Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007430.1 Kokia drynarioides strain JFW-HI SEQ_122051, 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: 17473
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34


Found at i:1188 original size:18 final size:19

Alignment explanation


    Indices: 1147--1189  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 19

       1137 AGGCTATATT

                               
       1147 TTTTATATTTAAAATATAA
          1 TTTTATATTTAAAATATAA

             *           *     
       1166 -CTTATATTTAAATTA-AA
          1 TTTTATATTTAAAATATAA

                   
       1183 TTTTATA
          1 TTTTATA

       1190 AATAATTGAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 3
        0.77            0.12        0.12

Matches are distributed among these distances:
  17    2  0.10
  18   18  0.90

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTTTATATTTAAAATATAA

Found at i:1366 original size:21 final size:22

Alignment explanation


    Indices: 1342--1400  Score: 52
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       1332 ATAACAACAT

                              *   
       1342 TTATCATTATAAAATT-TTTAA
          1 TTATCATTATAAAATTATATAA

                 *                   
       1363 TTAT-TTTATTTAAATATTATATAA
          1 TTATCATTA--TAAA-ATTATATAA

                           
       1387 TTATCATT-TAAAAT
          1 TTATCATTATAAAAT

       1401 AAATAATATA


Statistics
Matches: 30,  Mismatches: 3, Indels: 10
        0.70            0.07        0.23

Matches are distributed among these distances:
  20    3  0.10
  21    6  0.20
  22    8  0.27
  23    3  0.10
  24    8  0.27
  25    2  0.07

ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54


Consensus pattern (22 bp):   
TTATCATTATAAAATTATATAA

Found at i:1750 original size:9 final size:10

Alignment explanation


    Indices: 1725--1749  Score: 50
    Period size: 10  Copynumber: 2.5  Consensus size: 10

       1715 GTATTTTATT

                      
       1725 TTTTTTAAAA
          1 TTTTTTAAAA

                      
       1735 TTTTTTAAAA
          1 TTTTTTAAAA

                 
       1745 TTTTT
          1 TTTTT

       1750 ATTTTTAATA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   15  1.00

ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68


Consensus pattern (10 bp):   
TTTTTTAAAA

Found at i:1781 original size:18 final size:17

Alignment explanation


    Indices: 1736--1784  Score: 57
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       1726 TTTTTAAAAT

                          *  
       1736 TTTTTAA-A-ATTTTTA
          1 TTTTTAATATATTTATA

                             
       1751 TTTTTAATATATTTATA
          1 TTTTTAATATATTTATA

                     *       
       1768 TTTTTAAATTTATTTAT
          1 TTTTT-AATATATTTAT

       1785 TGATGTGACA


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  15    7  0.24
  16    1  0.03
  17   11  0.38
  18   10  0.34

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (17 bp):   
TTTTTAATATATTTATA

Found at i:8073 original size:18 final size:19

Alignment explanation


    Indices: 8026--8073  Score: 55
    Period size: 18  Copynumber: 2.6  Consensus size: 19

       8016 AATTCTTTAT

                           *   
       8026 TATAATATTTT-AATTAAA
          1 TATAATATTTTAAATAAAA

             *     *           
       8044 TTTAATAATTTAAATAAAA
          1 TATAATATTTTAAATAAAA

                        
       8063 TAT-ATATTTTA
          1 TATAATATTTTA

       8074 TTTTAAATTA


Statistics
Matches: 24,  Mismatches: 5, Indels: 2
        0.77            0.16        0.06

Matches are distributed among these distances:
  18   16  0.67
  19    8  0.33

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (19 bp):   
TATAATATTTTAAATAAAA

Found at i:14112 original size:15 final size:16

Alignment explanation


    Indices: 14092--14124  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

      14082 TCAACAGTTC

                        *   
      14092 AATCAT-TAAAATATT
          1 AATCATATAAAAAATT

                            
      14107 AATCATATAAAAAATT
          1 AATCATATAAAAAATT

              
      14123 AA
          1 AA

      14125 GAATGTAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15    6  0.38
  16   10  0.62

ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33


Consensus pattern (16 bp):   
AATCATATAAAAAATT
Done.