Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01001594.1 Hibiscus syriacus cultivar Beakdansim tig00003175_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: 91407
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35


Found at i:504 original size:3 final size:3

Alignment explanation


    Indices: 491--579  Score: 126
    Period size: 3  Copynumber: 29.0  Consensus size: 3

        481 CTTTTTATCC

                                                                          
        491 ATT ATTT ATT ATT ATT GATT ATT ATT ATT ATT ATT ATT ACTT ATT ATT
          1 ATT A-TT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT

                                          *   *                    
        539 ATT ATT ATT ATT ATT ATT ATT ATC ATC ATT ATT A-T ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

        580 TAAATATATA


Statistics
Matches: 80,  Mismatches: 2, Indels: 8
        0.89            0.02        0.09

Matches are distributed among these distances:
   2    2  0.03
   3   69  0.86
   4    9  0.11

ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63


Consensus pattern (3 bp):   
ATT

Found at i:1073 original size:15 final size:16

Alignment explanation


    Indices: 1053--1082  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

       1043 CGGAGAAGGA

                            
       1053 AGAGAAA-AAAAAAAC
          1 AGAGAAAGAAAAAAAC

                           
       1068 AGAGAAAGAAAAAAA
          1 AGAGAAAGAAAAAAA

       1083 ACTACTAAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00


Consensus pattern (16 bp):   
AGAGAAAGAAAAAAAC

Found at i:12797 original size:15 final size:16

Alignment explanation


    Indices: 12771--12800  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      12761 TTTTTAAAAA

                            
      12771 AATAATAATAATTTAT
          1 AATAATAATAATTTAT

                           
      12787 AATAA-AATAATTTA
          1 AATAATAATAATTTA

      12801 ACCACCAAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (16 bp):   
AATAATAATAATTTAT

Found at i:61356 original size:20 final size:21

Alignment explanation


    Indices: 61310--61370  Score: 79
    Period size: 20  Copynumber: 2.9  Consensus size: 21

      61300 TTCCCCTGTG

                                   
      61310 GGGGGAATCGGTTCCCCTTCAAA
          1 GGGGGAATCGGTT-CCC-TCAAA

                                 
      61333 GGGGGAATCGGTTCCCTC-AA
          1 GGGGGAATCGGTTCCCTCAAA

                 *    *       
      61353 GGGGGGATCGATTCCCTC
          1 GGGGGAATCGGTTCCCTC

      61371 TGCACCAAAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  20   18  0.50
  21    2  0.06
  22    3  0.08
  23   13  0.36

ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21


Consensus pattern (21 bp):   
GGGGGAATCGGTTCCCTCAAA

Found at i:75589 original size:15 final size:16

Alignment explanation


    Indices: 75561--75590  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      75551 TCAAAAATAA

                            
      75561 AATAAAATTAATTTAT
          1 AATAAAATTAATTTAT

                           
      75577 AATAAAA-TAATTTA
          1 AATAAAATTAATTTA

      75591 ACCACCAAAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    7  0.50
  16    7  0.50

ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40


Consensus pattern (16 bp):   
AATAAAATTAATTTAT
Done.