Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021084.1 Corchorus olitorius cultivar O-4 contig21117, 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: 28775
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:6246 original size:15 final size:15

Alignment explanation


    Indices: 6216--6257  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       6206 TTACTCTGCT

                            
       6216 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       6232 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       6247 TTGCTTTCTGT
          1 TTGTTTTCTGT

       6258 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:8114 original size:13 final size:13

Alignment explanation


    Indices: 8096--8122  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       8086 CTTCCCTTCA

                         
       8096 AATGAATGGGTCG
          1 AATGAATGGGTCG

                         
       8109 AATGAATGGGTCG
          1 AATGAATGGGTCG

             
       8122 A
          1 A

       8123 TGGAGAGAAG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.33, C:0.07, G:0.37, T:0.22


Consensus pattern (13 bp):   
AATGAATGGGTCG

Found at i:12360 original size:58 final size:58

Alignment explanation


    Indices: 12269--12378  Score: 168
    Period size: 58  Copynumber: 1.9  Consensus size: 58

      12259 GATAGAAAGC

                                  *     *              *               
      12269 ATATATAACATAAAGTTTGCAACTTTTAGCCTGTAGGAATAATTTAA-AGTTAATTCAT
          1 ATATATAACATAAAGTTTGCAAATTTTAACCTGTAGGAA-AATATAATAGTTAATTCAT

                    *                                           
      12327 ATATATAAGATAAAGTTTGCAAATTTTAACCTGTAGGAAAATATAATAGTTA
          1 ATATATAACATAAAGTTTGCAAATTTTAACCTGTAGGAAAATATAATAGTTA

      12379 TATTTGGAGG


Statistics
Matches: 47,  Mismatches: 4, Indels: 2
        0.89            0.08        0.04

Matches are distributed among these distances:
  57    6  0.13
  58   41  0.87

ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36


Consensus pattern (58 bp):   
ATATATAACATAAAGTTTGCAAATTTTAACCTGTAGGAAAATATAATAGTTAATTCAT

Found at i:12600 original size:84 final size:84

Alignment explanation


    Indices: 12457--12627  Score: 315
    Period size: 84  Copynumber: 2.0  Consensus size: 84

      12447 CTAAAAGAAT

                                                                  *          
      12457 CAAAGTAAATAGGATTTGTATTAAGATCATAAATATCCAAATGATTCTCATAAATCTAAAAACCA
          1 CAAAGTAAATAGGATTTGTATTAAGATCATAAATATCCAAATGATTCTCATAAAACTAAAAACCA

                               
      12522 ATTTGATTAAAAGAGTCAG
         66 ATTTGATTAAAAGAGTCAG

                  *                                                      *   
      12541 CAAAGTGAATAGGATTTGTATTAAGATCATAAATATCCAAATGATTCTCATAAAACTAAAATCCA
          1 CAAAGTAAATAGGATTTGTATTAAGATCATAAATATCCAAATGATTCTCATAAAACTAAAAACCA

                               
      12606 ATTTGATTAAAAGAGTCAG
         66 ATTTGATTAAAAGAGTCAG

               
      12625 CAA
          1 CAA

      12628 TGTCAATGCA


Statistics
Matches: 84,  Mismatches: 3, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  84   84  1.00

ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29


Consensus pattern (84 bp):   
CAAAGTAAATAGGATTTGTATTAAGATCATAAATATCCAAATGATTCTCATAAAACTAAAAACCA
ATTTGATTAAAAGAGTCAG

Found at i:15934 original size:30 final size:30

Alignment explanation


    Indices: 15898--15954  Score: 82
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      15888 CGTTCTCCAA

                                            
      15898 CCTTCTTCCT-C-TCTGGCCAAAAAAAAAAAT
          1 CCTTCTTCCTCCATCT--CCAAAAAAAAAAAT

                                       
      15928 CCTTCTTCCTCCATCTCCAAAAAAAAA
          1 CCTTCTTCCTCCATCTCCAAAAAAAAA

      15955 CTTCTCAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  30   21  0.84
  31    1  0.04
  32    3  0.12

ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26


Consensus pattern (30 bp):   
CCTTCTTCCTCCATCTCCAAAAAAAAAAAT
Done.