Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020868.1 Corchorus olitorius cultivar O-4 contig20901, 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: 8988
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3068 original size:17 final size:16

Alignment explanation


    Indices: 3014--3064  Score: 66
    Period size: 17  Copynumber: 3.1  Consensus size: 16

       3004 ACTCACCCCC

                   *         
       3014 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATC-A

                             
       3031 AGATCACCAGTGATGCA
          1 AGATCACCAGTGAT-CA

                    *       
       3048 AGATCACCGGTGATCA
          1 AGATCACCAGTGATCA

             
       3064 A
          1 A

       3065 AGATTACATG


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   27  0.87
  18    1  0.03

ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22


Consensus pattern (16 bp):   
AGATCACCAGTGATCA

Found at i:4546 original size:102 final size:103

Alignment explanation


    Indices: 4369--4572  Score: 340
    Period size: 102  Copynumber: 2.0  Consensus size: 103

       4359 TAATATGGTG

                  *                                                          
       4369 ATAATTCAGAGATTTTCAAAAAAACCCCATCACAATGAAATCTTGATATGGGGGACCTACATAGT
          1 ATAATTAAGAGATTTTCAAAAAAACCCCATCACAATGAAATCTTGATATGGGGGACCTACATAGT

                             *                    
       4434 ATTTATTTTAAAATTAGTTAAACCTTGAACTAAAATTC
         66 ATTTATTTTAAAATTAGCTAAACCTTGAACTAAAATTC

                             *         *                                     
       4472 ATAATTAAGAGATTTT-TAAAAAACCCTATCACAATGAAATCTTGATATGGGGGA-CTCACATAG
          1 ATAATTAAGAGATTTTCAAAAAAACCCCATCACAATGAAATCTTGATATGGGGGACCT-ACATAG

                            *                     
       4535 TATTTATTTTAAAATTGGCTAAACCTTGAACTAAAATT
         65 TATTTATTTTAAAATTAGCTAAACCTTGAACTAAAATT

       4573 GTGCCCCTAA


Statistics
Matches: 95,  Mismatches: 5, Indels: 3
        0.92            0.05        0.03

Matches are distributed among these distances:
 101    2  0.02
 102   78  0.82
 103   15  0.16

ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33


Consensus pattern (103 bp):   
ATAATTAAGAGATTTTCAAAAAAACCCCATCACAATGAAATCTTGATATGGGGGACCTACATAGT
ATTTATTTTAAAATTAGCTAAACCTTGAACTAAAATTC

Found at i:7558 original size:178 final size:178

Alignment explanation


    Indices: 7286--7615  Score: 448
    Period size: 178  Copynumber: 1.9  Consensus size: 178

       7276 CCGATTAAGG

                 *                      *                            *    *  
       7286 TGATTTAAGTGTCTATTAAAAGATTGTTTCATCATCTACAACTTTCATGAAGAACTCGAAAATTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCAAAAACTA

                               *                     *              *  *     
       7351 AATTTAATGTTTCAAGTATCAAAAATGCTTCC-GAAAAATTTGTTGTTTCAGTTAATGGGAATAG
         66 AATTTAATGTTTCAAGTATAAAAAATGCTTCCAG-AAAATTAGTTGTTTCAGTTAACGGAAATAG

              *               *                              
       7415 ACGGTCCACTTAATATTATATAACTTTTATTCCAGATGTCTGATTGAGA
        130 ACAGTCCACTTAATATTACATAACTTTTATTCCAGATGTCTGATTGAGA

                          *  *    *         *            *      *            
       7464 TGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTTATGAAGGACTCAAAAACTA
          1 TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCAAAAACTA

                           *                    *             *              
       7529 AATTTAAT-TTTCGAGGTATAAAAAATGCTTCCAGAGAATTAGTTGTTTCGGTTAACGGAAATAG
         66 AATTTAATGTTTC-AAGTATAAAAAATGCTTCCAGAAAATTAGTTGTTTCAGTTAACGGAAATAG

                  *                
       7593 ACAGTCTACTTAATATTACATAA
        130 ACAGTCCACTTAATATTACATAA

       7616 TTTGTGCTTA


Statistics
Matches: 130,  Mismatches: 20, Indels: 4
        0.84            0.13        0.03

Matches are distributed among these distances:
 177    4  0.03
 178  125  0.96
 179    1  0.01

ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36


Consensus pattern (178 bp):   
TGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGAACTCAAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCCAGAAAATTAGTTGTTTCAGTTAACGGAAATAGA
CAGTCCACTTAATATTACATAACTTTTATTCCAGATGTCTGATTGAGA
Done.