Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024163.1 Corchorus olitorius cultivar O-4 contig24196, 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: 21051
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32


Found at i:1289 original size:11 final size:11

Alignment explanation


    Indices: 1273--1300  Score: 56
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       1263 CCCTGCAACT

                       
       1273 AAAAAAAATAA
          1 AAAAAAAATAA

                       
       1284 AAAAAAAATAA
          1 AAAAAAAATAA

                  
       1295 AAAAAA
          1 AAAAAA

       1301 CTAAGCAAAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07


Consensus pattern (11 bp):   
AAAAAAAATAA

Found at i:2466 original size:15 final size:15

Alignment explanation


    Indices: 2442--2487  Score: 56
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       2432 ATAAAAATTA

                 *         
       2442 AATATTTTTTATTTT
          1 AATATATTTTATTTT

                           
       2457 AATATATTTTATTTT
          1 AATATATTTTATTTT

             *   *          
       2472 ATTGAAATTTTATTTT
          1 AAT-ATATTTTATTTT

       2488 TGTTTAAAAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  15   16  0.59
  16   11  0.41

ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67


Consensus pattern (15 bp):   
AATATATTTTATTTT

Found at i:17252 original size:26 final size:25

Alignment explanation


    Indices: 17198--17252  Score: 58
    Period size: 25  Copynumber: 2.2  Consensus size: 25

      17188 TTTTTTTTTC

                                 *  *
      17198 TTTTTTGTGGAAACAATTAGTGATT
          1 TTTTTTGTGGAAACAATTAGTAATG

                        *              
      17223 TTTTTTGTTGGATA-AATTAGTAAATG
          1 TTTTTTG-TGGAAACAATTAGT-AATG

                
      17249 TTTT
          1 TTTT

      17253 ATAGATTATG


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  25   14  0.56
  26   11  0.44

ACGTcount: A:0.27, C:0.02, G:0.18, T:0.53


Consensus pattern (25 bp):   
TTTTTTGTGGAAACAATTAGTAATG

Found at i:19291 original size:21 final size:22

Alignment explanation


    Indices: 19253--19294  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

      19243 TTTTATTAAT

                *   *             
      19253 ATAATATATTTTTAAATTATAA
          1 ATAAAATAATTTTAAATTATAA

                                 
      19275 ATAAAATAATTTT-AATTATA
          1 ATAAAATAATTTTAAATTATA

      19295 CAATTAGTGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  21    7  0.39
  22   11  0.61

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (22 bp):   
ATAAAATAATTTTAAATTATAA

Found at i:20334 original size:111 final size:111

Alignment explanation


    Indices: 20212--20435  Score: 385
    Period size: 111  Copynumber: 2.0  Consensus size: 111

      20202 TTATTTCTGA

                                                            *     *          
      20212 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCCTTTATTAAATCCATGTTCAAAGCCAAAGAAGA
          1 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCCTTTATTAAATCCATGCTCAAAACCAAAGAAGA

                         *                                
      20277 ACCAAATTGAAAATAAGAATTAGATGAAAATATTGACATCAATGGC
         66 ACCAAATTGAAAACAAGAATTAGATGAAAATATTGACATCAATGGC

                 *                          *                                
      20323 AAAAAGAAAAATCTTGGACAAGGTATTCCTTCTTTTATTAAATCCATGCTCAAAACCAAAGAAGA
          1 AAAAAAAAAAATCTTGGACAAGGTATTCCTTCCTTTATTAAATCCATGCTCAAAACCAAAGAAGA

                     *                           *        
      20388 ACCAAATTGTAAACAAGAATTAGATGAAAATATTGACCTCAATGGC
         66 ACCAAATTGAAAACAAGAATTAGATGAAAATATTGACATCAATGGC

              
      20434 AA
          1 AA

      20436 TTTCTTCTTC


Statistics
Matches: 106,  Mismatches: 7, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 111  106  1.00

ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25


Consensus pattern (111 bp):   
AAAAAAAAAAATCTTGGACAAGGTATTCCTTCCTTTATTAAATCCATGCTCAAAACCAAAGAAGA
ACCAAATTGAAAACAAGAATTAGATGAAAATATTGACATCAATGGC
Done.