Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024605.1 Corchorus olitorius cultivar O-4 contig24638, 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: 10851
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:5447 original size:16 final size:15

Alignment explanation


    Indices: 5409--5450  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5399 ACAGAGGTTG

                           
       5409 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       5424 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       5439 ACTAGAAAACAA
          1 AC-AGAAAACAA

       5451 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA

Found at i:6837 original size:19 final size:18

Alignment explanation


    Indices: 6808--6843  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6798 TTGAAATAAA

                              
       6808 TCTTCAATGGTCTTCAAG
          1 TCTTCAATGGTCTTCAAG

                              
       6826 TCTTCAAATGGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       6844 ACACGAATTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    5  0.29
  19   12  0.71

ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAG

Found at i:8712 original size:22 final size:21

Alignment explanation


    Indices: 8670--8712  Score: 59
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       8660 TTGGAATGGC

                       *         
       8670 GATGGCACGGGCATGGCCGGT
          1 GATGGCACGGGAATGGCCGGT

                             *    
       8691 GATGGCACGGTGAATGGGCGGT
          1 GATGGCACGG-GAATGGCCGGT

       8713 AATGACTTGG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   10  0.53
  22    9  0.47

ACGTcount: A:0.16, C:0.19, G:0.49, T:0.16


Consensus pattern (21 bp):   
GATGGCACGGGAATGGCCGGT
Done.