Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017767.1 Corchorus olitorius cultivar O-4 contig17800, 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: 28350
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:952 original size:36 final size:36

Alignment explanation


    Indices: 905--974  Score: 106
    Period size: 36  Copynumber: 1.9  Consensus size: 36

        895 TTCAATAACC

                           *                     
        905 TTACATCTTTTGTGATTTTTG-TTATCATATTTCTTA
          1 TTACATCTTTTGT-AATTTTGATTATCATATTTCTTA

                  *                           
        941 TTACATTTTTTGTAATTTTGATTATCATATTTCT
          1 TTACATCTTTTGTAATTTTGATTATCATATTTCT

        975 CCAAAATCTC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  35    6  0.19
  36   25  0.81

ACGTcount: A:0.21, C:0.10, G:0.07, T:0.61


Consensus pattern (36 bp):   
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA

Found at i:1849 original size:39 final size:40

Alignment explanation


    Indices: 1795--1875  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       1785 ATACCTAAGA

                                             *      
       1795 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
       1834 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
       1874 AT
          1 AT

       1876 AGAAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:2110 original size:6 final size:6

Alignment explanation


    Indices: 2092--2121  Score: 51
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       2082 GTTTAGACTT

                                              
       2092 ATATAG TATATAG ATATAG ATATAG ATATA
          1 ATATAG -ATATAG ATATAG ATATAG ATATA

       2122 AATTTTGACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   6   17  0.74
   7    6  0.26

ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37


Consensus pattern (6 bp):   
ATATAG

Found at i:2811 original size:31 final size:31

Alignment explanation


    Indices: 2746--2838  Score: 118
    Period size: 31  Copynumber: 3.0  Consensus size: 31

       2736 TATTGCGTCA

                 *         *               
       2746 AGGACGTTTTGCCCCCTGAACTT-CAAA-TC
          1 AGGACATTTTGCCCCTTGAACTTCCAAATTC

                          *                
       2775 AGGACATTTTGCCCTTTGAACTTCCAAATTC
          1 AGGACATTTTGCCCCTTGAACTTCCAAATTC

                      *       *             
       2806 AGGACATTTTACCCCTTGTACTTCCCAAATTC
          1 AGGACATTTTGCCCCTTGAACTT-CCAAATTC

             
       2838 A
          1 A

       2839 ACACAATTTA


Statistics
Matches: 55,  Mismatches: 6, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  29   20  0.36
  30    4  0.07
  31   22  0.40
  32    9  0.16

ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32


Consensus pattern (31 bp):   
AGGACATTTTGCCCCTTGAACTTCCAAATTC

Found at i:16326 original size:16 final size:16

Alignment explanation


    Indices: 16300--16333  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      16290 ACTTGAGATC

                             
      16300 AATACTAAATATATTTT
          1 AATACTAAATAT-TTTT

                            
      16317 AATA-TAAATATTTTT
          1 AATACTAAATATTTTT

              
      16332 AA
          1 AA

      16334 AAATAATTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    6  0.35
  16    7  0.41
  17    4  0.24

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (16 bp):   
AATACTAAATATTTTT
Done.