Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019497.1 Corchorus olitorius cultivar O-4 contig19530, 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: 18729
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:662 original size:26 final size:26

Alignment explanation


    Indices: 614--665  Score: 68
    Period size: 26  Copynumber: 2.0  Consensus size: 26

        604 AAAATAGACA

                              *       
        614 AATTAAACTAAAAAACAATAAAATAG
          1 AATTAAACTAAAAAACAAAAAAATAG

                        * **          
        640 AATTAAACTAAAGATTAAAAAAATAG
          1 AATTAAACTAAAAAACAAAAAAATAG

        666 TTTGAGAAAA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  26   22  1.00

ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21


Consensus pattern (26 bp):   
AATTAAACTAAAAAACAAAAAAATAG

Found at i:2077 original size:76 final size:76

Alignment explanation


    Indices: 1940--2091  Score: 166
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       1930 ACAAGGACCC

                        *                                      *          ** 
       1940 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGCGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAAAT

                       
       2005 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       2016 CGACTCCAGCTGCGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGCGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       2078 AATGGGCTGTGTCA
         63 AATGGGCAGTGTCA

       2092 TAGCTCATCA


Statistics
Matches: 63,  Mismatches: 10, Indels: 6
        0.80            0.13        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   53  0.84
  77    6  0.10

ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGCGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAAAT
GGGCAGTGTCA

Found at i:7117 original size:42 final size:42

Alignment explanation


    Indices: 7066--7156  Score: 114
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       7056 AGTGCATTAC

                              *     * *                
       7066 CTAA-ATTCTACTTC-ATTTCTAGGTCATTCATCAAAATAAAG
          1 CTAATATTCTAC-TCGATCTCTAGATAATTCATCAAAATAAAG

                                         *            
       7107 CTAATATTCTACTCGATCTCTAGATAATTTATCAAAATAAAG
          1 CTAATATTCTACTCGATCTCTAGATAATTCATCAAAATAAAG

            *       
       7149 TTAATATT
          1 CTAATATT

       7157 AATTGTTGTT


Statistics
Matches: 43,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  41    6  0.14
  42   37  0.86

ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38


Consensus pattern (42 bp):   
CTAATATTCTACTCGATCTCTAGATAATTCATCAAAATAAAG

Found at i:10773 original size:21 final size:21

Alignment explanation


    Indices: 10746--10792  Score: 67
    Period size: 22  Copynumber: 2.2  Consensus size: 21

      10736 CTAAGATGCA

                  *  *            
      10746 TAAAAAAAATAAATCTTAAATC
          1 TAAAAACAAGAAAT-TTAAATC

                                 
      10768 TAAAAACAAGAAATTTAAATC
          1 TAAAAACAAGAAATTTAAATC

                
      10789 TAAA
          1 TAAA

      10793 CCTAAATTGG


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21   11  0.48
  22   12  0.52

ACGTcount: A:0.64, C:0.09, G:0.02, T:0.26


Consensus pattern (21 bp):   
TAAAAACAAGAAATTTAAATC
Done.