Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005511.1 Kokia drynarioides strain JFW-HI SEQ_119585, 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: 7121
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35


Found at i:1481 original size:48 final size:48

Alignment explanation


    Indices: 1281--1471  Score: 240
    Period size: 48  Copynumber: 4.0  Consensus size: 48

       1271 GTTGTTTATT

                          *      *   *          *            
       1281 TATGC-TTCATTAAGTGTTTTTTTTTTTAAATGCATGTTTGTTTAATAA
          1 TATGCATT-ATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAA

             *     *     *                              *   
       1329 TCTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAA
          1 TATGCATTATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAA

             *        *                     *           *   
       1377 TTTGCATTATAAACTGTTTTGTTTGTTAAATGAATCTTTGTTTAGTAA
          1 TATGCATTATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAA

                           *                          *    
       1425 TATGCATTATTAACTATTTTGTTTGTTAAATGCATCTTTGTTAAATA
          1 TATGCATTATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAATA

       1472 CCTTGCATTA


Statistics
Matches: 125,  Mismatches: 17, Indels: 2
        0.87            0.12        0.01

Matches are distributed among these distances:
  48  124  0.99
  49    1  0.01

ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52


Consensus pattern (48 bp):   
TATGCATTATTAACTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAA

Found at i:2015 original size:80 final size:80

Alignment explanation


    Indices: 1917--2067  Score: 214
    Period size: 80  Copynumber: 1.9  Consensus size: 80

       1907 AGGAGAAATC

                         *            *                      *               
       1917 CCATGCCTTTTCAGCTACATCAGATCTTAATGAAGAGACATGACTCATTGGCTTT-CCTACAAGA
          1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAG-TTTCCCTACAAGA

                            
       1981 GTTAAAAACGAAATTG
         65 GTTAAAAACGAAATTG

                       *        *           *  *                            *
       1997 CCATGCCTTTTTAACTACATTAGATCCTAATGGAGGGACATGACTCATTAGTTTCCCTACAAGAT
          1 CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGTTTCCCTACAAGAG

                  
       2062 TTAAAA
         66 TTAAAA

       2068 TGAAATTAGT


Statistics
Matches: 62,  Mismatches: 8, Indels: 2
        0.86            0.11        0.03

Matches are distributed among these distances:
  79    3  0.05
  80   59  0.95

ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30


Consensus pattern (80 bp):   
CCATGCCTTTTCAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGTTTCCCTACAAGAG
TTAAAAACGAAATTG

Found at i:3106 original size:19 final size:18

Alignment explanation


    Indices: 3065--3110  Score: 60
    Period size: 17  Copynumber: 2.6  Consensus size: 18

       3055 AAAAAGTGAT

                               
       3065 GAAAAAAGTA-GAGAAAAA
          1 GAAAAAA-TACGAGAAAAA

                              
       3083 G-AAAAATACGAGAAAAA
          1 GAAAAAATACGAGAAAAA

                       
       3100 GTAAAAAATAC
          1 G-AAAAAATAC

       3111 AAAAATATTT


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  16    2  0.08
  17   14  0.56
  18    1  0.04
  19    8  0.32

ACGTcount: A:0.70, C:0.04, G:0.17, T:0.09


Consensus pattern (18 bp):   
GAAAAAATACGAGAAAAA

Found at i:6131 original size:18 final size:18

Alignment explanation


    Indices: 6108--6142  Score: 61
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       6098 AAAATTAGGA

                     *        
       6108 GATTCAATCTTTCTTGCT
          1 GATTCAATCATTCTTGCT

                             
       6126 GATTCAATCATTCTTGC
          1 GATTCAATCATTCTTGC

       6143 CTAAACAGTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.20, C:0.23, G:0.11, T:0.46


Consensus pattern (18 bp):   
GATTCAATCATTCTTGCT
Done.