# fasta36 -E 1.7 -F 1.3 -m 10 -n mrna_s01.fasta mrnalib.fasta
FASTA searches a protein or DNA sequence data bank
 version 36.3.5c Dec, 2011(preload8)
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: mrna_s01.fasta
  1>>>gi|255708421:1-99 Mus musculus myoglobin (Mb), transcript varia - 99 nt
Library: mrnalib.fasta
   178611 residues in   250 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 0.6048+/-0.0187; mu= 57.5189+/- 1.259
 mean_var=109.2865+/-49.006, 0's: 0 Z-trim(83.7): 6  B-trim: 0 in 0/14
 Lambda= 0.122685
 statistics sampled from 218 (219) to 218 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
 ktup: 3, E-join: 0.25 (0.93), E-opt: 0.05 (0.61), width:  16
 Scan time:  0.050

The best scores are:                                      opt bits E(250)
gi|284005422|ref|NM_001171502.1| Oryctolagus c ( 429) [f]   99 23.6     1.4
gi|284005386|ref|NM_001171415.1| Oryctolagus c ( 429) [f]   99 23.6     1.4
gi|284005381|ref|NM_001171414.1| Oryctolagus c ( 429) [f]   99 23.6     1.4
gi|23308614|ref|NM_152952.1| Danio rerio cytog (5188) [f]   80 23.6     1.4
gi|291415427|ref|XM_002723908.1| PREDICTED: Or ( 423) [f]   99 23.6     1.4

>>>gi|255708421:1-99, 99 nt vs mrnalib.fasta library
; pg_name: fasta36
; pg_ver: 36.3.5c Dec, 2011(preload8)
; pg_argv:  fasta36 -E 1.7 -F 1.3 -m 10 -n mrna_s01.fasta mrnalib.fasta; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: +5/-4 (5:-4)
; pg_open-ext: -12 -4
; pg_ktup: 3
; pg_join_E(): 0.25 (0.93)
; pg_optcut_E(): 0.05 (0.61)
; mp_extrap: 60000 218
; mp_stats:  Expectation_n fit: rho(ln(x))= 0.6048+/-0.0187; mu= 57.5189+/- 1.259  mean_var=109.2865+/-49.006, 0's: 0 Z-trim(83.7): 6  B-trim: 0 in 0/14  Lambda= 0.122685
; mp_KS: -0.0000 (N=0) at  20
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4  ktup: 3, E-join: 0.25 (0.93), E-opt: 0.05 (0.61), width:  16
>>gi|284005422|ref|NM_001171502.1| Oryctolagus cuniculus hemoglobin, zeta (HBZ_2), mRNA
; fa_frame: f
; fa_initn:  79
; fa_init1:  66
; fa_opt:  99
; fa_z-score: 90.0
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.738
; bs_sim: 0.738
; bs_overlap: 42
>gi|255708421 ..
; sq_len: 99
; sq_offset: 1
; sq_type: D
; al_start: 34
; al_stop: 75
; al_display_start: 4
GGAACTGTTTTAGAAACAGAACATCATCTTCAACATCCAGAGGACTGTCA
TCCTTGTCCCTGTGGGTGAGGGAAACAAACACTTGGCTTCAATGTC
>gi|284005422|ref|NM_001171502.1| ..
; sq_len: 429
; sq_offset: 1
; sq_type: D
; al_start: 12
; al_stop: 52
; al_display_start: 1
-------------------ATGTCTCTGACCAAGAGCGAGAGGACCATCA
T-CATGTCCCTCTGGGACAAGGTCTCCTCCCAGTCTGAGGCCATCGGCAC
TGAGGCCCTGGAGAGGCTCT
>>gi|284005386|ref|NM_001171415.1| Oryctolagus cuniculus zeta globin (HBZ0), mRNA
; fa_frame: f
; fa_initn:  73
; fa_init1:  66
; fa_opt:  99
; fa_z-score: 90.0
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.738
; bs_sim: 0.738
; bs_overlap: 42
>gi|255708421 ..
; sq_len: 99
; sq_offset: 1
; sq_type: D
; al_start: 34
; al_stop: 75
; al_display_start: 4
GGAACTGTTTTAGAAACAGAACATCATCTTCAACATCCAGAGGACTGTCA
TCCTTGTCCCTGTGGGTGAGGGAAACAAACACTTGGCTTCAATGTC
>gi|284005386|ref|NM_001171415.1| ..
; sq_len: 429
; sq_offset: 1
; sq_type: D
; al_start: 12
; al_stop: 52
; al_display_start: 1
-------------------ATGTCTCTGACCAAGAGCGAGAGGACCATCA
T-CATGTCCCTCTGGGACAAGGTCTCCTCCCAGTCTGAGGCCATCGGCAC
TGAGGCCCTGGAGAGGCTCT
>>gi|284005381|ref|NM_001171414.1| Oryctolagus cuniculus hemoglobin subunit zeta (RA_M008_JSM295ECF), mRNA
; fa_frame: f
; fa_initn:  90
; fa_init1:  66
; fa_opt:  99
; fa_z-score: 90.0
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.738
; bs_sim: 0.738
; bs_overlap: 42
>gi|255708421 ..
; sq_len: 99
; sq_offset: 1
; sq_type: D
; al_start: 34
; al_stop: 75
; al_display_start: 4
GGAACTGTTTTAGAAACAGAACATCATCTTCAACATCCAGAGGACTGTCA
TCCTTGTCCCTGTGGGTGAGGGAAACAAACACTTGGCTTCAATGTC
>gi|284005381|ref|NM_001171414.1| ..
; sq_len: 429
; sq_offset: 1
; sq_type: D
; al_start: 12
; al_stop: 52
; al_display_start: 1
-------------------ATGTCTCTGACCAAGAGCGAGAGGACCATCA
T-CATGTCCCTCTGGGACAAGGTCTCCTCCCAGTCTGAGGCCATCGGCAC
TGAGGCCCTGGAGAGGCTCT
>>gi|23308614|ref|NM_152952.1| Danio rerio cytoglobin 1 (cygb1), mRNA
; fa_frame: f
; fa_initn: 115
; fa_init1:  78
; fa_opt:  80
; fa_z-score: 70.4
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.800
; bs_sim: 0.800
; bs_overlap: 25
>gi|255708421 ..
; sq_len: 99
; sq_offset: 1
; sq_type: D
; al_start: 13
; al_stop: 37
; al_display_start: 1
------------------TCGGGAACTGTTTTAGAAACAGAACATCATCT
TCAACATCCAGAGGACTGTCATCCTTGTCCCTGTGGGTGAGGGAAACAAA
CACTTGGCTTCAATGTC
>gi|23308614|ref|NM_152952.1| ..
; sq_len: 5188
; sq_offset: 1
; sq_type: D
; al_start: 416
; al_stop: 440
; al_display_start: 386
CAACACACTGGTGGAAAACCTGCGAGATGCTGACAAACTCAACACCATCT
TCAACCAGATGGGCAAATCACACGCGCTGCGCCACAAGGTGGACCCTGTT
TACTTCAAAATTCTGGCCGG
>>gi|291415427|ref|XM_002723908.1| PREDICTED: Oryctolagus cuniculus zeta globin-like (LOC100357627), mRNA
; fa_frame: f
; fa_initn:  91
; fa_init1:  66
; fa_opt:  99
; fa_z-score: 90.0
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.738
; bs_sim: 0.738
; bs_overlap: 42
>gi|255708421 ..
; sq_len: 99
; sq_offset: 1
; sq_type: D
; al_start: 34
; al_stop: 75
; al_display_start: 4
GGAACTGTTTTAGAAACAGAACATCATCTTCAACATCCAGAGGACTGTCA
TCCTTGTCCCTGTGGGTGAGGGAAACAAACACTTGGCTTCAATGTC
>gi|291415427|ref|XM_002723908.1| ..
; sq_len: 423
; sq_offset: 1
; sq_type: D
; al_start: 12
; al_stop: 52
; al_display_start: 1
-------------------ATGTCTCTGACCAAGAGCGAGAGGACCATCA
T-CATGTCCCTCTGGGACAAGGTCTCCTCCCAGTCTGAGGCCATCGGCAC
TGAGGCCCTGGAGAGGCTCT

>>><<<
>>>///

99 residues in 1 query   sequences
178611 residues in 250 library sequences
 Tcomplib [36.3.5c Dec, 2011(preload8)] (4 proc in memory [0G])
 start: Tue May  8 01:06:58 2012 done: Tue May  8 01:06:58 2012
 Total Scan time:  0.050 Total Display time:  0.010

Function used was FASTA [36.3.5c Dec, 2011(preload8)]