AutoCloner

Multiple sequence alignment - TraesCS3B01G457800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3B01G457800	chr3B	100.000	2627	0	0	1	2627	700233828	700236454	0.000000e+00	4852.0
1	TraesCS3B01G457800	chr3B	89.278	1315	120	10	865	2160	700073478	700072166	0.000000e+00	1628.0
2	TraesCS3B01G457800	chr3B	74.558	283	52	14	2360	2627	11864130	11863853	3.580000e-19	106.0
3	TraesCS3B01G457800	chr3A	91.239	1267	91	9	865	2115	663452096	663450834	0.000000e+00	1707.0
4	TraesCS3B01G457800	chr3A	89.652	1266	113	8	864	2115	663441953	663440692	0.000000e+00	1596.0
5	TraesCS3B01G457800	chr3D	86.809	1501	139	29	865	2320	529496650	529495164	0.000000e+00	1620.0
6	TraesCS3B01G457800	chr3D	90.185	1192	87	8	911	2099	529503848	529502684	0.000000e+00	1526.0
7	TraesCS3B01G457800	chr3D	88.618	123	12	1	334	454	523301179	523301057	5.860000e-32	148.0
8	TraesCS3B01G457800	chr3D	74.558	283	52	14	2360	2627	523300113	523300390	3.580000e-19	106.0
9	TraesCS3B01G457800	chr7D	84.928	1108	159	6	974	2074	624769085	624770191	0.000000e+00	1114.0
10	TraesCS3B01G457800	chr7D	100.000	32	0	0	2360	2391	25385672	25385641	2.820000e-05	60.2
11	TraesCS3B01G457800	chr4A	84.044	1103	160	8	988	2074	604105220	604104118	0.000000e+00	1048.0
12	TraesCS3B01G457800	chr4A	80.882	1088	182	17	1008	2073	663696139	663695056	0.000000e+00	833.0
13	TraesCS3B01G457800	chr2D	81.920	1073	152	28	1028	2074	13770230	13771286	0.000000e+00	869.0
14	TraesCS3B01G457800	chr2D	74.539	271	55	11	2360	2621	27636268	27636003	3.580000e-19	106.0
15	TraesCS3B01G457800	chr6B	90.769	455	21	8	2	454	58814441	58814876	2.910000e-164	588.0
16	TraesCS3B01G457800	chr6B	92.040	201	16	0	634	834	508199413	508199613	1.540000e-72	283.0
17	TraesCS3B01G457800	chr6B	75.000	284	50	14	2360	2627	496415640	496415918	7.690000e-21	111.0
18	TraesCS3B01G457800	chr5D	94.096	271	10	4	2	271	430984256	430983991	8.750000e-110	407.0
19	TraesCS3B01G457800	chr5D	94.792	192	8	2	263	453	430976834	430976644	5.500000e-77	298.0
20	TraesCS3B01G457800	chr5D	84.444	270	19	3	2360	2627	430975743	430975991	7.260000e-61	244.0
21	TraesCS3B01G457800	chr2A	90.984	244	20	1	2386	2627	638312484	638312241	7.010000e-86	327.0
22	TraesCS3B01G457800	chr2A	95.531	179	7	1	274	452	638311411	638311588	4.280000e-73	285.0
23	TraesCS3B01G457800	chr5B	93.500	200	12	1	638	836	666300992	666300793	1.980000e-76	296.0
24	TraesCS3B01G457800	chr5B	94.271	192	10	1	636	826	589201020	589201211	2.560000e-75	292.0
25	TraesCS3B01G457800	chr5B	94.149	188	9	2	639	825	346616157	346616343	4.280000e-73	285.0
26	TraesCS3B01G457800	chr7B	96.089	179	7	0	647	825	617829299	617829121	2.560000e-75	292.0
27	TraesCS3B01G457800	chr7B	93.651	189	10	2	639	826	518678794	518678981	5.540000e-72	281.0
28	TraesCS3B01G457800	chr6A	94.475	181	10	0	644	824	586033068	586032888	1.990000e-71	279.0
29	TraesCS3B01G457800	chr2B	93.158	190	12	1	636	825	777642251	777642439	7.160000e-71	278.0
30	TraesCS3B01G457800	chr4B	92.670	191	14	0	640	830	667396711	667396901	2.580000e-70	276.0
31	TraesCS3B01G457800	chrUn	78.199	211	43	3	227	436	30434079	30434287	5.900000e-27	132.0
32	TraesCS3B01G457800	chr5A	78.199	211	43	3	227	436	666945896	666946104	5.900000e-27	132.0
33	TraesCS3B01G457800	chr1A	100.000	31	0	0	2361	2391	20415908	20415878	1.020000e-04	58.4
34	TraesCS3B01G457800	chr7A	100.000	29	0	0	2332	2360	376628339	376628311	1.000000e-03	54.7

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3B01G457800	chr3B	700233828	700236454	2626	False	4852	4852	100.000	1	2627	1	chr3B.!!$F1	2626
1	TraesCS3B01G457800	chr3B	700072166	700073478	1312	True	1628	1628	89.278	865	2160	1	chr3B.!!$R2	1295
2	TraesCS3B01G457800	chr3A	663450834	663452096	1262	True	1707	1707	91.239	865	2115	1	chr3A.!!$R2	1250
3	TraesCS3B01G457800	chr3A	663440692	663441953	1261	True	1596	1596	89.652	864	2115	1	chr3A.!!$R1	1251
4	TraesCS3B01G457800	chr3D	529495164	529496650	1486	True	1620	1620	86.809	865	2320	1	chr3D.!!$R2	1455
5	TraesCS3B01G457800	chr3D	529502684	529503848	1164	True	1526	1526	90.185	911	2099	1	chr3D.!!$R3	1188
6	TraesCS3B01G457800	chr7D	624769085	624770191	1106	False	1114	1114	84.928	974	2074	1	chr7D.!!$F1	1100
7	TraesCS3B01G457800	chr4A	604104118	604105220	1102	True	1048	1048	84.044	988	2074	1	chr4A.!!$R1	1086
8	TraesCS3B01G457800	chr4A	663695056	663696139	1083	True	833	833	80.882	1008	2073	1	chr4A.!!$R2	1065
9	TraesCS3B01G457800	chr2D	13770230	13771286	1056	False	869	869	81.920	1028	2074	1	chr2D.!!$F1	1046

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
539	540	0.109597	CAATGCTTCGTTGCCCACTC	60.11	55.0	0.62	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2333	2438	0.108329	CATAGACCAAACGTCCGCCT	60.108	55.0	0.0	0.0	43.08	5.52	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
23	24	6.668541	GCACATGTATCAATGACTTACTGT	57.331	37.500	0.00	0.00	3.55
24	25	7.076842	GCACATGTATCAATGACTTACTGTT	57.923	36.000	0.00	0.00	3.16
25	26	7.182761	GCACATGTATCAATGACTTACTGTTC	58.817	38.462	0.00	0.00	3.18
26	27	7.148423	GCACATGTATCAATGACTTACTGTTCA	60.148	37.037	0.00	0.00	3.18
27	28	8.886719	CACATGTATCAATGACTTACTGTTCAT	58.113	33.333	0.00	0.00	2.57
28	29	9.102757	ACATGTATCAATGACTTACTGTTCATC	57.897	33.333	0.00	0.00	2.92
29	30	9.101655	CATGTATCAATGACTTACTGTTCATCA	57.898	33.333	0.00	0.00	3.07
30	31	9.671279	ATGTATCAATGACTTACTGTTCATCAA	57.329	29.630	0.00	0.00	2.57
31	32	9.500785	TGTATCAATGACTTACTGTTCATCAAA	57.499	29.630	0.00	0.00	2.69
34	35	7.742151	TCAATGACTTACTGTTCATCAAATCG	58.258	34.615	0.00	0.00	3.34
35	36	7.387673	TCAATGACTTACTGTTCATCAAATCGT	59.612	33.333	0.00	0.00	3.73
36	37	7.672983	ATGACTTACTGTTCATCAAATCGTT	57.327	32.000	0.00	0.00	3.85
37	38	6.887368	TGACTTACTGTTCATCAAATCGTTG	58.113	36.000	0.00	35.95	4.10
38	39	6.481976	TGACTTACTGTTCATCAAATCGTTGT	59.518	34.615	0.00	36.07	3.32
39	40	6.658831	ACTTACTGTTCATCAAATCGTTGTG	58.341	36.000	0.00	36.07	3.33
40	41	6.260050	ACTTACTGTTCATCAAATCGTTGTGT	59.740	34.615	0.00	36.07	3.72
41	42	7.439955	ACTTACTGTTCATCAAATCGTTGTGTA	59.560	33.333	0.00	36.07	2.90
42	43	5.985781	ACTGTTCATCAAATCGTTGTGTAC	58.014	37.500	0.00	36.07	2.90
43	44	5.758296	ACTGTTCATCAAATCGTTGTGTACT	59.242	36.000	0.00	36.07	2.73
44	45	6.926826	ACTGTTCATCAAATCGTTGTGTACTA	59.073	34.615	0.00	36.07	1.82
45	46	7.439955	ACTGTTCATCAAATCGTTGTGTACTAA	59.560	33.333	0.00	36.07	2.24
46	47	7.569297	TGTTCATCAAATCGTTGTGTACTAAC	58.431	34.615	0.00	36.07	2.34
47	48	7.224949	TGTTCATCAAATCGTTGTGTACTAACA	59.775	33.333	12.05	36.07	2.41
60	61	5.726980	TGTACTAACACCGTATCACCTTT	57.273	39.130	0.00	0.00	3.11
61	62	6.100404	TGTACTAACACCGTATCACCTTTT	57.900	37.500	0.00	0.00	2.27

Showing 1 to 25 of 662 entries

Previous1 2 3 4 5…27Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.668541	ACAGTAAGTCATTGATACATGTGC	57.331	37.500	9.11	0.69	0.00	4.57
1	2	8.255394	TGAACAGTAAGTCATTGATACATGTG	57.745	34.615	9.11	0.00	0.00	3.21
2	3	9.102757	GATGAACAGTAAGTCATTGATACATGT	57.897	33.333	2.69	2.69	0.00	3.21
3	4	9.101655	TGATGAACAGTAAGTCATTGATACATG	57.898	33.333	0.00	0.00	0.00	3.21
4	5	9.671279	TTGATGAACAGTAAGTCATTGATACAT	57.329	29.630	0.00	0.00	0.00	2.29
5	6	9.500785	TTTGATGAACAGTAAGTCATTGATACA	57.499	29.630	0.00	0.00	0.00	2.29
8	9	8.393366	CGATTTGATGAACAGTAAGTCATTGAT	58.607	33.333	0.00	0.00	0.00	2.57
9	10	7.387673	ACGATTTGATGAACAGTAAGTCATTGA	59.612	33.333	0.00	0.00	0.00	2.57
10	11	7.521529	ACGATTTGATGAACAGTAAGTCATTG	58.478	34.615	0.00	0.00	0.00	2.82
11	12	7.672983	ACGATTTGATGAACAGTAAGTCATT	57.327	32.000	0.00	0.00	0.00	2.57
12	13	7.173218	ACAACGATTTGATGAACAGTAAGTCAT	59.827	33.333	0.00	0.00	36.48	3.06
13	14	6.481976	ACAACGATTTGATGAACAGTAAGTCA	59.518	34.615	0.00	0.00	36.48	3.41
14	15	6.792250	CACAACGATTTGATGAACAGTAAGTC	59.208	38.462	0.00	0.00	36.48	3.01
15	16	6.260050	ACACAACGATTTGATGAACAGTAAGT	59.740	34.615	0.00	0.00	36.48	2.24
16	17	6.658831	ACACAACGATTTGATGAACAGTAAG	58.341	36.000	0.00	0.00	36.48	2.34
17	18	6.612247	ACACAACGATTTGATGAACAGTAA	57.388	33.333	0.00	0.00	36.48	2.24
18	19	6.926826	AGTACACAACGATTTGATGAACAGTA	59.073	34.615	0.00	0.00	36.48	2.74
19	20	5.758296	AGTACACAACGATTTGATGAACAGT	59.242	36.000	0.00	0.00	36.48	3.55
20	21	6.228273	AGTACACAACGATTTGATGAACAG	57.772	37.500	0.00	0.00	36.48	3.16
21	22	7.224949	TGTTAGTACACAACGATTTGATGAACA	59.775	33.333	0.00	0.00	36.48	3.18
22	23	7.569297	TGTTAGTACACAACGATTTGATGAAC	58.431	34.615	0.00	0.00	36.48	3.18
23	24	7.716768	TGTTAGTACACAACGATTTGATGAA	57.283	32.000	0.00	0.00	36.48	2.57
38	39	5.726980	AAAGGTGATACGGTGTTAGTACA	57.273	39.130	0.00	0.00	0.00	2.90
39	40	5.349543	CCAAAAGGTGATACGGTGTTAGTAC	59.650	44.000	0.00	0.00	0.00	2.73
40	41	5.481105	CCAAAAGGTGATACGGTGTTAGTA	58.519	41.667	0.00	0.00	0.00	1.82

Showing 1 to 25 of 695 entries

Previous1 2 3 4 5…28Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.