Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004619.1 Corchorus capsularis cultivar CVL-1 contig04631, 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: 2179
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:1213 original size:18 final size:18

Alignment explanation


    Indices: 1190--1225  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       1180 AAGGTAAGCC

                              
       1190 TATTTATTTCTGGTTCTA
          1 TATTTATTTCTGGTTCTA

                              
       1208 TATTTATTTCTGGTTCTA
          1 TATTTATTTCTGGTTCTA

       1226 AGAGTAGTAG


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

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61


Consensus pattern (18 bp):   
TATTTATTTCTGGTTCTA

Found at i:1828 original size:19 final size:18

Alignment explanation


    Indices: 1795--1842  Score: 62
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       1785 AATAGAGTAT

                              
       1795 TATTAATATAAATTAATA
          1 TATTAATATAAATTAATA

                *              
       1813 TATTTATATAAAATTAATA
          1 TATTAATAT-AAATTAATA

              *         
       1832 TAATAA-ATAAA
          1 TATTAATATAAA

       1843 ATATGCATTA


Statistics
Matches: 26,  Mismatches: 3, Indels: 3
        0.81            0.09        0.09

Matches are distributed among these distances:
  17    3  0.12
  18   10  0.38
  19   13  0.50

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (18 bp):   
TATTAATATAAATTAATA

Found at i:1877 original size:18 final size:16

Alignment explanation


    Indices: 1835--1868  Score: 68
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       1825 ATTAATATAA

                            
       1835 TAAATAAAATATGCAT
          1 TAAATAAAATATGCAT

                            
       1851 TAAATAAAATATGCAT
          1 TAAATAAAATATGCAT

              
       1867 TA
          1 TA

       1869 TATATAAAAC


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

Matches are distributed among these distances:
  16   18  1.00

ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32


Consensus pattern (16 bp):   
TAAATAAAATATGCAT
Done.