Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014745.1 Corchorus olitorius cultivar O-4 contig14778, 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: 8152
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:4095 original size:2 final size:2

Alignment explanation


    Indices: 4088--4116  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

       4078 TGTGCATGTA

                                                       
       4088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       4117 GACACACACA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6677 original size:30 final size:30

Alignment explanation


    Indices: 6643--6829  Score: 347
    Period size: 30  Copynumber: 6.2  Consensus size: 30

       6633 AAATGTCACC

                                          
       6643 TGTCATGGTCTTACAATTGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                            *             
       6673 TGTCATGGTCTTACAAATGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                            *             
       6703 TGTCATGGTCTTACAAATGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                                          
       6733 TGTCATGGTCTTACAATTGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                                          
       6763 TGTCATGGTCTTACAATTGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                        *                 
       6793 TGTCATGGTCTTGCAATTGACACCAGAAGT
          1 TGTCATGGTCTTACAATTGACACCAGAAGT

                   
       6823 TGTCATG
          1 TGTCATG

       6830 AAAATTATTG


Statistics
Matches: 154,  Mismatches: 3, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  30  154  1.00

ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29


Consensus pattern (30 bp):   
TGTCATGGTCTTACAATTGACACCAGAAGT

Found at i:6848 original size:28 final size:28

Alignment explanation


    Indices: 6808--7047  Score: 237
    Period size: 28  Copynumber: 7.8  Consensus size: 28

       6798 TGGTCTTGCA

                                        
       6808 ATTGACACCAGAAGTTGTCATGAAAATT
          1 ATTGACACCAGAAGTTGTCATGAAAATT

                                   *        
       6836 ATTGACACCAGAAGTTGTCATACCAAATTATT
          1 ATTGACACCAGAAGTTGTCAT--GAAA--ATT

                                          
       6868 ATCTTGACACCAGAAGTTGTCATGAAAATT
          1 A--TTGACACCAGAAGTTGTCATGAAAATT

                   *               *        
       6898 ATTGACATCAGAAGTTGTCATATCAAATTATT
          1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT

                                          
       6930 ATCTTGACACCAGAAGTTGTCATGAAAATT
          1 A--TTGACACCAGAAGTTGTCATGAAAATT

                                   *        
       6960 ATTGACACCAGAAGTTGTCATATCAAATTATT
          1 ATTGACACCAGAAGTTGTC--ATGAAA--ATT

                                               
       6992 ATCTTGACACCAGAAGTTGTCATGCTGAGGAAATT
          1 A--TTGACACCAGAAGTTGTCA---TGA--AAATT

                                 
       7027 ATTGACACCAGAAGTTGTCAT
          1 ATTGACACCAGAAGTTGTCAT

       7048 CCCAAGATTG


Statistics
Matches: 181,  Mismatches: 8, Indels: 44
        0.78            0.03        0.19

Matches are distributed among these distances:
  28   56  0.31
  30   22  0.12
  32   21  0.12
  33   19  0.10
  34   55  0.30
  35    6  0.03
  37    2  0.01

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31


Consensus pattern (28 bp):   
ATTGACACCAGAAGTTGTCATGAAAATT

Found at i:6891 original size:62 final size:62

Alignment explanation


    Indices: 6809--7052  Score: 407
    Period size: 62  Copynumber: 3.9  Consensus size: 62

       6799 GGTCTTGCAA

                                                                          
       6809 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATACCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATACCAAATTATTATC

                                              *              *            
       6871 TTGACACCAGAAGTTGTCATGAAAATTATTGACATCAGAAGTTGTCATATCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATACCAAATTATTATC

                                                             *            
       6933 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATATCAAATTATTATC
          1 TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATACCAAATTATTATC

                                                                 *    
       6995 TTGACACCAGAAGTTGTCATGCTGAGGAAATTATTGACACCAGAAGTTGTCATCCCAA
          1 TTGACACCAGAAGTTGTCA---TGA--AAATTATTGACACCAGAAGTTGTCATACCAA

       7053 GATTGGAATT


Statistics
Matches: 172,  Mismatches: 5, Indels: 5
        0.95            0.03        0.03

Matches are distributed among these distances:
  62  140  0.81
  65    3  0.02
  67   29  0.17

ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31


Consensus pattern (62 bp):   
TTGACACCAGAAGTTGTCATGAAAATTATTGACACCAGAAGTTGTCATACCAAATTATTATC

Done.