Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024234.1 Corchorus olitorius cultivar O-4 contig24267, 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: 3610
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30


Found at i:1774 original size:19 final size:18

Alignment explanation


    Indices: 1745--1780  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       1735 TGAAAATAAT

                              
       1745 TCTTCAATTGTCTTCAAA
          1 TCTTCAATTGTCTTCAAA

                              
       1763 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATTGTCTTCAA

       1781 TAAGTCTTCA


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:0.28, C:0.22, G:0.06, T:0.44


Consensus pattern (18 bp):   
TCTTCAATTGTCTTCAAA

Found at i:3012 original size:22 final size:21

Alignment explanation


    Indices: 2988--3028  Score: 82
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2978 AATTTTATCA

                                 
       2988 AAAATTGGGGAAATAAGATCG
          1 AAAATTGGGGAAATAAGATCG

                                
       3009 AAAATTGGGGAAATAAGATC
          1 AAAATTGGGGAAATAAGATC

       3029 AATCAAAAAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.49, C:0.05, G:0.27, T:0.20


Consensus pattern (21 bp):   
AAAATTGGGGAAATAAGATCG

Found at i:3358 original size:30 final size:29

Alignment explanation


    Indices: 3319--3375  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       3309 GTTTATTAAT

                                           
       3319 GAAACTTGAAAATTAAAGACATAAGATAAAA
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAA

                                       
       3350 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

       3376 CTAATCCTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAA
Done.