Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01009424.1 Hibiscus syriacus cultivar Beakdansim tig00113399_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: 27176
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32


Found at i:5830 original size:135 final size:134

Alignment explanation


    Indices: 5461--5848  Score: 437
    Period size: 130  Copynumber: 2.9  Consensus size: 134

       5451 GACGACACTG

                 *  *          *                     *                  *   *
       5461 CTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACATGGTTCC-ACTCTGC
          1 CTCATACGTGATGAAGAG-TTCTTGGCCATCTTTAGG-AAGGTGATAACATGGTTCCTACGC-GA

              *                *               *          *   *         *    
       5525 TGGGGACGGCTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCATGGGAT
         63 TGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCATAGGAT

              * ** 
       5590 GATATTA
        128 GACACGA

                   *                                        *                
       5597 CTCATACATGATGAAGAGTTCTTGGCCATC--TA--AAGGTGATAACACGGTTCCTACGCGATGA
          1 CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGA

                                *        *                *                  
       5658 GGACGGCTGGTTATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGA-AGGATGA
         66 GGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-ATAGGATGA

                 
       5722 CACGA
        130 CACGA

                 *                                          *                
       5727 CTCATGCGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGCGATG
          1 CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAA-GGTGATAACATGGTTCCTACGCGATG

                *              **     ***                            
       5792 AGGATGGCTGGTTATCTAATATTGACGTTGCTCCTACGTGATGAGGAGATCTGGTCA
         65 AGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCA

       5849 GCTGATGTTG


Statistics
Matches: 212,  Mismatches: 33, Indels: 16
        0.81            0.13        0.06

Matches are distributed among these distances:
 130  104  0.49
 131    4  0.02
 132    2  0.01
 133    2  0.01
 134    3  0.01
 135   82  0.39
 136   15  0.07

ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28


Consensus pattern (134 bp):   
CTCATACGTGATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGA
GGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCATAGGATGAC
ACGA

Found at i:6788 original size:16 final size:16

Alignment explanation


    Indices: 6767--6800  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       6757 CTTTATTTAT

                             
       6767 TTTTTC-TTCTTTTTCA
          1 TTTTTCATT-TTTTTCA

                            
       6783 TTTTTCATTTTTTTCA
          1 TTTTTCATTTTTTTCA

              
       6799 TT
          1 TT

       6801 CATTTTTTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   15  0.88
  17    2  0.12

ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76


Consensus pattern (16 bp):   
TTTTTCATTTTTTTCA
Done.