Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016115.1 Corchorus olitorius cultivar O-4 contig16148, 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: 17434
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:5834 original size:37 final size:37

Alignment explanation


    Indices: 5784--5862  Score: 131
    Period size: 37  Copynumber: 2.1  Consensus size: 37

       5774 AGCACAGTCA

                                                 
       5784 TAAGAACCAACAGAACAAATACCAACTAAACAACAGC
          1 TAAGAACCAACAGAACAAATACCAACTAAACAACAGC

                             *  *                
       5821 TAAGAACCAACAGAACATATGCCAACTAAACAACAGC
          1 TAAGAACCAACAGAACAAATACCAACTAAACAACAGC

            *    
       5858 AAAGA
          1 TAAGA

       5863 GAAAAAGAAA


Statistics
Matches: 39,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  37   39  1.00

ACGTcount: A:0.56, C:0.25, G:0.10, T:0.09


Consensus pattern (37 bp):   
TAAGAACCAACAGAACAAATACCAACTAAACAACAGC

Found at i:10259 original size:6 final size:6

Alignment explanation


    Indices: 10243--10274  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

      10233 CAGGCTGCAC

                   *                             
      10243 CACAAT GACAAT CACAAT CACAAT CACAAT CA
          1 CACAAT CACAAT CACAAT CACAAT CACAAT CA

      10275 TTTGTTAACG


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.50, C:0.31, G:0.03, T:0.16


Consensus pattern (6 bp):   
CACAAT

Found at i:10430 original size:39 final size:38

Alignment explanation


    Indices: 10304--10451  Score: 235
    Period size: 38  Copynumber: 3.9  Consensus size: 38

      10294 TCGAGTCTAG

                                                  
      10304 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                                                  
      10341 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

                               *  * *              
      10379 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA

               *                  *           
      10418 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
          1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT

      10452 ATACACAGCC


Statistics
Matches: 103,  Mismatches: 6, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  37    7  0.07
  38   62  0.60
  39   34  0.33

ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24


Consensus pattern (38 bp):   
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA

Found at i:10438 original size:77 final size:75

Alignment explanation


    Indices: 10304--10451  Score: 233
    Period size: 77  Copynumber: 1.9  Consensus size: 75

      10294 TCGAGTCTAG

                                                                             
      10304 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
          1 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG

                      
      10369 TCCACTCTTA
         66 TCCACTCTTA

                               *  * *                 *                  *   
      10379 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
          1 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG

                    
      10444 GGTCCACT
         64 GGTCCACT

      10452 ATACACAGCC


Statistics
Matches: 66,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  75    7  0.11
  76   24  0.36
  77   35  0.53

ACGTcount: A:0.22, C:0.35, G:0.19, T:0.24


Consensus pattern (75 bp):   
CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA

Found at i:13543 original size:25 final size:25

Alignment explanation


    Indices: 13509--13557  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      13499 GATTGGTTTG

                                     
      13509 TAGAGACCGAGCGAGAGTGCTCAAA
          1 TAGAGACCGAGCGAGAGTGCTCAAA

                       *       *    
      13534 TAGAGACCGAGTGAGAGTGTTCAA
          1 TAGAGACCGAGCGAGAGTGCTCAA

      13558 GATTGTTTGG


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16


Consensus pattern (25 bp):   
TAGAGACCGAGCGAGAGTGCTCAAA

Found at i:14137 original size:29 final size:30

Alignment explanation


    Indices: 14086--14162  Score: 79
    Period size: 31  Copynumber: 2.6  Consensus size: 30

      14076 TGAATTTGTG

                                       *** 
      14086 AAGTTCAAGGGGG-AAAATCTCCTT-ATTTA
          1 AAGTTC-AGGGGGCAAAATCTCCTTGACACA

                                           
      14115 AAGTTCAGGGGGCAAAA-CGTCCTTGACACA
          1 AAGTTCAGGGGGCAAAATC-TCCTTGACACA

                              
      14145 ATAGTTCAGGGGGCAAAA
          1 A-AGTTCAGGGGGCAAAA

      14163 AAGCTGATAA


Statistics
Matches: 41,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  28    7  0.17
  29   15  0.37
  30    3  0.07
  31   16  0.39

ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22


Consensus pattern (30 bp):   
AAGTTCAGGGGGCAAAATCTCCTTGACACA
Done.