Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023123.1 Corchorus olitorius cultivar O-4 contig23156, 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: 15780
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:5001 original size:25 final size:26

Alignment explanation


    Indices: 4956--5014  Score: 77
    Period size: 25  Copynumber: 2.3  Consensus size: 26

       4946 TAAATAAAAA

                            *          
       4956 TTTTTTATGACGCAGGGAAAA-TTATT
          1 TTTTTTATGACGCAGGAAAAACTT-TT

                      *               
       4982 TTTTTTATGATGCA-GAAAAACTTTT
          1 TTTTTTATGACGCAGGAAAAACTTTT

                    
       5007 TTTTTTAT
          1 TTTTTTAT

       5015 AAAACGCAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  25   15  0.50
  26   15  0.50

ACGTcount: A:0.29, C:0.07, G:0.14, T:0.51


Consensus pattern (26 bp):   
TTTTTTATGACGCAGGAAAAACTTTT

Found at i:5036 original size:27 final size:25

Alignment explanation


    Indices: 4997--5050  Score: 74
    Period size: 27  Copynumber: 2.1  Consensus size: 25

       4987 TATGATGCAG

                                      
       4997 AAAAACTTTTTTTTTT-ATAAAACGC
          1 AAAAACTTTTTTTTTTCA-AAAACGC

                                       
       5022 AAAAACTCTTCTTTTTTTCAAAAACGC
          1 AAAAACT-TT-TTTTTTTCAAAAACGC

              
       5049 AA
          1 AA

       5051 CACAAAACAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  25    7  0.27
  26    2  0.08
  27   16  0.62
  28    1  0.04

ACGTcount: A:0.41, C:0.17, G:0.04, T:0.39


Consensus pattern (25 bp):   
AAAAACTTTTTTTTTTCAAAAACGC

Found at i:5483 original size:16 final size:15

Alignment explanation


    Indices: 5445--5486  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5435 ACAGAGGTTG

                   *    *  
       5445 ACAGAAAGCAATTAA
          1 ACAGAAAACAATGAA

                           
       5460 ACAGAAAACAATGAA
          1 ACAGAAAACAATGAA

                        
       5475 ACTAGAAAACAA
          1 AC-AGAAAACAA

       5487 AGCAAAGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  15   15  0.62
  16    9  0.38

ACGTcount: A:0.64, C:0.14, G:0.12, T:0.10


Consensus pattern (15 bp):   
ACAGAAAACAATGAA

Found at i:12960 original size:13 final size:13

Alignment explanation


    Indices: 12942--12967  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      12932 AATTTAATAA

                         
      12942 AAATAAAAATTGG
          1 AAATAAAAATTGG

                         
      12955 AAATAAAAATTGG
          1 AAATAAAAATTGG

      12968 GTTGCCTCCC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23


Consensus pattern (13 bp):   
AAATAAAAATTGG
Done.