Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009606.1 Corchorus olitorius cultivar O-4 contig09638, 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: 8916
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:728 original size:25 final size:24

Alignment explanation


    Indices: 680--748  Score: 111
    Period size: 25  Copynumber: 2.8  Consensus size: 24

        670 GTGGGTGTAC

                   *                
        680 ATGTTTATGGTATACCTTTGATGG
          1 ATGTTTACGGTATACCTTTGATGG

                                     
        704 ATGTTTACGGTATACCCTTTGATGG
          1 ATGTTTACGGTATA-CCTTTGATGG

            *                   
        729 GTGTTTACGGTATACCTTTG
          1 ATGTTTACGGTATACCTTTG

        749 GTTGGTATTC


Statistics
Matches: 42,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  24   19  0.45
  25   23  0.55

ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43


Consensus pattern (24 bp):   
ATGTTTACGGTATACCTTTGATGG

Found at i:6020 original size:18 final size:18

Alignment explanation


    Indices: 5997--6031  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       5987 TGTACATGTG

                   *   *      
       5997 TATATATGTATCTTGTCC
          1 TATATATATATATTGTCC

                             
       6015 TATATATATATATTGTC
          1 TATATATATATATTGTC

       6032 AAATAAAAAG


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51


Consensus pattern (18 bp):   
TATATATATATATTGTCC

Found at i:7176 original size:26 final size:26

Alignment explanation


    Indices: 7147--7198  Score: 79
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       7137 TCTGCGTAGG

                                       
       7147 TTTTTATATTTATT-TCAATAGTCGCA
          1 TTTTTATATTTATTAT-AATAGTCGCA

                   *                  
       7173 TTTTTATTTTTATTATAATAGTCGCA
          1 TTTTTATATTTATTATAATAGTCGCA

       7199 AAAAAAATTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  26   23  0.96
  27    1  0.04

ACGTcount: A:0.27, C:0.10, G:0.08, T:0.56


Consensus pattern (26 bp):   
TTTTTATATTTATTATAATAGTCGCA
Done.