AutoCloner

Multiple sequence alignment - TraesCS3B01G386600

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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	TraesCS3B01G386600	chr3B	100.000	6190	0	0	1	6190	607379125	607385314	0.000000e+00	11431.0
1	TraesCS3B01G386600	chr3B	76.577	1046	163	42	4205	5180	750207916	750206883	3.330000e-137	499.0
2	TraesCS3B01G386600	chr3B	79.661	118	15	5	2354	2471	750209975	750209867	6.650000e-10	76.8
3	TraesCS3B01G386600	chr3B	90.909	55	5	0	2213	2267	730819340	730819394	2.390000e-09	75.0
4	TraesCS3B01G386600	chr3A	94.420	4731	146	42	1518	6190	601560264	601555594	0.000000e+00	7166.0
5	TraesCS3B01G386600	chr3A	90.138	1156	60	13	379	1516	601561412	601560293	0.000000e+00	1454.0
6	TraesCS3B01G386600	chr3A	76.634	719	120	25	4193	4875	697749012	697748306	2.740000e-93	353.0
7	TraesCS3B01G386600	chr3A	81.119	286	32	14	4912	5180	697748175	697747895	6.290000e-50	209.0
8	TraesCS3B01G386600	chr3A	88.776	98	8	3	1305	1402	697751477	697751383	3.920000e-22	117.0
9	TraesCS3B01G386600	chr3A	83.051	118	11	4	2354	2471	697750820	697750712	1.420000e-16	99.0
10	TraesCS3B01G386600	chr3D	93.146	4844	188	50	278	5043	459462603	459467380	0.000000e+00	6974.0
11	TraesCS3B01G386600	chr3D	98.179	1153	19	1	5040	6190	459467451	459468603	0.000000e+00	2012.0
12	TraesCS3B01G386600	chr3D	86.441	118	12	3	118	231	459462206	459462323	6.510000e-25	126.0
13	TraesCS3B01G386600	chr3D	90.909	55	5	0	2213	2267	80261241	80261187	2.390000e-09	75.0
14	TraesCS3B01G386600	chr3D	100.000	34	0	0	5424	5457	459468035	459468068	5.180000e-06	63.9
15	TraesCS3B01G386600	chr6A	89.583	528	49	2	5663	6190	22803754	22804275	0.000000e+00	665.0
16	TraesCS3B01G386600	chr6A	89.831	413	40	2	5779	6190	22695844	22696255	4.250000e-146	529.0
17	TraesCS3B01G386600	chr6A	80.288	416	41	17	5151	5537	22695232	22695635	6.110000e-70	276.0
18	TraesCS3B01G386600	chr6A	77.593	482	47	28	4913	5365	22802944	22803393	1.040000e-57	235.0
19	TraesCS3B01G386600	chr6A	79.387	359	48	17	4900	5247	22694887	22695230	4.830000e-56	230.0
20	TraesCS3B01G386600	chr6A	79.147	211	32	9	2790	2994	204743043	204742839	1.080000e-27	135.0
21	TraesCS3B01G386600	chr6A	81.081	148	19	2	5392	5539	22803498	22803636	6.560000e-20	110.0
22	TraesCS3B01G386600	chr6A	92.105	38	3	0	4925	4962	204739495	204739458	3.000000e-03	54.7
23	TraesCS3B01G386600	chr6D	89.414	529	48	5	5663	6190	24261999	24262520	0.000000e+00	660.0
24	TraesCS3B01G386600	chr6D	90.073	413	39	2	5779	6190	24230796	24231207	9.130000e-148	534.0
25	TraesCS3B01G386600	chr6D	77.370	654	78	41	5151	5753	24230163	24230797	2.150000e-84	324.0
26	TraesCS3B01G386600	chr6D	86.139	202	23	2	5051	5247	24229960	24230161	4.860000e-51	213.0
27	TraesCS3B01G386600	chr6D	81.757	148	18	2	5392	5539	24261743	24261881	1.410000e-21	115.0
28	TraesCS3B01G386600	chr6D	88.462	78	7	2	4780	4856	24229733	24229809	6.610000e-15	93.5
29	TraesCS3B01G386600	chr6D	92.105	38	3	0	4925	4962	143647123	143647160	3.000000e-03	54.7
30	TraesCS3B01G386600	chr6B	89.143	525	54	3	5663	6187	39339167	39339688	0.000000e+00	651.0
31	TraesCS3B01G386600	chr6B	79.612	412	44	21	5153	5537	39197850	39198248	6.160000e-65	259.0
32	TraesCS3B01G386600	chr6B	84.653	202	26	2	5051	5247	39197644	39197845	4.900000e-46	196.0
33	TraesCS3B01G386600	chr6B	81.333	150	15	5	5392	5539	39338911	39339049	6.560000e-20	110.0
34	TraesCS3B01G386600	chr6B	92.105	38	3	0	4925	4962	255672747	255672784	3.000000e-03	54.7
35	TraesCS3B01G386600	chr5A	87.382	531	56	5	5663	6190	465111733	465111211	3.190000e-167	599.0
36	TraesCS3B01G386600	chr5A	82.192	219	31	7	2773	2987	427067831	427068045	1.370000e-41	182.0
37	TraesCS3B01G386600	chr5A	79.253	241	43	6	2818	3053	666232890	666232652	1.790000e-35	161.0
38	TraesCS3B01G386600	chr2A	87.382	531	56	6	5663	6190	425812698	425813220	3.190000e-167	599.0
39	TraesCS3B01G386600	chr1D	78.062	743	129	20	4466	5177	3435358	3434619	7.370000e-119	438.0
40	TraesCS3B01G386600	chr1D	90.000	50	5	0	4339	4388	436190988	436190939	1.440000e-06	65.8
41	TraesCS3B01G386600	chr5D	83.333	204	26	7	2788	2987	329617444	329617245	1.370000e-41	182.0
42	TraesCS3B01G386600	chr4D	79.167	240	45	4	2818	3053	485387036	485386798	1.790000e-35	161.0
43	TraesCS3B01G386600	chr4D	89.362	47	3	2	5151	5196	381837114	381837069	2.410000e-04	58.4
44	TraesCS3B01G386600	chr4B	78.750	240	46	4	2818	3053	618593466	618593228	8.310000e-34	156.0
45	TraesCS3B01G386600	chr1B	90.000	50	5	0	4339	4388	591111305	591111256	1.440000e-06	65.8
46	TraesCS3B01G386600	chr1A	90.000	50	5	0	4339	4388	533449240	533449191	1.440000e-06	65.8
47	TraesCS3B01G386600	chr7B	100.000	28	0	0	5315	5342	47335390	47335417	1.100000e-02	52.8
48	TraesCS3B01G386600	chr7B	100.000	28	0	0	5315	5342	47595189	47595216	1.100000e-02	52.8

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	TraesCS3B01G386600	chr3B	607379125	607385314	6189	False	11431.000000	11431	100.000000	1	6190	1	chr3B.!!$F1	6189
1	TraesCS3B01G386600	chr3B	750206883	750209975	3092	True	287.900000	499	78.119000	2354	5180	2	chr3B.!!$R1	2826
2	TraesCS3B01G386600	chr3A	601555594	601561412	5818	True	4310.000000	7166	92.279000	379	6190	2	chr3A.!!$R1	5811
3	TraesCS3B01G386600	chr3D	459462206	459468603	6397	False	2293.975000	6974	94.441500	118	6190	4	chr3D.!!$F1	6072
4	TraesCS3B01G386600	chr6A	22694887	22696255	1368	False	345.000000	529	83.168667	4900	6190	3	chr6A.!!$F1	1290
5	TraesCS3B01G386600	chr6A	22802944	22804275	1331	False	336.666667	665	82.752333	4913	6190	3	chr6A.!!$F2	1277
6	TraesCS3B01G386600	chr6D	24261743	24262520	777	False	387.500000	660	85.585500	5392	6190	2	chr6D.!!$F3	798
7	TraesCS3B01G386600	chr6D	24229733	24231207	1474	False	291.125000	534	85.511000	4780	6190	4	chr6D.!!$F2	1410
8	TraesCS3B01G386600	chr6B	39338911	39339688	777	False	380.500000	651	85.238000	5392	6187	2	chr6B.!!$F3	795
9	TraesCS3B01G386600	chr6B	39197644	39198248	604	False	227.500000	259	82.132500	5051	5537	2	chr6B.!!$F2	486
10	TraesCS3B01G386600	chr5A	465111211	465111733	522	True	599.000000	599	87.382000	5663	6190	1	chr5A.!!$R1	527
11	TraesCS3B01G386600	chr2A	425812698	425813220	522	False	599.000000	599	87.382000	5663	6190	1	chr2A.!!$F1	527
12	TraesCS3B01G386600	chr1D	3434619	3435358	739	True	438.000000	438	78.062000	4466	5177	1	chr1D.!!$R1	711

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
96	97	0.035881	TGAGAGGCTGGCAGTTTGAG	59.964	55.000	17.16	0.00	0.00	3.02	F
97	98	0.036022	GAGAGGCTGGCAGTTTGAGT	59.964	55.000	17.16	0.00	0.00	3.41	F
99	100	0.036022	GAGGCTGGCAGTTTGAGTCT	59.964	55.000	17.16	0.00	0.00	3.24	F
1415	1675	0.104120	GGTGAGCACCCAAACCAAAC	59.896	55.000	8.48	0.00	45.68	2.93	F
1418	1678	0.104120	GAGCACCCAAACCAAACCAC	59.896	55.000	0.00	0.00	0.00	4.16	F
2513	2827	0.108992	GTAGTGGTCGCCATGTCGAA	60.109	55.000	0.00	0.00	40.43	3.71	F
2515	2829	0.670546	AGTGGTCGCCATGTCGAAAG	60.671	55.000	0.00	0.00	40.43	2.62	F
2715	3490	0.692476	CACCAGGACCATGGACTTCA	59.308	55.000	21.47	0.00	43.57	3.02	F
3527	4304	1.064946	CTTCTACGCCTGCGAGAGG	59.935	63.158	19.52	12.42	46.13	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1411	1671	0.249955	GATGCATTGGGGGTGGTTTG	59.750	55.000	0.00	0.00	0.00	2.93	R
1889	2186	0.334676	GTTTGGGGGATCCATGGACA	59.665	55.000	18.99	7.31	46.52	4.02	R
1918	2215	1.933021	AGTGATTAGTCCACCGACCA	58.067	50.000	0.00	0.00	40.12	4.02	R
2715	3490	0.108615	CGCTTCCAGTTCTCGTGGAT	60.109	55.000	0.00	0.00	43.78	3.41	R
3311	4086	1.480212	AATGCACCACGAGGAGGACA	61.480	55.000	5.68	0.00	38.69	4.02	R
3950	4798	0.250338	ACTGACCTTCCCGAACAAGC	60.250	55.000	0.00	0.00	0.00	4.01	R
4448	5796	6.582636	TCAGTTATGTTACCTCCATTAGCTG	58.417	40.000	0.00	0.00	0.00	4.24	R
4663	6020	6.595326	TGCGACTAGACAAAGATGAAATTGAT	59.405	34.615	0.00	0.00	0.00	2.57	R
5292	6918	1.196127	GTACTTTGTACAACCCAGCGC	59.804	52.381	8.07	0.00	0.00	5.92	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	3.769739	TGTTCATCAAGCACAGTACCT	57.230	42.857	0.00	0.00	0.00	3.08
21	22	3.402110	TGTTCATCAAGCACAGTACCTG	58.598	45.455	0.00	0.00	37.52	4.00
22	23	2.099141	TCATCAAGCACAGTACCTGC	57.901	50.000	5.19	5.19	34.37	4.85
23	24	1.347378	TCATCAAGCACAGTACCTGCA	59.653	47.619	14.00	0.00	37.08	4.41
24	25	2.026915	TCATCAAGCACAGTACCTGCAT	60.027	45.455	14.00	1.17	37.08	3.96
25	26	3.197549	TCATCAAGCACAGTACCTGCATA	59.802	43.478	14.00	1.62	37.08	3.14
26	27	2.972625	TCAAGCACAGTACCTGCATAC	58.027	47.619	14.00	0.00	37.08	2.39
27	28	1.660607	CAAGCACAGTACCTGCATACG	59.339	52.381	14.00	0.00	37.08	3.06
28	29	0.175760	AGCACAGTACCTGCATACGG	59.824	55.000	14.00	0.00	37.08	4.02
29	30	0.174845	GCACAGTACCTGCATACGGA	59.825	55.000	8.01	0.00	34.37	4.69
30	31	1.202533	GCACAGTACCTGCATACGGAT	60.203	52.381	8.01	0.00	34.37	4.18
31	32	2.035449	GCACAGTACCTGCATACGGATA	59.965	50.000	8.01	0.00	34.37	2.59
32	33	3.639538	CACAGTACCTGCATACGGATAC	58.360	50.000	4.87	1.43	34.37	2.24
58	59	2.504032	CCATGTGGCGTACGGGAT	59.496	61.111	18.39	0.00	0.00	3.85
59	60	1.594293	CCATGTGGCGTACGGGATC	60.594	63.158	18.39	0.00	0.00	3.36
60	61	1.441729	CATGTGGCGTACGGGATCT	59.558	57.895	18.39	0.00	0.00	2.75
61	62	0.179084	CATGTGGCGTACGGGATCTT	60.179	55.000	18.39	0.00	0.00	2.40
62	63	0.179084	ATGTGGCGTACGGGATCTTG	60.179	55.000	18.39	0.00	0.00	3.02
63	64	1.520787	GTGGCGTACGGGATCTTGG	60.521	63.158	18.39	0.00	0.00	3.61
64	65	1.985662	TGGCGTACGGGATCTTGGT	60.986	57.895	18.39	0.00	0.00	3.67
65	66	1.227176	GGCGTACGGGATCTTGGTC	60.227	63.158	18.39	0.00	0.00	4.02
66	67	1.588139	GCGTACGGGATCTTGGTCG	60.588	63.158	18.39	0.00	0.00	4.79
67	68	1.805254	CGTACGGGATCTTGGTCGT	59.195	57.895	7.57	0.00	39.30	4.34
68	69	0.524816	CGTACGGGATCTTGGTCGTG	60.525	60.000	7.57	0.00	37.10	4.35
69	70	0.804933	GTACGGGATCTTGGTCGTGC	60.805	60.000	0.00	0.00	37.10	5.34

Showing 1 to 25 of 185 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	5.396328	TGCGTATCCGTATGCAGGTACTG	62.396	52.174	0.00	0.00	45.42	2.74
14	15	1.268899	GCGTATCCGTATGCAGGTACT	59.731	52.381	0.00	0.00	41.50	2.73
15	16	1.001048	TGCGTATCCGTATGCAGGTAC	60.001	52.381	0.00	0.00	45.42	3.34
16	17	1.320507	TGCGTATCCGTATGCAGGTA	58.679	50.000	0.00	0.00	45.42	3.08
17	18	2.120765	TGCGTATCCGTATGCAGGT	58.879	52.632	0.00	0.00	45.42	4.00
21	22	1.324718	CGTACTGCGTATCCGTATGC	58.675	55.000	0.00	0.00	42.09	3.14
22	23	1.324718	GCGTACTGCGTATCCGTATG	58.675	55.000	0.00	0.00	43.66	2.39
23	24	3.761481	GCGTACTGCGTATCCGTAT	57.239	52.632	0.00	0.00	43.66	3.06
41	42	1.594293	GATCCCGTACGCCACATGG	60.594	63.158	10.49	4.58	38.53	3.66
42	43	0.179084	AAGATCCCGTACGCCACATG	60.179	55.000	10.49	0.00	0.00	3.21
43	44	0.179084	CAAGATCCCGTACGCCACAT	60.179	55.000	10.49	0.00	0.00	3.21
44	45	1.216977	CAAGATCCCGTACGCCACA	59.783	57.895	10.49	0.00	0.00	4.17
45	46	1.520787	CCAAGATCCCGTACGCCAC	60.521	63.158	10.49	0.85	0.00	5.01
46	47	1.952102	GACCAAGATCCCGTACGCCA	61.952	60.000	10.49	0.00	0.00	5.69
47	48	1.227176	GACCAAGATCCCGTACGCC	60.227	63.158	10.49	0.00	0.00	5.68
48	49	1.588139	CGACCAAGATCCCGTACGC	60.588	63.158	10.49	0.00	0.00	4.42
49	50	0.524816	CACGACCAAGATCCCGTACG	60.525	60.000	8.69	8.69	33.62	3.67
50	51	0.804933	GCACGACCAAGATCCCGTAC	60.805	60.000	0.00	0.00	33.62	3.67
51	52	1.514087	GCACGACCAAGATCCCGTA	59.486	57.895	0.00	0.00	33.62	4.02
52	53	2.264794	GCACGACCAAGATCCCGT	59.735	61.111	0.00	0.00	35.46	5.28
53	54	1.672854	TAGGCACGACCAAGATCCCG	61.673	60.000	0.00	0.00	43.14	5.14
54	55	0.179081	GTAGGCACGACCAAGATCCC	60.179	60.000	0.00	0.00	43.14	3.85
55	56	0.824759	AGTAGGCACGACCAAGATCC	59.175	55.000	0.00	0.00	43.14	3.36
56	57	1.534175	CGAGTAGGCACGACCAAGATC	60.534	57.143	0.00	0.00	43.14	2.75
57	58	0.456221	CGAGTAGGCACGACCAAGAT	59.544	55.000	0.00	0.00	43.14	2.40

Showing 1 to 25 of 212 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.