Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012579.1 Corchorus olitorius cultivar O-4 contig12612, 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: 10208
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31


Found at i:1077 original size:76 final size:76

Alignment explanation


    Indices: 941--1090  Score: 171
    Period size: 76  Copynumber: 2.0  Consensus size: 76

        931 CAAGTACCCC

                                                              *    *      *  
        941 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGGACCCAGGTG
          1 GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATG

                       
       1006 GGCGGTGTCAT
         66 GGCGGTGTCAT

                   *     *              *                *           *       
       1017 GACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCAT-TTGTTTCGCCTGATCACCCAG
          1 GACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGCACCCAG

                  *     
       1079 ATGGGCTGTGTC
         63 ATGGGCGGTGTC

       1091 TTAGCTCATC


Statistics
Matches: 62,  Mismatches: 9, Indels: 6
        0.81            0.12        0.08

Matches are distributed among these distances:
  75    5  0.08
  76   51  0.82
  77    6  0.10

ACGTcount: A:0.15, C:0.29, G:0.30, T:0.26


Consensus pattern (76 bp):   
GACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGCACCCAGATG
GGCGGTGTCAT

Found at i:2063 original size:27 final size:26

Alignment explanation


    Indices: 2020--2070  Score: 75
    Period size: 27  Copynumber: 1.9  Consensus size: 26

       2010 ATGATTTAGG

                      *                
       2020 GGTTACTAACTCCCTTTTTTCTTTTGA
          1 GGTTACTAACACCCTTTTTT-TTTTGA

                        *           
       2047 GGTTACTAACACTCTTTTTTTTTT
          1 GGTTACTAACACCCTTTTTTTTTT

       2071 CAGAGGGACA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  26    4  0.18
  27   18  0.82

ACGTcount: A:0.16, C:0.20, G:0.10, T:0.55


Consensus pattern (26 bp):   
GGTTACTAACACCCTTTTTTTTTTGA

Found at i:8196 original size:16 final size:17

Alignment explanation


    Indices: 8167--8204  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       8157 AAAAATAAAT

                             
       8167 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       8184 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 
       8200 AAAAA
          1 AAAAA

       8205 GATAAGGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG

Found at i:9913 original size:76 final size:76

Alignment explanation


    Indices: 9776--9927  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       9766 ACAAGGACCC

                              *                                *           * 
       9776 CGACTCCACCTGGGCGCCGACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       9841 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *     *              *                            **     
       9852 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                   *      
       9914 GATGGGCTGTGTCA
         63 GATGGGCAGTGTCA

       9928 TAGCTCATCA


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:0.17, C:0.29, G:0.30, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Done.