Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016959.1 Corchorus olitorius cultivar O-4 contig16992, 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: 4574
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27


Found at i:2998 original size:42 final size:42

Alignment explanation


    Indices: 2952--3042  Score: 119
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       2942 CTAGTATCAC

                           *                * *   *   
       2952 GCCCGGCCATGCCCGGCACCACAAGCCTCAGCTGCGCCTCAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                              * *         *           
       2994 GCCCGGCCATGCCCGCCATCTCAAGCCTCATCCGAGCCACAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                   
       3036 GCCCGGC
          1 GCCCGGC

       3043 TAGGACCGGC


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.16, C:0.48, G:0.23, T:0.12


Consensus pattern (42 bp):   
GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

Found at i:3196 original size:29 final size:28

Alignment explanation


    Indices: 3153--3250  Score: 90
    Period size: 28  Copynumber: 3.5  Consensus size: 28

       3143 ATCTAAGGGA

                           *              
       3153 ATTTTGGGTCATTTTCAAAATCCA-GGGGC
          1 ATTTT-GGTCATTTTTAAAAT-CAGGGGGC

                            * * *       
       3182 ATTTTGGTCATTTTTACACTTAGGGGGC
          1 ATTTTGGTCATTTTTAAAATCAGGGGGC

                            * * *  *  * 
       3210 ATTTTGGTCATTTTTACACTTAGAGGTC
          1 ATTTTGGTCATTTTTAAAATCAGGGGGC

                         
       3238 ATTTTGGTCATTT
          1 ATTTTGGTCATTT

       3251 GTACTTCAGG


Statistics
Matches: 62,  Mismatches: 6, Indels: 3
        0.87            0.08        0.04

Matches are distributed among these distances:
  27    1  0.02
  28   56  0.90
  29    5  0.08

ACGTcount: A:0.20, C:0.14, G:0.21, T:0.44


Consensus pattern (28 bp):   
ATTTTGGTCATTTTTAAAATCAGGGGGC

Found at i:3208 original size:28 final size:28

Alignment explanation


    Indices: 3177--3250  Score: 130
    Period size: 28  Copynumber: 2.6  Consensus size: 28

       3167 TCAAAATCCA

                                        
       3177 GGGGCATTTTGGTCATTTTTACACTTAG
          1 GGGGCATTTTGGTCATTTTTACACTTAG

                                        
       3205 GGGGCATTTTGGTCATTTTTACACTTAG
          1 GGGGCATTTTGGTCATTTTTACACTTAG

            *  *              
       3233 AGGTCATTTTGGTCATTT
          1 GGGGCATTTTGGTCATTT

       3251 GTACTTCAGG


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   44  1.00

ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45


Consensus pattern (28 bp):   
GGGGCATTTTGGTCATTTTTACACTTAG

Found at i:3269 original size:26 final size:27

Alignment explanation


    Indices: 3175--3284  Score: 111
    Period size: 28  Copynumber: 4.1  Consensus size: 27

       3165 TTTCAAAATC

                                *       
       3175 CAGGGGCATTTTGGTCATTTTTACACTT
          1 CAGGGGCATTTTGGTCATTTGTA-ACTT

                                 *       
       3203 -AGGGGGCATTTTGGTCATTTTTACACTT
          1 CA-GGGGCATTTTGGTCATTTGTA-ACTT

                  *                     
       3231 -AGAGGTCATTTTGGTCATTTGT-ACTT
          1 CAG-GGGCATTTTGGTCATTTGTAACTT

                    *       *          
       3257 CAGGGGCACTTTGGTCTTTTGT-ACTT
          1 CAGGGGCATTTTGGTCATTTGTAACTT

              
       3283 CA
          1 CA

       3285 TTACTAGCTT


Statistics
Matches: 74,  Mismatches: 5, Indels: 8
        0.85            0.06        0.09

Matches are distributed among these distances:
  26   26  0.35
  27    4  0.05
  28   44  0.59

ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43


Consensus pattern (27 bp):   
CAGGGGCATTTTGGTCATTTGTAACTT
Done.