Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015938.1 Corchorus capsularis cultivar CVL-1 contig15959, 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: 9246
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:5267 original size:21 final size:20

Alignment explanation


    Indices: 5227--5266  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5217 CAAAATTAAC

                                
       5227 CCTATTTTTATGGTCATTTT
          1 CCTATTTTTATGGTCATTTT

                      *          
       5247 CCTATGTTTTTTGGT-ATTTT
          1 CCTAT-TTTTATGGTCATTTT

       5267 TATGGGTGAT


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

Matches are distributed among these distances:
  20   10  0.56
  21    8  0.44

ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62


Consensus pattern (20 bp):   
CCTATTTTTATGGTCATTTT

Found at i:6899 original size:20 final size:20

Alignment explanation


    Indices: 6874--6915  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6864 TTTTCTTAAG

                  *             
       6874 TAATTTTCTTAGCTTTAGTT
          1 TAATTTACTTAGCTTTAGTT

                             *  
       6894 TAATTTACTTAGCTTTATTT
          1 TAATTTACTTAGCTTTAGTT

              
       6914 TA
          1 TA

       6916 GATTAATTGT


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.24, C:0.10, G:0.07, T:0.60


Consensus pattern (20 bp):   
TAATTTACTTAGCTTTAGTT

Found at i:7195 original size:15 final size:13

Alignment explanation


    Indices: 7162--7202  Score: 57
    Period size: 14  Copynumber: 3.1  Consensus size: 13

       7152 TAATAATTCC

                         
       7162 TTATTTTT-ATTT
          1 TTATTTTTCATTT

                          
       7174 TTATTTTTCAATTT
          1 TTATTTTTC-ATTT

                          
       7188 TTAGTTTTTCATTT
          1 TTA-TTTTTCATTT

             
       7202 T
          1 T

       7203 CGTTTAAGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  12    8  0.31
  14   12  0.46
  15    6  0.23

ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76


Consensus pattern (13 bp):   
TTATTTTTCATTT
Done.