AutoCloner

Multiple sequence alignment - TraesCS2B01G540700

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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	TraesCS2B01G540700	chr2B	100.000	2849	0	0	1	2849	737109345	737106497	0.000000e+00	5262
1	TraesCS2B01G540700	chr2B	91.768	2223	126	22	4	2197	737098065	737095871	0.000000e+00	3038
2	TraesCS2B01G540700	chr2B	89.438	1619	79	27	695	2263	737160815	737159239	0.000000e+00	1958
3	TraesCS2B01G540700	chr2B	91.447	1251	68	11	642	1862	737246292	737245051	0.000000e+00	1681
4	TraesCS2B01G540700	chr2B	91.374	1252	68	12	642	1862	737227237	737225995	0.000000e+00	1677
5	TraesCS2B01G540700	chr2B	89.798	1235	76	11	806	2015	737272380	737271171	0.000000e+00	1537
6	TraesCS2B01G540700	chr2B	83.201	631	83	5	6	636	737248357	737247750	8.920000e-155	556
7	TraesCS2B01G540700	chr2B	82.884	631	85	5	6	636	737229303	737228696	1.930000e-151	545
8	TraesCS2B01G540700	chr2B	86.308	409	30	9	1860	2248	737244948	737244546	3.390000e-114	422
9	TraesCS2B01G540700	chr2B	89.583	144	14	1	2191	2333	737095712	737095569	6.270000e-42	182
10	TraesCS2B01G540700	chr2A	90.281	1780	108	23	600	2333	737735574	737733814	0.000000e+00	2268
11	TraesCS2B01G540700	chr2A	89.250	1693	111	28	694	2333	737880627	737878953	0.000000e+00	2052
12	TraesCS2B01G540700	chr2A	86.726	1567	139	23	806	2333	738007000	738005464	0.000000e+00	1677
13	TraesCS2B01G540700	chr2A	90.909	858	52	11	694	1536	737838564	737837718	0.000000e+00	1129
14	TraesCS2B01G540700	chr2A	86.184	608	75	7	1	601	737736263	737735658	0.000000e+00	649
15	TraesCS2B01G540700	chr2A	87.105	411	37	7	1938	2333	737837322	737836913	4.330000e-123	451
16	TraesCS2B01G540700	chr2A	88.685	327	15	4	2545	2849	568290191	568290517	2.070000e-101	379
17	TraesCS2B01G540700	chr2A	95.890	219	7	1	2333	2551	568289917	568290133	1.260000e-93	353
18	TraesCS2B01G540700	chr2A	92.857	112	5	2	2334	2445	568296621	568296729	2.940000e-35	159
19	TraesCS2B01G540700	chr2D	87.779	1702	127	30	694	2333	606156651	606154969	0.000000e+00	1916
20	TraesCS2B01G540700	chr2D	89.564	1514	94	20	853	2332	606188757	606187274	0.000000e+00	1862
21	TraesCS2B01G540700	chr2D	85.696	1573	145	23	807	2333	606214859	606213321	0.000000e+00	1585
22	TraesCS2B01G540700	chr2D	90.466	944	42	12	694	1626	606164505	606163599	0.000000e+00	1201
23	TraesCS2B01G540700	chr2D	87.602	613	53	8	1739	2333	606162004	606161397	0.000000e+00	689
24	TraesCS2B01G540700	chr2D	85.435	666	92	3	17	680	606189758	606189096	0.000000e+00	688
25	TraesCS2B01G540700	chr2D	90.066	151	7	5	694	842	606189109	606188965	3.750000e-44	189
26	TraesCS2B01G540700	chrUn	89.985	1308	86	18	1064	2333	386125594	386124294	0.000000e+00	1648
27	TraesCS2B01G540700	chrUn	84.298	242	16	12	694	921	30267131	30266898	1.720000e-52	217
28	TraesCS2B01G540700	chrUn	85.279	197	28	1	440	636	477697385	477697190	4.810000e-48	202

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	TraesCS2B01G540700	chr2B	737106497	737109345	2848	True	5262.000000	5262	100.000000	1	2849	1	chr2B.!!$R1	2848
1	TraesCS2B01G540700	chr2B	737159239	737160815	1576	True	1958.000000	1958	89.438000	695	2263	1	chr2B.!!$R2	1568
2	TraesCS2B01G540700	chr2B	737095569	737098065	2496	True	1610.000000	3038	90.675500	4	2333	2	chr2B.!!$R4	2329
3	TraesCS2B01G540700	chr2B	737271171	737272380	1209	True	1537.000000	1537	89.798000	806	2015	1	chr2B.!!$R3	1209
4	TraesCS2B01G540700	chr2B	737225995	737229303	3308	True	1111.000000	1677	87.129000	6	1862	2	chr2B.!!$R5	1856
5	TraesCS2B01G540700	chr2B	737244546	737248357	3811	True	886.333333	1681	86.985333	6	2248	3	chr2B.!!$R6	2242
6	TraesCS2B01G540700	chr2A	737878953	737880627	1674	True	2052.000000	2052	89.250000	694	2333	1	chr2A.!!$R1	1639
7	TraesCS2B01G540700	chr2A	738005464	738007000	1536	True	1677.000000	1677	86.726000	806	2333	1	chr2A.!!$R2	1527
8	TraesCS2B01G540700	chr2A	737733814	737736263	2449	True	1458.500000	2268	88.232500	1	2333	2	chr2A.!!$R3	2332
9	TraesCS2B01G540700	chr2A	737836913	737838564	1651	True	790.000000	1129	89.007000	694	2333	2	chr2A.!!$R4	1639
10	TraesCS2B01G540700	chr2A	568289917	568290517	600	False	366.000000	379	92.287500	2333	2849	2	chr2A.!!$F2	516
11	TraesCS2B01G540700	chr2D	606154969	606156651	1682	True	1916.000000	1916	87.779000	694	2333	1	chr2D.!!$R1	1639
12	TraesCS2B01G540700	chr2D	606213321	606214859	1538	True	1585.000000	1585	85.696000	807	2333	1	chr2D.!!$R2	1526
13	TraesCS2B01G540700	chr2D	606161397	606164505	3108	True	945.000000	1201	89.034000	694	2333	2	chr2D.!!$R3	1639
14	TraesCS2B01G540700	chr2D	606187274	606189758	2484	True	913.000000	1862	88.355000	17	2332	3	chr2D.!!$R4	2315
15	TraesCS2B01G540700	chrUn	386124294	386125594	1300	True	1648.000000	1648	89.985000	1064	2333	1	chrUn.!!$R2	1269

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
508	534	0.245539	GGGTAGACGTAGCACAAGCA	59.754	55.0	0.0	0.0	45.49	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2088	5559	0.171903	GCTAGGCCGTCGAACTGTAA	59.828	55.0	0.0	0.0	0.0	2.41	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
34	35	1.279840	GAGTTGCGGCCGATATTGC	59.720	57.895	33.48	10.77	0.00	3.56
37	38	0.317020	GTTGCGGCCGATATTGCTTC	60.317	55.000	33.48	8.18	0.00	3.86
40	41	1.444119	GCGGCCGATATTGCTTCCAA	61.444	55.000	33.48	0.00	35.01	3.53
51	52	0.899717	TGCTTCCAACTCATTGCCCC	60.900	55.000	0.00	0.00	34.17	5.80
197	198	1.999735	CGTTGTTGTAGCATGGTCGAT	59.000	47.619	0.00	0.00	0.00	3.59
294	318	2.599597	GCAGATGGATGGGTGGCT	59.400	61.111	0.00	0.00	0.00	4.75
428	454	2.955660	GGGAGAAACCATTGTGTTGACA	59.044	45.455	0.00	0.00	41.20	3.58
436	462	2.290367	CCATTGTGTTGACAGAGCGAAA	59.710	45.455	0.00	0.00	32.26	3.46
492	518	2.122989	AGGTGACTCGTGGTGGGT	60.123	61.111	0.00	0.00	32.90	4.51
508	534	0.245539	GGGTAGACGTAGCACAAGCA	59.754	55.000	0.00	0.00	45.49	3.91
532	559	1.521457	GGGAGATTGTGCGCGATCA	60.521	57.895	25.70	4.64	37.85	2.92
572	599	3.361977	GCAACGTTCACCCGGCAT	61.362	61.111	0.00	0.00	0.00	4.40
587	614	1.466167	CGGCATGCCAGATATAAGTGC	59.534	52.381	34.93	4.60	35.37	4.40
729	2338	6.492254	ACGTTTGGTTTATCTCTCAAACAAC	58.508	36.000	15.06	0.00	45.19	3.32
778	2388	2.678471	ACGATACGGAACCGGATTTT	57.322	45.000	9.46	0.00	43.85	1.82
931	2779	2.171725	GCCGAGACAACCGCATACC	61.172	63.158	0.00	0.00	0.00	2.73
1016	2864	2.722706	CGCACATGACGAACACATTCAG	60.723	50.000	0.00	0.00	34.14	3.02
1305	3156	3.222855	CTGAGCCTCCGCCTCGAT	61.223	66.667	0.00	0.00	34.57	3.59
1476	3327	2.291043	GGAAGCCCCGAGACCAAGA	61.291	63.158	0.00	0.00	0.00	3.02
1536	3387	0.620121	AGAGAAGGGGAAGGGAGCAG	60.620	60.000	0.00	0.00	0.00	4.24
1964	5423	1.267806	GTGGTGTTGAGACTTGCATGG	59.732	52.381	4.44	0.00	0.00	3.66
1967	5430	2.821969	GGTGTTGAGACTTGCATGGAAT	59.178	45.455	0.00	0.00	0.00	3.01
1990	5453	7.849804	ATCTGCGTTGATATAATACAATCCC	57.150	36.000	0.00	0.00	0.00	3.85
2004	5467	2.105821	ACAATCCCTGTTTTGTCCGAGA	59.894	45.455	0.00	0.00	32.99	4.04
2011	5474	4.700213	CCCTGTTTTGTCCGAGATACAAAT	59.300	41.667	2.56	0.00	44.05	2.32
2059	5529	5.724328	TCTAGCGAAAGAGACAACATTCAT	58.276	37.500	0.00	0.00	0.00	2.57
2076	5546	8.581263	CAACATTCATCAAATCAGAAAATCGAC	58.419	33.333	0.00	0.00	0.00	4.20
2080	5551	7.127917	TCATCAAATCAGAAAATCGACGAAA	57.872	32.000	0.00	0.00	0.00	3.46
2081	5552	7.580600	TCATCAAATCAGAAAATCGACGAAAA	58.419	30.769	0.00	0.00	0.00	2.29
2082	5553	8.236586	TCATCAAATCAGAAAATCGACGAAAAT	58.763	29.630	0.00	0.00	0.00	1.82
2083	5554	9.489393	CATCAAATCAGAAAATCGACGAAAATA	57.511	29.630	0.00	0.00	0.00	1.40
2154	5639	4.774660	TCCCTACACCAAACAAACTACA	57.225	40.909	0.00	0.00	0.00	2.74
2161	5646	8.397906	CCTACACCAAACAAACTACATATCATG	58.602	37.037	0.00	0.00	0.00	3.07
2167	5652	8.404765	CCAAACAAACTACATATCATGCATGTA	58.595	33.333	25.43	16.88	37.74	2.29
2218	5871	6.131961	AGGGGAAGATTAAACCTCAATCATG	58.868	40.000	0.00	0.00	35.30	3.07
2260	5914	1.565305	CTCCCTCATTTCTTCGCTCG	58.435	55.000	0.00	0.00	0.00	5.03
2363	6021	0.403655	TGTGTGTGTGTGGCCCATAT	59.596	50.000	0.00	0.00	0.00	1.78
2372	6030	3.255032	GGCCCATATGCCCACTCT	58.745	61.111	0.00	0.00	46.11	3.24
2376	6034	2.257207	GCCCATATGCCCACTCTAGTA	58.743	52.381	0.00	0.00	0.00	1.82
2434	6092	5.189180	AGAGAGAATTCCAGAATTTTCCCG	58.811	41.667	16.04	0.00	40.65	5.14
2438	6096	6.025749	AGAATTCCAGAATTTTCCCGAAAC	57.974	37.500	7.05	0.00	40.77	2.78
2543	6201	1.677552	CTTTGGGGGCGTGAGTACT	59.322	57.895	0.00	0.00	0.00	2.73
2554	6276	1.228769	TGAGTACTGGCGGAGGTGT	60.229	57.895	0.00	0.00	0.00	4.16
2658	6380	1.337071	GTGAGGTGTGTCTCGTGAAGA	59.663	52.381	0.00	0.00	36.61	2.87
2661	6383	2.032620	AGGTGTGTCTCGTGAAGAAGT	58.967	47.619	0.00	0.00	35.21	3.01
2720	6446	2.414994	AGATTGGATCTGGCTGTGTG	57.585	50.000	0.00	0.00	38.44	3.82
2739	6482	1.306997	TAGGGCAGGGGAAGAGGTG	60.307	63.158	0.00	0.00	0.00	4.00
2776	6519	2.922740	ACACACACGTACAGGGATTT	57.077	45.000	0.00	0.00	0.00	2.17
2787	6530	0.449388	CAGGGATTTGAAGCTCGTGC	59.551	55.000	0.07	0.07	40.05	5.34
2804	6547	1.171549	TGCGGTGCTGCATCTGAAAA	61.172	50.000	11.64	0.00	40.62	2.29
2805	6548	0.039256	GCGGTGCTGCATCTGAAAAA	60.039	50.000	11.64	0.00	34.15	1.94
2806	6549	1.689959	CGGTGCTGCATCTGAAAAAC	58.310	50.000	11.64	0.00	0.00	2.43
2811	6554	4.156556	GGTGCTGCATCTGAAAAACTCATA	59.843	41.667	5.27	0.00	32.14	2.15
2844	6588	1.995542	AGAAGATTTGGGCAAGGGAGA	59.004	47.619	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.501223	ATCGGCCGCAACTCGAAGAA	62.501	55.000	23.51	0.00	41.67	2.52
12	13	0.597637	ATATCGGCCGCAACTCGAAG	60.598	55.000	23.51	0.00	41.67	3.79
34	35	0.609131	ACGGGGCAATGAGTTGGAAG	60.609	55.000	0.00	0.00	35.83	3.46
37	38	1.586028	CAACGGGGCAATGAGTTGG	59.414	57.895	0.00	0.00	39.95	3.77
40	41	1.228552	AAGCAACGGGGCAATGAGT	60.229	52.632	3.39	0.00	35.83	3.41
146	147	3.423154	GTAGCTGGTGGTGTGCGC	61.423	66.667	0.00	0.00	0.00	6.09
158	159	2.716017	GCGAGCAGGAGTGGTAGCT	61.716	63.158	0.00	0.00	45.97	3.32
197	198	4.966787	GGGGTGCTTCAACCGGCA	62.967	66.667	0.00	0.00	43.24	5.69
229	253	1.334160	TCCTGCAACTCGAAGGTGTA	58.666	50.000	0.18	0.00	34.77	2.90
383	407	4.729918	CAGAGCACACCCCCTGCC	62.730	72.222	0.00	0.00	35.01	4.85
428	454	2.696187	GTCTCCCTTATCCTTTCGCTCT	59.304	50.000	0.00	0.00	0.00	4.09
436	462	1.739338	CGCAGCGTCTCCCTTATCCT	61.739	60.000	6.65	0.00	0.00	3.24
482	508	1.308069	GCTACGTCTACCCACCACGA	61.308	60.000	0.00	0.00	37.00	4.35
492	518	1.135373	GCTCTGCTTGTGCTACGTCTA	60.135	52.381	0.00	0.00	40.48	2.59
508	534	2.586792	GCACAATCTCCCGGCTCT	59.413	61.111	0.00	0.00	0.00	4.09
532	559	1.081376	GACGACGCGCATAGCCTAT	60.081	57.895	5.73	0.00	44.76	2.57
572	599	4.778213	AAGGAAGCACTTATATCTGGCA	57.222	40.909	0.00	0.00	0.00	4.92
707	2289	8.696410	TTTGTTGTTTGAGAGATAAACCAAAC	57.304	30.769	0.00	0.00	44.93	2.93
744	2354	4.088648	CGTATCGTTTTCCAAATGCAGTC	58.911	43.478	0.00	0.00	0.00	3.51
778	2388	1.002403	TAGGTCCGAATCCAGCCCA	59.998	57.895	0.00	0.00	0.00	5.36
871	2695	3.745803	GAGGAGACCGCCGACGTT	61.746	66.667	0.00	0.00	37.70	3.99
931	2779	1.008875	CGGCGGGATCGATGTGTATG	61.009	60.000	0.54	0.00	39.00	2.39
1133	2984	1.445238	GCAGAGAGTCTCACCGCAC	60.445	63.158	22.05	1.19	32.06	5.34
1140	2991	2.101380	GCGTCCGCAGAGAGTCTC	59.899	66.667	12.54	12.54	41.49	3.36
1476	3327	1.296715	CTTGGGTAGCTTCGGCAGT	59.703	57.895	0.00	0.00	44.74	4.40
1936	5395	2.167693	AGTCTCAACACCACGACTTCAA	59.832	45.455	0.00	0.00	33.21	2.69
1937	5396	1.754803	AGTCTCAACACCACGACTTCA	59.245	47.619	0.00	0.00	33.21	3.02
1938	5397	2.510768	AGTCTCAACACCACGACTTC	57.489	50.000	0.00	0.00	33.21	3.01
1939	5398	2.550978	CAAGTCTCAACACCACGACTT	58.449	47.619	0.00	0.00	44.86	3.01
1964	5423	8.391106	GGGATTGTATTATATCAACGCAGATTC	58.609	37.037	0.00	0.00	0.00	2.52
1967	5430	6.873605	CAGGGATTGTATTATATCAACGCAGA	59.126	38.462	0.00	0.00	0.00	4.26
1990	5453	8.169268	GTCTTATTTGTATCTCGGACAAAACAG	58.831	37.037	5.16	4.90	46.70	3.16
2039	5502	4.318332	TGATGAATGTTGTCTCTTTCGCT	58.682	39.130	0.00	0.00	0.00	4.93
2051	5521	7.482743	CGTCGATTTTCTGATTTGATGAATGTT	59.517	33.333	0.00	0.00	0.00	2.71
2076	5546	7.616716	GCCGTCGAACTGTAAGATATATTTTCG	60.617	40.741	7.86	7.86	37.43	3.46
2080	5551	5.243283	AGGCCGTCGAACTGTAAGATATATT	59.757	40.000	0.00	0.00	37.43	1.28
2081	5552	4.765856	AGGCCGTCGAACTGTAAGATATAT	59.234	41.667	0.00	0.00	37.43	0.86
2082	5553	4.139786	AGGCCGTCGAACTGTAAGATATA	58.860	43.478	0.00	0.00	37.43	0.86
2083	5554	2.957006	AGGCCGTCGAACTGTAAGATAT	59.043	45.455	0.00	0.00	37.43	1.63
2084	5555	2.372264	AGGCCGTCGAACTGTAAGATA	58.628	47.619	0.00	0.00	37.43	1.98
2085	5556	1.183549	AGGCCGTCGAACTGTAAGAT	58.816	50.000	0.00	0.00	37.43	2.40
2087	5558	1.798079	GCTAGGCCGTCGAACTGTAAG	60.798	57.143	0.00	0.00	42.29	2.34
2088	5559	0.171903	GCTAGGCCGTCGAACTGTAA	59.828	55.000	0.00	0.00	0.00	2.41
2167	5652	1.849039	AGGAAGCTGGTCCTTATGCAT	59.151	47.619	3.79	3.79	46.42	3.96
2218	5871	1.001020	TCATGGTGGTGGACATGCC	60.001	57.895	0.00	0.00	43.11	4.40
2248	5902	1.618861	CACGAGACGAGCGAAGAAAT	58.381	50.000	0.00	0.00	0.00	2.17
2260	5914	0.667792	GTCACTTCTGGGCACGAGAC	60.668	60.000	0.00	0.00	44.43	3.36
2434	6092	4.455533	TGCTCTGACACCATGTTATGTTTC	59.544	41.667	0.00	0.00	0.00	2.78
2438	6096	4.193865	TGATGCTCTGACACCATGTTATG	58.806	43.478	0.00	0.00	0.00	1.90
2515	6173	3.407967	CCCCAAAGGCCGGAGCTA	61.408	66.667	5.05	0.00	39.73	3.32
2527	6185	2.589157	CCAGTACTCACGCCCCCAA	61.589	63.158	0.00	0.00	0.00	4.12
2543	6201	2.904866	GCAACAACACCTCCGCCA	60.905	61.111	0.00	0.00	0.00	5.69
2624	6346	0.979665	CCTCACCAGCTTCTTCTCCA	59.020	55.000	0.00	0.00	0.00	3.86
2629	6351	0.839946	ACACACCTCACCAGCTTCTT	59.160	50.000	0.00	0.00	0.00	2.52
2658	6380	1.666209	GCACACCACACCTGCAACTT	61.666	55.000	0.00	0.00	0.00	2.66
2661	6383	2.044551	TGCACACCACACCTGCAA	60.045	55.556	0.00	0.00	37.97	4.08
2701	6426	1.632409	ACACACAGCCAGATCCAATCT	59.368	47.619	0.00	0.00	41.15	2.40
2720	6446	1.307084	ACCTCTTCCCCTGCCCTAC	60.307	63.158	0.00	0.00	0.00	3.18
2739	6482	2.160417	GTGTACACTGCTGCCAAATCTC	59.840	50.000	18.92	0.00	0.00	2.75
2767	6510	1.813513	CACGAGCTTCAAATCCCTGT	58.186	50.000	0.00	0.00	0.00	4.00
2776	6519	4.299547	AGCACCGCACGAGCTTCA	62.300	61.111	2.73	0.00	39.10	3.02
2787	6530	1.267806	AGTTTTTCAGATGCAGCACCG	59.732	47.619	4.07	0.00	0.00	4.94
2804	6547	4.160329	TCTCCTCACCAAGTGTATGAGTT	58.840	43.478	8.30	0.00	38.56	3.01
2805	6548	3.779444	TCTCCTCACCAAGTGTATGAGT	58.221	45.455	8.30	0.00	38.56	3.41
2806	6549	4.464244	TCTTCTCCTCACCAAGTGTATGAG	59.536	45.833	0.00	0.00	39.70	2.90
2811	6554	4.392940	CAAATCTTCTCCTCACCAAGTGT	58.607	43.478	0.00	0.00	34.79	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.