# /Users/pjcock/Downloads/Software/fasta-35.4.1/bin/fasta35 -m 10 -Q -H -B -E 0.1 -L -n -r +3/-2 NC_002127.ffn NC_002695.ffn
FASTA searches a protein or DNA sequence data bank
 version 35.04 Jun. 29, 2008
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: NC_002127.ffn
  1>>>ref|NC_002127.1|:413-736 - 324 nt
Library: NC_002695.ffn 4744434 residues in  5230 sequences

4744434 residues in  5230 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 3.2253+/-0.0011; mu= 14.3262+/- 0.073
 mean_var=39.3286+/- 8.052, 0's: 0 Z-trim: 0  B-trim: 2 in 1/43
 Lambda= 0.204513
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +3/-2 matrix (3:-2) ktup: 6
 join: 35, opt: 20, open/ext: -12/-4, width:  16
 Scan time:  1.660
!! No sequences with E() < 0.100000
  2>>>ref|NC_002127.1|:c1351-971 - 381 nt
Library: NC_002695.ffn 4744434 residues in  5230 sequences

4744434 residues in  5230 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 1.8467+/-0.00109; mu= 22.5671+/- 0.073
 mean_var=40.1160+/- 8.182, 0's: 0 Z-trim: 2  B-trim: 0 in 0/44
 Lambda= 0.202496
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +3/-2 matrix (3:-2) ktup: 6
 join: 35, opt: 20, open/ext: -12/-4, width:  16
 Scan time:  1.770

The best scores are:                                      opt z-sc E(5230)
ref|NC_002695.1|:1970775-1971404               ( 630) [f]   91 139.3   0.045

>>>ref|NC_002127.1|:c1351-971, 381 nt vs NC_002695.ffn library
; pg_name: /Users/pjcock/Downloads/Software/fasta-35.4.1/bin/fasta35
; pg_ver: 35.03
; pg_argv: /Users/pjcock/Downloads/Software/fasta-35.4.1/bin/fasta35 -m 10 -Q -H -B -E 0.1 -L -n -r +3/-2 NC_002127.ffn NC_002695.ffn
; pg_name_alg: FASTA
; pg_ver_rel: 3.5 Sept 2006
; pg_matrix: +3/-2 (3:-2)
; pg_open-ext: -12 -4
; pg_ktup: 6
; pg_optcut: 20
; pg_cgap: 35
; mp_extrap: 60000 5228
; mp_stats:  Expectation_n fit: rho(ln(x))= 1.8467+/-0.00109; mu= 22.5671+/- 0.073  mean_var=40.1160+/- 8.182, 0's: 0 Z-trim: 2  B-trim: 0 in 0/44  Lambda= 0.202496
; mp_KS: -0.0000 (N=1079006385) at  20
; mp_Algorithm: FASTA (3.5 Sept 2006) [optimized]
; mp_Parameters: +3/-2 matrix (3:-2) ktup: 6  join: 35, opt: 20, open/ext: -12/-4, width:  16
>>ref|NC_002695.1|:1970775-1971404
; fa_frame: f
; fa_initn:  54
; fa_init1:  54
; fa_opt:  91
; fa_z-score: 139.3
; fa_bits: 35.2
; fa_expect:  0.045
; bs_ident: 0.578
; bs_sim: 0.578
; bs_overlap: 102
>ref|NC_00212 ..
; sq_len: 381
; sq_offset: 1
; sq_type: D
; al_start: 4
; al_stop: 105
; al_display_start: 1
---------------------------ATGAAAAAAGATAAAAAATATCA
AATAGAAGCAATAAAAAATAAAGATAAAACTTTATTTATTGTCTATGCTA
CTGATATTTATAGCCCGAGCGAATTTTTCTCAAAAATCGAATCCGACTTG
AAGAAAAAGAAAAGCAAGGGTGATGTTTTT
>ref|NC_002695.1|:1970775-1971404 ..
; sq_len: 630
; sq_offset: 1
; sq_type: D
; al_start: 313
; al_stop: 414
; al_display_start: 283
AACTATTTTCAGAGTGTCATGGCAGAACACAGAGAAAATAAAACAAGTAA
TAAAATATTAATGGAAAAAATAAATTCTTGTTTATTTAGACCTGATTCTA
ATCACTTTTCTTGCCCGGAGTCATTTTTGACATGCCCGATAACGCTGGAC
ACACCTGAGACTGGGGTGTTCATGAGAAAC
; al_cons:
                              : : :: :::::: :  : :
 : :  :  :::  :::: : : ::     ::::::::      :: :::
 : :  ::: : :::::     ::::::  ::
  3>>>ref|NC_002127.1|:c2388-1348 - 1041 nt
Library: NC_002695.ffn 4744434 residues in  5230 sequences

4744434 residues in  5230 sequences
Statistics:  Expectation_n fit: rho(ln(x))= 3.0829+/-0.00118; mu= 17.6472+/- 0.080
 mean_var=43.5957+/- 8.728, 0's: 0 Z-trim: 0  B-trim: 0 in 0/44
 Lambda= 0.194246
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +3/-2 matrix (3:-2) ktup: 6
 join: 40, opt: 25, open/ext: -12/-4, width:  16
 Scan time:  3.060
!! No sequences with E() < 0.100000
>>><<<


1746 residues in 3 query   sequences
4744434 residues in 5230 library sequences
 Scomplib [35.03]
 start: Tue Jul 15 16:47:15 2008 done: Tue Jul 15 16:47:22 2008
 Total Scan time:  6.490 Total Display time:  0.010

Function used was FASTA [version 35.04 Jun. 29, 2008]
