Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001076.1 Corchorus olitorius cultivar O-4 contig01076, 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: 4388
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39


Found at i:1558 original size:28 final size:29

Alignment explanation


    Indices: 1517--1571  Score: 103
    Period size: 28  Copynumber: 1.9  Consensus size: 29

       1507 TTTCAGTTGT

                                         
       1517 GACAATTAAGCCCTCTGATTCTCAATTGG
          1 GACAATTAAGCCCTCTGATTCTCAATTGG

                                       
       1546 GACAA-TAAGCCCTCTGATTCTCAATT
          1 GACAATTAAGCCCTCTGATTCTCAATT

       1572 TTTGGACAAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  28   21  0.81
  29    5  0.19

ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31


Consensus pattern (29 bp):   
GACAATTAAGCCCTCTGATTCTCAATTGG

Found at i:1778 original size:2 final size:2

Alignment explanation


    Indices: 1773--1803  Score: 53
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1763 TGTGTGTGTG

                           *                              
       1773 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1804 TATTTTGGTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:2438 original size:140 final size:139

Alignment explanation


    Indices: 2181--2461  Score: 413
    Period size: 140  Copynumber: 2.0  Consensus size: 139

       2171 CGATAAGAAA

                *       *      *                              *              
       2181 ATTGTATAACTTTACATCAGTAAACTTTTATAAATAATGAAGATTATCAACTTTCATATCTAAAC
          1 ATTGCATAACTTCACATCAATAAACTTTTATAAATAATGAAGATTATCAAATTTCATATCTAAAC

                              *                                              
       2246 TTACTATAAAAGTTATAACGGTTAAAAAAAGAAAAACTATAAGGGGTTATTAACAAATTCAGTAA
         66 TTACTATAAAAGTTATAAAGGTT-AAAAAAGAAAAACTATAAGGGGTTATTAACAAATTCAGTAA

                  *   
       2311 CTTACTGAGT
        130 CTTACTAAGT

                             *                        *                     *
       2321 ATTGCATAACTTCACATTAATAAACTTTTATAAATAATGAAGGTTATCAAATTTCATATCTAAAG
          1 ATTGCATAACTTCACATCAATAAACTTTTATAAATAATGAAGATTATCAAATTTCATATCTAAAC

                                             *         *                     
       2386 TTACTATAAAATTAGTTATAAAGGTT-AAAAA-CAAAACTATATGGGGTTATTAACAAATTCAGT
         66 TTACTAT-AAA--AGTTATAAAGGTTAAAAAAGAAAAACTATAAGGGGTTATTAACAAATTCAGT

                        
       2449 AACTTACTAAGT
        128 AACTTACTAAGT

             
       2461 A
          1 A

       2462 ATTTTTGTAA


Statistics
Matches: 127,  Mismatches: 11, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 140  107  0.84
 141    8  0.06
 143   12  0.09

ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34


Consensus pattern (139 bp):   
ATTGCATAACTTCACATCAATAAACTTTTATAAATAATGAAGATTATCAAATTTCATATCTAAAC
TTACTATAAAAGTTATAAAGGTTAAAAAAGAAAAACTATAAGGGGTTATTAACAAATTCAGTAAC
TTACTAAGT

Found at i:3341 original size:10 final size:10

Alignment explanation


    Indices: 3326--3356  Score: 53
    Period size: 10  Copynumber: 3.1  Consensus size: 10

       3316 CGTTTTATTC

                      
       3326 AAATATCCAT
          1 AAATATCCAT

                    * 
       3336 AAATATCCGT
          1 AAATATCCAT

                      
       3346 AAATATCCAT
          1 AAATATCCAT

             
       3356 A
          1 A

       3357 TTATATTAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.48, C:0.19, G:0.03, T:0.29


Consensus pattern (10 bp):   
AAATATCCAT
Done.