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GenomeScan 1.0	Date run:  4-Feb-2002	Time: 17:31:55

Sequence homework_seq : 60000 bp : 36.99% C+G : Isochore 1 ( 0 - 43 C+G%)

Options:  	GenoaOnly	BothStrands

Parameter matrix: HumanIso.smat

Predicted genes/exons:

explanation

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.01 Init +   4639   4718   80  0  2   59  119    97 0.000  49.07
 1.02 Intr +  12955  13008   54  1  0   62  108    19 0.000  17.23
 1.03 Intr +  22201  22278   78  1  0   76   71    49 0.000  19.75
 1.04 Intr +  23778  23866   89  0  2   28   84    76 0.000  18.94
 1.05 Intr +  24473  24612  140  0  2   91   26    89 0.000  27.03
 1.06 Intr +  28856  28958  103  1  1   73   82    15 0.000  18.29
 1.07 Intr +  31443  31488   46  1  1   14  109    54 0.000  17.63
 1.08 Intr +  32810  32886   77  2  2   67   57    74 0.000  20.77
 1.09 Intr +  33872  37297 3426  0  0   75   40  2101 0.000 1054.84
 1.10 Intr +  37700  37788   89  0  2   83   98    23 0.000  22.57
 1.11 Intr +  46159  46327  169  0  1   14   93   155 0.000  28.32
 1.12 Intr +  52118  52244  127  0  1    7  116   133 0.000  29.90
 1.13 Intr +  54211  54401  191  1  2  107   58   162 0.000  35.37
 1.14 Intr +  57494  57804  311  0  2   96   59   336 0.000  98.33

Genoa hits used in predictions: 69 nonredundant hits

explanation

Genoa hit name      	Target protein                  	P.beg	P.end	 G.beg	 G.end	 RF	Program	E-val
--------------      	--------------                  	-----	-----	 -----	 -----	 --	-------	-----

Hit5.1_Hit3.1.i     	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1493	 1498	 52275	 54194	  1	BLASTX	6e-24
Hit6.1_Hit5.1.i     	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1452	 1450	 46362	 52084	  0	BLASTX	2.6e-23
Hit4.1_Hit7.1.i     	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  147	  148	 24642	 28826	  1	BLASTX	3e-17
Hit1.45L_Hit9.1.i   	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1365	 1365	 37329	 37669	  0	BLASTX	1e-14
Hit9.1_Hit6.1.i     	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1394	 1394	 37818	 46126	  0	BLASTX	1e-14
Hit10.1_Hit4.1.i    	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  100	  102	 23895	 24445	  0	BLASTX	5e-14
Hit8.1_Hit10.1.i    	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   71	   71	 22309	 23746	  0	BLASTX	6e-14
Hit11.1_Hit13.1.i   	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   26	   25	  4746	 12917	  1	BLASTX	2e-08
Hit13.1_Hit8.1.i    	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   45	   42	 13039	 22160	  1	BLASTX	2e-08
Hit1.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  233	  258	 33901	 33975	  0	BLASTX	0.00599
Hit1.2              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  258	  283	 33976	 34050	  0	BLASTX	0.00599
Hit1.3              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  283	  308	 34051	 34125	  0	BLASTX	0.00599
Hit1.4              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  308	  333	 34126	 34200	  0	BLASTX	0.00599
Hit1.5              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  333	  358	 34201	 34275	  0	BLASTX	0.00599
Hit1.6              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  358	  383	 34276	 34350	  0	BLASTX	0.00599
Hit1.7              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  383	  408	 34351	 34425	  0	BLASTX	0.00599
Hit1.8              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  408	  433	 34426	 34500	  0	BLASTX	0.00599
Hit1.9              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  433	  458	 34501	 34575	  0	BLASTX	0.00599
Hit1.10             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  458	  483	 34576	 34650	  0	BLASTX	0.00599
Hit1.11             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  483	  508	 34651	 34725	  0	BLASTX	0.00599
Hit1.12             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  508	  533	 34726	 34800	  0	BLASTX	0.00599
Hit1.13             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  533	  558	 34801	 34875	  0	BLASTX	0.00599
Hit1.14             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  558	  583	 34876	 34950	  0	BLASTX	0.00599
Hit1.15             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  583	  608	 34951	 35025	  0	BLASTX	0.00599
Hit1.16             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  608	  633	 35026	 35100	  0	BLASTX	0.00599
Hit1.17             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  633	  658	 35101	 35175	  0	BLASTX	0.00599
Hit1.18             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  658	  683	 35176	 35250	  0	BLASTX	0.00599
Hit1.19             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  683	  708	 35251	 35325	  0	BLASTX	0.00599
Hit1.20             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  708	  733	 35326	 35400	  0	BLASTX	0.00599
Hit1.21             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  733	  758	 35401	 35475	  0	BLASTX	0.00599
Hit1.22             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  758	  783	 35476	 35550	  0	BLASTX	0.00599
Hit1.23             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  783	  808	 35551	 35625	  0	BLASTX	0.00599
Hit1.24             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  808	  833	 35626	 35700	  0	BLASTX	0.00599
Hit1.25             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  833	  858	 35701	 35775	  0	BLASTX	0.00599
Hit1.26             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  858	  883	 35776	 35850	  0	BLASTX	0.00599
Hit1.27             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  883	  908	 35851	 35925	  0	BLASTX	0.00599
Hit1.28             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  908	  933	 35926	 36000	  0	BLASTX	0.00599
Hit1.29             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  933	  958	 36001	 36075	  0	BLASTX	0.00599
Hit1.30             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  958	  983	 36076	 36150	  0	BLASTX	0.00599
Hit1.31             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  983	 1008	 36151	 36225	  0	BLASTX	0.00599
Hit1.32             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1008	 1033	 36226	 36300	  0	BLASTX	0.00599
Hit1.33             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1033	 1058	 36301	 36375	  0	BLASTX	0.00599
Hit1.34             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1058	 1083	 36376	 36450	  0	BLASTX	0.00599
Hit1.35             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1083	 1108	 36451	 36525	  0	BLASTX	0.00599
Hit1.36             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1108	 1133	 36526	 36600	  0	BLASTX	0.00599
Hit1.37             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1133	 1158	 36601	 36675	  0	BLASTX	0.00599
Hit1.38             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1158	 1183	 36676	 36750	  0	BLASTX	0.00599
Hit1.39             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1183	 1208	 36751	 36825	  0	BLASTX	0.00599
Hit1.40             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1208	 1233	 36826	 36900	  0	BLASTX	0.00599
Hit1.41             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1233	 1258	 36901	 36975	  0	BLASTX	0.00599
Hit1.42             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1258	 1283	 36976	 37050	  0	BLASTX	0.00599
Hit1.43             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1283	 1308	 37051	 37125	  0	BLASTX	0.00599
Hit1.44             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1308	 1333	 37126	 37200	  0	BLASTX	0.00599
Hit1.45L            	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1333	 1365	 37201	 37299	  0	BLASTX	0.00599
Hit2.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1567	 1599	 57523	 57616	  0	BLASTX	9.28e-18
Hit2.2              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1599	 1630	 57617	 57710	  0	BLASTX	9.28e-18
Hit2.3L             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1630	 1660	 57711	 57804	  0	BLASTX	9.28e-18
Hit3.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1498	 1556	 54224	 54400	  1	BLASTX	4e-38
Hit4.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  102	  147	 24475	 24612	  0	BLASTX	1e-26
Hit5.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1450	 1493	 52114	 52245	  0	BLASTX	6e-24
Hit6.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1394	 1452	 46156	 46332	  0	BLASTX	2e-23
Hit7.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  148	  182	 28856	 28960	  1	BLASTX	3e-17
Hit8.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   42	   71	 22190	 22279	  1	BLASTX	1e-14
Hit9.1              	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	 1365	 1394	 37699	 37788	  0	BLASTX	1e-14
Hit10.1             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   71	  100	 23776	 23865	  0	BLASTX	5e-14
Hit11.1             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	    1	   26	  4639	  4716	  0	BLASTX	2e-11
Hit12.1             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  197	  222	 32808	 32885	  2	BLASTX	2e-11
Hit13.1             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	   25	   45	 12947	 13009	  1	BLASTX	2e-08
Hit14.1             	homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown	  181	  196	 31439	 31486	  1	BLASTX	1e-05


Predicted peptide sequence(s):


>homework_seq|GenomeScan_predicted_peptide_1|1660_aa:homework_seq|GenomeScan_predicted_peptide_1|1660_aa:gi|728984|spUnknown:1498..1556:E=4e-38
MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQ
CPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKD
EVSIIQSMGYRNRAKRLLQSEPENPSLETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIE
LGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEISLDSAKKAACEFSETDVTNTEHHQP
SNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENSSLLLTKDRMNVEK
AEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPCS
ENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDE
YSGSSEKIDLLASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENL
IIGAFVTEPQIIQERPLTNKLKRKRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQ
NGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEKESAFKTKAEPISSSISNMELELNIH
NSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSEEIKKKKYNQMPVR
HSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKEF
VNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQE
SISLLEVSTLGKAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSR
ETSIEMEESELDAQYLQNTFKVSKRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTF
ECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKDKPVDNAKCSIKGGSRFCLSSQFRGN
ETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSMSPEREMGNENIPS
TVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKLN
AMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSH
ASQVCSETPDDLLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQG
YRRGAKKLESSEENLSSEDEELPCFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLL
SLKNSLNDCSNQVILAKASQEHHLSEETKCSASLFSSQCSELEDLTANTNTQDPFLIGSS
KQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEAASGCESETSVSED
CSGLSSQSDILTTQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALEDL
RNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCP
SLDDRWYMHSCSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTP
YLESGISLFSDDPESDPSEDRAPESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDT
AGYNAMEESVSREKPELTASTERVNKRMSMVVSGLTPEEF

 


Explanation

Predicted genes/exons

Gn.Ex : gene number, exon number (for reference)
Type  : Init = Initial exon (ATG to 5' splice site)
        Intr = Internal exon (3' splice site to 5' splice site)
        Term = Terminal exon (3' splice site to stop codon)
        Sngl = Single-exon gene (ATG to stop)
        Prom = Promoter (TATA box / initation site)
        PlyA = poly-A signal (consensus: AATAAA)
S     : DNA strand (+ = input strand; - = opposite strand)
Begin : beginning of exon or signal (numbered on input strand)
End   : end point of exon or signal (numbered on input strand)
Len   : length of exon or signal (bp)
Fr    : reading frame (a forward strand codon ending at x has frame x mod 3)
Ph    : net phase of exon (exon length modulo 3)
I/Ac  : initiation signal or 3' splice site score (tenth bit units)
Do/T  : 5' splice site or termination signal score (tenth bit units)
CodRg : coding region score (tenth bit units)
P     : probability of exon (not calculated for GenomeScan)
Tscr  : exon score (depends on length, I/Ac, Do/T and CodRg scores)


Genoa hits used

Genoa hit name: names ending in ".i" are predicted introns
Target Protein: protein in which the hit is located
P.beg         : position of beginning in protein
P.end         : position of end in protein
G.beg         : position of beginning in DNA (nucleotide position on forward strand)
G.end         : position of end in DNA (nucleotide position on forward strand)
RF            : reading frame (forward strand codon ending at x has frame x mod 3)
Program       : name of program used for alignments, for reference
E-val         : probability that this is not a correct prediction


Comments

The SCORE of a predicted feature (e.g., exon or splice site) is a
log-odds measure of the quality of the feature based on local sequence
properties. For example, a predicted 5' splice site with
score > 100 is strong; 50-100 is moderate; 0-50 is weak; and
below 0 is poor (more than likely not a real donor site).

The PROBABILITY of a predicted exon is the estimated probability under
GenomeScan's model of genomic sequence structure that the exon is correct.
This probability depends in general on global as well as local sequence
properties, e.g., it depends on how well the exon fits with neighboring
exons.  It has been shown that predicted exons with higher probabilities
are more likely to be correct than those with lower probabilities.