Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021073.1 Corchorus olitorius cultivar O-4 contig21106, 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: 3569
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37


Found at i:32 original size:15 final size:14

Alignment explanation


    Indices: 4--39  Score: 54
    Period size: 15  Copynumber: 2.5  Consensus size: 14

          1 CTA

                          
          4 TTTTTTCTGGGTTT
          1 TTTTTTCTGGGTTT

                      *    
         18 TTTTTTACTGTGTTT
          1 TTTTTT-CTGGGTTT

                   
         33 TTTTTTC
          1 TTTTTTC

         40 ATATTTTTAG


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  14    7  0.35
  15   13  0.65

ACGTcount: A:0.03, C:0.08, G:0.14, T:0.75


Consensus pattern (14 bp):   
TTTTTTCTGGGTTT

Found at i:2165 original size:197 final size:197

Alignment explanation


    Indices: 1829--2185  Score: 527
    Period size: 197  Copynumber: 1.8  Consensus size: 197

       1819 TGAGCCCGTG

                              *              *         *             *       
       1829 TGTCACGGTCCACACCAACTTGTGAGGTATTGTTCGCTTTGACTCATTAGATCCGGCTCAATGAA
          1 TGTCACGGTCCACACCAAATTGTGAGGTATTGTCCGCTTTGACCCATTAGATCCGGCCCAATGAA

            *      *                       *                                *
       1894 TCTCACGGTTTTGTCCACAAAAAGCGCCTCATAAGTTCAAATGGTGCGAACACTTATATCCCAAG
         66 CCTCACGATTTTGTCCACAAAAAGCGCCTCACAAGTTCAAATGGTGCGAACACTTATATCCCAAA

            * *       *                                                      
       1959 GCTAACTCTAGTACACAACCGATGTGGGATCATCACTAGTACTCCTAGAGCCAGCCCTGATACCA
        131 ACCAACTCTAATACACAACCGATGTGGGATCATCACTAGTACTCCTAGAGCCAGCCCTGATACCA

              
       2024 AA
        196 AA

                     *                               *                      *
       2026 TGTCACGGTTCACACCAAATTGTGAGGTATTGTCCGCTTTGCCCCATT-GAATCCGGCCCAATGG
          1 TGTCACGGTCCACACCAAATTGTGAGGTATTGTCCGCTTTGACCCATTAG-ATCCGGCCCAATGA

            *              *                         *     *                 
       2090 GCCTCACGATTTTGTTCACAAAAAGCGCCTCACAAGTTCAAGTGGTGTGAACACTTATATCCCAA
         65 ACCTCACGATTTTGTCCACAAAAAGCGCCTCACAAGTTCAAATGGTGCGAACACTTATATCCCAA

                              *            
       2155 AACCAACTCTAATACACAGCCGATGTGGGAT
        130 AACCAACTCTAATACACAACCGATGTGGGAT

       2186 TCATGGCTCA


Statistics
Matches: 140,  Mismatches: 19, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
 196    1  0.01
 197  139  0.99

ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26


Consensus pattern (197 bp):   
TGTCACGGTCCACACCAAATTGTGAGGTATTGTCCGCTTTGACCCATTAGATCCGGCCCAATGAA
CCTCACGATTTTGTCCACAAAAAGCGCCTCACAAGTTCAAATGGTGCGAACACTTATATCCCAAA
ACCAACTCTAATACACAACCGATGTGGGATCATCACTAGTACTCCTAGAGCCAGCCCTGATACCA
AA

Found at i:3150 original size:21 final size:21

Alignment explanation


    Indices: 3124--3166  Score: 68
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       3114 CAAGTTTTGG

                       *    *    
       3124 AAATATGTATCCACTATTATA
          1 AAATATGTATCAACTAGTATA

                                 
       3145 AAATATGTATCAACTAGTATA
          1 AAATATGTATCAACTAGTATA

             
       3166 A
          1 A

       3167 TATTTGTTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.47, C:0.12, G:0.07, T:0.35


Consensus pattern (21 bp):   
AAATATGTATCAACTAGTATA

Found at i:3326 original size:22 final size:22

Alignment explanation


    Indices: 3298--3340  Score: 86
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       3288 GCCAAGATTT

                                  
       3298 TCTAATTTCTCATCCCTTTCTC
          1 TCTAATTTCTCATCCCTTTCTC

                                 
       3320 TCTAATTTCTCATCCCTTTCT
          1 TCTAATTTCTCATCCCTTTCT

       3341 ATGGTTCTAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   21  1.00

ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51


Consensus pattern (22 bp):   
TCTAATTTCTCATCCCTTTCTC
Done.