Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003445.1 Kokia drynarioides strain JFW-HI SEQ_116233, 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: 1669
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30


Found at i:1203 original size:29 final size:29

Alignment explanation


    Indices: 1154--1311  Score: 96
    Period size: 29  Copynumber: 5.4  Consensus size: 29

       1144 ACACCTGGAC

                                           
       1154 ATGGTAATTTTTAGAAAGTTCGGGGTTAAAA
          1 ATGG-AATTTTTAG-AAGTTCGGGGTTAAAA

               *                  *        
       1185 ATATG-ATTTTTAGAAGTTC-GAGTTCAAAA
          1 AT-GGAATTTTTAGAAGTTCGGGGTT-AAAA

                                           
       1214 ATGGAATTTTTAGACA-TTCGAGGGTT-AAA
          1 ATGGAATTTTTAGA-AGTTCG-GGGTTAAAA

               *       *    *  **         
       1243 ATGTAATTTTTGGAAAATTTAGGGTT-AAA
          1 ATGGAATTTTTAG-AAGTTCGGGGTTAAAA

               *    *          *          
       1272 ATGTAATTCTTAGAAGTTTAGGGG-TAAAA
          1 ATGGAATTTTTAGAAG-TTCGGGGTTAAAA

                        
       1301 ATGTG-ATTTTT
          1 ATG-GAATTTTT

       1312 GAAAATTTTA


Statistics
Matches: 101,  Mismatches: 15, Indels: 24
        0.72            0.11        0.17

Matches are distributed among these distances:
  28    8  0.08
  29   74  0.73
  30   12  0.12
  31    6  0.06
  32    1  0.01

ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39


Consensus pattern (29 bp):   
ATGGAATTTTTAGAAGTTCGGGGTTAAAA

Found at i:1285 original size:58 final size:57

Alignment explanation


    Indices: 1211--1319  Score: 132
    Period size: 58  Copynumber: 1.9  Consensus size: 57

       1201 TTCGAGTTCA

                       *                  *                             
       1211 AAAATGGAATTTTTAGACA-TTCGA-GGGTTAAAATGTAATTTTTGGAAAATTTAGGGTT
          1 AAAATGGAATTCTTAGA-AGTT-GAGGGGTAAAAATGTAATTTTT-GAAAATTTAGGGTT

                  *              *              *              
       1269 AAAATGTAATTCTTAGAAGTTTAGGGGTAAAAATGTGATTTTTGAAAATTT
          1 AAAATGGAATTCTTAGAAGTTGAGGGGTAAAAATGTAATTTTTGAAAATTT

       1320 TAAAGGTCCA


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  57   10  0.23
  58   34  0.77

ACGTcount: A:0.38, C:0.03, G:0.21, T:0.39


Consensus pattern (57 bp):   
AAAATGGAATTCTTAGAAGTTGAGGGGTAAAAATGTAATTTTTGAAAATTTAGGGTT

Found at i:1370 original size:30 final size:30

Alignment explanation


    Indices: 1240--1385  Score: 111
    Period size: 30  Copynumber: 4.9  Consensus size: 30

       1230 TTCGAGGGTT

                   *                      *
       1240 AAAATGTAATTTTTGGAAAA-TTTAGGG-TT
          1 AAAATGTGATTTTT-GAAAAGTTTAGGGATC

                   *   *    *          * *
       1269 AAAATGTAATTCTT-AGAAGTTTAGGGGTA
          1 AAAATGTGATTTTTGAAAAGTTTAGGGATC

                               *     *     
       1298 AAAATGTGATTTTTGAAAATTTTAAAGG-TC
          1 AAAATGTGATTTTTGAAAAGTTT-AGGGATC

            *     **                      
       1328 CAAATGCAATTTTTGAAAAGTTTAGGGATC
          1 AAAATGTGATTTTTGAAAAGTTTAGGGATC

                 *         * *          
       1358 AAAATATGATTTTTGGATAGTTTAGGGA
          1 AAAATGTGATTTTTGAAAAGTTTAGGGA

       1386 CCTTTTAGGC


Statistics
Matches: 92,  Mismatches: 20, Indels: 9
        0.76            0.17        0.07

Matches are distributed among these distances:
  27    3  0.03
  28    7  0.08
  29   29  0.32
  30   50  0.54
  31    3  0.03

ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38


Consensus pattern (30 bp):   
AAAATGTGATTTTTGAAAAGTTTAGGGATC
Done.