Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015317.1 Corchorus capsularis cultivar CVL-1 contig15338, 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: 10134
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35


Found at i:4609 original size:17 final size:17

Alignment explanation


    Indices: 4587--4620  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       4577 GAAATCTAGC

                              
       4587 TATTCCTTG-TATCATTT
          1 TATTCC-TGATATCATTT

                             
       4604 TATTCCTGATATCATTT
          1 TATTCCTGATATCATTT

       4621 GATTTTGTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    2  0.12
  17   14  0.88

ACGTcount: A:0.21, C:0.18, G:0.06, T:0.56


Consensus pattern (17 bp):   
TATTCCTGATATCATTT

Found at i:5641 original size:16 final size:16

Alignment explanation


    Indices: 5591--5641  Score: 75
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       5581 AAGTCTTTTC

                          * 
       5591 TTTCATTTTATTTAAT
          1 TTTCATTTTATTTATT

                         *  
       5607 TTTCATTTTATTTCTT
          1 TTTCATTTTATTTATT

                 *          
       5623 TTTCAGTTTATTTATT
          1 TTTCATTTTATTTATT

               
       5639 TTT
          1 TTT

       5642 TTCATTTTCT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   31  1.00

ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73


Consensus pattern (16 bp):   
TTTCATTTTATTTATT

Found at i:5654 original size:17 final size:16

Alignment explanation


    Indices: 5596--5657  Score: 54
    Period size: 17  Copynumber: 3.6  Consensus size: 16

       5586 TTTTCTTTCA

                              
       5596 TTTTATTTAATTTTCATT
          1 TTTTATTT--TTTTCATT

                   *          
       5614 TTATT-TCTTTTTCAGTT
          1 TT-TTATTTTTTTCA-TT

                             
       5631 TATTTATTTTTTTCATT
          1 T-TTTATTTTTTTCATT

                      
       5648 TTCTTATTTT
          1 TT-TTATTTT

       5658 CCATTCAATA


Statistics
Matches: 37,  Mismatches: 2, Indels: 11
        0.74            0.04        0.22

Matches are distributed among these distances:
  16    7  0.19
  17   15  0.41
  18   13  0.35
  19    2  0.05

ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74


Consensus pattern (16 bp):   
TTTTATTTTTTTCATT
Done.