Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016982.1 Corchorus olitorius cultivar O-4 contig17015, 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: 27436
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34


Found at i:5652 original size:37 final size:37

Alignment explanation


    Indices: 5583--5653  Score: 97
    Period size: 37  Copynumber: 1.9  Consensus size: 37

       5573 ACATAATTAT

                              * **  *            
       5583 TCATAAAGTTATGTCTATTTGGAATGACATGTATTGA
          1 TCATAAAGTTATGTCTATATCAAAAGACATGTATTGA

                                       *      
       5620 TCATAAAGTTATGTCTATATCAAAAGATATGTAT
          1 TCATAAAGTTATGTCTATATCAAAAGACATGTAT

       5654 GTTGATCAAG


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  37   29  1.00

ACGTcount: A:0.37, C:0.08, G:0.15, T:0.39


Consensus pattern (37 bp):   
TCATAAAGTTATGTCTATATCAAAAGACATGTATTGA

Found at i:8189 original size:37 final size:38

Alignment explanation


    Indices: 8139--8214  Score: 109
    Period size: 37  Copynumber: 2.0  Consensus size: 38

       8129 AATTATTCAT

                          *  **                   
       8139 AAAGTTATGTCTATTTGGGAAGACATGTA-TTGATCAA
          1 AAAGTTATGTCTATATGAAAAGACATGTACTTGATCAA

                                                   
       8176 AAAGTTATGTCTATATGAAAAGACATGTACGTTGATCAA
          1 AAAGTTATGTCTATATGAAAAGACATGTAC-TTGATCAA

       8215 GTATATAAAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  37   26  0.76
  39    8  0.24

ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33


Consensus pattern (38 bp):   
AAAGTTATGTCTATATGAAAAGACATGTACTTGATCAA

Found at i:13287 original size:18 final size:18

Alignment explanation


    Indices: 13264--13298  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      13254 AAGGGAGAGA

                              
      13264 TGGTGGCAGTTTGAGTGG
          1 TGGTGGCAGTTTGAGTGG

                   *         
      13282 TGGTGGCGGTTTGAGTG
          1 TGGTGGCAGTTTGAGTG

      13299 TTTGAGGTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.09, C:0.06, G:0.51, T:0.34


Consensus pattern (18 bp):   
TGGTGGCAGTTTGAGTGG

Found at i:25009 original size:30 final size:30

Alignment explanation


    Indices: 24937--25014  Score: 83
    Period size: 29  Copynumber: 2.7  Consensus size: 30

      24927 TTGCTTATTC

                  *                      * 
      24937 TATCTTTC-AATTG-TTGATTTGAATTGCCA
          1 TATCTTGCTAATTGATTGA-TTGAATTGCAA

                                          
      24966 TATCTTGCT-ATTGATTGATTGAATTGCAA
          1 TATCTTGCTAATTGATTGATTGAATTGCAA

                    *            
      24995 TTAT-TTGTTAATTGATTGAT
          1 -TATCTTGCTAATTGATTGAT

      25015 AGATTGTTTG


Statistics
Matches: 42,  Mismatches: 3, Indels: 7
        0.81            0.06        0.13

Matches are distributed among these distances:
  29   25  0.60
  30   17  0.40

ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50


Consensus pattern (30 bp):   
TATCTTGCTAATTGATTGATTGAATTGCAA

Found at i:27065 original size:45 final size:45

Alignment explanation


    Indices: 27012--27108  Score: 142
    Period size: 45  Copynumber: 2.2  Consensus size: 45

      27002 AGTACATTAC

                       *              *        *         
      27012 CTAA-ATTCTAGTACTCCATCTCTAGGTAATTCATTAAAATAAAA
          1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA

                         *                              *
      27056 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
          1 CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA

                    
      27101 CTAATATT
          1 CTAATATT

      27109 AATTGTTACT


Statistics
Matches: 47,  Mismatches: 5, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  44    4  0.09
  45   43  0.91

ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35


Consensus pattern (45 bp):   
CTAATATTCTACTACTCCATCTCTAGATAATTCATCAAAATAAAA
Done.