Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010227.1 Corchorus olitorius cultivar O-4 contig10259, 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: 7570
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:65 original size:21 final size:18

Alignment explanation


    Indices: 23--57  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

         13 AATTATTACA

                              
         23 TTGTTCATGAACAATTTT
          1 TTGTTCATGAACAATTTT

                 *           
         41 TTGTTTATGAACAATTT
          1 TTGTTCATGAACAATTT

         58 CATTTTGTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51


Consensus pattern (18 bp):   
TTGTTCATGAACAATTTT

Found at i:1730 original size:75 final size:75

Alignment explanation


    Indices: 1643--1781  Score: 197
    Period size: 75  Copynumber: 1.9  Consensus size: 75

       1633 AAGATCTTGA

                              *    *   *  *         *                        
       1643 TTTGTGGAATTCTAGTTTTGATGTAAAGTTTTCTGCTGAAGTCTTGAGATTGTCAAAAATTGATG
          1 TTTGTGGAATTCTAGTTTGGATGCAAAATTCTCTGCTGAAATCTTGAGATTGTCAAAAATTGATG

                      
       1708 ACTTTGAAGG
         66 ACTTTGAAGG

                   *     *                            *  *                  
       1718 TTTGTGGGATTCTGGTTTGGATGCAAAATTCTCTGCTGAAATTTTTAGATTGTCAAAAATTGAT
          1 TTTGTGGAATTCTAGTTTGGATGCAAAATTCTCTGCTGAAATCTTGAGATTGTCAAAAATTGAT

       1782 CTTGATGGGT


Statistics
Matches: 55,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  75   55  1.00

ACGTcount: A:0.27, C:0.09, G:0.23, T:0.42


Consensus pattern (75 bp):   
TTTGTGGAATTCTAGTTTGGATGCAAAATTCTCTGCTGAAATCTTGAGATTGTCAAAAATTGATG
ACTTTGAAGG

Found at i:5950 original size:179 final size:178

Alignment explanation


    Indices: 5626--6090  Score: 535
    Period size: 179  Copynumber: 2.6  Consensus size: 178

       5616 CCAAAAAATA

                                **  *      *  *                              
       5626 AATTTTTCAGAAGCATTTTTGGTATTTGAAAAATCAAATTTAGCTTTC-ATGTCCTTCATGAAAG
          1 AATTTTTCAGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGA-GTCCTTCATGAAAG

               *      *                 *            *              **       
       5690 TTGCAGATCACGAAACAACCTTTTAACAAACACTTGAATCATCTCAATCGGACATCTTGAGCAAA
         65 TTGTAGATCATGAAACAACCTTTTAACAGACACTTGAATCACCTCAATCGGACATCCGGAGCAAA

              *      *                    **             *    
       5755 AATTATGTATTATTAAGTGGACCGTCCATTTTCGCTAAAC-GAAAGAACT
        130 AAGTATGTAATATTAAGTGGACCGTCCATTCCCG-TAAACTGAAACAACT

                   *                                                *        
       5804 AATTTTTTAGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCTGAGTCCTACATGAAAG
          1 AATTTTTCAGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTC-GAGTCCTTCATGAAAG

                       *   *  *       *            *                         
       5869 TTGTAGATCATAAAATAAACTTTTAAGAGACACTTGAATAACCTCAAT-GAGACATCCGGAG-AA
         65 TTGTAGATCATGAAACAACCTTTTAACAGACACTTGAATCACCTCAATCG-GACATCCGGAGCAA

                                   *             *             
       5932 AAAGTATTGTAATATTAAGTGGATCGTCCATTCCCGTTAACTGAAACAACT
        129 AAAGTA-TGTAATATTAAGTGGACCGTCCATTCCCGTAAACTGAAACAACT

            *       *   *                            *  *         *          
       5983 CATTTTTCGGAAAC-TTTTTTGATACTTGAAACATTAAATTCAGTTTTCGAGTCTTTCATGAAAG
          1 AATTTTTCAGAAGCATTTTTT-ATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAG

                        *             *    *            
       6047 TTGTAGATCATGGAACAACCTTTTAATAGACGCTTGAATCACCT
         65 TTGTAGATCATGAAACAACCTTTTAACAGACACTTGAATCACCT

       6091 TGATAGGATA


Statistics
Matches: 241,  Mismatches: 40, Indels: 12
        0.82            0.14        0.04

Matches are distributed among these distances:
 178  111  0.46
 179  129  0.54
 180    1  0.00

ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34


Consensus pattern (178 bp):   
AATTTTTCAGAAGCATTTTTTATACTTGAAACATTAAATTTAGCTTTCGAGTCCTTCATGAAAGT
TGTAGATCATGAAACAACCTTTTAACAGACACTTGAATCACCTCAATCGGACATCCGGAGCAAAA
AGTATGTAATATTAAGTGGACCGTCCATTCCCGTAAACTGAAACAACT

Found at i:6959 original size:20 final size:21

Alignment explanation


    Indices: 6914--6959  Score: 51
    Period size: 19  Copynumber: 2.3  Consensus size: 21

       6904 AATTTATAAA

                          *      
       6914 ACATATAAAAAATATTAAAAT
          1 ACATATAAAAAATAATAAAAT

                      *        * 
       6935 A-ATAT-AAATATAATAAATT
          1 ACATATAAAAAATAATAAAAT

                  
       6954 ACATAT
          1 ACATAT

       6960 TAATTTGTAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 3
        0.78            0.11        0.11

Matches are distributed among these distances:
  19   12  0.57
  20    8  0.38
  21    1  0.05

ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33


Consensus pattern (21 bp):   
ACATATAAAAAATAATAAAAT
Done.