Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021626.1 Corchorus olitorius cultivar O-4 contig21659, 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: 6847
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:5980 original size:29 final size:30

Alignment explanation


    Indices: 5924--5980  Score: 71
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       5914 AAGAAAATAA

                     *     *   *   *      
       5924 TTTTTTTTTCATAACGCAGGGACGAAACTT
          1 TTTTTTTTTAATAACCCAGAGACAAAACTT

                                        
       5954 TTTTTTTTTAATAACCCA-AGACAAAAC
          1 TTTTTTTTTAATAACCCAGAGACAAAAC

       5981 AAATTTTTTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 1
        0.82            0.14        0.04

Matches are distributed among these distances:
  29    7  0.30
  30   16  0.70

ACGTcount: A:0.33, C:0.18, G:0.11, T:0.39


Consensus pattern (30 bp):   
TTTTTTTTTAATAACCCAGAGACAAAACTT

Found at i:6008 original size:30 final size:30

Alignment explanation


    Indices: 5974--6051  Score: 101
    Period size: 30  Copynumber: 2.6  Consensus size: 30

       5964 ATAACCCAAG

                                            
       5974 ACAAAACAAATTTTTTTTTTC-GACGCAAAA-
          1 ACAAAAC--ATTTTTTTTTTCTGACGCAAAAC

                                           
       6004 AC-AAACATTTTTTTTTTCTTGACGCAAAAC
          1 ACAAAACATTTTTTTTTTC-TGACGCAAAAC

                               
       6034 ACAAAAC-TTTTTTTTTTC
          1 ACAAAACATTTTTTTTTTC

       6052 AAAAACGCAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 8
        0.85            0.00        0.15

Matches are distributed among these distances:
  27   12  0.27
  29   13  0.30
  30   15  0.34
  31    4  0.09

ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41


Consensus pattern (30 bp):   
ACAAAACATTTTTTTTTTCTGACGCAAAAC

Found at i:6009 original size:29 final size:29

Alignment explanation


    Indices: 5977--6051  Score: 86
    Period size: 27  Copynumber: 2.6  Consensus size: 29

       5967 ACCCAAGACA

                                          
       5977 AAACAAATTTTTTTTTTC-GACGCAAAAAC
          1 AAACAAATTTTTTTTTTCTGACGC-AAAAC

                                          
       6006 AAAC--ATTTTTTTTTTCTTGACGCAAAAC
          1 AAACAAATTTTTTTTTTC-TGACGCAAAAC

                   *           
       6034 ACAA-AACTTTTTTTTTTC
          1 A-AACAAATTTTTTTTTTC

       6052 AAAAACGCAA


Statistics
Matches: 40,  Mismatches: 1, Indels: 9
        0.80            0.02        0.18

Matches are distributed among these distances:
  27   12  0.30
  28    6  0.15
  29   11  0.28
  30   11  0.28

ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43


Consensus pattern (29 bp):   
AAACAAATTTTTTTTTTCTGACGCAAAAC

Found at i:6435 original size:15 final size:16

Alignment explanation


    Indices: 6411--6449  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       6401 AGAGGTTGAA

                 *          
       6411 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       6426 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                    
       6442 AGAAAACA
          1 AGAAAACA

       6450 GAGCAAAGTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.62
  16    8  0.38

ACGTcount: A:0.62, C:0.13, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.