Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016264.1 Corchorus olitorius cultivar O-4 contig16297, 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: 11138
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:2109 original size:13 final size:12

Alignment explanation


    Indices: 2088--2122  Score: 61
    Period size: 13  Copynumber: 2.8  Consensus size: 12

       2078 AATAAAGTAA

                        
       2088 TAATACTATTAT
          1 TAATACTATTAT

                         
       2100 TAATTACTATTAT
          1 TAA-TACTATTAT

                      
       2113 TAATACTATT
          1 TAATACTATT

       2123 TCAATGTCTT


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

Matches are distributed among these distances:
  12   10  0.45
  13   12  0.55

ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51


Consensus pattern (12 bp):   
TAATACTATTAT

Found at i:3901 original size:8 final size:9

Alignment explanation


    Indices: 3865--3902  Score: 60
    Period size: 9  Copynumber: 4.3  Consensus size: 9

       3855 CTCAAATTAC

                     
       3865 TTATGGAAA
          1 TTATGGAAA

               *     
       3874 TTAAGGAAA
          1 TTATGGAAA

                     
       3883 TTATGGAAA
          1 TTATGGAAA

                     
       3892 TTAT-GAAA
          1 TTATGGAAA

               
       3900 TTA
          1 TTA

       3903 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:5255 original size:49 final size:47

Alignment explanation


    Indices: 5178--5318  Score: 151
    Period size: 49  Copynumber: 2.9  Consensus size: 47

       5168 CAAGCAATCA

                *      *                                    
       5178 TTTACTTTTCACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT

                     *                        * *          *  
       5226 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTAAAGACAAAATTGATCT
          1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTT-TATACAAAATTGAACT

                        *         *                      
       5275 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
          1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA

       5319 TTGGCACGCT


Statistics
Matches: 77,  Mismatches: 11, Indels: 11
        0.78            0.11        0.11

Matches are distributed among these distances:
  47   15  0.19
  48   21  0.27
  49   34  0.44
  50    7  0.09

ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50


Consensus pattern (47 bp):   
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT

Found at i:6321 original size:15 final size:15

Alignment explanation


    Indices: 6301--6337  Score: 56
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       6291 TGCTAGGGTG

                           
       6301 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                    *      
       6316 AATGGTGCGAACAAC
          1 AATGGTGCAAACAAC

              *    
       6331 AAGGGTG
          1 AATGGTG

       6338 TGAACAATAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   20  1.00

ACGTcount: A:0.41, C:0.16, G:0.30, T:0.14


Consensus pattern (15 bp):   
AATGGTGCAAACAAC

Found at i:6342 original size:15 final size:15

Alignment explanation


    Indices: 6304--6344  Score: 55
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6294 TAGGGTGAAT

                 *        *
       6304 GGTGCAAACAACAAT
          1 GGTGCGAACAACAAG

                           
       6319 GGTGCGAACAACAAG
          1 GGTGCGAACAACAAG

                *      
       6334 GGTGTGAACAA
          1 GGTGCGAACAA

       6345 TAATGGAAAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  15   23  1.00

ACGTcount: A:0.41, C:0.17, G:0.29, T:0.12


Consensus pattern (15 bp):   
GGTGCGAACAACAAG
Done.