Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014395.1 Corchorus capsularis cultivar CVL-1 contig14416, 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: 7627
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:519 original size:29 final size:28

Alignment explanation


    Indices: 466--520  Score: 83
    Period size: 29  Copynumber: 1.9  Consensus size: 28

        456 CCGAATTAGT

                                        
        466 GATGGAAATATCATTAAAAACTTTTTAC
          1 GATGGAAATATCATTAAAAACTTTTTAC

                              *  *     
        494 GATGGAAATATTCATTAATAATTTTTT
          1 GATGGAAATA-TCATTAAAAACTTTTT

        521 CTCAACAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  28   10  0.42
  29   14  0.58

ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42


Consensus pattern (28 bp):   
GATGGAAATATCATTAAAAACTTTTTAC

Found at i:6374 original size:3 final size:3

Alignment explanation


    Indices: 6366--6403  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

       6356 TACCTTTCCT

                                                              
       6366 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT

       6404 CTTTGAAGAA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:7533 original size:2 final size:2

Alignment explanation


    Indices: 7522--7566  Score: 76
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       7512 AGGAGAATTG

                                                                          
       7522 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                   
       7562 TA TA T
          1 TA TA T

       7567 GCTTCCTTGT


Statistics
Matches: 41,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   39  0.95

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


Consensus pattern (2 bp):   
TA

Done.