Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004769.1 Kokia drynarioides strain JFW-HI SEQ_118374, 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: 25380
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:16722 original size:39 final size:39

Alignment explanation


    Indices: 16667--16756  Score: 126
    Period size: 39  Copynumber: 2.3  Consensus size: 39

      16657 CAGTTATCAA

                     * *     *        *     *      
      16667 AATACTGAACTAGCAGTGACACTGTAGACACTGCAATAC
          1 AATACTGAATTGGCAGTAACACTGTAAACACTACAATAC

                                                   
      16706 AATACTGAATTGGCAGTAACACTGTAAACACTACAATAC
          1 AATACTGAATTGGCAGTAACACTGTAAACACTACAATAC

               *        
      16745 AATTCTGAATTG
          1 AATACTGAATTG

      16757 ACGGTGTGCT


Statistics
Matches: 45,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  39   45  1.00

ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24


Consensus pattern (39 bp):   
AATACTGAATTGGCAGTAACACTGTAAACACTACAATAC

Found at i:25218 original size:20 final size:20

Alignment explanation


    Indices: 25195--25271  Score: 65
    Period size: 22  Copynumber: 3.9  Consensus size: 20

      25185 AAATTTTAAT

                                
      25195 AAAAATTATTAAAAATTAGG
          1 AAAAATTATTAAAAATTAGG

                               *   
      25215 AAAAAAATTATTAAAAA-TCGTG
          1 --AAAAATTATTAAAAATTAG-G

                                *
      25237 AAAAATTA-T-AAAATATA-T
          1 AAAAATTATTAAAAAT-TAGG

                              
      25255 AAAAA-TATTAAAAATTA
          1 AAAAATTATTAAAAATTA

      25272 TAAAATTTTA


Statistics
Matches: 47,  Mismatches: 3, Indels: 14
        0.73            0.05        0.22

Matches are distributed among these distances:
  17    2  0.04
  18   12  0.26
  19    6  0.13
  20    9  0.19
  21    2  0.04
  22   16  0.34

ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30


Consensus pattern (20 bp):   
AAAAATTATTAAAAATTAGG

Found at i:25230 original size:10 final size:10

Alignment explanation


    Indices: 25174--25276  Score: 63
    Period size: 10  Copynumber: 10.5  Consensus size: 10

      25164 ATAAAGGTTA

                *     
      25174 TAAATATTAT
          1 TAAAAATTAT

                **   *
      25184 TAAATTTTAA
          1 TAAAAATTAT

                      
      25194 TAAAAATTAT
          1 TAAAAATTAT

                       *
      25204 TAAAAATTAGGA
          1 TAAAAATTA--T

            *         
      25216 AAAAAATTAT
          1 TAAAAATTAT

                   ** 
      25226 TAAAAATCGT
          1 TAAAAATTAT

            *         
      25236 GAAAAATTA-
          1 TAAAAATTAT

                      
      25245 T-AAAA-TAT
          1 TAAAAATTAT

                       
      25253 ATAAAAA-TAT
          1 -TAAAAATTAT

                      
      25263 TAAAAATTA-
          1 TAAAAATTAT

                 
      25272 TAAAA
          1 TAAAA

      25277 TTTTATAAAG


Statistics
Matches: 72,  Mismatches: 15, Indels: 13
        0.72            0.15        0.13

Matches are distributed among these distances:
   7    2  0.03
   8    4  0.06
   9   12  0.17
  10   46  0.64
  12    8  0.11

ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34


Consensus pattern (10 bp):   
TAAAAATTAT

Found at i:25273 original size:20 final size:20

Alignment explanation


    Indices: 25193--25276  Score: 70
    Period size: 18  Copynumber: 4.3  Consensus size: 20

      25183 TTAAATTTTA

                                 *
      25193 ATAAAAATTATTAAAAATTAGG
          1 ATAAAAATTATTAAAAA-TA-T

             *                 * 
      25215 AAAAAAATTATTAAAAATCGT
          1 ATAAAAATTATTAAAAAT-AT

             *                  
      25236 -GAAAAATTA-T-AAAATAT
          1 ATAAAAATTATTAAAAATAT

                                
      25253 ATAAAAA-TATTAAAAAT-T
          1 ATAAAAATTATTAAAAATAT

                  
      25271 ATAAAA
          1 ATAAAA

      25277 TTTTATAAAG


Statistics
Matches: 52,  Mismatches: 6, Indels: 12
        0.74            0.09        0.17

Matches are distributed among these distances:
  17    3  0.06
  18   18  0.35
  19    6  0.12
  20    8  0.15
  21    1  0.02
  22   16  0.31

ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30


Consensus pattern (20 bp):   
ATAAAAATTATTAAAAATAT
Done.