Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001618.1 Corchorus olitorius cultivar O-4 contig01618, 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, 784

Length: 1307
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28


Found at i:55 original size:21 final size:21

Alignment explanation


    Indices: 31--91  Score: 122
    Period size: 21  Copynumber: 2.9  Consensus size: 21

         21 GAGCTCTCCT

                                 
         31 TCATGTCTCAACATATTCTTC
          1 TCATGTCTCAACATATTCTTC

                                 
         52 TCATGTCTCAACATATTCTTC
          1 TCATGTCTCAACATATTCTTC

                               
         73 TCATGTCTCAACATATTCT
          1 TCATGTCTCAACATATTCT

         92 CATTAGTTTT


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   40  1.00

ACGTcount: A:0.25, C:0.28, G:0.05, T:0.43


Consensus pattern (21 bp):   
TCATGTCTCAACATATTCTTC

Found at i:744 original size:24 final size:25

Alignment explanation


    Indices: 716--766  Score: 68
    Period size: 24  Copynumber: 2.1  Consensus size: 25

        706 AAAGAGTAAC

                       *  *          
        716 AATAAAATAAATAAGCAAGA-AAAT
          1 AATAAAATAAAGAACCAAGATAAAT

                    *                
        740 AATAAAATTAAGAACCAAGATAAAT
          1 AATAAAATAAAGAACCAAGATAAAT

              
        765 AA
          1 AA

        767 ATACTCCAAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  24   17  0.74
  25    6  0.26

ACGTcount: A:0.69, C:0.06, G:0.08, T:0.18


Consensus pattern (25 bp):   
AATAAAATAAAGAACCAAGATAAAT

Found at i:1243 original size:27 final size:27

Alignment explanation


    Indices: 1196--1249  Score: 74
    Period size: 28  Copynumber: 2.0  Consensus size: 27

       1186 AAATCAATTA

                                        
       1196 GAAATCATAAAAACATAAAGATAAATAT
          1 GAAATCATAAAAACA-AAAGATAAATAT

                            *          
       1224 GAAATCATAAAATAC-CAAGATAAATA
          1 GAAATCATAAAA-ACAAAAGATAAATA

       1250 ATCAGGTTAA


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

Matches are distributed among these distances:
  27   10  0.42
  28   12  0.50
  29    2  0.08

ACGTcount: A:0.63, C:0.09, G:0.07, T:0.20


Consensus pattern (27 bp):   
GAAATCATAAAAACAAAAGATAAATAT
Done.