Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011375.1 Corchorus olitorius cultivar O-4 contig11408, 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, 927

Length: 1546
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36


Found at i:299 original size:153 final size:152

Alignment explanation


    Indices: 1--389  Score: 564
    Period size: 153  Copynumber: 2.5  Consensus size: 152

                       *              **                                *    
          1 TTTGGGCCTATTGGGGCCTATTAGTTTTGTTTTGAATCGTCTTCGATTTGGCAACCCTCATTGC-
          1 TTTGGGCCTATCGGGGCCTATTAGTTACGTTTTGAATCGTCTTCGATTT-GCAACCCTCAATGCT

                                                  *                          
         65 TTTCTTTCCATGTTTATGCCCTAACTATAATCACTTTGGTGAGATTAGTCCACTGTGAAGTTTTT
         65 TTTCTTTCCATGTTTATGCCCTAACTATAATCACTTTGCTGAGATTAGTCCACTGTGAAGTTTTT

                              *    
        130 AGCTCATTTGGAACACTTTTTAT
        130 AGCTCATTTGGAACACTTGTTAT

                              *      *                                       
        153 TTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATGCTT
          1 TTTGGGCCTATCGGGGCCTATTAGTTACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATGCTT

                         *    *              *                               
        218 TTCTTTCCATTGTATATGGCCTAACTATAATCATTTTGCTGAGATTAGTCCACTGTGAAGTTTTT
         66 TTCTTTCCA-TGTTTATGCCCTAACTATAATCACTTTGCTGAGATTAGTCCACTGTGAAGTTTTT

             *                     
        283 ATCTCATTTGGAACACTTGTTAT
        130 AGCTCATTTGGAACACTTGTTAT

                         ***          *                      *             * 
        306 TTTGGGCCTATCGACACCTATTAGTTCCGTTTTGAATCGTCTTCGATCTGGCAACCCTCAATGAT
          1 TTTGGGCCTATCGGGGCCTATTAGTTACGTTTTGAATCGTCTTCGAT-TTGCAACCCTCAATGCT

              *                
        371 TTACTTTCCAATGTTTATG
         65 TTTCTTTCC-ATGTTTATG

        390 ACCTGATTGA


Statistics
Matches: 211,  Mismatches: 22, Indels: 6
        0.88            0.09        0.03

Matches are distributed among these distances:
 151   13  0.06
 152   54  0.26
 153  113  0.54
 154   30  0.14
 155    1  0.00

ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41


Consensus pattern (152 bp):   
TTTGGGCCTATCGGGGCCTATTAGTTACGTTTTGAATCGTCTTCGATTTGCAACCCTCAATGCTT
TTCTTTCCATGTTTATGCCCTAACTATAATCACTTTGCTGAGATTAGTCCACTGTGAAGTTTTTA
GCTCATTTGGAACACTTGTTAT

Found at i:453 original size:40 final size:40

Alignment explanation


    Indices: 397--475  Score: 133
    Period size: 40  Copynumber: 2.0  Consensus size: 40

        387 ATGACCTGAT

                                                    
        397 TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
          1 TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC

                                   *                
        437 TGATGCGCCACA-GACTCATCATTGTCTTGAAGATGCTAG
          1 TGATGCGCCA-AGGACTCATCATGGTCTTGAAGATGCTAG

        476 GAGATCATTG


Statistics
Matches: 37,  Mismatches: 1, Indels: 2
        0.93            0.03        0.05

Matches are distributed among these distances:
  40   36  0.97
  41    1  0.03

ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27


Consensus pattern (40 bp):   
TGATGCGCCAAGGACTCATCATGGTCTTGAAGATGCTAGC
Done.