AutoCloner

Multiple sequence alignment - TraesCS3A01G477200

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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	TraesCS3A01G477200	chr3A	100.000	4995	0	0	1	4995	709071945	709066951	0.000000e+00	9225.0
1	TraesCS3A01G477200	chr3A	87.097	93	9	3	168	258	177112487	177112396	8.850000e-18	102.0
2	TraesCS3A01G477200	chr3D	94.991	2935	106	12	992	3924	573921648	573918753	0.000000e+00	4567.0
3	TraesCS3A01G477200	chr3D	88.563	682	35	10	263	911	573922323	573921652	0.000000e+00	787.0
4	TraesCS3A01G477200	chr3D	94.316	475	24	3	3993	4466	573912230	573911758	0.000000e+00	725.0
5	TraesCS3A01G477200	chr3D	84.211	247	39	0	1649	1895	514680942	514680696	1.800000e-59	241.0
6	TraesCS3A01G477200	chr3B	96.195	2129	76	4	1326	3452	763226839	763228964	0.000000e+00	3478.0
7	TraesCS3A01G477200	chr3B	91.160	871	46	6	3516	4366	763229058	763229917	0.000000e+00	1153.0
8	TraesCS3A01G477200	chr3B	89.346	413	30	5	4443	4849	763230257	763230661	1.600000e-139	507.0
9	TraesCS3A01G477200	chr3B	84.685	444	23	14	263	687	763225702	763226119	7.790000e-108	401.0
10	TraesCS3A01G477200	chr3B	81.731	520	29	20	779	1292	763226379	763226838	1.700000e-99	374.0
11	TraesCS3A01G477200	chr3B	89.524	105	8	2	4891	4995	763230783	763230884	4.060000e-26	130.0
12	TraesCS3A01G477200	chr3B	78.395	162	20	13	4628	4782	17036588	17036741	1.910000e-14	91.6
13	TraesCS3A01G477200	chr3B	96.226	53	1	1	4369	4420	763230206	763230258	8.910000e-13	86.1
14	TraesCS3A01G477200	chr2B	80.123	488	77	12	1431	1899	785984549	785984063	3.700000e-91	346.0
15	TraesCS3A01G477200	chr2B	81.081	111	16	5	4661	4770	523080696	523080590	3.200000e-12	84.2
16	TraesCS3A01G477200	chr2B	97.826	46	1	0	134	179	769490320	769490365	4.150000e-11	80.5
17	TraesCS3A01G477200	chr2B	80.180	111	17	4	4661	4770	523078456	523078350	1.490000e-10	78.7
18	TraesCS3A01G477200	chr1D	86.312	263	36	0	1644	1906	7372271	7372533	2.280000e-73	287.0
19	TraesCS3A01G477200	chr1D	90.000	90	9	0	4842	4931	482101126	482101215	3.160000e-22	117.0
20	TraesCS3A01G477200	chr1D	88.372	86	8	2	175	258	464288588	464288673	8.850000e-18	102.0
21	TraesCS3A01G477200	chr1D	87.273	55	7	0	68	122	87066400	87066346	4.170000e-06	63.9
22	TraesCS3A01G477200	chr1A	85.878	262	37	0	1645	1906	9532815	9532554	3.810000e-71	279.0
23	TraesCS3A01G477200	chr1A	86.957	92	10	2	168	258	588010744	588010654	8.850000e-18	102.0
24	TraesCS3A01G477200	chr1A	82.301	113	13	5	30	137	120378395	120378505	1.910000e-14	91.6
25	TraesCS3A01G477200	chr1B	85.171	263	39	0	1644	1906	9647615	9647877	2.290000e-68	270.0
26	TraesCS3A01G477200	chr6D	76.891	476	85	11	1443	1895	426109778	426109305	3.860000e-61	246.0
27	TraesCS3A01G477200	chr6D	94.118	51	2	1	134	183	472504271	472504321	5.360000e-10	76.8
28	TraesCS3A01G477200	chr6D	95.000	40	2	0	4083	4122	12560094	12560055	4.170000e-06	63.9
29	TraesCS3A01G477200	chr7B	80.986	284	54	0	1644	1927	745446456	745446739	5.030000e-55	226.0
30	TraesCS3A01G477200	chr5B	81.683	202	22	9	1	187	223958701	223958500	2.410000e-33	154.0
31	TraesCS3A01G477200	chr5B	93.103	58	2	2	132	187	223957663	223957606	3.200000e-12	84.2
32	TraesCS3A01G477200	chr5B	97.561	41	1	0	68	108	610296140	610296100	2.490000e-08	71.3
33	TraesCS3A01G477200	chr5B	100.000	35	0	0	224	258	337159873	337159839	1.160000e-06	65.8
34	TraesCS3A01G477200	chr6A	80.180	222	19	16	4430	4629	13785502	13785284	5.210000e-30	143.0
35	TraesCS3A01G477200	chr6A	79.508	122	21	3	4661	4781	33916169	33916051	3.200000e-12	84.2
36	TraesCS3A01G477200	chr6A	78.689	122	22	3	4661	4781	33918290	33918172	1.490000e-10	78.7
37	TraesCS3A01G477200	chr2A	83.453	139	20	2	1	137	651135639	651135776	5.250000e-25	126.0
38	TraesCS3A01G477200	chr2A	96.000	50	2	0	132	181	10978613	10978662	1.150000e-11	82.4
39	TraesCS3A01G477200	chr2A	93.617	47	2	1	141	186	724591193	724591147	8.970000e-08	69.4
40	TraesCS3A01G477200	chr4A	83.333	126	20	1	2	127	89019914	89020038	1.140000e-21	115.0
41	TraesCS3A01G477200	chr4A	81.034	116	17	4	4661	4775	715943693	715943582	2.480000e-13	87.9
42	TraesCS3A01G477200	chr4A	81.707	82	11	4	4843	4923	106101399	106101477	1.160000e-06	65.8
43	TraesCS3A01G477200	chr7D	87.778	90	11	0	4842	4931	623354303	623354214	6.840000e-19	106.0
44	TraesCS3A01G477200	chr6B	88.372	86	8	2	175	258	537452708	537452623	8.850000e-18	102.0
45	TraesCS3A01G477200	chr6B	86.585	82	5	4	4085	4161	21009070	21009150	8.910000e-13	86.1
46	TraesCS3A01G477200	chr6B	75.926	162	24	13	4629	4783	706024434	706024587	8.970000e-08	69.4
47	TraesCS3A01G477200	chr6B	75.625	160	24	11	4631	4783	706025228	706025379	1.160000e-06	65.8
48	TraesCS3A01G477200	chrUn	88.095	84	9	1	4842	4925	87112775	87112857	1.140000e-16	99.0
49	TraesCS3A01G477200	chr5D	85.417	96	12	2	175	268	558966819	558966914	1.140000e-16	99.0
50	TraesCS3A01G477200	chr7A	97.917	48	1	0	132	179	682268284	682268237	3.200000e-12	84.2
51	TraesCS3A01G477200	chr7A	95.918	49	2	0	132	180	569392764	569392716	4.150000e-11	80.5
52	TraesCS3A01G477200	chr4B	95.918	49	2	0	132	180	621846166	621846214	4.150000e-11	80.5
53	TraesCS3A01G477200	chr2D	85.897	78	8	3	4847	4923	467181318	467181243	4.150000e-11	80.5
54	TraesCS3A01G477200	chr2D	95.238	42	1	1	218	258	492711675	492711634	1.160000e-06	65.8
55	TraesCS3A01G477200	chr4D	88.060	67	6	2	4848	4913	137275279	137275214	1.490000e-10	78.7
56	TraesCS3A01G477200	chr4D	84.337	83	9	4	4842	4923	360836450	360836529	1.490000e-10	78.7
57	TraesCS3A01G477200	chr4D	84.932	73	7	4	4842	4913	191160211	191160280	2.490000e-08	71.3

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	TraesCS3A01G477200	chr3A	709066951	709071945	4994	True	9225.000000	9225	100.000000	1	4995	1	chr3A.!!$R2	4994
1	TraesCS3A01G477200	chr3D	573918753	573922323	3570	True	2677.000000	4567	91.777000	263	3924	2	chr3D.!!$R3	3661
2	TraesCS3A01G477200	chr3B	763225702	763230884	5182	False	875.585714	3478	89.838143	263	4995	7	chr3B.!!$F2	4732

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
127	128	0.107214	TTGGACTGGGAATGGATCGC	60.107	55.0	0.00	0.00	41.21	4.58	F
175	176	0.255890	GCCCCATTGGAGTTGCTCTA	59.744	55.0	3.62	0.00	35.39	2.43	F
1911	2175	0.112412	TGGGAGCTTTGAAACCCTCC	59.888	55.0	7.39	10.04	42.49	4.30	F
2364	2628	0.179215	GTTGAAGATGCGAAGGTGCG	60.179	55.0	0.00	0.00	37.81	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1911	2175	0.182537	TGTTGTCCAGTGGAACCCTG	59.817	55.000	15.09	37.80	4.45	R
2150	2414	3.004106	GCAATATGATGCCACTCCTTGTC	59.996	47.826	0.00	40.49	3.18	R
3400	3664	0.031857	CCTCTAGATGTCAGCTGCGG	59.968	60.000	9.47	0.00	5.69	R
4030	4371	0.178998	GCCAGGGACATGATGATGCT	60.179	55.000	0.00	32.14	3.79	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
20	21	3.274281	AAAATGGAGGGAAATGGTGGT	57.726	42.857	0.00	0.00	0.00	4.16
21	22	2.236489	AATGGAGGGAAATGGTGGTG	57.764	50.000	0.00	0.00	0.00	4.17
22	23	0.336048	ATGGAGGGAAATGGTGGTGG	59.664	55.000	0.00	0.00	0.00	4.61
23	24	1.682344	GGAGGGAAATGGTGGTGGC	60.682	63.158	0.00	0.00	0.00	5.01
24	25	1.384191	GAGGGAAATGGTGGTGGCT	59.616	57.895	0.00	0.00	0.00	4.75
25	26	0.967380	GAGGGAAATGGTGGTGGCTG	60.967	60.000	0.00	0.00	0.00	4.85
26	27	1.228862	GGGAAATGGTGGTGGCTGT	60.229	57.895	0.00	0.00	0.00	4.40
27	28	1.250840	GGGAAATGGTGGTGGCTGTC	61.251	60.000	0.00	0.00	0.00	3.51
28	29	0.539438	GGAAATGGTGGTGGCTGTCA	60.539	55.000	0.00	0.00	0.00	3.58
29	30	0.598065	GAAATGGTGGTGGCTGTCAC	59.402	55.000	3.25	3.25	45.34	3.67
36	37	2.571757	GTGGCTGTCACCGATCGA	59.428	61.111	18.66	0.00	40.39	3.59
37	38	1.805945	GTGGCTGTCACCGATCGAC	60.806	63.158	18.66	7.65	40.39	4.20
38	39	2.579787	GGCTGTCACCGATCGACG	60.580	66.667	18.66	7.07	42.18	5.12
54	55	4.772231	CGGACCCGGGGAGAGGAA	62.772	72.222	27.92	0.00	35.56	3.36
55	56	2.040779	GGACCCGGGGAGAGGAAT	60.041	66.667	27.92	0.00	0.00	3.01
56	57	1.235112	GGACCCGGGGAGAGGAATA	59.765	63.158	27.92	0.00	0.00	1.75
57	58	0.832559	GGACCCGGGGAGAGGAATAG	60.833	65.000	27.92	0.00	0.00	1.73
58	59	0.832559	GACCCGGGGAGAGGAATAGG	60.833	65.000	27.92	0.00	0.00	2.57
59	60	2.217745	CCCGGGGAGAGGAATAGGC	61.218	68.421	14.71	0.00	0.00	3.93
60	61	2.574955	CCGGGGAGAGGAATAGGCG	61.575	68.421	0.00	0.00	0.00	5.52
61	62	2.744377	GGGGAGAGGAATAGGCGC	59.256	66.667	0.00	0.00	0.00	6.53
62	63	2.340443	GGGAGAGGAATAGGCGCG	59.660	66.667	0.00	0.00	0.00	6.86
63	64	2.499827	GGGAGAGGAATAGGCGCGT	61.500	63.158	8.43	8.08	0.00	6.01
64	65	1.300233	GGAGAGGAATAGGCGCGTG	60.300	63.158	13.84	0.00	0.00	5.34
65	66	1.951631	GAGAGGAATAGGCGCGTGC	60.952	63.158	13.78	13.78	41.71	5.34

Showing 1 to 25 of 334 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	2.905736	CACCACCATTTCCCTCCATTTT	59.094	45.455	0.00	0.00	0.00	1.82
1	2	2.539302	CACCACCATTTCCCTCCATTT	58.461	47.619	0.00	0.00	0.00	2.32
2	3	1.273211	CCACCACCATTTCCCTCCATT	60.273	52.381	0.00	0.00	0.00	3.16
3	4	0.336048	CCACCACCATTTCCCTCCAT	59.664	55.000	0.00	0.00	0.00	3.41
4	5	1.773635	CCACCACCATTTCCCTCCA	59.226	57.895	0.00	0.00	0.00	3.86
5	6	1.682344	GCCACCACCATTTCCCTCC	60.682	63.158	0.00	0.00	0.00	4.30
6	7	0.967380	CAGCCACCACCATTTCCCTC	60.967	60.000	0.00	0.00	0.00	4.30
7	8	1.077265	CAGCCACCACCATTTCCCT	59.923	57.895	0.00	0.00	0.00	4.20
8	9	1.228862	ACAGCCACCACCATTTCCC	60.229	57.895	0.00	0.00	0.00	3.97
9	10	0.539438	TGACAGCCACCACCATTTCC	60.539	55.000	0.00	0.00	0.00	3.13
10	11	0.598065	GTGACAGCCACCACCATTTC	59.402	55.000	0.00	0.00	39.86	2.17
11	12	2.732289	GTGACAGCCACCACCATTT	58.268	52.632	0.00	0.00	39.86	2.32
12	13	4.500265	GTGACAGCCACCACCATT	57.500	55.556	0.00	0.00	39.86	3.16
19	20	1.805945	GTCGATCGGTGACAGCCAC	60.806	63.158	16.41	0.00	44.95	5.01
20	21	2.571757	GTCGATCGGTGACAGCCA	59.428	61.111	16.41	0.00	36.37	4.75
21	22	2.579787	CGTCGATCGGTGACAGCC	60.580	66.667	16.41	0.00	36.11	4.85
37	38	2.651841	TATTCCTCTCCCCGGGTCCG	62.652	65.000	21.85	3.89	39.44	4.79
38	39	0.832559	CTATTCCTCTCCCCGGGTCC	60.833	65.000	21.85	0.00	0.00	4.46
39	40	0.832559	CCTATTCCTCTCCCCGGGTC	60.833	65.000	21.85	0.00	0.00	4.46
40	41	1.236282	CCTATTCCTCTCCCCGGGT	59.764	63.158	21.85	0.00	0.00	5.28
41	42	2.217745	GCCTATTCCTCTCCCCGGG	61.218	68.421	15.80	15.80	0.00	5.73
42	43	2.574955	CGCCTATTCCTCTCCCCGG	61.575	68.421	0.00	0.00	0.00	5.73
43	44	3.052081	CGCCTATTCCTCTCCCCG	58.948	66.667	0.00	0.00	0.00	5.73
44	45	2.744377	GCGCCTATTCCTCTCCCC	59.256	66.667	0.00	0.00	0.00	4.81
45	46	2.340443	CGCGCCTATTCCTCTCCC	59.660	66.667	0.00	0.00	0.00	4.30

Showing 1 to 25 of 334 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.