Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016587.1 Corchorus olitorius cultivar O-4 contig16620, 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: 22861
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32


Found at i:7813 original size:19 final size:21

Alignment explanation


    Indices: 7777--7815  Score: 64
    Period size: 19  Copynumber: 2.0  Consensus size: 21

       7767 TTGAAATTCT

                                 
       7777 TCTTCAATATTGGTCTTCAAA
          1 TCTTCAATATTGGTCTTCAAA

                                
       7798 TCTTCAA-ATT-GTCTTCAA
          1 TCTTCAATATTGGTCTTCAA

       7816 TAAGTCTTCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19    8  0.44
  20    3  0.17
  21    7  0.39

ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44


Consensus pattern (21 bp):   
TCTTCAATATTGGTCTTCAAA

Found at i:17739 original size:19 final size:18

Alignment explanation


    Indices: 17715--17753  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      17705 AAATATCTCC

                  *            
      17715 AATTAGGGCTAATTGCACA
          1 AATTAGAGC-AATTGCACA

                   *          
      17734 AATTAGATCAATTGCACA
          1 AATTAGAGCAATTGCACA

              
      17752 AA
          1 AA

      17754 AAATAAGAAC


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  18   11  0.61
  19    7  0.39

ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26


Consensus pattern (18 bp):   
AATTAGAGCAATTGCACA

Found at i:21478 original size:32 final size:32

Alignment explanation


    Indices: 21431--21576  Score: 229
    Period size: 32  Copynumber: 4.5  Consensus size: 32

      21421 TAAAAGCAAT

                                ** *          
      21431 TAAATATAGCGGCGTTTTGTAATGTAGACGCCGC
          1 TAAATA-AG-GGCGTTTTGTTCTATAGACGCCGC

                                 *          
      21465 TAAATAAGGGCGTTTTGTTCTGTAGACGCCGC
          1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC

                                            
      21497 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC
          1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC

                                         *  
      21529 TAAATAAGGGCGTTTTGTTCTATAGACGCAGC
          1 TAAATAAGGGCGTTTTGTTCTATAGACGCCGC

                            
      21561 TAAATAAGGGCGTTTT
          1 TAAATAAGGGCGTTTT

      21577 CTTTTCACAC


Statistics
Matches: 108,  Mismatches: 4, Indels: 2
        0.95            0.04        0.02

Matches are distributed among these distances:
  32  100  0.93
  33    2  0.02
  34    6  0.06

ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32


Consensus pattern (32 bp):   
TAAATAAGGGCGTTTTGTTCTATAGACGCCGC

Done.