Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003129.1 Corchorus capsularis cultivar CVL-1 contig03137, 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: 11306
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:6304 original size:28 final size:29

Alignment explanation


    Indices: 6241--6313  Score: 112
    Period size: 28  Copynumber: 2.6  Consensus size: 29

       6231 CTATGACGTC

                   *    *                
       6241 TCCCTCTGATGTGTCAGGCGAAAAATTCT
          1 TCCCTCTAATGTATCAGGCGAAAAATTCT

                                         
       6270 TCCCTCTAATGTATCAGGCG-AAAATTCT
          1 TCCCTCTAATGTATCAGGCGAAAAATTCT

              *             
       6298 TCTCTCTAATGTATCA
          1 TCCCTCTAATGTATCA

       6314 CACAACAAGT


Statistics
Matches: 41,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  28   23  0.56
  29   18  0.44

ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34


Consensus pattern (29 bp):   
TCCCTCTAATGTATCAGGCGAAAAATTCT

Found at i:6326 original size:28 final size:28

Alignment explanation


    Indices: 6262--6328  Score: 73
    Period size: 28  Copynumber: 2.4  Consensus size: 28

       6252 TGTCAGGCGA

                *     *             **  
       6262 AAAATTCTTCCCTCTAATGTATCAGGCG
          1 AAAAGTCTTCTCTCTAATGTATCACACG

                *                       
       6290 AAAATTCTTCTCTCTAATGTATCACAC-
          1 AAAAGTCTTCTCTCTAATGTATCACACG

                        
       6317 AACAAGTCTTCT
          1 AA-AAGTCTTCT

       6329 GATGCTTCCG


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  27    2  0.06
  28   32  0.94

ACGTcount: A:0.31, C:0.25, G:0.09, T:0.34


Consensus pattern (28 bp):   
AAAAGTCTTCTCTCTAATGTATCACACG

Found at i:6891 original size:156 final size:155

Alignment explanation


    Indices: 6626--7013  Score: 387
    Period size: 156  Copynumber: 2.5  Consensus size: 155

       6616 GGTTCGAGCC

                             *                *                  *           
       6626 CTCCTTCATGGTGAACTAGGTTTCACACCCCAAATTGTCCTTAAATGAAAAACGTGCATAAGTTT
          1 CTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCATAAGTTT

                      *   * *                                  *       * *   
       6691 TTCATTATAAGTCTGATTGAGATGAAACTTTGCCAAGGGACTTAGATTATTTCC-TCAAGACTAT
         66 TTCATTATAAATCTCAATGAGATG-AACTTTGCCAAGGGACTTAGATTATTCCCAT-AAAAATAT

             *        *    *         *  
       6755 GGAAAAAATTCTAAGTAAAACCT-AGCT
        129 GAAAAAAATTATAAGCAAAA-CTGAACT

                  *                    *                                     
       6782 CTCCTTGATGGTGAACTTGGTTTCTA-TCCCCAAACTGTCCTTAAATGAAAAACATGCATAAGTT
          1 CTCCTTCATGGTGAACTTGGTTTC-ACACCCCAAACTGTCCTTAAATGAAAAACATGCATAAGTT

                   *               *        *                                
       6846 TTTCATTCTAAATC-CAATGAAGCTG-A-TTTTCCACCAGTAGG-CTTAGATTATTCCCATAAAA
         65 TTTCATTATAAATCTCAATG-AGATGAACTTTGCCA--AG--GGACTTAGATTATTCCCATAAAA

                                           
       6907 ATATGAAAAAAATTATAAGCAAAACTGAACT
        125 ATATGAAAAAAATTATAAGCAAAACTGAACT

                      *     *                           *                    
       6938 C-CCTATCATAGTGAAGTTGGTTTCACACCCCAAACTGTTCTTAATTGAAAATGAAAAACATGCA
          1 CTCCT-TCATGGTGAACTTGGTTTCACACCCCAAACTG-TC---CTT--AAATGAAAAACATGCA

                        
       7002 TAAGTTTTTCAT
         59 TAAGTTTTTCAT

       7014 CTTAAGTTCG


Statistics
Matches: 193,  Mismatches: 23, Indels: 26
        0.80            0.10        0.11

Matches are distributed among these distances:
 153    6  0.03
 154    1  0.01
 155   11  0.06
 156  139  0.72
 157    6  0.03
 160    2  0.01
 162   28  0.15

ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32


Consensus pattern (155 bp):   
CTCCTTCATGGTGAACTTGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCATAAGTTT
TTCATTATAAATCTCAATGAGATGAACTTTGCCAAGGGACTTAGATTATTCCCATAAAAATATGA
AAAAAATTATAAGCAAAACTGAACT

Found at i:7818 original size:19 final size:19

Alignment explanation


    Indices: 7796--7838  Score: 52
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       7786 ATTTAGCTAT

                     *          
       7796 ATATAAAT-GAATAAAATAA
          1 ATATAAATACAATAAAA-AA

                  *            
       7815 ATATAAGTACAATAAAAAA
          1 ATATAAATACAATAAAAAA

                 
       7834 ATATA
          1 ATATA

       7839 GATAAAATGT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  19   14  0.67
  20    7  0.33

ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26


Consensus pattern (19 bp):   
ATATAAATACAATAAAAAA
Done.