Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014552.1 Corchorus olitorius cultivar O-4 contig14585, 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: 5044
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35


Found at i:3107 original size:33 final size:33

Alignment explanation


    Indices: 3066--3167  Score: 127
    Period size: 33  Copynumber: 3.1  Consensus size: 33

       3056 TATGCCAATT

                                             
       3066 AATTTGATCTTGACATCTTTGTTTCTTCCATTC
          1 AATTTGATCTTGACATCTTTGTTTCTTCCATTC

                                  *     *     *
       3099 AATTTGATCTTGACATC-TTG-ATCTTGACATCTT
          1 AATTTGATCTTGACATCTTTGTTTCTT-CCAT-TC

            **                               
       3132 TGTTTGATCTTGACATCTTTGTTTCTTCCATTC
          1 AATTTGATCTTGACATCTTTGTTTCTTCCATTC

               
       3165 AAT
          1 AAT

       3168 CATTTGTTGC


Statistics
Matches: 55,  Mismatches: 10, Indels: 8
        0.75            0.14        0.11

Matches are distributed among these distances:
  31    4  0.07
  32    6  0.11
  33   35  0.64
  34    6  0.11
  35    4  0.07

ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50


Consensus pattern (33 bp):   
AATTTGATCTTGACATCTTTGTTTCTTCCATTC

Found at i:3121 original size:14 final size:14

Alignment explanation


    Indices: 3102--3131  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       3092 TCCATTCAAT

                          
       3102 TTGATCTTGACATC
          1 TTGATCTTGACATC

                          
       3116 TTGATCTTGACATC
          1 TTGATCTTGACATC

              
       3130 TT
          1 TT

       3132 TGTTTGATCT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47


Consensus pattern (14 bp):   
TTGATCTTGACATC

Found at i:3140 original size:19 final size:19

Alignment explanation


    Indices: 3116--3155  Score: 80
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       3106 TCTTGACATC

                               
       3116 TTGATCTTGACATCTTTGT
          1 TTGATCTTGACATCTTTGT

                               
       3135 TTGATCTTGACATCTTTGT
          1 TTGATCTTGACATCTTTGT

              
       3154 TT
          1 TT

       3156 CTTCCATTCA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55


Consensus pattern (19 bp):   
TTGATCTTGACATCTTTGT

Found at i:3752 original size:27 final size:27

Alignment explanation


    Indices: 3714--3788  Score: 132
    Period size: 27  Copynumber: 2.8  Consensus size: 27

       3704 GACTGTTGCC

                                       
       3714 GCAGTGGATCCTCCCACTTCGACCCCA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                         *           * 
       3741 GCAGTGGATCCTCACACTTCGACCCTA
          1 GCAGTGGATCCTCCCACTTCGACCCCA

                                 
       3768 GCAGTGGATCCTCCCACTTCG
          1 GCAGTGGATCCTCCCACTTCG

       3789 CCTCGGGTCG


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   45  1.00

ACGTcount: A:0.19, C:0.40, G:0.20, T:0.21


Consensus pattern (27 bp):   
GCAGTGGATCCTCCCACTTCGACCCCA
Done.