Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016057.1 Corchorus capsularis cultivar CVL-1 contig16078, 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: 26053
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:2318 original size:21 final size:21

Alignment explanation


    Indices: 2254--2308  Score: 92
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       2244 TAATCCTATG

                                 
       2254 TTGGAGGTTTCTTATTTATAT
          1 TTGGAGGTTTCTTATTTATAT

              **                 
       2275 TTTTAGGTTTCTTATTTATAT
          1 TTGGAGGTTTCTTATTTATAT

                         
       2296 TTGGAGGTTTCTT
          1 TTGGAGGTTTCTT

       2309 TATGATATTT


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.05, G:0.18, T:0.60


Consensus pattern (21 bp):   
TTGGAGGTTTCTTATTTATAT

Found at i:6932 original size:19 final size:18

Alignment explanation


    Indices: 6908--6943  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       6898 TGAAGATTTC

                               
       6908 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       6927 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       6944 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:8246 original size:15 final size:16

Alignment explanation


    Indices: 8226--8259  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       8216 AATTGCTTTC

                         *  
       8226 TTAGTTA-ATTTACTT
          1 TTAGTTAGATTTAATT

                            
       8241 TTAGTTAGATTTAATT
          1 TTAGTTAGATTTAATT

               
       8257 TTA
          1 TTA

       8260 ATTCTTCTTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    7  0.41
  16   10  0.59

ACGTcount: A:0.29, C:0.03, G:0.09, T:0.59


Consensus pattern (16 bp):   
TTAGTTAGATTTAATT

Found at i:15118 original size:24 final size:23

Alignment explanation


    Indices: 15091--15137  Score: 60
    Period size: 24  Copynumber: 2.0  Consensus size: 23

      15081 AGTTATTTAG

                                     
      15091 TTTATGCTT-TATCTTTAATTTTTC
          1 TTTAT-CTTATATCTTT-ATTTTTC

                      *            
      15115 TTTATCTTATGTCTTTATTTTTC
          1 TTTATCTTATATCTTTATTTTTC

      15138 AAGTTTCATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  23   10  0.48
  24   11  0.52

ACGTcount: A:0.15, C:0.13, G:0.04, T:0.68


Consensus pattern (23 bp):   
TTTATCTTATATCTTTATTTTTC

Found at i:16675 original size:19 final size:18

Alignment explanation


    Indices: 16651--16686  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      16641 TGAAGATTTC

                               
      16651 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      16670 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      16687 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.