Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012432.1 Corchorus olitorius cultivar O-4 contig12465, 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: 18264
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:60 original size:10 final size:10

Alignment explanation


    Indices: 39--90  Score: 50
    Period size: 10  Copynumber: 5.2  Consensus size: 10

         29 AGGGATCAGT

                   *  
         39 AAAGGATAGG
          1 AAAGGATGGG

             *        
         49 ATAGGATGGG
          1 AAAGGATGGG

             *      * 
         59 ATAGGATGAG
          1 AAAGGATGGG

                  *   
         69 AAAGGAGGGG
          1 AAAGGATGGG

                  *   
         79 AAAGGAAGGG
          1 AAAGGATGGG

              
         89 AA
          1 AA

         91 TGACCAATCC


Statistics
Matches: 35,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  10   35  1.00

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


Consensus pattern (10 bp):   
AAAGGATGGG

Found at i:8958 original size:170 final size:170

Alignment explanation


    Indices: 8676--9139  Score: 662
    Period size: 170  Copynumber: 2.7  Consensus size: 170

       8666 ACCTCATTAA

                                           *   *                        *    
       8676 AATCATTTTCTAGCTACGCCACTGTGTGAATAGGTCTCGGAACCAACTGCTGAAACAACCGTGCA
          1 AATCATTTTCTAGCTACGCCACTGTGTGAATGGGTTTCGGAACCAACTGCTGAAACAACCATGCA

                                   **  *       *                             
       8741 AAACTATGACAAGCATTAAAGCTTTGCTTAACATCACAATATTTTCTCTTGACACCTCAATGTAA
         66 AAACTATGACAAGCATTAAAGCTCCGCCTAACATCGCAATATTTTCTCTTGACACCTCAATGTAA

                  *                *                 
       8806 ATTTTATCTTCTGAA-TTGGAGTTCTTCTCAACATCAC-AC
        131 ATTTTACCTTCT-AACTTGGAGTACTTCTCAACATCACGAC

                                    *   *          *            *        *   
       8845 TAATCATTTTCTAGCTACGCCACTATGTAAATGGGTTTCAGAACCAACTGCTAAAACAACCTTGC
          1 -AATCATTTTCTAGCTACGCCACTGTGTGAATGGGTTTCGGAACCAACTGCTGAAACAACCATGC

                       *   *          *                                 *    
       8910 AAAACTATGACGAGCGTTAAAGCTCCACCTAACATCGCAATATTTTCTCTTGACACCTCATTGTA
         65 AAAACTATGACAAGCATTAAAGCTCCGCCTAACATCGCAATATTTTCTCTTGACACCTCAATGTA

                                                     
       8975 AATTTTACCTTCTAACTTGGAGTACTTCTCAACATCACGAC
        130 AATTTTACCTTCTAACTTGGAGTACTTCTCAACATCACGAC

                            *                                      * **    * 
       9016 AATCATTTTCTAGCTATGCCACTGTGTGAATGGGTTTCGGAACCAACTGCTGAAATAGTCATGTA
          1 AATCATTTTCTAGCTACGCCACTGTGTGAATGGGTTTCGGAACCAACTGCTGAAACAACCATGCA

                   *          *               *                        
       9081 AAACTATAACAAGCATTAGAGCTCCGCCTAACATAGCAATATTTTCTCTTGACACCTCA
         66 AAACTATGACAAGCATTAAAGCTCCGCCTAACATCGCAATATTTTCTCTTGACACCTCA

       9140 TTGCTTTTTG


Statistics
Matches: 259,  Mismatches: 33, Indels: 4
        0.88            0.11        0.01

Matches are distributed among these distances:
 169    2  0.01
 170  255  0.98
 171    2  0.01

ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31


Consensus pattern (170 bp):   
AATCATTTTCTAGCTACGCCACTGTGTGAATGGGTTTCGGAACCAACTGCTGAAACAACCATGCA
AAACTATGACAAGCATTAAAGCTCCGCCTAACATCGCAATATTTTCTCTTGACACCTCAATGTAA
ATTTTACCTTCTAACTTGGAGTACTTCTCAACATCACGAC

Found at i:9452 original size:29 final size:30

Alignment explanation


    Indices: 9390--9460  Score: 81
    Period size: 29  Copynumber: 2.4  Consensus size: 30

       9380 GAGAGGGACT

                             *           *
       9390 AAAACGTCCAAAATTTAGAGTTTAGGAGAT
          1 AAAACGTCCAAAATTTAAAGTTTAGGAGAC

                *                     * * 
       9420 AAAATGTCCAAAA-TTAAAGTTTAGGGGGC
          1 AAAACGTCCAAAATTTAAAGTTTAGGAGAC

                 *      
       9449 AAAACATCCAAA
          1 AAAACGTCCAAA

       9461 CCATAGAAGT


Statistics
Matches: 34,  Mismatches: 7, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  29   22  0.65
  30   12  0.35

ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23


Consensus pattern (30 bp):   
AAAACGTCCAAAATTTAAAGTTTAGGAGAC

Found at i:11726 original size:78 final size:78

Alignment explanation


    Indices: 11592--11752  Score: 286
    Period size: 78  Copynumber: 2.1  Consensus size: 78

      11582 GTTTTCTACT

                                * *         *                                
      11592 TAAAATAGTAAAATGGTAAACTGAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATAAAATAGTTACAAAGATATTAGATTTAATCAAATAAAAATAGA

                         
      11657 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                                                               *             
      11670 TAAAATAGTAAAATGGTAAAATAAAATAGTTACAAAGATATTAGATTTAATTAAATAAAAATAGA
          1 TAAAATAGTAAAATGGTAAAATAAAATAGTTACAAAGATATTAGATTTAATCAAATAAAAATAGA

                         
      11735 GTTTTTAGTTGAG
         66 GTTTTTAGTTGAG

                 
      11748 TAAAA
          1 TAAAA

      11753 CTATAAATCT


Statistics
Matches: 79,  Mismatches: 4, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  78   79  1.00

ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33


Consensus pattern (78 bp):   
TAAAATAGTAAAATGGTAAAATAAAATAGTTACAAAGATATTAGATTTAATCAAATAAAAATAGA
GTTTTTAGTTGAG

Found at i:12823 original size:17 final size:18

Alignment explanation


    Indices: 12786--12824  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      12776 ACCTCTATAA

                      *     * 
      12786 AATAATATTCTATAAATT
          1 AATAATATTCGATAAAAT

                              
      12804 AATAATATT-GATAAAAT
          1 AATAATATTCGATAAAAT

                
      12821 AATA
          1 AATA

      12825 TTTTTGTCCG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17   10  0.53
  18    9  0.47

ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38


Consensus pattern (18 bp):   
AATAATATTCGATAAAAT
Done.