Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008688.1 Corchorus olitorius cultivar O-4 contig08715, 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: 4576
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43


Found at i:117 original size:41 final size:41

Alignment explanation


    Indices: 64--148  Score: 120
    Period size: 41  Copynumber: 2.1  Consensus size: 41

         54 GTTCATGTTT

                                               *       
         64 TTTCTTTTTATCTCACCTAGGGTTTA-ATGTGTTTTTTGAGGG
          1 TTTCTTTTTATCTCACCTAGGGTTTATAT-TGTTTGTT-AGGG

                            *                        
        106 TTTC-TTTTATCTCACTTAGGGTTTATATTGTTTGTTAGGG
          1 TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG

               
        146 TTT
          1 TTT

        149 GACTTTCATG


Statistics
Matches: 40,  Mismatches: 2, Indels: 4
        0.87            0.04        0.09

Matches are distributed among these distances:
  40    7  0.17
  41   27  0.68
  42    6  0.15

ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55


Consensus pattern (41 bp):   
TTTCTTTTTATCTCACCTAGGGTTTATATTGTTTGTTAGGG

Found at i:806 original size:29 final size:29

Alignment explanation


    Indices: 774--835  Score: 124
    Period size: 29  Copynumber: 2.1  Consensus size: 29

        764 TTTCCTTGAG

                                         
        774 TTGTCTCTGATTACTTTTCCTCACTTTAT
          1 TTGTCTCTGATTACTTTTCCTCACTTTAT

                                         
        803 TTGTCTCTGATTACTTTTCCTCACTTTAT
          1 TTGTCTCTGATTACTTTTCCTCACTTTAT

                
        832 TTGT
          1 TTGT

        836 TTCCTATCAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.13, C:0.23, G:0.08, T:0.56


Consensus pattern (29 bp):   
TTGTCTCTGATTACTTTTCCTCACTTTAT

Found at i:1411 original size:14 final size:13

Alignment explanation


    Indices: 1392--1421  Score: 51
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       1382 AGACTACATG

                          
       1392 TTTCTTTTCTTTTT
          1 TTTCTTTT-TTTTT

                         
       1406 TTTCTTTTTTTTT
          1 TTTCTTTTTTTTT

               
       1419 TTT
          1 TTT

       1422 ATCTCAGGTG


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    8  0.50
  14    8  0.50

ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90


Consensus pattern (13 bp):   
TTTCTTTTTTTTT
Done.