Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021832.1 Corchorus olitorius cultivar O-4 contig21865, 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: 17222
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27


Found at i:12569 original size:16 final size:16

Alignment explanation


    Indices: 12540--12573  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      12530 CTTTTTATTA

                            
      12540 TTATTATTATTATTTC
          1 TTATTATTATTATTTC

                             
      12556 TTATATATTA-TATTTC
          1 TTAT-TATTATTATTTC

              
      12572 TT
          1 TT

      12574 TGTGAACCAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68


Consensus pattern (16 bp):   
TTATTATTATTATTTC

Found at i:13205 original size:39 final size:38

Alignment explanation


    Indices: 13162--13588  Score: 186
    Period size: 39  Copynumber: 10.7  Consensus size: 38

      13152 TTTATCTTAG

                                               *   
      13162 CAAACCTGCTTAGGTCCTTGTTTAGAACTTTCGTTCAAT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAA-TTTCGTTTAAT

                   **      *     *        *         
      13201 CAAACCTATTTAGGTTCTTGTGTAGAATTCCCGTTTAAGT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAATT-TCGTTTAA-T

             *                 *        *           
      13241 -GAACCTGCTTAGGT-CTACGTTTAGGAGTTTCGTTTAAT
          1 CAAACCTGCTTAGGTCCT-TGTTTA-GAATTTCGTTTAAT

             *                   *  *               
      13279 CGAACCTGCTTAGGTCCTTGTGTAAAATTTCTGTTTAAGT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAATTTC-GTTTAA-T

             *                    *      *     * *  *
      13319 -GAACCTGCTTAGGAT-CTCTGCTTAGAGCTTT-GATCAAG
          1 CAAACCTGCTTAGG-TCCT-TGTTTAGA-ATTTCGTTTAAT

            *                   *                            *
      13357 GAAACCTGCTTAGGTCTATGTTTAGAATCTCATTAGAATTTCTGTTTAAG
          1 CAAACCTGCTTAGGTC----CTT-G----T--TTAGAATTTC-GTTTAAT

            *                 *   *     *  * *   *
      13407 AAAACCTGCTTAGGTCCTCGTTCAGAATCTCATGTAAG
          1 CAAACCTGCTTAGGTCCTTGTTTAGAATTTCGTTTAAT

                               *               *    
      13445 CAAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAAGT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAA-TTTCGTTTAA-T

            *         *      *                      
      13485 AAAACCTGCTCAGGTCCCTGTTTAGAATTTCCGTTTAAGT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAATTT-CGTTTAA-T

             *     *  *        * *       *         
      13525 -GAACCTACTGAGGT-CTACGCTTAGAATCTCGTTTAAT
          1 CAAACCTGCTTAGGTCCT-TGTTTAGAATTTCGTTTAAT

             *                 *        
      13562 CGAACCTGCTTAGGTCC-TCTTTAGAAT
          1 CAAACCTGCTTAGGTCCTTGTTTAGAAT

      13589 CTCGCATTAG


Statistics
Matches: 293,  Mismatches: 63, Indels: 66
        0.69            0.15        0.16

Matches are distributed among these distances:
  37    8  0.03
  38   59  0.20
  39  144  0.49
  40   45  0.15
  41    4  0.01
  42    1  0.00
  43    2  0.01
  45    1  0.00
  46    1  0.00
  48    3  0.01
  49    5  0.02
  50   20  0.07

ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37


Consensus pattern (38 bp):   
CAAACCTGCTTAGGTCCTTGTTTAGAATTTCGTTTAAT

Found at i:13293 original size:78 final size:78

Alignment explanation


    Indices: 13164--13331  Score: 221
    Period size: 78  Copynumber: 2.2  Consensus size: 78

      13154 TATCTTAGCA

                            *                            *      *        *   
      13164 AACCTGCTTAGGTCCTTGTTTAGAACTTTCGTTCAATCAAACCTATTTAGGTTCTTGTGTAGAAT
          1 AACCTGCTTAGGTCCTCGTTTAGAACTTTCGTTCAATCAAACCTACTTAGGTCCTTGTGTAAAAT

                         
      13229 TCCCGTTTAAGTG
         66 TCCCGTTTAAGTG

                                    * *       *    *     *                   
      13242 AACCTGCTTAGGT-CTACGTTTAGGAGTTTCGTTTAATCGAACCTGCTTAGGTCCTTGTGTAAAA
          1 AACCTGCTTAGGTCCT-CGTTTAGAACTTTCGTTCAATCAAACCTACTTAGGTCCTTGTGTAAAA

              * *         
      13306 TTTCTGTTTAAGTG
         65 TTCCCGTTTAAGTG

                        
      13320 AACCTGCTTAGG
          1 AACCTGCTTAGG

      13332 ATCTCTGCTT


Statistics
Matches: 78,  Mismatches: 11, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  77    2  0.03
  78   76  0.97

ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39


Consensus pattern (78 bp):   
AACCTGCTTAGGTCCTCGTTTAGAACTTTCGTTCAATCAAACCTACTTAGGTCCTTGTGTAAAAT
TCCCGTTTAAGTG

Found at i:13500 original size:40 final size:40

Alignment explanation


    Indices: 13446--13524  Score: 113
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      13436 TCATGTAAGC

                     *      *            *          
      13446 AAACCTGCTTAGGTCCTTATTTAGAATTTTCGTTCAAGTA
          1 AAACCTGCTCAGGTCCCTATTTAGAATTTCCGTTCAAGTA

                              *               *    
      13486 AAACCTGCTCAGGTCCCTGTTTAGAATTTCCGTTTAAGT
          1 AAACCTGCTCAGGTCCCTATTTAGAATTTCCGTTCAAGT

      13525 GAACCTACTG


Statistics
Matches: 34,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  40   34  1.00

ACGTcount: A:0.25, C:0.20, G:0.16, T:0.38


Consensus pattern (40 bp):   
AAACCTGCTCAGGTCCCTATTTAGAATTTCCGTTCAAGTA
Done.