Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014505.1 Corchorus olitorius cultivar O-4 contig14538, 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: 10961
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35


Found at i:3203 original size:76 final size:76

Alignment explanation


    Indices: 3066--3217  Score: 175
    Period size: 76  Copynumber: 2.0  Consensus size: 76

       3056 ACAAGGACCC

                                           *                   *           * 
       3066 CGACTCCACCTGGGCGCCCACATGGATGCCTTAAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGATGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                        
       3131 GGG-TAGTGTCA
         66 GGGCT-GTGTCA

                    *     *           *  *                           **      
       3142 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTGAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
          1 CGACTCCACCTGGGCGCCCACATGG-ATGCCTGAAGCACCCATGTGGTTT-GCCTGAGAACCCAG

                         
       3205 ATGGGCTGTGTCA
         64 ATGGGCTGTGTCA

       3218 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   52  0.81
  77    8  0.12

ACGTcount: A:0.18, C:0.29, G:0.28, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGATGCCTGAAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCTGTGTCA

Found at i:4167 original size:44 final size:44

Alignment explanation


    Indices: 4101--4187  Score: 147
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       4091 GGACAAAATG

                        *                               
       4101 GGGTTTATTAGGTAATGACACGGGGAAAACATGCACCATGGTTT
          1 GGGTTTATTAGGCAATGACACGGGGAAAACATGCACCATGGTTT

                             *     *                   
       4145 GGGTTTATTAGGCAATGCCACGGTGAAAACATGCACCATGGTT
          1 GGGTTTATTAGGCAATGACACGGGGAAAACATGCACCATGGTT

       4188 GTTACAGATA


Statistics
Matches: 40,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  44   40  1.00

ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26


Consensus pattern (44 bp):   
GGGTTTATTAGGCAATGACACGGGGAAAACATGCACCATGGTTT

Found at i:5623 original size:21 final size:21

Alignment explanation


    Indices: 5597--5641  Score: 81
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       5587 GCTTTCTTCA

                   *             
       5597 TATTAATTTTTTGCTTTGTTT
          1 TATTAATGTTTTGCTTTGTTT

                                 
       5618 TATTAATGTTTTGCTTTGTTT
          1 TATTAATGTTTTGCTTTGTTT

               
       5639 TAT
          1 TAT

       5642 AGTGACTATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.16, C:0.04, G:0.11, T:0.69


Consensus pattern (21 bp):   
TATTAATGTTTTGCTTTGTTT

Found at i:5824 original size:44 final size:44

Alignment explanation


    Indices: 5756--5841  Score: 136
    Period size: 44  Copynumber: 2.0  Consensus size: 44

       5746 GCGAAATGGG

                      *        *                        
       5756 GTTTATCAGGTAATGCCACTGGGAAAACATGCACCATGGTTGGA
          1 GTTTATCAGGCAATGCCACGGGGAAAACATGCACCATGGTTGGA

                  *                     *             
       5800 GTTTATTAGGCAATGCCACGGGGAAAACTTGCACCATGGTTG
          1 GTTTATCAGGCAATGCCACGGGGAAAACATGCACCATGGTTG

       5842 TTACAGATAT


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  44   38  1.00

ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26


Consensus pattern (44 bp):   
GTTTATCAGGCAATGCCACGGGGAAAACATGCACCATGGTTGGA

Found at i:10611 original size:2 final size:2

Alignment explanation


    Indices: 10604--10644  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      10594 TGTAATACCG

                                                                         
      10604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10645 TAGGTGATTA


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.