Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015520.1 Corchorus olitorius cultivar O-4 contig15553, 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: 3281
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34


Found at i:384 original size:28 final size:28

Alignment explanation


    Indices: 353--427  Score: 82
    Period size: 28  Copynumber: 2.7  Consensus size: 28

        343 TTAAGATATC

                    *                *  
        353 AAAATTACTGTTTTGCCCTTGGTCATCT
          1 AAAATTACAGTTTTGCCCTTGGTCAACT

                           *   *    *    
        381 AAAATTACCA-TTTTACCCCTGGTTAACT
          1 AAAATTA-CAGTTTTGCCCTTGGTCAACT

                                
        409 -AAATTACAGTTTTGCCCTT
          1 AAAATTACAGTTTTGCCCTT

        428 AAATGCCGGA


Statistics
Matches: 38,  Mismatches: 7, Indels: 5
        0.76            0.14        0.10

Matches are distributed among these distances:
  26    2  0.05
  27   14  0.37
  28   21  0.55
  29    1  0.03

ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40


Consensus pattern (28 bp):   
AAAATTACAGTTTTGCCCTTGGTCAACT

Found at i:3062 original size:178 final size:177

Alignment explanation


    Indices: 2697--3074  Score: 440
    Period size: 178  Copynumber: 2.1  Consensus size: 177

       2687 TCATAAGCTC

                   *     *         *  *    *                 *         *     
       2697 AAATTATGTAATAGTAAGTAGACTGTTTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCA
          1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAGCA

                 *          *                                     *          
       2762 TTTTTTATACCTTGAATATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAGATCATGGAAC
         66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAAATCATGGAAC

               *               *     *          *     *  * 
       2827 AACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCG
        131 AACATTTCAAGAGACACTTAAATCACCTCAATCAGAAATCTGAAGAG

                                *                  *                         
       2874 AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTATCCGAAACAACAAATT-TTTCGAAAG
          1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-GAAAG

                                                       *                     
       2938 CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAAATCATGG
         64 CATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAAATCATGG

                 *    *  *                      **              
       3002 AACAATATTTTAATAGACACTTAAATCACCAT-AATTGGATAATC-GAAGAG
        128 AACAACATTTCAAGAGACACTTAAATCACC-TCAATCAGA-AATCTGAAGAG

                         *    *    
       3052 AATATTATATAATGTTAAATAGA
          1 AA-ATTATATAATATTAAGTAGA

       3075 TCGTTTAGCC


Statistics
Matches: 168,  Mismatches: 27, Indels: 11
        0.82            0.13        0.05

Matches are distributed among these distances:
 177   10  0.06
 178  153  0.91
 179    5  0.03

ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34


Consensus pattern (177 bp):   
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGAAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTGCATGAAAGTTGTAAATCATGGAAC
AACATTTCAAGAGACACTTAAATCACCTCAATCAGAAATCTGAAGAG
Done.