AutoCloner

Multiple sequence alignment - TraesCS7D01G299600

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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	TraesCS7D01G299600	chr7D	100.000	5139	0	0	1	5139	379572346	379567208	0.000000e+00	9491
1	TraesCS7D01G299600	chr7D	96.364	220	7	1	1	220	221660589	221660807	1.360000e-95	361
2	TraesCS7D01G299600	chr7D	95.909	220	8	1	1	220	42752398	42752180	6.330000e-94	355
3	TraesCS7D01G299600	chr7D	88.095	126	13	2	4418	4542	222777619	222777743	1.150000e-31	148
4	TraesCS7D01G299600	chr7B	92.786	3535	170	34	898	4411	374727097	374723627	0.000000e+00	5036
5	TraesCS7D01G299600	chr7B	74.914	291	47	20	4755	5036	624187579	624187852	5.440000e-20	110
6	TraesCS7D01G299600	chr7A	91.289	1986	105	16	310	2283	427822408	427820479	0.000000e+00	2647
7	TraesCS7D01G299600	chr7A	89.877	1877	141	32	2542	4411	427820019	427818185	0.000000e+00	2368
8	TraesCS7D01G299600	chr7A	95.503	467	12	3	2042	2499	427820481	427820015	0.000000e+00	737
9	TraesCS7D01G299600	chr7A	92.045	528	28	8	4625	5139	670181455	670181981	0.000000e+00	730
10	TraesCS7D01G299600	chr7A	92.505	507	21	9	4642	5139	36305997	36305499	0.000000e+00	710
11	TraesCS7D01G299600	chr7A	90.393	229	21	1	4417	4644	36306269	36306041	3.010000e-77	300
12	TraesCS7D01G299600	chr7A	80.952	231	29	13	4417	4644	681253116	681252898	8.850000e-38	169
13	TraesCS7D01G299600	chr3D	93.699	730	12	5	4417	5139	477408578	477407876	0.000000e+00	1062
14	TraesCS7D01G299600	chr3D	85.233	386	50	6	315	695	9273061	9272678	1.730000e-104	390
15	TraesCS7D01G299600	chr3D	96.364	220	7	1	1	220	428692347	428692129	1.360000e-95	361
16	TraesCS7D01G299600	chr3D	87.097	124	13	3	4417	4539	8307743	8307864	2.500000e-28	137
17	TraesCS7D01G299600	chr3D	86.614	127	14	3	4417	4542	517801285	517801409	2.500000e-28	137
18	TraesCS7D01G299600	chr6A	94.499	509	16	6	4641	5139	521470301	521469795	0.000000e+00	774
19	TraesCS7D01G299600	chr3B	93.137	510	15	12	4641	5139	17348440	17348940	0.000000e+00	730
20	TraesCS7D01G299600	chr3A	93.528	479	16	7	4675	5139	689387235	689386758	0.000000e+00	699
21	TraesCS7D01G299600	chr3A	76.549	452	59	30	4697	5138	725331931	725332345	2.430000e-48	204
22	TraesCS7D01G299600	chr1B	85.572	402	45	10	310	702	610971064	610971461	4.790000e-110	409
23	TraesCS7D01G299600	chr4B	85.422	391	51	3	310	695	647764455	647764844	8.010000e-108	401
24	TraesCS7D01G299600	chr4B	82.222	405	63	8	310	708	39046779	39047180	1.770000e-89	340
25	TraesCS7D01G299600	chr6D	85.166	391	51	4	310	695	15694443	15694055	1.340000e-105	394
26	TraesCS7D01G299600	chr6D	95.909	220	8	1	1	220	307313935	307313717	6.330000e-94	355
27	TraesCS7D01G299600	chr2A	84.211	399	56	4	310	703	431581739	431581343	1.040000e-101	381
28	TraesCS7D01G299600	chr4A	83.374	409	59	5	308	708	16961681	16961274	2.260000e-98	370
29	TraesCS7D01G299600	chr1D	96.789	218	6	1	4	221	211858977	211858761	3.780000e-96	363
30	TraesCS7D01G299600	chr1D	83.503	394	56	6	308	695	16676089	16675699	4.890000e-95	359
31	TraesCS7D01G299600	chr2D	96.364	220	7	1	1	220	386374135	386373917	1.360000e-95	361
32	TraesCS7D01G299600	chr2D	96.330	218	7	1	1	218	268474185	268474401	1.760000e-94	357
33	TraesCS7D01G299600	chr2D	86.508	126	13	4	4417	4541	361422419	361422297	8.980000e-28	135
34	TraesCS7D01G299600	chr5B	96.330	218	7	1	1	218	287455865	287456081	1.760000e-94	357
35	TraesCS7D01G299600	chr4D	95.909	220	8	1	1	220	222130280	222130498	6.330000e-94	355
36	TraesCS7D01G299600	chr2B	87.903	124	10	5	4417	4538	784729288	784729168	1.930000e-29	141
37	TraesCS7D01G299600	chr5D	87.805	123	10	4	4417	4537	53896877	53896758	6.940000e-29	139

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	TraesCS7D01G299600	chr7D	379567208	379572346	5138	True	9491.000000	9491	100.000	1	5139	1	chr7D.!!$R2	5138
1	TraesCS7D01G299600	chr7B	374723627	374727097	3470	True	5036.000000	5036	92.786	898	4411	1	chr7B.!!$R1	3513
2	TraesCS7D01G299600	chr7A	427818185	427822408	4223	True	1917.333333	2647	92.223	310	4411	3	chr7A.!!$R3	4101
3	TraesCS7D01G299600	chr7A	670181455	670181981	526	False	730.000000	730	92.045	4625	5139	1	chr7A.!!$F1	514
4	TraesCS7D01G299600	chr7A	36305499	36306269	770	True	505.000000	710	91.449	4417	5139	2	chr7A.!!$R2	722
5	TraesCS7D01G299600	chr3D	477407876	477408578	702	True	1062.000000	1062	93.699	4417	5139	1	chr3D.!!$R3	722
6	TraesCS7D01G299600	chr6A	521469795	521470301	506	True	774.000000	774	94.499	4641	5139	1	chr6A.!!$R1	498
7	TraesCS7D01G299600	chr3B	17348440	17348940	500	False	730.000000	730	93.137	4641	5139	1	chr3B.!!$F1	498

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
990	999	0.035820	TCGTTTCCCCAATTCCCTCG	60.036	55.000	0.00	0.00	0.00	4.63	F
991	1000	0.322187	CGTTTCCCCAATTCCCTCGT	60.322	55.000	0.00	0.00	0.00	4.18	F
994	1003	0.330267	TTCCCCAATTCCCTCGTTCC	59.670	55.000	0.00	0.00	0.00	3.62	F
995	1004	1.076995	CCCCAATTCCCTCGTTCCC	60.077	63.158	0.00	0.00	0.00	3.97	F
996	1005	1.076995	CCCAATTCCCTCGTTCCCC	60.077	63.158	0.00	0.00	0.00	4.81	F
1029	1038	1.078848	CCACAAGAAGAGGAGCCCG	60.079	63.158	0.00	0.00	0.00	6.13	F
2046	2060	2.094026	CCTAAAGTTGGCTTCATTGGGC	60.094	50.000	0.00	0.00	33.01	5.36	F
4015	4334	0.105778	GGATAGCAGGACTCCAGCAC	59.894	60.000	14.46	5.71	38.55	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2444	2706	1.580845	GGCATATCATGTCGCCTGCC	61.581	60.000	10.21	10.21	41.50	4.85	R
2517	2826	3.266636	TCAGAAACGTCAAACTTGAGCA	58.733	40.909	0.00	0.00	37.98	4.26	R
2856	3167	3.751698	AGAGATCAACGCCCAAACTAAAC	59.248	43.478	0.00	0.00	0.00	2.01	R
3011	3322	8.034313	TGGACTAGAGAAACCATTATTAGCAT	57.966	34.615	0.00	0.00	0.00	3.79	R
3063	3374	3.243101	CCTGCATCACATCATCAAGCTTC	60.243	47.826	0.00	0.00	0.00	3.86	R
3084	3395	1.303309	CCTTCTCGTTGCATCCATCC	58.697	55.000	0.00	0.00	0.00	3.51	R
4115	4434	0.376152	CATCACAGCACGCATTCTCC	59.624	55.000	0.00	0.00	0.00	3.71	R
4885	5254	5.063204	ACTCTCGTCCAACAAATCAAATGA	58.937	37.500	0.00	0.00	0.00	2.57	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	Self end TH	Hairpin	End Stability
23	24	6.968263	TCATGGAACTACAACCAATTGAAA	57.032	33.333	7.12	0.00	39.69	2.69
24	25	7.537596	TCATGGAACTACAACCAATTGAAAT	57.462	32.000	7.12	0.00	39.69	2.17
25	26	7.961351	TCATGGAACTACAACCAATTGAAATT	58.039	30.769	7.12	0.00	39.69	1.82
26	27	7.871973	TCATGGAACTACAACCAATTGAAATTG	59.128	33.333	7.12	10.72	44.12	2.32
50	51	8.884124	TGGAATTTCATCAGAAGTTTTATCCT	57.116	30.769	0.00	0.00	34.32	3.24
51	52	9.973661	TGGAATTTCATCAGAAGTTTTATCCTA	57.026	29.630	0.00	0.00	34.32	2.94
55	56	8.806429	TTTCATCAGAAGTTTTATCCTATGCA	57.194	30.769	0.00	0.00	34.71	3.96
56	57	8.985315	TTCATCAGAAGTTTTATCCTATGCAT	57.015	30.769	3.79	3.79	0.00	3.96
57	58	8.613060	TCATCAGAAGTTTTATCCTATGCATC	57.387	34.615	0.19	0.00	0.00	3.91
58	59	8.435187	TCATCAGAAGTTTTATCCTATGCATCT	58.565	33.333	0.19	0.00	0.00	2.90
59	60	8.504815	CATCAGAAGTTTTATCCTATGCATCTG	58.495	37.037	0.19	0.00	33.61	2.90
60	61	6.994496	TCAGAAGTTTTATCCTATGCATCTGG	59.006	38.462	0.19	7.45	33.26	3.86
61	62	6.769822	CAGAAGTTTTATCCTATGCATCTGGT	59.230	38.462	0.19	0.00	0.00	4.00
62	63	7.284034	CAGAAGTTTTATCCTATGCATCTGGTT	59.716	37.037	0.19	5.01	0.00	3.67
63	64	7.500559	AGAAGTTTTATCCTATGCATCTGGTTC	59.499	37.037	0.19	5.33	0.00	3.62
64	65	6.662755	AGTTTTATCCTATGCATCTGGTTCA	58.337	36.000	0.19	0.00	0.00	3.18
65	66	7.293073	AGTTTTATCCTATGCATCTGGTTCAT	58.707	34.615	0.19	0.00	0.00	2.57
66	67	7.446625	AGTTTTATCCTATGCATCTGGTTCATC	59.553	37.037	0.19	0.00	0.00	2.92
67	68	3.391506	TCCTATGCATCTGGTTCATCG	57.608	47.619	0.19	0.00	0.00	3.84
68	69	2.700371	TCCTATGCATCTGGTTCATCGT	59.300	45.455	0.19	0.00	0.00	3.73
69	70	2.804527	CCTATGCATCTGGTTCATCGTG	59.195	50.000	0.19	0.00	0.00	4.35
70	71	2.696989	ATGCATCTGGTTCATCGTGA	57.303	45.000	0.00	0.00	0.00	4.35
71	72	2.696989	TGCATCTGGTTCATCGTGAT	57.303	45.000	0.00	0.00	0.00	3.06
72	73	2.554142	TGCATCTGGTTCATCGTGATC	58.446	47.619	0.00	0.00	0.00	2.92
73	74	2.093553	TGCATCTGGTTCATCGTGATCA	60.094	45.455	0.00	0.00	0.00	2.92

Showing 1 to 25 of 442 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.968263	TTTCAATTGGTTGTAGTTCCATGA	57.032	33.333	5.42	0.00	36.69	3.07
1	2	8.020861	CAATTTCAATTGGTTGTAGTTCCATG	57.979	34.615	5.42	0.00	41.54	3.66
24	25	9.312904	AGGATAAAACTTCTGATGAAATTCCAA	57.687	29.630	0.00	0.00	0.00	3.53
25	26	8.884124	AGGATAAAACTTCTGATGAAATTCCA	57.116	30.769	0.00	0.00	0.00	3.53
29	30	9.412460	TGCATAGGATAAAACTTCTGATGAAAT	57.588	29.630	0.00	0.00	0.00	2.17
30	31	8.806429	TGCATAGGATAAAACTTCTGATGAAA	57.194	30.769	0.00	0.00	0.00	2.69
31	32	8.985315	ATGCATAGGATAAAACTTCTGATGAA	57.015	30.769	0.00	0.00	0.00	2.57
32	33	8.435187	AGATGCATAGGATAAAACTTCTGATGA	58.565	33.333	0.00	0.00	0.00	2.92
33	34	8.504815	CAGATGCATAGGATAAAACTTCTGATG	58.495	37.037	0.00	0.00	33.52	3.07
34	35	7.664731	CCAGATGCATAGGATAAAACTTCTGAT	59.335	37.037	11.34	0.00	33.52	2.90
35	36	6.994496	CCAGATGCATAGGATAAAACTTCTGA	59.006	38.462	11.34	0.00	33.52	3.27
36	37	6.769822	ACCAGATGCATAGGATAAAACTTCTG	59.230	38.462	21.12	10.57	32.26	3.02
37	38	6.904626	ACCAGATGCATAGGATAAAACTTCT	58.095	36.000	21.12	0.00	0.00	2.85
38	39	7.283127	TGAACCAGATGCATAGGATAAAACTTC	59.717	37.037	21.12	13.39	0.00	3.01
39	40	7.118723	TGAACCAGATGCATAGGATAAAACTT	58.881	34.615	21.12	6.04	0.00	2.66
40	41	6.662755	TGAACCAGATGCATAGGATAAAACT	58.337	36.000	21.12	0.00	0.00	2.66
41	42	6.942532	TGAACCAGATGCATAGGATAAAAC	57.057	37.500	21.12	8.29	0.00	2.43
42	43	6.427853	CGATGAACCAGATGCATAGGATAAAA	59.572	38.462	21.12	5.57	0.00	1.52
43	44	5.934043	CGATGAACCAGATGCATAGGATAAA	59.066	40.000	21.12	5.32	0.00	1.40
44	45	5.012046	ACGATGAACCAGATGCATAGGATAA	59.988	40.000	21.12	6.13	0.00	1.75
45	46	4.528206	ACGATGAACCAGATGCATAGGATA	59.472	41.667	21.12	9.24	0.00	2.59
46	47	3.326006	ACGATGAACCAGATGCATAGGAT	59.674	43.478	21.12	11.56	0.00	3.24
47	48	2.700371	ACGATGAACCAGATGCATAGGA	59.300	45.455	21.12	2.96	0.00	2.94
48	49	2.804527	CACGATGAACCAGATGCATAGG	59.195	50.000	14.46	14.46	0.00	2.57
49	50	3.721035	TCACGATGAACCAGATGCATAG	58.279	45.455	0.00	0.00	0.00	2.23

Showing 1 to 25 of 481 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.