Search to RefSeqBP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: RefSeq49_BP.fasta
33,088 sequences; 17,681,374 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_001035655.1| hypothetical protein LOC539395 [Bos taurus]. 94 2e-19
Alignment gi|XP_002685664.1| PREDICTED: collagen, type XVI, alpha 1 [Bos ... 49 6e-06
Alignment gi|XP_583549.3| PREDICTED: collagen, type XVI, alpha 1 [Bos tau... 49 6e-06
Alignment gi|NP_001070299.1| collagen alpha-1(III) chain [Bos taurus]. 49 8e-06
>ref|NP_001035655.1| hypothetical protein LOC539395 [Bos taurus].
Length = 218
Score = 93.6 bits (231), Expect = 2e-19
Identities = 52/77 (67%), Positives = 52/77 (67%)
Frame = +3
Query: 540 GRTGRSFSSRLQDSRSLDXXXXXXXXXXXXXXXEYXXXXXXXXTISSPLELEGTVSRHGD 719
GR GRSFSSRLQDSRSLD E TISSPLELEGTVSRHGD
Sbjct: 16 GRGGRSFSSRLQDSRSLDGLSGACGGPASSGGAESGAGGGRRATISSPLELEGTVSRHGD 75
Query: 720 LTHFVANNLQLKIRLSG 770
LTHFVANNLQLKIRLSG
Sbjct: 76 LTHFVANNLQLKIRLSG 92
>ref|XP_002685664.1| PREDICTED: collagen, type XVI, alpha 1 [Bos taurus].
Length = 1613
Score = 48.9 bits (115), Expect = 6e-06
Identities = 48/162 (29%), Positives = 61/162 (37%), Gaps = 6/162 (3%)
Frame = +3
Query: 24 EPPRPSQPGRTNSSVPAPNCGMESPRG---RPGPEADLLALGEQQAAIFGG--GPGRTPS 188
+P P PG+ +CG P+G RPG E + A+G Q G GP P
Sbjct: 1256 KPGHPGLPGQKG------DCGKPGPQGSSGRPGAEGEPGAMGPQGRPGPPGHVGPPGPPG 1309
Query: 189 EP-PAGLRLSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGAES 365
+P PAG+ G + G R P G P EP D + P G +
Sbjct: 1310 QPGPAGISAVGPKGDRGATG-ERGLLGLPGQPGPPGHPGPPGEPGMDGAAGKEGPPGKQG 1368
Query: 366 CLGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
G PGP+ D P P K + R G PGG G
Sbjct: 1369 LYGPPGPKGD---------PGPSGQKGQAGEKGRAGMPGGPG 1401
>ref|XP_583549.3| PREDICTED: collagen, type XVI, alpha 1 [Bos taurus].
Length = 1613
Score = 48.9 bits (115), Expect = 6e-06
Identities = 48/162 (29%), Positives = 61/162 (37%), Gaps = 6/162 (3%)
Frame = +3
Query: 24 EPPRPSQPGRTNSSVPAPNCGMESPRG---RPGPEADLLALGEQQAAIFGG--GPGRTPS 188
+P P PG+ +CG P+G RPG E + A+G Q G GP P
Sbjct: 1256 KPGHPGLPGQKG------DCGKPGPQGSSGRPGAEGEPGAMGPQGRPGPPGHVGPPGPPG 1309
Query: 189 EP-PAGLRLSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGAES 365
+P PAG+ G + G R P G P EP D + P G +
Sbjct: 1310 QPGPAGISAVGPKGDRGATG-ERGLLGLPGQPGPPGHPGPPGEPGMDGAAGKEGPPGKQG 1368
Query: 366 CLGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
G PGP+ D P P K + R G PGG G
Sbjct: 1369 LYGPPGPKGD---------PGPSGQKGQAGEKGRAGMPGGPG 1401
>ref|NP_001070299.1| collagen alpha-1(III) chain [Bos taurus].
Length = 1466
Score = 48.5 bits (114), Expect = 8e-06
Identities = 49/161 (30%), Positives = 59/161 (36%)
Frame = +3
Query: 9 TRPLKEPPRPSQPGRTNSSVPAPNCGMESPRGRPGPEADLLALGEQQAAIFGGGPGRTPS 188
T P+ P QPG S G+ PRG PG + G A F G PG+
Sbjct: 764 TGPIGPPGPAGQPGDKGESGAPGVPGIAGPRGGPGERGE---QGPPGPAGFPGAPGQN-G 819
Query: 189 EPPAGLRLSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGAESC 368
EP A GE A +G P A+ G P + + E G G P GA
Sbjct: 820 EPGA----KGERGAPGEKGEGGPPGAAGPAGGSGPAGPPGPQGVKGERGSPGGP-GAAGF 874
Query: 369 LGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
G GP P + NP PP A + G PG G
Sbjct: 875 PGGRGPPGPPGSN---GNPGPPGSSGAPGKDGPPGPPGSNG 912
Database: RefSeq49_BP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 17,681,374
Number of sequences in database: 33,088
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33088
Number of Hits to DB: 34,695,472
Number of extensions: 1242562
Number of successful extensions: 9984
Number of sequences better than 1.0e-05: 4
Number of HSP's gapped: 9475
Number of HSP's successfully gapped: 4
Length of query: 304
Length of database: 17,681,374
Length adjustment: 102
Effective length of query: 202
Effective length of database: 14,306,398
Effective search space: 2889892396
Effective search space used: 2889892396
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Animal-Genome cDNA 20110601C-014135
Search to RefSeqCP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: RefSeq49_CP.fasta
33,336 sequences; 18,874,504 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_850131.1| PREDICTED: hypothetical protein XP_845038 [Cani... 228 5e-60
Alignment gi|XP_544444.2| PREDICTED: similar to procollagen, type XVI, al... 50 4e-06
>ref|XP_850131.1| PREDICTED: hypothetical protein XP_845038 [Canis familiaris].
Length = 351
Score = 228 bits (582), Expect = 5e-60
Identities = 138/236 (58%), Positives = 146/236 (61%), Gaps = 8/236 (3%)
Frame = +3
Query: 87 MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA 266
MES RGRPGPEADL A GEQQAA++GGGPGR PSEPP+GL S + EAENV G RHP A
Sbjct: 1 MESSRGRPGPEADLPAPGEQQAALWGGGPGRAPSEPPSGLPPSAQGEAENVGGARRHPAA 60
Query: 267 SPKPSGCSFVHRPEREPR-EDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDK 443
SPK VHR ERE R +DE GRRGTPS APG ++PEPPE +
Sbjct: 61 SPKTPSRGAVHRAEREARDDDESGRRGTPS-------APG----SRAGEACEDPEPPEAE 109
Query: 444 PASERVCRRGSPGGGGM--XXXXXXXXXXXXXXXGRTGRSFSSRLQDSRSLD-----XXX 602
PASER CRRGS GGGGM GR GRSFSSRLQDSRSLD
Sbjct: 110 PASERGCRRGSAGGGGMEAEPREGDEEEEEAAAAGRAGRSFSSRLQDSRSLDGLSGACGG 169
Query: 603 XXXXXXXXXXXXEYXXXXXXXXTISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 770
E TISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG
Sbjct: 170 GGGGGAGSAGGAEPGAGSGRRATISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 225
>ref|XP_544444.2| PREDICTED: similar to procollagen, type XVI, alpha 1 [Canis
familiaris].
Length = 1502
Score = 49.7 bits (117), Expect = 4e-06
Identities = 52/164 (31%), Positives = 65/164 (39%), Gaps = 12/164 (7%)
Frame = +3
Query: 36 PSQPGRT-NSSVPAP--NCGMESP---RGRPGPEADLLALGEQQAAIFGG--GPGRTPSE 191
P G+T + +P P +CG P GRPG E + A+G Q G GP P +
Sbjct: 1140 PGFKGKTGHPGLPGPKGDCGKPGPPGSSGRPGAEGEPGAMGPQGRPGPPGHIGPPGPPGQ 1199
Query: 192 P-PAGLR---LSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGA 359
P PAG+ L G+ A G P P P G P EP D + P G
Sbjct: 1200 PGPAGISAMGLKGDRGATGERGLLGLP-GQPGPPGHP---GPPGEPGADGAAGKEGPPGK 1255
Query: 360 ESCLGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
+ G PGP+ D P P K + R G PGG G
Sbjct: 1256 QGLYGPPGPKGD---------PGPSGQKGQAGEKGRAGMPGGPG 1290
Database: RefSeq49_CP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,874,504
Number of sequences in database: 33,336
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33336
Number of Hits to DB: 36,193,751
Number of extensions: 1277418
Number of successful extensions: 10238
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 9785
Number of HSP's successfully gapped: 2
Length of query: 304
Length of database: 18,874,504
Length adjustment: 102
Effective length of query: 202
Effective length of database: 15,474,232
Effective search space: 3125794864
Effective search space used: 3125794864
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqSP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: RefSeq49_SP.fasta
24,897 sequences; 11,343,932 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|XP_003358326.1| PREDICTED: uncharacterized protein C17orf59 ... 379 e-105
Alignment gi|XP_003127801.1| PREDICTED: LOW QUALITY PROTEIN: collagen alp... 50 1e-06
Alignment gi|XP_003361043.1| PREDICTED: collagen alpha-1(II) chain-like, ... 49 5e-06
>ref|XP_003358326.1| PREDICTED: uncharacterized protein C17orf59 homolog [Sus scrofa].
Length = 354
Score = 379 bits (973), Expect = e-105
Identities = 190/228 (83%), Positives = 190/228 (83%)
Frame = +3
Query: 87 MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA 266
MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA
Sbjct: 1 MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA 60
Query: 267 SPKPSGCSFVHRPEREPREDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDKP 446
SPKPSGCSFVHRPEREPREDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDKP
Sbjct: 61 SPKPSGCSFVHRPEREPREDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDKP 120
Query: 447 ASERVCRRGSPGGGGMXXXXXXXXXXXXXXXGRTGRSFSSRLQDSRSLDXXXXXXXXXXX 626
ASERVCRRGSPGGGGM GRTGRSFSSRLQDSRSLD
Sbjct: 121 ASERVCRRGSPGGGGMDVEQEKEDDEEEAAAGRTGRSFSSRLQDSRSLDGLSGACGGSGS 180
Query: 627 XXXXEYXXXXXXXXTISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 770
EY TISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG
Sbjct: 181 AGGAEYGPGGGRRATISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 228
>ref|XP_003127801.1| PREDICTED: LOW QUALITY PROTEIN: collagen alpha-1(XVI) chain-like [Sus
scrofa].
Length = 1618
Score = 50.4 bits (119), Expect = 1e-06
Identities = 50/164 (30%), Positives = 62/164 (37%), Gaps = 9/164 (5%)
Frame = +3
Query: 27 PPRPSQPGRTNSSVPAPNCGMESP---RGRPGPEADLLALGEQQAAIFGG--GPGRTPSE 191
P +PG P +CG P GRPG E + A+G Q G GP P +
Sbjct: 1256 PGFKGKPGHPGLPGPKGDCGKPGPPGSSGRPGAEGEPGAMGPQGRPGPPGHIGPPGPPGQ 1315
Query: 192 P-PAGLR---LSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGA 359
P PAG+ L G+ + G P P P G P EP D + P G
Sbjct: 1316 PGPAGISAVGLKGDRGSPGERGLLGLP-GQPGPPGHP---GPPGEPGMDGAAGKEGPPGK 1371
Query: 360 ESCLGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
+ G PGP+ D P P K + R G PGG G
Sbjct: 1372 QGLYGPPGPKGD---------PGPSGQKGQAGEKGRAGMPGGPG 1406
>ref|XP_003361043.1| PREDICTED: collagen alpha-1(II) chain-like, partial [Sus scrofa].
Length = 1540
Score = 48.5 bits (114), Expect = 5e-06
Identities = 55/183 (30%), Positives = 64/183 (34%), Gaps = 21/183 (11%)
Frame = +3
Query: 6 STRPLKEPPRPSQPGRTNSSVPAPNCGMESPRGRPGPEADLLALGEQQAAIFGGGPGRTP 185
S P+ P + GRT PA G G+PGP +G F G PG
Sbjct: 402 SPGPMGPRGLPGERGRTG---PAGAAGARGNDGQPGPAGPPGPVGPAGGPGFPGAPGAKG 458
Query: 186 SEPPAGLRLSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGAES 365
P G R G E A+ G +P SP P+G S P + G G P G
Sbjct: 459 EAGPTGAR--GPEGAQGPRGEPGNP-GSPGPAGAS--GNPGTDGIPGAKGSAGAP-GIAG 512
Query: 366 CLGAPGPEHDP-----------------HGSLRLKNPEPP--EDKPASERVCR--RGSPG 482
G PGP P G K + P E PA E R RG PG
Sbjct: 513 APGFPGPRGPPGPQGATGPLGPKGQTGEPGIAGFKGEQGPKGEPGPAGEEGKRGARGEPG 572
Query: 483 GGG 491
G G
Sbjct: 573 GAG 575
Database: RefSeq49_SP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 11,343,932
Number of sequences in database: 24,897
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24897
Number of Hits to DB: 22,744,941
Number of extensions: 840977
Number of successful extensions: 6764
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 6285
Number of HSP's successfully gapped: 3
Length of query: 304
Length of database: 11,343,932
Length adjustment: 99
Effective length of query: 205
Effective length of database: 8,879,129
Effective search space: 1820221445
Effective search space used: 1820221445
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 33 (17.3 bits)
Search to RefSeqMP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: RefSeq49_MP.fasta
30,036 sequences; 15,617,559 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_082281.2| hypothetical protein LOC71923 [Mus musculus]. 217 1e-56
Alignment gi|NP_082542.3| collagen alpha-1(XVI) chain precursor [Mus musc... 49 7e-06
Alignment gi|NP_031768.2| collagen alpha-1(I) chain precursor [Mus muscul... 49 7e-06
>ref|NP_082281.2| hypothetical protein LOC71923 [Mus musculus].
Length = 360
Score = 217 bits (552), Expect = 1e-56
Identities = 126/234 (53%), Positives = 138/234 (58%), Gaps = 6/234 (2%)
Frame = +3
Query: 87 MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA 266
ME+ +GR GPE +L E QAA F G P RTPS+PP+ LSGEEEAE+V +SRHPRA
Sbjct: 1 MEAAQGRLGPEPELSVGAEHQAATFSGRPSRTPSKPPSVRTLSGEEEAESVGVSSRHPRA 60
Query: 267 SPKPSGCSFVHRPEREPREDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDKP 446
SPK S H PE + ED+ R TPSGA G PG EH P S PEP ED+P
Sbjct: 61 SPKTWSGSIAHGPELDTWEDKPSSRATPSGARGRRGVPGSEHAPPPSSWYPEPEPSEDQP 120
Query: 447 ASERVCRRGSPGGGGM------XXXXXXXXXXXXXXXGRTGRSFSSRLQDSRSLDXXXXX 608
++ RVCRRGSPGG M GR GRSF SRLQDSRSLD
Sbjct: 121 SALRVCRRGSPGGVEMNVELPQQEGDDDDDEDEEAAAGRAGRSFPSRLQDSRSLDGLSGA 180
Query: 609 XXXXXXXXXXEYXXXXXXXXTISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 770
E TISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG
Sbjct: 181 CGGGGSSSSGETGAGGGRRATISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 234
>ref|NP_082542.3| collagen alpha-1(XVI) chain precursor [Mus musculus].
Length = 1580
Score = 48.5 bits (114), Expect = 7e-06
Identities = 50/161 (31%), Positives = 62/161 (38%), Gaps = 9/161 (5%)
Frame = +3
Query: 36 PSQPGRT-NSSVPAP--NCGMESP---RGRPGPEADLLALGEQQAAIFGGGPGRT--PSE 191
P G+T + +P P +CG P GRPG E + A+G Q G PG P +
Sbjct: 1221 PGFKGKTGHPGLPGPKGDCGKPGPPGSSGRPGAEGEPGAMGPQGRP---GPPGHLGPPGQ 1277
Query: 192 P-PAGLRLSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGAESC 368
P P GL G + V G R P G P EP D + P G +
Sbjct: 1278 PGPPGLSTVGLKGDRGVPG-ERGLAGLPGQPGTPGHPGPPGEPGSDGAAGKEGPPGKQGL 1336
Query: 369 LGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
G PGP+ D P P K + R G PGG G
Sbjct: 1337 YGPPGPKGD---------PGPAGQKGQAGEKGRSGMPGGPG 1368
>ref|NP_031768.2| collagen alpha-1(I) chain precursor [Mus musculus].
Length = 1453
Score = 48.5 bits (114), Expect = 7e-06
Identities = 50/167 (29%), Positives = 62/167 (37%), Gaps = 8/167 (4%)
Frame = +3
Query: 15 PLKEPPRPSQPGRTNSSVPAPNCGMESPRGRPGPEADLLALGEQQAAIFGGGPGRT-PSE 191
P EP P + G P G+ RGRPGP A G A G PG T P+
Sbjct: 274 PKGEPGSPGENGAPGQMGPR---GLPGERGRPGPPGTAGARGNDGAVGAAGPPGPTGPTG 330
Query: 192 P---PAGLRLSGEEEAENVEGTS--RHPRASPKPSGCSFVHRPEREPREDELGRRGTPSG 356
P P + GE + G+ + R P P G + P P G G P G
Sbjct: 331 PPGFPGAVGAKGEAGPQGARGSEGPQGVRGEPGPPGPAGAAGPAGNP-----GADGQP-G 384
Query: 357 AESCLGAPGPEHDP--HGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
A+ GAPG P G+ P+ P P + G PG G
Sbjct: 385 AKGANGAPGIAGAPGFPGARGPSGPQGPSGPPGPKG--NSGEPGAPG 429
Database: RefSeq49_MP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 15,617,559
Number of sequences in database: 30,036
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 30036
Number of Hits to DB: 28,969,084
Number of extensions: 960082
Number of successful extensions: 6825
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 6463
Number of HSP's successfully gapped: 3
Length of query: 304
Length of database: 15,617,559
Length adjustment: 101
Effective length of query: 203
Effective length of database: 12,583,923
Effective search space: 2554536369
Effective search space used: 2554536369
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to RefSeqHP_Rel49
BLASTX 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: RefSeq49_HP.fasta
32,964 sequences; 18,297,164 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Alignment gi|NP_060092.2| hypothetical protein LOC54785 [Homo sapiens]. 269 2e-72
Alignment gi|NP_001847.3| collagen alpha-1(XVI) chain precursor [Homo sap... 49 8e-06
>ref|NP_060092.2| hypothetical protein LOC54785 [Homo sapiens].
Length = 357
Score = 269 bits (688), Expect = 2e-72
Identities = 145/229 (63%), Positives = 154/229 (67%), Gaps = 1/229 (0%)
Frame = +3
Query: 87 MESPRGRPGPEADLLALGEQQAAIFGGGPGRTPSEPPAGLRLSGEEEAENVEGTSRHPRA 266
MES RGRPGPE DLLA+ E QA +FGGGPGRT SEPPAGLR+SGEEE ENV G +RHPR
Sbjct: 1 MESSRGRPGPETDLLAVAEHQALVFGGGPGRTSSEPPAGLRVSGEEETENVGGANRHPRT 60
Query: 267 SPKPSGCSFVHRPEREPREDELGRRGTPSGAESCLGAPGPEHDPHGSLRLKNPEPPEDKP 446
SPK S C VHRPERE E+E G +GT SGA S GAPG EH+P S R KNP PPE KP
Sbjct: 61 SPKTSSCGVVHRPEREALENEPGPQGTLSGAGSRRGAPGAEHEPSLSSRHKNPAPPEGKP 120
Query: 447 ASERVCRRGSPGGG-GMXXXXXXXXXXXXXXXGRTGRSFSSRLQDSRSLDXXXXXXXXXX 623
+S R CRRG PGGG + R GRSFSSRLQDSRSLD
Sbjct: 121 SSGRDCRRGGPGGGMDVEQQEEEDNDEEAAAGSRAGRSFSSRLQDSRSLDGLSEACGGAG 180
Query: 624 XXXXXEYXXXXXXXXTISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 770
E TISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG
Sbjct: 181 SSGSAESGAGGGRRATISSPLELEGTVSRHGDLTHFVANNLQLKIRLSG 229
>ref|NP_001847.3| collagen alpha-1(XVI) chain precursor [Homo sapiens].
Length = 1604
Score = 48.5 bits (114), Expect = 8e-06
Identities = 51/164 (31%), Positives = 66/164 (40%), Gaps = 12/164 (7%)
Frame = +3
Query: 36 PSQPGRT-NSSVPAP--NCGMESP---RGRPGPEADLLALGEQQAAIFGG--GPGRTPSE 191
P G+T + +P P +CG P GRPG E + A+G Q G GP P +
Sbjct: 1242 PGFKGKTGHPGLPGPKGDCGKPGPPGSTGRPGAEGEPGAMGPQGRPGPPGHVGPPGPPGQ 1301
Query: 192 P-PAGLR---LSGEEEAENVEGTSRHPRASPKPSGCSFVHRPEREPREDELGRRGTPSGA 359
P PAG+ L G+ A G + P P P G P EP D + P G
Sbjct: 1302 PGPAGISAVGLKGDRGATGERGLAGLP-GQPGPPGHP---GPPGEPGTDGAAGKEGPPGK 1357
Query: 360 ESCLGAPGPEHDPHGSLRLKNPEPPEDKPASERVCRRGSPGGGG 491
+ G PGP+ DP + K + R G PGG G
Sbjct: 1358 QGFYGPPGPKGDPGAA---------GQKGQAGEKGRAGMPGGPG 1392
Database: RefSeq49_HP.fasta
Posted date: Oct 17, 2011 1:42 PM
Number of letters in database: 18,297,164
Number of sequences in database: 32,964
Lambda K H
0.318 0.134 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 32964
Number of Hits to DB: 35,013,954
Number of extensions: 1205455
Number of successful extensions: 9302
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 8737
Number of HSP's successfully gapped: 2
Length of query: 304
Length of database: 18,297,164
Length adjustment: 102
Effective length of query: 202
Effective length of database: 14,934,836
Effective search space: 3016836872
Effective search space used: 3016836872
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 34 (17.7 bits)
Search to Sscrofa10_2
BLASTN 2.2.24 [Aug-08-2010]
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.
Query= 20110601C-014135
(914 letters)
Database: Sscrofa_10.2.fasta
4582 sequences; 2,808,509,378 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Sscrofa_Chr12 1463 0.0
>Sscrofa_Chr12
|| Length = 63588571
Score = 1463 bits (738), Expect = 0.0
Identities = 862/916 (94%), Gaps = 3/916 (0%)
Strand = Plus / Minus
Query: 1 gcgcctctaca-cgccccttaaaggagccgccaaggccttcccagccggggcgaaccaat 59
||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881430 gcgcctctacaacgccccttaaaggagccgccaaggccttcccagccggggcgaaccaat 55881371
Query: 60 tcctcggttcctgcccccaactgcggtatggagtcgcctcgggggcggcctgggcccgag 119
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881370 tcctcggttcctgcccccaactgcggtatggagtcgcctcgggggcggcctgggcccgag 55881311
Query: 120 gcggaccttctggctctaggagaacagcaagccgcgatcttcggcggcggcccgggccga 179
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881310 gcggaccttctggctctaggagaacagcaagccgcgatcttcggcggcggcccgggccga 55881251
Query: 180 acgccctctgagccgcccgcaggcctccggctgtccggagaggaagaggccgagaacgtt 239
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881250 acgccctctgagccgcccgcaggcctccggctgtccggagaggaagaggccgagaacgtt 55881191
Query: 240 gagggcacgagccgccaccccagggcgtccccaaagccttcgggctgcagcttcgtccac 299
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881190 gagggcacgagccgccaccccagggcgtccccaaagccttcgggctgcagcttcgtccac 55881131
Query: 300 cggccggaacgggagcctcgggaggatgagctgggccggcgagggaccccttctggggca 359
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881130 cggccggaacgggagcctcgggaggatgagctgggccggcgagggaccccttctggggca 55881071
Query: 360 gagagctgcctgggggcgccgggtcccgagcatgatccgcatgggtccttgcggctcaag 419
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881070 gagagctgcctgggggcgccgggtcccgagcatgatccgcatgggtccttgcggctcaag 55881011
Query: 420 aaccctgagccgccagaggacaagcctgcatctgagagggtctgccgtcgggggagccct 479
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55881010 aaccctgagccgccagaggacaagcctgcatctgagagggtctgccgtcgggggagccct 55880951
Query: 480 ggaggcggcgggatggatgttgagcaggagaaggaagacgatgaggaggaggcggcagcc 539
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880950 ggaggcggcgggatggatgttgagcaggagaaggaagacgatgaggaggaggcggcagcc 55880891
Query: 540 ggcaggactggccgttcgttctccagccgccttcaggacagccgcagcctggacgggctg 599
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880890 ggcaggactggccgttcgttctccagccgccttcaggacagccgcagcctggacgggctg 55880831
Query: 600 agcggggcgtgcggaggctccgggtccgcagggggtgccgagtatnnnnnnnnnnnnnnn 659
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880830 agcggggcgtgcggaggctccgggtccgcagggggtgccgagtatggcccgggcggcggg 55880771
Query: 660 nnnnnnnnnaccatctccagccccctggagctcgagggcacggtgagccgccatggcgac 719
|||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880770 cggcgcgccaccatctccagccccctggagctcgagggcacggtgagccgccatggcgac 55880711
Query: 720 ctcacccactttgtcgccaacaatctgcaactgaagatccgtctgagcggcgnnnnnnnn 779
||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880710 ctcacccactttgtcgccaacaatctgcaactgaagatccgtctgagcggcgcccctcaa 55880651
Query: 780 nnnnnnnnnnnnnnnnntgcgcggccctgttcagctccgacacccactccggccatccct 839
|||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55880650 cccccgccccctgcccctgcgcggccctgttcagctccgacacccactccggccatccct 55880591
Query: 840 cccatcgatcccgacgtgctgcgggacctggagcggctgaatcgggnagctgggc-gcag 898
|||||||||||||||||||||||||||||||||||||||| ||||| |||||||| ||||
Sbjct: 55880590 cccatcgatcccgacgtgctgcgggacctggagcggctgagtcggg-agctgggcggcag 55880532
Query: 899 gntggaccgtctgctt 914
| ||||||||||||||
Sbjct: 55880531 ggtggaccgtctgctt 55880516
Database: Sscrofa_10.2.fasta
Posted date: Nov 16, 2011 10:34 AM
Number of letters in database: 2,808,509,378
Number of sequences in database: 4582
Lambda K H
1.37 0.711 1.31
Gapped
Lambda K H
1.37 0.711 1.31
Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 4582
Number of Hits to DB: 15,922,502
Number of extensions: 109
Number of successful extensions: 109
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 109
Number of HSP's successfully gapped: 3
Length of query: 914
Length of database: 2,808,509,378
Length adjustment: 21
Effective length of query: 893
Effective length of database: 2,808,413,156
Effective search space: 2507912948308
Effective search space used: 2507912948308
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
X3: 50 (99.1 bits)
S1: 18 (36.2 bits)
S2: 29 (58.0 bits)