Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023817.1 Corchorus olitorius cultivar O-4 contig23850, 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: 8622
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36


Found at i:211 original size:31 final size:31

Alignment explanation


    Indices: 176--259  Score: 84
    Period size: 29  Copynumber: 2.8  Consensus size: 31

        166 GGATGGACTT

                                  *        
        176 ATTTGAGATTTTTCGCAAAGTTGGGGCCCAA
          1 ATTTGAGATTTTTCGCAAAGTTCGGGCCCAA

                                          **
        207 ATTT--GATCTTTTC-CAAAGTTCGGGCCCTT
          1 ATTTGAGAT-TTTTCGCAAAGTTCGGGCCCAA

                  *    * *          
        236 ATTTGATATTTATGGCAAAGTTCG
          1 ATTTGAGATTTTTCGCAAAGTTCG

        260 AGAACCTATT


Statistics
Matches: 43,  Mismatches: 6, Indels: 8
        0.75            0.11        0.14

Matches are distributed among these distances:
  29   20  0.47
  30    8  0.19
  31   15  0.35

ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38


Consensus pattern (31 bp):   
ATTTGAGATTTTTCGCAAAGTTCGGGCCCAA

Found at i:225 original size:29 final size:30

Alignment explanation


    Indices: 185--259  Score: 89
    Period size: 29  Copynumber: 2.5  Consensus size: 30

        175 TATTTGAGAT

                         *                
        185 TTTTCGCAAAGTTGGGGCCCAAATTTGATC
          1 TTTTCGCAAAGTTCGGGCCCAAATTTGATC

                                **       *
        215 TTTTC-CAAAGTTCGGGCCCTTATTTGATA
          1 TTTTCGCAAAGTTCGGGCCCAAATTTGATC

                 *          
        244 TTTATGGCAAAGTTCG
          1 TTT-TCGCAAAGTTCG

        260 AGAACCTATT


Statistics
Matches: 38,  Mismatches: 5, Indels: 3
        0.83            0.11        0.07

Matches are distributed among these distances:
  29   23  0.61
  30    6  0.16
  31    9  0.24

ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37


Consensus pattern (30 bp):   
TTTTCGCAAAGTTCGGGCCCAAATTTGATC

Found at i:936 original size:16 final size:14

Alignment explanation


    Indices: 917--951  Score: 54
    Period size: 14  Copynumber: 2.5  Consensus size: 14

        907 AGATATTTGA

                           
        917 ATATAT-TTATATAT
          1 ATATATATTATAT-T

                          
        931 ATATATATTATATT
          1 ATATATATTATATT

                   
        945 ATATATA
          1 ATATATA

        952 AATAGAGTAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14   14  0.70
  15    6  0.30

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (14 bp):   
ATATATATTATATT
Done.