Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010968.1 Corchorus olitorius cultivar O-4 contig11000, 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, 703

Length: 1173
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36


Found at i:281 original size:154 final size:154

Alignment explanation


    Indices: 1--729  Score: 1086
    Period size: 154  Copynumber: 4.7  Consensus size: 154

                  *        **                     * *                  *    *
          1 CTTTCCTTTGTTTATTTCCTAACTATAATCATTTTGGTGATATTAGTCCACTTTGAAGTATTTAT
          1 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG

                       *    *    *             *    *      **                
         66 CTCATTTGGAAAACTTTTTATATTGGGCCTAAT-GGGGCCTATTAGTTCCGTTTTGAATCGTCTT
         66 CTCATTTGGAACACTTGTTATTTTGGGCCT-ATCGAGGCCCATTAGTGACGTTTTGAATCGTCTT

            *                       *
        130 AGATTTGACAACCCTCAATGCTTTC
        130 CGATTTGACAACCCTCAATGCTTTT

                   *                                            *            
        155 CTTTCCAATGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAG
          1 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG

                         *             *                    *                
        220 CTCATTTGGAACAGTTGTTATTTTGGGTCTATCGAGGCCCATTAGTGAGGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC

                  *             *   
        285 GATTTGGCAACCCTCAATGCATTT
        131 GATTTGACAACCCTCAATGCTTTT

                         *                *                        *         
        309 CTTTCCATTGTTTTTGGCCTAACTATAATCGTTTTGGTAAGATTAGTCCACTTTGTAGTTTTTAG
          1 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG

                                                                             
        374 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC

                       *     *       
        439 GATTT-AGCAAACCTCATTGCTTTT
        131 GATTTGA-CAACCCTCAATGCTTTT

                                                                   **        
        463 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGTCGTTTTTAG
          1 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG

                                                                             
        528 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
         66 CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC

                  *                 
        593 GATTTGGCAACCCTCAATGCTTTT
        131 GATTTGACAACCCTCAATGCTTTT

                                                                            *
        617 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAT
          1 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG

              *                   *         *  *             
        682 CTAATTTGGAACACTT-TATATGTTGGGCCTAACGGGGCCCATTAGTGA
         66 CTCATTTGGAACACTTGT-TATTTTGGGCCTATCGAGGCCCATTAGTGA

        730 TGCGTCAAGG


Statistics
Matches: 523,  Mismatches: 48, Indels: 8
        0.90            0.08        0.01

Matches are distributed among these distances:
 153    3  0.01
 154  520  0.99

ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42


Consensus pattern (154 bp):   
CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTAAGATTAGTCCACTTTGAAGTTTTTAG
CTCATTTGGAACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTGACGTTTTGAATCGTCTTC
GATTTGACAACCCTCAATGCTTTT

Found at i:859 original size:21 final size:21

Alignment explanation


    Indices: 833--945  Score: 165
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        823 TGCTAGAAGT

                                  
        833 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        854 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        875 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        896 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                  *        *     
        917 TCATTGAAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        938 TCATTGGA
          1 TCATTGGA

        946 AATGCCTAAG


Statistics
Matches: 85,  Mismatches: 6, Indels: 2
        0.91            0.06        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   83  0.98

ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:876 original size:42 final size:42

Alignment explanation


    Indices: 829--945  Score: 182
    Period size: 42  Copynumber: 2.8  Consensus size: 42

        819 AAGATGCTAG

                                                       
        829 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAG-AAGGTTCCAAGCTCATTGGAGAAGGTTCC

                                    *                 
        871 AAGTTCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC

               *      *        *             
        913 AAGATCATTGAAGAAGGTTTCAAGCTCATTGGA
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGA

        946 AATGCCTAAG


Statistics
Matches: 69,  Mismatches: 5, Indels: 2
        0.91            0.07        0.03

Matches are distributed among these distances:
  41    2  0.03
  42   67  0.97

ACGTcount: A:0.31, C:0.15, G:0.26, T:0.27


Consensus pattern (42 bp):   
AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
Done.