Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015894.1 Corchorus olitorius cultivar O-4 contig15927, 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: 10445
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:789 original size:31 final size:32

Alignment explanation


    Indices: 734--825  Score: 168
    Period size: 31  Copynumber: 2.9  Consensus size: 32

        724 ATGATAATTC

                                            
        734 TTGTGGTTCTTAACCCTTTTATTATAAGGTTT
          1 TTGTGGTTCTTAACCCTTTTATTATAAGGTTT

                                            
        766 TTGTGGTTCTTAACCC-TTTATTATAAGGTTT
          1 TTGTGGTTCTTAACCCTTTTATTATAAGGTTT

                 *                       
        797 TTGTGATTCTTAACCCTTTTATTATAAGG
          1 TTGTGGTTCTTAACCCTTTTATTATAAGG

        826 GGAAACTATG


Statistics
Matches: 58,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  31   30  0.52
  32   28  0.48

ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51


Consensus pattern (32 bp):   
TTGTGGTTCTTAACCCTTTTATTATAAGGTTT

Found at i:5950 original size:38 final size:38

Alignment explanation


    Indices: 5899--5979  Score: 144
    Period size: 38  Copynumber: 2.1  Consensus size: 38

       5889 AGCCTAACTT

                                            *     
       5899 TGATTTCCTATATATATAACATATAGTAAGATTACACA
          1 TGATTTCCTATATATATAACATATAGTAAGATGACACA

                                             *    
       5937 TGATTTCCTATATATATAACATATAGTAAGATGGCACA
          1 TGATTTCCTATATATATAACATATAGTAAGATGACACA

                 
       5975 TGATT
          1 TGATT

       5980 AAAGACTATT


Statistics
Matches: 41,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  38   41  1.00

ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37


Consensus pattern (38 bp):   
TGATTTCCTATATATATAACATATAGTAAGATGACACA

Found at i:6240 original size:21 final size:23

Alignment explanation


    Indices: 6199--6243  Score: 67
    Period size: 21  Copynumber: 2.0  Consensus size: 23

       6189 AACTTGTTAC

                                   
       6199 TATAAACTTTCAGCAATAATTAA
          1 TATAAACTTTCAGCAATAATTAA

                 *                 
       6222 TATAAGCTTT-AGC-ATAATTAA
          1 TATAAACTTTCAGCAATAATTAA

             
       6243 T
          1 T

       6244 TGAGTCAGTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    9  0.43
  22    3  0.14
  23    9  0.43

ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38


Consensus pattern (23 bp):   
TATAAACTTTCAGCAATAATTAA

Found at i:7038 original size:26 final size:27

Alignment explanation


    Indices: 7008--7064  Score: 71
    Period size: 29  Copynumber: 2.1  Consensus size: 27

       6998 AGTATTTTAA

                                       
       7008 ATTTTATACA-TTCATCAAATTATCAG
          1 ATTTTATACAGTTCATCAAATTATCAG

                   *  *                  
       7034 ATTTTTTTTATAGTTCATCAAATTATCAG
          1 A--TTTTATACAGTTCATCAAATTATCAG

              
       7063 AT
          1 AT

       7065 AGGTTACAAG


Statistics
Matches: 26,  Mismatches: 2, Indels: 5
        0.79            0.06        0.15

Matches are distributed among these distances:
  26    1  0.04
  27    1  0.04
  28    7  0.27
  29   17  0.65

ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47


Consensus pattern (27 bp):   
ATTTTATACAGTTCATCAAATTATCAG

Found at i:7620 original size:22 final size:22

Alignment explanation


    Indices: 7590--7632  Score: 77
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7580 TATTAAAATT

                *                 
       7590 GGTCCTTTCAAATAATTTTTTA
          1 GGTCATTTCAAATAATTTTTTA

                                 
       7612 GGTCATTTCAAATAATTTTTT
          1 GGTCATTTCAAATAATTTTTT

       7633 TTTTCTACAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   20  1.00

ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51


Consensus pattern (22 bp):   
GGTCATTTCAAATAATTTTTTA
Done.