Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021540.1 Corchorus olitorius cultivar O-4 contig21573, 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: 8689
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:383 original size:11 final size:12

Alignment explanation


    Indices: 354--387  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

        344 TAATATAATT

                 *      
        354 TAATTCTTAAAA
          1 TAATTATTAAAA

                        
        366 TAATTATTAAAA
          1 TAATTATTAAAA

                       
        378 -AATTATTAAA
          1 TAATTATTAAA

        388 CGGGTTTTTG


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11   10  0.48
  12   11  0.52

ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41


Consensus pattern (12 bp):   
TAATTATTAAAA

Found at i:1732 original size:2 final size:2

Alignment explanation


    Indices: 1725--1757  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1715 AGACAGTAAA

                                                             
       1725 AT 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 AT A

       1758 GAAGTTATTT


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

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4663 original size:37 final size:37

Alignment explanation


    Indices: 4608--4678  Score: 115
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       4598 TTTACCTACT

                                     *           
       4608 ACTCCCTCCGTCCCATATTATCTGTTCCTTTTGGATC
          1 ACTCCCTCCGTCCCATATTATCTGTACCTTTTGGATC

                   *     *                    
       4645 ACTCCCTTCGTCCTATATTATCTGTACCTTTTGG
          1 ACTCCCTCCGTCCCATATTATCTGTACCTTTTGG

       4679 GTCAAAGTTT


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  37   31  1.00

ACGTcount: A:0.14, C:0.32, G:0.11, T:0.42


Consensus pattern (37 bp):   
ACTCCCTCCGTCCCATATTATCTGTACCTTTTGGATC

Found at i:7575 original size:2 final size:2

Alignment explanation


    Indices: 7568--7601  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       7558 ATATAGTCTT

                                        *                     
       7568 TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       7602 CATGAAATGC


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.