Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010425.1 Corchorus olitorius cultivar O-4 contig10457, 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: 2564
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31


Found at i:526 original size:21 final size:21

Alignment explanation


    Indices: 500--541  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        490 TAAGGAAGAA

                                 
        500 GTTTCAAGCTCATCAGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

                          *      
        521 GTTTCAAGCTCATCGGAGTTG
          1 GTTTCAAGCTCATCAGAGTTG

        542 CCTAAGATGC


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33


Consensus pattern (21 bp):   
GTTTCAAGCTCATCAGAGTTG

Found at i:1603 original size:154 final size:154

Alignment explanation


    Indices: 1308--1730  Score: 659
    Period size: 154  Copynumber: 2.8  Consensus size: 154

       1298 CAAGGCTAGA

                                                                             
       1308 TTTTTCATTCCATTG-TTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
          1 TTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT

                                                                             
       1372 TTTAGCTCATTAAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCA
         66 TTTAGCTCATTAAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCA

                                    
       1437 TCTTCGATTTGGCAAACCTCAATG
        131 TCTTCGATTTGGCAAACCTCAATG

                  *                                       *                  
       1461 TTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGGTTAGTCCACTGTGAAGTT
          1 TTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT

            * *    *   **        *                          *     *         *
       1526 ATCAGCTAATTCGGAACACTTTTTATTTTGGGCCTATCGGGGCCCATTCGTTCCGTTTTGAATCG
         66 TTTAGCTCATTAAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCA

                           *        
       1591 TCTTCGATTTGGCAACCCTCAATG
        131 TCTTCGATTTGGCAAACCTCAATG

            *     *                                   *             *     *  
       1615 CTTTTCGTTCCATTGTTTATGGCCTAACTATAATCATTTTGGGGAGATTAGTCCACCGTGAAATT
          1 TTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT

                *      *                         *             
       1680 TTTAACTCATTTAGAACACTTGTTATTTTGGGCCTATAGGGGCCCATTAGT
         66 TTTAGCTCATTAAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGT

       1731 GATGTTTTGA


Statistics
Matches: 242,  Mismatches: 27, Indels: 1
        0.90            0.10        0.00

Matches are distributed among these distances:
 153   14  0.06
 154  228  0.94

ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40


Consensus pattern (154 bp):   
TTTTTCATTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTT
TTTAGCTCATTAAGAACACTTGTTATTTTGGGCCTATCGGGGCCCATTAGTTCCATTTTGAATCA
TCTTCGATTTGGCAAACCTCAATG

Found at i:2163 original size:11 final size:11

Alignment explanation


    Indices: 2147--2184  Score: 58
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       2137 CTAAGGGTAA

                       
       2147 AGGAAAAAGCT
          1 AGGAAAAAGCT

                       
       2158 AGGAAAAAGCT
          1 AGGAAAAAGCT

                 **    
       2169 AGGAAGGAGCT
          1 AGGAAAAAGCT

                 
       2180 AGGAA
          1 AGGAA

       2185 GGACCCTACT


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.50, C:0.08, G:0.34, T:0.08


Consensus pattern (11 bp):   
AGGAAAAAGCT

Done.