Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016462.1 Corchorus capsularis cultivar CVL-1 contig16483, 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: 31226
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:15302 original size:7 final size:7

Alignment explanation


    Indices: 15290--15317  Score: 56
    Period size: 7  Copynumber: 4.0  Consensus size: 7

      15280 TCAGCCGTGC

                   
      15290 CCTGTCG
          1 CCTGTCG

                   
      15297 CCTGTCG
          1 CCTGTCG

                   
      15304 CCTGTCG
          1 CCTGTCG

                   
      15311 CCTGTCG
          1 CCTGTCG

      15318 GGTTCATTAT


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:0.00, C:0.43, G:0.29, T:0.29


Consensus pattern (7 bp):   
CCTGTCG

Found at i:24132 original size:12 final size:13

Alignment explanation


    Indices: 24115--24147  Score: 50
    Period size: 12  Copynumber: 2.5  Consensus size: 13

      24105 AAAGGAAGAA

                         
      24115 AAAGAAAGAAA-C
          1 AAAGAAAGAAAGC

                         
      24127 AAAGAAAGAAAGC
          1 AAAGAAAGAAAGC

                    
      24140 AAGAGAAA
          1 AA-AGAAA

      24148 AGGAATGAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12   11  0.58
  13    3  0.16
  14    5  0.26

ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00


Consensus pattern (13 bp):   
AAAGAAAGAAAGC

Found at i:30983 original size:29 final size:30

Alignment explanation


    Indices: 30944--31013  Score: 97
    Period size: 29  Copynumber: 2.4  Consensus size: 30

      30934 ACCGAACCGT

                                   ***    
      30944 CAAATAAGCCCCTGAACTATT-ATTTCGGC
          1 CAAATAAGCCCCTGAACTATTAAAAACGGC

                              *           
      30973 CAAATAAGCCCCTGAACTCTTAAAAACGGC
          1 CAAATAAGCCCCTGAACTATTAAAAACGGC

                       
      31003 CAAATAAGCCC
          1 CAAATAAGCCC

      31014 TGTTGCCAAG


Statistics
Matches: 36,  Mismatches: 4, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  29   20  0.56
  30   16  0.44

ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20


Consensus pattern (30 bp):   
CAAATAAGCCCCTGAACTATTAAAAACGGC

Done.