Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015270.1 Corchorus olitorius cultivar O-4 contig15303, 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: 27870
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31


Found at i:11732 original size:76 final size:76

Alignment explanation


    Indices: 11595--11746  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      11585 ACAAGGACCC

                  *                                            *           * 
      11595 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      11660 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
      11671 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
      11733 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

      11747 TAGCTCTTCA


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:12598 original size:21 final size:21

Alignment explanation


    Indices: 12552--12598  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      12542 TAGTTTTAGG

                  *           *  
      12552 GTTTTTCAATTTAAGTTTCTT
          1 GTTTTTAAATTTAAGTTTATT

                                  
      12573 GTTTTTAAATTTAAGATTTATT
          1 GTTTTTAAATTTAAG-TTTATT

                 
      12595 -TTTT
          1 GTTTT

      12599 ATGCATCTTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  21   18  0.78
  22    5  0.22

ACGTcount: A:0.23, C:0.04, G:0.09, T:0.64


Consensus pattern (21 bp):   
GTTTTTAAATTTAAGTTTATT

Found at i:19780 original size:20 final size:21

Alignment explanation


    Indices: 19747--19793  Score: 60
    Period size: 20  Copynumber: 2.2  Consensus size: 21

      19737 GTCAAAGTTG

                     *           
      19747 AAGAAAAAATGAAAAAA-AAA
          1 AAGAAAAAAGGAAAAAAGAAA

                 *                
      19767 AAGAAGAAAGGAAAAAATGAAA
          1 AAGAAAAAAGGAAAAAA-GAAA

                 
      19789 AAGAA
          1 AAGAA

      19794 TCAATAAACA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20   15  0.65
  22    8  0.35

ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04


Consensus pattern (21 bp):   
AAGAAAAAAGGAAAAAAGAAA

Found at i:23978 original size:7 final size:6

Alignment explanation


    Indices: 23954--23990  Score: 56
    Period size: 6  Copynumber: 6.0  Consensus size: 6

      23944 GATCCCATTC

                *                                     
      23954 AGAAGA AGAAAA AGAAAA AGAAAA AGAAAAA AGAAAA
          1 AGAAAA AGAAAA AGAAAA AGAAAA AG-AAAA AGAAAA

      23991 CTTGGCCTAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
   6   23  0.79
   7    6  0.21

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (6 bp):   
AGAAAA

Found at i:24127 original size:14 final size:13

Alignment explanation


    Indices: 24110--24150  Score: 55
    Period size: 13  Copynumber: 3.1  Consensus size: 13

      24100 TTTTTCCAAA

                          
      24110 AAAAATGGGTTTTC
          1 AAAAAT-GGTTTTC

                         
      24124 AAAAATGGTTTTC
          1 AAAAATGGTTTTC

                * *      
      24137 AAAATTTGTTTTC
          1 AAAAATGGTTTTC

             
      24150 A
          1 A

      24151 CGAGGATGCT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  13   19  0.76
  14    6  0.24

ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41


Consensus pattern (13 bp):   
AAAAATGGTTTTC

Found at i:27766 original size:13 final size:13

Alignment explanation


    Indices: 27748--27773  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      27738 TGAGAAATAA

                         
      27748 AACTTGGTTGATT
          1 AACTTGGTTGATT

                         
      27761 AACTTGGTTGATT
          1 AACTTGGTTGATT

      27774 TTTTTTGTGA


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46


Consensus pattern (13 bp):   
AACTTGGTTGATT
Done.