Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014492.1 Kokia drynarioides strain JFW-HI SEQ_129531, 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: 4684
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26


Found at i:58 original size:21 final size:22

Alignment explanation


    Indices: 4--58  Score: 69
    Period size: 20  Copynumber: 2.5  Consensus size: 22

          1 TAC

                                   *
          4 TGTTATTTTTGCTGTTGTTTTGGT
          1 TGTTATTTTT--TGTTGTTTTGGA

                                  
         28 TGTTA-TTTTTGTTG-TTTGGA
          1 TGTTATTTTTTGTTGTTTTGGA

                       
         48 TGTTATTTTTT
          1 TGTTATTTTTT

         59 ATGCGTTTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  20   10  0.34
  21   10  0.34
  23    4  0.14
  24    5  0.17

ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69


Consensus pattern (22 bp):   
TGTTATTTTTTGTTGTTTTGGA

Found at i:231 original size:10 final size:9

Alignment explanation


    Indices: 166--232  Score: 50
    Period size: 8  Copynumber: 7.1  Consensus size: 9

        156 TATCTTAATA

                     
        166 TAAT-TTTT
          1 TAATGTTTT

                      
        174 TAATGTATTT
          1 TAATGT-TTT

                      
        184 TAAAT-TTTT
          1 T-AATGTTTT

             *       
        193 TTAT-TTTT
          1 TAATGTTTT

                        
        201 TAATGTTTGTTT
          1 TAATG--T-TTT

                     
        213 TAATGTTTT
          1 TAATGTTTT

                      
        222 TAAGTGTTTT
          1 TAA-TGTTTT

             
        232 T
          1 T

        233 GATATATTAT


Statistics
Matches: 49,  Mismatches: 2, Indels: 14
        0.75            0.03        0.22

Matches are distributed among these distances:
   8   13  0.27
   9   11  0.22
  10   13  0.27
  11    4  0.08
  12    8  0.16

ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69


Consensus pattern (9 bp):   
TAATGTTTT

Found at i:321 original size:17 final size:17

Alignment explanation


    Indices: 291--338  Score: 60
    Period size: 17  Copynumber: 2.8  Consensus size: 17

        281 TGGGCCCAAC

                            * 
        291 AAAATTTAAATTTATTTT
          1 AAAA-TTAAATTTATTAT

                    *        
        309 AAAATTAAGTTTATTAT
          1 AAAATTAAATTTATTAT

               *         
        326 AAATTTAAATTTA
          1 AAAATTAAATTTA

        339 AATTTATTTA


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  17   22  0.85
  18    4  0.15

ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50


Consensus pattern (17 bp):   
AAAATTAAATTTATTAT

Found at i:332 original size:23 final size:22

Alignment explanation


    Indices: 306--351  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 22

        296 TTAAATTTAT

                       *           
        306 TTTAAAATTAAGTTTATTATAAA
          1 TTTAAAATTAAATTTATT-TAAA

                  *               
        329 TTTAAATTTAAATTTATTTAAA
          1 TTTAAAATTAAATTTATTTAAA

             
        351 T
          1 T

        352 AATGTCCCAT


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

Matches are distributed among these distances:
  22    5  0.24
  23   16  0.76

ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52


Consensus pattern (22 bp):   
TTTAAAATTAAATTTATTTAAA

Found at i:4363 original size:22 final size:21

Alignment explanation


    Indices: 4322--4364  Score: 52
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       4312 CCCAAACAAA

                           *     
       4322 TAGAGGAAAAATACAGGCGAT
          1 TAGAGGAAAAATACACGCGAT

                                   
       4343 TAGAGGAGAAAAT-CGACGCGAT
          1 TAGAGGA-AAAATAC-ACGCGAT

       4365 GCAGGGAGTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  21    8  0.42
  22   11  0.58

ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14


Consensus pattern (21 bp):   
TAGAGGAAAAATACACGCGAT
Done.