Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010079.1 Corchorus olitorius cultivar O-4 contig10111, 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: 9915
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--37  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

          1 TATTACA

                                                        
          8 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         38 GAAAAAAACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3297 original size:16 final size:16

Alignment explanation


    Indices: 3268--3300  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       3258 AGATTATCAC

                            
       3268 CTTTCTGTTAAATTTG
          1 CTTTCTGTTAAATTTG

                             
       3284 CTTTCATGTT-AATTTG
          1 CTTTC-TGTTAAATTTG

             
       3300 C
          1 C

       3301 CAGCTAAGGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   12  0.75
  17    4  0.25

ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55


Consensus pattern (16 bp):   
CTTTCTGTTAAATTTG

Found at i:5193 original size:18 final size:18

Alignment explanation


    Indices: 5167--5203  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       5157 AACAGGTACC

                *         *   
       5167 TACACAACTTCCTATTTA
          1 TACAAAACTTCCTACTTA

                              
       5185 TACAAAACTTCCTACTTA
          1 TACAAAACTTCCTACTTA

             
       5203 T
          1 T

       5204 TTCCAAAGAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38


Consensus pattern (18 bp):   
TACAAAACTTCCTACTTA
Done.