Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018399870.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3104.0, 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: 3830
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.29

Warning! 984 characters in sequence are not A, C, G, or T


Found at i:2457 original size:171 final size:167

Alignment explanation


    Indices: 1995--2750  Score: 510
    Period size: 171  Copynumber: 4.4  Consensus size: 167

       1985 NNNNNNNNNN

                       *         *  *                * *                     
       1995 GAAGAAAAAAGTATTCATTGACAAAAAAAGTCCA-TTATAGCCGCCCATTCTTTCAAAAGCTTTA
          1 GAAGAAAAAA-CATTCATTG-TAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCTTTA

                           *    **                          *        *       
       2059 TTACTCGCTTTAAATAGTTTGGTAATCTCATAATTGATTTTAAGTTGATTTTTTTTACATTTTTG
         64 TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTATATTTTTG

                      * *               *   * *      
       2124 ATTAAAACAGGTTATAATTGAATGTCTGTCTCAAAAAACAT
        128 ATTAAAACAGATAATAATTGAATGTCT-ACTCGAGAAACAT

                     *               *               *     *         *       
       2165 GAAGAAAAAGCTATTCATTGCTAAGGAAAGTCCATTTATACAT-ACCTATTCTTTCAGAAGCTTT
          1 GAAGAAAAAAC-ATTCATTG-TAAGAAAAGTCCATTTATA-GTCACCCATTCTTTCAAAAGCTTT

                                             **********                      
       2229 ATTACTCGCTTTAAATGGTTTTATAATCTCATANNNNNNNNNNAGTTGAATTTTTTTATATTTTT
         63 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTATATTTTT

                                                   ** 
       2294 GATTAAAACAGATAATAATTGAATGTCTAACTCGAGAAATGT
        127 GATTAAAACAGATAATAATTGAATGTCT-ACTCGAGAAACAT

                                                                *            
       2336 GAAGAAAAATACATTCATTAGTAAGAAAAGTCCA-TTATAGTCACCCATTC-CTCTAAAAGGC-T
          1 GAAGAAAAA-ACATTCATT-GTAAGAAAAGTCCATTTATAGTCACCCATTCTTTC-AAAA-GCTT

                    *                        *          *                  * 
       2398 TATTACTCTCTTTAAA-GAGTTTTATAATCTCAAAATTGATTTTGAGTTCAATGTTTTTTACTTT
         62 TATTACTCGCTTTAAATG-GTTTTATAATCTCATAATTGATTTTAAGTT-AAT-TTTTTTA-TAT

                              *                   *         
       2462 TTTTG-TTAAAATC-GATCATAATT-ATATGTCTACGTTGAGAAACAT
        123 TTTTGATTAAAA-CAGATAATAATTGA-ATGTCTAC-TCGAGAAACAT

            *  *                 *    *     *      *     *     *         *   
       2507 AAAAAAAAAGACATTCATTGGCAAGACAAGTCAATTTATTGTCACACATTCCTTCAAAAGCCTTA
          1 GAAGAAAAA-ACATTCATT-GTAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCTTTA

                  *                ******************                *       
       2572 TTACTCACTTTAAATGGTTTTA-NNNNNNNNNNNNNNNNNNAAGTTGAATTTTTTTACATTTTTG
         64 TTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTATATTTTTG

               *                             *      * 
       2636 -TTTAAACAGACT-ATAATTGAATGTCTACCTCAAGAAACGT
        128 ATTAAAACAGA-TAATAATTGAATGTCTA-CTCGAGAAACAT

                      *   *                *         *        *              
       2676 GAAGAAAAAAAATTTATTGATAAGAAAAGTCAATTTATAGTTACCCATTCCTTCAAAAGCTTTAT
          1 GAAGAAAAAACATTCATTG-TAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCTTTAT

                      
       2741 TACTCGCTTT
         65 TACTCGCTTT

       2751 NNNNNNNNNN


Statistics
Matches: 457,  Mismatches: 106, Indels: 48
        0.75            0.17        0.08

Matches are distributed among these distances:
 167    1  0.00
 168   56  0.12
 169   45  0.10
 170   93  0.20
 171  209  0.46
 172   50  0.11
 173    3  0.01

ACGTcount: A:0.35, C:0.13, G:0.12, T:0.36


Consensus pattern (167 bp):   
GAAGAAAAAACATTCATTGTAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGCTTTATT
ACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTATATTTTTGATT
AAAACAGATAATAATTGAATGTCTACTCGAGAAACAT

Found at i:3229 original size:170 final size:171

Alignment explanation


    Indices: 2934--3284  Score: 431
    Period size: 170  Copynumber: 2.1  Consensus size: 171

       2924 CCATTCTTTT

                                         *        *                 *        
       2934 AAAAGCCTTATTACTCGCTTTAAATTATTTTATAATCTCATAAGTAATTTTAAGTTGAATGGTTT
          1 AAAAGCCTTATTACTCGCTTTAAATTATTCTATAATCTAATAAGTAATTTTAAGTTAAATGGTTT

                   **            *                                        *  
       2999 TACATTTTTAGTTAAAACAAAGTAGAAATGAATGTCTACCTCAAGAAACATGACGAAAAAGGGAT
         66 TACATTTCCAGTTAAAACAAACTAGAAATGAATGTCTACCTCAAGAAACATGACGAAAAAGGCAT

                                        *            
       3064 TCATTGACAAGAAAAGTCCATTTATAGTTACCTATTCCCTC
        131 TCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCCCTC

                             *                         *                **   
       3105 -AAAGCCTTATTACTCGTTTTAAATTATTCTATAATCTAATAATTAATTTTAAGTTAAATTTTTT
          1 AAAAGCCTTATTACTCGCTTTAAATTATTCTATAATCTAATAAGTAATTTTAAGTTAAATGGTTT

             *                *      *  *   *                 *             *
       3169 TTCATTTGCCA-TTAAAATAAACTATAATTGATTG-CTTACCTCAAGAAATATGTA-GAAAAAGT
         66 TACATTT-CCAGTTAAAACAAACTAGAAATGAATGTC-TACCTCAAGAAACATG-ACGAAAAAGG

                *     *          *                  **  
       3231 CATTTATTGAGAAGAAAAGTCTATTTATAGTCACCTATTCTTTC
        128 CATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCCCTC

                      
       3275 AAAAGCCTTA
          1 AAAAGCCTTA

       3285 NNNNNNNNNN


Statistics
Matches: 152,  Mismatches: 24, Indels: 8
        0.83            0.13        0.04

Matches are distributed among these distances:
 169    1  0.01
 170  140  0.92
 171   11  0.07

ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38


Consensus pattern (171 bp):   
AAAAGCCTTATTACTCGCTTTAAATTATTCTATAATCTAATAAGTAATTTTAAGTTAAATGGTTT
TACATTTCCAGTTAAAACAAACTAGAAATGAATGTCTACCTCAAGAAACATGACGAAAAAGGCAT
TCATTGACAAGAAAAGTCCATTTATAGTCACCTATTCCCTC
Done.