Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017502.1 Corchorus olitorius cultivar O-4 contig17535, 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: 13784
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:528 original size:13 final size:13

Alignment explanation


    Indices: 506--540  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

        496 ATAAAATTTA

                         
        506 AATTAATAAAAGG
          1 AATTAATAAAAGG

                 *       
        519 AATTAGTAAAAGG
          1 AATTAATAAAAGG

                     
        532 AATTAATAA
          1 AATTAATAA

        541 TAAGATTATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26


Consensus pattern (13 bp):   
AATTAATAAAAGG

Found at i:1322 original size:11 final size:11

Alignment explanation


    Indices: 1306--1336  Score: 62
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       1296 CTTGGGCCTA

                       
       1306 CCAGGCGTGGC
          1 CCAGGCGTGGC

                       
       1317 CCAGGCGTGGC
          1 CCAGGCGTGGC

                     
       1328 CCAGGCGTG
          1 CCAGGCGTG

       1337 CAAGCCATGC


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.10, C:0.35, G:0.45, T:0.10


Consensus pattern (11 bp):   
CCAGGCGTGGC

Found at i:2554 original size:13 final size:13

Alignment explanation


    Indices: 2536--2565  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

       2526 GGTTTTACTC

                         
       2536 TGATTTATGACTT
          1 TGATTTATGACTT

                      *  
       2549 TGATTTATGATTT
          1 TGATTTATGACTT

                
       2562 TGAT
          1 TGAT

       2566 ATTAATGGTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.23, C:0.03, G:0.17, T:0.57


Consensus pattern (13 bp):   
TGATTTATGACTT

Found at i:7014 original size:41 final size:40

Alignment explanation


    Indices: 6887--7020  Score: 119
    Period size: 41  Copynumber: 3.3  Consensus size: 40

       6877 CTAGCATATA

                      *        *        *             
       6887 AAATCAGGGATCAAATTGATTCAAATAGTAAC-TAAAATCCT
          1 AAATCAGGGACCAAATTGAATCAAATAGCAACAT-AAA-CCT

                     * *      *       *     *  *     
       6928 AAATCAGGGGCTAAATTGCATCAAATGGTCAATATTAA-CT
          1 AAATCAGGGACCAAATTGAATCAAATAG-CAACATAAACCT

                                     *                
       6968 CAAATCAGGGACCAAATTGAATCAATTAGCAAACATAAACCT
          1 -AAATCAGGGACCAAATTGAATCAAATAGC-AACATAAACCT

                       
       7010 AAATCAGGGAC
          1 AAATCAGGGAC

       7021 TAAGGTGAAA


Statistics
Matches: 72,  Mismatches: 16, Indels: 10
        0.73            0.16        0.10

Matches are distributed among these distances:
  40    3  0.04
  41   62  0.86
  42    6  0.08
  43    1  0.01

ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23


Consensus pattern (40 bp):   
AAATCAGGGACCAAATTGAATCAAATAGCAACATAAACCT

Found at i:9620 original size:27 final size:27

Alignment explanation


    Indices: 9583--9649  Score: 107
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       9573 AGTGAGCTTA

                                      *
       9583 AAATGACCAAAATGCCCCTGAATGTGT
          1 AAATGACCAAAATGCCCCTGAATGTGC

                                *      
       9610 AAATGACCAAAATGCCCCTGGATGTGC
          1 AAATGACCAAAATGCCCCTGAATGTGC

                   *     
       9637 AAATGACAAAAAT
          1 AAATGACCAAAAT

       9650 ACCCATAGAT


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  27   37  1.00

ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAATGTGC

Found at i:9660 original size:27 final size:27

Alignment explanation


    Indices: 9604--9660  Score: 69
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       9594 ATGCCCCTGA

                 *       *     *   * * 
       9604 ATGTGTAAATGACCAAAATGCCCCTGG
          1 ATGTGCAAATGACAAAAATACCCATAG

                                       
       9631 ATGTGCAAATGACAAAAATACCCATAG
          1 ATGTGCAAATGACAAAAATACCCATAG

               
       9658 ATG
          1 ATG

       9661 ACCCTAACGC


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  27   25  1.00

ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21


Consensus pattern (27 bp):   
ATGTGCAAATGACAAAAATACCCATAG

Found at i:13384 original size:13 final size:13

Alignment explanation


    Indices: 13362--13396  Score: 61
    Period size: 13  Copynumber: 2.7  Consensus size: 13

      13352 ATAAAATTTA

                         
      13362 AATTAATAAAAGG
          1 AATTAATAAAAGG

                 *       
      13375 AATTAGTAAAAGG
          1 AATTAATAAAAGG

                     
      13388 AATTAATAA
          1 AATTAATAA

      13397 TAAGATTATA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26


Consensus pattern (13 bp):   
AATTAATAAAAGG
Done.