Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000677.1 Corchorus capsularis cultivar CVL-1 contig00677, 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: 8161
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:4705 original size:2 final size:2

Alignment explanation


    Indices: 4698--4728  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       4688 CATTCGTGAC

                                                          
       4698 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4729 CATAAGATGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:5058 original size:21 final size:19

Alignment explanation


    Indices: 5014--5060  Score: 58
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       5004 AAGATTTGCA

                 *           * 
       5014 TTCCTTAAAAATATTTCTT
          1 TTCCTCAAAAATATTTCAT

                                 
       5033 TTCCTCAAAAATATTTAACAT
          1 TTCCTCAAAAATATTT--CAT

                   
       5054 TTCCTCA
          1 TTCCTCA

       5061 GCTTCTCCTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  19   15  0.62
  21    9  0.38

ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45


Consensus pattern (19 bp):   
TTCCTCAAAAATATTTCAT

Found at i:7645 original size:19 final size:19

Alignment explanation


    Indices: 7606--7645  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       7596 AATTGAGTTT

                       **   *  
       7606 TTTGAGTCAGTTTGTTGAG
          1 TTTGAGTCAGTCAGTTCAG

                               
       7625 TTTGAGTCAGTCAGTTCAG
          1 TTTGAGTCAGTCAGTTCAG

              
       7644 TT
          1 TT

       7646 AGTCACACTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.17, C:0.10, G:0.28, T:0.45


Consensus pattern (19 bp):   
TTTGAGTCAGTCAGTTCAG
Done.