Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023177.1 Corchorus olitorius cultivar O-4 contig23210, 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: 6820
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:2964 original size:154 final size:154

Alignment explanation


    Indices: 2460--2951  Score: 788
    Period size: 154  Copynumber: 3.2  Consensus size: 154

       2450 TGGCGCATCA

                  *                                                          
       2460 GAAGTTGTTAGCTCATTTGGAACACTTGTTATGTTGGGCCTATCGGGGCCCATTAGTGACATTTC
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTGGGCCTATCGGGGCCCATTAGTGACATTT-

                                      *                *                     
       2525 T-AATCGTCTTCGATTGGGCAAACCTGAATGCTTTTCTTTCCACTGTTTATGGCCTAACTATAAT
         65 TGAATCGTCTTCGATTGGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAAT

                                     
       2589 CATTTTGGTGAGATTAGTCCACTGT
        130 CATTTTGGTGAGATTAGTCCACTGT

                          *                 *           *               *    
       2614 GAAGTTTTTAGCTCCTTTGGAACACTTGTTATTTTGGGCCTATCTGGGCCCATTAGTGACGTTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTGGGCCTATCGGGGCCCATTAGTGACATTTT

                       *   *      *                                   *      
       2679 GAATCGTCTTCAATTTGGCAAATCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACCATAATC
         66 GAATCGTCTTCGATTGGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                                  * 
       2744 ATTTTGGTGAGATTAGTCCACTAT
        131 ATTTTGGTGAGATTAGTCCACTGT

                  *      *                 *    *           *                
       2768 GAAGTTCTTAGCTTATTTGGAACACTTGTTAAGTTGAGCCTATCGGGGTCCATTAGTGACATTTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTGGGCCTATCGGGGCCCATTAGTGACATTTT

                                     *                               *       
       2833 GAATCGTCTTCGATTGGGCAAACCTTAATGCTTTTCTTTCCATTGTTTATGGCCTAAGTATAATC
         66 GAATCGTCTTCGATTGGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC

                        *           
       2898 ATTTTGGTGAGAGTAGTCCACTGT
        131 ATTTTGGTGAGATTAGTCCACTGT

                                          
       2922 GAAGTTTTTAGCTCATTTGGAACACTTGTT
          1 GAAGTTTTTAGCTCATTTGGAACACTTGTT

       2952 CTTTTGGTCC


Statistics
Matches: 306,  Mismatches: 31, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
 153    1  0.00
 154  305  1.00

ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39


Consensus pattern (154 bp):   
GAAGTTTTTAGCTCATTTGGAACACTTGTTATGTTGGGCCTATCGGGGCCCATTAGTGACATTTT
GAATCGTCTTCGATTGGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATC
ATTTTGGTGAGATTAGTCCACTGT

Found at i:6721 original size:21 final size:21

Alignment explanation


    Indices: 6697--6788  Score: 159
    Period size: 21  Copynumber: 4.4  Consensus size: 21

       6687 CTTAGGCAAT

                         *       
       6697 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       6718 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                 
       6739 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGGAACCTTC

                                  
       6760 TCCAATGAGCTTGGAA-CTTGC
          1 TCCAATGAGCTTGGAACCTT-C

                    
       6781 TCCAATGA
          1 TCCAATGA

       6789 TCTCCTAGCA


Statistics
Matches: 69,  Mismatches: 1, Indels: 2
        0.96            0.01        0.03

Matches are distributed among these distances:
  20    3  0.04
  21   66  0.96

ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28


Consensus pattern (21 bp):   
TCCAATGAGCTTGGAACCTTC

Done.