04

ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21


Consensus pattern (38 bp):   
GGACCTAAGCAGGTTTCAACAAACGAGATACTAAGCGG

Found at i:3026 original size:38 final size:38

Alignment explanation


    Indices: 2982--3061  Score: 124
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       2972 CAGAAATTCT

                                             *    
       2982 AATGAGATTCTAAACATAGACCTAAACAGGTTTCCTTA
          1 AATGAGATTCTAAACATAGACCTAAACAGGTTTACTTA

                           *    *    *            
       3020 AATGAGATTCTAAACGTAGATCTAAGCAGGTTTACTTA
          1 AATGAGATTCTAAACATAGACCTAAACAGGTTTACTTA

                
       3058 AATG
          1 AATG

       3062 GCAACTCTAA


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  38   38  1.00

ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30


Consensus pattern (38 bp):   
AATGAGATTCTAAACATAGACCTAAACAGGTTTACTTA

Found at i:7538 original size:2 final size:2

Alignment explanation


    Indices: 7531--7559  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       7521 TGAGAAAGAG

                                                       
       7531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       7560 GAAAAATAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.