Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013065.1 Corchorus olitorius cultivar O-4 contig13098, 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: 21484
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--137  Score: 260
    Period size: 2  Copynumber: 69.5  Consensus size: 2

                                                                          
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         43 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                                                          
         85 TC T- TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                               
        125 TC TC TC TC TC TC T
          1 TC TC TC TC TC TC T

        138 TTTAACATTT


Statistics
Matches: 133,  Mismatches: 0, Indels: 4
        0.97            0.00        0.03

Matches are distributed among these distances:
   1    2  0.02
   2  131  0.98

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:1859 original size:2 final size:2

Alignment explanation


    Indices: 1852--1883  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       1842 TCACCAGTAC

                                                           
       1852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1884 TCAGGAACGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7019 original size:13 final size:12

Alignment explanation


    Indices: 6993--7017  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       6983 TTAAGAATAT

                        
       6993 ATTATTTTTCAA
          1 ATTATTTTTCAA

                        
       7005 ATTATTTTTCAA
          1 ATTATTTTTCAA

             
       7017 A
          1 A

       7018 ATATGGAGGA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56


Consensus pattern (12 bp):   
ATTATTTTTCAA

Found at i:7464 original size:10 final size:10

Alignment explanation


    Indices: 7446--7482  Score: 56
    Period size: 10  Copynumber: 3.7  Consensus size: 10

       7436 ATATAAATCA

                      
       7446 AAACCGACCG
          1 AAACCGACCG

                *     
       7456 AAACAGACCG
          1 AAACCGACCG

                     *
       7466 AAACCGACCA
          1 AAACCGACCG

                   
       7476 AAACCGA
          1 AAACCGA

       7483 TTAGTTGGTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  10   24  1.00

ACGTcount: A:0.49, C:0.35, G:0.16, T:0.00


Consensus pattern (10 bp):   
AAACCGACCG

Found at i:7664 original size:34 final size:34

Alignment explanation


    Indices: 7613--7678  Score: 89
    Period size: 34  Copynumber: 1.9  Consensus size: 34

       7603 TAAAAATTTG

                                *      *      
       7613 ATTTGGAGAAAACAATTTTTGAATTTTTAAGTAT
          1 ATTTGGAGAAAACAATTTTTAAATTTTAAAGTAT

                     *                       
       7647 ATTTGGATGCAAA-AATTTTTAAATTTTAAAGT
          1 ATTTGGA-GAAAACAATTTTTAAATTTTAAAGT

       7679 GTTACACAAA


Statistics
Matches: 28,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
  34   24  0.86
  35    4  0.14

ACGTcount: A:0.39, C:0.03, G:0.14, T:0.44


Consensus pattern (34 bp):   
ATTTGGAGAAAACAATTTTTAAATTTTAAAGTAT

Found at i:8238 original size:21 final size:21

Alignment explanation


    Indices: 8214--8253  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       8204 TAGAAGAAAA

                                 
       8214 CAAAATTTATAGAGAGGTTAT
          1 CAAAATTTATAGAGAGGTTAT

                *       *      
       8235 CAAATTTTATAGGGAGGTT
          1 CAAAATTTATAGAGAGGTT

       8254 TTTACAGTTT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.38, C:0.05, G:0.23, T:0.35


Consensus pattern (21 bp):   
CAAAATTTATAGAGAGGTTAT

Found at i:9922 original size:23 final size:23

Alignment explanation


    Indices: 9881--9924  Score: 63
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       9871 CTAACCCTAT

                          *        
       9881 TTTTTTCTTTCTTTCTTTTATAG
          1 TTTTTTCTTTCTTTATTTTATAG

                                  
       9904 TTTTTTC-TTCTTTTATTTTAT
          1 TTTTTTCTTTC-TTTATTTTAT

       9925 TTATTTATAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    3  0.16
  23   16  0.84

ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77


Consensus pattern (23 bp):   
TTTTTTCTTTCTTTATTTTATAG
Done.