>CHM223 (CHM223Q) /CSM/CH/CHM2-A/CHM223Q.Seq.d/
AACAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAATATATAT
ATATAAAATAAAATGTCTGATTATATGATGAATGATGATTCCCAAGATAATCCACATGCA
GATATATCGCAAGAGGATGTTTGGACAGTTATTAGTGCATATTTTCAAGANAAAGGTTTA
GTTAGACAACAATTAGATTCATTTGATGAGTTTATTCAAAATACAATGCAAGAAATTATA
GATGAATCACCACCAATTACATTAAGACCTGAATCACAACATCATCCANGTCAAGCAGTA
GTTAGTAATAATGTATCAACATTTTCAGTTAAATTTGGACAAATTTATCTTAGTAAACCA
ACAGCAGAAATTGATGGTGTATCACAACAAGTTACACCAAATCAAGCAAGAATTAGAAAT
TTAACCTATTCAGCACCATTATCTGTGGATATTACGAAAACGGTGATGACAGGATCAAAG
AGTAAAGGTGATGAAAGAAGAACCGATGANGTATTAAAGAGAATTTTCATTGGTAAAGTA
CCAATTATGTTACGTTCACAATATTGTATGTTGAATGAAGCAGATGATAGAGATTTAACA
ACGATGGGAGAATGTTCATTCGATCAAXXXXXXXXXXCGGTGATAAGTTCTCTTCTCGTC
ATGGTCAAAAAGGTACTTGTGGTATGGCTTATCGTCAAGAGGATTTACCATTCACTGTTG
AAGGTATCGTTCCAGATATCATTGTAAATCCACATGCTATTCCATCTCGTATGACCATTG
GTCAATTGATTGAATGTCTTCTTGGTAAAGTATCTGCTTCAACTGGTGATGAAGGTGATG
CTACCCCATTCACTGATGTCACTGTAGAAGCTATTTCACAAGCACTACACAAAATTGGTT
ATCAAATGACTGGTCATGAAGTTATGTATAATGGTCACACTGGTCGTCGTATGGATGCTC
AAATCTTTATTGGTCCAACTTATTATCAACGTTTAAAACATATGGTGGATGATAAAATTC
ACAGTCGTTCAAGAGGTCCTGTTCAAATTTTAACCCGTCAACCTGTAGAAGGTCGTTCTC
GTGATGGTGGTTTACGTTTTGGTGAGATGGAAAGAGATTGTATGATTTCTCATGGTGCAG
CTCAATTCTTAAAAGAACGTTTATTCGATCAATCAGATAGTTATCGTGTTCATATTTGTG
ATATTTGTGGTCTCATTGCAATTGCAAATCTAAAAAAGAATTCATTTAAATGTCGTAGAT
GTAAAAATAAAACTCAAATTTCTCAAATTAGAATGCCATATGCTGCAAAACTTTTATTCC
AAGAATTAATGTCAATGTCAATTGCTCCACGTATGTTTACTCAAACTTAATTTAAAATTT
TAAAT

nktktktktktktktktniyi*NKMSDYMMNDDSQDNPHADISQEDVWTVISAYFQXKGL
VRQQLDSFDEFIQNTMQEIIDESPPITLRPESQHHPXQAVVSNNVSTFSVKFGQIYLSKP
TAEIDGVSQQVTPNQARIRNLTYSAPLSVDITKTVMTGSKSKGDERRTDXVLKRIFIGKV
PIMLRSQYCMLNEADDRDLTTMGECSFDQ---

---GDKFSSRHGQKGTCGMAYRQEDLPFTVEGIVPDIIVNPHAIPSRMTIGQLIECLLGK
VSASTGDEGDATPFTDVTVEAISQALHKIGYQMTGHEVMYNGHTGRRMDAQIFIGPTYYQ
RLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLRFGEMERDCMISHGAAQFLKERLFD
QSDSYRVHICDICGLIAIANLKKNSFKCRRCKNKTQISQIRMPYAAKLLFQELMSMSIAP
RMFTQT*fkiln

Frame A:
nktktktktktktktktniyi*NKMSDYMMNDDSQDNPHADISQEDVWTVISAYFQXKGL
VRQQLDSFDEFIQNTMQEIIDESPPITLRPESQHHPXQAVVSNNVSTFSVKFGQIYLSKP
TAEIDGVSQQVTPNQARIRNLTYSAPLSVDITKTVMTGSKSKGDERRTDXVLKRIFIGKV
PIMLRSQYCMLNEADDRDLTTMGECSFDQ---

---r**vlfsswskrylwyglssrgftihc*ryrsryhckstcysisydhwsid*mssw*
sicfnw**r*cypih*chcrsyftsttqnwlsndws*syv*wshwssygcsnlywsnlls
tfktygg**nsqsfkrscsnfnpstcrrsfs*wwftfw*dgkrlydfswcssilkrtfir
sir*lscsyl*ylwshcnckskkefi*ms*m*k*nsnfsn*naiccktfiprinvnvncs
tyvysnli*nfk

Frame B:
tkqkqkqkqkqkqkqkqiyiykikclii**mmipkiihmqiyrkrmfgqllvhifkxkv*
ldnn*ihlmslfkiqckkl*mnhhqlh*dlnhniixvkq*lvimyqhfqlnldkfilvnq
qqklmvyhnklhqikqelei*piqhhylwilrkr**qdqrvkvmkeepmxy*refslvky
qlcyvhnivc*mkqmiei*qrwenvhsi---

---GDKFSSRHGQKGTCGMAYRQEDLPFTVEGIVPDIIVNPHAIPSRMTIGQLIECLLGK
VSASTGDEGDATPFTDVTVEAISQALHKIGYQMTGHEVMYNGHTGRRMDAQIFIGPTYYQ
RLKHMVDDKIHSRSRGPVQILTRQPVEGRSRDGGLRFGEMERDCMISHGAAQFLKERLFD
QSDSYRVHICDICGLIAIANLKKNSFKCRRCKNKTQISQIRMPYAAKLLFQELMSMSIAP
RMFTQT*fkiln

Frame C:
qnknknknknknknknkyiyik*nv*lyde**fpr*stcryiargcldsy*cifsrxrfs
*ttirfi**vyskynarnyr*ittnyikt*ittssxssss***cinifs*iwtnls**tn
srn*wcittsytksskn*kfnlfstiicgyyengddrike*r**kknr*xikenfhw*st
nyvtftilyve*sr**rfnndgrmfirs---

---vissllvmvkkvlvvwlivkriyhsllkvsfqisl*ihmlfhlv*plvn*lnvflvk
yllqlvmkvmlphslmsl*klfhkhytklvik*lvmklcimvtlvvvwmlksllvqliin
v*niwwmikftvvqevlfkf*pvnl*kvvlvmvvyvlvrwkeiv*flmvqlns*knvysi
nqivivfifvifvvslqlqi*krihlnvvdvkiklkflklechmlqnfyskn*cqcqllh
vcllklnlkf*

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CHM223 (CHM223Q) /CSM/CH/CHM2-A/CHM223Q.Seq.d/                       2524   0.0
AHN418 (AHN418Q) /CSM/AH/AHN4-A/AHN418Q.Seq.d/                       1475   0.0
AHM462 (AHM462Q) /CSM/AH/AHM4-C/AHM462Q.Seq.d/                       1475   0.0
SHF407 (SHF407Q) /CSM/SH/SHF4-A/SHF407Q.Seq.d/                       1445   0.0
AFI586 (AFI586Q) /CSM/AF/AFI5-D/AFI586Q.Seq.d/                       1407   0.0
SHK610 (SHK610Q) /CSM/SH/SHK6-A/SHK610Q.Seq.d/                       1392   0.0
VSD745 (VSD745Q) /CSM/VS/VSD7-B/VSD745Q.Seq.d/                       1354   0.0
AFB635 (AFB635Q) /CSM/AF/AFB6-B/AFB635Q.Seq.d/                       1265   0.0
AHA856 (AHA856Q) /CSM/AH/AHA8-C/AHA856Q.Seq.d/                       1148   0.0
CHK802 (CHK802Q) /CSM/CH/CHK8-A/CHK802Q.Seq.d/                        963   0.0

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

BU803755| polymerase (RNA) II (DNA directed) polypeptide B (140kD) [Homo sapiens], mRNA sequence.   143   1e-49  6
CV671939|CV671939.1 RE-3-SJ-L_H03_RE-3-SJ-LH03-T7 Schistosoma japonicum reverse cDNA Schistosoma japonicum cDNA, mRNA sequence.   147   1e-44  5
BU776977|BU776977.1 SJEDEG10 SJE Schistosoma japonicum cDNA, mRNA sequence.   147   1e-44  5
CV672573|CV672573.1 RET7SJ_03C05.T7 Schistosoma japonicum reverse cDNA Schistosoma japonicum cDNA, mRNA sequence.   147   2e-43  5
AX489154|AX489154.1 Sequence 6454 from Patent WO02053728.          88   5e-42  7
AY485615|AY485615.1 Candida tropicalis DNA-dependent RNA polymerase II second largest subunit gene, partial cds.    80   1e-41  8
AF107787|AF107787.1 Candida albicans DNA-dependent RNA polymerase II RPB140 (RPB2) gene, partial cds.    96   4e-39  6
CF449439|CF449439.1 EST685784 normalized cDNA library of onion Allium cepa cDNA clone ACACP96, mRNA sequence.    88   2e-37  6
U28403|U28403.1 Lycopersicon esculentum RNA polymerase II subunit 2 (rpb2) mRNA, complete cds.    82   9e-34  3
CF667663|CF667663.1 RTCNT1_31_F07.g1_A029 Root control Pinus taeda cDNA clone RTCNT1_31_F07_A029 5', mRNA sequence.    82   1e-33  6

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54J75) RecName: Full=DNA-directed RNA polymerase II subunit rp...   495   e-138
DQ058637_1(DQ058637|pid:none) Linanthus californicus RNA polymer...   421   e-116
DQ020641_1(DQ020641|pid:none) Petunia x hybrida RNA polymerase I...   421   e-116
DQ020642_1(DQ020642|pid:none) Antirrhinum majus RNA polymerase I...   420   e-116
AP008209_2128(AP008209|pid:none) Oryza sativa (japonica cultivar...   420   e-116
DQ058627_1(DQ058627|pid:none) Rhododendron macrophyllum RNA poly...   419   e-116
DQ020640_1(DQ020640|pid:none) Nicotiana sylvestris RNA polymeras...   419   e-116
Z19121_1(Z19121|pid:none) A.thaliana gene for RNA polymerase II ...   419   e-115
Z19120_1(Z19120|pid:none) A.thaliana mRNA for RNA polymerase II ...   419   e-115
BT068015_1(BT068015|pid:none) Zea mays full-length cDNA clone ZM...   416   e-114

 psg: 0.75  gvh: 0.41  alm: 0.40  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  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 

	 60.0 %: cytoplasmic
	 20.0 %: nuclear
	  8.0 %: mitochondrial
	  4.0 %: cytoskeletal
	  4.0 %: vesicles of secretory system
	  4.0 %: endoplasmic reticulum

>> prediction for CHM223 is cyt

>CHM223F.Seq
AACAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAATATATAT
ATATAAAATAAAATGTCTGATTATATGATGAATGATGATTCCCAAGATAATCCACATGCA
GATATATCGCAAGAGGATGTTTGGACAGTTATTAGTGCATATTTTCAAGANAAAGGTTTA
GTTAGACAACAATTAGATTCATTTGATGAGTTTATTCAAAATACAATGCAAGAAATTATA
GATGAATCACCACCAATTACATTAAGACCTGAATCACAACATCATCCANGTCAAGCAGTA
GTTAGTAATAATGTATCAACATTTTCAGTTAAATTTGGACAAATTTATCTTAGTAAACCA
ACAGCAGAAATTGATGGTGTATCACAACAAGTTACACCAAATCAAGCAAGAATTAGAAAT
TTAACCTATTCAGCACCATTATCTGTGGATATTACGAAAACGGTGATGACAGGATCAAAG
AGTAAAGGTGATGAAAGAAGAACCGATGANGTATTAAAGAGAATTTTCATTGGTAAAGTA
CCAATTATGTTACGTTCACAATATTGTATGTTGAATGAAGCAGATGATAGAGATTTAACA
ACGATGGGAGAATGTTCATTCGATCAANNNNNNNNNN

>CHM223Z.Seq
NNNNNNNNNNCGGTGATAAGTTCTCTTCTCGTCATGGTCAAAAAGGTACTTGTGGTATGG
CTTATCGTCAAGAGGATTTACCATTCACTGTTGAAGGTATCGTTCCAGATATCATTGTAA
ATCCACATGCTATTCCATCTCGTATGACCATTGGTCAATTGATTGAATGTCTTCTTGGTA
AAGTATCTGCTTCAACTGGTGATGAAGGTGATGCTACCCCATTCACTGATGTCACTGTAG
AAGCTATTTCACAAGCACTACACAAAATTGGTTATCAAATGACTGGTCATGAAGTTATGT
ATAATGGTCACACTGGTCGTCGTATGGATGCTCAAATCTTTATTGGTCCAACTTATTATC
AACGTTTAAAACATATGGTGGATGATAAAATTCACAGTCGTTCAAGAGGTCCTGTTCAAA
TTTTAACCCGTCAACCTGTAGAAGGTCGTTCTCGTGATGGTGGTTTACGTTTTGGTGAGA
TGGAAAGAGATTGTATGATTTCTCATGGTGCAGCTCAATTCTTAAAAGAACGTTTATTCG
ATCAATCAGATAGTTATCGTGTTCATATTTGTGATATTTGTGGTCTCATTGCAATTGCAA
ATCTAAAAAAGAATTCATTTAAATGTCGTAGATGTAAAAATAAAACTCAAATTTCTCAAA
TTAGAATGCCATATGCTGCAAAACTTTTATTCCAAGAATTAATGTCAATGTCAATTGCTC
CACGTATGTTTACTCAAACTTAATTTAAAATTTTAAAT

>CHM223P.Seq
AACAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAAAACAAATATATAT
ATATAAAATAAAATGTCTGATTATATGATGAATGATGATTCCCAAGATAATCCACATGCA
GATATATCGCAAGAGGATGTTTGGACAGTTATTAGTGCATATTTTCAAGANAAAGGTTTA
GTTAGACAACAATTAGATTCATTTGATGAGTTTATTCAAAATACAATGCAAGAAATTATA
GATGAATCACCACCAATTACATTAAGACCTGAATCACAACATCATCCANGTCAAGCAGTA
GTTAGTAATAATGTATCAACATTTTCAGTTAAATTTGGACAAATTTATCTTAGTAAACCA
ACAGCAGAAATTGATGGTGTATCACAACAAGTTACACCAAATCAAGCAAGAATTAGAAAT
TTAACCTATTCAGCACCATTATCTGTGGATATTACGAAAACGGTGATGACAGGATCAAAG
AGTAAAGGTGATGAAAGAAGAACCGATGANGTATTAAAGAGAATTTTCATTGGTAAAGTA
CCAATTATGTTACGTTCACAATATTGTATGTTGAATGAAGCAGATGATAGAGATTTAACA
ACGATGGGAGAATGTTCATTCGATCAA----------CGGTGATAAGTTCTCTTCTCGTC
ATGGTCAAAAAGGTACTTGTGGTATGGCTTATCGTCAAGAGGATTTACCATTCACTGTTG
AAGGTATCGTTCCAGATATCATTGTAAATCCACATGCTATTCCATCTCGTATGACCATTG
GTCAATTGATTGAATGTCTTCTTGGTAAAGTATCTGCTTCAACTGGTGATGAAGGTGATG
CTACCCCATTCACTGATGTCACTGTAGAAGCTATTTCACAAGCACTACACAAAATTGGTT
ATCAAATGACTGGTCATGAAGTTATGTATAATGGTCACACTGGTCGTCGTATGGATGCTC
AAATCTTTATTGGTCCAACTTATTATCAACGTTTAAAACATATGGTGGATGATAAAATTC
ACAGTCGTTCAAGAGGTCCTGTTCAAATTTTAACCCGTCAACCTGTAGAAGGTCGTTCTC
GTGATGGTGGTTTACGTTTTGGTGAGATGGAAAGAGATTGTATGATTTCTCATGGTGCAG
CTCAATTCTTAAAAGAACGTTTATTCGATCAATCAGATAGTTATCGTGTTCATATTTGTG
ATATTTGTGGTCTCATTGCAATTGCAAATCTAAAAAAGAATTCATTTAAATGTCGTAGAT
GTAAAAATAAAACTCAAATTTCTCAAATTAGAATGCCATATGCTGCAAAACTTTTATTCC
AAGAATTAATGTCAATGTCAATTGCTCCACGTATGTTTACTCAAACTTAATTTAAAATTT
TAAAT