HOXC9_ENSG00000180806_3e5.protein.info Alignment Results

Overview on processed synteny regions for HOXC9_ENSG00000180806_3e5.protein.info

Rank	AlnScore	RatioSum	logRatioSum	focalRatioSum	TargetGenome	chr	startPos	endPos	hitsCount	queryCov	meanIdentity	ori	score	compara
1	8687	28.72	6.44	10.1	Danio_rerio	23	33742961	33744799	2	99.6%	73.2%	1	373.4	ortholog_one2many: hoxc9a
2	6537	25	7.58	9.58	Danio_rerio	23	35245633	35247471	2	99.6%	73.2%	-1	373.4	ortholog_one2many: hoxc9a
3	4150	10.18	0.22	2.54	Danio_rerio	11
4	3798	6.71	-2.51	2.56	Danio_rerio	9	1948806	1949904	2	99.2%	50.2%	-1	265.33	noComparaHits: hoxd9a
5	3108	6.79	-0.26	2.83	Danio_rerio	3	23033313	23036559	2	69.6%	66.3%	1	228.02	noComparaHits: hoxb9a
6	2361	6.32	-0.89	1.94	Danio_rerio	19	10511297	10512339	2	78.1%	52.6%	1	188.24	noComparaHits: hoxa9a
7	2323	4.71	-1.51	1.95	Danio_rerio	16	15964987	15966531	2	100%	47.1%	-1	195.28	noComparaHits: hoxa9b
8	1346	2.7	-0.34	0.93	Danio_rerio	12
9	844	2	0	0.25	Danio_rerio	3

Data table for reference protein loci

QueryProtein(s)=ENSP00000302836 (contained in p6)
QueryGenome=Homo_sapiens

ref-loci	geneName	protID	transID	geneID	protName	chr	startPos	endPos	meanPos	ori	numExons	protLength	selfscore
p1	CALCOCO1	ENSP00000262059	ENST00000262059	ENSG00000012822	NP_065949.1	12	52391995	52405293	52396060	-1	14	691	1323.65
p2	HOXC13	ENSP00000243056	ENST00000243056	ENSG00000123364	HXC13_HUMAN	12	52618958	52625307	52619450	1	2	330	594.81
p3	HOXC12	ENSP00000243103	ENST00000243103	ENSG00000123407	HXC12_HUMAN	12	52634981	52636617	52635401	1	2	282	373.27
p4	HOXC11	ENSP00000243082	ENST00000243082	ENSG00000123388	HXC11_HUMAN	12	52653293	52655464	52653746	1	2	304	438.74
p5	HOXC10	ENSP00000307321	ENST00000303460	ENSG00000180818	HXC10_HUMAN	12	52665311	52669497	52665821	1	2	342	650.79
p6	HOXC9	ENSP00000302836	ENST00000303450	ENSG00000180806	HXC9_HUMAN	12	52680240	52682725	52680627	1	2	260	510.33
p7	HOXC8	ENSP00000040584	ENST00000040584	ENSG00000037965	HXC8_HUMAN	12	52689336	52691432	52689696	1	2	242	430.42
p8	HOXC6	ENSP00000243108	ENST00000243108	ENSG00000197757	HXC6_HUMAN	12	52708573	52710013	52708921	1	2	235	451.9
p9	HOXC5	ENSP00000309336	ENST00000312492	ENSG00000172789	HXC5_HUMAN	12	52713174	52714543	52713504	1	2	222	429.02
p10	HOXC4	ENSP00000305973	ENST00000303406	ENSG00000198353	HXC4_HUMAN	12	52733974	52735256	52734367	1	2	264	520.55
p11	SMUG1	ENSP00000338606	ENST00000337581	ENSG00000123415	SMUG1_HUMAN	12	52862147	52863991	52862549	-1	2	270	521.25
p12	CBX5	ENSP00000209875	ENST00000209875	ENSG00000094916	CBX5_HUMAN	12	52921806	52937701	52932122	-1	4	191	371.21
p13	HNRPA1	ENSP00000341826	ENST00000340913	ENSG00000135486	ROA1_HUMAN	12	52960859	52964364	52962510	1	10	372	523.89
p14	NFE2	ENSP00000312436	ENST00000312156	ENSG00000123405	NFE2_HUMAN	12	52972425	52975299	52972980	-1	2	373	699.37

total length of ref-loci (on slice) = 583305 (58e4)

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.glob01.23.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 32869533:34032121 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=28.72 log_scoreRatio_sum=6.44 focal_scoreRatio_sum=10.1
AlnScore=8687 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	+/+	ENSP00000262059	CALCOCO1	q1	q1	417.53	23	33632270	33649214	-1	11	69.5%	44%	1563	0.89 / 0.68 = 1.31	ortholog_one2many: calcoco1	1
p2	q2	+/+	ENSP00000243056	HOXC13	q2	q2	467.87	23	33701520	33704218	1	3	91.8%	77.3%	915	0.53 / 0.21 = 2.52	ortholog_one2many: hoxc13a	1
p3	q3	+/+	ENSP00000243103	HOXC12	q3	q3	340.66	23	33711191	33712771	1	2	100%	65.2%	834	0.49 / 0.08 = 6.13	ortholog_one2many: A2BE68_DANRE	1
p4	q4	+/+	ENSP00000243082	HOXC11	q4	q4	385.72	23	33722501	33724786	1	2	100%	64.2%	966	0.34 / 0.12 = 2.83	ortholog_one2many: hoxc11a	1
p5	q5	+/+	ENSP00000307321	HOXC10	q5	q5	246.32	23	33731209	33733955	1	2	94.4%	45.9%	1005	0.57 / 0.62 = 0.92	noComparaHits: hoxc10a	2
p6	q6	+/+	ENSP00000302836	HOXC9	q6	q6	373.4	23	33742961	33744799	1	2	99.6%	73.2%	780	0.52 / 0.26 = 2	ortholog_one2many: hoxc9a	1
p7	q7	+/+	ENSP00000040584	HOXC8	q7	q7	403.32	23	33749039	33751053	1	2	100%	82%	750	0.33 / 0.06 = 5.5	ortholog_one2many: hoxc8a	1
p8	q8	+/+	ENSP00000243108	HOXC6	q8	q8	339.25	23	33763064	33764351	1	2	98.3%	73.1%	696	0.55 / 0.24 = 2.29	ortholog_one2many: hoxc6a	1
p9	q9	+/+	ENSP00000309336	HOXC5	q9	q9	209.71	23	33766330	33767846	1	2	100%	53.6%	699	0.62 / 0.51 = 1.22	noComparaHits: hoxc5a	1
p10	q10	+/+	ENSP00000305973	HOXC4	q10	q10	351.92	23	33778655	33779978	1	2	100%	70.1%	804	0.51 / 0.32 = 1.59	ortholog_one2many: hoxc4a	1
---	q11	gapp	-	-	-	q11	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gapq	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q12	+/+	ENSP00000209875	CBX5	q12	q12	257.85	23	33946797	33950790	-1	4	97.4%	68.8%	567	0.36 / 0.3 = 1.2	ortholog_one2one: zgc:158601	1
p13	q13	+/+	ENSP00000341826	HNRPA1	q13	q13	445.25	23	33954708	33956426	1	5	87.4%	69.4%	990	0.03 / 0.15 = 0.2	noComparaHits: hnrpa1	1
p14	q14	+/+	ENSP00000312436	NFE2	q14	q14	212.66	23	33959217	33960940	-1	3	47.2%	62.5%	528	0.7 / 0.69 = 1.01	ortholog_one2one: nfe2	1

region 2

syntenyRegion: Danio_rerio.glob02.23.minQN4.fac2.02.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 23 -i 34749250:35906424 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=25 log_scoreRatio_sum=7.58 focal_scoreRatio_sum=9.58
AlnScore=6537 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000243056	HOXC13	q1	q1	467.87	23	35287148	35289846	-1	3	91.8%	77.3%	915	0.53 / 0.21 = 2.52	ortholog_one2many: hoxc13a	1
p3	q2	+/+	ENSP00000243103	HOXC12	q2	q2	340.66	23	35277627	35279207	-1	2	100%	65.2%	834	0.49 / 0.08 = 6.13	ortholog_one2many: A2BE68_DANRE	1
p4	q3	+/+	ENSP00000243082	HOXC11	q3	q3	385.72	23	35265648	35267933	-1	2	100%	64.2%	966	0.34 / 0.12 = 2.83	ortholog_one2many: hoxc11a	1
p5	q4	+/+	ENSP00000307321	HOXC10	q4	q4	246.32	23	35256479	35259225	-1	2	94.4%	45.9%	1005	0.57 / 0.62 = 0.92	noComparaHits: hoxc10a	2
p6	q5	+/+	ENSP00000302836	HOXC9	q5	q5	373.4	23	35245633	35247471	-1	2	99.6%	73.2%	780	0.52 / 0.26 = 2	ortholog_one2many: hoxc9a	1
p7	q6	+/+	ENSP00000040584	HOXC8	q6	q6	403.32	23	35239379	35241393	-1	2	100%	82%	750	0.33 / 0.06 = 5.5	ortholog_one2many: hoxc8a	1
p8	q7	+/+	ENSP00000243108	HOXC6	q7	q7	339.25	23	35226124	35227411	-1	2	98.3%	73.1%	696	0.55 / 0.24 = 2.29	ortholog_one2many: hoxc6a	1
p9	q8	+/+	ENSP00000309336	HOXC5	q8	q8	209.71	23	35222629	35224145	-1	2	100%	53.6%	699	0.62 / 0.51 = 1.22	noComparaHits: hoxc5a	1
p10	q9	+/+	ENSP00000305973	HOXC4	q9	q9	351.92	23	35210505	35211828	-1	2	100%	70.1%	804	0.51 / 0.32 = 1.59	ortholog_one2many: hoxc4a	1
p11	---	gape	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000312436	NFE2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 3

syntenyRegion: Danio_rerio.glob03.11.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 11 -i 114757:1255217 -f 86e4 some_geneID_to_be_selected
scoreRatio_sum=10.18 log_scoreRatio_sum=0.22 focal_scoreRatio_sum=2.54
AlnScore=4150 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	+/+	ENSP00000262059	CALCOCO1	q1	q1	274.78	11	509350	520707	-1	7	53.7%	39.3%	1176	0.89 / 0.79 = 1.13	ortholog_one2many: tceb3	2
p2	q2	+/+	ENSP00000243056	HOXC13	q2	q2	391.12	11	547278	549837	1	3	87.6%	68.7%	867	0.53 / 0.34 = 1.56	ortholog_one2many: hoxc13b	2
p3	q3	+/+	ENSP00000243103	HOXC12	q3	q3	261.11	11	559045	560166	1	2	96.5%	55.1%	816	0.49 / 0.3 = 1.63	ortholog_one2many: hoxc12b	2
p4	q4	+/+	ENSP00000243082	HOXC11	q4	q4	358.97	11	566782	568428	1	2	93.8%	68.7%	858	0.34 / 0.18 = 1.89	ortholog_one2many: hoxc11b	2
p5	---	gapq	ENSP00000307321	HOXC10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gapq	ENSP00000302836	HOXC9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gapq	ENSP00000040584	HOXC8	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	q5	+/+	ENSP00000243108	HOXC6	q5	q5	325.53	11	589745	590852	1	2	98.7%	72.6%	702	0.55 / 0.27 = 2.04	ortholog_one2many: hoxc6b	2
p9	---	gapq	ENSP00000309336	HOXC5	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gapq	ENSP00000305973	HOXC4	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	q6	+/+	ENSP00000338606	SMUG1	q6	q6	313.2	11	604600	606878	-1	2	90%	63.9%	732	0.73 / 0.39 = 1.87	ortholog_one2one: Q0P412_DANRE	1
p12	---	gapq	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	q7	+/+	ENSP00000341826	HNRPA1	q7	q7	241.88	11	1252244	1255217	1	3	44.1%	72.6%	492	0.03 / 0.53 = 0.06	ortholog_one2many: zgc:66127	5
p14	---	gape	ENSP00000312436	NFE2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 4

syntenyRegion: Danio_rerio.glob04.9.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 9 -i 1645138:2801668 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=6.71 log_scoreRatio_sum=-2.51 focal_scoreRatio_sum=2.56
AlnScore=3798 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000243056	HOXC13	q1	q1	170.99	9	1971944	1974397	-1	2	62.1%	47.5%	642	0.53 / 0.71 = 0.75	noComparaHits: hoxd13a	6
p3	q2	+/+	ENSP00000243103	HOXC12	q2	q2	185.78	9	1966604	1968848	-1	2	70.9%	49.8%	600	0.49 / 0.5 = 0.98	noComparaHits: hoxd12a	3
p4	q3	+/+	ENSP00000243082	HOXC11	q3	q3	258.64	9	1960574	1962309	-1	2	94.7%	51.2%	879	0.34 / 0.41 = 0.83	noComparaHits: hoxd11a	3
p5	q4	+/+	ENSP00000307321	HOXC10	q4	q4	262.51	9	1952491	1954123	-1	2	92.7%	49.8%	918	0.57 / 0.59 = 0.97	noComparaHits: hoxd10a	1
p6	q5	+/+	ENSP00000302836	HOXC9	q5	q5	265.33	9	1948806	1949904	-1	2	99.2%	50.2%	855	0.52 / 0.48 = 1.08	noComparaHits: hoxd9a	2
p7	---	gapq	ENSP00000040584	HOXC8	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gapq	ENSP00000243108	HOXC6	q6	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000309336	HOXC5	q6	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	q6	+/+	ENSP00000305973	HOXC4	q6	q6	253.01	9	1933948	1934984	-1	2	85.2%	59.3%	669	0.51 / 0.51 = 1	between_species_paralog: hoxd4a	3
p11	---	gapq	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gapq	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	q7	+/+	ENSP00000341826	HNRPA1	q7	q7	396.66	9	1665747	1674145	-1	5	64.2%	81%	723	0.03 / 0.24 = 0.13	noComparaHits: zgc:153703	2
p14	q8	+/+	ENSP00000312436	NFE2	q8	q8	189.52	9	1651108	1652013	1	1	79.1%	41.8%	906	0.7 / 0.72 = 0.97	between_species_paralog: nfe2l2	3

region 5

syntenyRegion: Danio_rerio.glob06.3.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 3 -i 22020980:23155579 -f 85e4 some_geneID_to_be_selected
scoreRatio_sum=6.79 log_scoreRatio_sum=-0.26 focal_scoreRatio_sum=2.83
AlnScore=3108 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000243056	HOXC13	q1	q1	263.22	3	23010220	23011494	1	2	82.7%	54.6%	837	0.53 / 0.55 = 0.96	noComparaHits: hoxb13a	4
p3	---	gapq	ENSP00000243103	HOXC12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gapq	ENSP00000243082	HOXC11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	q2	+/+	ENSP00000307321	HOXC10	q2	q2	131.08	3	23026681	23026944	1	1	25.7%	75%	264	0.57 / 0.79 = 0.72	noComparaHits: hoxb10a	4
p6	q3	+/+	ENSP00000302836	HOXC9	q3	q3	228.02	3	23033313	23036559	1	2	69.6%	66.3%	549	0.52 / 0.55 = 0.95	noComparaHits: hoxb9a	3
p7	q4	+/+	ENSP00000040584	HOXC8	q4	q4	288.91	3	23044100	23045539	1	2	95.5%	63.5%	687	0.33 / 0.32 = 1.03	between_species_paralog: hoxb8a	2
---	q5	gapp	-	-	-	q5	-	-	-	-	-	-	-	-	-	-	-	-
p8	q6	+/+	ENSP00000243108	HOXC6	q6	q6	191.4	3	23059516	23061226	1	2	88.5%	50.9%	654	0.55 / 0.57 = 0.96	noComparaHits: hoxb6a ; hoxb3a	3
p9	q7	+/+	ENSP00000309336	HOXC5	q7	q7	185.55	3	23063599	23065002	1	3	98.2%	43.5%	807	0.62 / 0.56 = 1.11	noComparaHits: hoxb5a ; hoxb3a	3
p10	q8	+/+	ENSP00000305973	HOXC4	q8	q8	268.49	3	23077620	23079288	1	2	95.8%	57.9%	735	0.51 / 0.48 = 1.06	between_species_paralog: hoxb4a	2
p11	---	gapq	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gapq	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gapq	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gapq	ENSP00000312436	NFE2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
---	q9	gape	-	-	-	q9	-	-	-	-	-	-	-	-	-	-	-	-

region 6

syntenyRegion: Danio_rerio.glob05.19.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 19 -i 9622051:10784864 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=6.32 log_scoreRatio_sum=-0.89 focal_scoreRatio_sum=1.94
AlnScore=2361 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	+/+	ENSP00000262059	CALCOCO1	q1	q1	224.89	19	10340251	10358170	-1	5	36.6%	41.9%	762	0.89 / 0.83 = 1.07	between_species_paralog: si:ch211-204j16.2	3
p2	q2	+/+	ENSP00000243056	HOXC13	q2	q2	266.04	19	10490790	10491767	1	2	82.7%	54.6%	831	0.53 / 0.55 = 0.96	noComparaHits: hoxa13a	3
p3	---	gapq	ENSP00000243103	HOXC12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	q3	+/+	ENSP00000243082	HOXC11	q3	q3	141.64	19	10498425	10499255	1	1	93.1%	35.3%	831	0.34 / 0.67 = 0.51	noComparaHits: hoxa11a	5
p5	---	gapq	ENSP00000307321	HOXC10	q4	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	q4	+/+	ENSP00000302836	HOXC9	q4	q4	188.24	19	10511297	10512339	1	2	78.1%	52.6%	600	0.52 / 0.63 = 0.83	noComparaHits: hoxa9a	5
p7	---	gapq	ENSP00000040584	HOXC8	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gapq	ENSP00000243108	HOXC6	q5	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	q5	+/+	ENSP00000309336	HOXC5	q5	q5	188.37	19	10520701	10521966	1	3	98.2%	47.9%	765	0.62 / 0.56 = 1.11	noComparaHits: hoxa5a	2
p10	q6	+/+	ENSP00000305973	HOXC4	q6	q6	247.73	19	10528752	10529933	1	2	95.5%	52.5%	735	0.51 / 0.52 = 0.98	between_species_paralog: hoxa4a	4
---	q7	gapp	-	-	-	q7	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gapq	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gapq	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gapq	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	q8	/+	ENSP00000312436	NFE2	q8	q8	128.62	19	10694984	10695640	1	1	59.8%	38.1%	657	0.7 / 0.81 = 0.86	between_species_paralog: nfe2l3	6

region 7

syntenyRegion: Danio_rerio.glob07.16.minQN4.fac2.01.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 16 -i 15834923:16991908 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=4.71 log_scoreRatio_sum=-1.51 focal_scoreRatio_sum=1.95
AlnScore=2323 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	q1	+/+	ENSP00000243056	HOXC13	q1	q1	256.18	16	15984775	15985935	-1	2	77.6%	55.8%	741	0.53 / 0.56 = 0.95	noComparaHits: hoxa13b	5
p3	---	gapq	ENSP00000243103	HOXC12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	q2	+/+	ENSP00000243082	HOXC11	q2	q2	244.56	16	15975493	15977082	-1	2	87.8%	52.7%	807	0.34 / 0.44 = 0.77	noComparaHits: hoxa11b	4
p5	q3	+/+	ENSP00000307321	HOXC10	q3	q3	218.16	16	15969590	15971748	-1	2	70.5%	50.8%	726	0.57 / 0.66 = 0.86	noComparaHits: hoxa10b	3
p6	q4	+/+	ENSP00000302836	HOXC9	q4	q4	195.28	16	15964987	15966531	-1	2	100%	47.1%	774	0.52 / 0.61 = 0.85	noComparaHits: hoxa9b	4
p7	---	gapq	ENSP00000040584	HOXC8	q3	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gapq	ENSP00000243108	HOXC6	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gapq	ENSP00000309336	HOXC5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	q5	+/+	ENSP00000305973	HOXC4	q5	q5	104.81	16	15953680	15954720	-1	2	43.6%	51.7%	357	0.51 / 0.79 = 0.65	noComparaHits: hoxa2b	noData
p11	---	gapq	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q6	+/+	ENSP00000209875	CBX5	q6	q6	158.93	16	15834923	15841562	1	4	88.5%	46.5%	504	0.36 / 0.57 = 0.63	between_species_paralog: cbx3b	5
p13	---	gape	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000312436	NFE2	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 26131270:27271634 -f 86e4 some_geneID_to_be_selected
scoreRatio_sum=2.7 log_scoreRatio_sum=-0.34 focal_scoreRatio_sum=0.93
AlnScore=1346 (based on relative scores)
AlnType: reversed (decreasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000243056	HOXC13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000243103	HOXC12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000243082	HOXC11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gaps	ENSP00000307321	HOXC10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gaps	ENSP00000302836	HOXC9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	q1	+/+	ENSP00000040584	HOXC8	q1	q1	236.46	12	26478731	26480927	-1	2	99.6%	53.4%	726	0.33 / 0.45 = 0.73	between_species_paralog: hoxb8b	3
p8	q2	+/+	ENSP00000243108	HOXC6	q2	q2	177.32	12	26470491	26471559	-1	2	86%	49.3%	627	0.55 / 0.6 = 0.92	noComparaHits: hoxb6b	4
p9	q3	+/+	ENSP00000309336	HOXC5	q3	q3	173.94	12	26467745	26468987	-1	3	58.1%	65.2%	414	0.62 / 0.59 = 1.05	noComparaHits: hoxb5b	4
p10	---	gape	ENSP00000305973	HOXC4	q3	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gape	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	---	gape	ENSP00000209875	CBX5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p13	---	gape	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	---	gape	ENSP00000312436	NFE2	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-

region 9

syntenyRegion: Danio_rerio.glob10.3.minQN4.fac2.02.blastresult [View in Ensembl]
retrieve target region: getEnsemblProteins.pl -h Danio_rerio -l 3 -i 19321565:20477670 -f 87e4 some_geneID_to_be_selected
scoreRatio_sum=2 log_scoreRatio_sum=0 focal_scoreRatio_sum=0.25
AlnScore=844 (based on relative scores)
AlnType: normal (increasing chromosome positions)
QueryProtein(s)=ENSP00000302836 (contained in p6)
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	ENSP00000262059	CALCOCO1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p2	---	gaps	ENSP00000243056	HOXC13	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p3	---	gaps	ENSP00000243103	HOXC12	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p4	---	gaps	ENSP00000243082	HOXC11	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p5	---	gaps	ENSP00000307321	HOXC10	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p6	---	gaps	ENSP00000302836	HOXC9	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p7	---	gaps	ENSP00000040584	HOXC8	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p8	---	gaps	ENSP00000243108	HOXC6	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p9	---	gaps	ENSP00000309336	HOXC5	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p10	---	gaps	ENSP00000305973	HOXC4	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p11	---	gaps	ENSP00000338606	SMUG1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p12	q1	/+	ENSP00000209875	CBX5	q1	q1	237.79	3	19879838	19884549	1	4	96.3%	62.2%	537	0.36 / 0.35 = 1.03	between_species_paralog: cbx1	2
p13	---	gapq	ENSP00000341826	HNRPA1	noMatch	---	-	-	-	-	-	-	-	-	-	-	-	-
p14	q2	+/+	ENSP00000312436	NFE2	q2	q2	189.43	3	19888301	19891446	-1	3	65.4%	42.1%	738	0.7 / 0.72 = 0.97	between_species_paralog: nfe2l1	4

[ref-loci]	[top]	[up]
[previous]	1	[next]

[ref-loci]	[top]	[up]
[previous]	2	[next]

[ref-loci]	[top]	[up]
[previous]	3	[next]

[ref-loci]	[top]	[up]
[previous]	4	[next]

[ref-loci]	[top]	[up]
[previous]	5	[next]