Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024870.1 Corchorus olitorius cultivar O-4 contig24903, 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: 20362
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:1348 original size:176 final size:177

Alignment explanation


    Indices: 1034--1355  Score: 443
    Period size: 176  Copynumber: 1.8  Consensus size: 177

       1024 CACTTGTGTA

                     *           * *               *           *         *   
       1034 ATATTAAGTTGACCGTCTATTTCTATTAACCGAAACAACTAATTCTTTGGACGCATTTTTTTATA
          1 ATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAGCA--TTTTGATA

                                          *                 *  *             
       1099 CCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATTATTAAACAACCTTTCA
         64 CCTTGAACATTAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGAAACAACCTTTCA

                      *                                      
       1164 AGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAGTTATATG
        129 AGAGACACTTAAATCATCTCAATCAGACATCTGGAGCAAAAGTTATATG

                                    *      *                                 
       1213 ATATTAAGTGGACCGTCTATTCCCGTTAACCTAAACAACAAATT-TTTCGGAAGCA-TTTGATA-
          1 ATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTT-GGAAGCATTTTGATAC

                                                                *     *    * 
       1275 CTTGAAACATTAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGGAACAATCTTTTA
         65 CTTG-AACATTAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGAAACAACCTTTCA

             *              
       1340 ATAGACACTTAAATCA
        129 AGAGACACTTAAATCA

       1356 CCTTAATCGG


Statistics
Matches: 125,  Mismatches: 16, Indels: 7
        0.84            0.11        0.05

Matches are distributed among these distances:
 175    4  0.03
 176   74  0.59
 178    3  0.02
 179   44  0.35

ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Consensus pattern (177 bp):   
ATATTAAGTGGACCGTCTATTCCCATTAACCGAAACAACAAATTCTTTGGAAGCATTTTGATACC
TTGAACATTAAATTTAGTTTTCGAGTCCCTCATGAAAGTTGTAGATCATGAAACAACCTTTCAAG
AGACACTTAAATCATCTCAATCAGACATCTGGAGCAAAAGTTATATG

Found at i:12067 original size:27 final size:27

Alignment explanation


    Indices: 12029--12112  Score: 159
    Period size: 27  Copynumber: 3.1  Consensus size: 27

      12019 ACGGCCAATG

                  *                    
      12029 CAATATCTTCTTTCTAACCGACTTAAA
          1 CAATATATTCTTTCTAACCGACTTAAA

                                       
      12056 CAATATATTCTTTCTAACCGACTTAAA
          1 CAATATATTCTTTCTAACCGACTTAAA

                                       
      12083 CAATATATTCTTTCTAACCGACTTAAA
          1 CAATATATTCTTTCTAACCGACTTAAA

               
      12110 CAA
          1 CAA

      12113 CTAAAAAAAT


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  27   56  1.00

ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36


Consensus pattern (27 bp):   
CAATATATTCTTTCTAACCGACTTAAA
Done.