Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008543.1 Corchorus capsularis cultivar CVL-1 contig08564, 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: 8915
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35


Found at i:1705 original size:39 final size:39

Alignment explanation


    Indices: 1662--1737  Score: 134
    Period size: 39  Copynumber: 1.9  Consensus size: 39

       1652 AAGTTTGTGA

                                                   
       1662 GTCTGAAAGAATAGGAGAAGACTGGTTTTGAGTAAGGGT
          1 GTCTGAAAGAATAGGAGAAGACTGGTTTTGAGTAAGGGT

                               * *               
       1701 GTCTGAAAGAATAGGAGAATATTGGTTTTGAGTAAGG
          1 GTCTGAAAGAATAGGAGAAGACTGGTTTTGAGTAAGG

       1738 ATGTTGTTAT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  39   35  1.00

ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28


Consensus pattern (39 bp):   
GTCTGAAAGAATAGGAGAAGACTGGTTTTGAGTAAGGGT

Found at i:4703 original size:12 final size:13

Alignment explanation


    Indices: 4681--4709  Score: 58
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       4671 GTCTATTATC

                         
       4681 AAAAACAAAAAAA
          1 AAAAACAAAAAAA

                         
       4694 AAAAACAAAAAAA
          1 AAAAACAAAAAAA

               
       4707 AAA
          1 AAA

       4710 TTTTGTCACC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00


Consensus pattern (13 bp):   
AAAAACAAAAAAA

Found at i:8278 original size:15 final size:15

Alignment explanation


    Indices: 8258--8295  Score: 67
    Period size: 15  Copynumber: 2.5  Consensus size: 15

       8248 GTTCAAGTGG

                      *    
       8258 GGGAGGGGTGTGGTA
          1 GGGAGGGGTGGGGTA

                           
       8273 GGGAGGGGTGGGGTA
          1 GGGAGGGGTGGGGTA

                    
       8288 GGGAGGGG
          1 GGGAGGGG

       8296 GAGGAGTTGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.13, C:0.00, G:0.74, T:0.13


Consensus pattern (15 bp):   
GGGAGGGGTGGGGTA
Done.