Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017635.1 Corchorus olitorius cultivar O-4 contig17668, 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: 5461
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30


Found at i:588 original size:35 final size:35

Alignment explanation


    Indices: 534--603  Score: 113
    Period size: 35  Copynumber: 2.0  Consensus size: 35

        524 CCGGGTAGTG

                   *  *   *                    
        534 CAAATTTGATTGAATGCTCCAGAAGAGCTAGTATT
          1 CAAATTTCATCGAAGGCTCCAGAAGAGCTAGTATT

                                               
        569 CAAATTTCATCGAAGGCTCCAGAAGAGCTAGTATT
          1 CAAATTTCATCGAAGGCTCCAGAAGAGCTAGTATT

        604 GTTTTATCTG


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  35   32  1.00

ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29


Consensus pattern (35 bp):   
CAAATTTCATCGAAGGCTCCAGAAGAGCTAGTATT

Found at i:887 original size:18 final size:19

Alignment explanation


    Indices: 864--899  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

        854 TAAACAAGAA

                               
        864 GTTTATTGATT-GCATTAT
          1 GTTTATTGATTGGCATTAT

                    *         
        882 GTTTATTGTTTGGCATTA
          1 GTTTATTGATTGGCATTA

        900 CCGTTTAGGC


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

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56


Consensus pattern (19 bp):   
GTTTATTGATTGGCATTAT

Found at i:5172 original size:21 final size:21

Alignment explanation


    Indices: 5128--5172  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5118 GGTGCCCACA

                            *  * 
       5128 TGGTTTCCTTGAGCACGCATG
          1 TGGTTTCCTTGAGCACCCAGG

                  *      *       
       5149 TGGTTTGCTTGAGGACCCAGG
          1 TGGTTTCCTTGAGCACCCAGG

               
       5170 TGG
          1 TGG

       5173 GCGGTGTCAC


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.13, C:0.20, G:0.36, T:0.31


Consensus pattern (21 bp):   
TGGTTTCCTTGAGCACCCAGG

Found at i:5243 original size:76 final size:76

Alignment explanation


    Indices: 5106--5250  Score: 179
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       5096 ACAAGGACCC

                                                  *            *    *      * 
       5106 CGACTCCACCTGGGTGCCCACATGGTTTCCTTGAGCACGCATGTGGTTTGCTTGAGGACCCAGGT
          1 CGACTCCACCTGGGTGCCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT

                       
       5171 GGGCGGTGTCA
         66 GGGCGGTGTCA

                    *                    *                            *      
       5182 CGACTCCAGCTGGGTGCCCACATGGTTT-GTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGTGCCCACATGGTTTCCT-TG-AGCACCCATGTGGTTT-GCCTGAGCACCCA

                   
       5244 GATGGGC
         63 GATGGGC

       5251 TATGTCATAG


Statistics
Matches: 59,  Mismatches: 7, Indels: 6
        0.82            0.10        0.08

Matches are distributed among these distances:
  75    5  0.08
  76   52  0.88
  77    2  0.03

ACGTcount: A:0.16, C:0.29, G:0.30, T:0.25


Consensus pattern (76 bp):   
CGACTCCACCTGGGTGCCCACATGGTTTCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGAT
GGGCGGTGTCA

Done.