Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014826.1 Corchorus olitorius cultivar O-4 contig14859, 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: 7422
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Found at i:2205 original size:85 final size:84

Alignment explanation


    Indices: 2076--2243  Score: 248
    Period size: 85  Copynumber: 2.0  Consensus size: 84

       2066 TTTTGGGTAA

                     *              * *       *    *                         
       2076 TAATTGATTTTGGGTTATGGGTTTTTGGAAAAAATTATTTTTTTATGACTTTTTGGGTTGAATTG
          1 TAATTGATTATGGGTTATGGGTTTCTAGAAAAAAATATTGTTTTATGACTTTTTGGGTTGAATTG

                                 
       2141 TTTATG-GATTTTTTCGATAG
         66 TTTATGAG-TTTTTT-GATAG

                                                *           *                
       2161 TAATTGATTATGGGTTATGGGTTTCTAGAAAAAAATGTTGTTTTATGATTTTTTGGGTTGAATTG
          1 TAATTGATTATGGGTTATGGGTTTCTAGAAAAAAATATTGTTTTATGACTTTTTGGGTTGAATTG

                              
       2226 TTTATGAGTTTTTTGATA
         66 TTTATGAGTTTTTTGATA

       2244 TTTTTGGAAA


Statistics
Matches: 75,  Mismatches: 7, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  84    4  0.05
  85   70  0.93
  86    1  0.01

ACGTcount: A:0.24, C:0.02, G:0.23, T:0.52


Consensus pattern (84 bp):   
TAATTGATTATGGGTTATGGGTTTCTAGAAAAAAATATTGTTTTATGACTTTTTGGGTTGAATTG
TTTATGAGTTTTTTGATAG

Found at i:4389 original size:2 final size:2

Alignment explanation


    Indices: 4376--4409  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       4366 AGGAGATTAT

                      *                                         
       4376 TA TA TA TG TA TA TA -A TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4410 TATTAAGTTA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:5278 original size:31 final size:31

Alignment explanation


    Indices: 5243--5303  Score: 79
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       5233 TTCGGCTCAT

                            * *             
       5243 CTGGATTCA-GGTCATTCGGGTCTCGGGTTTG
          1 CTGGATTCAGGGTCATGCAGGT-TCGGGTTTG

                   *                      
       5274 CTGGATTTAGGGTCATGCAGGTTCGGGTTT
          1 CTGGATTCAGGGTCATGCAGGTTCGGGTTT

       5304 TGGCCTCAGG


Statistics
Matches: 26,  Mismatches: 3, Indels: 2
        0.84            0.10        0.06

Matches are distributed among these distances:
  31   16  0.62
  32   10  0.38

ACGTcount: A:0.11, C:0.16, G:0.36, T:0.36


Consensus pattern (31 bp):   
CTGGATTCAGGGTCATGCAGGTTCGGGTTTG

Found at i:6133 original size:19 final size:19

Alignment explanation


    Indices: 6097--6135  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       6087 ATTTGATCCA

                         *     
       6097 TATATATATAATAGATTTT
          1 TATATATATAATACATTTT

                                
       6116 TATACTATAT-ATACATTTT
          1 TATA-TATATAATACATTTT

             
       6135 T
          1 T

       6136 CTTAGGTAAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  19   13  0.72
  20    5  0.28

ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54


Consensus pattern (19 bp):   
TATATATATAATACATTTT
Done.