Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018381.1 Corchorus olitorius cultivar O-4 contig18414, 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: 16427
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:42 original size:29 final size:29

Alignment explanation


    Indices: 4--108  Score: 99
    Period size: 29  Copynumber: 3.6  Consensus size: 29

          1 TAA

                                          
          4 TTGCTCAAATAAGGGTCTGATCTTTTAATT
          1 TTGCTCAAATAAGGG-CTGATCTTTTAATT

                              *  *         *
         34 TTGC-CAAATAAGGGCCTAATGTTTGTCAA-A
          1 TTGCTCAAATAAGGG-CTGATCTTT-T-AATT

            *                      *      
         64 ATGCTCAAATAAGGGCATGATCTCTTAATT
          1 TTGCTCAAATAAGGGC-TGATCTTTTAATT

                            
         94 TTGC-CAAATAAGGGC
          1 TTGCTCAAATAAGGGC

        109 CTAACGTTTG


Statistics
Matches: 60,  Mismatches: 10, Indels: 11
        0.74            0.12        0.14

Matches are distributed among these distances:
  29   30  0.50
  30   13  0.22
  31   17  0.28

ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Consensus pattern (29 bp):   
TTGCTCAAATAAGGGCTGATCTTTTAATT

Found at i:76 original size:31 final size:31

Alignment explanation


    Indices: 38--201  Score: 117
    Period size: 31  Copynumber: 5.4  Consensus size: 31

         28 TTAATTTTGC

                                           
         38 CAAATAAGGGCCTAATGTTTGTCAAAATGCT
          1 CAAATAAGGGCCTAATGTTTGTCAAAATGCT

                       * *  * *       **    
         69 CAAATAAGGGCATGATCTCT-T-AATTTTGC-
          1 CAAATAAGGGCCTAATGTTTGTCAA-AATGCT

                           *     *         
         98 CAAATAAGGGCCTAACGTTTGCCAAAATGCT
          1 CAAATAAGGGCCTAATGTTTGTCAAAATGCT

                        **  *        **     
        129 CAAATAAGGGCCCGATCTTT-T-AATTTGGC-
          1 CAAATAAGGGCCTAATGTTTGTCAAAAT-GCT

                     **                     
        158 CAAATAAGGATCTAATGTTTG-CTAAAATGCT
          1 CAAATAAGGGCCTAATGTTTGTC-AAAATGCT

                         
        189 CAAATAAGGGCCT
          1 CAAATAAGGGCCT

        202 GACATCGAAA


Statistics
Matches: 94,  Mismatches: 30, Indels: 18
        0.66            0.21        0.13

Matches are distributed among these distances:
  29   35  0.37
  30   11  0.12
  31   48  0.51

ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29


Consensus pattern (31 bp):   
CAAATAAGGGCCTAATGTTTGTCAAAATGCT

Found at i:200 original size:60 final size:60

Alignment explanation


    Indices: 5--203  Score: 301
    Period size: 60  Copynumber: 3.3  Consensus size: 60

          1 TAAT

                          *                                              
          5 TGCTCAAATAAGGGTCTGATCTTTTAATTTTGCCAAATAAGGGCCTAATGTTTG-TCAAAA
          1 TGCTCAAATAAGGGCCTGATCTTTTAATTTTGCCAAATAAGGGCCTAATGTTTGCT-AAAA

                           *      *                         *      *    
         65 TGCTCAAATAAGGGCATGATCTCTTAATTTTGCCAAATAAGGGCCTAACGTTTGCCAAAA
          1 TGCTCAAATAAGGGCCTGATCTTTTAATTTTGCCAAATAAGGGCCTAATGTTTGCTAAAA

                            *             *           **                
        125 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGATCTAATGTTTGCTAAAA
          1 TGCTCAAATAAGGGCCTGATCTTTTAATTTTGCCAAATAAGGGCCTAATGTTTGCTAAAA

                               
        185 TGCTCAAATAAGGGCCTGA
          1 TGCTCAAATAAGGGCCTGA

        204 CATCGAAAAT


Statistics
Matches: 124,  Mismatches: 14, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
  60  124  1.00

ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31


Consensus pattern (60 bp):   
TGCTCAAATAAGGGCCTGATCTTTTAATTTTGCCAAATAAGGGCCTAATGTTTGCTAAAA

Found at i:4199 original size:19 final size:19

Alignment explanation


    Indices: 4177--4228  Score: 54
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       4167 GGGCTGAAAT

                               
       4177 TAATTAATTATTAAATAAA
          1 TAATTAATTATTAAATAAA

                         * * *  
       4196 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAAATAAA

                           
       4215 TAATT-ATTATTAAA
          1 TAATTAATTATTAAA

       4229 AGTTTCACAT


Statistics
Matches: 26,  Mismatches: 5, Indels: 5
        0.72            0.14        0.14

Matches are distributed among these distances:
  18    9  0.35
  19   16  0.62
  20    1  0.04

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (19 bp):   
TAATTAATTATTAAATAAA
Done.