TBLASTN 2.2.17 [Aug-26-2007]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,
Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005.
Query= sla/lp_dsp
(448 letters)
Database: genoma.fa
14 sequences; 23,462,190 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Plasmodium_knowlesi_strain_H|PK4.chr13|2007-02-22|ds-DNA|Plasmod... 241 7e-64
Plasmodium_knowlesi_strain_H|chr02|2007-02-22|ds-DNA|Plasmodium_... 35 0.081
Plasmodium_knowlesi_strain_H|PK4.chr06|2007-02-22|ds-DNA|Plasmod... 30 2.8
Plasmodium_knowlesi_strain_H|PK4.chr12.pseudo|2007-02-22|ds-DNA|... 28 9.2
>Plasmodium_knowlesi_strain_H|PK4.chr13|2007-02-22|ds-
DNA|Plasmodium_knowlesi_Sanger
Length = 2200295
Score = 241 bits (615), Expect = 7e-64, Method: Composition-based stats.
Identities = 139/383 (36%), Positives = 206/383 (53%), Gaps = 41/383 (10%)
Frame = -2
Query: 65 NYPHKVGLGEREARIACKLVARRHYNFGHGIGR--------------------------- 97
N V +GERE RI LV ++ FGHGIGR
Sbjct: 151777 NSEKNVKIGERENRIYSALVRNKYIGFGHGIGR*AARSAHTHMNGCVRIYTSI*TLIRGF 151598
Query: 98 ---------SGDLLEAQPKAAGSTLLARLTNALILDLIRGIGLPSCAGCFLVPMCTGMTL 148
SG+L + QPK+AG+++LA+ T + + DLIR G+ C +++P TGM L
Sbjct: 151597 LTQLCPLRRSGNLDDVQPKSAGNSILAKATTSFVKDLIRSFGIKGCEDVYILPYATGMCL 151418
Query: 149 TLCLQSLRKRRPGARYVLWSRIDQKSCFKAITATGLVPVVIPCLIKGESLNTNVDLFREK 208
+ CL +K R + YV+ SRID K+C+K I L +V+ + K E L TN++
Sbjct: 151417 STCLLYTKKEREKSEYVIVSRIDHKTCYKCIDFCALKYLVVDMVYKDEELFTNLNEIERL 151238
Query: 209 IKSLGVDSILCLYTTTSCFAPRNSDDIAEVSKLSKQWQIPHLVNNAYGLQAKEIVNQLE- 267
I++ G + I C+ + TS +APRNSDDI +++ + K++ +PH++NNA+GLQ + +++
Sbjct: 151237 IQTYG-EKICCVMSVTSSYAPRNSDDIVKIAHICKRYNVPHIINNAFGLQCNYLCKEIQK 151061
Query: 268 CANRVGRIDYFVQSSDKNLLVPVGSAIVASFNESVLHDVASTYAGRASGSQSLDVLMTLL 327
C GR+D+ VQS DKN LVPV IV S ++ + ++ Y GR LD+ +TLL
Sbjct: 151060 CFESKGRVDFVVQSCDKNFLVPVNGGIVFSSDKKKMKELKKHYPGRTPVHAYLDLFITLL 150881
Query: 328 SLGRNGFRLLFDQRGENFNYLRENLRKFAEPRGEIVIDSRFNSISLAITLATLAGD---- 383
LG+ L +R ENF++L+E + +I + N IS+AI L L
Sbjct: 150880 ELGKKKILNLRKEREENFSWLQEKVSTLCSKYNLTLIKASKNKISMAINLNELYNICHIL 150701
Query: 384 QMKSITKLGSMLHMRGVSGARVI 406
KSIT LGS+L R V+G RVI
Sbjct: 150700 NPKSITLLGSLLFYRNVTGHRVI 150632
>Plasmodium_knowlesi_strain_H|chr02|2007-02-22|ds-
DNA|Plasmodium_knowlesi_Sanger
Length = 726886
Score = 35.0 bits (79), Expect = 0.081, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 26/55 (47%)
Frame = -1
Query: 194 KGESLNTNVDLFREKIKSLGVDSILCLYTTTSCFAPRNSDDIAEVSKLSKQWQIP 248
KG ++ T FR + S +C+ S FAP N ++AEV K K+ P
Sbjct: 347419 KGATVRTQCSFFRWDK*TFFFQSTMCIIVEGSVFAPLNVQNVAEVEKEYKKGNYP 347255
>Plasmodium_knowlesi_strain_H|PK4.chr06|2007-02-22|ds-
DNA|Plasmodium_knowlesi_Sanger
Length = 1053092
Score = 30.0 bits (66), Expect = 2.8, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 29/58 (50%)
Frame = -1
Query: 127 RGIGLPSCAGCFLVPMCTGMTLTLCLQSLRKRRPGARYVLWSRIDQKSCFKAITATGL 184
R + P+ LVP+C G+ TL SL +RRP Y +R+ C A T++ +
Sbjct: 537167 RRVVKPTKTTSSLVPICDGLV*TLRT*SLFRRRPSCLYQCGTRMFCGIC*MATTSSAV 536994
>Plasmodium_knowlesi_strain_H|PK4.chr12.pseudo|2007-02-22|ds-
DNA|Plasmodium_knowlesi_Sanger
Length = 3128370
Score = 28.1 bits (61), Expect = 9.2, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Frame = +2
Query: 64 NNYPHKVGLGEREARIACKLVARRHYNFGHGIGRSG----DLLEAQPKAA 109
++Y H V L + I + +R++ F HG+G SG LL+ P A
Sbjct: 922238 SSYLHGVNLQPTQLFIKMFFIRKRYFGFSHGLGISGVIHRRLLKEVPNCA 922387
Database: genoma.fa
Posted date: Mar 7, 2008 11:49 AM
Number of letters in database: 23,462,190
Number of sequences in database: 14
Lambda K H
0.320 0.136 0.403
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 14
Number of Hits to DB: 11,817,076
Number of extensions: 175379
Number of successful extensions: 835
Number of sequences better than 10.0: 5
Number of HSP's gapped: 832
Number of HSP's successfully gapped: 6
Length of query: 448
Length of database: 7,820,730
Length adjustment: 101
Effective length of query: 347
Effective length of database: 7,819,316
Effective search space: 2713302652
Effective search space used: 2713302652
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (28.1 bits)
# TBLASTN 2.2.17 [Aug-26-2007]
# Query: sla/lp_dsp
# Database: genoma.fa
# Fields: Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score
sla/lp_dsp Plasmodium_knowlesi_strain_H|PK4.chr13|2007-02-22|ds-DNA|Plasmodium_knowlesi_Sanger 36.29 383 203 4 65 406 151777 150632 7e-64 241
sla/lp_dsp Plasmodium_knowlesi_strain_H|chr02|2007-02-22|ds-DNA|Plasmodium_knowlesi_Sanger 32.73 55 37 0 194 248 347419 347255 0.081 35.0
sla/lp_dsp Plasmodium_knowlesi_strain_H|PK4.chr06|2007-02-22|ds-DNA|Plasmodium_knowlesi_Sanger 32.76 58 39 0 127 184 537167 536994 2.8 30.0
sla/lp_dsp Plasmodium_knowlesi_strain_H|PK4.chr12.pseudo|2007-02-22|ds-DNA|Plasmodium_knowlesi_Sanger 32.00 50 30 1 64 109 922238 922387 9.2 28.1
