Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010579.1 Corchorus capsularis cultivar CVL-1 contig10600, 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: 22923
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:10156 original size:24 final size:24

Alignment explanation


    Indices: 10124--10171  Score: 96
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      10114 CAAAATCAAG

                                    
      10124 TATATGAGTAATCATATTAGGTCT
          1 TATATGAGTAATCATATTAGGTCT

                                    
      10148 TATATGAGTAATCATATTAGGTCT
          1 TATATGAGTAATCATATTAGGTCT

      10172 CAATTATCTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42


Consensus pattern (24 bp):   
TATATGAGTAATCATATTAGGTCT

Found at i:20651 original size:23 final size:21

Alignment explanation


    Indices: 20598--20657  Score: 66
    Period size: 23  Copynumber: 2.7  Consensus size: 21

      20588 TATATAATTC

                       *         *
      20598 TATATATCATATAATTAATTTG
          1 TATATAT-ATAAAATTAATTTA

                                    
      20620 TATATTATATAAATATTAATATTA
          1 TATA-TATATAAA-ATTAAT-TTA

                          
      20644 TATATATATAAAAT
          1 TATATATATAAAAT

      20658 AATCCGAAAA


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  22   10  0.30
  23   17  0.52
  24    6  0.18

ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48


Consensus pattern (21 bp):   
TATATATATAAAATTAATTTA

Found at i:22846 original size:2 final size:2

Alignment explanation


    Indices: 22839--22923  Score: 170
    Period size: 2  Copynumber: 42.5  Consensus size: 2

      22829 ACAGAAGGGG

                                                                          
      22839 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                                          
      22881 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

             
      22923 G
          1 G


Statistics
Matches: 83,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   83  1.00

ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00


Consensus pattern (2 bp):   
GA

Done.