Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018165.1 Corchorus olitorius cultivar O-4 contig18198, 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: 99739
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:20513 original size:31 final size:31

Alignment explanation


    Indices: 20478--20542  Score: 112
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      20468 GATTCTCTTA

                                           
      20478 AAAATATATCAAGGAGTTTTATTTTTGGCAC
          1 AAAATATATCAAGGAGTTTTATTTTTGGCAC

                     *          *          
      20509 AAAATATATTAAGGAGTTTTTTTTTTGGCAC
          1 AAAATATATCAAGGAGTTTTATTTTTGGCAC

               
      20540 AAA
          1 AAA

      20543 GAAAGCAAAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40


Consensus pattern (31 bp):   
AAAATATATCAAGGAGTTTTATTTTTGGCAC

Found at i:37564 original size:31 final size:31

Alignment explanation


    Indices: 37526--37585  Score: 120
    Period size: 31  Copynumber: 1.9  Consensus size: 31

      37516 TATGATTTGA

                                           
      37526 TTGGAAATTAAAACTTCCCAATAGATCAGGG
          1 TTGGAAATTAAAACTTCCCAATAGATCAGGG

                                         
      37557 TTGGAAATTAAAACTTCCCAATAGATCAG
          1 TTGGAAATTAAAACTTCCCAATAGATCAG

      37586 AGTGAACCCT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27


Consensus pattern (31 bp):   
TTGGAAATTAAAACTTCCCAATAGATCAGGG

Found at i:68519 original size:24 final size:24

Alignment explanation


    Indices: 68488--68568  Score: 87
    Period size: 24  Copynumber: 3.4  Consensus size: 24

      68478 CTCCTCTCGT

                       *             
      68488 ACCCGAGCC-ATCAGGTCCACTTGC
          1 ACCCGAGCCTAGCA-GTCCACTTGC

                                     
      68512 -CCCTGAGCCTAGCAGTCCACTTGC
          1 ACCC-GAGCCTAGCAGTCCACTTGC

                       *       *     
      68536 ACCCGAGCCTACCAGTCC-TTTCGC
          1 ACCCGAGCCTAGCAGTCCACTT-GC

                     
      68560 ACCCGAGCC
          1 ACCCGAGCC

      68569 ATCCATGCCA


Statistics
Matches: 50,  Mismatches: 3, Indels: 8
        0.82            0.05        0.13

Matches are distributed among these distances:
  23    5  0.10
  24   39  0.78
  25    6  0.12

ACGTcount: A:0.19, C:0.44, G:0.20, T:0.17


Consensus pattern (24 bp):   
ACCCGAGCCTAGCAGTCCACTTGC

Found at i:74370 original size:16 final size:16

Alignment explanation


    Indices: 74319--74377  Score: 66
    Period size: 16  Copynumber: 3.7  Consensus size: 16

      74309 TGTGACTTCC

                 *     *    
      74319 TTTCCCTTCCTCCCTA
          1 TTTCCTTTCCTTCCTA

                     *   *   
      74335 TTTCCTTTTTCTTACTA
          1 TTTCC-TTTCCTTCCTA

                            
      74352 TTTCCTTTCCTTCCTA
          1 TTTCCTTTCCTTCCTA

                       
      74368 TTT-CTTTCCT
          1 TTTCCTTTCCT

      74378 CCCAACCAAA


Statistics
Matches: 36,  Mismatches: 6, Indels: 3
        0.80            0.13        0.07

Matches are distributed among these distances:
  15    7  0.19
  16   17  0.47
  17   12  0.33

ACGTcount: A:0.07, C:0.36, G:0.00, T:0.58


Consensus pattern (16 bp):   
TTTCCTTTCCTTCCTA

Found at i:92846 original size:32 final size:32

Alignment explanation


    Indices: 92785--92846  Score: 79
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      92775 TATATAGTAT

                *                *  *       
      92785 TATATTATTATATGATCATAATAATGAAAATG
          1 TATAGTATTATATGATCATAAAAAGGAAAATG

                         *  *             
      92817 TATAGTATTATATTATTATAAAAAGGAAAA
          1 TATAGTATTATATGATCATAAAAAGGAAAA

      92847 AGGTAAAACC


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  32   25  1.00

ACGTcount: A:0.50, C:0.02, G:0.10, T:0.39


Consensus pattern (32 bp):   
TATAGTATTATATGATCATAAAAAGGAAAATG

Found at i:93892 original size:14 final size:14

Alignment explanation


    Indices: 93869--93900  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

      93859 TCATTGGGAC

                 *        
      93869 ACAACCACTAGTTT
          1 ACAACAACTAGTTT

                          
      93883 ACAACAACTAGTTT
          1 ACAACAACTAGTTT

                
      93897 ACAA
          1 ACAA

      93901 TCTCGCACAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25


Consensus pattern (14 bp):   
ACAACAACTAGTTT

Found at i:94236 original size:2 final size:2

Alignment explanation


    Indices: 94231--94268  Score: 62
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      94221 GAATCGGGTC

                                                                       
      94231 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A- AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      94269 CAAAACATAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   32  0.94

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


Consensus pattern (2 bp):   
AT

Done.