Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011182.1 Corchorus capsularis cultivar CVL-1 contig11203, 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: 21482
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33


Found at i:159 original size:2 final size:2

Alignment explanation


    Indices: 152--198  Score: 69
    Period size: 2  Copynumber: 23.5  Consensus size: 2

        142 TTCGTACTCT

                               *                                           
        152 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
          1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
        194 TA TA T
          1 TA TA T

        199 GGAGAGTACT


Statistics
Matches: 41,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
   1    1  0.02
   2   38  0.93
   3    2  0.05

ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:12380 original size:2 final size:2

Alignment explanation


    Indices: 12373--12397  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      12363 GTTTCTTGTT

                                                 
      12373 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

      12398 GTATGTATGT


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


Consensus pattern (2 bp):   
TA

Found at i:12402 original size:4 final size:4

Alignment explanation


    Indices: 12395--12437  Score: 86
    Period size: 4  Copynumber: 10.8  Consensus size: 4

      12385 TATATATATA

                                                                 
      12395 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
          1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT

      12438 TACAATGTAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   39  1.00

ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51


Consensus pattern (4 bp):   
TATG

Found at i:14131 original size:14 final size:14

Alignment explanation


    Indices: 14112--14139  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      14102 GGCATGGGTG

                          
      14112 GTATAGGCAAAACA
          1 GTATAGGCAAAACA

                          
      14126 GTATAGGCAAAACA
          1 GTATAGGCAAAACA

      14140 ACTCTTGCTG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14


Consensus pattern (14 bp):   
GTATAGGCAAAACA
Done.