Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008220.1 Kokia drynarioides strain JFW-HI SEQ_122884, 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: 13514
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36


Found at i:2396 original size:28 final size:27

Alignment explanation


    Indices: 2339--2394  Score: 80
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       2329 CTTTTATTTG

                                  *    
       2339 AAATTTATTTTATTATTGAATATATTA
          1 AAATTTATTTTATTATTGAATAGATTA

                                        
       2366 AAATATTA-TTTATTA-TGAATAGATTA
          1 AAAT-TTATTTTATTATTGAATAGATTA

               
       2392 AAA
          1 AAA

       2395 AAAATTGGGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  26   13  0.48
  27   11  0.41
  28    3  0.11

ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48


Consensus pattern (27 bp):   
AAATTTATTTTATTATTGAATAGATTA

Found at i:3740 original size:2 final size:2

Alignment explanation


    Indices: 3735--3775  Score: 57
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       3725 TTTATTTTTT

                                                    *                     
       3735 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TCA T- TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T

       3776 TTTCCTGATT


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.91
   3    2  0.06

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


Consensus pattern (2 bp):   
TA

Found at i:9320 original size:30 final size:30

Alignment explanation


    Indices: 9259--9327  Score: 88
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       9249 TTTCGTTGAT

                      *                    
       9259 TGTTTTGTCATTTTTCGATAACGTTAGTGAC
          1 TGTTTTGTCAATTTTC-ATAACGTTAGTGAC

                                            
       9290 TGTTTTGTCACATTTTC-TAA-GTTGAGTGAC
          1 TGTTTTGTCA-ATTTTCATAACGTT-AGTGAC

                    
       9320 TGTTTTGT
          1 TGTTTTGT

       9328 TAAATGTAAC


Statistics
Matches: 35,  Mismatches: 1, Indels: 5
        0.85            0.02        0.12

Matches are distributed among these distances:
  29    3  0.09
  30   17  0.49
  31   10  0.29
  32    5  0.14

ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51


Consensus pattern (30 bp):   
TGTTTTGTCAATTTTCATAACGTTAGTGAC
Done.