Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009733.1 Corchorus olitorius cultivar O-4 contig09765, 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: 1803
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39


Found at i:693 original size:123 final size:127

Alignment explanation


    Indices: 555--809  Score: 392
    Period size: 131  Copynumber: 2.0  Consensus size: 127

        545 CATTGTTTAA

                   *                                  *  *                   
        555 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTATTTGAATCTAATAT-CTT-T-AT
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAT

                     *      *                                             
        617 A-ATTTTTACCATTTTTCTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATAT
         66 ATATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATAT

                                                                             
        678 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACA
          1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATA-A

                                                                    *        
        743 TATTTTATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
         65 TA---TATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATA

             
        808 T
        127 T

             
        809 A
          1 A

        810 TTTCTTAAAT


Statistics
Matches: 118,  Mismatches: 6, Indels: 8
        0.89            0.05        0.06

Matches are distributed among these distances:
 123   53  0.45
 124    3  0.03
 125    1  0.01
 127    3  0.03
 131   58  0.49

ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50


Consensus pattern (127 bp):   
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAAT
ATATTTTTAACATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTATTTAAATAT

Found at i:831 original size:14 final size:13

Alignment explanation


    Indices: 795--833  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        785 TATATATTAG

                         
        795 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
        808 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
        822 AATTTTTTAAAT
          1 AATTTTTTAAAT

        834 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA

Found at i:1099 original size:15 final size:15

Alignment explanation


    Indices: 1053--1100  Score: 53
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       1043 TTCATCATTT

                            
       1053 TTTAAAA-CTAATTAA
          1 TTTAAAATCTAATT-A

                     *  *   
       1068 GTTTAAAATTTATTTA
          1 -TTTAAAATCTAATTA

                           
       1084 TTTAAAATCTAATTA
          1 TTTAAAATCTAATTA

              
       1099 TT
          1 TT

       1101 GTGATTAACC


Statistics
Matches: 27,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  15   15  0.56
  16    8  0.30
  17    4  0.15

ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50


Consensus pattern (15 bp):   
TTTAAAATCTAATTA
Done.