Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004983.1 Corchorus capsularis cultivar CVL-1 contig05001, 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: 6384
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35


Found at i:1159 original size:16 final size:16

Alignment explanation


    Indices: 1138--1172  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       1128 TAATATTGAA

                            
       1138 TTCAGGTATTTTCAGG
          1 TTCAGGTATTTTCAGG

                            
       1154 TTCAGGTATTTTCAGG
          1 TTCAGGTATTTTCAGG

               
       1170 TTC
          1 TTC

       1173 GAGTTCGGGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46


Consensus pattern (16 bp):   
TTCAGGTATTTTCAGG

Found at i:1571 original size:21 final size:21

Alignment explanation


    Indices: 1525--1571  Score: 85
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       1515 CTTTCCTTCC

                *                
       1525 TTTACATGATGTAACAAGCTT
          1 TTTAGATGATGTAACAAGCTT

                                 
       1546 TTTAGATGATGTAACAAGCTT
          1 TTTAGATGATGTAACAAGCTT

                 
       1567 TTTAG
          1 TTTAG

       1572 CTTGTGACCA


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40


Consensus pattern (21 bp):   
TTTAGATGATGTAACAAGCTT

Found at i:5357 original size:10 final size:10

Alignment explanation


    Indices: 5342--5372  Score: 53
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       5332 TTCTTGTGTA

                      
       5342 AAAAAAAAAG
          1 AAAAAAAAAG

                      
       5352 AAAAAAAAAG
          1 AAAAAAAAAG

                       
       5362 AAAAAAGAAAG
          1 AAAAAA-AAAG

       5373 GCAATTTTTT


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

Matches are distributed among these distances:
  10   16  0.80
  11    4  0.20

ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00


Consensus pattern (10 bp):   
AAAAAAAAAG
Done.