Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015934.1 Corchorus olitorius cultivar O-4 contig15967, 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: 7360
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:2056 original size:21 final size:20

Alignment explanation


    Indices: 2010--2080  Score: 67
    Period size: 21  Copynumber: 3.5  Consensus size: 20

       2000 AATTTCCTTA

                   *             
       2010 TTTCCTTCTTCTTCTTTTT-T
          1 TTTCCTTTTTCTT-TTTTTCT

                                  
       2030 TGTTCCTTTTTCTTTTCTTTCT
          1 T-TTCCTTTTTCTTTT-TTTCT

                        *       
       2052 TTTCC--TTTCTATTTTTCT
          1 TTTCCTTTTTCTTTTTTTCT

                       
       2070 TTTCCCTTTTT
          1 TTT-CCTTTTT

       2081 GGGCCAAGCC


Statistics
Matches: 43,  Mismatches: 2, Indels: 11
        0.77            0.04        0.20

Matches are distributed among these distances:
  18    8  0.19
  19    9  0.21
  20    3  0.07
  21   21  0.49
  22    2  0.05

ACGTcount: A:0.01, C:0.24, G:0.01, T:0.73


Consensus pattern (20 bp):   
TTTCCTTTTTCTTTTTTTCT

Found at i:3849 original size:32 final size:33

Alignment explanation


    Indices: 3797--3862  Score: 98
    Period size: 32  Copynumber: 2.0  Consensus size: 33

       3787 CTCCCCACTT

                          *              *   
       3797 TGTCCTCCTATTAATTGCTTCTTCAATCTGATC
          1 TGTCCTCCTATTAAATGCTTCTTCAATCTAATC

                  *                          
       3830 TGTCCTGCT-TTAAATGCTTCTTCAATCTAATC
          1 TGTCCTCCTATTAAATGCTTCTTCAATCTAATC

             
       3862 T
          1 T

       3863 CTCAGAAACT


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  32   22  0.73
  33    8  0.27

ACGTcount: A:0.20, C:0.26, G:0.09, T:0.45


Consensus pattern (33 bp):   
TGTCCTCCTATTAAATGCTTCTTCAATCTAATC

Found at i:5447 original size:45 final size:45

Alignment explanation


    Indices: 5395--5481  Score: 156
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       5385 TACCTAAATT

                           *                     *       
       5395 CTACTCCATCTCTAGGTAATTCATCAAAATAAAGCTATTATTCTA
          1 CTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA

                                                      
       5440 CTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT
          1 CTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATT

       5482 AATTGTTGTT


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  45   40  1.00

ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34


Consensus pattern (45 bp):   
CTACTCCATCTCTAGATAATTCATCAAAATAAAGCTAATATTCTA

Found at i:6609 original size:4 final size:4

Alignment explanation


    Indices: 6600--6636  Score: 74
    Period size: 4  Copynumber: 9.2  Consensus size: 4

       6590 GGGCTGGTTA

                                                          
       6600 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
          1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A

       6637 CCTTTTGGCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   33  1.00

ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24


Consensus pattern (4 bp):   
AAAT

Done.