Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017360.1 Corchorus olitorius cultivar O-4 contig17393, 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: 15840
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27


Found at i:11343 original size:37 final size:36

Alignment explanation


    Indices: 11269--11388  Score: 122
    Period size: 37  Copynumber: 3.3  Consensus size: 36

      11259 AAGGAGCTGG

                                     *           
      11269 AAAA-AAAAACTGTG-CCTAAAACAAAAAGAGGTCGA
          1 AAAACAAAAACTG-GACCTAAAACAGAAAGAGGTCGA

                                   *              
      11304 AAAACAAAAACAT-GACCTAAAATAGAAAGAGGTCGGA
          1 AAAACAAAAAC-TGGACCTAAAACAGAAAGAGGTC-GA

                                       *        * 
      11341 AAAGA-AAAAACTGGACCTAAAACAGAGAGAGGTCATA
          1 AAA-ACAAAAACTGGACCTAAAACAGAAAGAGGTC-GA

                       
      11378 AAAACTAAAAA
          1 AAAAC-AAAAA

      11389 GGAGGGGTTC


Statistics
Matches: 71,  Mismatches: 6, Indels: 13
        0.79            0.07        0.14

Matches are distributed among these distances:
  35    5  0.07
  36   25  0.35
  37   35  0.49
  38    6  0.08

ACGTcount: A:0.58, C:0.13, G:0.17, T:0.11


Consensus pattern (36 bp):   
AAAACAAAAACTGGACCTAAAACAGAAAGAGGTCGA

Found at i:12270 original size:59 final size:59

Alignment explanation


    Indices: 12194--12664  Score: 698
    Period size: 59  Copynumber: 8.0  Consensus size: 59

      12184 TGAGTTTCAG

                                                            *          
      12194 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCCGTTAGAGAGT
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

                                *    *      *    *                  *  
      12253 TTTCAATTCAAAATCTTATCATGTTCTTAAAACCCTGGTCGAGGTCTCTGTTAGAGTGT
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

                                                  *                    *
      12312 TTTCAATTCAAAATCTTATCCTGTTTTTAAAA-CTCTGGTCGAGGTCTCTGTTAGAGAGA
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATC-CTGTTCGAGGTCTCTGTTAGAGAGT

                                        *       *                      
      12371 TTTCAATTCAAAATCTTATCCTGTTTTTGAAATCCTATTCGAGGTCTCTGTTAGAGAGT
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

                                                                       
      12430 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

                 *              *                            *       * 
      12489 TTTCAGTTCAAAATCTTATCTTGTTTTTAAAATCCTGTTCGAGGTCTCTATTAGAGATT
          1 TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

                 *   *                                                  
      12548 TTTCAGTTCGAAATCTTAT-CTCG-TTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT
          1 TTTCAATTCAAAATCTTATCCT-GTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

              *                  *  *                          * *      
      12606 TTCCAATTCAAAATCTCT-TCTTGCTTTTAAAATCCTGTTCGAGGTCTCTGGTCGAGAGT
          1 TTTCAATTCAAAATCT-TATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

      12665 CTATATTTTC


Statistics
Matches: 376,  Mismatches: 30, Indels: 12
        0.90            0.07        0.03

Matches are distributed among these distances:
  58   50  0.13
  59  325  0.86
  60    1  0.00

ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41


Consensus pattern (59 bp):   
TTTCAATTCAAAATCTTATCCTGTTTTTAAAATCCTGTTCGAGGTCTCTGTTAGAGAGT

Found at i:13151 original size:29 final size:29

Alignment explanation


    Indices: 12902--13141  Score: 320
    Period size: 29  Copynumber: 8.2  Consensus size: 29

      12892 TAATTGATCA

                    *                    
      12902 TTTT-CACGTCCAGGGGCATTATGGTCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

                ** **                     
      12930 TTTTATATGTCCAGGGGCATTATGGTCATT
          1 TTTTGCACATCCAGGGGCATTATGGTCA-T

                                         
      12960 TTTTGCACATCCAGGGGCATTATGGTCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

               *    *             *      *
      12989 TTTAGCACCTCCAGGGGGCATTTTGGTCAC
          1 TTTTGCACATCCA-GGGGCATTATGGTCAT

                                 *       
      13019 TTTTGCACATCCAGGGGCATTTTGGTCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

                                    *    
      13048 TTTTGCACATCCAGGGGCATTATGATCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

               *    *            *       
      13077 TTTAGCACCTCCAGGGGCATTTTGGTCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

                       *                 
      13106 TTTTGCACATCTAGGGGCATTATGGTCAT
          1 TTTTGCACATCCAGGGGCATTATGGTCAT

                   
      13135 TTTTGCA
          1 TTTTGCA

      13142 TGTTCTGGGG


Statistics
Matches: 186,  Mismatches: 23, Indels: 5
        0.87            0.11        0.02

Matches are distributed among these distances:
  28    4  0.02
  29  132  0.71
  30   50  0.27

ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37


Consensus pattern (29 bp):   
TTTTGCACATCCAGGGGCATTATGGTCAT

Done.