Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008302.1 Hibiscus syriacus cultivar Beakdansim tig00110988_pilon, 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: 3402722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 17 of 17

Found at i:3392355 original size:49 final size:49

Alignment explanation


    Indices: 3392278--3392407  Score: 217
    Period size: 49  Copynumber: 2.7  Consensus size: 49

    3392268 TTAAATAAAT

                *                                            
    3392278 AAATAAATTATAACAAATTAGATACCAACTAAATCTAAAAGCTGTCTAA
          1 AAATCAATTATAACAAATTAGATACCAACTAAATCTAAAAGCTGTCTAA

                                                     *       
    3392327 AAATCAATTATAACAAATTAGATACCAACTAAATCTAAAAGGTGTCTAA
          1 AAATCAATTATAACAAATTAGATACCAACTAAATCTAAAAGCTGTCTAA

                               *             
    3392376 AAATC-ATCTATAACAAATCAGATACCAACTAA
          1 AAATCAAT-TATAACAAATTAGATACCAACTAA

    3392408 TTATAGCTTC


Statistics
Matches: 77,  Mismatches: 3, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  48    2  0.03
  49   75  0.97

ACGTcount: A:0.52, C:0.16, G:0.06, T:0.25


Consensus pattern (49 bp):   
AAATCAATTATAACAAATTAGATACCAACTAAATCTAAAAGCTGTCTAA

Found at i:3394132 original size:19 final size:20

Alignment explanation


    Indices: 3394108--3394165  Score: 73
    Period size: 22  Copynumber: 2.9  Consensus size: 20

    3394098 TGCAGAAATG

                       *        
    3394108 GTATCGGTACCGTAATAG-A
          1 GTATCGGTACCATAATAGTA

                                  
    3394127 GTATCGGTACCATAGTATAGTA
          1 GTATCGGTACCATA--ATAGTA

                  *          
    3394149 GTATCGATACCATAATA
          1 GTATCGGTACCATAATA

    3394166 TAGAAGTATC


Statistics
Matches: 34,  Mismatches: 2, Indels: 5
        0.83            0.05        0.12

Matches are distributed among these distances:
  19   13  0.38
  20    3  0.09
  21    4  0.12
  22   14  0.41

ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29


Consensus pattern (20 bp):   
GTATCGGTACCATAATAGTA

Found at i:3394154 original size:22 final size:21

Alignment explanation


    Indices: 3394122--3394200  Score: 106
    Period size: 22  Copynumber: 3.7  Consensus size: 21

    3394112 CGGTACCGTA

                       *         
    3394122 ATAGAGTATCGGTACCATAGT
          1 ATAGAGTATCGATACCATAGT

                                * 
    3394143 ATAGTAGTATCGATACCATAAT
          1 ATAG-AGTATCGATACCATAGT

                               *  
    3394165 ATAGAAGTATCGATACCATGGT
          1 ATAG-AGTATCGATACCATAGT

                           
    3394187 AT-GAGTATCGATAC
          1 ATAGAGTATCGATAC

    3394201 TATTGAGCTA


Statistics
Matches: 52,  Mismatches: 5, Indels: 3
        0.87            0.08        0.05

Matches are distributed among these distances:
  20   11  0.21
  21    5  0.10
  22   36  0.69

ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29


Consensus pattern (21 bp):   
ATAGAGTATCGATACCATAGT

Found at i:3394637 original size:55 final size:55

Alignment explanation


    Indices: 3394519--3394675  Score: 262
    Period size: 55  Copynumber: 2.9  Consensus size: 55

    3394509 TACCAAATGA

                   *                                       *       
    3394519 CACTTTGCGTGCAAAACTAAGAAATTCATAATAAG-TTATGAATTTCTGTATGGG
          1 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG

                            *                                      
    3394573 CACTTTGTGTGCAAAATTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG
          1 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG

                       *              *                     
    3394628 CACTTTGTGTGAAAAACTAAGAAATTTATAATAAGTTTATGAATTTCC
          1 CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCC

    3394676 ATATTGGTAG


Statistics
Matches: 96,  Mismatches: 6, Indels: 1
        0.93            0.06        0.01

Matches are distributed among these distances:
  54   33  0.34
  55   63  0.66

ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36


Consensus pattern (55 bp):   
CACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG

Found at i:3395059 original size:46 final size:46

Alignment explanation


    Indices: 3394972--3395059  Score: 122
    Period size: 46  Copynumber: 1.9  Consensus size: 46

    3394962 TTAGATGAAG

                   *                *      *    *         
    3394972 AACAGTGCATAATTGGCATGAAATTATGACATAAATGAAAATGTAT
          1 AACAGTGAATAATTGGCATGAAATGATGACACAAATAAAAATGTAT

                                        *    *        
    3395018 AACAGTGAATAATTGGCATGAAATGATGCCACATATAAAAAT
          1 AACAGTGAATAATTGGCATGAAATGATGACACAAATAAAAAT

    3395060 ACATAGCGGT


Statistics
Matches: 36,  Mismatches: 6, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  46   36  1.00

ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26


Consensus pattern (46 bp):   
AACAGTGAATAATTGGCATGAAATGATGACACAAATAAAAATGTAT

Found at i:3400980 original size:52 final size:54

Alignment explanation


    Indices: 3400880--3401000  Score: 183
    Period size: 52  Copynumber: 2.3  Consensus size: 54

    3400870 AATAAGCTAT

                           *                   *       *          
    3400880 TTAAGTTTCGGGTTTGAAGAGATATATTTGATGCTGCATTATATTGAATAGTGA
          1 TTAAGTTTCGGGTTTCAAGAGATATATTTGATGCTACATTATACTGAATAGTGA

                                   *                              
    3400934 TTAAGTTTCGGGTTTCAAGAGA-GT-TTTGATGCTACATTATACTGAATAGTGA
          1 TTAAGTTTCGGGTTTCAAGAGATATATTTGATGCTACATTATACTGAATAGTGA

                    *      
    3400986 TTAAGTTTAGGGTTT
          1 TTAAGTTTCGGGTTT

    3401001 TAATTTTTTG


Statistics
Matches: 62,  Mismatches: 5, Indels: 2
        0.90            0.07        0.03

Matches are distributed among these distances:
  52   40  0.65
  53    1  0.02
  54   21  0.34

ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41


Consensus pattern (54 bp):   
TTAAGTTTCGGGTTTCAAGAGATATATTTGATGCTACATTATACTGAATAGTGA

Done.