Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018793.1 Corchorus olitorius cultivar O-4 contig18826, 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, 928

Length: 1547
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30


Found at i:754 original size:15 final size:15

Alignment explanation


    Indices: 734--764  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        724 AATAGTCCAA

                           
        734 AATGCAAACATGACT
          1 AATGCAAACATGACT

                           
        749 AATGCAAACATGACT
          1 AATGCAAACATGACT

             
        764 A
          1 A

        765 GTGTAAATAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19


Consensus pattern (15 bp):   
AATGCAAACATGACT

Found at i:959 original size:29 final size:28

Alignment explanation


    Indices: 916--1037  Score: 156
    Period size: 29  Copynumber: 4.2  Consensus size: 28

        906 GCTTAAAGTA

                                        
        916 AAAATGACCAAAATGCCCCTGGATGTGC
          1 AAAATGACCAAAATGCCCCTGGATGTGC

                                 *  *     
        944 ACAAATGACCAAAATGCCCCTAGAGGTGCC
          1 A-AAATGACCAAAATGCCCCTGGATGTG-C

             *        *                  
        974 AGAATGACCATAATGCCCCTGGA-GATGC
          1 AAAATGACCAAAATGCCCCTGGATG-TGC

                       *                 
       1002 GAAAATGACCATAATGCCCCTGGATGTGC
          1 -AAAATGACCAAAATGCCCCTGGATGTGC

                   
       1031 AAAATGA
          1 AAAATGA

       1038 TCACTTAAGA


Statistics
Matches: 83,  Mismatches: 6, Indels: 10
        0.84            0.06        0.10

Matches are distributed among these distances:
  28   10  0.12
  29   70  0.84
  30    3  0.04

ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGGATGTGC

Found at i:1390 original size:59 final size:59

Alignment explanation


    Indices: 1271--1546  Score: 511
    Period size: 59  Copynumber: 4.7  Consensus size: 59

       1261 GAAATATAGG

                                                                        
       1271 CTCTC-AACCAGAGACCTCGAACAGGATTTT-AAAACAAGATAAGATTTTGAATTGAAAA
          1 CTCTCTAA-CAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA

                                                                       
       1329 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
          1 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA

                              *                                        
       1388 CTCTCTAACAGAGACCTCAAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
          1 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA

                                                                       
       1447 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA
          1 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA

                              *                      
       1506 CTCTCTAACAGAGACCTCAAACAGGATTTTAAAAACAAGAT
          1 CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGAT

       1547 G


Statistics
Matches: 213,  Mismatches: 3, Indels: 3
        0.97            0.01        0.01

Matches are distributed among these distances:
  58   27  0.13
  59  186  0.87

ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25


Consensus pattern (59 bp):   
CTCTCTAACAGAGACCTCGAACAGGATTTTAAAAACAAGATAAGATTTTGAATTGAAAA

Done.