Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006780.1 Corchorus olitorius cultivar O-4 contig06805, 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, 916

Length: 1527
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38


Found at i:587 original size:18 final size:20

Alignment explanation


    Indices: 567--604  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        557 AAGGGTAATT

                     *          
        567 AAAA-AAAATTGTTTTCATA
          1 AAAAGAAAAGTGTTTTCATA

                               
        586 AAAAGAAAAGTGTTTTCAT
          1 AAAAGAAAAGTGTTTTCAT

        605 GATAAAGGAG


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    4  0.24
  20   13  0.76

ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34


Consensus pattern (20 bp):   
AAAAGAAAAGTGTTTTCATA

Found at i:611 original size:21 final size:20

Alignment explanation


    Indices: 566--611  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        556 AAAGGGTAAT

                *    *          
        566 TAAAAAAAATTGTTTTCATA
          1 TAAAGAAAAGTGTTTTCATA

            *                    
        586 AAAAGAAAAGTGTTTTCATGA
          1 TAAAGAAAAGTGTTTTCAT-A

                 
        607 TAAAG
          1 TAAAG

        612 GAGAAGAGGT


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

Matches are distributed among these distances:
  20   16  0.76
  21    5  0.24

ACGTcount: A:0.50, C:0.04, G:0.13, T:0.33


Consensus pattern (20 bp):   
TAAAGAAAAGTGTTTTCATA

Found at i:1477 original size:18 final size:19

Alignment explanation


    Indices: 1444--1479  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       1434 TGAAGATTTA

                               
       1444 TTGAAGACAAATTGAAGAT
          1 TTGAAGACAAATTGAAGAT

                     *        
       1463 TTGAAGAC-CATTGAAGA
          1 TTGAAGACAAATTGAAGA

       1480 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.44, C:0.08, G:0.22, T:0.25


Consensus pattern (19 bp):   
TTGAAGACAAATTGAAGAT
Done.