Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024579.1 Corchorus olitorius cultivar O-4 contig24612, 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: 9417
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30


Found at i:608 original size:15 final size:15

Alignment explanation


    Indices: 588--616  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

        578 GAATGATTTG

                           
        588 TATTTTAATTTCTTA
          1 TATTTTAATTTCTTA

                          
        603 TATTTTAATTTCTT
          1 TATTTTAATTTCTT

        617 CTAATTAATA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69


Consensus pattern (15 bp):   
TATTTTAATTTCTTA

Found at i:906 original size:24 final size:24

Alignment explanation


    Indices: 850--924  Score: 98
    Period size: 24  Copynumber: 3.1  Consensus size: 24

        840 ATAATTATAA

                  *               *  
        850 TTCTTTCAAATATTCTCTCTAAATT
          1 TTCTTTAAAATATTCTCTCT-ATTT

               *                    
        875 TTCATTAAAATATTCTCTCTATTT
          1 TTCTTTAAAATATTCTCTCTATTT

                                     
        899 TTCTTTAAAATA-TCTTCTCTATTT
          1 TTCTTTAAAATATTC-TCTCTATTT

              
        923 TT
          1 TT

        925 AATTGCTCAA


Statistics
Matches: 45,  Mismatches: 4, Indels: 3
        0.87            0.08        0.06

Matches are distributed among these distances:
  23    2  0.04
  24   25  0.56
  25   18  0.40

ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56


Consensus pattern (24 bp):   
TTCTTTAAAATATTCTCTCTATTT

Found at i:9384 original size:2 final size:2

Alignment explanation


    Indices: 9377--9410  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       9367 AAATAAAGGA

                                                              
       9377 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

       9411 TCGATTG


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):   
AT

Done.