Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021081.1 Corchorus olitorius cultivar O-4 contig21114, 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: 3453
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26


Found at i:1835 original size:13 final size:13

Alignment explanation


    Indices: 1795--1845  Score: 57
    Period size: 14  Copynumber: 3.8  Consensus size: 13

       1785 TTGTCAACCA

                        *
       1795 AAAAGTCAACGGT
          1 AAAAGTCAACGGG

            *         *   
       1808 CAAAGTCAATAGGG
          1 AAAAGTCAA-CGGG

                         
       1822 AAAAGTCAACGGG
          1 AAAAGTCAACGGG

                       
       1835 AAAAAGTCAAC
          1 -AAAAGTCAAC

       1846 TTGATGATGT


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  13   11  0.35
  14   20  0.65

ACGTcount: A:0.49, C:0.16, G:0.24, T:0.12


Consensus pattern (13 bp):   
AAAAGTCAACGGG

Found at i:1951 original size:28 final size:29

Alignment explanation


    Indices: 1888--1958  Score: 101
    Period size: 28  Copynumber: 2.5  Consensus size: 29

       1878 ATGGCGTGGA

                                         
       1888 AGGATGACGTGGCAGGTCGACTGGTCAAC
          1 AGGATGACGTGGCAGGTCGACTGGTCAAC

             *      *        *           
       1917 ATG-TGACATGGCAGGTTGACTGGTCAAC
          1 AGGATGACGTGGCAGGTCGACTGGTCAAC

                           
       1945 -GGATGACGTGGCAG
          1 AGGATGACGTGGCAG

       1959 ATGACGTGAC


Statistics
Matches: 36,  Mismatches: 5, Indels: 3
        0.82            0.11        0.07

Matches are distributed among these distances:
  27    1  0.03
  28   33  0.92
  29    2  0.06

ACGTcount: A:0.24, C:0.18, G:0.38, T:0.20


Consensus pattern (29 bp):   
AGGATGACGTGGCAGGTCGACTGGTCAAC

Found at i:2595 original size:20 final size:20

Alignment explanation


    Indices: 2570--2610  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       2560 TTTCACCCCG

                   *  *         
       2570 TGTATTTTCTTTTTTAGAAA
          1 TGTATTTGCTATTTTAGAAA

                                
       2590 TGTATTTGCTATTTTAGAAA
          1 TGTATTTGCTATTTTAGAAA

             
       2610 T
          1 T

       2611 TAAGAAAATC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56


Consensus pattern (20 bp):   
TGTATTTGCTATTTTAGAAA

Found at i:3036 original size:2 final size:2

Alignment explanation


    Indices: 3029--3085  Score: 62
    Period size: 2  Copynumber: 28.0  Consensus size: 2

       3019 CCGACCGATG

                                           *  *  *                          
       3029 AT AT AT AT AT AT AT AT AT AT GGT TT TT AT AT AT AT CAT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT -AT AT AT AT

                                
       3073 AT AT AT AT A- AT AT
          1 AT AT AT AT AT AT AT

       3086 CTTCTTCGTC


Statistics
Matches: 49,  Mismatches: 3, Indels: 6
        0.84            0.05        0.10

Matches are distributed among these distances:
   1    1  0.02
   2   45  0.92
   3    3  0.06

ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51


Consensus pattern (2 bp):   
AT

Done.