Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022306.1 Corchorus olitorius cultivar O-4 contig22339, 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: 2009
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35


Found at i:525 original size:13 final size:13

Alignment explanation


    Indices: 503--547  Score: 58
    Period size: 12  Copynumber: 3.6  Consensus size: 13

        493 GGAAATGTTC

                 *       
        503 TATAACTGCTTTA
          1 TATAAATGCTTTA

                         
        516 TATAAATGCTTTA
          1 TATAAATGCTTTA

                    *    
        529 TA-AAATGTTTTA
          1 TATAAATGCTTTA

                    
        541 -ATAAATG
          1 TATAAATG

        548 TTTTGGGTGC


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  11    1  0.03
  12   14  0.48
  13   14  0.48

ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44


Consensus pattern (13 bp):   
TATAAATGCTTTA

Found at i:1265 original size:31 final size:31

Alignment explanation


    Indices: 1222--1309  Score: 133
    Period size: 31  Copynumber: 2.9  Consensus size: 31

       1212 ACTAATATGT

                                          *
       1222 CCAAA-AAAAACATAAGGGATTTTTTTGTCT
          1 CCAAAGAAAAACATAAGGGATTTTTTTGTCC

            **                             
       1252 TTAAAGAAAAACATAAGGGATTTTTTTGTCC
          1 CCAAAGAAAAACATAAGGGATTTTTTTGTCC

                      *                
       1283 CCAAAGAAAAGCATAAGGGATTTTTTT
          1 CCAAAGAAAAACATAAGGGATTTTTTT

       1310 AGTATTTAGT


Statistics
Matches: 51,  Mismatches: 6, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  30    3  0.06
  31   48  0.94

ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33


Consensus pattern (31 bp):   
CCAAAGAAAAACATAAGGGATTTTTTTGTCC

Found at i:1626 original size:154 final size:155

Alignment explanation


    Indices: 1456--1884  Score: 580
    Period size: 156  Copynumber: 2.8  Consensus size: 155

       1446 TAATTCCCTA

                        *               *                             *      
       1456 AAAAT-GTAAAATTAAAATAGTTATAAAAATATT-GAATTTAATTAAATAAAAATAGAATTTTTG
          1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAG-ATTTAATTAAATAAAAATAGAGTTTTTG

            *                         *    *                                 
       1519 GTGAAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAAAAAAATTCTAATA
         65 TTGAAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAAATTCTAATA

                                 *    
       1584 TATCTAA-CTTTTTAATTAAATTAGT
        130 TATCTAAGCTTTTTAATTAAAATAGT

                                           *        *                      **
       1609 AAAATGGTAAAAATAAAATAGTTATAAATATGTTAGATTTGATTAAATAAAAATAGAGTTCTTAA
          1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTT-TTTG

                *      *                                                     
       1674 TTGAGA-AAAATTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAAATTCTAATA
         65 TTGAAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAAATTCTAATA

                     *                 
       1738 TATCTAAGTTTTTTTAATTAAAATAGT
        130 TATCTAAG-CTTTTTAATTAAAATAGT

                          *     *     *      *     *                         
       1765 AAAATGGTAAAAATGAAATATTTATATATATATAAGATTAAATTAAATAAAAATAGAGTTTTTAG
          1 AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTTTTT-G

                         *     *                           *  *     
       1830 TTG-AATAAAACTATAAAAATTTAAACAATGACATTTAAGAAATATAATTGAAAAA
         65 TTGAAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAA

       1885 TAAGGGTATA


Statistics
Matches: 240,  Mismatches: 29, Indels: 11
        0.86            0.10        0.04

Matches are distributed among these distances:
 153    5  0.02
 154  109  0.45
 155   10  0.04
 156  116  0.48

ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36


Consensus pattern (155 bp):   
AAAATGGTAAAAATAAAATAGTTATAAATATATTAGATTTAATTAAATAAAAATAGAGTTTTTGT
TGAAATAAAACTGTAAAAGTTTAAACAATGACATTTAAGAAATATATTTAAAAAAATTCTAATAT
ATCTAAGCTTTTTAATTAAAATAGT

Found at i:1875 original size:79 final size:76

Alignment explanation


    Indices: 1650--1884  Score: 169
    Period size: 77  Copynumber: 3.0  Consensus size: 76

       1640 GTTAGATTTG

                                  *              *     *                     
       1650 ATTAAATAAAAATAGAGTTCTTAATTGAGA-AAAATTGTAAAAGTTTAAACAATGACATTTAAGA
          1 ATTAAATAAAAATAGAGTT-TTTATTGA-ATAAAA-TATAAAAATTTAAACAATGACATTTAAGA

                           
       1714 AATATATTTAAAAAA
         63 AATATA-TTAAAAAA

                *    * **                                 *          *     * 
       1729 ATTCTAATATATCTA-AGTTTTT-TT-AATTAAAATAGT-AAAATGGTAAA-AATGAAATATTTA
          1 ATT-AAATAAAAATAGAGTTTTTATTGAA-TAAAATA-TAAAAAT-TTAAACAATGACAT-TTAA

            * *            *  
       1789 TATATATA-TAAGATTAA
         61 GAAATATATTAA-A-AAA

                                                                             
       1806 ATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAATTTAAACAATGACATTTAAGAA
          1 ATTAAATAAAAATAGAGTTTTTA-TTGAATAAAA-TATAAAAATTTAAACAATGACATTTAAGAA

                    *     
       1871 ATATAATTGAAAAA
         64 ATAT-ATTAAAAAA

       1885 TAAGGGTATA


Statistics
Matches: 115,  Mismatches: 24, Indels: 34
        0.66            0.14        0.20

Matches are distributed among these distances:
  75    4  0.03
  76   21  0.18
  77   32  0.28
  78    2  0.02
  79   29  0.25
  80   25  0.22
  81    2  0.02

ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35


Consensus pattern (76 bp):   
ATTAAATAAAAATAGAGTTTTTATTGAATAAAATATAAAAATTTAAACAATGACATTTAAGAAAT
ATATTAAAAAA
Done.