Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001387.1 Corchorus capsularis cultivar CVL-1 contig01387, 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: 7296
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35


Found at i:1058 original size:12 final size:13

Alignment explanation


    Indices: 1029--1062  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       1019 AGTATATACC

                *        
       1029 AATTACTCTCTCT
          1 AATTTCTCTCTCT

                         
       1042 AATTTCTCTCT-T
          1 AATTTCTCTCTCT

                     
       1054 AATTTCTCT
          1 AATTTCTCT

       1063 TTTTTTTTGT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.21, C:0.26, G:0.00, T:0.53


Consensus pattern (13 bp):   
AATTTCTCTCTCT

Found at i:2692 original size:4 final size:4

Alignment explanation


    Indices: 2683--2717  Score: 70
    Period size: 4  Copynumber: 8.8  Consensus size: 4

       2673 ATGTGGTGAG

                                                       
       2683 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
          1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA

       2718 TATATATATA


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

Matches are distributed among these distances:
   4   31  1.00

ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26


Consensus pattern (4 bp):   
ATAC

Found at i:2722 original size:2 final size:2

Alignment explanation


    Indices: 2715--2756  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       2705 ACATACATAC

                                 *                                        
       2715 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2757 TCCATTGATT


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5850 original size:46 final size:46

Alignment explanation


    Indices: 5777--5866  Score: 126
    Period size: 46  Copynumber: 2.0  Consensus size: 46

       5767 TCAATCAATC

                  *     **        *              *        
       5777 ATTTGCGGATATTTACATTCCAGTTCATAGAGTCATAGTTGAGTTG
          1 ATTTGCCGATATCCACATTCCACTTCATAGAGTCATAATTGAGTTG

                                *                       
       5823 ATTTGCCGATATCCACATTCTACTTCATAGAGTCATAATTGAGT
          1 ATTTGCCGATATCCACATTCCACTTCATAGAGTCATAATTGAGT

       5867 CCCCAATGGG


Statistics
Matches: 38,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  46   38  1.00

ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38


Consensus pattern (46 bp):   
ATTTGCCGATATCCACATTCCACTTCATAGAGTCATAATTGAGTTG
Done.