Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007904.1 Corchorus capsularis cultivar CVL-1 contig07925, 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: 17917
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32


Found at i:1859 original size:2 final size:2

Alignment explanation


    Indices: 1854--1908  Score: 110
    Period size: 2  Copynumber: 27.5  Consensus size: 2

       1844 GTGTGTATCA

                                                                          
       1854 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                               
       1896 AG AG AG AG AG AG A
          1 AG AG AG AG AG AG A

       1909 TTGTAAGGAT


Statistics
Matches: 53,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   53  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:3269 original size:134 final size:134

Alignment explanation


    Indices: 3029--3300  Score: 481
    Period size: 134  Copynumber: 2.0  Consensus size: 134

       3019 CACATTCATT

                                                 *            *      *       
       3029 TATTGCAAATCAGAGTTGCTTACTGTTCTGTTGAGTTTTCAATTGCTCCCTCTATCTGTACTATT
          1 TATTGCAAATCAGAGTTGCTTACTGTTCTGTTGAGTTCTCAATTGCTCCCACTATCTATACTATT

                  *                                                          
       3094 TAATCTGGTCGCACTAACACTCTGTCTTGCAGAAGAGTTAGTTACTCTTGAAAAGATTTTTAAGT
         66 TAATCTCGTCGCACTAACACTCTGTCTTGCAGAAGAGTTAGTTACTCTTGAAAAGATTTTTAAGT

                
       3159 GGGC
        131 GGGC

                       *                                                     
       3163 TATTGCAAATCCGAGTTGCTTACTGTTCTGTTGAGTTCTCAATTGCTCCCACTATCTATACTATT
          1 TATTGCAAATCAGAGTTGCTTACTGTTCTGTTGAGTTCTCAATTGCTCCCACTATCTATACTATT

                *                        *                                   
       3228 TAATTTCGTCGCACTAACACTCTGTCTTGTAGAAGAGTTAGTTACTCTTGAAAAGATTTTTAAGT
         66 TAATCTCGTCGCACTAACACTCTGTCTTGCAGAAGAGTTAGTTACTCTTGAAAAGATTTTTAAGT

                
       3293 GGGC
        131 GGGC

                
       3297 TATT
          1 TATT

       3301 CACCCCCCTC


Statistics
Matches: 131,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 134  131  1.00

ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39


Consensus pattern (134 bp):   
TATTGCAAATCAGAGTTGCTTACTGTTCTGTTGAGTTCTCAATTGCTCCCACTATCTATACTATT
TAATCTCGTCGCACTAACACTCTGTCTTGCAGAAGAGTTAGTTACTCTTGAAAAGATTTTTAAGT
GGGC

Found at i:9453 original size:2 final size:2

Alignment explanation


    Indices: 9446--9482  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       9436 TTCATTCCTA

                                                                   
       9446 AT AT AT AT 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 AT AT AT AT A

       9483 AAGAAGAAGT


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:9906 original size:18 final size:18

Alignment explanation


    Indices: 9883--9921  Score: 69
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       9873 CATTGAAAAA

                              
       9883 TGACATGGGTATGCAAAT
          1 TGACATGGGTATGCAAAT

                   *          
       9901 TGACATGTGTATGCAAAT
          1 TGACATGGGTATGCAAAT

               
       9919 TGA
          1 TGA

       9922 AAAATGATTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31


Consensus pattern (18 bp):   
TGACATGGGTATGCAAAT

Found at i:13230 original size:10 final size:10

Alignment explanation


    Indices: 13215--13239  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

      13205 TAACTCCAAT

                      
      13215 TATGGACTTA
          1 TATGGACTTA

                      
      13225 TATGGACTTA
          1 TATGGACTTA

                 
      13235 TATGG
          1 TATGG

      13240 GATGAATATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40


Consensus pattern (10 bp):   
TATGGACTTA
Done.