Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022206.1 Corchorus olitorius cultivar O-4 contig22239, 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: 17562
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:7779 original size:33 final size:33

Alignment explanation


    Indices: 7742--7823  Score: 146
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       7732 CGTTCATGTG

                                             
       7742 CCCTTAAATCATAGTCCTCAATTCATCATTGTA
          1 CCCTTAAATCATAGTCCTCAATTCATCATTGTA

                                            *
       7775 CCCTTAAATCATAGTCCTCAATTCATCATTGTG
          1 CCCTTAAATCATAGTCCTCAATTCATCATTGTA

                   *        
       7808 CCCTTAAGTCATAGTC
          1 CCCTTAAATCATAGTC

       7824 TTGAAGCCAT


Statistics
Matches: 47,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  33   47  1.00

ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35


Consensus pattern (33 bp):   
CCCTTAAATCATAGTCCTCAATTCATCATTGTA

Found at i:7880 original size:109 final size:112

Alignment explanation


    Indices: 7761--8013  Score: 370
    Period size: 113  Copynumber: 2.3  Consensus size: 112

       7751 CATAGTCCTC

                         *       *                                           
       7761 AATTCATCATTGTACCCTTAAATCATAGTCCTCAATTCATCATTGTGCCCTTAAGTCATAGTCTT
          1 AATTCATCATTGTGCCCTTAAGTCATAGTCCTCAATTCATCATTGTGCCCTTAAGTCATAGT-TT

                       * **                                 
       7826 G-AAG-C-CA-TCTTAACTCGATCATGTGTGCCCACCCTTAATTGATT
         65 GTAAGCCACACGCCCAACTCGATCATGTGTGCCCACCCTTAATTGATT

                               *  *                               *          
       7870 AATTCATCATTGTGCCCTTGAGCCATAGTCCTCAATTCATCATTGTGCCCTTAATTCATAGTTTG
          1 AATTCATCATTGTGCCCTTAAGTCATAGTCCTCAATTCATCATTGTGCCCTTAAGTCATAGTTTG

                                          *                 
       7935 TAAGCCACACGGCCCAACTCGATCATGTGTTCCCACCCTTAATTGATT
         66 TAAGCCACAC-GCCCAACTCGATCATGTGTGCCCACCCTTAATTGATT

                     *                     
       7983 AATTCATCACTGTGCCCTTAAGTCATAGTCC
          1 AATTCATCATTGTGCCCTTAAGTCATAGTCC

       8014 GTAAGGCATT


Statistics
Matches: 127,  Mismatches: 12, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 108    3  0.02
 109   60  0.47
 110    1  0.01
 111    2  0.02
 113   61  0.48

ACGTcount: A:0.25, C:0.27, G:0.13, T:0.34


Consensus pattern (112 bp):   
AATTCATCATTGTGCCCTTAAGTCATAGTCCTCAATTCATCATTGTGCCCTTAAGTCATAGTTTG
TAAGCCACACGCCCAACTCGATCATGTGTGCCCACCCTTAATTGATT

Found at i:12540 original size:40 final size:40

Alignment explanation


    Indices: 12427--12547  Score: 172
    Period size: 40  Copynumber: 3.0  Consensus size: 40

      12417 TGTTACATGA

                  *                              *  
      12427 GTGGATTAGAACAAATTGTTTTTAATTTCATTTTTAACGT
          1 GTGGATCAGAACAAATTGTTTTTAATTTCATTTTTAATGT

                                                  * 
      12467 GTGGATCAGAACAAATTGTTTTTAATTTCATTTTTAATTT
          1 GTGGATCAGAACAAATTGTTTTTAATTTCATTTTTAATGT

                    *             **                 
      12507 GTGGATCAAAACAAATTGTTTTGGATTAT-ATTTTTAATGT
          1 GTGGATCAGAACAAATTGTTTTTAATT-TCATTTTTAATGT

             
      12547 G
          1 G

      12548 AATGACAGTA


Statistics
Matches: 73,  Mismatches: 7, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  40   72  0.99
  41    1  0.01

ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47


Consensus pattern (40 bp):   
GTGGATCAGAACAAATTGTTTTTAATTTCATTTTTAATGT

Found at i:12824 original size:89 final size:89

Alignment explanation


    Indices: 12673--12910  Score: 395
    Period size: 89  Copynumber: 2.7  Consensus size: 89

      12663 ACCCCAACAG

                                 *                  *             *          
      12673 TGGCTTACGTTGCTATAGAATATATACCAACAGCGGGGGGTGTTGGTATAGCCACAAACCAAAAA
          1 TGGCTTACGTTGCTATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAA

              *                     
      12738 ATGGTATGATTGGAGATATACCTA
         66 ATAGTATGATTGGAGATATACCTA

                                                 *                           
      12762 TGGCTTACGTTGCTATAGAATGTATACCAACAGCGGGTGGCGTTGGTATAGCCATAAACCAAAAA
          1 TGGCTTACGTTGCTATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAA

                                    
      12827 ATAGTATGATTGGAGATATACCTA
         66 ATAGTATGATTGGAGATATACCTA

            *     *                                        *            
      12851 CGGCTTCCGTTGCTATAGAATGTATACCAACAGCGGGGGGGCGTTGGCATAGCCATAAAC
          1 TGGCTTACGTTGCTATAGAATGTATACCAACAGC-GGGGGGCGTTGGTATAGCCATAAAC

      12911 AGCCAACAGG


Statistics
Matches: 139,  Mismatches: 9, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  89  116  0.83
  90   23  0.17

ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25


Consensus pattern (89 bp):   
TGGCTTACGTTGCTATAGAATGTATACCAACAGCGGGGGGCGTTGGTATAGCCATAAACCAAAAA
ATAGTATGATTGGAGATATACCTA
Done.