Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013662.1 Corchorus olitorius cultivar O-4 contig13695, 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: 39564
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:98 original size:55 final size:55

Alignment explanation


    Indices: 14--128  Score: 230
    Period size: 55  Copynumber: 2.1  Consensus size: 55

          4 GAGAGAGAAC

                                                                   
         14 ATGTCAAATTATCGGGCCCGATCCAAATCCAATAAAGGTTGAAAATAAGAGGAGT
          1 ATGTCAAATTATCGGGCCCGATCCAAATCCAATAAAGGTTGAAAATAAGAGGAGT

                                                                   
         69 ATGTCAAATTATCGGGCCCGATCCAAATCCAATAAAGGTTGAAAATAAGAGGAGT
          1 ATGTCAAATTATCGGGCCCGATCCAAATCCAATAAAGGTTGAAAATAAGAGGAGT

                 
        124 ATGTC
          1 ATGTC

        129 CAAGCTCAAA


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  55   60  1.00

ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23


Consensus pattern (55 bp):   
ATGTCAAATTATCGGGCCCGATCCAAATCCAATAAAGGTTGAAAATAAGAGGAGT

Found at i:2545 original size:42 final size:43

Alignment explanation


    Indices: 2494--2587  Score: 129
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       2484 AGTGCATTAC

                                  * *     *            
       2494 CTAA-ATTCTA-CTCCATCTCTGGGTAATTTATCAAAATAAAG
          1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG

                                                         
       2535 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG

                    
       2580 CTAATATT
          1 CTAATATT

       2588 AATTGTTGTT


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   36  0.78

ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG

Found at i:22396 original size:21 final size:21

Alignment explanation


    Indices: 22367--22406  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      22357 GAGTATGTAA

                                 
      22367 AGACCATTAGTACTGAACATT
          1 AGACCATTAGTACTGAACATT

                *              
      22388 AGACTATTAGTACTGAACA
          1 AGACCATTAGTACTGAACA

      22407 AAAGCCAAGT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28


Consensus pattern (21 bp):   
AGACCATTAGTACTGAACATT

Found at i:26479 original size:52 final size:52

Alignment explanation


    Indices: 26401--26503  Score: 188
    Period size: 52  Copynumber: 2.0  Consensus size: 52

      26391 ACACAGTATT

                                                                
      26401 ATGGCCATTTCGTTGTTTAAGAATTGTGTTTTTAAATTCCAGCTAATTTGTC
          1 ATGGCCATTTCGTTGTTTAAGAATTGTGTTTTTAAATTCCAGCTAATTTGTC

                      *                        *               
      26453 ATGGCCATTTTGTTGTTTAAGAATTGTGTTTTTAATTTCCAGCTAATTTGT
          1 ATGGCCATTTCGTTGTTTAAGAATTGTGTTTTTAAATTCCAGCTAATTTGT

      26504 GTTTTTAAAT


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  52   49  1.00

ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49


Consensus pattern (52 bp):   
ATGGCCATTTCGTTGTTTAAGAATTGTGTTTTTAAATTCCAGCTAATTTGTC

Found at i:26503 original size:24 final size:24

Alignment explanation


    Indices: 26476--26522  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      26466 TGTTTAAGAA

                        *           
      26476 TTGTGTTTTTAATTTCCAGCTAAT
          1 TTGTGTTTTTAAATTCCAGCTAAT

                                   
      26500 TTGTGTTTTTAAATTCCAGCTAA
          1 TTGTGTTTTTAAATTCCAGCTAA

      26523 GAATTGTGAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51


Consensus pattern (24 bp):   
TTGTGTTTTTAAATTCCAGCTAAT

Found at i:34152 original size:86 final size:88

Alignment explanation


    Indices: 34039--34204  Score: 198
    Period size: 92  Copynumber: 1.9  Consensus size: 88

      34029 TGAGTGGAGT

                          *       *                                          
      34039 TTTATAATTTGTTTTGACAATATAATGAGTTG-A-GT-TTATTATTA-A-CTATTAATGAAAAAT
          1 TTTATAATTTGTTTCGACAATAGAATGAG-TGCATGTATTATTATTATATCTATTAATGAAAAAT

                    *               
      34099 GACTAAAGTAATTATTATTTATTA
         65 GACTAAAGCAATTATTATTTATTA

                              *                  *                         * 
      34123 TTTATAATTTTGTTATCGGCAATAGAATGAGTGCATTTTATTATTATTATTATCTATTAATGAGA
          1 TTTATAA-TTTGTT-TCGACAATAGAATGAGTGCA-TGTATTATTATTA-TATCTATTAATGAAA

                             
      34188 AATGACTAAAGCAATTA
         62 AATGACTAAAGCAATTA

      34205 ATTTAACAAA


Statistics
Matches: 67,  Mismatches: 6, Indels: 10
        0.81            0.07        0.12

Matches are distributed among these distances:
  84    7  0.10
  85    8  0.12
  86   14  0.21
  88    1  0.01
  89    9  0.13
  91    1  0.01
  92   27  0.40

ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45


Consensus pattern (88 bp):   
TTTATAATTTGTTTCGACAATAGAATGAGTGCATGTATTATTATTATATCTATTAATGAAAAATG
ACTAAAGCAATTATTATTTATTA
Done.