Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023421.1 Corchorus olitorius cultivar O-4 contig23454, 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: 3381
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:307 original size:167 final size:168

Alignment explanation


    Indices: 31--528  Score: 795
    Period size: 169  Copynumber: 3.0  Consensus size: 168

         21 TACCCGGACC

                                                                             
         31 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA
          1 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA

                     *                                                     * 
         96 AACTTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAA-TTTTGATGAAAACTTTA
         66 AACTTTGAAATGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAACTTGA

                                                * 
        160 TAAAATGAAATGATACCCGGAGGTTTTATCAATTGCTT
        131 TAAAATGAAATGATACCCGGAGGTTTTATCAATTGCCT

                                                                             
        198 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA
          1 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA

                               *                                *            
        263 AACTTTGAAATGAGACCTTAAACAAGGATTTTAAACTTAAACATGAACTTTTAATGACAAACTTG
         66 AACTTTGAAATGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGA-AAACTTG

              *                                    
        328 ATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCT
        130 ATAAAATGAAATGATACCCGGAGGTTTTATCAATTGCCT

                                                    *                    *   
        367 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTCGTGCCCGGAGGACTTACCAACGCA
          1 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA

                *                 * *          *      * *   *     *          
        432 AACTCTG-AATAGAGACCTTGACCGAGGATTTT-AGCTTAAAAAAGAATTTTTGGTGAAAAACTT
         66 AACTTTGAAAT-GAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATG-AAAACTT

                                *             
        495 GATAAAATGAAATGATACCCAGAGGTTTTATCAA
        129 GATAAAATGAAATGATACCCGGAGGTTTTATCAA

        529 ATGGAAATAA


Statistics
Matches: 307,  Mismatches: 20, Indels: 7
        0.92            0.06        0.02

Matches are distributed among these distances:
 167  110  0.36
 168   66  0.21
 169  131  0.43

ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29


Consensus pattern (168 bp):   
GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA
AACTTTGAAATGAGACCTTGAACAAGGATTTTAAACTTAAACATGAACTTTTGATGAAAACTTGA
TAAAATGAAATGATACCCGGAGGTTTTATCAATTGCCT

Found at i:2225 original size:6 final size:6

Alignment explanation


    Indices: 2214--2255  Score: 70
    Period size: 6  Copynumber: 7.3  Consensus size: 6

       2204 TCAATTCCCT

                                                               
       2214 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT-- TTTTGA TT
          1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TT

       2256 GATTTTTTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   4    4  0.12
   6   30  0.88

ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71


Consensus pattern (6 bp):   
TTTTGA

Found at i:2279 original size:18 final size:18

Alignment explanation


    Indices: 2213--2284  Score: 81
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       2203 ATCAATTCCC

                             *
       2213 TTTTTGATTTTGATTTTG
          1 TTTTTGATTTTGATTTTT

            *                 
       2231 ATTTTGATTTTGATTTTT
          1 TTTTTGATTTTGATTTTT

                          *      
       2249 TTTGATTGATTTTTTATTTTT
          1 TTT--TTGA-TTTTGATTTTT

                  *        
       2270 TTTTTGTTTTTGATT
          1 TTTTTGATTTTGATT

       2285 GAATTTCTTG


Statistics
Matches: 45,  Mismatches: 6, Indels: 6
        0.79            0.11        0.11

Matches are distributed among these distances:
  18   25  0.56
  19    3  0.07
  20    4  0.09
  21   13  0.29

ACGTcount: A:0.12, C:0.00, G:0.12, T:0.75


Consensus pattern (18 bp):   
TTTTTGATTTTGATTTTT
Done.