# fasta36 -E 1.7 -F 1.3 -m 10 -n mrna_s02.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_s02.fasta
  1>>>gi|156718121:2361-2376 Bos taurus nucleoporin 43kDa (NU - 16 nt
Library: mrnalib.fasta
   178611 residues in   250 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 7.9681+/- 0.014; mu= -10.9438+/- 0.902
 mean_var=29.7386+/- 9.846, 0's: 0 Z-trim(80.0): 6  B-trim: 0 in 0/16
 Lambda= 0.235187
 statistics sampled from 176 (177) to 176 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
 ktup: 1, E-join: 0.25 (0.978), E-opt: 0.05 (0.472), width:  16
 Scan time:  0.060

The best scores are:                                      opt bits E(250)
gi|77681427|ref|NM_001016495.2| Xenopus (Silur ( 554) [f]   57 21.0     1.4
gi|53749657|ref|NM_182940.2| Danio rerio hemog ( 564) [f]   57 21.0     1.4
gi|158508631|ref|NM_030206.4| Mus musculus cyt (2331) [f]   62 20.9     1.5
gi|296217287|ref|XM_002754912.1| PREDICTED: Ca ( 627) [f]   57 20.8     1.5
gi|332211540|ref|XM_003254828.1| PREDICTED: No ( 640) [r]   57 20.8     1.5
gi|147903656|ref|NM_001086277.1| Xenopus laevi ( 677) [f]   57 20.8     1.6
gi|380013536|ref|XM_003690762.1| PREDICTED: Ap ( 707) [r]   57 20.7     1.7
gi|332211538|ref|XM_003254827.1| PREDICTED: No ( 713) [r]   57 20.7     1.7

>>>gi|156718121:2361-2376, 16 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_s02.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: 1
; pg_join_E(): 0.25 (0.978)
; pg_optcut_E(): 0.05 (0.472)
; mp_extrap: 60000 176
; mp_stats:  Expectation_n fit: rho(ln(x))= 7.9681+/- 0.014; mu= -10.9438+/- 0.902  mean_var=29.7386+/- 9.846, 0's: 0 Z-trim(80.0): 6  B-trim: 0 in 0/16  Lambda= 0.235187
; mp_KS: -0.0000 (N=0) at  30
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4  ktup: 1, E-join: 0.25 (0.978), E-opt: 0.05 (0.472), width:  16
>>gi|77681427|ref|NM_001016495.2| Xenopus (Silurana) tropicalis hemoglobin, epsilon 1 (hbe1), mRNA
; fa_frame: f
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 88.1
; fa_bits: 21.0
; fa_expect:    1.4
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 2
; al_stop: 16
; al_display_start: 1
-----------------------------GAAGAAGGAAAAAAAA
>gi|77681427|ref|NM_001016495.2| ..
; sq_len: 554
; sq_offset: 1
; sq_type: D
; al_start: 530
; al_stop: 544
; al_display_start: 500
ATTAATCAATGCCCTGTTTGTTATGCAATAAAGAATAAAAAAAAAAAAAA
AAAAA
>>gi|53749657|ref|NM_182940.2| Danio rerio hemoglobin alpha embryonic-1 (hbae1), mRNA
; fa_frame: f
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 87.9
; fa_bits: 21.0
; fa_expect:    1.4
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 2
; al_stop: 16
; al_display_start: 1
-----------------------------GAAGAAGGAAAAAAAA
>gi|53749657|ref|NM_182940.2| ..
; sq_len: 564
; sq_offset: 1
; sq_type: D
; al_start: 532
; al_stop: 546
; al_display_start: 502
TGAGACAATAAATTATGATGAAAAACATTAAAGAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAA
>>gi|158508631|ref|NM_030206.4| Mus musculus cytoglobin (Cygb), mRNA
; fa_frame: f
; fa_initn:  62
; fa_init1:  62
; fa_opt:  62
; fa_z-score: 76.3
; fa_bits: 20.9
; fa_expect:    1.5
; bs_ident: 0.875
; bs_sim: 0.875
; bs_overlap: 16
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 1
; al_stop: 16
; al_display_start: 1
------------------------------GAAGAAGGAAAAAAAA
>gi|158508631|ref|NM_030206.4| ..
; sq_len: 2331
; sq_offset: 1
; sq_type: D
; al_start: 1782
; al_stop: 1797
; al_display_start: 1752
GGGCTACACAGGAAGACCTCGGGTCAAACGGAAGAAAAAAAAAAAACATA
AAGATCTGGCTCCCCTCTCCTCTCCTCCCCTCCCCTCCCCTCCCCAAGGG
TTTGCCTGACTGGCTTGTCC
>>gi|296217287|ref|XM_002754912.1| PREDICTED: Callithrix jacchus hemoglobin subunit gamma-like (LOC100389093), mRNA
; fa_frame: f
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 86.3
; fa_bits: 20.8
; fa_expect:    1.5
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 1
; al_stop: 15
; al_display_start: 1
------------------------------GAAGAAGGAAAAAAAA
>gi|296217287|ref|XM_002754912.1| ..
; sq_len: 627
; sq_offset: 1
; sq_type: D
; al_start: 132
; al_stop: 146
; al_display_start: 102
ACTGCACAGGGCCTCACTGGAACTAGAGAAGAAGAAGGTAAAACAGGCTG
ACAAAAGAATTCCTGCTCCTAGTCCAGACACCATGAGTAATTTCACAGCT
GAGGACAAGGCTGCTATCAC
>>gi|332211540|ref|XM_003254828.1| PREDICTED: Nomascus leucogenys hemoglobin subunit gamma-1-like, transcript variant 2 (LOC100582529), mRNA
; fa_frame: r
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 86.0
; fa_bits: 20.8
; fa_expect:    1.5
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 16
; al_stop: 2
; al_display_start: 16
------------------------------TTTTTTTTCCTTCTTC
>gi|332211540|ref|XM_003254828.1| ..
; sq_len: 640
; sq_offset: 1
; sq_type: D
; al_start: 590
; al_stop: 604
; al_display_start: 560
TAAGAGATCACACATGATTTTCTTCAGCTCTTTTTTTTACATCTTTTTAA
ATATATGAGCCACAAAGGGTTTTATGTTGAG
>>gi|147903656|ref|NM_001086277.1| Xenopus laevis hemoglobin, alpha 2 (hba2), mRNA
; fa_frame: f
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 85.2
; fa_bits: 20.8
; fa_expect:    1.6
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 2
; al_stop: 16
; al_display_start: 1
-----------------------------GAAGAAGGAAAAAAAA
>gi|147903656|ref|NM_001086277.1| ..
; sq_len: 677
; sq_offset: 1
; sq_type: D
; al_start: 643
; al_stop: 657
; al_display_start: 613
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAA
AAAAAAAAAAAAAAA
>>gi|380013536|ref|XM_003690762.1| PREDICTED: Apis florea globin-like (LOC100870092), mRNA
; fa_frame: r
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 84.6
; fa_bits: 20.7
; fa_expect:    1.7
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 16
; al_stop: 2
; al_display_start: 16
------TTTTTTTTCCTTCTTC
>gi|380013536|ref|XM_003690762.1| ..
; sq_len: 707
; sq_offset: 1
; sq_type: D
; al_start: 7
; al_stop: 21
; al_display_start: 1
TTTTTCTTTTTTTTTTTTCTTTTCTTCCTTTCTTCCTTCCTTTTCTTTTT
TTTTTTTCTT
>--
; fa_frame: r
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 84.6
; fa_bits: 20.7
; fa_expect:    1.7
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 16
; al_stop: 2
; al_display_start: 16
------------------------------TTTTTTTTCCTTCTTC
>gi|380013536|ref|XM_003690762.1| ..
; sq_len: 707
; sq_offset: 1
; sq_type: D
; al_start: 46
; al_stop: 60
; al_display_start: 16
TTTCTTTTCTTCCTTTCTTCCTTCCTTTTCTTTTTTTTTTTTCTTTTGCC
CAACGCCCGTTTTCGCAACGGACGAGGAGCGATGGGAACGTTTCTACGTT
TCCTCGGGATTTCGTCATCG
>--
; fa_frame: r
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 84.6
; fa_bits: 20.7
; fa_expect:    1.7
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 15
; al_stop: 1
; al_display_start: 16
-----------------------------TTTTTTTTCCTTCTTC
>gi|380013536|ref|XM_003690762.1| ..
; sq_len: 707
; sq_offset: 1
; sq_type: D
; al_start: 645
; al_stop: 659
; al_display_start: 615
AACGGGACGAGTTAGTTTATCCGTCATTTCTTTTTTTCCTCCTCCCTTCC
CCTCCCCCCCCCTTCTTTAATTTAGTCACTTAAGAATTGCTTC
>>gi|332211538|ref|XM_003254827.1| PREDICTED: Nomascus leucogenys hemoglobin subunit gamma-1-like, transcript variant 1 (LOC100582529), mRNA
; fa_frame: r
; fa_initn:  57
; fa_init1:  57
; fa_opt:  57
; fa_z-score: 84.5
; fa_bits: 20.7
; fa_expect:    1.7
; bs_ident: 0.867
; bs_sim: 0.867
; bs_overlap: 15
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 16
; al_stop: 2
; al_display_start: 16
------------------------------TTTTTTTTCCTTCTTC
>gi|332211538|ref|XM_003254827.1| ..
; sq_len: 713
; sq_offset: 1
; sq_type: D
; al_start: 663
; al_stop: 677
; al_display_start: 633
TAAGAGATCACACATGATTTTCTTCAGCTCTTTTTTTTACATCTTTTTAA
ATATATGAGCCACAAAGGGTTTTATGTTGAG

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

16 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:  0.060 Total Display time:  0.000

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