Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024850.1 Corchorus olitorius cultivar O-4 contig24883, 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: 15297
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33


Found at i:107 original size:41 final size:42

Alignment explanation


    Indices: 17--100  Score: 107
    Period size: 41  Copynumber: 2.0  Consensus size: 42

          7 TGATCTAAGG

                    *                       *        *
         17 TAATATTTGTTAATTGATTTCAATTTTATCCCTAATTTAGAG
          1 TAATATTTATTAATTGATTTCAATTTTATCCCGAATTTAGAA

                       *                     *    *   
         59 TAATATTTATTTATTGA-TTCAATTTTATCCCGGATTTGGAA
          1 TAATATTTATTAATTGATTTCAATTTTATCCCGAATTTAGAA

             
        100 T
          1 T

        101 TTTATTTTTG


Statistics
Matches: 36,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  41   21  0.58
  42   15  0.42

ACGTcount: A:0.30, C:0.10, G:0.11, T:0.50


Consensus pattern (42 bp):   
TAATATTTATTAATTGATTTCAATTTTATCCCGAATTTAGAA

Found at i:730 original size:20 final size:22

Alignment explanation


    Indices: 707--746  Score: 66
    Period size: 20  Copynumber: 1.9  Consensus size: 22

        697 GAAAATGATC

                                  
        707 AAAATCA-AAAA-AAAAAGAGA
          1 AAAATCAGAAAATAAAAAGAGA

                                
        727 AAAATCAGAAAATAAAAAGA
          1 AAAATCAGAAAATAAAAAGA

        747 TGCAATAAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  20    7  0.39
  21    4  0.22
  22    7  0.39

ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07


Consensus pattern (22 bp):   
AAAATCAGAAAATAAAAAGAGA

Found at i:5287 original size:64 final size:64

Alignment explanation


    Indices: 5141--5420  Score: 375
    Period size: 64  Copynumber: 4.3  Consensus size: 64

       5131 ACATTAATTC

                                                 *   *                       
       5141 GATTCACCGAATCATCCTGAACTGT-TCGAAAATGTGTTGCTCCGAGCTCACTGAATTCCAATCT
          1 GATTCACCGAATCATCCTGAACTGTCT-GAAAATGTGCTGCACCGAGCTC-C-GAATTCCAATCT

             *
       5205 TC
         63 TT

                  *    *            *   *  *   *                            
       5207 GATTCATCGAAACATCCTGAACTGCCTGGAACTGTACTGCACCGAGCTCCGAATTCCAATCTTT
          1 GATTCACCGAATCATCCTGAACTGTCTGAAAATGTGCTGCACCGAGCTCCGAATTCCAATCTTT

                                     *                   *                  
       5271 GATTCACCGAATCATCCTGAACTGTTTGAAAATGTGCTGCACCGAACTCCGAATTCCAATCTTT
          1 GATTCACCGAATCATCCTGAACTGTCTGAAAATGTGCTGCACCGAGCTCCGAATTCCAATCTTT

                                   *                 **                      
       5335 GATTCACCGAATCATCCTGAACTATCT-AGAAATGTGCTGCTTCGAGCTCCGAATTCCAATCTTT
          1 GATTCACCGAATCATCCTGAACTGTCTGA-AAATGTGCTGCACCGAGCTCCGAATTCCAATCTTT

                                  
       5399 GATTCACCGAATCAATCCTGAA
          1 GATTCACCGAATC-ATCCTGAA

       5421 GAAAAAATTA


Statistics
Matches: 189,  Mismatches: 22, Indels: 7
        0.87            0.10        0.03

Matches are distributed among these distances:
  63    1  0.01
  64  139  0.74
  65    9  0.05
  66   39  0.21
  67    1  0.01

ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29


Consensus pattern (64 bp):   
GATTCACCGAATCATCCTGAACTGTCTGAAAATGTGCTGCACCGAGCTCCGAATTCCAATCTTT

Done.