Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: VEPZ01008872.1 Hibiscus syriacus cultivar Beakdansim tig00112107_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: 385822
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


File 2 of 2

Found at i:360335 original size:32 final size:32

Alignment explanation


    Indices: 360265--360335  Score: 88
    Period size: 32  Copynumber: 2.2  Consensus size: 32

     360255 ACAGATTAAG

                  *               *         
     360265 AAATGAGTACTTGAATTACATATACATGGACA
          1 AAATGATTACTTGAATTACATACACATGGACA

            **                   *        * 
     360297 TGATGATTACTTGAATTACATGCACATGGATA
          1 AAATGATTACTTGAATTACATACACATGGACA

                   
     360329 AAATGAT
          1 AAATGAT

     360336 AAATGAGTAT


Statistics
Matches: 31,  Mismatches: 8, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31


Consensus pattern (32 bp):   
AAATGATTACTTGAATTACATACACATGGACA

Found at i:370401 original size:15 final size:15

Alignment explanation


    Indices: 370381--370409  Score: 58
    Period size: 15  Copynumber: 1.9  Consensus size: 15

     370371 AACTAACATA

                           
     370381 AAAGTTGTTTTGCAC
          1 AAAGTTGTTTTGCAC

                          
     370396 AAAGTTGTTTTGCA
          1 AAAGTTGTTTTGCA

     370410 TTTTCTTGAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41


Consensus pattern (15 bp):   
AAAGTTGTTTTGCAC

Found at i:373132 original size:60 final size:60

Alignment explanation


    Indices: 372999--373114  Score: 146
    Period size: 60  Copynumber: 1.9  Consensus size: 60

     372989 ATCAGGTGAC

                  *                              *     *         *      
     372999 CATTTTATAACTTTTAATAGTCGAAAGACTCAACAAAGCAGCATCCTATAGTTTGAGAAA
          1 CATTTTGTAACTTTTAATAGTCGAAAGACTCAACAAAACAGCAACCTATAGTTCGAGAAA

                                    **               *                
     373059 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAAC-GTAACCTTATAG-TCGAG
          1 CATTTTGTAACTTTTAATAGTCGAAAGACTCAACAAAACAGCAACC-TATAGTTCGAG

     373115 GGACTATTTG


Statistics
Matches: 48,  Mismatches: 7, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  59    8  0.17
  60   40  0.83

ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30


Consensus pattern (60 bp):   
CATTTTGTAACTTTTAATAGTCGAAAGACTCAACAAAACAGCAACCTATAGTTCGAGAAA

Found at i:378540 original size:17 final size:18

Alignment explanation


    Indices: 378502--378540  Score: 55
    Period size: 17  Copynumber: 2.3  Consensus size: 18

     378492 TTCATAGATA

                              
     378502 ATATTTATTTTAAAATTT
          1 ATATTTATTTTAAAATTT

                  *           
     378520 -TATTTGTTTT-AAATTT
          1 ATATTTATTTTAAAATTT

                 
     378536 ATATT
          1 ATATT

     378541 ATTAATAGAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  16    6  0.32
  17   13  0.68

ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64


Consensus pattern (18 bp):   
ATATTTATTTTAAAATTT

Found at i:379040 original size:30 final size:30

Alignment explanation


    Indices: 378984--379040  Score: 71
    Period size: 30  Copynumber: 1.9  Consensus size: 30

     378974 ATAAACGAAC

                             *            
     378984 CAAACATGAATAGGATACTAAAATTTTAAA
          1 CAAACATGAATAGGATAATAAAATTTTAAA

                 *     *                
     379014 CAAACGTGAATCGGA-AATAAATATTTT
          1 CAAACATGAATAGGATAATAAA-ATTTT

     379041 CAAAAAATTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  29    5  0.22
  30   18  0.78

ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28


Consensus pattern (30 bp):   
CAAACATGAATAGGATAATAAAATTTTAAA

Done.