Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019455.1 Corchorus olitorius cultivar O-4 contig19488, 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: 8518
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38


Found at i:97 original size:33 final size:33

Alignment explanation


    Indices: 60--165  Score: 117
    Period size: 33  Copynumber: 3.2  Consensus size: 33

         50 TCATGGCTCA

                                          *  
         60 GTCGCGACCGGATCGCGACTTGACCATGGCCTG
          1 GTCGCGACCGGATCGCGACTTGACCATGGCATG

                      *            *         
         93 GTCGCGACCGTATCGCGACTTGATCATGGCATG
          1 GTCGCGACCGGATCGCGACTTGACCATGGCATG

                        *     *  * *           
        126 GTCGCG-CGCGGGTCGCGTCTGGGCCATGGTCA-G
          1 GTCGCGAC-CGGATCGCGACTTGACCATGG-CATG

                   
        159 GTCGCGA
          1 GTCGCGA

        166 TTCGGTCGTG


Statistics
Matches: 61,  Mismatches: 9, Indels: 5
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.95
  34    2  0.03

ACGTcount: A:0.13, C:0.30, G:0.37, T:0.20


Consensus pattern (33 bp):   
GTCGCGACCGGATCGCGACTTGACCATGGCATG

Found at i:4647 original size:2 final size:2

Alignment explanation


    Indices: 4640--4673  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       4630 GATATGCTAC

                                                              
       4640 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4674 CTCCCCCTGT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:7627 original size:36 final size:36

Alignment explanation


    Indices: 7580--7649  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       7570 TTCAATAACC

                  *      *                       
       7580 TTACATCTTTTGTGATTTT-AGTTATCATATTTCTTA
          1 TTACATATTTTGTAATTTTGA-TTATCATATTTCTTA

                                              
       7616 TTACATATTTTGTAATTTTGATTATCATATTTCT
          1 TTACATATTTTGTAATTTTGATTATCATATTTCT

       7650 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  36   30  0.97
  37    1  0.03

ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59


Consensus pattern (36 bp):   
TTACATATTTTGTAATTTTGATTATCATATTTCTTA
Done.