Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398850.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2132.0, 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: 2383
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.23

Warning! 971 characters in sequence are not A, C, G, or T


Found at i:287 original size:171 final size:171

Alignment explanation


    Indices: 1--755  Score: 764
    Period size: 171  Copynumber: 4.4  Consensus size: 171

                       *    *                                                
          1 AGAAATGTGAAAAAAATAGCATTCATTGGCAAGAAAAGTCTATTTATATCGTC-CC-ACTCCTTC
          1 AGAAATGTGAAGAAAAGAGCATTCATTGGCAAGAAAAGTC-ATTTATA--GTCACCTACTCCTTC

                            *          *                                     
         64 ATAAA-CC-ATATTACTCACTTTAAATGGTTTTTTAATCTCATAATTGATTTTAA-TTTAAATTT
         63 A-AAAGCCTA-ATTACACACTTTAAATAGTTTTTTAATCTCATAATTGATTTTAAGTTTAAATTT

                                *               * *      *
        126 TTTTACATTTTTGATTAAAAGAGACTATAATTGAATATGTATCTTG
        126 TTTTACATTTTTGATTAAAACAGACTATAATTGAATGTCTATCTTA

            *                 *         *                           *        
        172 GGAAATGTGAAGAAAAGAACATTCATTGACAAGAAAAGTTCATTTATAGTCACCTATTCCTTCAA
          1 AGAAATGTGAAGAAAAGAGCATTCATTGGCAAGAAAAG-TCATTTATAGTCACCTACTCCTTCAA

                          *              *                        *          
        237 AAGCCTAATTACACTCTTTAAATAGTTTTCTAATCTCATAATTGATTTTAAGTTGAAA-TTTTTT
         65 AAGCCTAATTACACACTTTAAATAGTTTTTTAATCTCATAATTGATTTTAAGTTTAAATTTTTTT

                    *             *            * * ** 
        301 ACATTTTTCATTAAAACAGACTCTAATTGAATGTCGAACACA
        130 ACATTTTTGATTAAAACAGACTATAATTGAATGTCTATCTTA

                 **           *                        *     * *  * *        
        343 AGAAACATGAAGAAAAGAACATTCATTGGCAAGAAAAGTTCATATATAGCCTCCCAATCCTTCAA
          1 AGAAATGTGAAGAAAAGAGCATTCATTGGCAAGAAAAG-TCATTTATAGTCACCTACTCCTTCAA

               *  *        *         *    *      *                           
        408 AAGGCTTATTACTA-GCTTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTT-AATTTTTT
         65 AAGCCTAATTAC-ACACTTTAAATAGTTTTTTAATCTCATAATTGATTTTAAGTTTAAATTTTTT

                   * *       *    *       *             
        471 TACATTTATAATTAAAAAAGACAATAATTGTATGTCTAT-TTCA
        129 TACATTTTTGATTAAAACAGACTATAATTGAATGTCTATCTT-A

                         *  *            *                      *            
        514 AGAAATGTGAAGAGAATAGCATTCATTGGGAAGAAAAGTCTATTTATA-TCATCTCACTCCTTCA
          1 AGAAATGTGAAGAAAAGAGCATTCATTGGCAAGAAAAGTC-ATTTATAGTCACCT-ACTCCTTCA

               *   *     *          *                                        
        578 AAACCCTTATTACTCACTTTAAATGGTTTTTTAATCTCATAATTGA-TTTAA-TTTAAATTTTTT
         64 AAAGCCTAATTACACACTTTAAATAGTTTTTTAATCTCATAATTGATTTTAAGTTTAAATTTTTT

                                                        *
        641 TACATTTTTGATTAAACACAGA-TAATAATTGAATGTCTATCTTG
        129 TACATTTTTGATTAAA-ACAGACT-ATAATTGAATGTCTATCTTA

                 *     *        *       **          *                *  *    
        685 AGAAACGTGGAGGAAAA-AGTATTCATTATCAAGAAAAGACCATTTATAGTCACCTATTCTTTCA
          1 AGAAATGT-GAAGAAAAGAGCATTCATTGGCAAGAAAAG-TCATTTATAGTCACCTACTCCTTCA

                   
        749 AAAGCCT
         64 AAAGCCT

        756 TATCACACGC


Statistics
Matches: 480,  Mismatches: 85, Indels: 38
        0.80            0.14        0.06

Matches are distributed among these distances:
 169    6  0.01
 170   38  0.08
 171  413  0.86
 172   23  0.05

ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37


Consensus pattern (171 bp):   
AGAAATGTGAAGAAAAGAGCATTCATTGGCAAGAAAAGTCATTTATAGTCACCTACTCCTTCAAA
AGCCTAATTACACACTTTAAATAGTTTTTTAATCTCATAATTGATTTTAAGTTTAAATTTTTTTA
CATTTTTGATTAAAACAGACTATAATTGAATGTCTATCTTA

Found at i:711 original size:342 final size:342

Alignment explanation


    Indices: 20--677  Score: 841
    Period size: 342  Copynumber: 1.9  Consensus size: 342

         10 AAAAAAATAG

                                    *    * *     *                           
         20 CATTCATTGGCAAGAAAAGTCTATTTATATCGTCCCACTCCTTCATAAACCATATTACTCACTTT
          1 CATTCATTGGCAAGAAAAGTCTATATATAGCCTCCCAATCCTTCATAAACCATATTACTCACTTT

                **    *      *                                 * *       *   
         85 AAATGGTTTTTTAATCTCATAATTGATTTTAATTTAAATTTTTTTACATTTTTGATTAAAAGAGA
         66 AAATAATTTTATAATCTAATAATTGATTTTAATTTAAATTTTTTTACATTTATAATTAAAAAAGA

             *            *      **                                          
        150 CTATAATTGAATATGTATCTTGGGAAATGTGAAGAAAAGAACATTCATTGACAAGAAAAGTTCAT
        131 CAATAATTGAATATCTATCTTAAGAAATGTGAAGAAAAGAACATTCATTGACAAGAAAAGTTCAT

                         *          *           *                            
        215 TTATAGTCACCTATTCCTTCAAAAGCCTAATTACACTCTTTAAATAGTTTTCTAATCTCATAATT
        196 TTATAGTCACCTACTCCTTCAAAACCCTAATTACACACTTTAAATAGTTTTCTAATCTCATAATT

                                                       *                     
        280 GATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAACAGACTCTAATTGAATGTCGAACACAAG
        261 GATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCGAACACAAG

                             
        345 AAACATGAAGAAAAGAA
        326 AAACATGAAGAAAAGAA

                                                               * *           
        362 CATTCATTGGCAAGAAAAGT-TCATATATAGCCTCCCAATCCTTCA-AAAGGCTTATTACT-AGC
          1 CATTCATTGGCAAGAAAAGTCT-ATATATAGCCTCCCAATCCTTCATAAA-CCATATTACTCA-C

                                                                             
        424 TTTAAATAATTTTATAATCTAATAATTGATTTTAAGTTT-AATTTTTTTACATTTATAATTAAAA
         63 TTTAAATAATTTTATAATCTAATAATTGATTTTAA-TTTAAATTTTTTTACATTTATAATTAAAA

                         *  *                       *  * *         **        
        488 AAGACAATAATTGTATGTCTAT-TTCAAGAAATGTGAAGAGAATAGCATTCATTGGGAAGAAAAG
        127 AAGACAATAATTGAATATCTATCTT-AAGAAATGTGAAGAAAAGAACATTCATTGACAAGAAAAG

                           *                   *     *          *     *      
        552 -TCTATTTATA-TCATCTCACTCCTTCAAAACCCTTATTACTCACTTTAAATGGTTTTTTAATCT
        191 TTC-ATTTATAGTCACCT-ACTCCTTCAAAACCCTAATTACACACTTTAAATAGTTTTCTAATCT

                              *                  *                           
        615 CATAATTGA-TTTAA-TTTAAATTTTTTTACATTTTTGATTAAACACAGA-TAATAATTGAATGT
        254 CATAATTGATTTTAAGTTGAAA-TTTTTTACATTTTTCATTAAA-ACAGACT-ATAATTGAATGT

             
        677 C
        316 C

        678 TATCTTGAGA


Statistics
Matches: 271,  Mismatches: 35, Indels: 20
        0.83            0.11        0.06

Matches are distributed among these distances:
 340    5  0.02
 341   40  0.15
 342  223  0.82
 343    3  0.01

ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39


Consensus pattern (342 bp):   
CATTCATTGGCAAGAAAAGTCTATATATAGCCTCCCAATCCTTCATAAACCATATTACTCACTTT
AAATAATTTTATAATCTAATAATTGATTTTAATTTAAATTTTTTTACATTTATAATTAAAAAAGA
CAATAATTGAATATCTATCTTAAGAAATGTGAAGAAAAGAACATTCATTGACAAGAAAAGTTCAT
TTATAGTCACCTACTCCTTCAAAACCCTAATTACACACTTTAAATAGTTTTCTAATCTCATAATT
GATTTTAAGTTGAAATTTTTTACATTTTTCATTAAAACAGACTATAATTGAATGTCGAACACAAG
AAACATGAAGAAAAGAA

Done.