Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012191.1 Corchorus olitorius cultivar O-4 contig12224, 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: 17393
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32


Found at i:6500 original size:10 final size:10

Alignment explanation


    Indices: 6485--6509  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       6475 CCTTTCTCAA

                      
       6485 GAACACTTAT
          1 GAACACTTAT

                      
       6495 GAACACTTAT
          1 GAACACTTAT

                 
       6505 GAACA
          1 GAACA

       6510 AAACCCACCC


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24


Consensus pattern (10 bp):   
GAACACTTAT

Found at i:7016 original size:22 final size:21

Alignment explanation


    Indices: 6991--7033  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       6981 TCAAGAGTGA

                 *                
       6991 TTTTGGCTGTGTTTGTCTTTTT
          1 TTTTGACTGTGTTTGT-TTTTT

                    *            
       7013 TTTTGACTTTGTTTGTTTTTT
          1 TTTTGACTGTGTTTGTTTTTT

       7034 GGTTCAATTT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21    5  0.26
  22   14  0.74

ACGTcount: A:0.02, C:0.07, G:0.19, T:0.72


Consensus pattern (21 bp):   
TTTTGACTGTGTTTGTTTTTT

Found at i:7372 original size:10 final size:10

Alignment explanation


    Indices: 7353--7395  Score: 52
    Period size: 10  Copynumber: 4.4  Consensus size: 10

       7343 ATGTTCTGAC

                 *    
       7353 TTTTGCTTTT
          1 TTTTGTTTTT

                 *    
       7363 TTTT-CTTTT
          1 TTTTGTTTTT

                     *
       7372 TTTTGTTTTG
          1 TTTTGTTTTT

                      
       7382 TTTTGTTTTT
          1 TTTTGTTTTT

                
       7392 TTTT
          1 TTTT

       7396 TAATTTTTCC


Statistics
Matches: 29,  Mismatches: 3, Indels: 2
        0.85            0.09        0.06

Matches are distributed among these distances:
   9    9  0.31
  10   20  0.69

ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86


Consensus pattern (10 bp):   
TTTTGTTTTT

Found at i:7375 original size:19 final size:19

Alignment explanation


    Indices: 7353--7394  Score: 59
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       7343 ATGTTCTGAC

                                
       7353 TTTTGCTTTT-TTTTCTTTT
          1 TTTTG-TTTTGTTTTCTTTT

                          *    
       7372 TTTTGTTTTGTTTTGTTTT
          1 TTTTGTTTTGTTTTCTTTT

                
       7391 TTTT
          1 TTTT

       7395 TTAATTTTTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    4  0.19
  19   17  0.81

ACGTcount: A:0.00, C:0.05, G:0.10, T:0.86


Consensus pattern (19 bp):   
TTTTGTTTTGTTTTCTTTT
Done.