Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021129.1 Corchorus olitorius cultivar O-4 contig21162, 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: 45082
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:470 original size:21 final size:20

Alignment explanation


    Indices: 437--479  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 20

        427 ATGTAACATC

                                 
        437 ATTTTTTTAATTTGTTATATT
          1 ATTTTTTTAATTTGTTAT-TT

                          *      
        458 ATTTTATTT-ATTTTTTATTT
          1 ATTTT-TTTAATTTGTTATTT

              
        478 AT
          1 AT

        480 ATTGCTGCTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  20    4  0.20
  21   13  0.65
  22    3  0.15

ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74


Consensus pattern (20 bp):   
ATTTTTTTAATTTGTTATTT

Found at i:13233 original size:18 final size:18

Alignment explanation


    Indices: 13210--13250  Score: 57
    Period size: 18  Copynumber: 2.3  Consensus size: 18

      13200 AAGGAAATCT

                               
      13210 CGCCGTCGTT-TTAGCTGC
          1 CGCCGTCGTTGTT-GCTGC

                          *   
      13228 CGCCGTCGTTGTTGTTGC
          1 CGCCGTCGTTGTTGCTGC

                 
      13246 CGCCG
          1 CGCCG

      13251 AAGAAGAAGA


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

Matches are distributed among these distances:
  18   19  0.90
  19    2  0.10

ACGTcount: A:0.02, C:0.34, G:0.32, T:0.32


Consensus pattern (18 bp):   
CGCCGTCGTTGTTGCTGC

Found at i:13751 original size:23 final size:22

Alignment explanation


    Indices: 13721--13764  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 22

      13711 TGAGATTTGG

                         *        
      13721 GAGAAGAAAGAAAGAGAGTTTA
          1 GAGAAGAAAGAAAAAGAGTTTA

                                  
      13743 GAGAGAGAAAGAAAAAGAGTTT
          1 GAGA-AGAAAGAAAAAGAGTTT

      13765 CAACTGGGCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  22    4  0.20
  23   16  0.80

ACGTcount: A:0.55, C:0.00, G:0.32, T:0.14


Consensus pattern (22 bp):   
GAGAAGAAAGAAAAAGAGTTTA

Found at i:14089 original size:7 final size:7

Alignment explanation


    Indices: 14073--14108  Score: 54
    Period size: 7  Copynumber: 5.1  Consensus size: 7

      14063 TCTACCCAAA

                 * 
      14073 AATTAAT
          1 AATTATT

                   
      14080 AATTATT
          1 AATTATT

               *   
      14087 AATGATT
          1 AATTATT

                   
      14094 AATTATT
          1 AATTATT

                   
      14101 AATTATT
          1 AATTATT

             
      14108 A
          1 A

      14109 TTAAGCTTAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   7   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (7 bp):   
AATTATT

Found at i:19325 original size:31 final size:28

Alignment explanation


    Indices: 19280--19346  Score: 89
    Period size: 31  Copynumber: 2.3  Consensus size: 28

      19270 CGTTTGAGAG

                *                         
      19280 GGGGCAAAACGTCCAAAATTGAGAATTCAA
          1 GGGGAAAAACGTCCAAAATTGA-AATTC-A

                      *                  
      19310 GGGGTAAAAATGTCCAAAATTGAAATTCA
          1 GGGG-AAAAACGTCCAAAATTGAAATTCA

                    
      19339 GGGGAAAA
          1 GGGGAAAA

      19347 TGGTGCTTTT


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  28    4  0.12
  29    5  0.15
  30    9  0.26
  31   16  0.47

ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18


Consensus pattern (28 bp):   
GGGGAAAAACGTCCAAAATTGAAATTCA

Found at i:38190 original size:16 final size:16

Alignment explanation


    Indices: 38154--38185  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

      38144 AAAGAAGTAG

                            
      38154 AAGGAAAGAAAGAAAC
          1 AAGGAAAGAAAGAAAC

                            
      38170 AAGGAAATGAAAGAAA
          1 AAGGAAA-GAAAGAAA

      38186 GAGGAGCCAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    7  0.47
  17    8  0.53

ACGTcount: A:0.69, C:0.03, G:0.25, T:0.03


Consensus pattern (16 bp):   
AAGGAAAGAAAGAAAC
Done.