Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013614.1 Corchorus olitorius cultivar O-4 contig13647, 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: 19012
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1511 original size:23 final size:23

Alignment explanation


    Indices: 1485--1529  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1475 ATATGAGTTG

                                    
       1485 ATGTTAGTGATATA-TATATGATC
          1 ATGTT-GTGATATACTATATGATC

                 *                
       1508 ATGTTTTGATATACTATATGAT
          1 ATGTTGTGATATACTATATGAT

       1530 GGATTATGCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    7  0.35
  23   13  0.65

ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47


Consensus pattern (23 bp):   
ATGTTGTGATATACTATATGATC

Found at i:11181 original size:76 final size:76

Alignment explanation


    Indices: 11044--11195  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      11034 ACAAGGACCC

                   *                                           *           * 
      11044 CGACTCCCCCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
      11109 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
      11120 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
      11182 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

      11196 TAGCCCTTCA


Statistics
Matches: 64,  Mismatches: 9, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  75    4  0.06
  76   54  0.84
  77    6  0.09

ACGTcount: A:0.16, C:0.30, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:17177 original size:21 final size:21

Alignment explanation


    Indices: 17144--17192  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      17134 AAGAATTGTA

                          **     
      17144 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
      17164 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
      17185 GCATTCCT
          1 GC-TTCCT

      17193 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT
Done.