Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397592.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1445.0, 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: 5693
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.33

Warning! 120 characters in sequence are not A, C, G, or T


Found at i:1571 original size:168 final size:170

Alignment explanation


    Indices: 1280--1588  Score: 532
    Period size: 168  Copynumber: 1.8  Consensus size: 170

       1270 AGTTTGAGTC

                 *        *              *                                   
       1280 TTTCTCAACGTCATGAGGTGTTGTCGTTTTAGTAATGTTGGCTATGTTGTAAAACCAAAACGTCT
          1 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACG-CT

             *              *                                                
       1345 TTTTGATGTGTCATTTTGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTT
         65 TCTTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTT

                                                     
       1410 AGTTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG
        130 AGTTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG

                                                   *                         
       1451 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTTGCTATGTTGTAAAACCAAAAC-C-T
          1 TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACGCTT

                       *                                                     
       1514 CTTGATGTGTCGTTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTA
         66 CTTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTA

                      
       1579 GTTGTCTTCT
        131 GTTGTCTTCT

       1589 GCCGGTGGTG


Statistics
Matches: 131,  Mismatches: 7, Indels: 3
        0.93            0.05        0.02

Matches are distributed among these distances:
 168   73  0.56
 169    1  0.01
 171   57  0.44

ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44


Consensus pattern (170 bp):   
TTTCTAAACGTCATAAGGTGTTGTCGTTTCAGTAATGTTGGCTATGTTGTAAAACCAAAACGCTT
CTTGATGTGTCATTTGGGTATTTGAGTTTGTTTAGTTTACTAAACGCTTGTAGGCTTGTCGTTTA
GTTGTCTTCTTGAAATTTCTGTTGAAGTGGCCGGTGGTGG

Found at i:2836 original size:19 final size:19

Alignment explanation


    Indices: 2799--2837  Score: 51
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2789 ATGCTTCTAA

                         *     
       2799 GTCATTAATTGTATAAAAT
          1 GTCATTAATTGTAGAAAAT

                   *      *    
       2818 GTCATTACTTGTAGGAAAT
          1 GTCATTAATTGTAGAAAAT

             
       2837 G
          1 G

       2838 GGGATAGAGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38


Consensus pattern (19 bp):   
GTCATTAATTGTAGAAAAT

Found at i:4292 original size:29 final size:28

Alignment explanation


    Indices: 4242--4415  Score: 147
    Period size: 28  Copynumber: 6.0  Consensus size: 28

       4232 TAACAACTTT

                 *                      
       4242 AACATGTTTGTCTTAATTTAGATAAGAA
          1 AACATATTTGTCTTAATTTAGATAAGAA

                 *      *                
       4270 AACATGTTTGATTTTAATTTAGATAAG-A
          1 AACATATTTG-TCTTAATTTAGATAAGAA

                                * *       
       4298 AACTATATTTGTCTTAATCTAAAATAAGAA
          1 AAC-ATATTTGTCTTAAT-TTAGATAAGAA

                        *       *    *     
       4328 AA-ATATTTTTTATCTTAATCTAGACAAGAA
          1 AACATA---TTTGTCTTAATTTAGATAAGAA

                                  *      
       4358 AACATATTTGTCTTAATTTAGACAAGATA
          1 AACATATTTGTCTTAATTTAGATAAGA-A

                       *                  
       4387 AA-ATATTTTCATCTTAATTATAGATAAGA
          1 AACATA-TTT-GTCTTAATT-TAGATAAGA

       4416 GTTGTCTTAA


Statistics
Matches: 120,  Mismatches: 14, Indels: 21
        0.77            0.09        0.14

Matches are distributed among these distances:
  28   45  0.38
  29   34  0.28
  30   20  0.17
  31   21  0.17

ACGTcount: A:0.43, C:0.08, G:0.10, T:0.40


Consensus pattern (28 bp):   
AACATATTTGTCTTAATTTAGATAAGAA

Found at i:4358 original size:59 final size:58

Alignment explanation


    Indices: 4242--4404  Score: 179
    Period size: 59  Copynumber: 2.8  Consensus size: 58

       4232 TAACAACTTT

                 *                         *  *   *  *     *    *     
       4242 AACATGTTTGTCTTAATTTAGATAAG-AAAACATGTTTGATTTTAATTTAGATAAG-A
          1 AACATATTTGTCTTAATTTAGATAAGAAAAATATTTTTCATCTTAATCTAGACAAGAA

                                * *                 *                   
       4298 AACTATATTTGTCTTAATCTAAAATAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
          1 AAC-ATATTTGTCTTAAT-TTAGATAAGAAAAATATTTTTCATCTTAATCTAGACAAGAA

                                  *                         
       4358 AACATATTTGTCTTAATTTAGACAAGATAAAATA-TTTTCATCTTAAT
          1 AACATATTTGTCTTAATTTAGATAAGA-AAAATATTTTTCATCTTAAT

       4405 TATAGATAAG


Statistics
Matches: 89,  Mismatches: 13, Indels: 8
        0.81            0.12        0.07

Matches are distributed among these distances:
  56    3  0.03
  57   13  0.15
  58   26  0.29
  59   43  0.48
  60    4  0.04

ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40


Consensus pattern (58 bp):   
AACATATTTGTCTTAATTTAGATAAGAAAAATATTTTTCATCTTAATCTAGACAAGAA

Done.