Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016113.1 Corchorus olitorius cultivar O-4 contig16146, 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: 3243
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28


Found at i:2288 original size:33 final size:33

Alignment explanation


    Indices: 2246--2312  Score: 125
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2236 TTTGTGAGTT

                                         *   
       2246 CAAGATCAAAATTCGCTTTTCAAAACAAGTTTG
          1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

                                             
       2279 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG
          1 CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

             
       2312 C
          1 C

       2313 TTTCCATTTG


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28


Consensus pattern (33 bp):   
CAAGATCAAAATTCGCTTTTCAAAACAAGATTG

Found at i:2339 original size:48 final size:48

Alignment explanation


    Indices: 2281--2393  Score: 147
    Period size: 48  Copynumber: 2.3  Consensus size: 48

       2271 CAAGTTTGCA

                                                             
       2281 AGATCAAAATTCGCTTTTCAAAACAAGATTGC-TTTCCATTTGTGAGCC
          1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTT-CATTTGTGAGCC

                *                 **                         *
       2329 AGATTAAAATTCGCTTTTCAAAGTAAGATTGCATTTCATTTGTGAGTCTA
          1 AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTTGTGAG-C-C

                     *     
       2379 AGATCAAAACTCGCT
          1 AGATCAAAATTCGCT

       2394 CTTCGAGGGG


Statistics
Matches: 56,  Mismatches: 6, Indels: 4
        0.85            0.09        0.06

Matches are distributed among these distances:
  48   39  0.70
  49    4  0.07
  50   13  0.23

ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35


Consensus pattern (48 bp):   
AGATCAAAATTCGCTTTTCAAAACAAGATTGCATTTCATTTGTGAGCC

Found at i:2960 original size:35 final size:35

Alignment explanation


    Indices: 2914--3243  Score: 476
    Period size: 35  Copynumber: 9.5  Consensus size: 35

       2904 CATTTTCCAA

                                                
       2914 AGATGACTCGGTGTAGCATCTTCAAAGTT-ATACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGA-ACTC

                                               
       2949 AGATGACTCGGTGTAGCATCTTCAAAGTTGAA-TC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

                                           *   
       2983 AGATGACTCGGTGTAGCATCTTCAAAGTTGACCTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

            *            *     *      *        
       3018 GGATGACTCGGTGCAGCATTTTCAAAATTGAACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

                                *               
       3053 AGATGACTCGGTGTAGCATCCTCAAAGTTGAA-TCC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACT-C

                     *   *     *      *        
       3088 AGATGACTCAGTGCAGCATTTTCAAAATTGAACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

                                               
       3123 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

                                   *            
       3158 AGATGACTCGGTGTAGCATCTTCGAAGTTGAA-TCC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACT-C

                                                
       3193 AGATGACTCGGTGTAGCATC-TCAAA-TTGAA-TCC
          1 AGATGACTCGGTGTAGCATCTTCAAAGTTGAACT-C

                              
       3226 AGATGACTCGGTGTAGCA
          1 AGATGACTCGGTGTAGCA


Statistics
Matches: 268,  Mismatches: 22, Indels: 12
        0.89            0.07        0.04

Matches are distributed among these distances:
  33   26  0.10
  34   39  0.15
  35  201  0.75
  36    2  0.01

ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28


Consensus pattern (35 bp):   
AGATGACTCGGTGTAGCATCTTCAAAGTTGAACTC

Done.