HOXA9_ENSG00000078399_5e5.protein.info Alignment Results

Overview on processed synteny regions for HOXA9_ENSG00000078399_5e5.protein.info

Rank	AlnScore	RatioSum	logRatioSum	focalRatioSum	TargetGenome	chr	startPos	endPos	hitsCount	queryCov	meanIdentity	ori	score	compara
1	4073	13.08	3.29	3.66	Danio_rerio	16	15965005	15966531	2	99.6%	48.9%	-1	226.96	noComparaHits: hoxa9b
2	5581	14.73	2.58	3.63	Danio_rerio	19	10511297	10512339	2	63.2%	58%	1	181.55	noComparaHits: hoxa9a
3	2119	4.66	-0.39	1.12	Danio_rerio	12
4	1490	2.62	-0.4	0.79	Danio_rerio	11
5	596	0.48	-0.72	0.05	Danio_rerio	23
6	3269	6.38	-0.74	2.52	Danio_rerio	9	1948806	1949904	2	99.6%	48%	-1	239.99	noComparaHits: hoxd9a
7	4690	10.53	-0.76	3.29	Danio_rerio	3	23033313	23036568	2	82.7%	54.2%	1	212.88	noComparaHits: hoxb9a
8	204	0.33	-1.1	0.05	Danio_rerio	24
9	3322	7.54	-1.98	3.02	Danio_rerio	23	33742961	33744781	2	98.5%	49.6%	1	238.58	noComparaHits: hoxc9a
10	3318	7.54	-1.98	3.02	Danio_rerio	23	35245651	35247471	2	98.5%	49.6%	-1	238.58	noComparaHits: hoxc9a

Data table for reference protein loci

QueryProtein(s)=ENSP00000343619 (contained in p11)
QueryGenome=Homo_sapiens

ref-loci	geneName	protID	transID	geneID	protName	chr	startPos	endPos	meanPos	ori	numExons	protLength	selfscore
p1	SKAP2	ENSP00000005587	ENST00000345317	ENSG00000005020	SKAP2_HUMAN	7	26676244	26870573	26733074	-1	12	359	747.13
p2	-	ENSP00000328286	ENST00000333401	ENSG00000184579	-	7	26988911	26989532	26989233	-1	2	198	336.79
p3	HOXA1	ENSP00000343246	ENST00000343060	ENSG00000105991	HXA1_HUMAN	7	27100584	27102056	27101547	-1	2	335	615.59
p4	HOXA2	ENSP00000222718	ENST00000222718	ENSG00000105996	HXA2_HUMAN	7	27106870	27108644	27107431	-1	2	376	679.66
p5	HOXA3	ENSP00000324884	ENST00000317201	ENSG00000105997	HXA3_HUMAN	7	27114059	27116784	27114719	-1	2	443	525.69
p6	Q96MZ3_HUMAN	ENSP00000297027	ENST00000297027	ENSG00000164519	Q96MZ3_HUMAN	7	27122158	27128119	27122347	1	2	128	207.82
p7	HOXA4	ENSP00000353151	ENST00000360046	ENSG00000197576	HXA4_HUMAN	7	27135369	27136877	27136392	-1	2	320	627.91
p8	HOXA5	ENSP00000222726	ENST00000222726	ENSG00000106004	HXA5_HUMAN	7	27147979	27149751	27149341	-1	2	270	517.03
p9	HOXA6	ENSP00000222728	ENST00000222728	ENSG00000106006	HXA6_HUMAN	7	27151802	27153893	27153537	-1	2	233	460.35
p10	HOXA7	ENSP00000242159	ENST00000242159	ENSG00000122592	HXA7_HUMAN	7	27161053	27162689	27162339	-1	2	230	444.86
p11	HOXA9	ENSP00000343619	ENST00000343483	ENSG00000078399	HXA9_HUMAN	7	27169747	27171601	27171188	-1	2	272	528.64
p12	HOXA10	ENSP00000283921	ENST00000283921	ENSG00000153807	HXA10_HUMAN	7	27178043	27180399	27179803	-1	2	393	663.81
p13	HOXA11	ENSP00000006015	ENST00000006015	ENSG00000005073	HXA11_HUMAN	7	27188940	27191288	27190812	-1	2	313	377.85
p14	HOXA13	ENSP00000222753	ENST00000222753	ENSG00000106031	HXA13_HUMAN	7	27204342	27206221	27205634	-1	2	388	607.14
p15	EVX1	ENSP00000222761	ENST00000222761	ENSG00000106038	EVX1_HUMAN	7	27249175	27252569	27251371	1	3	407	588.83
p16	A4D198_HUMAN	ENSP00000322111	ENST00000313812	ENSG00000177093	A4D198_HUMAN	7	27464307	27464999	27464649	-1	1	230	433.46
p17	HIBADH	ENSP00000265395	ENST00000265395	ENSG00000106049	3HIDH_HUMAN	7	27532358	27668932	27549219	-1	8	336	654.39

total length of ref-loci (on slice) = 992689 (99e4)

Parameter used for the loci-alignments

qLoci-Score_CutOff: 100 bits
qLoci-MaxProtOverlap: 40 aa
loci size factor: 2 (additional loci size constraint: 0 nt)
loci-grouping type: loci intervalls
max distance between non-highlighted (orange) target columns: 500000 nt
RelativeScore color index:

<=
33

<=
66

<=
100

<=
133

<=
166

<=
200

<=
233

<=
266

<=
300

<=
333

<=
366

<=
400

<=
433

<=
466

<=
500

<=
533

<=
566

<=
600

<=
633

<=
666

<=
700

<=
733

<=
766

<=
800

<=
833

<=
866

<=
900

<=
933

<=
966

<=
1000

relSc>1000

<=
33

<=
66

<=
100

<=
133

<=
166

<=
200

<=
233

<=
266

<=
300

<=
333

<=
366

<=
400

<=
433

<=
466

<=
500

<=
533

<=
566

<=
600

<=
633

<=
666

<=
700

<=
733

<=
766

<=
800

<=
833

<=
866

<=
900

<=
933

<=
966

<=
1000

relSc>1000

region 1

syntenyRegion: Danio_rerio.glob03.16.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 16 -i 15878347:17844753 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=13.08 log_scoreRatio_sum=3.29 focal_scoreRatio_sum=3.66
AlnScore=4073 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	q1	+/+	ENSP00000005587	SKAP2	q1	q1	385.44	16	15905869	15946733	-1	8	69.9%	66%	804	0.59 / 0.48 = 1.23	ortholog_one2one: skap2	1
p2	---	gapq	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gapq	ENSP00000343246	HOXA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	q2	+/+	ENSP00000222718	HOXA2	q2	q2	473.02	16	15953161	15954846	-1	2	98.9%	71%	1071	0.55 / 0.3 = 1.83	ortholog_one2one: hoxa2b	1
p5	---	gapq	ENSP00000324884	HOXA3	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gapq	ENSP00000353151	HOXA4	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gapq	ENSP00000222726	HOXA5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000222728	HOXA6	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gapq	ENSP00000242159	HOXA7	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	q3	+/+	ENSP00000343619	HOXA9	q3	q3	226.96	16	15965005	15966531	-1	2	99.6%	48.9%	774	0.55 / 0.57 = 0.96	noComparaHits: hoxa9b	3
p12	q4	+/+	ENSP00000283921	HOXA10	q4	q4	237.87	16	15969590	15971748	-1	2	65.4%	56%	696	0.65 / 0.64 = 1.02	noComparaHits: hoxa10b	1
p13	q5	+/+	ENSP00000006015	HOXA11	q5	q5	344.19	16	15975493	15977085	-1	2	87.2%	67%	813	0.25 / 0.08 = 3.13	ortholog_one2many: hoxa11b	1
p14	q6	+/+	ENSP00000222753	HOXA13	q6	q6	249.84	16	15984766	15985716	-1	2	50.3%	66.5%	579	0.58 / 0.58 = 1	ortholog_one2many: hoxa13b	3
p15	---	gapq	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gapq	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	q7	+/+	ENSP00000265395	HIBADH	q7	q7	507.48	16	15993005	16007851	-1	7	90.5%	82%	933	0.86 / 0.22 = 3.91	ortholog_one2many: hibadh	1

region 2

syntenyRegion: Danio_rerio.glob01.19.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 19 -i 8631227:10562315 -f 14e5 some_geneID_to_be_selected
scoreRatio_sum=14.73 log_scoreRatio_sum=2.58 focal_scoreRatio_sum=3.63
AlnScore=5581 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000343246	HOXA1	q1	q1	328.34	19	10547332	10548513	1	2	98.2%	56%	993	0.69 / 0.46 = 1.5	ortholog_one2one: hoxa1a	1
p4	q2	+/+	ENSP00000222718	HOXA2	q2	q2	133.33	19	10543546	10544525	1	2	49.2%	48.9%	510	0.55 / 0.8 = 0.69	noComparaHits:	3
p5	q3	+/+	ENSP00000324884	HOXA3	q3	q3	391.01	19	10538806	10540642	1	2	87.6%	57.9%	1149	0.26 / 0.25 = 1.04	ortholog_one2one: hoxa3a	2
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q4	+/+	ENSP00000353151	HOXA4	q4	q4	191.4	19	10528761	10529933	1	2	74.4%	47.1%	723	0.59 / 0.69 = 0.86	ortholog_one2one: hoxa4a	2
p8	q5	+/+	ENSP00000222726	HOXA5	q5	q5	331.87	19	10520701	10522002	1	2	100%	66.5%	825	0.41 / 0.35 = 1.17	ortholog_one2one: hoxa5a	1
p9	---	gapq	ENSP00000222728	HOXA6	q4	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gapq	ENSP00000242159	HOXA7	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	q6	+/+	ENSP00000343619	HOXA9	q6	q6	181.55	19	10511297	10512339	1	2	63.2%	58%	501	0.55 / 0.65 = 0.85	noComparaHits: hoxa9a	5
p12	---	gapq	ENSP00000283921	HOXA10	q6	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	q7	+/+	ENSP00000006015	HOXA11	q7	q7	337.14	19	10498422	10499983	1	2	91.7%	62.6%	858	0.25 / 0.1 = 2.5	ortholog_one2many: hoxa11a	2
p14	q8	+/+	ENSP00000222753	HOXA13	q8	q8	295.26	19	10490838	10491773	1	2	71.4%	60.2%	813	0.58 / 0.51 = 1.14	ortholog_one2many: hoxa13a	1
p15	q9	+/+	ENSP00000222761	EVX1	q9	q9	411.55	19	10480188	10482503	-1	3	95.3%	59.7%	1107	0.42 / 0.3 = 1.4	ortholog_one2one: evx1	1
p16	---	gapq	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	q10	+/+	ENSP00000265395	HIBADH	q10	q10	494.44	19	10363653	10418066	1	7	89.3%	72.9%	1047	0.86 / 0.24 = 3.58	ortholog_one2many: zgc:100804	2

region 3

syntenyRegion: Danio_rerio.glob08.12.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 12 -i 26131306:28039019 -f 14e5 some_geneID_to_be_selected
scoreRatio_sum=4.66 log_scoreRatio_sum=-0.39 focal_scoreRatio_sum=1.12
AlnScore=2119 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	q1	+/+	ENSP00000005587	SKAP2	q1	q1	327.37	12	26394051	26440888	-1	8	77.7%	49.8%	945	0.59 / 0.56 = 1.05	between_species_paralog: skap2	2
p2	---	gapq	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q2	+/+	ENSP00000343246	HOXA1	q2	q2	183.66	12	26456223	26457244	-1	2	97.9%	39.8%	939	0.69 / 0.7 = 0.99	noComparaHits: hoxb1b	3
p4	---	gapq	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gapq	ENSP00000324884	HOXA3	q3	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gapq	ENSP00000353151	HOXA4	q3	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	q3	+/+	ENSP00000222726	HOXA5	q3	q3	285.4	12	26467712	26468987	-1	2	98.1%	57.7%	816	0.41 / 0.44 = 0.93	between_species_paralog: hoxb5b	3
p9	q4	+/+	ENSP00000222728	HOXA6	q4	q4	232.94	12	26470452	26471559	-1	2	99.6%	58.1%	675	0.48 / 0.49 = 0.98	ortholog_one2one: hoxb6b	2
p10	q5	+/+	ENSP00000242159	HOXA7	q5	q5	149.51	12	26478803	26480924	-1	2	85.7%	46.8%	642	0.47 / 0.66 = 0.71	noComparaHits: hoxb8b	3
p11	---	gape	ENSP00000343619	HOXA9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000283921	HOXA10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000006015	HOXA11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000222753	HOXA13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 4

syntenyRegion: Danio_rerio.glob07.11.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 11 -i 4109:1929754 -f 14e5 some_geneID_to_be_selected
scoreRatio_sum=2.62 log_scoreRatio_sum=-0.4 focal_scoreRatio_sum=0.79
AlnScore=1490 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000343246	HOXA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gaps	ENSP00000324884	HOXA3	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gaps	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gaps	ENSP00000353151	HOXA4	q1	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gaps	ENSP00000222726	HOXA5	q1	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q1	+/+	ENSP00000222728	HOXA6	q1	q1	194.92	11	589745	590834	1	2	100%	47%	684	0.48 / 0.57 = 0.84	noComparaHits: hoxc6b	4
p10	---	gapq	ENSP00000242159	HOXA7	q1	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gapq	ENSP00000343619	HOXA9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gapq	ENSP00000283921	HOXA10	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	q2	+/+	ENSP00000006015	HOXA11	q2	q2	260.75	11	566842	568428	1	2	93.3%	51.2%	852	0.25 / 0.3 = 0.83	noComparaHits: hoxc11b	5
p14	q3	+/+	ENSP00000222753	HOXA13	q3	q3	232.94	11	547516	549822	1	2	58.5%	59.1%	642	0.58 / 0.61 = 0.95	noComparaHits: hoxc13b	5
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 5

syntenyRegion: Danio_rerio.glob11.23.minQN4.fac2.03.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 40370623:42333822 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=0.48 log_scoreRatio_sum=-0.72 focal_scoreRatio_sum=0.05
AlnScore=596 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000328286	-	q1	q1	201.04	23	42161159	42162169	1	3	75.8%	58.1%	480	0.19 / 0.4 = 0.48	between_species_paralog: HMGB2 (2 of 3)	3
p3	---	gape	ENSP00000343246	HOXA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gape	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gape	ENSP00000324884	HOXA3	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gape	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gape	ENSP00000353151	HOXA4	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gape	ENSP00000222726	HOXA5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gape	ENSP00000222728	HOXA6	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gape	ENSP00000242159	HOXA7	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gape	ENSP00000343619	HOXA9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000283921	HOXA10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000006015	HOXA11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000222753	HOXA13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 6

syntenyRegion: Danio_rerio.glob04.9.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 9 -i 1921957:3874634 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=6.38 log_scoreRatio_sum=-0.74 focal_scoreRatio_sum=2.52
AlnScore=3269 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000343246	HOXA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000222718	HOXA2	q1	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q1	+/+	ENSP00000324884	HOXA3	q1	q1	305.81	9	1922029	1923358	-1	2	84.4%	49.3%	1047	0.26 / 0.41 = 0.63	between_species_paralog: hoxd3a	3
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q2	+/+	ENSP00000353151	HOXA4	q2	q2	189.64	9	1933897	1934984	-1	2	45.9%	67.8%	429	0.59 / 0.69 = 0.86	between_species_paralog: hoxd4a	4
p8	---	gapq	ENSP00000222726	HOXA5	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000222728	HOXA6	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gapq	ENSP00000242159	HOXA7	q2	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	q3	+/+	ENSP00000343619	HOXA9	q3	q3	239.99	9	1948806	1949904	-1	2	99.6%	48%	855	0.55 / 0.54 = 1.02	noComparaHits: hoxd9a	1
p12	q4	+/+	ENSP00000283921	HOXA10	q4	q4	208.66	9	1952491	1953931	-1	2	42%	68.7%	480	0.65 / 0.68 = 0.96	noComparaHits: hoxd10a	2
p13	q5	+/+	ENSP00000006015	HOXA11	q5	q5	284.69	9	1960574	1962255	-1	2	91.1%	56.1%	825	0.25 / 0.24 = 1.04	noComparaHits: hoxd11a	4
p14	q6	+/+	ENSP00000222753	HOXA13	q6	q6	161.13	9	1971944	1974397	-1	2	57.7%	46.5%	651	0.58 / 0.73 = 0.79	noComparaHits: hoxd13a	6
p15	q7	+/+	ENSP00000222761	EVX1	q7	q7	358.87	9	1987346	1989676	1	4	74.2%	63.1%	918	0.42 / 0.39 = 1.08	between_species_paralog: evx2	2
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 7

syntenyRegion: Danio_rerio.glob02.3.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 3 -i 21211959:23186838 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=10.53 log_scoreRatio_sum=-0.76 focal_scoreRatio_sum=3.29
AlnScore=4690 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000343246	HOXA1	q1	q1	217.46	3	23124590	23126293	1	2	99.1%	45.1%	969	0.69 / 0.64 = 1.08	noComparaHits: hoxb1a	2
p4	q2	+/+	ENSP00000222718	HOXA2	q2	q2	299.12	3	23107926	23109945	1	2	99.5%	50.9%	1146	0.55 / 0.55 = 1	between_species_paralog: hoxb2a	2
p5	q3	+/+	ENSP00000324884	HOXA3	q3	q3	427.97	3	23101788	23103710	1	2	100%	56.2%	1245	0.26 / 0.18 = 1.44	between_species_paralog: hoxb3a	1
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q4	+/+	ENSP00000353151	HOXA4	q4	q4	206.55	3	23077620	23079309	1	2	71.9%	51.9%	678	0.59 / 0.67 = 0.88	between_species_paralog: hoxb4a	1
p8	q5	+/+	ENSP00000222726	HOXA5	q5	q5	291.03	3	23063599	23065038	1	2	100%	58.8%	858	0.41 / 0.43 = 0.95	between_species_paralog: hoxb5a	2
p9	q6	+/+	ENSP00000222728	HOXA6	q6	q6	250.55	3	23059516	23061253	1	2	99.1%	59.1%	681	0.48 / 0.45 = 1.07	between_species_paralog: hoxb6a	1
---	q7	gapp	-	-	-	q7	-	-	-	-	-	-	-	-	-	-	-	-
p10	q8	+/+	ENSP00000242159	HOXA7	q8	q8	141.78	3	23044103	23045506	1	2	86.5%	44.1%	654	0.47 / 0.68 = 0.69	noComparaHits: hoxb8a	4
p11	q9	+/+	ENSP00000343619	HOXA9	q9	q9	212.88	3	23033313	23036568	1	2	82.7%	54.2%	621	0.55 / 0.59 = 0.93	noComparaHits: hoxb9a	4
p12	q10	+/+	ENSP00000283921	HOXA10	q10	q10	131.43	3	23026693	23026944	1	1	21.1%	82.1%	252	0.65 / 0.8 = 0.81	noComparaHits: hoxb10a	5
p13	---	gapq	ENSP00000006015	HOXA11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	q11	+/+	ENSP00000222753	HOXA13	q11	q11	280.82	3	23010358	23011476	1	2	62.9%	63.4%	690	0.58 / 0.53 = 1.09	between_species_paralog: hoxb13a	2
p15	q12	+/+	ENSP00000222761	EVX1	q12	q12	167.47	3	22998210	22999095	-1	2	45.7%	51.1%	537	0.42 / 0.71 = 0.59	noComparaHits: eve1	3
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 8

syntenyRegion: Danio_rerio.glob09.24.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 24 -i 19763797:21724407 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=0.33 log_scoreRatio_sum=-1.1 focal_scoreRatio_sum=0.05
AlnScore=204 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000343246	HOXA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q1	+/+	ENSP00000324884	HOXA3	q1	q1	107.28	24	20272372	20274036	1	2	16%	70.4%	213	0.26 / 0.79 = 0.33	noComparaHits: pdx1	9
p6	---	gape	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gape	ENSP00000353151	HOXA4	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gape	ENSP00000222726	HOXA5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gape	ENSP00000222728	HOXA6	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gape	ENSP00000242159	HOXA7	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gape	ENSP00000343619	HOXA9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000283921	HOXA10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000006015	HOXA11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000222753	HOXA13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 9

syntenyRegion: Danio_rerio.glob05.23.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 31855395:33831080 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=7.54 log_scoreRatio_sum=-1.98 focal_scoreRatio_sum=3.02
AlnScore=3322 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
p1	---	gaps	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000343246	HOXA1	q3	q1	102.22	23	33830835	33831080	1	1	24.8%	71.1%	246	0.69 / 0.83 = 0.83	noComparaHits: hoxc1a	5
p4	---	gapq	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q2	+/+	ENSP00000324884	HOXA3	q2	q2	101.16	23	33795334	33795546	1	1	16%	74.6%	213	0.26 / 0.8 = 0.33	noComparaHits: hoxc3a	10
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q3	+/+	ENSP00000353151	HOXA4	q3	q3	190.35	23	33778862	33779867	1	2	55%	61.6%	483	0.59 / 0.69 = 0.86	between_species_paralog: hoxc4a	3
p8	---	gapq	ENSP00000222726	HOXA5	q4	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q4	+/+	ENSP00000222728	HOXA6	q4	q4	206.67	23	33763064	33767828	1	3	92.7%	49.4%	654	0.48 / 0.55 = 0.87	noComparaHits: hoxc6a ; hoxc5a	3
p10	q5	+/+	ENSP00000242159	HOXA7	q5	q5	151.27	23	33749042	33751044	1	2	80%	50.8%	534	0.47 / 0.65 = 0.72	noComparaHits: hoxc8a	2
p11	q6	+/+	ENSP00000343619	HOXA9	q6	q6	238.58	23	33742961	33744781	1	2	98.5%	49.6%	765	0.55 / 0.54 = 1.02	noComparaHits: hoxc9a	2
p12	q7	+/+	ENSP00000283921	HOXA10	q7	q7	182.6	23	33731209	33733955	1	2	64.9%	46.4%	729	0.65 / 0.72 = 0.9	noComparaHits: hoxc10a	3
p13	q8	+/+	ENSP00000006015	HOXA11	q8	q8	285.05	23	33722561	33724786	1	2	93.3%	55.5%	852	0.25 / 0.24 = 1.04	noComparaHits: hoxc11a	3
p14	q9	+/+	ENSP00000222753	HOXA13	q9	q9	242.45	23	33701748	33704206	1	2	62.1%	58.8%	678	0.58 / 0.6 = 0.97	noComparaHits: hoxc13a	4
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 10

syntenyRegion: Danio_rerio.glob06.23.minQN4.fac2.02.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 35047023:37012084 -f 15e5 some_geneID_to_be_selected
scoreRatio_sum=7.54 log_scoreRatio_sum=-1.98 focal_scoreRatio_sum=3.02
AlnScore=3318 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000343619 (contained in p11)
TargetGenome=Danio_rerio

ref-loci	target-loci	aln	protID	geneName	optQloci	target-loci	score	chr	startPos	endPos	ori	hits	queryCov	meanIdentity	hitsLength	intra_inter	compara	globalRank
---	q1	gaps	-	-	-	q1	-	-	-	-	-	-	-	-	-	-	-	-
p1	---	gapq	ENSP00000005587	SKAP2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gapq	ENSP00000328286	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q2	+/+	ENSP00000343246	HOXA1	q4	q2	102.22	23	35159197	35159442	-1	1	24.8%	71.1%	246	0.69 / 0.83 = 0.83	noComparaHits: hoxc1a	5
p4	---	gapq	ENSP00000222718	HOXA2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q3	+/+	ENSP00000324884	HOXA3	q5	q3	101.16	23	35194845	35195057	-1	1	16%	74.6%	213	0.26 / 0.8 = 0.33	noComparaHits: hoxc3a	10
p6	---	gapq	ENSP00000297027	Q96MZ3_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q4	+/+	ENSP00000353151	HOXA4	q4	q4	190.35	23	35210616	35211621	-1	2	55%	61.6%	483	0.59 / 0.69 = 0.86	between_species_paralog: hoxc4a	3
p8	---	gapq	ENSP00000222726	HOXA5	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q5	+/+	ENSP00000222728	HOXA6	q5	q5	206.67	23	35222647	35227411	-1	3	92.7%	49.4%	654	0.48 / 0.55 = 0.87	noComparaHits: hoxc5a ; hoxc6a	3
p10	q6	+/+	ENSP00000242159	HOXA7	q6	q6	151.27	23	35239388	35241390	-1	2	80%	50.8%	534	0.47 / 0.65 = 0.72	noComparaHits: hoxc8a	2
p11	q7	+/+	ENSP00000343619	HOXA9	q7	q7	238.58	23	35245651	35247471	-1	2	98.5%	49.6%	765	0.55 / 0.54 = 1.02	noComparaHits: hoxc9a	2
p12	q8	+/+	ENSP00000283921	HOXA10	q8	q8	182.6	23	35256479	35259225	-1	2	64.9%	46.4%	729	0.65 / 0.72 = 0.9	noComparaHits: hoxc10a	3
p13	q9	+/+	ENSP00000006015	HOXA11	q9	q9	285.05	23	35265648	35267873	-1	2	93.3%	55.5%	852	0.25 / 0.24 = 1.04	noComparaHits: hoxc11a	3
p14	q10	+/+	ENSP00000222753	HOXA13	q10	q10	242.45	23	35287160	35289618	-1	2	62.1%	58.8%	678	0.58 / 0.6 = 0.97	noComparaHits: hoxc13a	4
p15	---	gape	ENSP00000222761	EVX1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p16	---	gape	ENSP00000322111	A4D198_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p17	---	gape	ENSP00000265395	HIBADH	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

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