Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011664.1 Corchorus olitorius cultivar O-4 contig11697, 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, 976

Length: 1628
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36


Found at i:358 original size:154 final size:154

Alignment explanation


    Indices: 1--606  Score: 966
    Period size: 154  Copynumber: 3.9  Consensus size: 154

                                         *                                   
          1 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG-TACTTTTGGGCCTATCG
          1 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTA-TTTTGGGCCTATCG

            *            * *                                                 
         65 AGG-CCATTAGT-CCGTTTTGAATCGTCTTCGATTTGGTCAAACCTCAATTGCTTTTCTTTCCAT
         65 GGGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGG-CAAACCTCAA-TGCTTTTCTTTCCAT

                   * *                  
        128 TGTTTATAGCCTTAACTATAATCATTTT
        128 TGTTTATGGAC-TAACTATAATCATTTT

                 *                       *                                   
        156 GGTGACATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
          1 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                          *       *                                          
        221 GGCCCATTAGTGACGTTTTGAACCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
         66 GGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT

                  *                 
        286 TTATGGCCTAACTATAATCATTTT
        131 TTATGGACTAACTATAATCATTTT

                                                 *  *                        
        310 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTAGATCACTTGTTATTTTGGGCCTATCGG
          1 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                                          *                *               * 
        375 GGCCCATTAGTGACATTTTGAATCGTCTTCAATTTGGCAAACCTCAAGGCTTTTCTTTCCATTTT
         66 GGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT

                                    
        440 TTATGGACTAACTATAATCATTTT
        131 TTATGGACTAACTATAATCATTTT

                                                                             
        464 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
          1 GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGG

                       **                           *   *         *          
        529 GGCCCATTAGTTCCATTTTGAATCGTCTTCGATTTGGCAACCCTTAATGCTTTTGTTTCCATTGT
         66 GGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT

                         
        594 TTATGGACTAACT
        131 TTATGGACTAACT

        607 GATGCGCCAA


Statistics
Matches: 423,  Mismatches: 25, Indels: 7
        0.93            0.05        0.02

Matches are distributed among these distances:
 154  293  0.69
 155   87  0.21
 156   20  0.05
 157   23  0.05

ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41


Consensus pattern (154 bp):   
GGTGAGATTAGTCCACTGTGAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCTATCGG
GGCCCATTAGTGACATTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGT
TTATGGACTAACTATAATCATTTT

Found at i:738 original size:21 final size:21

Alignment explanation


    Indices: 712--824  Score: 156
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        702 TGCTAGAAGT

                                  
        712 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        733 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        754 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

             *               *  *
        775 TTATTGGAGAAGGTTCCTAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        796 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        817 TCATTGGA
          1 TCATTGGA

        825 ATTGCCTAAG


Statistics
Matches: 83,  Mismatches: 8, Indels: 2
        0.89            0.09        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   81  0.98

ACGTcount: A:0.28, C:0.15, G:0.27, T:0.29


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:755 original size:42 final size:42

Alignment explanation


    Indices: 708--824  Score: 173
    Period size: 42  Copynumber: 2.8  Consensus size: 42

        698 AAGATGCTAG

                                                       
        708 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTCC

                                    * *               
        750 AAGTTCATTGGAGAAGGTTCCAAGTTTATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC

            *  *               *             
        792 TAGATCATTGGAGAAGGTTTCAAGCTCATTGGA
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGA

        825 ATTGCCTAAG


Statistics
Matches: 67,  Mismatches: 7, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  41    2  0.03
  42   65  0.97

ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29


Consensus pattern (42 bp):   
AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
Done.