Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021877.1 Corchorus olitorius cultivar O-4 contig21910, 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: 10266
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33


Found at i:1432 original size:12 final size:12

Alignment explanation


    Indices: 1415--1440  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       1405 TTCAAGTCCA

                        
       1415 AAAATGACGTCG
          1 AAAATGACGTCG

                        
       1427 AAAATGACGTCG
          1 AAAATGACGTCG

              
       1439 AA
          1 AA

       1441 GTCCCTGCAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15


Consensus pattern (12 bp):   
AAAATGACGTCG

Found at i:7409 original size:8 final size:9

Alignment explanation


    Indices: 7373--7410  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       7363 CCCAAATTAC

                     
       7373 TTATGGAAA
          1 TTATGGAAA

               *     
       7382 TTAAGGAAA
          1 TTATGGAAA

                     
       7391 TTATGGAAA
          1 TTATGGAAA

                     
       7400 TTAT-GAAA
          1 TTATGGAAA

               
       7408 TTA
          1 TTA

       7411 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:8755 original size:49 final size:48

Alignment explanation


    Indices: 8683--8811  Score: 165
    Period size: 49  Copynumber: 2.7  Consensus size: 48

       8673 TTAAAGCAAT

                  *                            **           
       8683 CTTTTACTTT-AC-TGCACTTTTTCTCAATTTTTACTACAAAATTGAA
          1 CTTTTATTTTCACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAA

                                                            *
       8729 CTTTTATTTTCACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGAT
          1 CTTTTATTTTCACTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAA

                           *         *         
       8778 CTTTTAATTTTCA-TCGCACTTTTTATCAATTTTT
          1 CTTTT-ATTTTCACTTGCACTTTTTCTCAATTTTT

       8812 GGATAAAATT


Statistics
Matches: 73,  Mismatches: 6, Indels: 6
        0.86            0.07        0.07

Matches are distributed among these distances:
  46    9  0.12
  47    2  0.03
  48   19  0.26
  49   36  0.49
  50    7  0.10

ACGTcount: A:0.26, C:0.18, G:0.05, T:0.52


Consensus pattern (48 bp):   
CTTTTATTTTCACTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAA

Found at i:9688 original size:15 final size:15

Alignment explanation


    Indices: 9656--9696  Score: 64
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       9646 GAATGGTCAA

                           
       9656 AACAACAATGGTGCG
          1 AACAACAATGGTGCG

                         * 
       9671 AACAACAATGGTGTG
          1 AACAACAATGGTGCG

                 *     
       9686 AACAATAATGG
          1 AACAACAATGG

       9697 AAACGGTGCA


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.