Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016025.1 Corchorus olitorius cultivar O-4 contig16058, 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: 2116
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--999  Score: 1411
    Period size: 154  Copynumber: 6.5  Consensus size: 154

                       *                    *                 *        *     
          1 GAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACCAATGGGCCTCGATA
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA

                                          *              *                   
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCGAAAAACTTCACAGTTGACTAATCTCACCAAAATG
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG

                       *            
        131 ATTATAGTTAGTCCATAAACAATG
        131 ATTATAGTTAGGCCATAAACAATG

                   *                          *                       **     
        155 GAAAGAAGAGCATTGAGGTTTGCCAAATCGAAGAGGATTCAAAACGTCACTAATGGGCTTCGATA
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA

                      *   *     *     *            *               *         
        220 GGCCCAAAATGACATGTGTTTCAAATTAGCTAAAAACTTTACAGTGGACTAATCTTACCAAAATG
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG

                       *  *   *     
        285 ATTATAGTTAGTCCCTAACCAATG
        131 ATTATAGTTAGGCCATAAACAATG

                                                          **           *   * 
        309 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAA
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA

            *                           *                                    
        374 AGCCC-AAATAACAAGTGTTCCAAATGACCT-AAAACTTCACAGTGGACTAATCTCACCAAAATG
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG

                   * *              
        437 ATTATAGGTCGGCCATAAACAATG
        131 ATTATAGTTAGGCCATAAACAATG

                                    *                  *    *             *  
        461 G-AAG-AAAGACATT-AGGTTT-CTAAATCCGAAGACGATTCAGAACGACACTAATGGGACCCCG
          1 GAAAGAAAAG-CATTGAGGTTTGCCAAAT-CGAAGACGATTCAAAACGTCACTAATGGG-CCACG

                                           *                                 
        522 ATAGGCCCAAAATAACAAGTGTTCCAAATGACCT-AAAACTTCACAGTGGACTAATCTCACCGAA
         63 ATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AA

                        *          *     
        586 AATGGATTATAGGTAGGCCATAAGCAATG
        127 AAT-GATTATAGTTAGGCCATAAACAATG

                                                              *     *        
        615 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCACGATA
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA

                *                         *                                  
        680 GGCCAAAAATAACAAGTGTTCCAAATGAGCGAAAAACTTCACAGTGGACTAATCTCACCAAAATG
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG

                                   *
        745 ATTATAGTTAGGCCATAAACAATA
        131 ATTATAGTTAGGCCATAAACAATG

                            *                                 *     *        
        769 GAAAGAAAAGCATTGAAGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCACGATA
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA

                                           **        *   *             *     
        834 GGCCCAAAATAACAAGTGTTCCAAATGAGCTGGAAACTTCAAAGTTGACTAATCTCACCGAAATG
         66 GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG

                                    
        899 ATTATAGTTAGGCCATAAACAATG
        131 ATTATAGTTAGGCCATAAACAATG

                                                            *           * *  
        923 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCAAT
          1 GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCCACGAT

            *    *       
        987 TGGCCTAAAATAA
         65 AGGCCCAAAATAA

       1000 TTGTAGACAC


Statistics
Matches: 760,  Mismatches: 73, Indels: 24
        0.89            0.09        0.03

Matches are distributed among these distances:
 149    5  0.01
 150   36  0.05
 151   18  0.02
 152  103  0.14
 153   25  0.03
 154  458  0.60
 155   48  0.06
 156   62  0.08
 157    5  0.01

ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21


Consensus pattern (154 bp):   
GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCACGATA
GGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGGCCATAAACAATG

Found at i:1493 original size:22 final size:21

Alignment explanation


    Indices: 1468--1512  Score: 54
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1458 TTCACGTTTA

                  *         *     
       1468 TTTCTTCTTGAGCATACTCATT
          1 TTTCTTATTG-GCATAATCATT

                      *          
       1490 TTTCTTATTGTCATAATCATT
          1 TTTCTTATTGGCATAATCATT

              
       1511 TT
          1 TT

       1513 GTCTATTAGT


Statistics
Matches: 20,  Mismatches: 3, Indels: 1
        0.83            0.12        0.04

Matches are distributed among these distances:
  21   11  0.55
  22    9  0.45

ACGTcount: A:0.20, C:0.18, G:0.07, T:0.56


Consensus pattern (21 bp):   
TTTCTTATTGGCATAATCATT

Found at i:1509 original size:21 final size:22

Alignment explanation


    Indices: 1480--1525  Score: 60
    Period size: 21  Copynumber: 2.1  Consensus size: 22

       1470 TCTTCTTGAG

                *                  
       1480 CATACTCATTTT-TCTTATT-GT
          1 CATAATCATTTTGTC-TATTAGT

                                  
       1501 CATAATCATTTTGTCTATTAGT
          1 CATAATCATTTTGTCTATTAGT

               
       1523 CAT
          1 CAT

       1526 GTATATACAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  21   15  0.68
  22    7  0.32

ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52


Consensus pattern (22 bp):   
CATAATCATTTTGTCTATTAGT
Done.