Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000618.1 Corchorus olitorius cultivar O-4 contig00618, 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, 670

Length: 1117
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36


Found at i:593 original size:127 final size:118

Alignment explanation


    Indices: 367--937  Score: 718
    Period size: 127  Copynumber: 4.7  Consensus size: 118

        357 AATTTCCCAT

                         *                                                   
        367 TCCTGTTCGAGGTGTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTCTAAAATCCTG
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTT-TAAAATCCTG

                 *                                                        
        432 TTCGATGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTTTTAAAAAAAA
         65 TTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTG----TTTTT----AAAA

                                *                     *                      
        494 TCCTGTTCGAGGTCTCTGTTGGAGAGTTTTCAATTCAAAATCACATCTTGTTTTCTAAAATCCTG
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTT-TAAAATCCTG

                                                *                        
        559 TTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTACCTTGTTTTTTTAAAAAAAAA
         65 TTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTG--TTTTT-----AAAA

              *     *     *                            * *         **     *  
        620 TCATGTTCAAGGTCGCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTTAATCCCGT
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTTAAAATCCTGT

                           *           *         * *             
        685 TCGAGGTCTCTGTTAAAGAGTTTTCAACTCAAAATCTCATCTTG-TTTTAAAA
         66 TCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTAAAA

                                                       * *       *           
        737 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTAACCTTGTTTATAAAATCCTGT
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTTAAAATCCTGT

                                                   *             
        802 TCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT--AA
         66 TCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTAAAA

                                                     * *              *     *
        853 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTG-TTTTAAACTCCTGG
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTTAAAATCCTGT

                   *      *      
        917 TCGAGGTTTCTGTTTGAGAGT
         66 TCGAGGTCTCTGTTAGAGAGT

        938 CTATATTTCA


Statistics
Matches: 403,  Mismatches: 39, Indels: 16
        0.88            0.09        0.03

Matches are distributed among these distances:
 115   30  0.07
 116   49  0.12
 117  102  0.25
 118    4  0.01
 122    4  0.01
 125   54  0.13
 126   55  0.14
 127  105  0.26

ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42


Consensus pattern (118 bp):   
TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTTAAAATCCTGT
TCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTAAAA

Found at i:698 original size:59 final size:59

Alignment explanation


    Indices: 367--937  Score: 718
    Period size: 59  Copynumber: 9.5  Consensus size: 59

        357 AATTTCCCAT

                         *                             *                
        367 TCCTGTTCGAGGTGTCTGTTAGAGAGTTTTCAATTCAAAATCTCATCTTGTTTTCTAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTT-TAAAA

                      *                                  *                   
        427 TCCTGTTCGATGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTTTTAAAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTG----TTTTT----AA

              
        492 AA
         58 AA

                                *                     **                
        494 TCCTGTTCGAGGTCTCTGTTGGAGAGTTTTCAATTCAAAATCACATCTTGTTTTCTAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTT-TAAAA

                                                     *   *                   
        554 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATATTACCTTGTTTTTTTAAAAAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTG--TTTTT-----AAA

             
        619 A
         59 A

              *     *     *                              *         **  
        620 TCATGTTCAAGGTCGCTGTTAGAGAGTTTTCAATTCAAAATCTTACCTTGTTTTTTTAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA

               *                 *           *         *               
        679 TCCCGTTCGAGGTCTCTGTTAAAGAGTTTTCAACTCAAAATCTCATCTTG-TTTTAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA

                                                       * *       *     
        737 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTAACCTTGTTTATAAAA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA

                                                                       
        796 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTT--AA
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA

                                                     *                *
        853 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATTTTATCTTG-TTTTAAAC
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA

                 *       *      *      
        911 TCCTGGTCGAGGTTTCTGTTTGAGAGT
          1 TCCTGTTCGAGGTCTCTGTTAGAGAGT

        938 CTATATTTCA


Statistics
Matches: 448,  Mismatches: 44, Indels: 40
        0.84            0.08        0.08

Matches are distributed among these distances:
  56    4  0.01
  57   51  0.11
  58   76  0.17
  59  103  0.23
  60   95  0.21
  61    1  0.00
  62    4  0.01
  63    5  0.01
  64   10  0.02
  66   50  0.11
  67   49  0.11

ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42


Consensus pattern (59 bp):   
TCCTGTTCGAGGTCTCTGTTAGAGAGTTTTCAATTCAAAATCTTATCTTGTTTTTAAAA
Done.