Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024557.1 Corchorus olitorius cultivar O-4 contig24590, 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: 3124
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32


Found at i:54 original size:35 final size:35

Alignment explanation


    Indices: 8--166  Score: 201
    Period size: 35  Copynumber: 4.5  Consensus size: 35

          1 CATATAA

                                     *         
          8 AAAACTTCTTGAAATGAGATCAACTATGATCAACG
          1 AAAACTTCTTGAAATGAGATCAACTCTGATCAACG

                  *        *                   **
         43 AAAACTCCTTGAAATAAGATCAACTCTGATCATAAAA
          1 AAAACTTCTTGAAATGAGATCAACTCTGATC--AACG

                          *                    
         80 AAAACTTCTTGAAAGGAGATCAACTCTGATCAACG
          1 AAAACTTCTTGAAATGAGATCAACTCTGATCAACG

                  *       **                *  
        115 AAAACTCCTTGAAACAAGATCAACTCTGATCATCG
          1 AAAACTTCTTGAAATGAGATCAACTCTGATCAACG

                       *     
        150 AAAACTTCTTGGAATGA
          1 AAAACTTCTTGAAATGA

        167 CCGCACTGGA


Statistics
Matches: 104,  Mismatches: 18, Indels: 4
        0.83            0.14        0.03

Matches are distributed among these distances:
  35   74  0.71
  37   30  0.29

ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25


Consensus pattern (35 bp):   
AAAACTTCTTGAAATGAGATCAACTCTGATCAACG

Found at i:119 original size:72 final size:72

Alignment explanation


    Indices: 1--147  Score: 258
    Period size: 72  Copynumber: 2.0  Consensus size: 72

                *                *                                  *        
          1 CATATAAAAAACTTCTTGAAATGAGATCAACTATGATCAACGAAAACTCCTTGAAATAAGATCAA
          1 CATAAAAAAAACTTCTTGAAAGGAGATCAACTATGATCAACGAAAACTCCTTGAAACAAGATCAA

                   
         66 CTCTGAT
         66 CTCTGAT

                                            *                                
         73 CATAAAAAAAACTTCTTGAAAGGAGATCAACTCTGATCAACGAAAACTCCTTGAAACAAGATCAA
          1 CATAAAAAAAACTTCTTGAAAGGAGATCAACTATGATCAACGAAAACTCCTTGAAACAAGATCAA

                   
        138 CTCTGAT
         66 CTCTGAT

               
        145 CAT
          1 CAT

        148 CGAAAACTTC


Statistics
Matches: 71,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  72   71  1.00

ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24


Consensus pattern (72 bp):   
CATAAAAAAAACTTCTTGAAAGGAGATCAACTATGATCAACGAAAACTCCTTGAAACAAGATCAA
CTCTGAT

Found at i:212 original size:54 final size:54

Alignment explanation


    Indices: 130--239  Score: 202
    Period size: 54  Copynumber: 2.0  Consensus size: 54

        120 TCCTTGAAAC

                          *                                       
        130 AAGATCAACTCTGATCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTG
          1 AAGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTG

                              *                                   
        184 AAGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCATCTG
          1 AAGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTG

              
        238 AA
          1 AA

        240 CACCTGTTTC


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25


Consensus pattern (54 bp):   
AAGATCAACTCTGACCATCGAAAACTTCTTGGAATGACCGCACTGGATCATCTG
Done.