Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011382.1 Corchorus olitorius cultivar O-4 contig11415, 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: 2294
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37


Found at i:1898 original size:16 final size:16

Alignment explanation


    Indices: 1877--1907  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1867 CCTTAAAAAT

                            
       1877 CCTTAAAAATCTTAAC
          1 CCTTAAAAATCTTAAC

                           
       1893 CCTTAAAAATCTTAA
          1 CCTTAAAAATCTTAA

       1908 TTAGTCAATT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32


Consensus pattern (16 bp):   
CCTTAAAAATCTTAAC

Found at i:1927 original size:61 final size:66

Alignment explanation


    Indices: 1860--2003  Score: 192
    Period size: 70  Copynumber: 2.2  Consensus size: 66

       1850 CACGAACTCA

                                              *                              
       1860 AAAATACCCTTAAAAATCCTTAA-A-AA-T-CT-TA-ACCCTTAAAAATCTTAATTAGTCAATTA
          1 AAAATACCCTTAAAAAT-CTTAATACAATTACTAAATACCCTTAAAAATCTTAATTAGTCAATTA

              
       1919 CT
         65 CT

                                                                             
       1921 AAAATACCCTTAAAAATCTTAATTAGTCAATTACTAAAATACCCTTAAAAATCTTAATTAGTCAA
          1 AAAATACCCTTAAAAATCTTAA-TA--CAATTACT-AAATACCCTTAAAAATCTTAATTAGTCAA

                 
       1986 TTACT
         62 TTACT

                         
       1991 AAAATACCCTTAA
          1 AAAATACCCTTAA

       2004 TATTATAGTA


Statistics
Matches: 72,  Mismatches: 1, Indels: 11
        0.86            0.01        0.13

Matches are distributed among these distances:
  60    5  0.07
  61   17  0.24
  62    1  0.01
  65    2  0.03
  66    1  0.01
  67    2  0.03
  69    1  0.01
  70   43  0.60

ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33


Consensus pattern (66 bp):   
AAAATACCCTTAAAAATCTTAATACAATTACTAAATACCCTTAAAAATCTTAATTAGTCAATTAC
T

Found at i:1930 original size:35 final size:35

Alignment explanation


    Indices: 1891--2003  Score: 226
    Period size: 35  Copynumber: 3.2  Consensus size: 35

       1881 AAAAATCTTA

                                               
       1891 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT
          1 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT

                                               
       1926 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT
          1 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT

                                               
       1961 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT
          1 ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT

                    
       1996 ACCCTTAA
          1 ACCCTTAA

       2004 TATTATAGTA


Statistics
Matches: 78,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   78  1.00

ACGTcount: A:0.45, C:0.19, G:0.03, T:0.34


Consensus pattern (35 bp):   
ACCCTTAAAAATCTTAATTAGTCAATTACTAAAAT

Found at i:2188 original size:30 final size:30

Alignment explanation


    Indices: 2153--2214  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       2143 TATAATTTTT

                      *  *                 
       2153 AATCATTAAACTTTTATTT-ATTAATTATAA
          1 AATCATTAAAATTCTATTTCA-TAATTATAA

                                          
       2183 AATCATTAAAATTCTATTTCATAATTATAA
          1 AATCATTAAAATTCTATTTCATAATTATAA

              
       2213 AA
          1 AA

       2215 AGATATTGAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30   28  0.97
  31    1  0.03

ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45


Consensus pattern (30 bp):   
AATCATTAAAATTCTATTTCATAATTATAA
Done.