Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018766.1 Corchorus olitorius cultivar O-4 contig18799, 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: 6632
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29


Found at i:84 original size:27 final size:27

Alignment explanation


    Indices: 8--137  Score: 100
    Period size: 27  Copynumber: 4.7  Consensus size: 27

          1 TTTAGCA

                                   *** *
          8 TGAGTCCCAACTGC-GGAGGCTTTGGCT
          1 TGAGTCCCAACTGCGGGA-GCTTCAACG

                   *    * *   *        
         35 TGAGTCCTAACTACCGGAACTTCAACG
          1 TGAGTCCCAACTGCGGGAGCTTCAACG

                                       * 
         62 TGAGTCCCAACTGCGGGAGCTTCATAGAG
          1 TGAGTCCCAACTGCGGGAGCTTCA-A-CG

               *               *    * *
         91 TGAATCCCAACTGCGGGAGTTTCAGCA
          1 TGAGTCCCAACTGCGGGAGCTTCAACG

                          *     
        118 TGAGTCCCAACTGCAGGAGC
          1 TGAGTCCCAACTGCGGGAGC

        138 GTCTTTCTCT


Statistics
Matches: 80,  Mismatches: 20, Indels: 6
        0.75            0.19        0.06

Matches are distributed among these distances:
  27   53  0.66
  28    4  0.05
  29   23  0.29

ACGTcount: A:0.24, C:0.27, G:0.28, T:0.22


Consensus pattern (27 bp):   
TGAGTCCCAACTGCGGGAGCTTCAACG

Found at i:519 original size:24 final size:24

Alignment explanation


    Indices: 492--565  Score: 94
    Period size: 24  Copynumber: 3.1  Consensus size: 24

        482 GCCAACCGTT

                            *       
        492 ATTCTACCGCAGAAGCTAACCACC
          1 ATTCTACCGCAGAAGCCAACCACC

                     *         *   *
        516 ATTCTACCGTAGAAGCCAATCACT
          1 ATTCTACCGCAGAAGCCAACCACC

                           *   *    
        540 ATTCTACCGCAGAAGTCAAGCACC
          1 ATTCTACCGCAGAAGCCAACCACC

              
        564 AT
          1 AT

        566 GTTGCCACAT


Statistics
Matches: 42,  Mismatches: 8, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  24   42  1.00

ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20


Consensus pattern (24 bp):   
ATTCTACCGCAGAAGCCAACCACC

Found at i:5565 original size:15 final size:16

Alignment explanation


    Indices: 5547--5584  Score: 69
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       5537 AGGTTGACAA

                            
       5547 AAAACAATTAAAC-AG
          1 AAAACAATTAAACTAG

                            
       5562 AAAACAATTAAACTAG
          1 AAAACAATTAAACTAG

                   
       5578 AAAACAA
          1 AAAACAA

       5585 AACAAAGTAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.68, C:0.13, G:0.05, T:0.13


Consensus pattern (16 bp):   
AAAACAATTAAACTAG

Done.