Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018363.1 Corchorus olitorius cultivar O-4 contig18396, 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: 51310
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:5876 original size:2 final size:2

Alignment explanation


    Indices: 5869--5893  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       5859 ATCAACTGAA

                                                 
       5869 TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC T

       5894 ATTTATATAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:11521 original size:38 final size:38

Alignment explanation


    Indices: 11469--11541  Score: 112
    Period size: 38  Copynumber: 1.9  Consensus size: 38

      11459 CACACACACT

                     *             *               
      11469 AAACTCAGTTTTTGTG-TTGTTGTCAAAAAAAAAAAAAA
          1 AAACTCAGTATTTGTGTTTG-TGCCAAAAAAAAAAAAAA

                                               
      11507 AAACTCAGTATTTGTGTTTGTGCCAAAAAAAAAAA
          1 AAACTCAGTATTTGTGTTTGTGCCAAAAAAAAAAA

      11542 GACTCAGTAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  38   29  0.91
  39    3  0.09

ACGTcount: A:0.47, C:0.10, G:0.14, T:0.30


Consensus pattern (38 bp):   
AAACTCAGTATTTGTGTTTGTGCCAAAAAAAAAAAAAA

Found at i:15826 original size:7 final size:7

Alignment explanation


    Indices: 15814--15841  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      15804 AGAAGAAAGC

                   
      15814 AAAGGCA
          1 AAAGGCA

                   
      15821 AAAGGCA
          1 AAAGGCA

                   
      15828 AAAGGCA
          1 AAAGGCA

                   
      15835 AAAGGCA
          1 AAAGGCA

      15842 GCTCATTTAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   21  1.00

ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00


Consensus pattern (7 bp):   
AAAGGCA

Found at i:21072 original size:13 final size:13

Alignment explanation


    Indices: 21054--21079  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      21044 TGATTTTAGC

                         
      21054 AATGTTAATGCTT
          1 AATGTTAATGCTT

                         
      21067 AATGTTAATGCTT
          1 AATGTTAATGCTT

      21080 TAACATGTGA


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

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46


Consensus pattern (13 bp):   
AATGTTAATGCTT

Found at i:23424 original size:19 final size:19

Alignment explanation


    Indices: 23390--23447  Score: 93
    Period size: 18  Copynumber: 3.2  Consensus size: 19

      23380 ATTTCCTTGA

                               
      23390 TTTCTTTTCC-TTTTTGTT
          1 TTTCTTTTCCTTTTTTGTT

                               
      23408 TTTCTTTTCCTTTTTTGTT
          1 TTTCTTTTCCTTTTTTGTT

                          *    
      23427 TTTCTTTT-CTTTTGTGTT
          1 TTTCTTTTCCTTTTTTGTT

               
      23445 TTT
          1 TTT

      23448 AATTTTTCAA


Statistics
Matches: 38,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
  18   22  0.58
  19   16  0.42

ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79


Consensus pattern (19 bp):   
TTTCTTTTCCTTTTTTGTT

Done.