HOXD9_ENSG00000128709_5e5.protein.info Alignment Results

Overview on processed synteny regions for HOXD9_ENSG00000128709_5e5.protein.info

Rank	AlnScore	RatioSum	logRatioSum	focalRatioSum	TargetGenome	chr	startPos	endPos	hitsCount	queryCov	meanIdentity	ori	score	compara
1	4326	11.41	1.76	3.78	Danio_rerio	9	1948809	1949904	3	68.1%	62.7%	-1	265.46	noComparaHits: hoxd9a
2	3017	7.61	-0.41	2.91	Danio_rerio	23	33742961	33744781	2	75.1%	55%	1	241.75	noComparaHits: hoxc9a
3	3013	7.61	-0.41	2.91	Danio_rerio	23	35245651	35247471	2	75.1%	55%	-1	241.75	noComparaHits: hoxc9a
4	2799	7.14	-0.92	2.32	Danio_rerio	19	10511297	10512327	2	57%	51%	1	172.75	noComparaHits: hoxa9a
5	2660	7.26	-0.85	2.42	Danio_rerio	3	23036335	23036565	1	22.8%	85.9%	1	133.9	noComparaHits: hoxb9a
6	1811	4.44	-0.63	2.06	Danio_rerio	16	15965008	15966531	2	66.1%	52.4%	-1	195.28	noComparaHits: hoxa9b
7	1303	3.38	-0.71	0.87	Danio_rerio	11
8	871	2.47	-0.6	0.61	Danio_rerio	12

Data table for reference protein loci

QueryProtein(s)=ENSP00000249499 (contained in p7)
QueryGenome=Homo_sapiens

ref-loci	geneName	protID	transID	geneID	protName	chr	startPos	endPos	meanPos	ori	numExons	protLength	selfscore
p1	KIAA1715	ENSP00000272748	ENST00000272748	ENSG00000144320	LNP_HUMAN	2	176502941	176568558	176520512	-1	12	428	832.9
p2	EVX2	ENSP00000312385	ENST00000308618	ENSG00000174279	EVX2_HUMAN	2	176653081	176656750	176653792	-1	3	476	758.65
p3	HOXD13	ENSP00000249505	ENST00000249505	ENSG00000128714	HXD13_HUMAN	2	176665889	176667704	176666387	1	2	335	600.45
p4	HOXD12	ENSP00000303578	ENST00000306412	ENSG00000170178	HXD12_HUMAN	2	176672776	176673734	176673190	1	3	278	514.91
p5	HOXD11	ENSP00000249504	ENST00000249504	ENSG00000128713	NP_067015.2	2	176680330	176682116	176680834	1	2	338	527.36
p6	HOXD10	ENSP00000249501	ENST00000249501	ENSG00000128710	HXD10_HUMAN	2	176689808	176692205	176690315	1	2	340	636.01
p7	HOXD9	ENSP00000249499	ENST00000249499	ENSG00000128709	HXD9_HUMAN	2	176695773	176697149	176696283	1	2	342	629.32
p8	Q8NAT4_HUMAN	ENSP00000316098	ENST00000313266	ENSG00000175892	Q8NAT4_HUMAN	2	176701687	176702151	176701915	-1	1	154	278.58
p9	HOXD8	ENSP00000315949	ENST00000313173	ENSG00000175879	HXD8_HUMAN	2	176703341	176704586	176703773	1	2	290	499.78
p10	HOXD4	ENSP00000302548	ENST00000306324	ENSG00000170166	HXD4_HUMAN	2	176724608	176725916	176724986	1	2	255	505.41
p11	HOXD3	ENSP00000249440	ENST00000249440	ENSG00000128652	HXD3_HUMAN	2	176742089	176745248	176744595	1	2	432	841.23
p12	HOXD1	ENSP00000328598	ENST00000331462	ENSG00000128645	HXD1_HUMAN	2	176761776	176763116	176762265	1	2	328	579.33
p13	-	ENSP00000346209	ENST00000331781	ENSG00000182553	-	2	176773882	176774226	176774050	-1	1	114	208.53
p14	MTX2	ENSP00000249442	ENST00000249442	ENSG00000128654	MTX2_HUMAN	2	176842604	176910638	176901860	1	10	263	549.05

total length of ref-loci (on slice) = 407698 (41e4)

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.glob01.9.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 9 -i 1485735:2296330 -f 61e4 some_geneID_to_be_selected
scoreRatio_sum=11.41 log_scoreRatio_sum=1.76 focal_scoreRatio_sum=3.78
AlnScore=4326 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	+/+	ENSP00000272748	KIAA1715	q1	q1	358.12	9	2011126	2074682	1	9	73.1%	53.1%	1005	0.9 / 0.57 = 1.58	ortholog_one2many: lnp	1
p2	q2	+/+	ENSP00000312385	EVX2	q2	q2	500.26	9	1987331	1989553	1	3	85.7%	68.8%	1137	0.6 / 0.34 = 1.76	ortholog_one2one: evx2	1
p3	q3	+/+	ENSP00000249505	HOXD13	q3	q3	165.01	9	1971944	1974445	-1	2	65.1%	43.2%	657	0.59 / 0.72 = 0.82	noComparaHits: hoxd13a	6
p4	q4	+/+	ENSP00000303578	HOXD12	q4	q4	109.61	9	1966604	1966846	-1	1	29.1%	70.4%	243	0.65 / 0.78 = 0.83	ortholog_one2one: hoxd12a	3
p5	q5	+/+	ENSP00000249504	HOXD11	q5	q5	268.63	9	1960571	1962261	-1	3	71.3%	60.4%	705	0.49 / 0.49 = 1	noComparaHits: hoxd11a	1
p6	q6	+/+	ENSP00000249501	HOXD10	q6	q6	440.28	9	1952491	1954201	-1	2	99.7%	69.7%	996	0.56 / 0.3 = 1.87	ortholog_one2one: hoxd10a	1
p7	q7	+/+	ENSP00000249499	HOXD9	q7	q7	265.46	9	1948809	1949904	-1	3	68.1%	62.7%	657	0.61 / 0.57 = 1.07	noComparaHits: hoxd9a	1
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000315949	HOXD8	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	q8	+/+	ENSP00000302548	HOXD4	q8	q8	280.12	9	1933885	1934984	-1	2	100%	60.9%	711	0.5 / 0.44 = 1.14	between_species_paralog: hoxd4a	1
p11	q9	+/+	ENSP00000249440	HOXD3	q9	q9	488.51	9	1921957	1923316	-1	2	90.5%	66.8%	1152	0.55 / 0.41 = 1.34	ortholog_one2one: hoxd3a	1
p12	---	gape	ENSP00000328598	HOXD1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 2

syntenyRegion: Danio_rerio.glob05.23.minQN4.fac2.02.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 33292385:34096581 -f 60e4 some_geneID_to_be_selected
scoreRatio_sum=7.61 log_scoreRatio_sum=-0.41 focal_scoreRatio_sum=2.91
AlnScore=3017 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000312385	EVX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000249505	HOXD13	q1	q1	254.07	23	33701670	33704197	1	2	79.1%	53.9%	750	0.59 / 0.57 = 1.04	noComparaHits: hoxc13a	1
p4	q2	+/+	ENSP00000303578	HOXD12	q2	q2	162.54	23	33711191	33712771	1	2	50%	60.8%	426	0.65 / 0.68 = 0.96	noComparaHits: A2BE68_DANRE	1
p5	q3	+/+	ENSP00000249504	HOXD11	q3	q3	233.43	23	33722558	33724783	1	3	64.5%	58.2%	636	0.49 / 0.55 = 0.89	noComparaHits: hoxc11a	4
p6	q4	+/+	ENSP00000249501	HOXD10	q4	q4	228.72	23	33731209	33733940	1	2	98.2%	46.2%	1005	0.56 / 0.64 = 0.88	noComparaHits: hoxc10a	3
p7	q5	+/+	ENSP00000249499	HOXD9	q5	q5	241.75	23	33742961	33744781	1	2	75.1%	55%	744	0.61 / 0.61 = 1	noComparaHits: hoxc9a	2
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q6	+/+	ENSP00000315949	HOXD8	q6	q6	229.78	23	33749264	33751014	1	2	56.2%	73.2%	483	0.55 / 0.54 = 1.02	between_species_paralog: hoxc8a	1
---	q7	gapp	-	-	-	q7	-	-	-	-	-	-	-	-	-	-	-	-
---	q8	gapp	-	-	-	q8	-	-	-	-	-	-	-	-	-	-	-	-
p10	q9	+/+	ENSP00000302548	HOXD4	q9	q9	245.62	23	33778655	33779888	1	2	92.5%	57.6%	714	0.5 / 0.51 = 0.98	between_species_paralog: hoxc4a	3
p11	---	gapq	ENSP00000249440	HOXD3	q9	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q10	+/+	ENSP00000328598	HOXD1	q10	q10	100.81	23	33830823	33831014	1	1	19.5%	84.4%	192	0.69 / 0.82 = 0.84	noComparaHits: hoxc1a	4
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 3

syntenyRegion: Danio_rerio.glob04.23.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 35106321:35900467 -f 60e4 some_geneID_to_be_selected
scoreRatio_sum=7.61 log_scoreRatio_sum=-0.41 focal_scoreRatio_sum=2.91
AlnScore=3013 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000312385	EVX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000249505	HOXD13	q1	q1	254.07	23	35287169	35289696	-1	2	79.1%	53.9%	750	0.59 / 0.57 = 1.04	noComparaHits: hoxc13a	1
p4	q2	+/+	ENSP00000303578	HOXD12	q2	q2	162.54	23	35277627	35279207	-1	2	50%	60.8%	426	0.65 / 0.68 = 0.96	noComparaHits: A2BE68_DANRE	1
p5	q3	+/+	ENSP00000249504	HOXD11	q3	q3	233.43	23	35265651	35267876	-1	3	64.5%	58.2%	636	0.49 / 0.55 = 0.89	noComparaHits: hoxc11a	4
p6	q4	+/+	ENSP00000249501	HOXD10	q4	q4	228.72	23	35256494	35259225	-1	2	98.2%	46.2%	1005	0.56 / 0.64 = 0.88	noComparaHits: hoxc10a	3
p7	q5	+/+	ENSP00000249499	HOXD9	q5	q5	241.75	23	35245651	35247471	-1	2	75.1%	55%	744	0.61 / 0.61 = 1	noComparaHits: hoxc9a	2
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q6	+/+	ENSP00000315949	HOXD8	q6	q6	229.78	23	35239418	35241168	-1	2	56.2%	73.2%	483	0.55 / 0.54 = 1.02	between_species_paralog: hoxc8a	1
---	q7	gapp	-	-	-	q7	-	-	-	-	-	-	-	-	-	-	-	-
---	q8	gapp	-	-	-	q8	-	-	-	-	-	-	-	-	-	-	-	-
p10	q9	+/+	ENSP00000302548	HOXD4	q9	q9	245.62	23	35210595	35211828	-1	2	92.5%	57.6%	714	0.5 / 0.51 = 0.98	between_species_paralog: hoxc4a	3
p11	---	gapq	ENSP00000249440	HOXD3	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q10	+/+	ENSP00000328598	HOXD1	q10,q11	q10	100.81	23	35159263	35159454	-1	1	19.5%	84.4%	192	0.69 / 0.82 = 0.84	noComparaHits: hoxc1a	4
p13	---	gapq	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gapq	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
---	q11	gape	-	-	-	q11	-	-	-	-	-	-	-	-	-	-	-	-

region 4

syntenyRegion: Danio_rerio.glob03.19.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 19 -i 9779001:10548546 -f 58e4 some_geneID_to_be_selected
scoreRatio_sum=7.14 log_scoreRatio_sum=-0.92 focal_scoreRatio_sum=2.32
AlnScore=2799 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000312385	EVX2	q1	q1	258.64	19	10480293	10481282	-1	2	48.5%	61.6%	669	0.6 / 0.65 = 0.92	between_species_paralog: evx1	2
p3	q2	+/+	ENSP00000249505	HOXD13	q2	q2	236.11	19	10490898	10491770	1	2	76.1%	50.3%	825	0.59 / 0.6 = 0.98	between_species_paralog: hoxa13a	3
p4	---	gapq	ENSP00000303578	HOXD12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q3	+/+	ENSP00000249504	HOXD11	q3	q3	250.32	19	10498419	10499980	1	3	66.9%	58.8%	717	0.49 / 0.52 = 0.94	noComparaHits: hoxa11a	3
p6	---	gapq	ENSP00000249501	HOXD10	q4	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q4	+/+	ENSP00000249499	HOXD9	q4	q4	172.75	19	10511297	10512327	1	2	57%	51%	543	0.61 / 0.72 = 0.85	noComparaHits: hoxa9a	4
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q5	+/+	ENSP00000315949	HOXD8	q5	q5	134.15	19	10520701	10521954	1	3	32.1%	62.4%	300	0.55 / 0.73 = 0.75	noComparaHits: hoxa5a	4
p10	q6	+/+	ENSP00000302548	HOXD4	q6	q6	215.34	19	10528752	10529879	1	2	89.8%	53.4%	681	0.5 / 0.57 = 0.88	between_species_paralog: hoxa4a	4
p11	q7	+/+	ENSP00000249440	HOXD3	q7	q7	310.04	19	10538878	10540642	1	2	90.5%	46.9%	1209	0.55 / 0.63 = 0.87	between_species_paralog: hoxa3a	3
p12	q8	+/+	ENSP00000328598	HOXD1	q8	q8	152.34	19	10547332	10548486	1	2	98.8%	37.3%	966	0.69 / 0.73 = 0.95	noComparaHits: hoxa1a	1
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 5

syntenyRegion: Danio_rerio.glob02.3.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 3 -i 22469490:23155711 -f 51e4 some_geneID_to_be_selected
scoreRatio_sum=7.26 log_scoreRatio_sum=-0.85 focal_scoreRatio_sum=2.42
AlnScore=2660 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000312385	EVX2	q1	q1	157.61	3	22998306	22999104	-1	2	34%	52.1%	450	0.6 / 0.79 = 0.76	noComparaHits: eve1	3
p3	q2	+/+	ENSP00000249505	HOXD13	q2	q2	247.73	3	23010325	23011473	1	2	75.8%	52.9%	729	0.59 / 0.58 = 1.02	between_species_paralog: hoxb13a	2
p4	---	gapq	ENSP00000303578	HOXD12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gapq	ENSP00000249504	HOXD11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	q3	+/+	ENSP00000249501	HOXD10	q3	q3	127.91	3	23026681	23026947	1	1	26.2%	71.9%	267	0.56 / 0.79 = 0.71	noComparaHits: hoxb10a	4
p7	q4	+/+	ENSP00000249499	HOXD9	q4	q4	133.9	3	23036335	23036565	1	1	22.8%	85.9%	231	0.61 / 0.78 = 0.78	noComparaHits: hoxb9a	5
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q5	+/+	ENSP00000315949	HOXD8	q5	q5	226.96	3	23044226	23045536	1	2	69%	61.6%	561	0.55 / 0.54 = 1.02	between_species_paralog: hoxb8a	2
---	q6	gapp	-	-	-	q6	-	-	-	-	-	-	-	-	-	-	-	-
---	q7	gapp	-	-	-	q7	-	-	-	-	-	-	-	-	-	-	-	-
---	q8	gapp	-	-	-	q8	-	-	-	-	-	-	-	-	-	-	-	-
p10	q9	+/+	ENSP00000302548	HOXD4	q9	q9	252.3	3	23077620	23079267	1	2	93.7%	56.3%	714	0.5 / 0.5 = 1	between_species_paralog: hoxb4a	2
p11	q10	+/+	ENSP00000249440	HOXD3	q10	q10	392.76	3	23101788	23103710	1	2	96.3%	54.8%	1248	0.55 / 0.53 = 1.04	between_species_paralog: hoxb3a	2
---	q11	gapp	-	-	-	q11	-	-	-	-	-	-	-	-	-	-	-	-
p12	q12	+/+	ENSP00000328598	HOXD1	q12	q12	147.76	3	23124773	23126284	1	2	77.4%	42.1%	783	0.69 / 0.74 = 0.93	noComparaHits: hoxb1a	2
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 6

syntenyRegion: Danio_rerio.glob06.16.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 16 -i 15198030:15996395 -f 60e4 some_geneID_to_be_selected
scoreRatio_sum=4.44 log_scoreRatio_sum=-0.63 focal_scoreRatio_sum=2.06
AlnScore=1811 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000312385	EVX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000249505	HOXD13	q1	q1	212.52	16	15984775	15985755	-1	2	60.9%	59.1%	564	0.59 / 0.64 = 0.92	between_species_paralog: hoxa13b	5
p4	---	gapq	ENSP00000303578	HOXD12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q2	+/+	ENSP00000249504	HOXD11	q2	q2	259.83	16	15975496	15977088	-1	3	87.3%	52%	861	0.49 / 0.5 = 0.98	noComparaHits: hoxa11b	2
p6	q3	+/+	ENSP00000249501	HOXD10	q3	q3	266.03	16	15969590	15971739	-1	2	93.8%	50.5%	951	0.56 / 0.58 = 0.97	noComparaHits: hoxa10b	2
p7	q4	+/+	ENSP00000249499	HOXD9	q4	q4	195.28	16	15965008	15966531	-1	2	66.1%	52.4%	636	0.61 / 0.68 = 0.9	noComparaHits: hoxa9b	3
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000315949	HOXD8	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	q5	+/+	ENSP00000302548	HOXD4	q5	q5	123.61	16	15953680	15954666	-1	3	49.4%	50%	378	0.5 / 0.75 = 0.67	noComparaHits: hoxa2b	10
p11	---	gape	ENSP00000249440	HOXD3	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000328598	HOXD1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 7

syntenyRegion: Danio_rerio.glob07.11.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 11 -i 242:590867 -f 44e4 some_geneID_to_be_selected
scoreRatio_sum=3.38 log_scoreRatio_sum=-0.71 focal_scoreRatio_sum=0.87
AlnScore=1303 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000312385	EVX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	q1	+/+	ENSP00000249505	HOXD13	q1	q1	228.37	11	547432	549807	1	2	75.8%	50.6%	741	0.59 / 0.61 = 0.97	noComparaHits: hoxc13b	4
p4	q2	+/+	ENSP00000303578	HOXD12	q2	q2	147.76	11	559045	560166	1	2	45.7%	58%	390	0.65 / 0.71 = 0.92	noComparaHits: hoxc12b	2
p5	q3	+/+	ENSP00000249504	HOXD11	q3	q3	214.77	11	566839	568425	1	3	84.3%	46.2%	840	0.49 / 0.59 = 0.83	noComparaHits: hoxc11b	5
p6	---	gapq	ENSP00000249501	HOXD10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gapq	ENSP00000249499	HOXD9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gapq	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000315949	HOXD8	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	q4	+/+	ENSP00000302548	HOXD4	q4	q4	120.3	11	590093	590867	1	2	45.1%	53%	333	0.5 / 0.76 = 0.66	noComparaHits: hoxc6b	noData
p11	---	gape	ENSP00000249440	HOXD3	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000328598	HOXD1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 8

syntenyRegion: Danio_rerio.glob08.12.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 12 -i 26456241:27186793 -f 55e4 some_geneID_to_be_selected
scoreRatio_sum=2.47 log_scoreRatio_sum=-0.6 focal_scoreRatio_sum=0.61
AlnScore=871 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000249499 (contained in p7)
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	ENSP00000272748	KIAA1715	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000312385	EVX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000249505	HOXD13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000303578	HOXD12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gaps	ENSP00000249504	HOXD11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gaps	ENSP00000249501	HOXD10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gaps	ENSP00000249499	HOXD9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gaps	ENSP00000316098	Q8NAT4_HUMAN	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q1	+/+	ENSP00000315949	HOXD8	q1	q1	179.09	12	26478746	26480927	-1	2	59%	58%	486	0.55 / 0.64 = 0.86	between_species_paralog: hoxb8b	3
---	q2	gapp	-	-	-	q2	-	-	-	-	-	-	-	-	-	-	-	-
p10	q3	+/+	ENSP00000302548	HOXD4	q3	q3	140.01	12	26467628	26468453	-1	2	48.2%	57.6%	375	0.5 / 0.72 = 0.69	noComparaHits: hoxb5b	6
p11	---	gapq	ENSP00000249440	HOXD3	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q4	+/+	ENSP00000328598	HOXD1	q4	q4	144.24	12	26456241	26456932	-1	2	58.5%	47.1%	609	0.69 / 0.75 = 0.92	noComparaHits: hoxb1b	3
p13	---	gape	ENSP00000346209	-	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000249442	MTX2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

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