Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012667.1 Corchorus olitorius cultivar O-4 contig12700, 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: 50809
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:7508 original size:2 final size:2

Alignment explanation


    Indices: 7501--7537  Score: 53
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       7491 CTTAAAAGTC

                                                                       
       7501 AT AT AT AT AT AT AT AT AT -T AT -T AT -T AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7538 TATTTTTAGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
   1    3  0.09
   2   29  0.91

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (2 bp):   
AT

Found at i:7530 original size:13 final size:13

Alignment explanation


    Indices: 7501--7540  Score: 57
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       7491 CTTAAAAGTC

                         
       7501 ATATATATATA-T
          1 ATATATATATATT

                          
       7513 ATATAT-TATTATT
          1 ATATATATA-TATT

                         
       7526 ATATATATATATT
          1 ATATATATATATT

              
       7539 AT
          1 AT

       7541 TTTTAGTGGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  11    2  0.08
  12    8  0.32
  13   13  0.52
  14    2  0.08

ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55


Consensus pattern (13 bp):   
ATATATATATATT

Found at i:15728 original size:12 final size:12

Alignment explanation


    Indices: 15711--15735  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      15701 ATATATCATG

                        
      15711 AAAAAAAAAGAA
          1 AAAAAAAAAGAA

                        
      15723 AAAAAAAAAGAA
          1 AAAAAAAAAGAA

             
      15735 A
          1 A

      15736 TCTTAGTTAG


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:0.92, C:0.00, G:0.08, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAAGAA

Found at i:21746 original size:34 final size:33

Alignment explanation


    Indices: 21707--21770  Score: 83
    Period size: 34  Copynumber: 1.9  Consensus size: 33

      21697 ATGTTCACAA

                  *                   *       
      21707 ATTTTCTAGCTAAATTTTACATCTTTCTATTCAC
          1 ATTTTCGAGCTAAATTTTACAT-TTTATATTCAC

                    *  *                  
      21741 ATTTTCGATCTTAATTTTACATTTTATATT
          1 ATTTTCGAGCTAAATTTTACATTTTATATT

      21771 ATTTTAAAAG


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  33    7  0.27
  34   19  0.73

ACGTcount: A:0.27, C:0.16, G:0.03, T:0.55


Consensus pattern (33 bp):   
ATTTTCGAGCTAAATTTTACATTTTATATTCAC

Found at i:25780 original size:26 final size:26

Alignment explanation


    Indices: 25744--25794  Score: 93
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      25734 AATAACGAGT

                                      
      25744 TTTTGCCTTTCTCAATTCATGCTTGA
          1 TTTTGCCTTTCTCAATTCATGCTTGA

                        *            
      25770 TTTTGCCTTTCTTAATTCATGCTTG
          1 TTTTGCCTTTCTCAATTCATGCTTG

      25795 GTTATGCAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.14, C:0.22, G:0.12, T:0.53


Consensus pattern (26 bp):   
TTTTGCCTTTCTCAATTCATGCTTGA

Found at i:31004 original size:41 final size:41

Alignment explanation


    Indices: 30922--31004  Score: 123
    Period size: 41  Copynumber: 2.0  Consensus size: 41

      30912 CTTTACTTAA

                                                *    
      30922 TCTGGTGAAAGCCTCAATTTGACTATGAACTTCCATCTTCT
          1 TCTGGTGAAAGCCTCAATTTGACTATGAACTTCCATATTCT

                       *  *                           
      30963 TCTGGTGAAAGGCTGAATTTGACTATGAAC-TCCAATATTCT
          1 TCTGGTGAAAGCCTCAATTTGACTATGAACTTCC-ATATTCT

             
      31004 T
          1 T

      31005 GCATCGTCCT


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  40    3  0.08
  41   35  0.92

ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36


Consensus pattern (41 bp):   
TCTGGTGAAAGCCTCAATTTGACTATGAACTTCCATATTCT

Found at i:39450 original size:40 final size:39

Alignment explanation


    Indices: 39396--39471  Score: 125
    Period size: 40  Copynumber: 1.9  Consensus size: 39

      39386 AAACGGCACA

                     *              *              
      39396 AAAATCAGGTGCAACCATATATAAGAGCTGATTGTTATC
          1 AAAATCAGGGGCAACCATATATAAAAGCTGATTGTTATC

                                                 
      39435 AAAATCAGGAGGCAACCATATATAAAAGCTGATTGTT
          1 AAAATCAGG-GGCAACCATATATAAAAGCTGATTGTT

      39472 TTCCAAAAGA


Statistics
Matches: 34,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  39    9  0.26
  40   25  0.74

ACGTcount: A:0.41, C:0.14, G:0.18, T:0.26


Consensus pattern (39 bp):   
AAAATCAGGGGCAACCATATATAAAAGCTGATTGTTATC
Done.