Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023672.1 Corchorus olitorius cultivar O-4 contig23705, 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: 6435
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:934 original size:12 final size:12

Alignment explanation


    Indices: 917--941  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        907 GCTTGACTAT

                        
        917 AATACTAAATGA
          1 AATACTAAATGA

                        
        929 AATACTAAATGA
          1 AATACTAAATGA

             
        941 A
          1 A

        942 GATGCGATTT


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

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24


Consensus pattern (12 bp):   
AATACTAAATGA

Found at i:1133 original size:25 final size:25

Alignment explanation


    Indices: 1105--1152  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       1095 TTAGTTGATT

                                     
       1105 AAATTAGATTTGAGCTACATGAATG
          1 AAATTAGATTTGAGCTACATGAATG

                   *               
       1130 AAATTAGCTTTGAGCTACATGAA
          1 AAATTAGATTTGAGCTACATGAA

       1153 CGCAAAATAC


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31


Consensus pattern (25 bp):   
AAATTAGATTTGAGCTACATGAATG

Found at i:2183 original size:22 final size:22

Alignment explanation


    Indices: 2155--2199  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2145 CTCAACATAT

                                  
       2155 ACCCGGGAAATGTGAATGCAAC
          1 ACCCGGGAAATGTGAATGCAAC

                                  
       2177 ACCCGGGAAATGTGAATGCAAC
          1 ACCCGGGAAATGTGAATGCAAC

             
       2199 A
          1 A

       2200 TGGGGGGCTC


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13


Consensus pattern (22 bp):   
ACCCGGGAAATGTGAATGCAAC

Found at i:5874 original size:16 final size:15

Alignment explanation


    Indices: 5836--5877  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       5826 ACAGAGGTTG

                   *       
       5836 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
       5851 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       5866 ACTAGAAAACAA
          1 AC-AGAAAACAA

       5878 AGCAAAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

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


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.