Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023566.1 Corchorus olitorius cultivar O-4 contig23599, 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: 2579
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:870 original size:13 final size:13

Alignment explanation


    Indices: 852--889  Score: 55
    Period size: 13  Copynumber: 3.2  Consensus size: 13

        842 CTTGGCCCAT

                         
        852 TTATTATTATTTA
          1 TTATTATTATTTA

                         
        865 TTATTATTATTT-
          1 TTATTATTATTTA

                         
        877 TT-TT-TTATTTA
          1 TTATTATTATTTA

              
        888 TT
          1 TT

        890 TTTTTTTTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  10    6  0.25
  11    4  0.17
  12    2  0.08
  13   12  0.50

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (13 bp):   
TTATTATTATTTA

Found at i:1946 original size:330 final size:332

Alignment explanation


    Indices: 1272--1992  Score: 852
    Period size: 330  Copynumber: 2.2  Consensus size: 332

       1262 TACAGGAGTA

                     *  *              *        *             *     *  *     
       1272 CTTTTCACGATTTTAATATCGTTTTTCATATTTTTTCT-GAATTAATTTCAAATTATATTGAAAC
          1 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCGAATTAATTTCTAATTAAATCGAAAC

                                        *               *                    
       1336 AAGATTCAGATGTACATAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTGGTTAGATAAAT
         66 AAGATTCAGATGTACATAAAAACAAATCATTAAATTCAATGTGGCTGAGATTTGGTTAGATAAAT

                          *       **                      *          *     * 
       1401 AAAGATATTTCAAGGAGTCCGGTGCCAAAAATCATGCAAAACAGAGTCGTGGCCCTGTAATGCGT
        131 AAAGATA-TTCAAGAAGTCCGGCACCAAAAATCATGCAAAACAGAGCCGTGGCCCTGAAATGCAT

                                 *                                 *         
       1466 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAGTTGACCCGA
        195 TTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA

                                *  *                    *       *   *      * 
       1531 AAGATATTTCCTCAAATTTTGGCTAAAATACTCAAAAAAAAATACATAAGTCGATATCAAAAAGA
        260 AAGATATTTCCTCAAATTTTAGCGAAAATACTCAAAAAAAAATAAATAAGTCAATACCAAAAAAA

                 *  
       1596 TTGAAGGG
        325 TTGAAAGG

                 *             *                          *                 *
       1604 CTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTTTCGAATTAAATTCTAATTAAATCGAAAT
          1 CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCGAATTAATTTCTAATTAAATCGAAAC

                            *                                              * 
       1669 AAGATTCAGATGCT-CGTAAAAA-AAATCATTAAA-TCTAATGTGGCTGAGATTTGGTTAGATGA
         66 AAGATTCAGATG-TACATAAAAACAAATCATTAAATTC-AATGTGGCTGAGATTTGGTTAGATAA

                                  *                      *          **       
       1731 ATATAA-ATA-TCAAGAAGTCTTGGCACCAAAAATCATGCAAAACTGAGCCG-GG-TTTGAAATG
        129 ATA-AAGATATTCAAGAAGTC-CGGCACCAAAAATCATGCAAAACAGAGCCGTGGCCCTGAAATG

                       *    *                  *                             
       1792 CATTTTTAGCCGAAAATCGTGATGATTAGTACATATGATTTCGGCT-AAATTTTGCAAAAATTGA
        192 CATTTTTAGCCAAAAACCGTGATGATTAGTAC--ACGATTTCGGCTAAAATTTTGCAAAAATTGA

                      *         *                    *             *     *   
       1856 CCCGAAAGATTTTTCCTC-ATTTTCTAGCGAAAATACTC-ATAAAAAATAAATAATTCAATGCCA
        255 CCCGAAAGATATTTCCTCAAATTT-TAGCGAAAATACTCAAAAAAAAATAAATAAGTCAATACCA

                         *
       1919 AAAAAATTGAAAGT
        319 AAAAAATTGAAAGG

                                       *       *     *           *      
       1933 CTTTTTCACGCTTCTAATATCGTTTTTTCTATTTTATTTCAAAATTAATTTCTGATTAAA
          1 C-TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTC-GAATTAATTTCTAATTAAA

       1993 AGGAAACAGG


Statistics
Matches: 329,  Mismatches: 50, Indels: 21
        0.82            0.12        0.05

Matches are distributed among these distances:
 329   69  0.21
 330   91  0.28
 331   54  0.16
 332   72  0.22
 333   42  0.13
 334    1  0.00

ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Consensus pattern (332 bp):   
CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCGAATTAATTTCTAATTAAATCGAAAC
AAGATTCAGATGTACATAAAAACAAATCATTAAATTCAATGTGGCTGAGATTTGGTTAGATAAAT
AAAGATATTCAAGAAGTCCGGCACCAAAAATCATGCAAAACAGAGCCGTGGCCCTGAAATGCATT
TTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAA
AGATATTTCCTCAAATTTTAGCGAAAATACTCAAAAAAAAATAAATAAGTCAATACCAAAAAAAT
TGAAAGG
Done.