Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398570.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1861.0, 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: 7089
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.30

Warning! 1089 characters in sequence are not A, C, G, or T


Found at i:303 original size:15 final size:15

Alignment explanation


    Indices: 265--322  Score: 59
    Period size: 15  Copynumber: 3.9  Consensus size: 15

        255 AAAAAAACCC

                           
        265 TTTTA-TTTATTTA-
          1 TTTTATTTTATTTAT

                       *    
        278 TTTTATTTTTAGTTAT
          1 TTTTA-TTTTATTTAT

                           
        294 TTTTATTTTATTTAT
          1 TTTTATTTTATTTAT

                           
        309 TCATTTA-TTTATTT
          1 T--TTTATTTTATTT

        323 CAACATTAAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
  13    5  0.13
  15   17  0.45
  16   12  0.32
  17    4  0.11

ACGTcount: A:0.21, C:0.02, G:0.02, T:0.76


Consensus pattern (15 bp):   
TTTTATTTTATTTAT

Found at i:341 original size:4 final size:4

Alignment explanation


    Indices: 266--322  Score: 50
    Period size: 4  Copynumber: 14.8  Consensus size: 4

        256 AAAAAACCCT

                                           *                           * 
        266 TTTA TTTA TTTA TTT- TATT- TTTA GTTA -TT- TTTA TTTTA TTTA TTCA
          1 TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA

                         
        312 TTTA TTTA TTT
          1 TTTA TTTA TTT

        323 CAACATTAAT


Statistics
Matches: 45,  Mismatches: 3, Indels: 10
        0.78            0.05        0.17

Matches are distributed among these distances:
   3    7  0.16
   4   34  0.76
   5    4  0.09

ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75


Consensus pattern (4 bp):   
TTTA

Found at i:4290 original size:172 final size:171

Alignment explanation


    Indices: 3995--4473  Score: 498
    Period size: 172  Copynumber: 2.8  Consensus size: 171

       3985 NNNNNNNCTT

                     *     *              *      *    *                    * 
       3995 GCTTTAAATAGTTTTGTAATCTCAAAATTGGTTTTAGATTAAATTTTTTTACATTTTTGGTTAGA
          1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAGTTTAATTTTTTTTACATTTTTGGTTAAA

             *                *  *     *       *                             
       4060 ATAGATTATAATTGAATGCCTGCC-C-TGTTAAACGTGAAGAAAAAGATATTCATTGGTAAGAAA
         66 ACAGATTATAATTGAATGTCTACCTCAAG--AAACATGAAGAAAAAGATATTCATTGGTAAGAAA

                           *       * *       *          
       4123 AGTCCATCTATAGT-TGCCCATTTCTTCAAAAGTCGTATTACTC
        129 AGTCCATCTATAGTCAG-CCATTCCATCAAAAGCCGTATTACTC

                            *                                  *             
       4166 GCTTTAAATGGTTTTACAATCTCAAAATTGATTTTAGGTTTAATTTTTTTTTCATTTTTGGTTAA
          1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTA-GTTTAATTTTTTTTACATTTTTGGTTAA

                *  *      *                  *     *      **            *    
       4231 AACATATCATAATTAAATGTCTACCTCAAGAAATATGAAAAAAAAGGCATTCATTGGTAAAAAAA
         65 AACAGATTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAA

            * **  *         *                *        
       4296 ATTTATTTATAGTCAGGCATTCCATCAAAAGCCTTATTACTC
        130 GTCCATCTATAGTCAGCCATTCCATCAAAAGCCGTATTACTC

            **          *         *      *          *                    *   
       4338 AATTTAAATGGTCTTATAATCTTAAAATTCATTTTAAGTTCAATTTTTTTTACATTTTCT-ATTA
          1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTT-AGTTTAATTTTTTTTACATTTT-TGGTTA

                                       *  *                          **      
       4402 AAACAGATTATAATTGAATGTCTACCTTAAAAAACATGAAGAAAAAGATATTCATTGACAAGAAA
         64 AAACAGATTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAA

                   
       4467 AGTCCAT
        129 AGTCCAT

       4474 TTATTGGGTT


Statistics
Matches: 247,  Mismatches: 55, Indels: 11
        0.79            0.18        0.04

Matches are distributed among these distances:
 171   32  0.13
 172  210  0.85
 173    4  0.02
 174    1  0.00

ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39


Consensus pattern (171 bp):   
GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAGTTTAATTTTTTTTACATTTTTGGTTAAA
ACAGATTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAGATATTCATTGGTAAGAAAAG
TCCATCTATAGTCAGCCATTCCATCAAAAGCCGTATTACTC
Done.