Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019855.1 Corchorus olitorius cultivar O-4 contig19888, 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: 15363
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:2939 original size:25 final size:24

Alignment explanation


    Indices: 2893--2940  Score: 60
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       2883 GAAGATTGAT

                         *          
       2893 CAGCATTGAGTAGTTGAAAGGAAG
          1 CAGCATTGAGTAGATGAAAGGAAG

                        *     *     
       2917 CAGCAGTTGAGTTGATGAGAGGAA
          1 CAGCA-TTGAGTAGATGAAAGGAA

       2941 AAAAGAAGGG


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  24    5  0.25
  25   15  0.75

ACGTcount: A:0.35, C:0.08, G:0.35, T:0.21


Consensus pattern (24 bp):   
CAGCATTGAGTAGATGAAAGGAAG

Found at i:2987 original size:12 final size:12

Alignment explanation


    Indices: 2970--2996  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       2960 CATTAATTCA

                        
       2970 AAGCAATTAAGT
          1 AAGCAATTAAGT

                        
       2982 AAGCAATTAAGT
          1 AAGCAATTAAGT

               
       2994 AAG
          1 AAG

       2997 GGAAATGAGT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22


Consensus pattern (12 bp):   
AAGCAATTAAGT

Found at i:5802 original size:19 final size:18

Alignment explanation


    Indices: 5778--5813  Score: 63
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       5768 TGAAGACTTA

                               
       5778 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                             
       5797 TTGAAGACAATTGAAGA
          1 TTGAAGACAATTGAAGA

       5814 ATTATTTTCA


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

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

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


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:7136 original size:22 final size:22

Alignment explanation


    Indices: 7094--7136  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       7084 TTTCTAATTA

                           **     
       7094 ATTGTTTTCTTTAATTTTCTTG
          1 ATTGTTTTCTTTAATAGTCTTG

                                  
       7116 ATTGTTTTC-TTACATAGTCTT
          1 ATTGTTTTCTTTA-ATAGTCTT

       7137 AATTACTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  21    3  0.17
  22   15  0.83

ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63


Consensus pattern (22 bp):   
ATTGTTTTCTTTAATAGTCTTG
Done.