AutoCloner

Multiple sequence alignment - TraesCS2B01G248700

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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	TraesCS2B01G248700	chr2B	100.000	5339	0	0	1	5339	255050558	255055896	0.000000e+00	9860.0
1	TraesCS2B01G248700	chr2B	83.140	344	45	3	2165	2495	704119609	704119952	8.690000e-78	302.0
2	TraesCS2B01G248700	chr2B	79.300	343	58	3	2165	2494	560456228	560456570	1.500000e-55	228.0
3	TraesCS2B01G248700	chr2D	96.114	5327	130	25	1	5282	198458653	198463947	0.000000e+00	8619.0
4	TraesCS2B01G248700	chr2D	82.267	344	46	4	2165	2494	614805489	614805147	3.150000e-72	283.0
5	TraesCS2B01G248700	chr2D	93.333	60	4	0	5280	5339	198463972	198464031	7.360000e-14	89.8
6	TraesCS2B01G248700	chr2D	94.737	38	2	0	2769	2806	116908939	116908976	5.770000e-05	60.2
7	TraesCS2B01G248700	chr2A	95.644	5326	148	27	1	5280	215747586	215752873	0.000000e+00	8473.0
8	TraesCS2B01G248700	chr2A	94.737	38	2	0	2769	2806	118444821	118444858	5.770000e-05	60.2
9	TraesCS2B01G248700	chr6A	83.824	340	43	3	2165	2494	489860952	489860615	4.010000e-81	313.0
10	TraesCS2B01G248700	chr6A	91.954	87	7	0	3605	3691	472952665	472952751	7.260000e-24	122.0
11	TraesCS2B01G248700	chr6A	87.500	56	3	2	5286	5339	297681851	297681904	1.610000e-05	62.1
12	TraesCS2B01G248700	chr4B	83.090	343	42	5	2165	2493	467104322	467104662	1.120000e-76	298.0
13	TraesCS2B01G248700	chr4B	81.924	343	49	3	2165	2494	484587528	484587186	1.460000e-70	278.0
14	TraesCS2B01G248700	chr4B	95.402	87	4	0	3608	3694	670403334	670403248	7.210000e-29	139.0
15	TraesCS2B01G248700	chr6B	81.924	343	48	3	2165	2494	660635173	660635514	1.460000e-70	278.0
16	TraesCS2B01G248700	chr6B	80.523	344	54	2	2165	2495	680878191	680878534	8.880000e-63	252.0
17	TraesCS2B01G248700	chr6B	84.793	217	29	2	2280	2493	487556348	487556563	1.160000e-51	215.0
18	TraesCS2B01G248700	chr6B	97.143	35	1	0	2772	2806	35701273	35701307	5.770000e-05	60.2
19	TraesCS2B01G248700	chr4D	80.780	359	55	3	2163	2508	298223882	298223525	8.810000e-68	268.0
20	TraesCS2B01G248700	chr4D	94.253	87	5	0	3608	3694	381882681	381882595	3.350000e-27	134.0
21	TraesCS2B01G248700	chr4D	92.222	90	7	0	3605	3694	509646443	509646354	1.560000e-25	128.0
22	TraesCS2B01G248700	chr3B	96.629	89	3	0	3603	3691	556504590	556504502	1.200000e-31	148.0
23	TraesCS2B01G248700	chr3B	91.765	85	4	2	3607	3691	224314659	224314740	1.220000e-21	115.0
24	TraesCS2B01G248700	chr1D	96.629	89	3	0	3603	3691	348128612	348128524	1.200000e-31	148.0
25	TraesCS2B01G248700	chr7A	91.489	47	4	0	5282	5328	69218127	69218173	1.240000e-06	65.8
26	TraesCS2B01G248700	chr7A	100.000	35	0	0	2165	2199	617606143	617606109	1.240000e-06	65.8
27	TraesCS2B01G248700	chr5B	97.143	35	1	0	2772	2806	234759829	234759863	5.770000e-05	60.2

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	TraesCS2B01G248700	chr2B	255050558	255055896	5338	False	9860.0	9860	100.0000	1	5339	1	chr2B.!!$F1	5338
1	TraesCS2B01G248700	chr2D	198458653	198464031	5378	False	4354.4	8619	94.7235	1	5339	2	chr2D.!!$F2	5338
2	TraesCS2B01G248700	chr2A	215747586	215752873	5287	False	8473.0	8473	95.6440	1	5280	1	chr2A.!!$F2	5279

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	Hairpin	End Stability	Orientation
918	926	0.033920	GGCCTTTCTTGGGTTGCTTG	59.966	55.000	0.00	4.01	F
1173	1181	0.460987	CAGCGATGAACCCTCCTGTC	60.461	60.000	0.00	3.51	F
2231	2239	1.207329	GGTCGTCCTCATGGTTTAGCT	59.793	52.381	34.23	3.32	F
3397	3422	3.030291	TGAATGCCTTTTTGTCTGGTGT	58.970	40.909	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2231	2239	1.341531	CCACCAAAACCACGGCAATAA	59.658	47.619	0.00	0.00	0.00	1.40	R
2355	2372	1.635487	TCCCAAATTCTGAGACCCCAG	59.365	52.381	0.00	0.00	35.55	4.45	R
3440	3465	1.207791	GGCCCTTGATCTCTTCCTCA	58.792	55.000	0.00	0.00	0.00	3.86	R
5035	5100	0.302890	GGACGAATGAAGCATGCTCG	59.697	55.000	22.93	21.58	32.49	5.03	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
380	382	2.869636	GCTCTCTACTGCTGCACTTGTT	60.870	50.000	0.00	0.00	0.00	2.83
404	406	6.698008	TTTTTGCAATCTCTTCAACTCTCA	57.302	33.333	0.00	0.00	0.00	3.27
538	544	1.222115	GACGTTGCTTTCTGTCGGCT	61.222	55.000	0.00	0.00	0.00	5.52
631	637	1.869754	CGACCGGCCATCTATCTTGTG	60.870	57.143	0.00	0.00	0.00	3.33
758	766	4.727507	TGAGTTCTGCTTCTAGATCCAC	57.272	45.455	0.00	0.00	0.00	4.02
781	789	7.043391	CCACTTTCGGCTTTCTTTTCTTTTTAG	60.043	37.037	0.00	0.00	0.00	1.85
841	849	2.159379	CGATGAGACGTGGATGAGTTCA	60.159	50.000	0.00	0.00	0.00	3.18
918	926	0.033920	GGCCTTTCTTGGGTTGCTTG	59.966	55.000	0.00	0.00	0.00	4.01
932	940	3.493176	GGTTGCTTGCAGATTCAGGTTTT	60.493	43.478	0.00	0.00	0.00	2.43
952	960	1.270094	TGATTGGTTTCGTCTGCTCGT	60.270	47.619	0.00	0.00	0.00	4.18
956	964	1.009389	GGTTTCGTCTGCTCGTCTGG	61.009	60.000	0.00	0.00	0.00	3.86
1173	1181	0.460987	CAGCGATGAACCCTCCTGTC	60.461	60.000	0.00	0.00	0.00	3.51
1431	1439	2.109799	CACCTATCTGGGCAGCCG	59.890	66.667	5.00	0.00	41.11	5.52
1635	1643	2.125552	CACCGCGATCTGAAGCCA	60.126	61.111	8.23	0.00	0.00	4.75
1671	1679	1.745141	GCGACCAAGGATGAGAATGCT	60.745	52.381	0.00	0.00	0.00	3.79
1915	1923	5.766150	TTGGATTTGACGAGTTTCAATGT	57.234	34.783	0.00	0.00	35.42	2.71
2231	2239	1.207329	GGTCGTCCTCATGGTTTAGCT	59.793	52.381	0.00	0.00	34.23	3.32
2235	2243	5.116882	GTCGTCCTCATGGTTTAGCTTATT	58.883	41.667	0.00	0.00	34.23	1.40
2236	2244	5.006746	GTCGTCCTCATGGTTTAGCTTATTG	59.993	44.000	0.00	0.00	34.23	1.90
2413	2430	6.938030	TGGTCTATTTGTATTGGTTTTCGTCT	59.062	34.615	0.00	0.00	0.00	4.18
2741	2765	9.343103	CATGTGTACTAACTACTAAGTGTCTTG	57.657	37.037	0.00	0.00	35.62	3.02
3389	3414	5.472148	TGCTCATAACTGAATGCCTTTTTG	58.528	37.500	0.00	0.00	0.00	2.44
3397	3422	3.030291	TGAATGCCTTTTTGTCTGGTGT	58.970	40.909	0.00	0.00	0.00	4.16
3440	3465	8.752005	TGCAGGTTATAGCTTCAAATCTTAAT	57.248	30.769	0.00	0.00	0.00	1.40
3619	3644	2.092538	CCTCTGAACTACTCCCTCCGTA	60.093	54.545	0.00	0.00	0.00	4.02
3640	3665	8.855110	TCCGTACCATAATATAGGACGTTTTTA	58.145	33.333	3.04	0.00	31.26	1.52
3908	3934	6.758886	GGGTGAGTATTCTAATCTGAACTGTG	59.241	42.308	0.00	0.00	0.00	3.66
3941	3967	7.898725	CAACTGATAGTGTTGTTTTCTTCAC	57.101	36.000	0.00	0.00	39.69	3.18
3991	4017	7.581213	TTCACAGGTTCACACTTCATTAATT	57.419	32.000	0.00	0.00	0.00	1.40
4504	4558	4.578928	TGTTTTGGACCTACTTTCTTCTGC	59.421	41.667	0.00	0.00	0.00	4.26
4508	4562	2.744741	GGACCTACTTTCTTCTGCAAGC	59.255	50.000	0.00	0.00	0.00	4.01
4610	4674	6.272822	AGGAACATAATTTGCAGGAAAGAC	57.727	37.500	0.00	0.00	0.00	3.01
4655	4719	9.681692	TTCTGTCACATTCTGTAAATGATTTTG	57.318	29.630	0.00	0.00	0.00	2.44
4750	4815	1.945394	AGAAGACACAGCAGCAACAAG	59.055	47.619	0.00	0.00	0.00	3.16
4760	4825	4.152223	ACAGCAGCAACAAGAAAAACAAAC	59.848	37.500	0.00	0.00	0.00	2.93
4813	4878	6.049790	GTCTAGGCTAGAATTGAAACCGATT	58.950	40.000	25.07	0.00	36.40	3.34
4873	4938	5.997746	ACATGGATAGCTAATTTACACGCAT	59.002	36.000	0.00	0.00	0.00	4.73
4881	4946	1.819928	ATTTACACGCATGCCTGTCA	58.180	45.000	22.99	11.89	0.00	3.58
4915	4980	3.855255	TGGTGATGTTTCTGTCCTTCA	57.145	42.857	0.00	0.00	0.00	3.02
4939	5004	7.039644	TCAGATTTCTCTTAACGGACTTCTTCT	60.040	37.037	0.00	0.00	0.00	2.85
4941	5006	8.245491	AGATTTCTCTTAACGGACTTCTTCTAC	58.755	37.037	0.00	0.00	0.00	2.59
4954	5019	6.097915	ACTTCTTCTACGTCAAAGATTGGA	57.902	37.500	11.91	0.00	31.89	3.53
4988	5053	5.416952	CCCTCTTTGACATTATCAGTGCTTT	59.583	40.000	0.00	0.00	38.99	3.51
5012	5077	6.385649	TTTCATGTCAAAGTTTGGTCTACC	57.614	37.500	15.47	0.00	0.00	3.18
5035	5100	4.505742	CCCCCTGCTCCTCTTTGATATTAC	60.506	50.000	0.00	0.00	0.00	1.89
5041	5106	5.221521	TGCTCCTCTTTGATATTACGAGCAT	60.222	40.000	4.41	0.00	44.69	3.79
5059	5124	2.030946	GCATGCTTCATTCGTCCACTAC	59.969	50.000	11.37	0.00	0.00	2.73
5060	5125	3.261580	CATGCTTCATTCGTCCACTACA	58.738	45.455	0.00	0.00	0.00	2.74
5258	5323	5.298989	ACACTTAACTGTTGGGTATGTCA	57.701	39.130	2.69	0.00	0.00	3.58
5272	5337	0.478072	ATGTCACCTCTTGGTTGGCA	59.522	50.000	0.00	0.00	46.05	4.92
5295	5387	7.094377	GGCAAACATTCTGTTGTCCTATAGAAA	60.094	37.037	0.00	0.00	40.14	2.52
5296	5388	7.965107	GCAAACATTCTGTTGTCCTATAGAAAG	59.035	37.037	0.00	0.00	40.14	2.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
384	386	5.311265	ACATGAGAGTTGAAGAGATTGCAA	58.689	37.500	0.00	0.00	0.00	4.08
385	387	4.903054	ACATGAGAGTTGAAGAGATTGCA	58.097	39.130	0.00	0.00	0.00	4.08
404	406	3.872696	TCCAAGAACATATGCACGACAT	58.127	40.909	1.58	0.00	43.18	3.06
538	544	7.654022	AATTGGGTAACAGACAAAAGAAAGA	57.346	32.000	0.00	0.00	39.74	2.52
758	766	7.167635	GGACTAAAAAGAAAAGAAAGCCGAAAG	59.832	37.037	0.00	0.00	0.00	2.62
781	789	9.606631	AGTAATAATTCATTCAAGAGACTGGAC	57.393	33.333	0.00	0.00	0.00	4.02
902	910	1.682854	TCTGCAAGCAACCCAAGAAAG	59.317	47.619	0.00	0.00	0.00	2.62
918	926	4.525912	ACCAATCAAAACCTGAATCTGC	57.474	40.909	0.00	0.00	37.67	4.26
932	940	1.270094	ACGAGCAGACGAAACCAATCA	60.270	47.619	5.12	0.00	37.03	2.57
952	960	2.896685	CCAAATTTACAACCCAGCCAGA	59.103	45.455	0.00	0.00	0.00	3.86
956	964	4.306600	CAGTTCCAAATTTACAACCCAGC	58.693	43.478	7.49	0.00	0.00	4.85
1431	1439	4.499183	CTCCACAGAACTCCACTATGTTC	58.501	47.826	0.00	0.00	41.84	3.18
1635	1643	0.598562	TCGCGAGCAAGAAGTTCTCT	59.401	50.000	3.71	0.00	35.13	3.10
1671	1679	0.111061	AATCAGTGGCCTTGAGCACA	59.889	50.000	3.32	0.00	46.50	4.57
1915	1923	1.341852	TCCACGACTCGGAATGAACAA	59.658	47.619	2.98	0.00	0.00	2.83
1984	1992	6.908825	ACATGGTATGTTTATGTCAACACAC	58.091	36.000	0.00	0.00	41.63	3.82
2122	2130	8.915871	AACATGGAATCAGATGTTTATTTTCG	57.084	30.769	0.00	0.00	39.27	3.46
2231	2239	1.341531	CCACCAAAACCACGGCAATAA	59.658	47.619	0.00	0.00	0.00	1.40
2235	2243	1.826054	CTCCACCAAAACCACGGCA	60.826	57.895	0.00	0.00	0.00	5.69
2236	2244	1.792118	GACTCCACCAAAACCACGGC	61.792	60.000	0.00	0.00	0.00	5.68
2355	2372	1.635487	TCCCAAATTCTGAGACCCCAG	59.365	52.381	0.00	0.00	35.55	4.45
2497	2519	3.742882	TGATTAGTTCTATCATGCGCTGC	59.257	43.478	9.73	0.00	0.00	5.25
2525	2547	3.243201	CGCAATGCCTCTAGAAAATTCCC	60.243	47.826	0.00	0.00	0.00	3.97
3221	3246	4.063689	GGATGTTCTGATCCAGCATACAG	58.936	47.826	0.00	0.00	41.59	2.74
3389	3414	5.238650	ACACACTTGCTTATAAACACCAGAC	59.761	40.000	0.00	0.00	0.00	3.51
3397	3422	5.943416	ACCTGCATACACACTTGCTTATAAA	59.057	36.000	0.00	0.00	39.60	1.40
3440	3465	1.207791	GGCCCTTGATCTCTTCCTCA	58.792	55.000	0.00	0.00	0.00	3.86
3599	3624	2.131776	ACGGAGGGAGTAGTTCAGAG	57.868	55.000	0.00	0.00	0.00	3.35
3619	3644	9.895138	AACTGTAAAAACGTCCTATATTATGGT	57.105	29.630	0.00	0.00	0.00	3.55
3941	3967	3.485463	TGTCTCACTGGTAAGGTTTGG	57.515	47.619	0.00	0.00	0.00	3.28
3991	4017	7.065324	GCAGGTGCATTATACAACTACACTAAA	59.935	37.037	0.00	0.00	41.59	1.85
4228	4278	2.440409	AGAGCGCCATCAAGAAAATGT	58.560	42.857	2.29	0.00	0.00	2.71
4504	4558	3.779759	TGTACTTGCAAAAACCAGCTTG	58.220	40.909	0.00	0.00	0.00	4.01
4508	4562	9.906660	TTTATTAGATGTACTTGCAAAAACCAG	57.093	29.630	0.00	0.00	0.00	4.00
4610	4674	3.691609	AGAAAGCTCTTGGAAATTAGGCG	59.308	43.478	0.00	0.00	0.00	5.52
4655	4719	7.604545	AGATACCTTTTGCTGTCTTCTCTAAAC	59.395	37.037	0.00	0.00	0.00	2.01
4750	4815	4.693095	TGAAAGGCCTTGTGTTTGTTTTTC	59.307	37.500	21.33	8.63	0.00	2.29
4760	4825	1.631405	TGGGATTGAAAGGCCTTGTG	58.369	50.000	21.33	0.00	0.00	3.33
4873	4938	4.623932	AAGAACTAGTCATTGACAGGCA	57.376	40.909	18.57	0.72	34.60	4.75
4881	4946	7.721399	AGAAACATCACCAAAGAACTAGTCATT	59.279	33.333	0.00	0.00	0.00	2.57
4915	4980	7.234661	AGAAGAAGTCCGTTAAGAGAAATCT	57.765	36.000	0.00	0.00	0.00	2.40
4939	5004	4.081862	CAGGGTAGTCCAATCTTTGACGTA	60.082	45.833	0.00	0.00	38.24	3.57
4941	5006	3.056107	TCAGGGTAGTCCAATCTTTGACG	60.056	47.826	0.00	0.00	38.24	4.35
4954	5019	2.258109	GTCAAAGAGGGTCAGGGTAGT	58.742	52.381	0.00	0.00	0.00	2.73
4988	5053	6.183360	GGGTAGACCAAACTTTGACATGAAAA	60.183	38.462	0.00	0.00	39.85	2.29
5012	5077	1.511613	TATCAAAGAGGAGCAGGGGG	58.488	55.000	0.00	0.00	0.00	5.40
5035	5100	0.302890	GGACGAATGAAGCATGCTCG	59.697	55.000	22.93	21.58	32.49	5.03
5041	5106	2.036604	TGTGTAGTGGACGAATGAAGCA	59.963	45.455	0.00	0.00	0.00	3.91
5059	5124	1.676006	ACCTCCAAAAGCTTTCGTGTG	59.324	47.619	13.10	6.89	0.00	3.82
5060	5125	1.947456	GACCTCCAAAAGCTTTCGTGT	59.053	47.619	13.10	5.88	0.00	4.49
5066	5131	3.217626	CAACTCAGACCTCCAAAAGCTT	58.782	45.455	0.00	0.00	0.00	3.74
5107	5172	1.804748	GAAGGTTGTCCAACATCGTCC	59.195	52.381	11.89	0.00	42.85	4.79
5146	5211	3.209410	CATTAGAGAGTTGGGATGGCAC	58.791	50.000	0.00	0.00	0.00	5.01
5147	5212	2.846206	ACATTAGAGAGTTGGGATGGCA	59.154	45.455	0.00	0.00	0.00	4.92
5148	5213	3.567478	ACATTAGAGAGTTGGGATGGC	57.433	47.619	0.00	0.00	0.00	4.40
5182	5247	5.189180	GGCTAACATGAAAGGATCAAGTCT	58.811	41.667	0.00	0.00	38.96	3.24
5186	5251	4.661222	TGTGGCTAACATGAAAGGATCAA	58.339	39.130	0.00	0.00	42.54	2.57
5295	5387	4.036852	GTGTCACAAAAGCTAAAAGAGGCT	59.963	41.667	0.00	0.00	40.85	4.58
5296	5388	4.036852	AGTGTCACAAAAGCTAAAAGAGGC	59.963	41.667	5.62	0.00	0.00	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.