Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008136.1 Corchorus olitorius cultivar O-4 contig08163, 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, 884

Length: 1474
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:344 original size:79 final size:79

Alignment explanation


    Indices: 255--462  Score: 353
    Period size: 79  Copynumber: 2.6  Consensus size: 79

        245 AAAGATTTGA

                                  * * *             *                        
        255 ATCATCAATCAAGAAGTTTTCAATCATAACATCAGACTCATAGTTATTTTTCAAGTTGACCGCAC
          1 ATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCAC

                          
        320 ATTGGTCCCTTTTC
         66 ATTGGTCCCTTTTC

                                                                             
        334 ATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCAC
          1 ATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCAC

                    *     
        399 ATTGGTCCTTTTTC
         66 ATTGGTCCCTTTTC

              *                                 *             
        413 ATTATCAATCAAGAAGTTTTCAGTTACAACATCAGATTCAGAGTTATTTT
          1 ATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTT

        463 CCAAAGTTAT


Statistics
Matches: 122,  Mismatches: 7, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  79  122  1.00

ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36


Consensus pattern (79 bp):   
ATCATCAATCAAGAAGTTTTCAGTTACAACATCAGACTCAGAGTTATTTTTCAAGTTGACCGCAC
ATTGGTCCCTTTTC

Found at i:1055 original size:50 final size:50

Alignment explanation


    Indices: 980--1253  Score: 442
    Period size: 50  Copynumber: 5.5  Consensus size: 50

        970 CTCTCTCCGA

                                                              
        980 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT
          1 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT

                                                              
       1030 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT
          1 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT

                                                              
       1080 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT
          1 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT

                                             *     *           
       1130 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGATTTCCGTTT-ATGAGTT
          1 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGA-GAGTT

                  *                     *     *     *   *    *
       1180 CAAGATTAAAATTCGCTTTTCAAAATAAGATTGCATTCCAGTTGTGAGTC
          1 CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT

               *         *          
       1230 CAATATCAAAATTTGCTTTTCAAA
          1 CAAGATCAAAATTCGCTTTTCAAA

       1254 GGGCATTTAA


Statistics
Matches: 209,  Mismatches: 13, Indels: 4
        0.92            0.06        0.02

Matches are distributed among these distances:
  49    1  0.00
  50  208  1.00

ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36


Consensus pattern (50 bp):   
CAAGATCAAAATTCGCTTTTCAAAATAAAATTGCTTTCCATTTGAGAGTT

Done.