Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023344.1 Corchorus olitorius cultivar O-4 contig23377, 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: 16065
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.31


Found at i:1238 original size:2 final size:2

Alignment explanation


    Indices: 1231--1263  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1221 CTTTAACTAG

                                                             
       1231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1264 GAGATGATCA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:8343 original size:371 final size:365

Alignment explanation


    Indices: 7777--8543  Score: 941
    Period size: 372  Copynumber: 2.1  Consensus size: 365

       7767 TTTGGTGGTG

                *       *                                                  * 
       7777 TTGGTAGAAGAAAAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTAACAGCTCAGTA
          1 TTGGCAGAAGAATAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTAACA-CTCAGCA

              *            *       ***          *     *** *                  
       7842 CATTGCTTATGAAGTTCAAAGTCCTTGCAACCCAAACATCTATGGATGGGTCCTGATAGTTGTAC
         65 CAATGCTTATGAAGTCCAAAGTCAACGCAACCCAAAAATCTACAAAAGGGTCCTGATAGTTGTAC

                *                  *           *     *               *       
       7907 CTCTTATGCGGCGCAACAACCATGAAGTAAGTCTTTGGTGGGCTTTTCAACAAGTAATAAAGGAT
        130 CTCTCATGCGGCGCAACAACCATAAAGTAAGTCTTCGGTGGACTTTTCAACAAGTAACAAAGGAT

             *                *           *               *              *   
       7972 GTTGGTGGCTAAAATGTTTAAGTAGAGAAATTTTTCCAAAAGTGGATAG-CGAAAAAAGGCGCAG
        195 GCTGGTGGCTAAAATGTTCAAGTAGAGAAAATTTTCCAAAAGTGGACAGTCGAAAAAAGGCACAG

                     *                   *                        *     *   *
       8036 TAGATGTCTTGGAAGAAATCACAAGTCTTGCAGTGAAAAACATATCCCAAACATTTACAGTGACG
        260 TAGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACATATCCCAAACATCTACAGCGACA

                            *       *                 
       8101 TAAACTACAAAATCA-GGATTTATTTTAAGGGTATGGTGAAC
        325 TAAACTACAAAATCATCG-TTTATCTTAAGGGTATGGTGAAC

                                                                             
       8142 TTGGCAGAAGAATAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTAGATC-CTCAGC
          1 TTGGCAGAAGAATAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTA-A-CACTCAGC

             *    *                                         *                
       8206 ATAATGTTTATGAAGGTCAGAGCCAAAGTCAACGCAACCCAAAAATCTGCAAAAGGGTCCTGATA
         64 ACAATGCTTATGAA-GT-----CCAAAGTCAACGCAACCCAAAAATCTACAAAAGGGTCCTGATA

                 *            **       **                              *     
       8271 GTTGTTCC-CTACATGCGTTGCAACAATTATAAAGTAA-TCTCTCGGTGGACTTTTCAATAAGTA
        123 GTTGTACCTCT-CATGCGGCGCAACAACCATAAAGTAAGTCT-TCGGTGGACTTTTCAACAAGTA

                                        **                             *   * 
       8334 ACAAAGGATGCTGGTGGCTAAAATGTTCCTGTAGAGAAAATTTTCCAAAAGTGGACAGTGGAAGA
        186 ACAAAGGATGCTGGTGGCTAAAATGTTCAAGTAGAGAAAATTTTCCAAAAGTGGACAGTCGAAAA

                      *                    *                                 
       8399 AAGGCACAGTTGATGTCTAGGAAGAAATCACGAGTCTTACAGTGAAAAACATATCCCAAACATCT
        251 AAGGCACAGTAGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACATATCCCAAACATCT

             *    *     *                      *             *
       8464 ATAGCGGCATAAGCTACAAAATCATCGTTTATCTTGAGGGTATGGTGAAT
        316 ACAGCGACATAAACTACAAAATCATCGTTTATCTTAAGGGTATGGTGAAC

                                          
       8514 TTGGCAGAAGAATAAGAGGGTGTGGGTGGA
          1 TTGGCAGAAGAATAAGAGGGTGTGGGTGGA

       8544 TAGGATTATC


Statistics
Matches: 340,  Mismatches: 50, Indels: 17
        0.84            0.12        0.04

Matches are distributed among these distances:
 365   68  0.20
 366    3  0.01
 367    1  0.00
 370    5  0.01
 371  130  0.38
 372  132  0.39
 373    1  0.00

ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25


Consensus pattern (365 bp):   
TTGGCAGAAGAATAAGAGGGTGTGGGTGGAAAGGCGGATTAATCTCAAGAGGTAACACTCAGCAC
AATGCTTATGAAGTCCAAAGTCAACGCAACCCAAAAATCTACAAAAGGGTCCTGATAGTTGTACC
TCTCATGCGGCGCAACAACCATAAAGTAAGTCTTCGGTGGACTTTTCAACAAGTAACAAAGGATG
CTGGTGGCTAAAATGTTCAAGTAGAGAAAATTTTCCAAAAGTGGACAGTCGAAAAAAGGCACAGT
AGATGTCTAGGAAGAAATCACAAGTCTTACAGTGAAAAACATATCCCAAACATCTACAGCGACAT
AAACTACAAAATCATCGTTTATCTTAAGGGTATGGTGAAC

Found at i:9835 original size:21 final size:22

Alignment explanation


    Indices: 9806--9853  Score: 89
    Period size: 21  Copynumber: 2.2  Consensus size: 22

       9796 CGACAAAAAT

                                  
       9806 AAAACTAAACTAAAAGCTCTTG
          1 AAAACTAAACTAAAAGCTCTTG

                                  
       9828 AAAA-TAAACTAAAAGCTCTTG
          1 AAAACTAAACTAAAAGCTCTTG

                 
       9849 AAAAC
          1 AAAAC

       9854 CCACTTCATC


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  21   21  0.84
  22    4  0.16

ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21


Consensus pattern (22 bp):   
AAAACTAAACTAAAAGCTCTTG

Found at i:14370 original size:11 final size:11

Alignment explanation


    Indices: 14354--14378  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      14344 GGGGAATAAT

                       
      14354 CAATCCAAAAA
          1 CAATCCAAAAA

                       
      14365 CAATCCAAAAA
          1 CAATCCAAAAA

               
      14376 CAA
          1 CAA

      14379 ACAATTTTCT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08


Consensus pattern (11 bp):   
CAATCCAAAAA
Done.