Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002510.1 Corchorus olitorius cultivar O-4 contig02510, 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: 2296
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--46  Score: 92
    Period size: 2  Copynumber: 23.0  Consensus size: 2

                                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                 
         43 TA TA
          1 TA TA

         47 CTAAATATTA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:1739 original size:2 final size:2

Alignment explanation


    Indices: 1722--1781  Score: 75
    Period size: 2  Copynumber: 27.5  Consensus size: 2

       1712 TAATTAATGC

                                                                            
       1722 AT AT CAT AT CAT AT AT AT CAT AT AT AT CAT AT AT AT CAT AT AT AT
          1 AT AT -AT AT -AT AT AT AT -AT AT AT AT -AT AT AT AT -AT AT AT AT

                                  
       1767 AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT A

       1782 ATGATAATAA


Statistics
Matches: 53,  Mismatches: 0, Indels: 10
        0.84            0.00        0.16

Matches are distributed among these distances:
   2   43  0.81
   3   10  0.19

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


Consensus pattern (2 bp):   
AT

Found at i:1741 original size:9 final size:9

Alignment explanation


    Indices: 1721--1781  Score: 99
    Period size: 9  Copynumber: 6.9  Consensus size: 9

       1711 CTAATTAATG

                      
       1721 CATATCATAT
          1 CATAT-ATAT

                     
       1731 CATATATAT
          1 CATATATAT

                     
       1740 CATATATAT
          1 CATATATAT

                     
       1749 CATATATAT
          1 CATATATAT

                     
       1758 CATATATAT
          1 CATATATAT

                     
       1767 -ATATATAT
          1 CATATATAT

                    
       1775 -ATATATA
          1 CATATATA

       1782 ATGATAATAA


Statistics
Matches: 51,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
   8   15  0.29
   9   31  0.61
  10    5  0.10

ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44


Consensus pattern (9 bp):   
CATATATAT

Found at i:2000 original size:17 final size:17

Alignment explanation


    Indices: 1978--2010  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       1968 TAAAGAAATC

                             
       1978 ATATCATATATATATAT
          1 ATATCATATATATATAT

                            
       1995 ATATCATATATATATA
          1 ATATCATATATATATA

       2011 ATGATAACAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45


Consensus pattern (17 bp):   
ATATCATATATATATAT

Found at i:2197 original size:228 final size:226

Alignment explanation


    Indices: 1747--2215  Score: 807
    Period size: 229  Copynumber: 2.1  Consensus size: 226

       1737 TATCATATAT

                                                      *                      
       1747 ATCATATATATCATATATATATATATATATATATAATGATAATAATATACACTACAAATATGAAA
          1 ATCATATATAT-ATATATATATATATATATATATAATGATAACAATATACACTACAAATATGAAA

                                            *                                
       1812 ACTCTTTAAATGTTGAGGCCTCCAAATCTCGATACGTGTCTCTAATTAATTCTAATATTAATTAT
         65 ACTCTTTAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTAATTAT

                                                                             
       1877 ATTGATATATTAATTAGAAAAAAGCCTTTCGTATATTTTAAGAAAGAACAATAATTTATCTTACA
        130 ATTGATATATTAATTAGAAAAAAGCCTTTCGTATATTTTAAGAAAGAACAATAATTTATCTTACA

                                             
       1942 AATTTTTAAGATTTTAATTAAAAAAATAAAGAA
        195 AATTTTTAAGATTTTAATTAAAAAAATAAAG-A

                                                           *               * 
       1975 ATCATATCATATATATATATATATCATATATATATAATGATAACAATGTACACTACAAATATGGA
          1 ATCATAT-ATATATATATATATAT-ATATATATATAATGATAACAATATACACTACAAATATGAA

                                                                        *    
       2040 AACTCTTTAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTCATTA
         64 AACTCTTTAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTAATTA

                        *                  *                           *     
       2105 TATTGATATATTGATTAGAAAAAAAGCCTTTGGTATA-TTTAAG-AAGAACAATAATTTCTCTTA
        129 TATTGATATATTAATTAG-AAAAAAGCCTTTCGTATATTTTAAGAAAGAACAATAATTTATCTTA

                                              
       2168 CAAATTTTTAAGATTTTAATTAAAAAAATAAAGA
        193 CAAATTTTTAAGATTTTAATTAAAAAAATAAAGA

                          
       2202 ATCATATATATATA
          1 ATCATATATATATA

       2216 ATGATAACAA


Statistics
Matches: 230,  Mismatches: 8, Indels: 8
        0.93            0.03        0.03

Matches are distributed among these distances:
 226    7  0.03
 227    8  0.03
 228   71  0.31
 229  127  0.55
 230   17  0.07

ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37


Consensus pattern (226 bp):   
ATCATATATATATATATATATATATATATATATAATGATAACAATATACACTACAAATATGAAAA
CTCTTTAAATGTTGAGGCCTCCAAATCTCGACACGTGTCTCTAATTAATTCTAATATTAATTATA
TTGATATATTAATTAGAAAAAAGCCTTTCGTATATTTTAAGAAAGAACAATAATTTATCTTACAA
ATTTTTAAGATTTTAATTAAAAAAATAAAGA
Done.