Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006079.1 Corchorus olitorius cultivar O-4 contig06104, 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, 654

Length: 1091
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40


Found at i:887 original size:125 final size:124

Alignment explanation


    Indices: 662--899  Score: 329
    Period size: 125  Copynumber: 1.9  Consensus size: 124

        652 CTTATTTTTC

                              *                                              
        662 AAATATATTTCTTAAATGCCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
          1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACT-AATTAAAAACTCTATTTTT

                                                *     *                 
        727 ATTTAATCAAATCTAATATATTTATAACTATTTTATTTTTACTATTTTACTATTTTAATT
         65 ATTTAATCAAATCTAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT

                                                  *        *         *       
        787 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTA-T-TTTACCAAAATTCTATTT
          1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTAATTA--AAAACTCTATTT

                     *          * *                            
        850 TTATTTAATTAAAT-TCAATTTTTTTATAACTATTTTATCTTTACCATTTT
         63 TTATTTAATCAAATCT-AATATATTTATAACTATTTTATCTTTACCATTTT

        900 TTTAGGGAAT


Statistics
Matches: 100,  Mismatches: 9, Indels: 8
        0.85            0.08        0.07

Matches are distributed among these distances:
 123    3  0.03
 124    1  0.01
 125   77  0.77
 126   19  0.19

ACGTcount: A:0.35, C:0.11, G:0.01, T:0.53


Consensus pattern (124 bp):   
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTAATTAAAAACTCTATTTTTA
TTTAATCAAATCTAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT

Found at i:963 original size:104 final size:103

Alignment explanation


    Indices: 834--1041  Score: 371
    Period size: 104  Copynumber: 2.0  Consensus size: 103

        824 AGTTTTATTT

                                                                   *         
        834 TACCAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTATAACTATTTTATCTTTACCATTT
          1 TACCAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTATAACTATTTTATCCTTACCATTT

                       *                          
        899 TTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
         66 TTTTAGGGAATCATCTTTACCATTTTAATTTTAAAAGA

                                       **                                    
        937 TACCAAAAATTCTATTTTTATTTAATTCGATTCAATTTTTTTATAACTATTTTATCCTTACCATT
          1 TACC-AAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTATAACTATTTTATCCTTACCATT

                                                   
       1002 TTTTTAGGGAATCATCTTTACCATTTTAATTTTAAAAGA
         65 TTTTTAGGGAATCATCTTTACCATTTTAATTTTAAAAGA

             
       1041 T
          1 T

       1042 GAGTTATTAT


Statistics
Matches: 100,  Mismatches: 4, Indels: 1
        0.95            0.04        0.01

Matches are distributed among these distances:
 103    4  0.04
 104   96  0.96

ACGTcount: A:0.32, C:0.12, G:0.04, T:0.51


Consensus pattern (103 bp):   
TACCAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTATAACTATTTTATCCTTACCATTT
TTTTAGGGAATCATCTTTACCATTTTAATTTTAAAAGA
Done.