Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023567.1 Corchorus olitorius cultivar O-4 contig23600, 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: 8502
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:1257 original size:18 final size:17

Alignment explanation


    Indices: 1199--1259  Score: 50
    Period size: 18  Copynumber: 3.4  Consensus size: 17

       1189 TTTTTCTATT

                *             
       1199 TTGGACTTTAGATTTATG
          1 TTGGGCTTTA-ATTTATG

                   *     *    *
       1217 TTGGGCCCTTAATGTATTT
          1 TTGGG-CTTTAATTTA-TG

                             
       1236 TTGGGCTTTAATTTATG
          1 TTGGGCTTTAATTTATG

                   
       1253 CTTGGGC
          1 -TTGGGC

       1260 CATTGTTGCT


Statistics
Matches: 33,  Mismatches: 7, Indels: 6
        0.72            0.15        0.13

Matches are distributed among these distances:
  17    1  0.03
  18   22  0.67
  19   10  0.30

ACGTcount: A:0.16, C:0.11, G:0.25, T:0.48


Consensus pattern (17 bp):   
TTGGGCTTTAATTTATG

Found at i:2126 original size:68 final size:68

Alignment explanation


    Indices: 2017--2926  Score: 1059
    Period size: 68  Copynumber: 13.5  Consensus size: 68

       2007 TAAAGCTTTA

                  *    *                  *                                  
       2017 TTTTCTCTTTCTAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

               
       2082 CTG
         66 CTG

                                       *                       *             
       2085 TTTTCTATTTCCAAAAATACCCTTTCGATCAAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

                
       2150 GC-G
         66 -CTG

                  *                                            *             
       2153 TTTTCTTTTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

                
       2218 GC-G
         66 -CTG

                  *                       *                     *            
       2221 TTTTCTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTACATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

            * *
       2286 GTA
         66 CTG

            *     *          **           *        *    **                   
       2289 CTTTCTTTTTCCAAAAACGCCCTTTCGGTCGAAGGGTCAATTTCAACTTTTTGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

            *  
       2354 GTG
         66 CTG

                                                                             
       2357 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

            *  
       2422 GTG
         66 CTG

                                                                             
       2425 TTTTCTATTTCC--AAA-ACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

            ** 
       2487 GGG
         66 CTG

                                          *                                  
       2490 TTTTCTATTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

            *  
       2555 GTG
         66 CTG

                                      *   *    *               *             
       2558 TTTTCTATTTCCAAAAATACCCTTTCTGTCGAAGGATCATTTTCGTCTTTTCGCATTTAAGTTTA
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA

                
       2623 GC-G
         66 -CTG

               *  *         *        *    *               *                  
       2626 TTTCCTTTTTCCAAAAGTACCCTTTTGGTCGAAGGGTCATTTTCGTATTTTGTGCATTTAAGTTT
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTT-TGCATTTAAGTTT

               *
       2691 ACTA
         65 ACTG

            *     *           *           *      * *    **      *            
       2695 CTTTCTTTTTCCAAAAATGCCCTTTCGGTCGAAGGGTTAATTTCAAC-TTTTCCATGTTTAAG-T
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCA--TTTAAGTT

                 
       2758 TA--G
         64 TACTG

               *        *                           *          *       **    
       2761 TTTACT-TTTCCCAAAATACCCTTTCGGTCAAAGGGTCA-ATTCTGTCGTTCTTGCATTCGAGTT
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTC-GTC-TTTTTGCATTTAAGTT

                 
       2824 TACT-
         64 TACTG

               *            *            *         *    *              *     
       2828 TTTGC--TTTCCAAAATTACCCTTTCGGTGAAAGGGTCAGTTTCATCTTTTTCGCATTTCAGTTT
          1 TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTT-GCATTTAAGTTT

                
       2891 A---
         65 ACTG

                               *                 
       2892 --TTCTACTTTCCAAAAATGCCCTTTCGGTCAAAGGG
          1 TTTTCTA-TTTCCAAAAATACCCTTTCGGTCAAAGGG

       2927 CTAGCTTTGT


Statistics
Matches: 739,  Mismatches: 82, Indels: 45
        0.85            0.09        0.05

Matches are distributed among these distances:
  62    2  0.00
  64    3  0.00
  65  124  0.17
  66   52  0.07
  67   18  0.02
  68  483  0.65
  69   57  0.08

ACGTcount: A:0.21, C:0.20, G:0.15, T:0.44


Consensus pattern (68 bp):   
TTTTCTATTTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTTGCATTTAAGTTTA
CTG

Found at i:6930 original size:19 final size:18

Alignment explanation


    Indices: 6906--6941  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6896 TGAAGACTTA

                               
       6906 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       6925 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       6942 ATTATTTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.