Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021866.1 Corchorus olitorius cultivar O-4 contig21899, 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: 5173
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33


Found at i:56 original size:38 final size:37

Alignment explanation


    Indices: 4--220  Score: 172
    Period size: 38  Copynumber: 5.7  Consensus size: 37

          1 TTT

                    *                              
          4 CCGTTTAACCAAACCTGCTTAGGTCCTTGTTTAGAACTC
          1 CCGTTTAATCAAACCTGCTTAGGT-CTTGTTTAGAA-TC

                                             *     *
         43 CCG-TTAAGT-AAACCTGCTTAGGTCTTCGTTTGGAAGTT
          1 CCGTTTAA-TCAAACCTGCTTAGGTCTT-GTTTAGAA-TC

            *                             *        
         81 TCGTTTAATCAAACCTGCTTAGGTTCTTGTGT-GAATTC
          1 CCGTTTAATCAAACCTGCTTAGG-TCTTGTTTAGAA-TC

                       *                  *       *
        119 CCGTTTGAAT-GAACCTGCTTAGGTCTATGCTTAGAATT
          1 CCGTTT-AATCAAACCTGCTTAGGTCT-TGTTTAGAATC

            *  *                       * *      * *
        157 TCGCTTAATCAAACCTGCTTAGGTCTACGCTTAGAGTTT
          1 CCGTTTAATCAAACCTGCTTAGGTCT-TGTTTAGA-ATC

            *                        
        196 TCGTTTAATCAAACCTGCTTAGGTC
          1 CCGTTTAATCAAACCTGCTTAGGTC

        221 CCTCTTTGTA


Statistics
Matches: 149,  Mismatches: 19, Indels: 20
        0.79            0.10        0.11

Matches are distributed among these distances:
  37    9  0.06
  38   81  0.54
  39   55  0.37
  40    4  0.03

ACGTcount: A:0.23, C:0.22, G:0.19, T:0.37


Consensus pattern (37 bp):   
CCGTTTAATCAAACCTGCTTAGGTCTTGTTTAGAATC

Found at i:211 original size:77 final size:75

Alignment explanation


    Indices: 14--453  Score: 229
    Period size: 77  Copynumber: 5.7  Consensus size: 75

          4 CCGTTTAACC

                             * *      * **                             *  *  
         14 AAACCTGCTTAGGTCCTTGTTTAGAACTCCCG-TTAAGTAAACCTGCTTAGGTCT-TCGTTTGGA
          1 AAACCTGCTTAGGT-CTCGCTTAGAATTTTCGTTTAA-TAAACCTGCTTAGGTCTAT-GCTTAGA

                   *     *
         77 AGTTTCGTTTAATC
         63 A-TTTCGCTTAATA

                             *           **         *                        
         91 AAACCTGCTTAGGTTCTTG-TGT-GAATTCCCGTTTGAATGAACCTGCTTAGGTCTATGCTTAGA
          1 AAACCTGCTTAGG-TCTCGCT-TAGAATTTTCGTTT-AATAAACCTGCTTAGGTCTATGCTTAGA

                        *
        154 ATTTCGCTTAATC
         63 ATTTCGCTTAATA

                                     *                            **     *   
        167 AAACCTGCTTAGGTCTACGCTTAGAGTTTTCGTTTAATCAAACCTGCTTAGGTCCCT-CTTTGTA
          1 AAACCTGCTTAGGTCT-CGCTTAGAATTTTCGTTTAAT-AAACCTGCTTAGGTCTATGCTTAG-A

                            
        231 ATCTT-GCCTTAGA-A
         63 AT-TTCG-CTTA-ATA

                   * * *                   *               *         *       
        245 AAACCTGATCAAGTCTCTGCTTAGAATTTTCATTTAGGA-AAACCTGTTTAGGGTCTCTGCTTAG
          1 AAACCTGCTTAGGTCTC-GCTTAGAATTTTCGTTTA--ATAAACCTGCTTA-GGTCTATGCTTAG

              *     * *     
        309 AGCTTT-GATCAAGT-
         62 A-ATTTCGCTTAA-TA

              *            * **      *  ** *                                 
        323 AAGCCTGCTTAGGTCCCTATATAGAGTTGCCATTTAAGTAAACCTGCTTAGGTCTATG-TTCAGA
          1 AAACCTGCTTAGGTCTCGCT-TAGAATTTTCGTTTAA-TAAACCTGCTTAGGTCTATGCTT-AGA

                  *    * 
        387 ATTTCGTTTAAGA
         63 ATTTCGCTTAATA

                               *                                   
        400 AAACCTGCTTAGGTTCTCGTTTAGAATTCTT-GTTTAATCAAACCTGCTTAGGTC
          1 AAACCTGCTTAGG-TCTCGCTTAGAATT-TTCGTTTAAT-AAACCTGCTTAGGTC

        454 CCCCCCCCTT


Statistics
Matches: 284,  Mismatches: 49, Indels: 60
        0.72            0.12        0.15

Matches are distributed among these distances:
  75    3  0.01
  76   49  0.17
  77  126  0.44
  78   89  0.31
  79   11  0.04
  80    6  0.02

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


Consensus pattern (75 bp):   
AAACCTGCTTAGGTCTCGCTTAGAATTTTCGTTTAATAAACCTGCTTAGGTCTATGCTTAGAATT
TCGCTTAATA

Found at i:446 original size:39 final size:39

Alignment explanation


    Indices: 355--452  Score: 119
    Period size: 38  Copynumber: 2.5  Consensus size: 39

        345 AGAGTTGCCA

                  *                  *             
        355 TTTAAGTAAACCTGCTTAGG-TCTATGTTCAGAATTTCG
          1 TTTAAGAAAACCTGCTTAGGTTCTACGTTCAGAATTTCG

                                         *        * 
        393 TTTAAGAAAACCTGCTTAGGTTCT-CGTTTAGAATTCTTG
          1 TTTAAGAAAACCTGCTTAGGTTCTACGTTCAGAATT-TCG

                 **              
        432 TTTAATCAAACCTGCTTAGGT
          1 TTTAAGAAAACCTGCTTAGGT

        453 CCCCCCCCCT


Statistics
Matches: 52,  Mismatches: 6, Indels: 3
        0.85            0.10        0.05

Matches are distributed among these distances:
  38   28  0.54
  39   24  0.46

ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40


Consensus pattern (39 bp):   
TTTAAGAAAACCTGCTTAGGTTCTACGTTCAGAATTTCG

Found at i:815 original size:27 final size:25

Alignment explanation


    Indices: 785--834  Score: 64
    Period size: 25  Copynumber: 1.9  Consensus size: 25

        775 TTTTGTAGTA

                                       
        785 TTGAAATTTCGGTTTTGAAACCAAAGC
          1 TTGAAATTTC--TTTTGAAACCAAAGC

                 *           *     
        812 TTGAATTTTCTTTTGAACCCAAA
          1 TTGAAATTTCTTTTGAAACCAAA

        835 TTCTTGAATT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   12  0.57
  27    9  0.43

ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38


Consensus pattern (25 bp):   
TTGAAATTTCTTTTGAAACCAAAGC
Done.