Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001431.1 Corchorus capsularis cultivar CVL-1 contig01431, 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, 622

Length: 1037
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41


Found at i:292 original size:58 final size:58

Alignment explanation


    Indices: 229--339  Score: 213
    Period size: 58  Copynumber: 1.9  Consensus size: 58

        219 TGGAAACATT

                                                                      
        229 TTGCAGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTG
          1 TTGCAGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTG

                               *                                 
        287 TTGCAGAGATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
          1 TTGCAGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTC

        340 AACTTTGCAG


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  58   52  1.00

ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38


Consensus pattern (58 bp):   
TTGCAGAGATTCCCTCCATAATGAGGATAACTTTGCAGAGCATTATTTTCTTCTTTTG

Found at i:349 original size:25 final size:25

Alignment explanation


    Indices: 315--370  Score: 112
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        305 TGATGAGGAT

                                     
        315 AACTTTGCAGAGCATTATTTTCTTC
          1 AACTTTGCAGAGCATTATTTTCTTC

                                     
        340 AACTTTGCAGAGCATTATTTTCTTC
          1 AACTTTGCAGAGCATTATTTTCTTC

                  
        365 AACTTT
          1 AACTTT

        371 TGACTTTTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   31  1.00

ACGTcount: A:0.25, C:0.20, G:0.11, T:0.45


Consensus pattern (25 bp):   
AACTTTGCAGAGCATTATTTTCTTC

Found at i:729 original size:74 final size:74

Alignment explanation


    Indices: 606--754  Score: 253
    Period size: 74  Copynumber: 2.0  Consensus size: 74

        596 AATCCATTGA

                                          *             *                    
        606 ACTTAGCATTTCTGCCATAAGCTTCTCATAGTCTTTCTTAGTTTTTGCTTGTGCCAATATAGTAC
          1 ACTTAGCATTTCTGCCATAAGCTTCTCATACTCTTTCTTAGTTTGTGCTTGTGCCAATATAGTAC

                     
        671 TAGCATTAG
         66 TAGCATTAG

                                      *            *                *        
        680 ACTTAGCATTTCTGCCATAAGCTTCTTATACTCTTTCTTGGTTTGTGCTTGTGCCAGTATAGTAC
          1 ACTTAGCATTTCTGCCATAAGCTTCTCATACTCTTTCTTAGTTTGTGCTTGTGCCAATATAGTAC

                     
        745 TAGCATTAG
         66 TAGCATTAG

             
        754 A
          1 A

        755 TTTTGCTTGT


Statistics
Matches: 70,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  74   70  1.00

ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42


Consensus pattern (74 bp):   
ACTTAGCATTTCTGCCATAAGCTTCTCATACTCTTTCTTAGTTTGTGCTTGTGCCAATATAGTAC
TAGCATTAG
Done.