Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010519.1 Corchorus capsularis cultivar CVL-1 contig10540, 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: 43672
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:5393 original size:17 final size:16

Alignment explanation


    Indices: 5371--5402  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

       5361 GGTTTTCTTG

                             
       5371 AAACCCTAAAATGGGAA
          1 AAACCCTAAAA-GGGAA

                           
       5388 AAACCCTAAAAGGGA
          1 AAACCCTAAAAGGGA

       5403 GGGGAGGGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    4  0.27
  17   11  0.73

ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09


Consensus pattern (16 bp):   
AAACCCTAAAAGGGAA

Found at i:6237 original size:7 final size:7

Alignment explanation


    Indices: 6225--6249  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       6215 CCTGCATTTG

                   
       6225 CCCTATT
          1 CCCTATT

                   
       6232 CCCTATT
          1 CCCTATT

                   
       6239 CCCTATT
          1 CCCTATT

                
       6246 CCCT
          1 CCCT

       6250 CTTATTATCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.12, C:0.48, G:0.00, T:0.40


Consensus pattern (7 bp):   
CCCTATT

Found at i:42472 original size:15 final size:15

Alignment explanation


    Indices: 42452--42505  Score: 51
    Period size: 15  Copynumber: 3.7  Consensus size: 15

      42442 TATATATATA

                           
      42452 TATATATATAGTGTT
          1 TATATATATAGTGTT

                           
      42467 TATATA-ATAGT-TT
          1 TATATATATAGTGTT

                        **   
      42480 TCACTAT-TATAAAGTT
          1 T-A-TATATATAGTGTT

                      
      42496 TATATATATA
          1 TATATATATA

      42506 TAAAGTTGGA


Statistics
Matches: 32,  Mismatches: 2, Indels: 10
        0.73            0.05        0.23

Matches are distributed among these distances:
  13    3  0.09
  14    9  0.28
  15   17  0.53
  16    3  0.09

ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50


Consensus pattern (15 bp):   
TATATATATAGTGTT
Done.