Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015883.1 Corchorus olitorius cultivar O-4 contig15916, 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: 14244
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:2342 original size:19 final size:18

Alignment explanation


    Indices: 2309--2344  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2299 TTGAAATTAT

                              
       2309 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       2327 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       2345 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:7693 original size:19 final size:18

Alignment explanation


    Indices: 7660--7695  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       7650 TTGAAATTAT

                              
       7660 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       7678 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       7696 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:10350 original size:27 final size:27

Alignment explanation


    Indices: 10308--10381  Score: 69
    Period size: 28  Copynumber: 2.7  Consensus size: 27

      10298 TTCATTTTCA

                   *   *                
      10308 AAGGGTAGTTTTGTAATTTA-AAATCTC
          1 AAGGGTAATTTAGTAATTTACAAATC-C

                                  **    
      10335 AAGGGTAATTTAGTAACTTTACTCATCC
          1 AAGGGTAATTTAGTAA-TTTACAAATCC

                    **         
      10363 AAGGGTAAAATAGTAATTT
          1 AAGGGTAATTTAGTAATTT

      10382 CATTTTTTTA


Statistics
Matches: 39,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  27   17  0.44
  28   19  0.49
  29    3  0.08

ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36


Consensus pattern (27 bp):   
AAGGGTAATTTAGTAATTTACAAATCC

Found at i:10724 original size:22 final size:22

Alignment explanation


    Indices: 10696--10738  Score: 70
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      10686 CCCTTCACCC

                                   
      10696 TTTTTTTTTCTT-TTCTTTTCTG
          1 TTTTTTTTTCTTCTT-TTTTCTG

                                 
      10718 TTTTTTTTTCTTCTTTTTTCT
          1 TTTTTTTTTCTTCTTTTTTCT

      10739 CCTCCCCCCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  22   18  0.90
  23    2  0.10

ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84


Consensus pattern (22 bp):   
TTTTTTTTTCTTCTTTTTTCTG
Done.