Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398748.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2031.0, 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, 998

Length: 1664
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.32

Warning! 233 characters in sequence are not A, C, G, or T


Found at i:489 original size:170 final size:161

Alignment explanation


    Indices: 285--601  Score: 348
    Period size: 170  Copynumber: 1.9  Consensus size: 161

        275 TTTAATGTTA

                       * *   *                           *   * *             
        285 AATTTTTCTACTTTTTTTGTTAAAAGAAATTATTATTGAATGTTTGCCTGGGAAAACATAAAGAA
          1 AATTTTTCTACATATTTGGTTAAAAGAAATTATTATTGAATGTTTACCTCGAAAAACATAAAGAA

              *             *      *            *        *       *           
        350 AATGCCATTCATTGGCCAGAAAAGTCCATTTATAGTTACACATGCTTTCAAA-TCCTAATTACTC
         66 AAAGCCATTCATTGGCAAGAAAAATCCATTTATAGTCACACATGCCTTCAAAGGCCTAATTACTC

                                                     
        414 GCTTTAAATGGTTTTATNNNNNNNNNNTTGATTTTAGTTTG
        131 GCTTTAAATGGTTTTAT----------TTGATTTTAGTTTG

                   *                 * *                            ** *     
        455 AATTTTTTTACATATTTGGTTAAAATAGATTATTATTGAATGTTTACCTCGAAAAATGTGAAGAA
          1 AATTTTTCTACATATTTGGTTAAAAGAAATTATTATTGAATGTTTACCTCGAAAAACATAAAGAA

                *          *                       *                         
        520 AAAGTCATTCATTGGTAAGAAAAATCCATTTATAGTCACCCATGCCTTCAAAGGCCTAATTACTC
         66 AAAGCCATTCATTGGCAAGAAAAATCCATTTATAGTCACACATGCCTTCAAAGGCCTAATTACTC

                             
        585 GCTTTAAATGGTTTTAT
        131 GCTTTAAATGGTTTTAT

        602 AATCTCGCTT


Statistics
Matches: 125,  Mismatches: 21, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
 170   97  0.78
 171   28  0.22

ACGTcount: A:0.32, C:0.13, G:0.13, T:0.38


Consensus pattern (161 bp):   
AATTTTTCTACATATTTGGTTAAAAGAAATTATTATTGAATGTTTACCTCGAAAAACATAAAGAA
AAAGCCATTCATTGGCAAGAAAAATCCATTTATAGTCACACATGCCTTCAAAGGCCTAATTACTC
GCTTTAAATGGTTTTATTTGATTTTAGTTTG

Found at i:1482 original size:170 final size:168

Alignment explanation


    Indices: 908--1663  Score: 515
    Period size: 170  Copynumber: 4.5  Consensus size: 168

        898 NNNTCATTGA

                *              *   *   *      *   ***    *    *    *    *    
        908 CAAGTAAAGTCCATTTATATTTACCCATGCCTTCAAAATTGTAATCACTCACTTTGAATGATTTT
          1 CAAGAAAAGTCCATTTATAGTTATCCAAGCCTTCGAAAGCCTAATTACTCGCTTTAAATGGTTTT

                          *   *  *                                 *    * ** 
        973 ATAATCTCATAATTGATTATATGTTGAA--TTTTTATATTTTTGGTTAAAATAGATTATAGTAAA
         66 ATAATCTCATAATTAATTTTAGGTTGAATTTTTTTATATTTTTGGTT-AAA-AGAATATAATTGA

                  *   *  *   **          *   *       
       1036 ATGTCTACCTTAAAAAATGTGAAGAAACAGCCAATCATT-G
        129 ATGTCTGCCTCAAGAAACATGAAGAAA-AACCATTCATTAG

                *       *         * *   *  *  **       *     *          * ***
       1076 ACAATAAAAGTCTATTTATAGTCACCCATGCTTTTAAAAGCCTTATTACGCGCTTTAAATAGNNN
          1 -CAAGAAAAGTCCATTTATAGTTATCCAAGCCTTCGAAAGCCTAATTACTCGCTTTAAATGGTTT

            *******               *       *      *                  *        
       1141 NNNNNNNTCATAATTAATTTTAAGTT-AA-ATTTTTACATTTTTGGTTAAAATAGATTATAATTG
         65 TATAATCTCATAATTAATTTTAGGTTGAATTTTTTTATATTTTTGGTT-AAA-AGAATATAATTG

               * *    *                                
       1204 AATATATGCCCCAAGAAACATGAAGAAAAAGCCATTCATTGAG
        128 AATGTCTGCCTCAAGAAACATGAAGAAAAA-CCATTCATT-AG

                            *    * *                           **       **   
       1247 -AA-AAAAGTCCATTTCTAGTCACCCAAGCAC-TCGAAAGCCTAATTACTCATTTTAAATAATTT
          1 CAAGAAAAGTCCATTTATAGTTATCCAAGC-CTTCGAAAGCCTAATTACTCGCTTTAAATGGTTT

                *          *                          *                      
       1309 TATACTCTCATAATTGATTTTAGGTTGAATTTTTTTATATTTATGGTTAAACAGAATATAATTGA
         65 TATAATCTCATAATTAATTTTAGGTTGAATTTTTTTATATTTTTGGTTAAA-AGAATATAATTGA

                  *   * *       *                    
       1374 ATGTCTACCTTAGGAAACATAAAGAAAAATCCATTCATTAG
        129 ATGTCTGCCTCAAGAAACATGAAGAAAAA-CCATTCATTAG

                   * *                        *              *               
       1415 CAAGAAAGGACCATTTATAGTTATCCAAGCCTTCAAAAGCCTAATTACTTGCTTTAAATGGTTTT
          1 CAAGAAAAGTCCATTTATAGTTATCCAAGCCTTCGAAAGCCTAATTACTCGCTTTAAATGGTTTT

                 *            *           *               *    *             
       1480 ATAATGTCATAATTAATTGTAGGTTGAATTGTTTTATATTTTTGGTGAAAATATATTATAATTGA
         66 ATAATCTCATAATTAATTTTAGGTTGAATTTTTTTATATTTTTGGTTAAAAGA-A-TATAATTGA

             * *                                    * 
       1545 AGGACTGCCTCAAG-AACATGAAGAAAAA-CACTATCATTGG
        129 ATGTCTGCCTCAAGAAACATGAAGAAAAACCA-T-TCATTAG

              *         *            * *     *        *            * *       
       1585 CAGGAAAAGTCCGTTTATAGTTATCTATGCCTTTGAAAGCCTTATTACTCGCTTTCAGTGGTTTT
          1 CAAGAAAAGTCCATTTATAGTTATCCAAGCCTTCGAAAGCCTAATTACTCGCTTTAAATGGTTTT

                          
       1650 ATAATCTCATAATT
         66 ATAATCTCATAATT

       1664 G


Statistics
Matches: 454,  Mismatches: 119, Indels: 27
        0.76            0.20        0.05

Matches are distributed among these distances:
 168   69  0.15
 169  174  0.38
 170  192  0.42
 171   19  0.04

ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36


Consensus pattern (168 bp):   
CAAGAAAAGTCCATTTATAGTTATCCAAGCCTTCGAAAGCCTAATTACTCGCTTTAAATGGTTTT
ATAATCTCATAATTAATTTTAGGTTGAATTTTTTTATATTTTTGGTTAAAAGAATATAATTGAAT
GTCTGCCTCAAGAAACATGAAGAAAAACCATTCATTAG
Done.