Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022721.1 Corchorus olitorius cultivar O-4 contig22754, 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: 8516
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:2473 original size:25 final size:25

Alignment explanation


    Indices: 2445--2493  Score: 80
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       2435 GATTGGTTTG

                   *   *             
       2445 TAGAGACTGAGTGAGAGTGCTCAAA
          1 TAGAGACCGAGCGAGAGTGCTCAAA

                                    
       2470 TAGAGACCGAGCGAGAGTGCTCAA
          1 TAGAGACCGAGCGAGAGTGCTCAA

       2494 GATTGTTTTG


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:3400 original size:25 final size:25

Alignment explanation


    Indices: 3366--3413  Score: 87
    Period size: 25  Copynumber: 1.9  Consensus size: 25

       3356 GATTGGTTTG

                                     
       3366 TAGAGACCGAGAGAGAGTGCTCAAA
          1 TAGAGACCGAGAGAGAGTGCTCAAA

                       *           
       3391 TAGAGACCGAGCGAGAGTGCTCA
          1 TAGAGACCGAGAGAGAGTGCTCA

       3414 GGATTGTTTG


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

Matches are distributed among these distances:
  25   22  1.00

ACGTcount: A:0.35, C:0.19, G:0.33, T:0.12


Consensus pattern (25 bp):   
TAGAGACCGAGAGAGAGTGCTCAAA

Found at i:5454 original size:8 final size:9

Alignment explanation


    Indices: 5418--5455  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       5408 CCCAAATTAC

                     
       5418 TTATGGAAA
          1 TTATGGAAA

               *     
       5427 TTAAGGAAA
          1 TTATGGAAA

                     
       5436 TTATGGAAA
          1 TTATGGAAA

                     
       5445 TTAT-GAAA
          1 TTATGGAAA

               
       5453 TTA
          1 TTA

       5456 AATGAATTAA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   8    7  0.26
   9   20  0.74

ACGTcount: A:0.47, C:0.00, G:0.18, T:0.34


Consensus pattern (9 bp):   
TTATGGAAA

Found at i:6808 original size:49 final size:47

Alignment explanation


    Indices: 6730--6856  Score: 136
    Period size: 48  Copynumber: 2.7  Consensus size: 47

       6720 CCAAGCAATC

                 *    *                                      
       6730 CTTTACTTTTCAC-TGCACTTTTTCTCAATTTTTACTA-CAAAATTGAA
          1 CTTTAATTTTTACTTGCACTTTTTCTCAATTTTTA--AGCAAAATTGAA

                *                                          *
       6777 CTTTTATTTTTACTTGCATCTTTTTCTCAATTTTTAAGCAAAATTGAT
          1 CTTTAATTTTTACTTGCA-CTTTTTCTCAATTTTTAAGCAAAATTGAA

                      *   *         *         
       6825 CTTTAATTTTCA-TCGCAC-TTTTATCAATTTTT
          1 CTTTAATTTTTACTTGCACTTTTTCTCAATTTTT

       6857 TTGACAAAAT


Statistics
Matches: 69,  Mismatches: 8, Indels: 8
        0.81            0.09        0.09

Matches are distributed among these distances:
  45   13  0.19
  46    1  0.01
  47   15  0.22
  48   23  0.33
  49   17  0.25

ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52


Consensus pattern (47 bp):   
CTTTAATTTTTACTTGCACTTTTTCTCAATTTTTAAGCAAAATTGAA

Found at i:7736 original size:15 final size:15

Alignment explanation


    Indices: 7704--7744  Score: 64
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       7694 GAATGGTCAA

                           
       7704 AACAACAATGGTGCG
          1 AACAACAATGGTGCG

                         * 
       7719 AACAACAATGGTGTG
          1 AACAACAATGGTGCG

                 *     
       7734 AACAATAATGG
          1 AACAACAATGG

       7745 AAATGGTGCA


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

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.44, C:0.15, G:0.24, T:0.17


Consensus pattern (15 bp):   
AACAACAATGGTGCG
Done.