Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017190.1 Corchorus olitorius cultivar O-4 contig17223, 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: 12194
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:3295 original size:22 final size:23

Alignment explanation


    Indices: 3270--3316  Score: 87
    Period size: 22  Copynumber: 2.1  Consensus size: 23

       3260 ACAAGGGCTT

                                   
       3270 AAGCTATATGATCAAAGTGC-AA
          1 AAGCTATATGATCAAAGTGCGAA

                                   
       3292 AAGCTATATGATCAAAGTGCGAA
          1 AAGCTATATGATCAAAGTGCGAA

              
       3315 AA
          1 AA

       3317 TACTGAATTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  22   20  0.83
  23    4  0.17

ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21


Consensus pattern (23 bp):   
AAGCTATATGATCAAAGTGCGAA

Found at i:3490 original size:27 final size:27

Alignment explanation


    Indices: 3460--3536  Score: 127
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       3450 AACAGTGAAC

                                       
       3460 TGCAAATGACTAAAATGCCCCTGAATG
          1 TGCAAATGACTAAAATGCCCCTGAATG

                        *             *
       3487 TGCAAATGACTACAATGCCCCTGAATT
          1 TGCAAATGACTAAAATGCCCCTGAATG

             *                     
       3514 TACAAATGACTAAAATGCCCCTG
          1 TGCAAATGACTAAAATGCCCCTG

       3537 GTTGATTCTA


Statistics
Matches: 46,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   46  1.00

ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23


Consensus pattern (27 bp):   
TGCAAATGACTAAAATGCCCCTGAATG

Found at i:4513 original size:76 final size:76

Alignment explanation


    Indices: 4363--4514  Score: 166
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       4353 ACAAGGGCCT

                                           **      *           *           * 
       4363 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCTATGTGGTTTGCTTGAGTACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGTACCCAGAT

             *         
       4428 GGGCAGTGTCA
         66 GAGCAGTGTCA

                    *     *              *                                   
       4439 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTAAAG-ACCCATGT-GTTTCGCCTGA-TCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTAAAGCACCCATGTGGTTT-GCCTGAGT-ACCCA

                   *      
       4501 GATGAGCTGTGTCA
         63 GATGAGCAGTGTCA

       4515 TAGCTTGGTA


Statistics
Matches: 63,  Mismatches: 10, Indels: 6
        0.80            0.13        0.08

Matches are distributed among these distances:
  75    5  0.08
  76   51  0.81
  77    7  0.11

ACGTcount: A:0.18, C:0.29, G:0.28, T:0.26


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGTACCCAGAT
GAGCAGTGTCA
Done.