Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398876.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2158.0, 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: 10911
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.20

Warning! 4982 characters in sequence are not A, C, G, or T


Found at i:2449 original size:31 final size:31

Alignment explanation


    Indices: 2411--2476  Score: 87
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       2401 AGACAATCAA

                      *     *     *        
       2411 TCTTGCCAATTAATACTTTTTTCTTCATGTT
          1 TCTTGCCAATGAATACCTTTTTATTCATGTT

                          *          *     
       2442 TCTTGCCAATGAATGCCTTTTTATTTATGTT
          1 TCTTGCCAATGAATACCTTTTTATTCATGTT

                
       2473 TCTT
          1 TCTT

       2477 AAGGTAGACA


Statistics
Matches: 30,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55


Consensus pattern (31 bp):   
TCTTGCCAATGAATACCTTTTTATTCATGTT

Found at i:6274 original size:172 final size:155

Alignment explanation


    Indices: 6060--6382  Score: 288
    Period size: 172  Copynumber: 2.0  Consensus size: 155

       6050 TTAAAGCAAA

                             *     *   **                            * *     
       6060 TAATAAGGCTTTTGAAGGTATGGGTAAGTATAAATAGACTTTTCTTGCCAAC-GAATGCTTTTTT
          1 TAATAAGGCTTTTGAAGCTATGGATAACAATAAATAGACTTTTCTTG-CAACTGAATACCTTTTT

                        *      *     *   ** *  *         **               *  
       6124 CTTCATGTTTCTCAAGGTATACATTGAATTGTTGTTTGTTTTAACCGAAAATGTACAAAGAATTC
         65 CTTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACAAAAAATGTACAAAGAAATC

                                                       
       6189 AAATTTAAATCAATTTTGAGATNNNNNNNNNNNNNNNNNCGAG
        130 AAATTTAAATCAATTTTGAGAT-----------------CGAG

                                     *         *            *                
       6232 TAATAAGGCTTTTGAAGCTATGGATGACAATAAATGGACTTTTCTTGCTACTGAATACCTTTTTC
          1 TAATAAGGCTTTTGAAGCTATGGATAACAATAAATAGACTTTTCTTGCAACTGAATACCTTTTTC

                     *                                             *         
       6297 TTCATGTTTTTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACAAAAAATGTACGAAGAAATCA
         66 TTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACAAAAAATGTACAAAGAAATCA

                                 
       6362 AATTTAAATCAATTTTGAGAT
        131 AATTTAAATCAATTTTGAGAT

       6383 TATAAAACCA


Statistics
Matches: 129,  Mismatches: 21, Indels: 2
        0.85            0.14        0.01

Matches are distributed among these distances:
 171    3  0.02
 172  126  0.98

ACGTcount: A:0.32, C:0.12, G:0.15, T:0.36


Consensus pattern (155 bp):   
TAATAAGGCTTTTGAAGCTATGGATAACAATAAATAGACTTTTCTTGCAACTGAATACCTTTTTC
TTCATGTTTCTAAAGGTAGACATTCAATCCTAGTCTGTTTTAACAAAAAATGTACAAAGAAATCA
AATTTAAATCAATTTTGAGATCGAG

Found at i:9574 original size:171 final size:168

Alignment explanation


    Indices: 9077--9583  Score: 433
    Period size: 171  Copynumber: 3.0  Consensus size: 168

       9067 NNNNNNNNNN

                                             *           *                *  
       9077 GTTTAACCAAAAATATAAAAAAAATT-AATCATAAAATCAATTATAGCATTACAAAACCATTGAA
          1 GTTTAACCAAAAATATAAAAAAAATTCAA-C-TTAAATCAATTATGGCATTACAAAACCATTTAA

             *                 *        *  *                              *  
       9141 ATCGAGTAATAAGGCTTTTGAAGGTATGAGTTACTATAAATGGACTTTTCTTGCCAATGAATACT
         64 AGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT

              ******** *     *                **  *   
       9206 NNNNNNNNNNTGTTTCTGAAGGTAGACATTCAATCCTAGTCT
        129 --TTTTTCTCTATTTCTCAAGGTAGACATTCAATTATAATCT

                           *  * * **       *           *   *               * 
       9248 GATTTAACCAAAAATGTATAGAGCATTCAAATTTAAATCAATTTTGGGATTACAAAACCATTTCA
          1 G-TTTAACCAAAAATATAAAAAAAATTC-AACTTAAATCAATTATGGCATTACAAAACCATTTAA

              *          *   **********                    *                 
       9313 AGTGAGTAATAAGACTTNNNNNNNNNNGGGTGACTATAAATGGACTTCTCTTGCCAATGAATG-T
         64 AGCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCT

                             * *         *             
       9377 CTTTTTCTCTACGTTTCCCTAGGTAGACAATCAATTATAATCT
        129 -TTTTTCTCTA--TTTCTCAAGGTAGACATTCAATTATAATCT

                   *                                                         
       9420 GTTTAACTAAAAATATAAAAAAAATTCAACTTACAATCAATTATGGCATTACAAAACCATTTAAA
          1 GTTTAACCAAAAATATAAAAAAAATTCAACTTA-AATCAATTATGGCATTACAAAACCATTTAAA

                   *                                **               *       
       9485 GCGAGTAGTAAGGCTTTTAAAGGTATGGGTGACTATAAATACACTTTTCTTGCCAATAAATGCTT
         65 GCGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTT

                                              
       9550 TTTTCTTCATATTTCTCAAGGTAGACATTCAATT
        130 TTTTC-TC-TATTTCTCAAGGTAGACATTCAATT

       9584 CTAGTCTGNN


Statistics
Matches: 251,  Mismatches: 76, Indels: 18
        0.73            0.22        0.05

Matches are distributed among these distances:
 170    6  0.02
 171  121  0.48
 172  120  0.48
 173    2  0.01
 174    2  0.01

ACGTcount: A:0.36, C:0.14, G:0.13, T:0.33


Consensus pattern (168 bp):   
GTTTAACCAAAAATATAAAAAAAATTCAACTTAAATCAATTATGGCATTACAAAACCATTTAAAG
CGAGTAATAAGGCTTTTAAAGGTATGGGTGACTATAAATGGACTTTTCTTGCCAATGAATGCTTT
TTTCTCTATTTCTCAAGGTAGACATTCAATTATAATCT
Done.