Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009693.1 Corchorus olitorius cultivar O-4 contig09725, 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: 9907
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:906 original size:13 final size:13

Alignment explanation


    Indices: 867--910  Score: 63
    Period size: 12  Copynumber: 3.4  Consensus size: 13

        857 TTTCTTTGAC

                         
        867 TTACAAACGGAA-
          1 TTACAAACGGAAT

                          
        879 TTACAAACGGAAAT
          1 TTACAAACGG-AAT

               *         
        893 TTAGAAACGGAAT
          1 TTACAAACGGAAT

                 
        906 TTACA
          1 TTACA

        911 TCGGAAAAGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  12   10  0.36
  13    9  0.32
  14    9  0.32

ACGTcount: A:0.48, C:0.14, G:0.16, T:0.23


Consensus pattern (13 bp):   
TTACAAACGGAAT

Found at i:2957 original size:30 final size:30

Alignment explanation


    Indices: 2921--2977  Score: 114
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2911 AGCAATGGCC

                                          
       2921 AGAGAATTGGGAAGGAGATTGATGTTGGTT
          1 AGAGAATTGGGAAGGAGATTGATGTTGGTT

                                       
       2951 AGAGAATTGGGAAGGAGATTGATGTTG
          1 AGAGAATTGGGAAGGAGATTGATGTTG

       2978 AAGTAATGGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.32, C:0.00, G:0.40, T:0.28


Consensus pattern (30 bp):   
AGAGAATTGGGAAGGAGATTGATGTTGGTT

Found at i:5592 original size:18 final size:20

Alignment explanation


    Indices: 5569--5608  Score: 57
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       5559 TTTCTCATTG

                                
       5569 ATATCA-TCTTCATC-TAGC
          1 ATATCATTCTTCATCATAGC

                    *           
       5587 ATATCATTTTTCATCATAGC
          1 ATATCATTCTTCATCATAGC

              
       5607 AT
          1 AT

       5609 TCTGAGACAA


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

Matches are distributed among these distances:
  18    6  0.32
  19    7  0.37
  20    6  0.32

ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42


Consensus pattern (20 bp):   
ATATCATTCTTCATCATAGC

Found at i:6956 original size:29 final size:30

Alignment explanation


    Indices: 6924--6980  Score: 80
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       6914 AAGGAATGAG

                            *             
       6924 AATTAGTTTTA-AAAATACAATGGTTTGGA
          1 AATTAGTTTTATAAAACACAATGGTTTGGA

                 *         *            
       6953 AATTATTTTTATAAACCACAATGGTTTG
          1 AATTAGTTTTATAAAACACAATGGTTTG

       6981 ATCAAAAACT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  29   10  0.42
  30   14  0.58

ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40


Consensus pattern (30 bp):   
AATTAGTTTTATAAAACACAATGGTTTGGA
Done.