Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018400686.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3870.0, 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: 5143
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.27

Warning! 1122 characters in sequence are not A, C, G, or T


Found at i:2992 original size:7 final size:7

Alignment explanation


    Indices: 2980--3054  Score: 60
    Period size: 7  Copynumber: 10.3  Consensus size: 7

       2970 NNNNNNNNTT

                   
       2980 AAAATAA
          1 AAAATAA

                   *
       2987 AAAATATT
          1 AAAATA-A

                   
       2995 AAAATAA
          1 AAAATAA

              *   *
       3002 AATATAT
          1 AAAATAA

              *    
       3009 AATATAA
          1 AAAATAA

               *   
       3016 AAATTAA
          1 AAAATAA

               *    
       3023 AAATTAAA
          1 AAAAT-AA

                   
       3031 AAAATAA
          1 AAAATAA

              *    
       3038 AATATAA
          1 AAAATAA

                    
       3045 AAAATTAA
          1 AAAA-TAA

              
       3053 AA
          1 AA

       3055 TTTATATAAT


Statistics
Matches: 55,  Mismatches: 10, Indels: 5
        0.79            0.14        0.07

Matches are distributed among these distances:
   7   38  0.69
   8   17  0.31

ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25


Consensus pattern (7 bp):   
AAAATAA

Found at i:2998 original size:15 final size:15

Alignment explanation


    Indices: 2978--3055  Score: 69
    Period size: 15  Copynumber: 5.5  Consensus size: 15

       2968 NNNNNNNNNN

                           
       2978 TTAAAATAAAAAATA
          1 TTAAAATAAAAAATA

                       *   
       2993 TTAAAATAAAATATA
          1 TTAAAATAAAAAATA

                *          
       3008 -TAATAT-AAAAAT-
          1 TTAAAATAAAAAATA

             *              
       3020 TAAAAATTAAAAAA-A
          1 TTAAAA-TAAAAAATA

                            
       3035 -TAAAATATAAAAA-A
          1 TTAAAATA-AAAAATA

                   
       3049 TTAAAAT
          1 TTAAAAT

       3056 TTATATAATA


Statistics
Matches: 51,  Mismatches: 6, Indels: 12
        0.74            0.09        0.17

Matches are distributed among these distances:
  13   10  0.20
  14   16  0.31
  15   25  0.49

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (15 bp):   
TTAAAATAAAAAATA

Found at i:3055 original size:36 final size:36

Alignment explanation


    Indices: 2978--3056  Score: 97
    Period size: 36  Copynumber: 2.2  Consensus size: 36

       2968 NNNNNNNNNN

                            **             *  * 
       2978 TTAAAA-TAAAAAATATTAAAATAAAATATATAATA
          1 TTAAAATTAAAAAATAAAAAAATAAAATATAAAAAA

             *           *                      
       3013 TAAAAATTAAAAATTAAAAAAATAAAATATAAAAAA
          1 TTAAAATTAAAAAATAAAAAAATAAAATATAAAAAA

                    
       3049 TTAAAATT
          1 TTAAAATT

       3057 TATATAATAT


Statistics
Matches: 36,  Mismatches: 7, Indels: 1
        0.82            0.16        0.02

Matches are distributed among these distances:
  35    5  0.14
  36   31  0.86

ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29


Consensus pattern (36 bp):   
TTAAAATTAAAAAATAAAAAAATAAAATATAAAAAA

Found at i:3110 original size:15 final size:14

Alignment explanation


    Indices: 2983--3106  Score: 63
    Period size: 14  Copynumber: 8.6  Consensus size: 14

       2973 NNNNNTTAAA

                          *
       2983 ATAAAAAATATTAAA
          1 ATAAAAAATA-TAAT

                  *       
       2998 ATAAAATATATAAT
          1 ATAAAAAATATAAT

                   *     *
       3012 ATAAAAATTA-AAA
          1 ATAAAAAATATAAT

                        *   
       3025 ATTAAAAAAATAAAAT
          1 A-T-AAAAAATATAAT

                       *   
       3041 ATAAAAAATTAAAAT
          1 ATAAAAAA-TATAAT

            *  * *       * 
       3056 TTATATAATATAGGT
          1 ATAAAAAATATA-AT

             *  *        *
       3071 AGAATAAAT-TAAA
          1 ATAAAAAATATAAT

                  *       
       3084 ATAAAATATATAAT
          1 ATAAAAAATATAAT

                     
       3098 ATAAAAAAT
          1 ATAAAAAAT

       3107 TATATTAAAG


Statistics
Matches: 79,  Mismatches: 24, Indels: 13
        0.68            0.21        0.11

Matches are distributed among these distances:
  13    9  0.11
  14   34  0.43
  15   33  0.42
  16    3  0.04

ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30


Consensus pattern (14 bp):   
ATAAAAAATATAAT
Done.