BLASTN 2.2.10 [Oct-19-2004]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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= QCM3d10.yg.2.1
(683 letters)
Database: Pinus_nucl_with_EST.fasta
355,925 sequences; 217,277,237 total letters
Score E
Sequences producing significant alignments: (bits) Value
gb|CO197733.1|CO197733 GEO1_8_E04.g1_A029 Root gravitropism... 62 3e-008
gb|DN610972.1|DN610972 EST964022 Subtracted pine embryo lib... 42 0.029
gb|DR687879.1|DR687879 EST1077962 Normalized pine embryo li... 42 0.029
gb|DT627908.1|DT627908 EST1156657 Subtracted pine embryo li... 42 0.029
dbj|BD236453.1| Materials and method for modification of pl... 42 0.029
gb|DN609701.1|DN609701 EST962751 Subtracted pine embryo lib... 40 0.12
dbj|BD236455.1| Materials and method for modification of pl... 40 0.12
gb|BQ107573.1|BQ107573 NXLV099_D06_F NXLV (Nsf Xylem Late w... 38 0.46
gb|BQ196928.1|BQ196928 NXLV107_B12_F NXLV (Nsf Xylem Late w... 38 0.46
gb|CO169002.1|CO169002 NDL1_4_A12.b1_A029 Needles control P... 38 0.46
gb|CO169065.1|CO169065 NDL1_4_A12.g1_A029 Needles control P... 38 0.46
gb|CX650196.1|CX650196 COLD1_44_D02.b1_A029 Root cold Pinus... 38 0.46
gb|CX650274.1|CX650274 COLD1_44_D02.g1_A029 Root cold Pinus... 38 0.46
gb|DR057513.1|DR057513 RTNIT1_6_F04.b1_A029 Roots minus nit... 38 0.46
gb|DR057602.1|DR057602 RTNIT1_6_F04.g1_A029 Roots minus nit... 38 0.46
gb|DR078877.1|DR078877 RTFEPL1_7_A03.g1_A029 Roots plus add... 38 0.46
gb|DR742058.1|DR742058 RTCU1_1_A10.g1_A029 Roots plus added... 38 0.46
>gb|CO197733.1|CO197733 GEO1_8_E04.g1_A029 Root gravitropism April 2003 test Pinus taeda
cDNA clone GEO1_8_E04_A029 5', mRNA sequence
Length = 642
Score = 61.9 bits (31), Expect = 3e-008
Identities = 61/71 (85%)
Strand = Plus / Plus
Query: 427 attgataaatatgatctatatggacaagtggcataccccaagcaccataagcaatctgaa 486
||||| |||||||||||||||||| |||||||||| || || || || || ||||| |||
Sbjct: 365 attgacaaatatgatctatatggagaagtggcatatcctaaacatcacaaacaatcagaa 424
Query: 487 gttcctgatat 497
||| |||||||
Sbjct: 425 gttgctgatat 435
Score = 40.1 bits (20), Expect = 0.12
Identities = 50/60 (83%)
Strand = Plus / Plus
Query: 256 gctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagcatttggtgaa 315
||||||||||| || ||||| |||||||| || | ||| ||||||| || |||||||||
Sbjct: 194 gctcttgctcgacctgatcccaagaagaacatggccactttagtcaaggcttttggtgaa 253
>gb|DN610972.1|DN610972 EST964022 Subtracted pine embryo library, Lib_B Pinus taeda cDNA
clone PSAAW26, mRNA sequence
Length = 689
Score = 42.1 bits (21), Expect = 0.029
Identities = 54/65 (83%)
Strand = Plus / Plus
Query: 247 atgattcttgctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagca 306
|||||||||||| | | || || ||||| || || ||| |||||||||||||||||||
Sbjct: 298 atgattcttgctttatcacgacctgatcccaaaaaaaatctcactactctagtcaaagcg 357
Query: 307 tttgg 311
|||||
Sbjct: 358 tttgg 362
Score = 40.1 bits (20), Expect = 0.12
Identities = 74/92 (80%)
Strand = Plus / Plus
Query: 430 gataaatatgatctatatggacaagtggcataccccaagcaccataagcaatctgaagtt 489
||||||||||| | ||||| ||||| || || || ||||| || |||||||| || |||
Sbjct: 481 gataaatatgacttgtatgggcaagttgcttatccaaagcatcacaagcaatcagatgtt 540
Query: 490 cctgatatttatcgtttagctgcgagaacaaa 521
|| |||||||| ||| | ||||| | ||||||
Sbjct: 541 ccagatatttaccgtcttgctgcaaaaacaaa 572
>gb|DR687879.1|DR687879 EST1077962 Normalized pine embryo library, Lib_D Pinus taeda cDNA
clone PWABX65 3' end, mRNA sequence
Length = 746
Score = 42.1 bits (21), Expect = 0.029
Identities = 54/65 (83%)
Strand = Plus / Plus
Query: 247 atgattcttgctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagca 306
|||||||||||| | | || || ||||| || || ||| |||||||||||||||||||
Sbjct: 20 atgattcttgctttatcacgacctgatcccaaaaaaaatctcactactctagtcaaagcg 79
Query: 307 tttgg 311
|||||
Sbjct: 80 tttgg 84
>gb|DT627908.1|DT627908 EST1156657 Subtracted pine embryo library, Lib_B Pinus taeda cDNA
clone PIMCS08 5' end, mRNA sequence
Length = 690
Score = 42.1 bits (21), Expect = 0.029
Identities = 54/65 (83%)
Strand = Plus / Minus
Query: 247 atgattcttgctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagca 306
|||||||||||| | | || || ||||| || || ||| |||||||||||||||||||
Sbjct: 393 atgattcttgctttatcacgacctgatcccaaaaaaaatctcactactctagtcaaagcg 334
Query: 307 tttgg 311
|||||
Sbjct: 333 tttgg 329
Score = 40.1 bits (20), Expect = 0.12
Identities = 74/92 (80%)
Strand = Plus / Minus
Query: 430 gataaatatgatctatatggacaagtggcataccccaagcaccataagcaatctgaagtt 489
||||||||||| | ||||| ||||| || || || ||||| || |||||||| || |||
Sbjct: 210 gataaatatgacttgtatgggcaagttgcttatccaaagcatcacaagcaatcagatgtt 151
Query: 490 cctgatatttatcgtttagctgcgagaacaaa 521
|| |||||||| ||| | ||||| | ||||||
Sbjct: 150 ccagatatttaccgtcttgctgcaaaaacaaa 119
>dbj|BD236453.1| Materials and method for modification of plant cell wall
polysaccharides
Length = 415
Score = 42.1 bits (21), Expect = 0.029
Identities = 24/25 (96%)
Strand = Plus / Plus
Query: 287 tcactactctagtcaaagcatttgg 311
||||||||||||||||||| |||||
Sbjct: 237 tcactactctagtcaaagcgtttgg 261
>gb|DN609701.1|DN609701 EST962751 Subtracted pine embryo library, Lib_B Pinus taeda cDNA
clone PSAAG13, mRNA sequence
Length = 545
Score = 40.1 bits (20), Expect = 0.12
Identities = 74/92 (80%)
Strand = Plus / Plus
Query: 430 gataaatatgatctatatggacaagtggcataccccaagcaccataagcaatctgaagtt 489
||||||||||| | ||||| ||||| || || || ||||| || |||||||| || |||
Sbjct: 337 gataaatatgacttgtatgggcaagttgcttatccaaagcatcacaagcaatcagatgtt 396
Query: 490 cctgatatttatcgtttagctgcgagaacaaa 521
|| |||||||| ||| | ||||| | ||||||
Sbjct: 397 ccagatatttaccgtcttgctgcaaaaacaaa 428
Score = 38.2 bits (19), Expect = 0.46
Identities = 49/59 (83%)
Strand = Plus / Plus
Query: 247 atgattcttgctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagc 305
|||||||||||| | | || || ||||| || || ||| |||||||||||||||||||
Sbjct: 154 atgattcttgctttatcacgacctgatcccaaaaaaaatctcactactctagtcaaagc 212
>dbj|BD236455.1| Materials and method for modification of plant cell wall
polysaccharides
Length = 304
Score = 40.1 bits (20), Expect = 0.12
Identities = 50/60 (83%)
Strand = Plus / Plus
Query: 256 gctcttgctcgtccggatccgaagaagaatatcactactctagtcaaagcatttggtgaa 315
||||||||||| || ||||| |||||||| || | ||| ||||||| || |||||||||
Sbjct: 222 gctcttgctcgacctgatcccaagaagaacatggccactttagtcaaggcttttggtgaa 281
>gb|BQ107573.1|BQ107573 NXLV099_D06_F NXLV (Nsf Xylem Late wood Vertical) Pinus taeda cDNA
clone NXLV099_D06 5', mRNA sequence
Length = 443
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 225 aggaaggaaatggagatgg 243
>gb|BQ196928.1|BQ196928 NXLV107_B12_F NXLV (Nsf Xylem Late wood Vertical) Pinus taeda cDNA
clone NXLV107_B12 5', mRNA sequence
Length = 493
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 48 aggaaggaaatggagatgg 66
>gb|CO169002.1|CO169002 NDL1_4_A12.b1_A029 Needles control Pinus taeda cDNA clone
NDL1_4_A12_A029 3', mRNA sequence
Length = 635
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 303 aggaaggaaatggagatgg 321
>gb|CO169065.1|CO169065 NDL1_4_A12.g1_A029 Needles control Pinus taeda cDNA clone
NDL1_4_A12_A029 5', mRNA sequence
Length = 732
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 556 aggaaggaaatggagatgg 574
>gb|CX650196.1|CX650196 COLD1_44_D02.b1_A029 Root cold Pinus taeda cDNA clone
COLD1_44_D02_A029 3', mRNA sequence
Length = 836
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 469 aggaaggaaatggagatgg 487
>gb|CX650274.1|CX650274 COLD1_44_D02.g1_A029 Root cold Pinus taeda cDNA clone
COLD1_44_D02_A029 5', mRNA sequence
Length = 810
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 446 aggaaggaaatggagatgg 464
>gb|DR057513.1|DR057513 RTNIT1_6_F04.b1_A029 Roots minus nitrogen Pinus taeda cDNA clone
RTNIT1_6_F04_A029 3', mRNA sequence
Length = 886
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 398 cagctgttttgacttcagc 416
|||||||||||||||||||
Sbjct: 63 cagctgttttgacttcagc 81
>gb|DR057602.1|DR057602 RTNIT1_6_F04.g1_A029 Roots minus nitrogen Pinus taeda cDNA clone
RTNIT1_6_F04_A029 5', mRNA sequence
Length = 851
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 398 cagctgttttgacttcagc 416
|||||||||||||||||||
Sbjct: 305 cagctgttttgacttcagc 323
>gb|DR078877.1|DR078877 RTFEPL1_7_A03.g1_A029 Roots plus added iron Pinus taeda cDNA clone
RTFEPL1_7_A03_A029 5', mRNA sequence
Length = 799
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 398 cagctgttttgacttcagc 416
|||||||||||||||||||
Sbjct: 776 cagctgttttgacttcagc 794
>gb|DR742058.1|DR742058 RTCU1_1_A10.g1_A029 Roots plus added copper Pinus taeda cDNA clone
RTCU1_1_A10_A029 5', mRNA sequence
Length = 773
Score = 38.2 bits (19), Expect = 0.46
Identities = 19/19 (100%)
Strand = Plus / Plus
Query: 161 aggaaggaaatggagatgg 179
|||||||||||||||||||
Sbjct: 480 aggaaggaaatggagatgg 498
Database: Pinus_nucl_with_EST.fasta
Posted date: Feb 7, 2006 2:45 PM
Number of letters in database: 217,277,237
Number of sequences in database: 355,925
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 Hits to DB: 72,580
Number of Sequences: 355925
Number of extensions: 72580
Number of successful extensions: 19647
Number of sequences better than 0.5: 17
Number of HSP's better than 0.5 without gapping: 17
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 19612
Number of HSP's gapped (non-prelim): 35
length of query: 683
length of database: 217,277,237
effective HSP length: 19
effective length of query: 664
effective length of database: 210,514,662
effective search space: 139781735568
effective search space used: 139781735568
T: 0
A: 0
X1: 11 (21.8 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 19 (38.2 bits)