Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402907.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5956.0, 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, 659

Length: 1099
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35

Warning! 40 characters in sequence are not A, C, G, or T


Found at i:390 original size:170 final size:173

Alignment explanation


    Indices: 214--530  Score: 381
    Period size: 170  Copynumber: 1.8  Consensus size: 173

        204 NNNNNNTGGG

                    **         **     *                                   ** 
        214 CTTTTCTTGTCAATGAATGGGTTTTTGTTCACGTT-TCTCAAGGTAGACAATAAATTATAATTTG
          1 CTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTGTCTC-AGGTAGACAATAAATTATAATCCG

              *  *    *                   *   *                  *           
        278 TTTTAGCCAACAATAT-AAAAAAA-GTCAATTTACAATCAATTATGAGATTA-CAAACCATTTAA
         65 TTCTAACCAAAAATATAAAAAAAATGTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAA

             *       *                                  
        340 AGTGAGTAATAAGGCTTTTGAGGGAATGTGTTATTATAAATGGA
        130 AATGAGTAAAAAGGCTTTTGAGGGAATGTGTTATTATAAATGGA

                                           **           *    *        *      
        384 CTTTTCTTACCAATGAATGCCTTTTTCTTCATTTTGTCTCAGGTTGACATTAAATTATTATCCGT
          1 CTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTGTCTCAGGTAGACAATAAATTATAATCCGT

                                    *                 *             *        
        449 TCTAACCAAAAATATAAAAAAAATTTCAACTTAAAATCAATTCTGAGATTATAAAATCATTTAAA
         66 TCTAACCAAAAATATAAAAAAAATGTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA

                        *    
        514 ATGAGTAAAAAGTCTTT
        131 ATGAGTAAAAAGGCTTT

        531 CAAAGGCTTG


Statistics
Matches: 119,  Mismatches: 24, Indels: 5
        0.80            0.16        0.03

Matches are distributed among these distances:
 170   60  0.50
 171   11  0.09
 172   23  0.19
 173   25  0.21

ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38


Consensus pattern (173 bp):   
CTTTTCTTACCAATGAATGCCTTTTTCTTCACGTTGTCTCAGGTAGACAATAAATTATAATCCGT
TCTAACCAAAAATATAAAAAAAATGTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAA
ATGAGTAAAAAGGCTTTTGAGGGAATGTGTTATTATAAATGGA

Found at i:787 original size:170 final size:172

Alignment explanation


    Indices: 468--845  Score: 410
    Period size: 170  Copynumber: 2.2  Consensus size: 172

        458 AAATATAAAA

                                   *               *            *      *     
        468 AAAATTTCAACTTAAAATCAATTCTGAGATTAT-AAAATCATTTAAAATGAGTAAAAAGTCTTTC
          1 AAAA-TTCAACTTAAAATCAATTATGAGATTATAAAAATAATTTAAAATGAGGAAAAAGGCTTTC

                                *  *                *                    * * 
        532 AAAGGCTTGAGTGACAATAAGTGGACTTTTTATGCTAATGGATGACTTTTGATTCATGTTTTCTA
         65 AAAGGCTTGAGTGACAATAAATGCACTTTTTATGCTAATGAATGACTTTTGATTCATGTTTCCCA

               *                                 *     
        597 TAGTAGACATTCAATTATAATAT-ATTTAATAAAAAATG-AA-
        130 TAGCAGACATTCAATTATAATATCATTTAATAAAAAAAGTAAC

                      *                                            *         
        637 AAACATTCAAGTTAAAATCAATTATGAGATTATAAAAATAATTTAAAATGAGGAAGAAGGCTTTC
          1 AAA-ATTCAACTTAAAATCAATTATGAGATTATAAAAATAATTTAAAATGAGGAAAAAGGCTTTC

                            *                   *         **    **  *        
        702 AAAGGCTT-AGGTGACTATAAATGCACTTTTCT-TGTTAATGAATGGTTTTTTCTTTATGTTTCC
         65 AAAGGCTTGA-GTGACAATAAATGCACTTTT-TATGCTAATGAATGACTTTTGATTCATGTTTCC

                      *   * *       *  *                  
        765 CA-AGGCAGATATTTATTTATAATCTCTTTTAATAAAAAAAGTAAC
        128 CATA-GCAGACATTCAATTATAATATCATTTAATAAAAAAAGTAAC

                  *            *      *         
        810 AAAATTTAACTTAAAATCAGTTATGATATTATAAAA
          1 AAAATTCAACTTAAAATCAATTATGAGATTATAAAA

        846 CCATTNNNNN


Statistics
Matches: 172,  Mismatches: 29, Indels: 13
        0.80            0.14        0.06

Matches are distributed among these distances:
 169   31  0.18
 170   93  0.54
 171   14  0.08
 172   31  0.18
 173    3  0.02

ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37


Consensus pattern (172 bp):   
AAAATTCAACTTAAAATCAATTATGAGATTATAAAAATAATTTAAAATGAGGAAAAAGGCTTTCA
AAGGCTTGAGTGACAATAAATGCACTTTTTATGCTAATGAATGACTTTTGATTCATGTTTCCCAT
AGCAGACATTCAATTATAATATCATTTAATAAAAAAAGTAAC
Done.