Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009550.1 Corchorus capsularis cultivar CVL-1 contig09571, 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: 13780
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32


Found at i:7627 original size:178 final size:178

Alignment explanation


    Indices: 7305--7633  Score: 507
    Period size: 178  Copynumber: 1.8  Consensus size: 178

       7295 ATTATGGTTC

                 *                                           *    *          
       7305 GAACATCACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGGATATGAAGAAAACAT
          1 GAACAACACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGAATATAAAGAAAACAT

                                *             *                    *   *     
       7370 GTTAGGCTTAAGGGATATTTTAGTAATCAACCACGTGAGAAAAGACCAAAACGGGGCGATAAGGT
         66 GTTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGACGAAAAGGT

                   *                                        
       7435 CACTCCACATTAAAAGTTGATTGGGGATCCTTTAATAAGTTTCTGTGG
        131 CACTCCAAATTAAAAGTTGATTGGGGATCCTTTAATAAGTTTCTGTGG

                    *    *                            *         *            
       7483 GAACAACATTTATTAGAACTCAATGGCCAAATTACACACAAAGACAATGAATCTAAAGAAAACAT
          1 GAACAACACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGAATATAAAGAAAACAT

                      *                                             *        
       7548 GTTAGGCTTAGGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGATGAAAAGGT
         66 GTTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGACGAAAAGGT

             *                    
       7613 -TCTCCCAAATTAAAAGTTGAT
        131 CACT-CCAAATTAAAAGTTGAT

       7634 GGGAGCCTTT


Statistics
Matches: 135,  Mismatches: 15, Indels: 2
        0.89            0.10        0.01

Matches are distributed among these distances:
 177    2  0.01
 178  133  0.99

ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23


Consensus pattern (178 bp):   
GAACAACACTTATCAGAACTCAATGGCCAAATTACACACAAAAACAATGAATATAAAGAAAACAT
GTTAGGCTTAAGGGATATTTCAGTAATCAACCACATGAGAAAAGACCAAAACGGGACGAAAAGGT
CACTCCAAATTAAAAGTTGATTGGGGATCCTTTAATAAGTTTCTGTGG

Found at i:10615 original size:276 final size:273

Alignment explanation


    Indices: 10121--10644  Score: 831
    Period size: 276  Copynumber: 1.9  Consensus size: 273

      10111 TATTTAATGT

                                          *           *                    * 
      10121 TCAAAACTATTCCCTAAGGAGACACATGTCGACCCTTTAACCTTAACCCTGCATGTCCAGTCTGC
          1 TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCGTAACCCTGCATGTCCAGTCTAC

                         *         *                                         
      10186 TAAACTTCACTAATGGTGGATAAGATGATTTTCCTTAAAAAAATATACACTAAAAAGAAACATGT
         66 TAAACTTCACTAACGGTGGATAAAATGATTTTCCTTAAAAAAATATACACTAAAAAGAAACATGT

               *                                                             
      10251 CAATTCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTT
        131 CAACTCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTT

                  *                      *                                   
      10316 ACTTTTTGTAATAACCATAAACACTTCTAGGTTTAATTTAAGTAACATTATTATGGCTTTTTACT
        196 ACTTTTCGTAATAACCATAAACACTTCTAAG--T--TTTAAGTAACATTATTATGGCTTTTTACT

                             
      10381 TAATTAATGTTCAAAAA
        257 TAATTAATGTTCAAAAA

                                                                     *       
      10398 TCAAAACTATTCCCTAAGG-GTACACATGTCAACCCTTTAACCGTAACCCTGCATGTGCAGTCTA
          1 TCAAAACTATTCCCTAAGGAG-ACACATGTCAACCCTTTAACCGTAACCCTGCATGTCCAGTCTA

                                                                        *    
      10462 CTAAACTTCACTAACGGTGGATAAAAT-ATTTTTCCTT-AAAAAATATACACTAAAAAGACACAT
         65 CTAAACTTCACTAACGGTGGATAAAATGA-TTTTCCTTAAAAAAATATACACTAAAAAGAAACAT

                                  *      *                 *                 
      10525 GTCAAACT-TTTAACCCCGTTTTTACAATTTAATAGTAAACTACACTGATAGTGGATGTGATAAT
        129 GTC-AACTCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAAT

                                         *                          
      10589 TTTACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATGGC
        193 TTTACTTTTCGTAATAACCATAAACACTTCTAAGTTTTAAGTAACATTATTATGGC

      10645 AAAACTTTAG


Statistics
Matches: 230,  Mismatches: 14, Indels: 11
        0.90            0.05        0.04

Matches are distributed among these distances:
 272   21  0.09
 274    1  0.00
 276  114  0.50
 277   94  0.41

ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34


Consensus pattern (273 bp):   
TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCGTAACCCTGCATGTCCAGTCTAC
TAAACTTCACTAACGGTGGATAAAATGATTTTCCTTAAAAAAATATACACTAAAAAGAAACATGT
CAACTCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTT
ACTTTTCGTAATAACCATAAACACTTCTAAGTTTTAAGTAACATTATTATGGCTTTTTACTTAAT
TAATGTTCAAAAA

Found at i:13033 original size:20 final size:21

Alignment explanation


    Indices: 12996--13035  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      12986 AACCTGTTAA

                         *       
      12996 TTAAAGCGTGTCACTCGTGTC
          1 TTAAAGCGTGTCAATCGTGTC

                       *        
      13017 TTAAA-CGTGTTAATCGTGT
          1 TTAAAGCGTGTCAATCGTGT

      13036 TTTGACACGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38


Consensus pattern (21 bp):   
TTAAAGCGTGTCAATCGTGTC
Done.