Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011701.1 Corchorus olitorius cultivar O-4 contig11734, 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, 766

Length: 1277
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34


Found at i:464 original size:152 final size:154

Alignment explanation


    Indices: 1--488  Score: 734
    Period size: 153  Copynumber: 3.2  Consensus size: 154

                                               *  *                          
          1 AACACTTGTTATTTTGGGCCTATCGAGGCCCATTAATTCCGTTTTGAATCGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA

                                           *                            *    
         66 ACCCTCAATGCTTTTCTTTCCAATGTTTATGCCCTAACTATAATCATTTTGGTGAGATTACTCCA
         66 ACCCTCAATGCTTTTCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCA

                                    
        131 CTGTGAAGTTTTTAGCTCATTTGG
        131 CTGTGAAGTTTTTAGCTCATTTGG

                *  *                      *       *                  *       
        155 AACAATTTTTATTTTGGGCCTATCG-GAGCTCATTAGTGACGTTTTGAATCGTCTTCTATTT-GC
          1 AACACTTGTTATTTTGGGCCTATCGAG-GCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGC

                                   *        *             *                  
        218 AACCCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC-ATTAATAATTTTGGTGAGATTAGTC
         65 AACCCTCAATGCTTTTCTTTCCAATGTTTATGACCTAACTA-TAATCATTTTGGTGAGATTAGTC

                            *         
        282 CACTGTGAAGTTTTTACCTCATTTGG
        129 CACTGTGAAGTTTTTAGCTCATTTGG

                               *                             *               
        308 AACACTTGTTA-TTTGGGCATATCGAGGCCCATTAGTTACGTTTTGAATTGTCTTCGATTTGGCA
          1 AACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA

                          *                                        * *       
        372 ACCCTCAATGCTTTCCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGT-AAAATAGTCCA
         66 ACCCTCAATGCTTTTCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCA

              *      *             *
        436 CTTTGAAGTATTTAGCTCATTTGA
        131 CTGTGAAGTTTTTAGCTCATTTGG

                                         
        460 AACACTTGTTATTTTGGGCCTATCGAGGC
          1 AACACTTGTTATTTTGGGCCTATCGAGGC

        489 TGATGCGCCA


Statistics
Matches: 298,  Mismatches: 30, Indels: 13
        0.87            0.09        0.04

Matches are distributed among these distances:
 152   83  0.28
 153  162  0.54
 154   53  0.18

ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40


Consensus pattern (154 bp):   
AACACTTGTTATTTTGGGCCTATCGAGGCCCATTAGTTACGTTTTGAATCGTCTTCGATTTGGCA
ACCCTCAATGCTTTTCTTTCCAATGTTTATGACCTAACTATAATCATTTTGGTGAGATTAGTCCA
CTGTGAAGTTTTTAGCTCATTTGG

Found at i:621 original size:21 final size:21

Alignment explanation


    Indices: 595--812  Score: 316
    Period size: 21  Copynumber: 10.4  Consensus size: 21

        585 TGCTAGAAGT

                                  
        595 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                  
        616 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                     *  *       *
        637 TCATTGGAGCAGATTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                 
        658 TCATTGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        679 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                  
        700 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        721 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        742 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        763 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        784 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        805 TCATTGGA
          1 TCATTGGA

        813 AATGCCTAAG


Statistics
Matches: 182,  Mismatches: 12, Indels: 6
        0.91            0.06        0.03

Matches are distributed among these distances:
  20    3  0.02
  21  177  0.97
  22    2  0.01

ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Done.