Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014677.1 Corchorus olitorius cultivar O-4 contig14710, 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: 10360
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39


Found at i:612 original size:21 final size:22

Alignment explanation


    Indices: 588--635  Score: 64
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        578 TTGATTTAAC

                       *           
        588 TTATTTTGTTCTTAA-A-TAATT
          1 TTATTTT-TTCCTAATATTAATT

                                  
        609 TTATTTTTTCCTAATATTAATT
          1 TTATTTTTTCCTAATATTAATT

                 
        631 TTATT
          1 TTATT

        636 GGAAATTGAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  20    6  0.25
  21    8  0.33
  22   10  0.42

ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65


Consensus pattern (22 bp):   
TTATTTTTTCCTAATATTAATT

Found at i:8351 original size:98 final size:95

Alignment explanation


    Indices: 8242--8417  Score: 289
    Period size: 98  Copynumber: 1.8  Consensus size: 95

       8232 ACTTAACTAT

                                                         *                   
       8242 TATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTTAATATCTTTATAACTACTT
          1 TATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATAT-TTTATAACTA-TT

                                             
       8307 TATTTTTACCATTTTACTATTTTTTTCAAAATA
         64 T-TTTTTACCATTTTACTATTTTTTTCAAAATA

                                               *    *                 *      
       8340 TATAGTTTTATTCTACTAAAAACTCTATTTTCATTTAATTGAATTCAATATTTTATAATTATTTT
          1 TATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATTTTATAACTATTTT

                         
       8405 TTTTACCATTTTA
         66 TTTTACCATTTTA

       8418 ATTTAAAAAG


Statistics
Matches: 74,  Mismatches: 4, Indels: 3
        0.91            0.05        0.04

Matches are distributed among these distances:
  95   14  0.19
  96    3  0.04
  97    9  0.12
  98   48  0.65

ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53


Consensus pattern (95 bp):   
TATAGTTTTATTCTACTAAAAACTCTATTTTCATTCAATTAAATTCAATATTTTATAACTATTTT
TTTTACCATTTTACTATTTTTTTCAAAATA

Found at i:10150 original size:2 final size:2

Alignment explanation


    Indices: 10138--10198  Score: 88
    Period size: 2  Copynumber: 30.5  Consensus size: 2

      10128 CGGTTTTTAA

                                                         *                
      10138 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                     *                   
      10179 AT AT AT CT AT AT ACT AT AT A
          1 AT AT AT AT AT AT A-T AT AT A

      10199 AGTCTAAACT


Statistics
Matches: 53,  Mismatches: 4, Indels: 4
        0.87            0.07        0.07

Matches are distributed among these distances:
   1    1  0.02
   2   50  0.94
   3    2  0.04

ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.