Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402386.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5465.0, 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, 676

Length: 1128
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35


Found at i:161 original size:19 final size:18

Alignment explanation


    Indices: 117--163  Score: 60
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        107 TTCCTAAAGC

                               
        117 TTTTTTTCAAAAAAAATTA
          1 TTTTTTT-AAAAAAAATTA

                           *   
        136 -TTTTTTAAAAAACAGTTA
          1 TTTTTTTAAAAAA-AATTA

                      
        154 TTTTTTTAAA
          1 TTTTTTTAAA

        164 GAGTTTTTTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  17    6  0.24
  18   10  0.40
  19    9  0.36

ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51


Consensus pattern (18 bp):   
TTTTTTTAAAAAAAATTA

Found at i:338 original size:15 final size:15

Alignment explanation


    Indices: 315--352  Score: 51
    Period size: 15  Copynumber: 2.5  Consensus size: 15

        305 TCAAAATAAT

                        *  
        315 AAATAAAAA-ATTAA
          1 AAATAAAAATATCAA

                            
        329 AAATTAAAAATATCAA
          1 AAA-TAAAAATATCAA

                    
        345 AAATAAAA
          1 AAATAAAA

        353 TAAGTAAATA


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  14    3  0.14
  15   11  0.52
  16    7  0.33

ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21


Consensus pattern (15 bp):   
AAATAAAAATATCAA

Found at i:679 original size:37 final size:39

Alignment explanation


    Indices: 603--676  Score: 98
    Period size: 39  Copynumber: 1.9  Consensus size: 39

        593 AGATATCTCA

                 *      *                          
        603 TCAAATAAAAAATTATTGTTAAGAAAAAATTATAAAATT
          1 TCAAAAAAAAAAATATTGTTAAGAAAAAATTATAAAATT

                                         *       
        642 TCAAAAAAAAAAATA-TGTT-AGAAAAACTTTATAAA
          1 TCAAAAAAAAAAATATTGTTAAGAAAAA-ATTATAAA

        677 TTTTGTAAAG


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  37    7  0.23
  38   11  0.35
  39   13  0.42

ACGTcount: A:0.61, C:0.04, G:0.05, T:0.30


Consensus pattern (39 bp):   
TCAAAAAAAAAAATATTGTTAAGAAAAAATTATAAAATT

Found at i:707 original size:16 final size:15

Alignment explanation


    Indices: 688--729  Score: 52
    Period size: 16  Copynumber: 2.9  Consensus size: 15

        678 TTTGTAAAGA

                            
        688 CAAAATTATAAAATTT
          1 CAAAATTATAAAA-TT

                 *         
        704 CAAAAATATAAAATT
          1 CAAAATTATAAAATT

                         
        719 --AAATTATAAAA
          1 CAAAATTATAAAA

        730 AGTATAAAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  13   10  0.42
  15    2  0.08
  16   12  0.50

ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31


Consensus pattern (15 bp):   
CAAAATTATAAAATT

Found at i:736 original size:61 final size:61

Alignment explanation


    Indices: 612--737  Score: 148
    Period size: 61  Copynumber: 2.0  Consensus size: 61

        602 ATCAAATAAA

                      *                                  **           *   
        612 AAATTATTGTTAAGAAAAAATTATAAAATTTCAAAAAAAAAAATATGTTAGAAAAACTTTAT
          1 AAATTATTGTAAAGAAAAAATTATAAAATTTCAAAAAAAAAAATAAATTAGAAAAAC-GTAT

                           *                            *       *          
        674 AAATT-TTGTAAAGACAAAATTATAAAATTTCAAAAATATAAAATTAAATTATAAAAA-GTAT
          1 AAATTATTGTAAAGAAAAAATTATAAAATTTCAAAAA-A-AAAAATAAATTAGAAAAACGTAT

               
        735 AAA
          1 AAA

        738 ATTGTTCCCC


Statistics
Matches: 55,  Mismatches: 7, Indels: 5
        0.82            0.10        0.07

Matches are distributed among these distances:
  61   35  0.64
  62    6  0.11
  63   14  0.25

ACGTcount: A:0.60, C:0.03, G:0.06, T:0.32


Consensus pattern (61 bp):   
AAATTATTGTAAAGAAAAAATTATAAAATTTCAAAAAAAAAAATAAATTAGAAAAACGTAT
Done.