Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006323.1 Corchorus olitorius cultivar O-4 contig06348, 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, 658

Length: 1098
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33


Found at i:286 original size:6 final size:6

Alignment explanation


    Indices: 267--351  Score: 52
    Period size: 6  Copynumber: 14.0  Consensus size: 6

        257 CCTTATTTCC

                   *                                * *   *        
        267 TTTCTT CTTCTT TTT-TT TTTCTT TTTCTT TTTC-C ATTCAT TTT-TT
          1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT

              *                                           
        312 TTCCTTT TTTCCCTT TTTCCTT TTTCCTT TTT-TT TTTCTT
          1 TTTC-TT TTT--CTT TTT-CTT TTT-CTT TTTCTT TTTCTT

        352 CTTACCGCTG


Statistics
Matches: 63,  Mismatches: 9, Indels: 14
        0.73            0.10        0.16

Matches are distributed among these distances:
   5   16  0.25
   6   23  0.37
   7   18  0.29
   8    5  0.08
   9    1  0.02

ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76


Consensus pattern (6 bp):   
TTTCTT

Found at i:321 original size:8 final size:8

Alignment explanation


    Indices: 308--344  Score: 58
    Period size: 8  Copynumber: 4.8  Consensus size: 8

        298 TCCATTCATT

                    
        308 TTTTTTCC
          1 TTTTTTCC

                    
        316 TTTTTTCC
          1 TTTTTTCC

            *       
        324 CTTTTTCC
          1 TTTTTTCC

                    
        332 -TTTTTCC
          1 TTTTTTCC

                  
        339 TTTTTT
          1 TTTTTT

        345 TTTTCTTCTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
   7    7  0.26
   8   20  0.74

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (8 bp):   
TTTTTTCC

Found at i:321 original size:23 final size:22

Alignment explanation


    Indices: 282--344  Score: 69
    Period size: 23  Copynumber: 2.9  Consensus size: 22

        272 TCTTCTTTTT

                                  
        282 TTTTTCTTTTT-C-TTTTTCCA
          1 TTTTTCTTTTTCCTTTTTTCCA

                                   *
        302 TTCATTT-TTTTTCCTTTTTTCCC
          1 TT--TTTCTTTTTCCTTTTTTCCA

                                
        325 TTTTTCCTTTTTCCTTTTTT
          1 TTTTT-CTTTTTCCTTTTTT

        345 TTTTCTTCTT


Statistics
Matches: 36,  Mismatches: 1, Indels: 9
        0.78            0.02        0.20

Matches are distributed among these distances:
  20    2  0.06
  21    8  0.22
  22    4  0.11
  23   22  0.61

ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75


Consensus pattern (22 bp):   
TTTTTCTTTTTCCTTTTTTCCA

Found at i:464 original size:29 final size:29

Alignment explanation


    Indices: 432--488  Score: 87
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        422 CTGGGCCGCG

                            *            
        432 CGCTGGCCTGCCAATGTGCAGGCCCAGCA
          1 CGCTGGCCTGCCAATGCGCAGGCCCAGCA

                        **              
        461 CGCTGGCCTGCCTGTGCGCAGGCCCAGC
          1 CGCTGGCCTGCCAATGCGCAGGCCCAGC

        489 GGCCTGCTGG


Statistics
Matches: 25,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.12, C:0.40, G:0.33, T:0.14


Consensus pattern (29 bp):   
CGCTGGCCTGCCAATGCGCAGGCCCAGCA
Done.