Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003781.1 Kokia drynarioides strain JFW-HI SEQ_116760, 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: 2467
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41


Found at i:41 original size:25 final size:25

Alignment explanation


    Indices: 19--68  Score: 75
    Period size: 25  Copynumber: 2.0  Consensus size: 25

          9 TTATAATAAT

                       *             
         19 ATTATATTAATGTTAAATAAATATA
          1 ATTATATTAATATTAAATAAATATA

               *                     
         44 ATTTTATTAATATTAAATAAA-ATA
          1 ATTATATTAATATTAAATAAATATA

             
         68 A
          1 A

         69 AGAGTTTCCT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    4  0.17
  25   19  0.83

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


Consensus pattern (25 bp):   
ATTATATTAATATTAAATAAATATA

Found at i:346 original size:16 final size:16

Alignment explanation


    Indices: 325--362  Score: 76
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        315 TTGAGCTCTG

                            
        325 GACGACTGCACCTCCA
          1 GACGACTGCACCTCCA

                            
        341 GACGACTGCACCTCCA
          1 GACGACTGCACCTCCA

                  
        357 GACGAC
          1 GACGAC

        363 CCCAAGACCG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.26, C:0.42, G:0.21, T:0.11


Consensus pattern (16 bp):   
GACGACTGCACCTCCA

Found at i:1191 original size:25 final size:24

Alignment explanation


    Indices: 1144--1191  Score: 69
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       1134 GGAGAGATTT

                             **     
       1144 TTATTTTATTTAATATTCTTATAA
          1 TTATTTTATTTAATATTAATATAA

                                    
       1168 TTATATTTATTTAATATTAATATA
          1 TTAT-TTTATTTAATATTAATATA

       1192 GAATTTAAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    4  0.19
  25   17  0.81

ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60


Consensus pattern (24 bp):   
TTATTTTATTTAATATTAATATAA

Found at i:1311 original size:53 final size:50

Alignment explanation


    Indices: 1195--1313  Score: 116
    Period size: 53  Copynumber: 2.3  Consensus size: 50

       1185 TAATATAGAA

                                    *                  *  *   
       1195 TTTAAATTTATTATTTTATTTTTTGAACATATTTATTTATTTCCATTTAT
          1 TTTAAATTTATTATTTTATTTTTTCAACATATTTATTTATTTCAATATAT

                 *  *                                      *        
       1245 TTTATTATATATTATTTT-TTTCTTGTCAACAATAATTT-TTTATTTTAATATATT
          1 TTTA-AATTTATTATTTTATTT-TT-TCAAC-AT-ATTTATTTATTTCAATATA-T

                           
       1299 TTTAAATTTATTATT
          1 TTTAAATTTATTATT

       1314 ATGATATTTT


Statistics
Matches: 55,  Mismatches: 8, Indels: 9
        0.76            0.11        0.12

Matches are distributed among these distances:
  50    7  0.13
  51   13  0.24
  52    4  0.07
  53   22  0.40
  54    9  0.16

ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64


Consensus pattern (50 bp):   
TTTAAATTTATTATTTTATTTTTTCAACATATTTATTTATTTCAATATAT

Found at i:1320 original size:25 final size:25

Alignment explanation


    Indices: 1278--1326  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       1268 TGTCAACAAT

                 *     *             
       1278 AATTTTTTATTTTAATATATTTTTA
          1 AATTTATTATTATAATATATTTTTA

                         *    *     
       1303 AATTTATTATTATGATATTTTTTT
          1 AATTTATTATTATAATATATTTTT

       1327 TGAAAATATT


Statistics
Matches: 20,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  25   20  1.00

ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67


Consensus pattern (25 bp):   
AATTTATTATTATAATATATTTTTA
Done.