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Dicty_cDB
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U04842-1
Contig ID Contig-U04842-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U04842-1 (Contig-U04842-1Q) /CSM_Contig/Contig-U04842-1Q.Seq.d
ATCAATTTTTGAACTATTGTTTTTTTTTTATTTTTATATTTATTTATTTA
TTTATTTTAGTTCATTTATTTTTTTATTACTAAAAAAAAAAAAAAAAAAA
AAAAAANAAAAAAAAAAAGAAAAAAAAATATGGATATTTTAAATTATATA
AAAAAAAATTTAAAAATTAGAATTGAAACAACAAATCAATTAAATGATGC
CTTTAAAAAATAAAAATTTATGTTCTGTTGAATTTGATAATAAAGAAACT
TGGTTATCAAATACTCCATTAGAAGAACCAAATGCATATAAAAATATTAC
TCATCCCTCACAATTGGATGGTTTAGAAAATGGTGATTACCATATCTCCA
GTAACTTGGTAGTTTCAATCCTTAAAGAAAAATTAAAAGAAATTGAACAA
TTAAAACAAATTATTAAATCAAAAGACTATGATATAAACTATATATCAGC
ATATGGTGAAAGAAAATATCCAAATGGCAGTAAAAATGAATAAAATTATT
ATTTAATTTTTTGTGGGAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTA
GAGGGAATAAAATTTATTTCACTTCTTAAATAATAATAAGATATATATTA
AAATAA
Gap no gap
Contig length 606
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 2483498
End point 2482892
Strand (PLUS/MINUS) MINUS
Number of clones 4
Number of EST 4
Link to clone list U04842
List of clone(s) 

est1=SSJ425E,1,520
est2=SSH608E,109,529
est3=SSD344Z,118,528
est4=SSK646Z,144,607
Translated Amino Acid sequence 
sifellfffyfyiylfiyfssfiflllkkkkkkkkxkkkekkiwif*ii*kki*klelkq
qin*MMPLKNKNLCSVEFDNKETWLSNTPLEEPNAYKNITHPSQLDGLENGDYHISSNLV
VSILKEKLKEIEQLKQIIKSKDYDINYISAYGERKYPNGSKNE*nyylifcgkkkkkkkk
kflegikfisllk***diy*n
Translated Amino Acid sequence (All Frames) 
Frame A:
inf*tivfflflylfiylf*fiyffitkkkkkkkkxkkkrkknmdilnyikknlkiriet
tnqlndafkk*kfmfc*i***rnlvikysirrtkci*kyyssltigwfrkw*lpylq*lg
sfnp*rkikrn*tiktny*ikrl*yklyisiw*kkiskwq*k*ikllfnflwekkkkkkk
kifrgnkiyfts*iiiryilk*


Frame B:
sifellfffyfyiylfiyfssfiflllkkkkkkkkxkkkekkiwif*ii*kki*klelkq
qin*MMPLKNKNLCSVEFDNKETWLSNTPLEEPNAYKNITHPSQLDGLENGDYHISSNLV
VSILKEKLKEIEQLKQIIKSKDYDINYISAYGERKYPNGSKNE*nyylifcgkkkkkkkk
kflegikfisllk***diy*n


Frame C:
qflnycfffififiylfilvhlffyy*kkkkkkkxkkkkkkkygyfklykkkfkn*n*nn
ksik*cl*kikiyvllnliikklgyqilh*knqmhikilliphnwmv*kmvitispvtw*
fqslkkn*kklnn*nkllnqktmi*tiyqhmvkeniqmavkmnkiii*ffvgkkkkkkkk
nf*re*nlfhflnnnkiyiki
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04842-1 (Contig-U04842-1Q)
/CSM_Contig/Contig-U04842-1Q.Seq.d
         (606 letters)

Database: CSM
           6905 sequences; 5,674,871 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04842-1 (Contig-U04842-1Q) /CSM_Contig/Conti...   365  e-101
Contig-U14374-1 (Contig-U14374-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U11881-1 (Contig-U11881-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U11804-1 (Contig-U11804-1Q) /CSM_Contig/Conti...    38  0.011
Contig-U12717-1 (Contig-U12717-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U12585-1 (Contig-U12585-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U12500-1 (Contig-U12500-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U09498-1 (Contig-U09498-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U09287-1 (Contig-U09287-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U06402-1 (Contig-U06402-1Q) /CSM_Contig/Conti...    36  0.042

>Contig-U04842-1 (Contig-U04842-1Q) /CSM_Contig/Contig-U04842-1Q.Seq.d
          Length = 606

 Score =  365 bits (184), Expect = e-101
 Identities = 226/247 (91%)
 Strand = Plus / Plus

                                                                       
Query: 129 tatggatattttaaattatatnnnnnnnnntttaaaaattagaattgaaacaacaaatca 188
           |||||||||||||||||||||         ||||||||||||||||||||||||||||||
Sbjct: 129 tatggatattttaaattatataaaaaaaaatttaaaaattagaattgaaacaacaaatca 188

                                                                       
Query: 189 attaaatgatgcctttnnnnnnnnnnnntttatgttctgttgaatttgataataaagaaa 248
           ||||||||||||||||            ||||||||||||||||||||||||||||||||
Sbjct: 189 attaaatgatgcctttaaaaaataaaaatttatgttctgttgaatttgataataaagaaa 248

                                                                       
Query: 249 cttggttatcaaatactccattagaagaaccaaatgcatataaaaatattactcatccct 308
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 249 cttggttatcaaatactccattagaagaaccaaatgcatataaaaatattactcatccct 308

                                                                       
Query: 309 cacaattggatggtttagaaaatggtgattaccatatctccagtaacttggtagtttcaa 368
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 309 cacaattggatggtttagaaaatggtgattaccatatctccagtaacttggtagtttcaa 368

                  
Query: 369 tccttaa 375
           |||||||
Sbjct: 369 tccttaa 375


 Score =  184 bits (93), Expect = 7e-47
 Identities = 93/93 (100%)
 Strand = Plus / Plus

                                                                       
Query: 425 gactatgatataaactatatatcagcatatggtgaaagaaaatatccaaatggcagtaaa 484
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 425 gactatgatataaactatatatcagcatatggtgaaagaaaatatccaaatggcagtaaa 484

                                            
Query: 485 aatgaataaaattattatttaattttttgtggg 517
           |||||||||||||||||||||||||||||||||
Sbjct: 485 aatgaataaaattattatttaattttttgtggg 517


 Score =  123 bits (62), Expect = 2e-28
 Identities = 62/62 (100%)
 Strand = Plus / Plus

                                                                       
Query: 545 tttttagagggaataaaatttatttcacttcttaaataataataagatatatattaaaat 604
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 545 tttttagagggaataaaatttatttcacttcttaaataataataagatatatattaaaat 604

             
Query: 605 aa 606
           ||
Sbjct: 605 aa 606


 Score = 44.1 bits (22), Expect = 2e-04
 Identities = 22/22 (100%)
 Strand = Plus / Plus

                                
Query: 60 gttcatttatttttttattact 81
          ||||||||||||||||||||||
Sbjct: 60 gttcatttatttttttattact 81


 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                             
Query: 1  atcaatttttgaactattg 19
          |||||||||||||||||||
Sbjct: 1  atcaatttttgaactattg 19


>Contig-U14374-1 (Contig-U14374-1Q) /CSM_Contig/Contig-U14374-1Q.Seq.d
          Length = 310

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 23/24 (95%)
 Strand = Plus / Minus

                                   
Query: 486 atgaataaaattattatttaattt 509
           |||| |||||||||||||||||||
Sbjct: 229 atgattaaaattattatttaattt 206


>Contig-U11881-1 (Contig-U11881-1Q) /CSM_Contig/Contig-U11881-1Q.Seq.d
          Length = 3720

 Score = 38.2 bits (19), Expect = 0.011
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                               
Query: 492  aaaattattatttaatttt 510
            |||||||||||||||||||
Sbjct: 3702 aaaattattatttaatttt 3720


 Score = 30.2 bits (15), Expect = 2.6
 Identities = 15/15 (100%)
 Strand = Plus / Minus

                           
Query: 65   tttatttttttatta 79
            |||||||||||||||
Sbjct: 3596 tttatttttttatta 3582


  Database: CSM
    Posted date:  Jun 9, 2004  7:35 PM
  Number of letters in database: 5,674,871
  Number of sequences in database:  6905
  
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: 27,771
Number of Sequences: 6905
Number of extensions: 27771
Number of successful extensions: 2908
Number of sequences better than 10.0: 326
length of query: 606
length of database: 5,674,871
effective HSP length: 16
effective length of query: 590
effective length of database: 5,564,391
effective search space: 3282990690
effective search space used: 3282990690
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2009. 7. 3
Homology vs DNA 
Query= Contig-U04842-1 (Contig-U04842-1Q) /CSM_Contig/Contig-U04842-1Q.Seq.d
         (606 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

Searching..................................................done

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(C94269) Dictyostelium discoideum slug cDNA, clone SSK646.        291   e-150  3
(AU038354) Dictyostelium discoideum slug cDNA, clone SSH608.      299   e-124  2
(C91053) Dictyostelium discoideum slug cDNA, clone SSJ425.        299   e-124  2
(C92285) Dictyostelium discoideum slug cDNA, clone SSD344.        270   e-116  2
(AM432085) Vitis vinifera contig VV78X123534.4, whole genome...    52   0.025  1
(AU037422) Dictyostelium discoideum slug cDNA, clone SSD618.       38   0.031  3
(AU263293) Dictyostelium discoideum vegetative cDNA clone:VS...    38   0.032  3
(AC004709) Plasmodium falciparum chromosome 12, *** SEQUENCI...    40   0.049  8
(AE014822) Plasmodium falciparum 3D7 chromosome 14 section 7...    38   0.064  9
(X95276) Plasmodium falciparum complete gene map of plastid-...    40   0.072  3
(AL403171) T7 end of clone AT0AA007A04 of library AT0AA from...    50   0.099  1
(AL403167) T7 end of clone AT0AA007A02 of library AT0AA from...    50   0.099  1
(AP008209) Oryza sativa (japonica cultivar-group) genomic DN...    50   0.099  1
(AC119797) Oryza sativa Japonica Group chromosome 3 clone OS...    50   0.099  1
(AC105729) Oryza sativa Japonica Group chromosome 3 clone OJ...    50   0.099  1
(EA682205) Sequence 61084 from patent US 7365185.                  50   0.099  1
(EA644340) Sequence 23219 from patent US 7365185.                  50   0.099  1
(AC230459) Bos taurus clone CH240-508B10, WORKING DRAFT SEQU...    50   0.099  1
(ER893007) REAA2A05 FST of T-DNA insertion lines (Right Bord...    50   0.099  1
(CL755195) OR_BBa0122N21.f OR_BBa Oryza nivara genomic clone...    50   0.099  1
(AM486078) Vitis vinifera, whole genome shotgun sequence, co...    40   0.13   3
(AF437291) Saccharomyces castellii strain NRRL Y-12630 mitoc...    36   0.18   4
(AE014847) Plasmodium falciparum 3D7 chromosome 12, section ...    40   0.19   8
(AM618759) Entamoeba invadens IP1 GSS, clone inv114b04.q1k.        32   0.20   3
(J01471) Yeast (S.cerevisiae) mitochondrial apocytochrome b ...    36   0.21   2
(AM642671) Entamoeba dispar GSS, clone dispar97a06.p1k.            40   0.22   2
(AC011255) Homo sapiens chromosome 8 clone RP11-394D6 map 8,...    36   0.23   2
(AC026723) Homo sapiens chromosome 5 clone CTD-2209N14, comp...    36   0.23   2
(CT943669) Pan troglodytes chromosome X clone CH251-484K12 m...    36   0.24   4
(AF402141) Schizophyllum commune mitochondrial DNA, complete...    38   0.24   2
(AM609980) Entamoeba invadens IP1 GSS, clone inv111f10.q1k.        32   0.25   3
(AC210447) Oryza glaberrima clone OG_BBa0010M11, complete se...    46   0.32   3
(CR405706) Zebrafish DNA sequence from clone CH211-233D12 in...    48   0.39   1
(DD010736) Diagnosis of known genetic Parameters within the ...    48   0.39   1
(AX344564) Sequence 15 from Patent WO0200932.                      48   0.39   1
(AC117081) Dictyostelium discoideum chromosome 2 map 5862124...    48   0.39   1
(AC097502) Homo sapiens BAC clone RP11-340B18 from 4, comple...    48   0.39   1
(CU407321) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    48   0.39   1
(CT009482) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    48   0.39   1
(AZ670895) ENTLE93TF Entamoeba histolytica Sheared DNA Entam...    48   0.39   1
(ER893006) DBA2C09 FST of T-DNA insertion lines (Right Borde...    48   0.39   1
(EL550104) EST_omor_rgc_13473 omorrgc mixed_tissue Osmerus m...    48   0.39   1
(AM285304) Spiroplasma citri GII3-3X chromosome, contig Cont...    48   0.39   1
(AL929358) Plasmodium falciparum strain 3D7, chromosome 9; s...    36   0.48   7
(BQ452178) PfESToaa93b06.y1 Plasmodium falciparum 3D7 asexua...    36   0.52   2
(CT954305) N.leucogenys DNA sequence from clone CH271-269B20.      42   0.55   4
(CU104723) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    42   0.55   3
(BU498684) PfESToac01d09.y1 Plasmodium falciparum 3D7 asexua...    36   0.55   2
(V00696) Yeast (S. cerevisiae) mitochondrial gene for cytoch...    36   0.76   3
(FP085414) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    36   0.85   2
(EK327502) 1095467011680 Global-Ocean-Sampling_GS-31-01-01-1...    38   0.85   2
(CU929325) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    36   0.86   2
(DQ642846) Plasmodium falciparum HB3 apicoplast, complete ge...    40   0.86   4
(AF466146) Melipona bicolor mitochondrial genome, partial se...    36   0.93   3
(CR382399) Plasmodium falciparum chromosome 6, complete sequ...    36   1.1    6
(CG406341) ZMMBBb0261P02.f ZMMBBb Zea mays subsp. mays genom...    36   1.1    2
(DX535362) GH_MBb0064M11r GH_MBb Gossypium hirsutum genomic ...    44   1.1    2
(L36899) Saccharomyces cerevisiae mitochondrion origin of re...    36   1.3    3
(AC006281) Plasmodium falciparum chromosome 12 clone PFYACB8...    36   1.4    7
(AJ011856) Saccharomyces cerevisiae complete mitochondrial g...    34   1.4    5
(AM430250) Vitis vinifera contig VV78X027990.11, whole genom...    34   1.5    3
(CU633910) Zebrafish DNA sequence from clone CH1073-408O3 in...    46   1.6    1
(CU570688) Zebrafish DNA sequence from clone CH73-250A19 in ...    46   1.6    1
(CR376863) Zebrafish DNA sequence from clone DKEY-93F15 in l...    46   1.6    1
(BX957294) Zebrafish DNA sequence from clone DKEY-187I15 in ...    46   1.6    1
(BX248521) Zebrafish DNA sequence from clone CH211-243C14 in...    46   1.6    1
(BX088652) Zebrafish DNA sequence from clone DKEY-256M19 in ...    46   1.6    1
(CR380959) Candida glabrata strain CBS138 chromosome M compl...    46   1.6    1
(AP008210) Oryza sativa (japonica cultivar-group) genomic DN...    46   1.6    1
(AL732346) Oryza sativa genomic DNA, chromosome 4, BAC clone...    46   1.6    1
(AL732340) Oryza sativa genomic DNA, chromosome 4, BAC clone...    46   1.6    1
(AL606619) Oryza sativa genomic DNA, chromosome 4, BAC clone...    46   1.6    1
(AC146330) Medicago truncatula clone mth2-7g7, complete sequ...    46   1.6    1
(AL929357) Plasmodium falciparum strain 3D7, chromosome 9; s...    46   1.6    1
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720...    46   1.6    1
(AC148651) Medicago truncatula chromosome unknown clone mte1...    46   1.6    1
(CU929045) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   1.6    1
(CR628388) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    46   1.6    1
(AP010240) Lotus japonicus genomic DNA, chromosome 2, clone:...    46   1.6    1
(AC232934) Heliconius erato clone BBAM-41G22, WORKING DRAFT ...    46   1.6    1
(AC217737) Heliconius erato clone BBAM-38G6, WORKING DRAFT S...    46   1.6    1
(AC166038) Medicago truncatula clone mth2-107h21, WORKING DR...    46   1.6    1
(ER960070) CH260-111E05_T7 CHORI-260 Meleagris gallopavo gen...    46   1.6    1
(EJ337495) 1092963489670 Global-Ocean-Sampling_GS-28-01-01-1...    46   1.6    1
(ED750192) GM_WBb0116E17.f GM_WBb Glycine max genomic clone ...    46   1.6    1
(DU483935) 1098421043086 CHORI-243 Ovis aries genomic clone ...    46   1.6    1
(DU471327) 1098415665744 CHORI-243 Ovis aries genomic clone ...    46   1.6    1
(CL094729) ISB1-25H10_T7.1 ISB1 Xenopus (Silurana) tropicali...    46   1.6    1
(EC273421) TT1C915TV Tetrahymena thermophila SB210 cDNA libr...    46   1.6    1
(DC223010) Plasmodium berghei strain ANKA cDNA clone:MZ00677...    46   1.6    1
(DC219581) Plasmodium berghei strain ANKA cDNA clone:MZ00128...    46   1.6    1
(BW640583) Dugesia ryukyuensis mRNA, clone: Dr_sW_018_K16, 5...    46   1.6    1
(BB978622) Plasmodium berghei str. ANKA cDNA clone: OK008668...    46   1.6    1
(BB978444) Plasmodium berghei str. ANKA cDNA clone: OK008483...    46   1.6    1
(BB977006) Plasmodium berghei str. ANKA cDNA clone: OK006952...    46   1.6    1
(CP001078) Clostridium botulinum E3 str. Alaska E43, complet...    46   1.6    1
(AE014852) Plasmodium falciparum 3D7 chromosome 12, section ...    32   1.9    8
(AL359382) Human DNA sequence from clone RP11-631F7 on chrom...    42   2.2    2
(AM476325) Vitis vinifera contig VV78X261077.5, whole genome...    34   2.3    3
(C93421) Dictyostelium discoideum slug cDNA, clone SSM822.         36   2.3    2
(AC129214) Mus musculus BAC clone RP24-426N11 from 16, compl...    40   2.4    4
(AM442958) Vitis vinifera contig VV78X237810.12, whole genom...    38   2.4    3
(ET912777) CHO_OF202xk24r1.ab1 CHO_OF Nicotiana tabacum geno...    38   2.5    2
(BI642947) TZF49 TZF (Sapwood-heartwood transition zone of b...    38   2.6    2
(BH794792) ME_MBa0003H11f Manihot esculenta Manihot esculent...    40   2.7    2
(AF250324) Homo sapiens chromosome 4q35 BAC clones RPCI-11-4...    40   2.8    2
(CS468864) Sequence 55 from Patent EP1748080.                      34   3.0    2
(CS468863) Sequence 54 from Patent EP1748080.                      34   3.0    2
(CS419341) Sequence 55 from Patent WO2006094836.                   34   3.0    2
(CS419340) Sequence 54 from Patent WO2006094836.                   34   3.0    2
(AM447380) Vitis vinifera contig VV78X158201.8, whole genome...    40   3.0    3
(AF015463) Plasmodium falciparum microsatellite 14e sequence.      36   3.0    2
(AC202519) Medicago truncatula clone mth2-75c11, WORKING DRA...    32   3.1    2
(AM429188) Vitis vinifera contig VV78X040868.15, whole genom...    38   3.1    2
(FH644893) CHO_OF4984xb06f1.ab1 CHO_OF4 Nicotiana tabacum ge...    38   3.2    2
(AY257663) Bostrychia radicans isolate BZ3051 cytochrome oxi...    32   3.3    3
(AM460235) Vitis vinifera, whole genome shotgun sequence, co...    34   3.3    2
(AJ926240) Theileria annulata EST, clone tam013e10_q1k.            40   3.8    2
(AF389855) Sus scrofa estrogen sulfotransferase mRNA, comple...    32   3.9    2
(EB240933) PEG003-C-217348-501 Normalized Pedal-Pleural Gang...    34   4.0    2
(CZ266477) bes02_CH257_289E23_CYPAC72_AV228_055 CHORI-257 Gr...    34   4.0    2
(DN111857) 1111003 MARC 4PIG Sus scrofa cDNA 3', mRNA sequence.    32   4.1    2
(DN111491) 1110619 MARC 4PIG Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW322782) rlin03_l18.y1 lin Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW658131) rtra04_o16r1.y1 tra Sus scrofa cDNA 5', mRNA sequ...    32   4.1    2
(EW322322) rlin37_b2.y1 lin Sus scrofa cDNA 5', mRNA sequence.     32   4.1    2
(EW318282) rlin18_m6.y1 lin Sus scrofa cDNA 5', mRNA sequence.     32   4.1    2
(EW326331) rlin34_h5.y1 lin Sus scrofa cDNA 5', mRNA sequence.     32   4.1    2
(CZ266498) bes02_CH257_273C6_CYPAC71_AV227_039 CHORI-257 Gre...    34   4.1    2
(EW318612) rlin38_p14.y1 lin Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW663626) rtra07_b20r1.y1 tra Sus scrofa cDNA 5', mRNA sequ...    32   4.1    2
(EW005996) rcsk10_g23.y1 csk Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW531396) rret07_i22.y1 ret Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW325003) rlin36_c9.y1 lin Sus scrofa cDNA 5', mRNA sequence.     32   4.1    2
(EW657453) rtra03_f2r1.y1 tra Sus scrofa cDNA 5', mRNA seque...    32   4.1    2
(EW318411) rlin37_b18.y1 lin Sus scrofa cDNA 5', mRNA sequence.    32   4.1    2
(EW439213) rnco1917b_k9.y2 nco Sus scrofa cDNA 5', mRNA sequ...    32   4.1    2
(EU477789) Stictalia sp. 1 JCT-2008 16S ribosomal RNA gene, ...    34   4.1    2
(EW323733) rlin20_b16.y1 lin Sus scrofa cDNA 5', mRNA sequence.    32   4.2    2
(CU302336) Medicago truncatula chromosome 5 clone mth2-81g16...    38   4.2    4
(EW296279) ruio25_g14.y1 kid Sus scrofa cDNA 5', mRNA sequence.    32   4.2    2
(AC005308) Plasmodium falciparum chromosome 12 clone PFYAC49...    32   4.3    9
(AE014837) Plasmodium falciparum 3D7 chromosome 11 section 2...    32   4.5    7
(AP010279) Lotus japonicus genomic DNA, chromosome 2, clone:...    38   4.7    3
(CW952344) TcB38.1_D03_SP6 Tribolium BAC library Tribolium c...    38   4.8    2
(U16955) Plasmodium falciparum ATPase 2 gene, complete cds.        32   4.9    4
(AM480706) Vitis vinifera contig VV78X145784.6, whole genome...    34   5.0    3
(AX346868) Sequence 1939 from Patent WO0200928.                    42   5.4    2
(AZ615233) 1M0444P19F Mouse 10kb plasmid UUGC1M library Mus ...    40   5.6    2
(BA000026) Mycoplasma penetrans HF-2 DNA, complete genome.         40   5.8    9
(BX927103) Zebrafish DNA sequence from clone DKEY-262M23 in ...    38   6.0    3
(AC096863) Genomic sequence for Mus musculus, clone RP23-110...    40   6.0    2
(CR762392) Zebrafish DNA sequence from clone DKEY-265A11 in ...    44   6.1    1
(CR759833) Zebrafish DNA sequence from clone DKEYP-4F2 in li...    44   6.1    1
(BX004773) Zebrafish DNA sequence from clone DKEY-13D19.           44   6.1    1
(AC147246) Mus musculus BAC clone RP23-465M17 from chromosom...    44   6.1    1
(AC135640) Mus musculus BAC clone RP23-362A12 from chromosom...    44   6.1    1
(AC197178) Rhesus Macaque  BAC CH250-117L1 () complete seque...    44   6.1    1
(AC192197) Pan troglodytes BAC clone CH251-72K14 from chromo...    44   6.1    1
(AC148683) Macaca mulatta Major Histocompatibility Complex B...    44   6.1    1
(AC148667) Macaca mulatta Major Histocompatibility Complex B...    44   6.1    1
(AB128049) Macaca mulatta genes, MHC class I region, partial...    44   6.1    1
(EU427470) Phytophthora ramorum strain CBS 101553 mitochondr...    44   6.1    1
(DQ832718) Phytophthora ramorum mitochondrion, complete genome.    44   6.1    1
(AY654900) Kluyveromyces lactis mitochondrion, complete genome.    44   6.1    1
(AM485719) Vitis vinifera contig VV78X252403.11, whole genom...    44   6.1    1
(AM455759) Vitis vinifera, whole genome shotgun sequence, co...    44   6.1    1
(AC097368) Oryza sativa chromosome 3 BAC OSJNBb0017F17 genom...    44   6.1    1
(AC093017) Oryza sativa Japonica Group chromosome 3 clone OS...    44   6.1    1
(EA680240) Sequence 59119 from patent US 7365185.                  44   6.1    1
(DD010735) Diagnosis of known genetic Parameters within the ...    44   6.1    1
(AX344551) Sequence 2 from Patent WO0200932.                       44   6.1    1
(CR788268) Human DNA sequence from clone RP11-24B13 on chrom...    44   6.1    1
(AL355608) Human DNA sequence from clone RP11-567J2 on chrom...    44   6.1    1
(AL353729) Human DNA sequence from clone RP11-290L7 on chrom...    44   6.1    1
(AL353581) Human DNA sequence from clone RP11-65L19 on chrom...    44   6.1    1
(AL162233) Human DNA sequence from clone RP11-292B8 on chrom...    44   6.1    1
(AL161740) Human DNA sequence from clone RP6-239D12 on chrom...    44   6.1    1
(AC119424) Homo sapiens chromosome 3 clone RP11-475O23, comp...    44   6.1    1
(AC105751) Homo sapiens chromosome 3 clone RP11-908O9, compl...    44   6.1    1
(AC160444) Bos taurus clone CH240-83N22, WORKING DRAFT SEQUE...    44   6.1    1
(AC087573) Homo sapiens chromosome 8 clone RP11-79J19 map 8,...    44   6.1    1
(AC025861) Homo sapiens clone RP11-766D10, WORKING DRAFT SEQ...    44   6.1    1
(CU467658) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    44   6.1    1
(AL365177) Human DNA sequence *** SEQUENCING CANCELLED *** f...    44   6.1    1
(AC215532) Oryza officinalis clone OO__Ba0115A15, *** SEQUEN...    44   6.1    1
(AC212631) Solanum lycopersicum chromosome 7 clone C07HBa011...    44   6.1    1
(AC183461) Atelerix albiventris clone LB4-516K21, WORKING DR...    44   6.1    1
(AC172176) Atelerix albiventris clone LB4-359O9, WORKING DRA...    44   6.1    1
(AC171767) Atelerix albiventris clone LB4-512C8, WORKING DRA...    44   6.1    1
(AC170720) Atelerix albiventris clone LB4-367C8, WORKING DRA...    44   6.1    1
(AC164241) Bos taurus clone CH240-138D5, WORKING DRAFT SEQUE...    44   6.1    1
(CR859733) Pongo abelii mRNA; cDNA DKFZp469K1925 (from clone...    44   6.1    1
(BH499172) BOGCV37TR BOGC Brassica oleracea genomic clone BO...    44   6.1    1
(AZ741569) RPCI-24-141K22.TJ RPCI-24 Mus musculus genomic cl...    44   6.1    1
(FH281112) CHO_OF4182xg06r1.ab1 CHO_OF4 Nicotiana tabacum ge...    44   6.1    1
(ER607991) 1093016289611 Global-Ocean-Sampling_GS-36-01-01-2...    44   6.1    1
(EK311056) 1095462397131 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EK293881) 1095462340192 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EK276473) 1095462279358 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EK269254) 1095462248792 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EK267212) 1095462233267 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EK234927) 1095460196325 Global-Ocean-Sampling_GS-31-01-01-1...    44   6.1    1
(EJ779328) 1093011913668 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ764583) 1092963178822 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ706018) 1092956053932 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ660807) 1092955022717 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ655658) 1092955005148 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ655457) 1092955004547 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ653632) 1092954009575 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ648696) 1092953002866 Global-Ocean-Sampling_GS-30-02-01-1...    44   6.1    1
(EJ350606) 1092963584093 Global-Ocean-Sampling_GS-28-01-01-1...    44   6.1    1
(EJ252897) 1095347000309 Global-Ocean-Sampling_GS-27-01-01-1...    44   6.1    1
(EJ245307) 1095335013542 Global-Ocean-Sampling_GS-27-01-01-1...    44   6.1    1
(EJ162478) 1092344053535 Global-Ocean-Sampling_GS-27-01-01-1...    44   6.1    1
(EJ081112) 1095460034252 Global-Ocean-Sampling_GS-26-01-01-1...    44   6.1    1
(EJ050060) 1095454144024 Global-Ocean-Sampling_GS-26-01-01-1...    44   6.1    1
(EJ049256) 1095454135400 Global-Ocean-Sampling_GS-26-01-01-1...    44   6.1    1
(EJ031772) 1095454049031 Global-Ocean-Sampling_GS-26-01-01-1...    44   6.1    1
(EI457527) PV_GBa0059K10.f PV_GBa Phaseolus vulgaris genomic...    44   6.1    1
(EI450928) PV_GBa0050G23.f PV_GBa Phaseolus vulgaris genomic...    44   6.1    1
(ED163747) AUAC-aak54d02.b1 Ascaris suum whole genome shotgu...    44   6.1    1
(DX413132) SOYB480TH LargeInsertSoybeanGenLibBuild4 Glycine ...    44   6.1    1
(AL344304) Tetraodon nigroviridis genome survey sequence SP6...    44   6.1    1
(AL324891) Tetraodon nigroviridis genome survey sequence SP6...    44   6.1    1
(AL320486) Tetraodon nigroviridis genome survey sequence T7 ...    44   6.1    1
(AL286216) Tetraodon nigroviridis genome survey sequence PUC...    44   6.1    1
(AL284551) Tetraodon nigroviridis genome survey sequence T7 ...    44   6.1    1
(AL246517) Tetraodon nigroviridis genome survey sequence PUC...    44   6.1    1
(AL229468) Tetraodon nigroviridis genome survey sequence PUC...    44   6.1    1
(AL191286) Tetraodon nigroviridis genome survey sequence T7 ...    44   6.1    1
(AL179399) Tetraodon nigroviridis genome survey sequence T7 ...    44   6.1    1
(DE409981) Bombyx mori genomic DNA, BAC clone:10G6D.               44   6.1    1
(CZ970815) 170475 Tomato MboI BAC Library Solanum lycopersic...    44   6.1    1
(BZ515652) BOMQU05TR BO_2_3_KB Brassica oleracea genomic clo...    44   6.1    1
(AG423799) Mus musculus molossinus DNA, clone:MSMg01-296B11....    44   6.1    1
(DY286713) IC0AAA65DC04RM1 CitNFL Citrus clementina cDNA 5',...    44   6.1    1
(DN305049) PL05007B1B06 cDNA from sexually mature hermaphodi...    44   6.1    1
(DN295569) PL03020A2B06 cDNA from sexually mature hermaphodi...    44   6.1    1
(CD006123) VVB063B02_326800 An expressed sequence tag databa...    44   6.1    1
(FC716366) CBBG10767.rev CBBG Lottia gigantea 12,15,18h embr...    44   6.1    1
(EW874427) G894P533FJ15.T0 Ixodes scapularis Pooled Non-infe...    44   6.1    1
(AC141756) Apis mellifera clone CH224-60D18, WORKING DRAFT S...    38   7.1    2
(AP010406) Lotus japonicus genomic DNA, chromosome 3, clone:...    36   7.1    4
(CT737236) Pan troglodytes chromosome X clone CH251-15O05 ma...    36   7.1    4
(FE521398) li0672411 Radiata pine mature earlywood cDNA libr...    38   7.6    2
(AY955840) Paracoccidioides brasiliensis strain Pb18 mitocho...    32   7.8    5
(AC026971) Homo sapiens chromosome 18 clone RP11-591I15 map ...    38   7.9    5
(AE014824) Plasmodium falciparum 3D7 chromosome 14 section 9...    36   8.1    6
(AE014820) Plasmodium falciparum 3D7 chromosome 14 section 5...    36   8.1    6
(CU795515) A BAC library has been constructed from PN40024 g...    32   8.2    3
(AE014836) Plasmodium falciparum 3D7 chromosome 11 section 1...    34   8.2    6
(AL035476) Plasmodium falciparum MAL4P3.                           34   8.3    8
(CL055132) CH216-80J13_RM1.1 CH216 Xenopus (Silurana) tropic...    30   8.4    3
(AC022249) Homo sapiens clone RP11-24G14, WORKING DRAFT SEQU...    42   8.4    4
(CR356232) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS...    36   9.0    3
(CR382398) Plasmodium falciparum chromosome 6, complete sequ...    32   9.3    9
(DX478842) Cpl21133 Papaya Genomic DNA BAC Library Carica pa...    36   9.4    2
(EX851959) CBNC9315.fwd CBNC Phycomyces blakesleeanus NRRL15...    34   9.4    3
(CT039142) Sus scrofa genomic clone CH242-9I21, genomic surv...    40   9.7    2
(ET106276) QM0AAC12BG04FM1 CCH3 Citrus clementina genomic cl...    34   9.8    2
(AC142307) Pan troglodytes BAC clone RP43-131H12 from chromo...    40   9.8    5
(BH492351) BOGVQ48TR BOGV Brassica oleracea genomic clone BO...    34   9.8    2

>(C94269) Dictyostelium discoideum slug cDNA, clone SSK646.
          Length = 463

 Score =  291 bits (147), Expect(3) = e-150
 Identities = 150/151 (99%)
 Strand = Plus / Plus


Query: 221 tgttctgttgaatttgataataaagaaacttggttatcaaatactccattagaagaacca 280
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 77  tgttctgttgaatttgataataaagaaacttggttatcaaatactccattagaagaacca 136


Query: 281 aatgcatataaaaatattactcatccctcacaattggatggtttagaaaatggtgattac 340
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 137 aatgcatataaaaatattactcatccctcacaattggatggtttagaaaatggtgattac 196


Query: 341 catatctccagtaacttggtagtttcaatcc 371
           |||||| ||||||||||||||||||||||||
Sbjct: 197 catatcaccagtaacttggtagtttcaatcc 227

 Score =  176 bits (89), Expect(3) = e-150
 Identities = 92/93 (98%)
 Strand = Plus / Plus


Query: 425 gactatgatataaactatatatcagcatatggtgaaagaaaatatccaaatggcagtaaa 484
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 281 gactatgatataaactatatatcagcatatggtgaaagaaaatatccaaatggcagtaaa 340


Query: 485 aatgaataaaattattatttaattttttgtggg 517
           |||||||||||||||| ||||||||||||||||
Sbjct: 341 aatgaataaaattattttttaattttttgtggg 373

 Score =  123 bits (62), Expect(3) = e-150
 Identities = 62/62 (100%)
 Strand = Plus / Plus


Query: 545 tttttagagggaataaaatttatttcacttcttaaataataataagatatatattaaaat 604
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 401 tttttagagggaataaaatttatttcacttcttaaataataataagatatatattaaaat 460


Query: 605 aa 606
           ||
Sbjct: 461 aa 462

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 542,477,545
Number of extensions: 43340904
Number of successful extensions: 3823767
Number of sequences better than 10.0: 263
Length of query: 606
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 583
Effective length of database: 99,442,330,388
Effective search space: 57974878616204
Effective search space used: 57974878616204
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.31
Homology vs Protein 
Query= Contig-U04842-1 (Contig-U04842-1Q) /CSM_Contig/Contig-U04842-1Q.Seq.d
         (606 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE017261_786(AE017261|pid:none) Picrophilus torridus DSM 9790, c...    33   6.3

>AE017261_786(AE017261|pid:none) Picrophilus torridus DSM 9790,
            complete genome.
          Length = 1637

 Score = 33.1 bits (74), Expect = 6.3
 Identities = 18/41 (43%), Positives = 24/41 (58%)
 Frame = +2

Query: 236  DNKETWLSNTPLEEPNAYKNITHPSQLDGLENGDYHISSNL 358
            DNK T  +N  + E NAY N+    Q+  L  G Y++SSNL
Sbjct: 1290 DNK-TIYNNVNITENNAYINVNSSKQIYVLPQGKYNVSSNL 1329

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: 3268448
Number of Hits to DB: 563,583,921
Number of extensions: 8792402
Number of successful extensions: 19527
Number of sequences better than 10.0: 1
Number of HSP's gapped: 19523
Number of HSP's successfully gapped: 1
Length of query: 202
Length of database: 1,061,185,681
Length adjustment: 122
Effective length of query: 80
Effective length of database: 662,435,025
Effective search space: 52994802000
Effective search space used: 52994802000
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: 30 (16.2 bits)
PSORT 

 psg: 0.65  gvh: 0.26  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.16  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 44.0 %: nuclear
	 40.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  4.0 %: mitochondrial

>> prediction for Contig-U04842-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 4
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0