Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015677.1 Corchorus olitorius cultivar O-4 contig15710, 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: 23770
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:659 original size:330 final size:330

Alignment explanation


    Indices: 1--791  Score: 920
    Period size: 330  Copynumber: 2.4  Consensus size: 330

                                         *                *       *   *    * 
          1 ATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTGTACGAGTTTCTAAATCCT
          1 ATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGTATCTGAATCTT

            *            *            *                                      
         66 ATTTCGATTTAATCAGAAATTAATTTTGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAA
         66 GTTTCGATTTAATTAGAAATTAA-TTCG-AA-AAAATAGGAAAAACGATATTAGAAGCGTGAAAA

              * *       *       *         *                   *  *           
        131 AGGCTTTCAACTTTTTTTGCGTTGAATTATTTATTTTTTATGAGTATTTTCGCTAGAAAACAAGG
        128 AGCCCTTCAACTCTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAGAAAACAAGG

                                                *       *  *   **            
        196 AAAAATCTTTCGAGTCAATTTTTGCAAAATTTAGCCGAAATCGTGTATTAATTATCACGGTTTTC
        193 AAAAATCTTTCGAGTCAATTTTTGCAAAATTTAGCCAAAATCGTATACTAACCATCACGGTTTTC

                     ** *  *     *                                           
        261 GACTAAAAATTCGTTTCGGGATCCGGCTTAGTTTTGCATGATTTTTAGTGCCAAGACTCCTTGAA
        258 GACTAAAAAAGCATTACGGGACCCGGCTTAGTTTTGCATGATTTTTAGTGCCAAGACTCCTTGAA

                     
        326 ATAT-TTAT
        323 ATATCTT-T

                                        *        *                           
        334 ATTCATCTAACCAAATCTCAGCCACATTAAATTTAAGAATTTGTTTTTACGAGTATCTGAATCTT
          1 ATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGTATCTGAATCTT

                                       *               *              *      
        399 GTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACAATATTAGAAGCGT-TAAAAGC
         66 GTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGC

                                                                        **   
        463 CCTTCAA-TCTTTTTG-ATATCGAATTATATATTTTTTATGAGTATTTTAGCCA-AAAATTGAGG
        131 CCTTCAACTCTTTTTGCAT-T-GAATTATATATTTTTTATGAGTATTTTAGCCAGAAAA-CAAGG

               *                                                             
        525 AAATATCTTTCG-GTTCAATTTTTG-AAGAATTTTAGCCAAAATCGTATACT-ACCATCACGGTT
        193 AAAAATCTTTCGAG-TCAATTTTTGCAA-AA-TTTAGCCAAAATCGTATACTAACCATCACGGTT

              * *                                               *     *      
        587 TTTGGCTAAAAAAGCATTACAGGG-CCACGGCTCT-GTTTTGCATGATTTTTGGTGCCGAGACTC
        255 TTCGACTAAAAAAGCATTAC-GGGACC-CGGCT-TAGTTTTGCATGATTTTTAGTGCCAAGACTC

                          
        650 CTTGAAATATCTTT
        317 CTTGAAATATCTTT

               *      *      *   *       *  *                 *   *  *       
        664 ATTTATCTAATCAAATCACAGGCACATTGGATGTAAGGATTTGTTTTTA-TATGCATTTGAATCT
          1 ATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGA-GTATCTGAATCT

                  *                              *              *  *        
        728 TGTTTCCATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAATCGTGAAAA
         65 TGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAA

        792 GTCGTCAAAT


Statistics
Matches: 390,  Mismatches: 55, Indels: 27
        0.83            0.12        0.06

Matches are distributed among these distances:
 327    1  0.00
 328   15  0.04
 329   92  0.24
 330  167  0.43
 331   30  0.08
 332    6  0.02
 333   79  0.20

ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Consensus pattern (330 bp):   
ATTCATCTAACCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGTATCTGAATCTT
GTTTCGATTTAATTAGAAATTAATTCGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGC
CCTTCAACTCTTTTTGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAGAAAACAAGGAAA
AATCTTTCGAGTCAATTTTTGCAAAATTTAGCCAAAATCGTATACTAACCATCACGGTTTTCGAC
TAAAAAAGCATTACGGGACCCGGCTTAGTTTTGCATGATTTTTAGTGCCAAGACTCCTTGAAATA
TCTTT

Found at i:6772 original size:1 final size:1

Alignment explanation


    Indices: 6766--6805  Score: 53
    Period size: 1  Copynumber: 40.0  Consensus size: 1

       6756 GTAAAGAAAG

                                      ***           
       6766 AAAAAAAAAAAAAAAAAAAAAAAAAAGGCAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

       6806 CCCATCAACT


Statistics
Matches: 36,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:0.93, C:0.03, G:0.05, T:0.00


Consensus pattern (1 bp):   
A

Found at i:19576 original size:10 final size:10

Alignment explanation


    Indices: 19561--19590  Score: 60
    Period size: 10  Copynumber: 3.0  Consensus size: 10

      19551 GATGATTCAA

                      
      19561 ATTTGATTAG
          1 ATTTGATTAG

                      
      19571 ATTTGATTAG
          1 ATTTGATTAG

                      
      19581 ATTTGATTAG
          1 ATTTGATTAG

      19591 GTGGCACCAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   20  1.00

ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50


Consensus pattern (10 bp):   
ATTTGATTAG
Done.