Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000212.1 Kokia drynarioides strain JFW-HI SEQ_110907, 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: 7780
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:2023 original size:5 final size:5

Alignment explanation


    Indices: 1999--2053  Score: 60
    Period size: 5  Copynumber: 10.8  Consensus size: 5

       1989 AAAAAATTAG

                                                  *                 
       1999 TTTA- TTTAT TTTCAAT TTTAT TTTAT TTTAT CTTAT TTT-T TTTAAT
          1 TTTAT TTTAT TTT--AT TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT

                      
       2045 TTTAT TTTA
          1 TTTAT TTTA

       2054 ATTATGCACT


Statistics
Matches: 44,  Mismatches: 2, Indels: 9
        0.80            0.04        0.16

Matches are distributed among these distances:
   4    8  0.18
   5   27  0.61
   6    4  0.09
   7    5  0.11

ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75


Consensus pattern (5 bp):   
TTTAT

Found at i:3374 original size:24 final size:22

Alignment explanation


    Indices: 3332--3375  Score: 61
    Period size: 24  Copynumber: 1.9  Consensus size: 22

       3322 CCAATTAGGG

                                  
       3332 AATTATTGTTTAGATTTAATCA
          1 AATTATTGTTTAGATTTAATCA

                    *             
       3354 AATTATCTTTTTAGAATTTAAT
          1 AATTAT-TGTTTAG-ATTTAAT

       3376 TTGGATCCAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    6  0.32
  23    6  0.32
  24    7  0.37

ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52


Consensus pattern (22 bp):   
AATTATTGTTTAGATTTAATCA

Found at i:6190 original size:22 final size:22

Alignment explanation


    Indices: 6160--6240  Score: 99
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       6150 AAAAAAATAT

                *         **      
       6160 TCAACTATATTGGCGTAATCAA
          1 TCAATTATATTGGCACAATCAA

                                  
       6182 TCAATTATATTGGCACAATCAA
          1 TCAATTATATTGGCACAATCAA

             *         * **       
       6204 TTAATTATATTTGTGCAATCAA
          1 TCAATTATATTGGCACAATCAA

                           
       6226 TCAATTATATTGGCA
          1 TCAATTATATTGGCA

       6241 TAATACATCC


Statistics
Matches: 48,  Mismatches: 11, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  22   48  1.00

ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37


Consensus pattern (22 bp):   
TCAATTATATTGGCACAATCAA
Done.