Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017951.1 Corchorus olitorius cultivar O-4 contig17984, 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: 23969
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:8815 original size:2 final size:2

Alignment explanation


    Indices: 8810--8834  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8800 ATTAAAAAAA

                                                 
       8810 AC AC AC AC AC AC AC AC AC AC AC AC A
          1 AC AC AC AC AC AC AC AC AC AC AC AC A

       8835 TTTTATATTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00


Consensus pattern (2 bp):   
AC

Found at i:13928 original size:68 final size:69

Alignment explanation


    Indices: 13803--13948  Score: 222
    Period size: 68  Copynumber: 2.1  Consensus size: 69

      13793 TCTTCTTAGG

                *         **                                    *            
      13803 CCTGGTTTGGCGTTGTGTTTGGAGATAAAAAAAAACTGCTTTTGACCCAAAATGCAATACCAAAT
          1 CCTGATTTGGCGTTACGTTTGGAGATAAAAAAAAACTGCTTTTGACCCAAAACGCAATACCAAAT

                
      13868 AAAT
         66 AAAT

                                              **                             
      13872 CCTGATTTGGCGTTACGTTTGGAGAT-AAAAAAAGTTGCTTTTGACCCAAAACGCAATACCAAAT
          1 CCTGATTTGGCGTTACGTTTGGAGATAAAAAAAAACTGCTTTTGACCCAAAACGCAATACCAAAT

                
      13936 AAAT
         66 AAAT

             *       
      13940 CATGATTTG
          1 CCTGATTTG

      13949 TGGCAAAAGC


Statistics
Matches: 70,  Mismatches: 7, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  68   47  0.67
  69   23  0.33

ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29


Consensus pattern (69 bp):   
CCTGATTTGGCGTTACGTTTGGAGATAAAAAAAAACTGCTTTTGACCCAAAACGCAATACCAAAT
AAAT

Found at i:16716 original size:28 final size:28

Alignment explanation


    Indices: 16683--16743  Score: 86
    Period size: 28  Copynumber: 2.2  Consensus size: 28

      16673 ACAAAATGTC

                    *       *           
      16683 CCAAAATTGAAATTCATAGGTAAAATAT
          1 CCAAAATTAAAATTCAGAGGTAAAATAT

                          *  *          
      16711 CCAAAATTAAAATTTAGGGGTAAAATAT
          1 CCAAAATTAAAATTCAGAGGTAAAATAT

                 
      16739 CCAAA
          1 CCAAA

      16744 CGCACTTCAA


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.51, C:0.11, G:0.11, T:0.26


Consensus pattern (28 bp):   
CCAAAATTAAAATTCAGAGGTAAAATAT

Found at i:20282 original size:60 final size:60

Alignment explanation


    Indices: 20203--20331  Score: 204
    Period size: 60  Copynumber: 2.1  Consensus size: 60

      20193 TGGCTAATTG

                     *    *             *            *    *             
      20203 CTCAAATAAGGGTCTGATCTTTTAATTTGGCCAAATAAGGGTCTAATGATTGCCAAAATA
          1 CTCAAATAAAGGTCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATA

                                                            *           
      20263 CTCAAATAAAGGTCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGTTTGCCAAAATA
          1 CTCAAATAAAGGTCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATA

                     
      20323 CTCAAATAA
          1 CTCAAATAA

      20332 GGACCTAGCA


Statistics
Matches: 63,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  60   63  1.00

ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29


Consensus pattern (60 bp):   
CTCAAATAAAGGTCCGATCTTTTAATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATA

Found at i:20350 original size:60 final size:60

Alignment explanation


    Indices: 20226--20350  Score: 144
    Period size: 60  Copynumber: 2.1  Consensus size: 60

      20216 CTGATCTTTT

                 *            *    *                         *    *  ***
      20226 AATTTGGCCAAATAAGGGTCTAATGATTGCCAAAATACTCAAATAAAGGTCCGATCTTTT
          1 AATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATACTCAAATAAAGGACCGAGCTCGA

                                     *                          *        
      20286 AATTTAGCCAAATAAGGGCCTAACGTTTGCCAAAATACTCAAAT-AAGGACCTAGCATCGA
          1 AATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATACTCAAATAAAGGACCGAGC-TCGA

                 
      20346 AATTT
          1 AATTT

      20351 TTTACGCGTC


Statistics
Matches: 54,  Mismatches: 10, Indels: 2
        0.82            0.15        0.03

Matches are distributed among these distances:
  59    8  0.15
  60   46  0.85

ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27


Consensus pattern (60 bp):   
AATTTAGCCAAATAAGGGCCTAACGATTGCCAAAATACTCAAATAAAGGACCGAGCTCGA

Found at i:20477 original size:60 final size:59

Alignment explanation


    Indices: 20376--20539  Score: 184
    Period size: 60  Copynumber: 2.7  Consensus size: 59

      20366 AACTGACGTT

                           *     *           *  *                   *   
      20376 AGGCCCTTATTTGAGTATTTTCGATAATGTTAGGCCTTTATTTGGCCAAATTAAAAGATC
          1 AGGCCCTTATTTGAGCATTTTGGA-AATGTTAGACCCTTATTTGGCCAAATTAAAAAATC

            *                               *                           
      20436 GGGCCCTTATTTGAGCATTTTGGTAAATGTTATACCCTTATTTGGCCAAATTAAAAAATC
          1 AGGCCCTTATTTGAGCATTTTGG-AAATGTTAGACCCTTATTTGGCCAAATTAAAAAATC

             ** *         *            **               
      20496 ATACACTTATTTGAACATTTTGGCAAACATTAGACCCTTATTTG
          1 AGGCCCTTATTTGAGCATTTTGG-AAATGTTAGACCCTTATTTG

      20540 AGCAGTTAGC


Statistics
Matches: 87,  Mismatches: 16, Indels: 2
        0.83            0.15        0.02

Matches are distributed among these distances:
  60   86  0.99
  61    1  0.01

ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38


Consensus pattern (59 bp):   
AGGCCCTTATTTGAGCATTTTGGAAATGTTAGACCCTTATTTGGCCAAATTAAAAAATC
Done.