# /Users/pjcock/Downloads/Software/fasta-35.4.4/bin/fasta35 -H -q -E 0.05 -m 10 query.txt orchid_cds.txt
FASTA searches a protein or DNA sequence data bank
 version 35.04 Jan. 15, 2009
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: query.txt
  1>>>query - 131 nt
Library: orchid_cds.txt     573 residues in     1 sequences

    573 residues in     1 sequences
Statistics: (shuffled [500]) MLE statistics: Lambda= 0.1428;  K=0.01152
Algorithm: FASTA (3.5 Sept 2006) [optimized]
Parameters: +5/-4 matrix (5:-4) ktup: 6
 join: 46, opt: 31, open/ext: -12/-4, width:  16
 Scan time:  0.030

The best scores are:                                      opt bits E(1)
gi|116660610|gb|EG558221.1|EG558221 CR03001A07 ( 573) [r]  646 139.6 7.2e-38

>>>query, 131 nt vs orchid_cds.txt library
; pg_name: /Users/pjcock/Downloads/Software/fasta-35.4.4/bin/fasta35
; pg_ver: 35.04
; pg_argv: /Users/pjcock/Downloads/Software/fasta-35.4.4/bin/fasta35 -H -q -E 0.05 -m 10 query.txt orchid_cds.txt
; pg_name_alg: FASTA
; pg_ver_rel: 3.5 Sept 2006
; pg_matrix: +5/-4 (5:-4)
; pg_open-ext: -12 -4
; pg_ktup: 6
; pg_optcut: 31
; pg_cgap: 46
; mp_extrap: 60000 500
; mp_stats: (shuffled [500]) MLE statistics: Lambda= 0.1428;  K=0.01152
; mp_KS: -0.0000 (N=0) at   0
; mp_Algorithm: FASTA (3.5 Sept 2006) [optimized]
; mp_Parameters: +5/-4 matrix (5:-4) ktup: 6  join: 46, opt: 31, open/ext: -12/-4, width:  16
>>gi|116660610|gb|EG558221.1|EG558221 CR03001A07 Root CR03 cDNA library Catharanthus roseus cDNA clone CR03001A07 5', mRNA sequence
; fa_frame: r
; fa_initn: 646
; fa_init1: 646
; fa_opt: 646
; fa_z-score: 712.3
; fa_bits: 139.6
; fa_expect: 7.2e-38
; bs_ident: 0.992
; bs_sim: 0.992
; bs_overlap: 131
>query ..
; sq_len: 131
; sq_offset: 132
; sq_type: D
; al_start: 131
; al_stop: 1
; al_display_start: 131
------------------------------GCAACGCTTCAAGAACTGGA
ATTAGGAACCGTGACAACGATTAATGAGGAGATTTATGAAGAGGGTTCTT
CGATTTTAGGCCAATCGGAAGGAATTATGTAGCAAGTCCATCAGAAAATG
GAAGAAGTCAT
>gi|116660610|gb|EG558221.1|EG558221 ..
; sq_len: 573
; sq_offset: 1
; sq_type: D
; al_start: 360
; al_stop: 490
; al_display_start: 330
CAAGGGTTGATTATGTCATATCCAGCCGTTGCAACGCTTCAAGAACTGGA
ATTAGGAACCGTGACAACGATTAATGAGGAGATTTATGAAGAGGGTTCTT
CGATTTTAGGCCAATCGGAAGGAATTATGTAGCAAGTCCATCAGAAAATG
GAAGTAGTCATCATATGATGATGGCAATGACAGTAAGTTTTAATAATAAT
AATAATGGTGATCATGATGAGAAGATTAAGGATGGATTAA
; al_cons:
                              ::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::
::::::::::::::::::::::::::::::::::::::::::::::::::
:::: ::::::
>>><<<


131 residues in 1 query   sequences
573 residues in 1 library sequences
 Scomplib [35.04]
 start: Tue Jan 27 18:10:06 2009 done: Tue Jan 27 18:10:06 2009
 Total Scan time:  0.030 Total Display time:  0.010

Function used was FASTA [version 35.04 Jan. 15, 2009]