Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010174.1 Kokia drynarioides strain JFW-HI SEQ_124979, 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: 12144
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:11333 original size:119 final size:119

Alignment explanation


    Indices: 11182--11562  Score: 591
    Period size: 119  Copynumber: 3.2  Consensus size: 119

      11172 AAATTCGTCA

                                                                 *           
      11182 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACAACGCGGTCATCTTCCTAATGAGATACTG
          1 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACAACGCGGTCATCTTCCTGATGAGATACTG

                                   *                  *        *  
      11247 AGAAGAAGACCAAATCAAACCCACGCGCGATGAACAAATCTTTGAACCCCAGCT
         66 AGAAGAAGACCAAATCAAACCCATGCGCGATGAACAAATCTTCGAACCCCAACT

                             * *  *                                          
      11301 TCCTGATGAGATACAGATAGGCAGATTGAAACAAACAACGCGGTCATCTTCCTGATGAGATACTG
          1 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACAACGCGGTCATCTTCCTGATGAGATACTG

                     *                         *                  
      11366 AGAAGAAGAGCAAATCAAACCCATGCGCGATGAACGAATCTTCGAACCCCAACT
         66 AGAAGAAGACCAAATCAAACCCATGCGCGATGAACAAATCTTCGAACCCCAACT

                                                *    *                *   *  
      11420 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATGAAATAGTG
          1 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACAACGCGGTCATCTTCCTGATGAGATACTG

                                      *          *               *  
      11485 AGAAGAAGACCAAATCAAACCCATGCTCGATGTGAACTAATCTTCGAACCCCACCT
         66 AGAAGAAGACCAAATCAAACCCATGCGCGA--TGAACAAATCTTCGAACCCCAACT

                          *       
      11541 TCCTGATGAGATACTGAGAAGC
          1 TCCTGATGAGATACAGAGAAGC

      11563 AGGTCGAAGT


Statistics
Matches: 239,  Mismatches: 21, Indels: 2
        0.91            0.08        0.01

Matches are distributed among these distances:
 119  196  0.82
 121   43  0.18

ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19


Consensus pattern (119 bp):   
TCCTGATGAGATACAGAGAAGCGGATTGAAACAAACAACGCGGTCATCTTCCTGATGAGATACTG
AGAAGAAGACCAAATCAAACCCATGCGCGATGAACAAATCTTCGAACCCCAACT

Found at i:12041 original size:17 final size:17

Alignment explanation


    Indices: 12011--12090  Score: 124
    Period size: 17  Copynumber: 4.7  Consensus size: 17

      12001 GGCCTATTGG

                 *           
      12011 AATTTGAATTTATTTTA
          1 AATTTAAATTTATTTTA

              *    *         
      12028 AAATTAAGTTTATTTTA
          1 AATTTAAATTTATTTTA

                             
      12045 AATTTAAATTTATTTTA
          1 AATTTAAATTTATTTTA

                          *  
      12062 AATTTAAATTTATTATA
          1 AATTTAAATTTATTTTA

                        
      12079 AATTTAAATTTA
          1 AATTTAAATTTA

      12091 AAATGTCCAA


Statistics
Matches: 57,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   57  1.00

ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55


Consensus pattern (17 bp):   
AATTTAAATTTATTTTA

Found at i:12050 original size:6 final size:6

Alignment explanation


    Indices: 12011--12092  Score: 66
    Period size: 6  Copynumber: 14.3  Consensus size: 6

      12001 GGCCTATTGG

                 *         *       *     *      *                  
      12011 AATTTG AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTT-
          1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA

             *                                           
      12056 ATTTTA AATTTA AATTT- -ATTATA AATTTA AATTTA AA
          1 AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA AA

      12093 ATGTCCAATT


Statistics
Matches: 61,  Mismatches: 9, Indels: 12
        0.74            0.11        0.15

Matches are distributed among these distances:
   4    3  0.05
   5   13  0.21
   6   42  0.69
   7    3  0.05

ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54


Consensus pattern (6 bp):   
AATTTA
Done.