Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022848.1 Corchorus olitorius cultivar O-4 contig22881, 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: 9169
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33


Found at i:205 original size:6 final size:6

Alignment explanation


    Indices: 194--235  Score: 68
    Period size: 6  Copynumber: 7.0  Consensus size: 6

        184 TCAGCTACCA

                                                             
        194 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTTT GTTTTT -TTTTT
          1 GTTTTT GTTTTT GTTTTT GTTTTT G-TTTTT GTTTTT GTTTTT

        236 ACGAAAGCTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
   5    5  0.14
   6   24  0.69
   7    6  0.17

ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86


Consensus pattern (6 bp):   
GTTTTT

Found at i:1320 original size:2 final size:2

Alignment explanation


    Indices: 1313--1348  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1303 TAAGATAGTA

                                                                 
       1313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1349 GAAATTAAAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:7168 original size:19 final size:17

Alignment explanation


    Indices: 7144--7190  Score: 58
    Period size: 19  Copynumber: 2.6  Consensus size: 17

       7134 GCCTCACTTA

                              
       7144 TTTCCCCTCTTTTCTCAT
          1 TTTCCCCTCTTTTC-CAT

                   *       *  
       7162 CTTTCCCTTCTTTTCGAT
          1 -TTTCCCCTCTTTTCCAT

                       
       7180 TTTCCCCTCTT
          1 TTTCCCCTCTT

       7191 CTGTTCCCAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  17   10  0.40
  18    2  0.08
  19   13  0.52

ACGTcount: A:0.04, C:0.38, G:0.02, T:0.55


Consensus pattern (17 bp):   
TTTCCCCTCTTTTCCAT
Done.