Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019544.1 Corchorus olitorius cultivar O-4 contig19577, 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: 16917
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33


Found at i:823 original size:2 final size:2

Alignment explanation


    Indices: 818--851  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

        808 AACTATACAG

                                                              
        818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        852 GGCCCAACTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:10844 original size:21 final size:21

Alignment explanation


    Indices: 10820--10864  Score: 81
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      10810 AAAACCTGGC

                *                
      10820 CATCGACAATGATTATAATGG
          1 CATCCACAATGATTATAATGG

                                 
      10841 CATCCACAATGATTATAATGG
          1 CATCCACAATGATTATAATGG

               
      10862 CAT
          1 CAT

      10865 TGGATCAGTT


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:0.38, C:0.18, G:0.16, T:0.29


Consensus pattern (21 bp):   
CATCCACAATGATTATAATGG

Found at i:14689 original size:18 final size:18

Alignment explanation


    Indices: 14666--14701  Score: 56
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      14656 TAAAATTGAG

                               
      14666 TATATATT-TATTTATTAT
          1 TATATATTATA-TTATTAT

                              
      14684 TATATATTATATTATTAT
          1 TATATATTATATTATTAT

      14702 CTAAGTAAAG


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18   15  0.88
  19    2  0.12

ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64


Consensus pattern (18 bp):   
TATATATTATATTATTAT

Found at i:16189 original size:330 final size:330

Alignment explanation


    Indices: 15588--16200  Score: 1077
    Period size: 330  Copynumber: 1.9  Consensus size: 330

      15578 GAGAGTTTGC

                                     *                     *       *         
      15588 TAGTGAGATTGTTATGATTGTTGATTGTAATTGATTGATTTGATAGTTGAAATTTGTGGCATAAG
          1 TAGTGAGATTGTTATGATTGTTGATCGTAATTGATTGATTTGATAGTGGAAATTTATGGCATAAG

                          *            *                                     
      15653 TCCACAAGAAAATTTTCTTTGTTGTTTTTGCTTTTTTATTTGTTTGGTTAATTCCTGGGATATTC
         66 TCCACAAGAAAATTGTCTTTGTTGTTTCTGCTTTTTTATTTGTTTGGTTAATTCCTGGGATATTC

                        *                                                 *  
      15718 GAAGTTAAAACAGGTTCAGACACAGTGCACCTACCAGTTGAGCTAATAACTCGGGTGAACTCGAC
        131 GAAGTTAAAACAAGTTCAGACACAGTGCACCTACCAGTTGAGCTAATAACTCGGGTGAACTCAAC

                                                                         *   
      15783 ATCTTTAAACTACCTTAAACTTTGATAATTAATTATAAAGAAAAAAAATGTCTTAAATGTCTTCT
        196 ATCTTTAAACTACCTTAAACTTTGATAATTAATTATAAAGAAAAAAAATGTCTTAAATGTCCTCT

                                                                             
      15848 TGTGCCCCCTTACCATTTTTAAACTTTCCTAGTGAGATTGTTATGTCTTAAACTACTTTAAACTT
        261 TGTGCCCCCTTACCATTTTTAAACTTTCCTAGTGAGATTGTTATGTCTTAAACTACTTTAAACTT

                 
      15913 TGCTA
        326 TGCTA

                                                              *              
      15918 TAGTGAGATTGTTATGATTGTTGATCGTAATTGATTGATTTGATAGTGGAGATTTATGGCAT-AG
          1 TAGTGAGATTGTTATGATTGTTGATCGTAATTGATTGATTTGATAGTGGAAATTTATGGCATAAG

                                                                             
      15982 ATCCACAAGAAAATTGTCTTTGTTGTTTCTGCTTTTTTTATTTGTTTGGTTAATTCCTGGGATAT
         66 -TCCACAAGAAAATTGTCTTTGTTGTTTCTGC-TTTTTTATTTGTTTGGTTAATTCCTGGGATAT

                 *      *       *                                            
      16047 TCGAATTTAAAATAAGTTCATACACAGTGCACCTACCAGTTGAGCTAATAACTCGGGTGAACTCA
        129 TCGAAGTTAAAACAAGTTCAGACACAGTGCACCTACCAGTTGAGCTAATAACTCGGGTGAACTCA

                           *                                                 
      16112 ACATCTTTAAACTACTTTAAACTTTGATAATTAATTATAAAG-AAAAAAATGTCTTAAATGTCCT
        194 ACATCTTTAAACTACCTTAAACTTTGATAATTAATTATAAAGAAAAAAAATGTCTTAAATGTCCT

                                     
      16176 CTTGTGCCCCCTTACCATTTTTAAA
        259 CTTGTGCCCCCTTACCATTTTTAAA

      16201 AAGGATGCTC


Statistics
Matches: 268,  Mismatches: 13, Indels: 4
        0.94            0.05        0.01

Matches are distributed among these distances:
 329    2  0.01
 330  133  0.50
 331  133  0.50

ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40


Consensus pattern (330 bp):   
TAGTGAGATTGTTATGATTGTTGATCGTAATTGATTGATTTGATAGTGGAAATTTATGGCATAAG
TCCACAAGAAAATTGTCTTTGTTGTTTCTGCTTTTTTATTTGTTTGGTTAATTCCTGGGATATTC
GAAGTTAAAACAAGTTCAGACACAGTGCACCTACCAGTTGAGCTAATAACTCGGGTGAACTCAAC
ATCTTTAAACTACCTTAAACTTTGATAATTAATTATAAAGAAAAAAAATGTCTTAAATGTCCTCT
TGTGCCCCCTTACCATTTTTAAACTTTCCTAGTGAGATTGTTATGTCTTAAACTACTTTAAACTT
TGCTA
Done.