Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000104.1 Corchorus olitorius cultivar O-4 contig00104, 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: 2288
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:873 original size:14 final size:13

Alignment explanation


    Indices: 854--899  Score: 56
    Period size: 14  Copynumber: 3.3  Consensus size: 13

        844 ATTCACTGAA

                          
        854 TTTTTTGTTTTCTT
          1 TTTTTTGTTTT-TT

                          
        868 TTTTTTGTTGTTTT
          1 TTTTTTGTT-TTTT

            *             
        882 GTTTTTGTTTTTGT
          1 TTTTTTGTTTTT-T

                
        896 TTTT
          1 TTTT

        900 GCATTTTTTT


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  13    3  0.11
  14   23  0.82
  15    2  0.07

ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85


Consensus pattern (13 bp):   
TTTTTTGTTTTTT

Found at i:880 original size:17 final size:16

Alignment explanation


    Indices: 854--912  Score: 64
    Period size: 17  Copynumber: 3.4  Consensus size: 16

        844 ATTCACTGAA

                            
        854 TTTTTTGTTTTCTTTT
          1 TTTTTTGTTTTCTTTT

                        *    
        870 TTTTGTTGTTTTGTTTT
          1 TTTT-TTGTTTTCTTTT

                           *   
        887 TGTTTTTGTTTTTGCATTT
          1 T-TTTTTG-TTTT-CTTTT

                   
        906 TTTTTTG
          1 TTTTTTG

        913 CATATTTACT


Statistics
Matches: 36,  Mismatches: 3, Indels: 6
        0.80            0.07        0.13

Matches are distributed among these distances:
  16    4  0.11
  17   15  0.42
  18   13  0.36
  19    4  0.11

ACGTcount: A:0.02, C:0.03, G:0.14, T:0.81


Consensus pattern (16 bp):   
TTTTTTGTTTTCTTTT

Found at i:887 original size:6 final size:6

Alignment explanation


    Indices: 855--900  Score: 53
    Period size: 6  Copynumber: 8.0  Consensus size: 6

        845 TTCACTGAAT

                                    *                               
        855 TTTTTG TTTTCT- TTTTT- TTGTTG -TTTTG TTTTTG TTTTTG TTTTTG
          1 TTTTTG TTTT-TG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG

        901 CATTTTTTTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   5    9  0.26
   6   25  0.71
   7    1  0.03

ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83


Consensus pattern (6 bp):   
TTTTTG

Found at i:919 original size:14 final size:13

Alignment explanation


    Indices: 878--915  Score: 53
    Period size: 12  Copynumber: 3.1  Consensus size: 13

        868 TTTTTTGTTG

                        *
        878 TTTTGTTTTTG-T
          1 TTTTGTTTTTGCA

                         
        890 TTTTGTTTTTGCA
          1 TTTTGTTTTTGCA

                         
        903 TTTT-TTTTTGCA
          1 TTTTGTTTTTGCA

             
        915 T
          1 T

        916 ATTTACTGAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  12   20  0.83
  13    4  0.17

ACGTcount: A:0.05, C:0.05, G:0.13, T:0.76


Consensus pattern (13 bp):   
TTTTGTTTTTGCA
Done.