Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020437.1 Corchorus olitorius cultivar O-4 contig20470, 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: 18114
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32


Found at i:4445 original size:79 final size:79

Alignment explanation


    Indices: 4314--4471  Score: 298
    Period size: 79  Copynumber: 2.0  Consensus size: 79

       4304 CAAGTTTGGT

                                            *                                
       4314 TTGGTTATTGTAGATCACTTATCTTTGATTCATATTAAGTTTTTGCTACTAATTGTTGGTTCCTC
          1 TTGGTTATTGTAGATCACTTATCTTTGATTCACATTAAGTTTTTGCTACTAATTGTTGGTTCCTC

                          
       4379 AAGTAGGTCACGAG
         66 AAGTAGGTCACGAG

                                                                     *       
       4393 TTGGTTATTGTAGATCACTTATCTTTGATTCACATTAAGTTTTTGCTACTAATTGTTTGTTCCTC
          1 TTGGTTATTGTAGATCACTTATCTTTGATTCACATTAAGTTTTTGCTACTAATTGTTGGTTCCTC

                          
       4458 AAGTAGGTCACGAG
         66 AAGTAGGTCACGAG

       4472 AAGAGCGAAT


Statistics
Matches: 77,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  79   77  1.00

ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44


Consensus pattern (79 bp):   
TTGGTTATTGTAGATCACTTATCTTTGATTCACATTAAGTTTTTGCTACTAATTGTTGGTTCCTC
AAGTAGGTCACGAG

Found at i:15567 original size:16 final size:15

Alignment explanation


    Indices: 15546--15588  Score: 68
    Period size: 16  Copynumber: 2.7  Consensus size: 15

      15536 TTACTTTGTT

                            
      15546 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                            
      15562 TTGTTTTTCTGTTTAA
          1 TTG-TTTTCTGTTTAA

                       
      15578 TTGTTTTCTGT
          1 TTGTTTTCTGT

      15589 CAACCTCTGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  15    8  0.31
  16   12  0.46
  17    6  0.23

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:15967 original size:31 final size:28

Alignment explanation


    Indices: 15929--15986  Score: 80
    Period size: 31  Copynumber: 2.0  Consensus size: 28

      15919 GCGTCGTTTT

                         *                 
      15929 GAAAAAAAAAATTGTTTTGTGTTTTTGCGTC
          1 GAAAAAAAAAA-TCTTTT-TG-TTTTGCGTC

                                       
      15960 GAAAAAAAAAATCTTTTTGTTTTGCGT
          1 GAAAAAAAAAATCTTTTTGTTTTGCGT

      15987 TTTTAATTTT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28    8  0.31
  29    2  0.08
  30    5  0.19
  31   11  0.42

ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41


Consensus pattern (28 bp):   
GAAAAAAAAAATCTTTTTGTTTTGCGTC
Done.