Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024470.1 Corchorus olitorius cultivar O-4 contig24503, 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: 1806
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35


Found at i:1130 original size:30 final size:30

Alignment explanation


    Indices: 1090--1161  Score: 135
    Period size: 30  Copynumber: 2.4  Consensus size: 30

       1080 CAGTTGGCCA

                 *                        
       1090 CGGGCCTTGCCACGGTTTTAGAGTTTTCAG
          1 CGGGCTTTGCCACGGTTTTAGAGTTTTCAG

                                          
       1120 CGGGCTTTGCCACGGTTTTAGAGTTTTCAG
          1 CGGGCTTTGCCACGGTTTTAGAGTTTTCAG

                        
       1150 CGGGCTTTGCCA
          1 CGGGCTTTGCCA

       1162 TGGATAATTT


Statistics
Matches: 41,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  30   41  1.00

ACGTcount: A:0.12, C:0.24, G:0.31, T:0.33


Consensus pattern (30 bp):   
CGGGCTTTGCCACGGTTTTAGAGTTTTCAG

Found at i:1577 original size:23 final size:23

Alignment explanation


    Indices: 1547--1592  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1537 GATTATTCTG

                                   
       1547 TTAAATTTCCTTTCACTCTCTCT
          1 TTAAATTTCCTTTCACTCTCTCT

                                   
       1570 TTAAATTTCCTTTCACTCTCTCT
          1 TTAAATTTCCTTTCACTCTCTCT

       1593 GAAAAATTAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.17, C:0.30, G:0.00, T:0.52


Consensus pattern (23 bp):   
TTAAATTTCCTTTCACTCTCTCT

Found at i:1607 original size:24 final size:23

Alignment explanation


    Indices: 1549--1600  Score: 77
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       1539 TTATTCTGTT

                                 **
       1549 AAATTTCCTTTCACTCTCTCTTT
          1 AAATTTCCTTTCACTCTCTCTAA

                                    
       1572 AAATTTCCTTTCACTCTCTCTGAA
          1 AAATTTCCTTTCACTCTCTCT-AA

                 
       1596 AAATT
          1 AAATT

       1601 ATCTTTCCTT


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  23   21  0.81
  24    5  0.19

ACGTcount: A:0.25, C:0.27, G:0.02, T:0.46


Consensus pattern (23 bp):   
AAATTTCCTTTCACTCTCTCTAA
Done.