Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014986.1 Corchorus olitorius cultivar O-4 contig15019, 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: 10345
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:83 original size:28 final size:28

Alignment explanation


    Indices: 40--105  Score: 114
    Period size: 28  Copynumber: 2.3  Consensus size: 28

         30 CCTTTATCCA

                                          
         40 TGAGTTTTGATGTTATTTTACTTGAATGAT
          1 TGAG-TTT-ATGTTATTTTACTTGAATGAT

                                        
         70 TGAGTTTATGTTATTTTACTTGAATGAT
          1 TGAGTTTATGTTATTTTACTTGAATGAT

                    
         98 TGAGTTTA
          1 TGAGTTTA

        106 AGTTTTGATG


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  28   29  0.81
  29    3  0.08
  30    4  0.11

ACGTcount: A:0.24, C:0.03, G:0.20, T:0.53


Consensus pattern (28 bp):   
TGAGTTTATGTTATTTTACTTGAATGAT

Found at i:867 original size:121 final size:122

Alignment explanation


    Indices: 719--956  Score: 354
    Period size: 122  Copynumber: 2.0  Consensus size: 122

        709 ATCTTATTTT

                *                       *          **   *      *             
        719 AGCACACTGTTTTTCTTCTTAAATTTTATGAATTATGCAGCCAATC-TTTTTTATAAATCAAATG
          1 AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAACAACCGTTTTATATAAATCAAATG

                      *                                               
        783 CTAT-AATCAGAAATAGGAAATTGAGTTTTATGAGAAGTGGGAAACGTGAGTAGCAGC
         66 CTATAAAT-AAAAATAGGAAATTGAGTTTTATGAGAAGTGGGAAACGTGAGTAGCAGC

                    *                                            *  *        
        840 AGCAAACTTTTTTTCTTCTTAAATTTTAGGAATTATGCAAACAACCGTTTTATGTATATCAAATG
          1 AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAACAACCGTTTTATATAAATCAAATG

                               *                                
        905 CTATAAATAAAAATAGGAATTTGAGTTTTATGAGAAGTGGGAAACGTGAGTA
         66 CTATAAATAAAAATAGGAAATTGAGTTTTATGAGAAGTGGGAAACGTGAGTA

        957 AATGGAAGTA


Statistics
Matches: 104,  Mismatches: 11, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
 121   40  0.38
 122   61  0.59
 123    3  0.03

ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35


Consensus pattern (122 bp):   
AGCAAACTGTTTTTCTTCTTAAATTTTAGGAATTATGCAAACAACCGTTTTATATAAATCAAATG
CTATAAATAAAAATAGGAAATTGAGTTTTATGAGAAGTGGGAAACGTGAGTAGCAGC

Found at i:1340 original size:30 final size:31

Alignment explanation


    Indices: 1300--1361  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       1290 ATCGGTCACA

                 *        *                
       1300 TGTCATTTTTTG-TCCACGTGGCATGCCACG
          1 TGTCACTTTTTGATACACGTGGCATGCCACG

                                  **       
       1330 TGTCACTTTTTGATACACGTGGTGTGCCACG
          1 TGTCACTTTTTGATACACGTGGCATGCCACG

             
       1361 T
          1 T

       1362 CGTACACCGT


Statistics
Matches: 27,  Mismatches: 4, Indels: 1
        0.84            0.12        0.03

Matches are distributed among these distances:
  30   11  0.41
  31   16  0.59

ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37


Consensus pattern (31 bp):   
TGTCACTTTTTGATACACGTGGCATGCCACG

Found at i:8100 original size:20 final size:19

Alignment explanation


    Indices: 8075--8113  Score: 51
    Period size: 20  Copynumber: 2.0  Consensus size: 19

       8065 AATTAATAAG

                  *             
       8075 AAAGTTGAATCATCTAAAAA
          1 AAAGTTAAATCA-CTAAAAA

                      *        
       8095 AAAGTTAAATGACTAAAAA
          1 AAAGTTAAATCACTAAAAA

       8114 GAATACTTAT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23


Consensus pattern (19 bp):   
AAAGTTAAATCACTAAAAA
Done.