# fasta36 -E 1.7 -F 1.3 -m 10 -n mrna_mult.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_mult.fasta
  1>>>random_s00 - 15 nt
Library: mrnalib.fasta
   178611 residues in   250 sequences

Statistics: Altschul/Gish params: n0: 15 Lambda: 0.192 K: 0.177 H: 0.360
 statistics sampled from 59 (59) to 59 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
 ktup: 1, E-join: 0.25 (0.802), E-opt: 0.05 (0.126), width:  16
 Scan time:  0.050
!! No sequences with E() < 1.7
>>><<<
  2>>>gi|255708421:1-99 Mus musculus myoglobin (Mb), transcript varia - 99 nt
Library: mrnalib.fasta
   178611 residues in   250 sequences

Statistics: Altschul/Gish params: n0: 99 Lambda: 0.192 K: 0.177 H: 0.360
 statistics sampled from 211 (219) to 211 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: +5/-4 matrix (5:-4), open/ext: -12/-4
 ktup: 3, E-join: 0.25 (0.866), E-opt: 0.05 (0.368), width:  16
 Scan time:  0.040

The best scores are:                                      opt bits E(250)
gi|23308614|ref|NM_152952.1| Danio rerio cytog (5188) [r]   74 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_mult.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 (0.866)
; pg_optcut_E(): 0.05 (0.368)
; mp_extrap: 60000 211
; mp_stats: Altschul/Gish params: n0: 99 Lambda: 0.192 K: 0.177 H: 0.360
; 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: 3, E-join: 0.25 (0.866), E-opt: 0.05 (0.368), width:  16
>>gi|23308614|ref|NM_152952.1| Danio rerio cytoglobin 1 (cygb1), mRNA
; fa_frame: r
; fa_initn: 124
; fa_init1:  74
; fa_opt:  74
; fa_z-score: 70.3
; fa_bits: 23.6
; fa_expect:    1.4
; bs_ident: 0.818
; bs_sim: 0.818
; bs_overlap: 22
>gi|255708421 ..
; sq_len: 99
; sq_offset: 100
; sq_type: D
; al_start: 29
; al_stop: 8
; al_display_start: 59
CAAGGATGACAGTCCTCTGGATGTTGAAGATGATGTTCTGTTTCTAAAAC
AGTTCCCGA
>gi|23308614|ref|NM_152952.1| ..
; sq_len: 5188
; sq_offset: 1
; sq_type: D
; al_start: 3484
; al_stop: 3505
; al_display_start: 3454
CATTGTATAAAATACAACAAAATTTGTGTTTGATTTTTTTTGTCTAAAAC
AGCAAGAATGGATGAGTAATGAAATAATAAAAAAAACATAAAAAAATAAG
TAAAAAAATAACAGAAATAA

>>><<<
  3>>>gi|156718121:2361-2376 Bos taurus nucleoporin 43kDa (NU - 16 nt
Library: mrnalib.fasta
   178611 residues in   250 sequences

Statistics: Altschul/Gish params: n0: 16 Lambda: 0.192 K: 0.177 H: 0.360
 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 (0.903), E-opt: 0.05 (0.403), width:  16
 Scan time:  0.080

The best scores are:                                      opt bits E(250)
gi|47271416|ref|NM_131257.2| Danio rerio hemog ( 597) [f]   52 21.0     1.4
gi|332859474|ref|XM_001156938.2| PREDICTED: Pa ( 762) [f]   52 20.9     1.4
gi|332211534|ref|XM_003254825.1| PREDICTED: No ( 805) [r]   52 20.9     1.4
gi|23308614|ref|NM_152952.1| Danio rerio cytog (5188) [f]   52 20.9     1.4
gi|297689475|ref|XM_002822130.1| PREDICTED: Po (1158) [r]   52 20.9     1.4
gi|297689475|ref|XM_002822130.1| PREDICTED: Po (1158) [f]   52 20.9     1.4

>>>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_mult.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 (0.903)
; pg_optcut_E(): 0.05 (0.403)
; mp_extrap: 60000 176
; mp_stats: Altschul/Gish params: n0: 16 Lambda: 0.192 K: 0.177 H: 0.360
; 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 (0.903), E-opt: 0.05 (0.403), width:  16
>>gi|47271416|ref|NM_131257.2| Danio rerio hemoglobin alpha adult-1 (hbaa1), mRNA
; fa_frame: f
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 87.3
; fa_bits: 21.0
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 3
; al_stop: 16
; al_display_start: 1
----------------------------GAAGAAGGAAAAAAAA
>gi|47271416|ref|NM_131257.2| ..
; sq_len: 597
; sq_offset: 1
; sq_type: D
; al_start: 573
; al_stop: 586
; al_display_start: 543
GTCTGAATGAAATTTCTCAATAAAAGGCACAGAACTAAAAAAAAAAAAAA
AAAAA
>>gi|332859474|ref|XM_001156938.2| PREDICTED: Pan troglodytes myoglobin, transcript variant 11 (MB), mRNA
; fa_frame: f
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 85.3
; fa_bits: 20.9
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 3
; al_stop: 16
; al_display_start: 1
----------------------------GAAGAAGGAAAAAAAA
>gi|332859474|ref|XM_001156938.2| ..
; sq_len: 762
; sq_offset: 1
; sq_type: D
; al_start: 85
; al_stop: 98
; al_display_start: 55
AGCCATTGAGCGATCTTTGTCAAGCATCCCAGAAGGTATAAAAACGCCCT
TGGGGCCAGGCAGCCTCAAACCCCAGCTGTTGGGGCCAGGACACCCAGTG
AGCCCATACTTGCTCTTTTT
>>gi|332211534|ref|XM_003254825.1| PREDICTED: Nomascus leucogenys hemoglobin subunit gamma-2-like (LOC100581638), mRNA
; fa_frame: r
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 84.9
; fa_bits: 20.9
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 15
; al_stop: 2
; al_display_start: 16
-----------------------------TTTTTTTTCCTTCTTC
>gi|332211534|ref|XM_003254825.1| ..
; sq_len: 805
; sq_offset: 1
; sq_type: D
; al_start: 634
; al_stop: 647
; al_display_start: 604
TAAGAGATCACACATGATTTTCTTCAGCTCTTTTTTTACATCTTTTTAAA
TATATGAGCCACAAAGGGTTTATATTGAGGGATGTGTGTATGTGTATTTC
TGCTGCCTGTGTGTGTTTGT
>>gi|23308614|ref|NM_152952.1| Danio rerio cytoglobin 1 (cygb1), mRNA
; fa_frame: f
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 70.2
; fa_bits: 20.9
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 2
; al_stop: 15
; al_display_start: 1
-----------------------------GAAGAAGGAAAAAAAA
>gi|23308614|ref|NM_152952.1| ..
; sq_len: 5188
; sq_offset: 1
; sq_type: D
; al_start: 3548
; al_stop: 3561
; al_display_start: 3518
AGTAATGAAATAATAAAAAAAACATAAAAAAATAAGTAAAAAAATAACAG
AAATAATAATAATGATAACAAAAATGGTAAAAGTAAATAAAACTAAAATA
TTGTACAAACAGTAGAAAAC
>>gi|297689475|ref|XM_002822130.1| PREDICTED: Pongo abelii hemoglobin subunit gamma-like (LOC100439631), mRNA
; fa_frame: r
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 82.0
; fa_bits: 20.9
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 17
; sq_type: D
; al_start: 15
; al_stop: 2
; al_display_start: 16
-----------------------------TTTTTTTTCCTTCTTC
>gi|297689475|ref|XM_002822130.1| ..
; sq_len: 1158
; sq_offset: 1
; sq_type: D
; al_start: 984
; al_stop: 997
; al_display_start: 954
TAAGAGATCACACATGCTTTTCTTCAGCTCTTTTTTTACATCTTTTTAAA
TATATGAGCCACAAACAGTTTATATTGAGGGATGTGTGTATGTGTATTTC
TGCTGCTTGTGTGTGTTTGT
>>gi|297689475|ref|XM_002822130.1| PREDICTED: Pongo abelii hemoglobin subunit gamma-like (LOC100439631), mRNA
; fa_frame: f
; fa_initn:  52
; fa_init1:  52
; fa_opt:  52
; fa_z-score: 82.0
; fa_bits: 20.9
; fa_expect:    1.4
; bs_ident: 0.857
; bs_sim: 0.857
; bs_overlap: 14
>gi|156718121 ..
; sq_len: 16
; sq_offset: 1
; sq_type: D
; al_start: 2
; al_stop: 15
; al_display_start: 1
------------------GAAGAAGGAAAAAAAA
>gi|297689475|ref|XM_002822130.1| ..
; sq_len: 1158
; sq_offset: 1
; sq_type: D
; al_start: 20
; al_stop: 33
; al_display_start: 1
CCTCACTGGAGCTAAAGACAAGAAGGTAAAAGAGGCTGACAAAAGAAGTC
CTGGTATCCTCTATGGTGGGAGAAGAAAACTAGGTAAAAGGAAGAATAAA
TTAGAGAAAAATTGGAACGA

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

130 residues in 3 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:  0.170 Total Display time:  0.010

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