Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024764.1 Corchorus olitorius cultivar O-4 contig24797, 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: 8323
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34


Found at i:1149 original size:2 final size:2

Alignment explanation


    Indices: 1142--1171  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1132 GTGCATTTCA

                                                        
       1142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1172 TATGCACACA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:5570 original size:35 final size:35

Alignment explanation


    Indices: 5507--5578  Score: 90
    Period size: 35  Copynumber: 2.1  Consensus size: 35

       5497 GATCCTCTTT

                *                           *  
       5507 GATATTGGAGTTAGTAGGATATTAAGGTGTTTGGA
          1 GATACTGGAGTTAGTAGGATATTAAGGTGTTTAGA

                           *  * *  *           
       5542 GATACTGGAGTTAGTTGGGTTTTGAGGTGTTTAGA
          1 GATACTGGAGTTAGTAGGATATTAAGGTGTTTAGA

              
       5577 GA
          1 GA

       5579 ACTTAAGATC


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  35   31  1.00

ACGTcount: A:0.25, C:0.01, G:0.36, T:0.38


Consensus pattern (35 bp):   
GATACTGGAGTTAGTAGGATATTAAGGTGTTTAGA

Found at i:7351 original size:33 final size:33

Alignment explanation


    Indices: 7309--7376  Score: 120
    Period size: 33  Copynumber: 2.1  Consensus size: 33

       7299 TTGAACTAAG

                                              
       7309 TAACTATTAATTTCACTTCTTT-ATGCAAAGTTC
          1 TAACTATTAATTTCACTT-TTTAATGCAAAGTTC

                                             
       7342 TAACTATTAATTTCACTTTTTAATGCAAAGTTC
          1 TAACTATTAATTTCACTTTTTAATGCAAAGTTC

              
       7375 TA
          1 TA

       7377 TTTAATTAAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  32    3  0.09
  33   31  0.91

ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46


Consensus pattern (33 bp):   
TAACTATTAATTTCACTTTTTAATGCAAAGTTC

Found at i:8274 original size:13 final size:11

Alignment explanation


    Indices: 8156--8269  Score: 67
    Period size: 11  Copynumber: 10.8  Consensus size: 11

       8146 ATTATGCTAT

                   *   
       8156 TATATATCAAA
          1 TATATATAAAA

                 *  ** 
       8167 TATATTTATGA
          1 TATATATAAAA

                       
       8178 TATATATAAAA
          1 TATATATAAAA

                    *  
       8189 TATAT-T-TAA
          1 TATATATAAAA

                 *  ** 
       8198 T-TATTTATGA
          1 TATATATAAAA

                       
       8208 TATATATAAAA
          1 TATATATAAAA

              *  *     
       8219 TACATGT-AAA
          1 TATATATAAAA

                      *
       8229 -ATATATAAAT
          1 TATATATAAAA

                 *  ** 
       8239 TATATTTATGA
          1 TATATATAAAA

                       
       8250 TATATATAAAA
          1 TATATATAAAA

                     
       8261 TATATATAA
          1 TATATATAA

       8270 CAAATTTTTT


Statistics
Matches: 74,  Mismatches: 24, Indels: 10
        0.69            0.22        0.09

Matches are distributed among these distances:
   8    3  0.04
   9    8  0.11
  10    9  0.12
  11   54  0.73

ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44


Consensus pattern (11 bp):   
TATATATAAAA
Done.