Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005187.1 Corchorus capsularis cultivar CVL-1 contig05205, 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: 8638
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36


Found at i:3357 original size:59 final size:59

Alignment explanation


    Indices: 3226--3404  Score: 290
    Period size: 59  Copynumber: 3.0  Consensus size: 59

       3216 CTTGGTTAAG

                                      *                        *        
       3226 AAAAATTAAAATATCTTATTTC--TTCTTTTCATTATTTCTATCTTTTTAAAATTACTAT
          1 AAAAATTAAAATATCTTATTTCTTTTTTTTTCATTATTTCTAT-TTTTTAATATTACTAT

                                               *                       
       3284 AAAAATTAAAATATCTTATTTCTTTTTTTTTCATTGTTTCTATTTTTTAATATTACTAT
          1 AAAAATTAAAATATCTTATTTCTTTTTTTTTCATTATTTCTATTTTTTAATATTACTAT

                 *                                                      
       3343 AAAAAATAAAATATCTTATTTCTTTTTTTTTCATTATTTCTATTTTTTTAATATTACTAT
          1 AAAAATTAAAATATCTTATTTCTTTTTTTTTCATTATTTCTA-TTTTTTAATATTACTAT

              
       3403 AA
          1 AA

       3405 TGTGGGCCTC


Statistics
Matches: 113,  Mismatches: 5, Indels: 4
        0.93            0.04        0.03

Matches are distributed among these distances:
  58   22  0.19
  59   55  0.49
  60   36  0.32

ACGTcount: A:0.34, C:0.09, G:0.01, T:0.56


Consensus pattern (59 bp):   
AAAAATTAAAATATCTTATTTCTTTTTTTTTCATTATTTCTATTTTTTAATATTACTAT

Found at i:3397 original size:17 final size:18

Alignment explanation


    Indices: 3359--3402  Score: 54
    Period size: 18  Copynumber: 2.5  Consensus size: 18

       3349 TAAAATATCT

                   *         *
       3359 TATTTCTTTTTTTTTCAT
          1 TATTTCTATTTTTTTCAA

                              
       3377 TATTTCTATTTTTTT-AA
          1 TATTTCTATTTTTTTCAA

                *    
       3394 TATTACTAT
          1 TATTTCTAT

       3403 AATGTGGGCC


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  17    9  0.39
  18   14  0.61

ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70


Consensus pattern (18 bp):   
TATTTCTATTTTTTTCAA
Done.