Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022912.1 Corchorus olitorius cultivar O-4 contig22945, 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: 13711
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:148 original size:16 final size:16

Alignment explanation


    Indices: 127--157  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

        117 AAGAAGCAAT

                            
        127 AAAAGGTATTTTCAAA
          1 AAAAGGTATTTTCAAA

                           
        143 AAAAGGTATTTTCAA
          1 AAAAGGTATTTTCAA

        158 GTCATGTTCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32


Consensus pattern (16 bp):   
AAAAGGTATTTTCAAA

Found at i:1561 original size:2 final size:2

Alignment explanation


    Indices: 1554--1584  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1544 ATGCCGTAAA

                                           *              
       1554 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       1585 ATTGGTTTAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:10147 original size:13 final size:13

Alignment explanation


    Indices: 10117--10155  Score: 51
    Period size: 13  Copynumber: 3.0  Consensus size: 13

      10107 TTTTATTCTC

                    *   *
      10117 TTTTTCTTGCTTG
          1 TTTTTCTTTCTTT

            *            
      10130 CTTTTCTTTCTTT
          1 TTTTTCTTTCTTT

                         
      10143 TTTTTCTTTCTTT
          1 TTTTTCTTTCTTT

      10156 CTCCCTCAAC


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  13   22  1.00

ACGTcount: A:0.00, C:0.18, G:0.05, T:0.77


Consensus pattern (13 bp):   
TTTTTCTTTCTTT

Found at i:11111 original size:33 final size:33

Alignment explanation


    Indices: 11065--11128  Score: 110
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      11055 CCCTTTTTTC

                                             
      11065 TTTGGGTTATGCAAGCTTGTTTCAATTTAGATG
          1 TTTGGGTTATGCAAGCTTGTTTCAATTTAGATG

                    *             *        
      11098 TTTGGGTTTTGCAAGCTTGTTTTAATTTAGA
          1 TTTGGGTTATGCAAGCTTGTTTCAATTTAGA

      11129 AGAAACAATT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  33   29  1.00

ACGTcount: A:0.20, C:0.08, G:0.23, T:0.48


Consensus pattern (33 bp):   
TTTGGGTTATGCAAGCTTGTTTCAATTTAGATG
Done.