Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022559.1 Corchorus olitorius cultivar O-4 contig22592, 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: 2593
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33


Found at i:184 original size:27 final size:27

Alignment explanation


    Indices: 109--191  Score: 121
    Period size: 30  Copynumber: 3.0  Consensus size: 27

         99 CTACCACTAA

                         *             
        109 TAATAATTATTATTATAATAATAAGTT
          1 TAATAATTATTATAATAATAATAAGTT

                      *                   
        136 TAATAATTATAATACCACTAATAATAAGTT
          1 TAATAATTATTATA--A-TAATAATAAGTT

                                      
        166 TAATAATTATTATAATAATAATAAGT
          1 TAATAATTATTATAATAATAATAAGT

        192 CTAAATTAAC


Statistics
Matches: 50,  Mismatches: 3, Indels: 6
        0.85            0.05        0.10

Matches are distributed among these distances:
  27   23  0.46
  28    1  0.02
  29    1  0.02
  30   25  0.50

ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42


Consensus pattern (27 bp):   
TAATAATTATTATAATAATAATAAGTT

Found at i:328 original size:15 final size:18

Alignment explanation


    Indices: 295--330  Score: 51
    Period size: 15  Copynumber: 2.2  Consensus size: 18

        285 TTTTAATAAT

                              
        295 TATAATAATAAGTGATTA
          1 TATAATAATAAGTGATTA

                              
        313 TATAA-AATAA-TG-TTA
          1 TATAATAATAAGTGATTA

               
        328 TAT
          1 TAT

        331 TTTAGACTTT


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  15    6  0.33
  16    2  0.11
  17    5  0.28
  18    5  0.28

ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42


Consensus pattern (18 bp):   
TATAATAATAAGTGATTA

Found at i:469 original size:2 final size:2

Alignment explanation


    Indices: 457--497  Score: 64
    Period size: 2  Copynumber: 20.0  Consensus size: 2

        447 AGTTTAGACT

                               *                                        
        457 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        498 AATTAATCAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:2194 original size:22 final size:23

Alignment explanation


    Indices: 2160--2203  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       2150 CTAGCATTAG

                             *     
       2160 CATAATAGCAGTA-TAGCAAAAT
          1 CATAATAGCAGTAGTAGAAAAAT

                                   
       2182 CATAATA-CTAGTAGTAGAAAAA
          1 CATAATAGC-AGTAGTAGAAAAA

       2204 GAGTCAATAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  21    1  0.05
  22   11  0.58
  23    7  0.37

ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23


Consensus pattern (23 bp):   
CATAATAGCAGTAGTAGAAAAAT
Done.