Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021353.1 Corchorus olitorius cultivar O-4 contig21386, 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: 26551
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34


Found at i:1842 original size:16 final size:17

Alignment explanation


    Indices: 1811--1851  Score: 57
    Period size: 16  Copynumber: 2.5  Consensus size: 17

       1801 CGCACCCTTG

                     *       
       1811 TATTAATATCATATATA
          1 TATTAATATAATATATA

                             
       1828 TATTAAT-TAATATATA
          1 TATTAATATAATATATA

              *     
       1844 TAATAATA
          1 TATTAATA

       1852 CATATAGAAA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  16   14  0.67
  17    7  0.33

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46


Consensus pattern (17 bp):   
TATTAATATAATATATA

Found at i:1856 original size:16 final size:16

Alignment explanation


    Indices: 1814--1857  Score: 54
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       1804 ACCCTTGTAT

                            *
       1814 TAATATCATATATATAT
          1 TAATA-CATATATATAA

                             
       1831 TAATTA-ATATATATAA
          1 TAA-TACATATATATAA

                       
       1847 TAATACATATA
          1 TAATACATATA

       1858 GAAAATTTAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 5
        0.80            0.03        0.17

Matches are distributed among these distances:
  15    2  0.08
  16   17  0.71
  17    3  0.12
  18    2  0.08

ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43


Consensus pattern (16 bp):   
TAATACATATATATAA

Found at i:22945 original size:20 final size:20

Alignment explanation


    Indices: 22908--22958  Score: 66
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      22898 CAAAGTTAAG

                         *       
      22908 AAAAACACAAAAATGAAAAAC
          1 AAAAACA-AAAAACGAAAAAC

                      *        *
      22929 AAAAACAAAATACGAAAAAT
          1 AAAAACAAAAAACGAAAAAC

                      
      22949 AAAAACAAAA
          1 AAAAACAAAA

      22959 CTAAAGGAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  20   20  0.74
  21    7  0.26

ACGTcount: A:0.78, C:0.12, G:0.04, T:0.06


Consensus pattern (20 bp):   
AAAAACAAAAAACGAAAAAC
Done.