AutoCloner

Multiple sequence alignment - TraesCS7D01G303400

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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	TraesCS7D01G303400	chr7D	100.000	2552	0	0	1	2552	383975640	383973089	0.000000e+00	4713.0
1	TraesCS7D01G303400	chr7D	86.641	262	33	2	2177	2436	199355919	199355658	3.210000e-74	289.0
2	TraesCS7D01G303400	chr7D	94.340	159	9	0	626	784	383974926	383974768	7.050000e-61	244.0
3	TraesCS7D01G303400	chr7D	94.340	159	9	0	715	873	383975015	383974857	7.050000e-61	244.0
4	TraesCS7D01G303400	chr7D	97.143	70	2	0	626	695	383974837	383974768	4.460000e-23	119.0
5	TraesCS7D01G303400	chr7D	97.143	70	2	0	804	873	383975015	383974946	4.460000e-23	119.0
6	TraesCS7D01G303400	chr7A	95.579	2511	105	5	3	2508	432695719	432693210	0.000000e+00	4017.0
7	TraesCS7D01G303400	chr7A	82.635	334	46	7	2177	2508	209155820	209155497	4.160000e-73	285.0
8	TraesCS7D01G303400	chr7A	95.597	159	7	0	626	784	432695005	432694847	3.260000e-64	255.0
9	TraesCS7D01G303400	chr7A	95.597	159	7	0	715	873	432695094	432694936	3.260000e-64	255.0
10	TraesCS7D01G303400	chr7A	97.143	70	2	0	626	695	432694916	432694847	4.460000e-23	119.0
11	TraesCS7D01G303400	chr7A	97.143	70	2	0	804	873	432695094	432695025	4.460000e-23	119.0
12	TraesCS7D01G303400	chr7B	92.522	2474	126	18	1	2463	378391542	378389117	0.000000e+00	3489.0
13	TraesCS7D01G303400	chr7B	83.019	318	40	10	2178	2491	163488642	163488335	2.500000e-70	276.0
14	TraesCS7D01G303400	chr7B	94.340	159	9	0	715	873	378390928	378390770	7.050000e-61	244.0
15	TraesCS7D01G303400	chr7B	93.082	159	11	0	626	784	378390839	378390681	1.530000e-57	233.0
16	TraesCS7D01G303400	chr7B	94.805	77	4	0	804	880	378390928	378390852	1.240000e-23	121.0
17	TraesCS7D01G303400	chr7B	95.714	70	3	0	626	695	378390750	378390681	2.080000e-21	113.0
18	TraesCS7D01G303400	chr7B	75.824	182	27	12	223	397	316405034	316404863	2.720000e-10	76.8
19	TraesCS7D01G303400	chr5D	82.036	334	52	7	2180	2508	460939880	460939550	6.950000e-71	278.0
20	TraesCS7D01G303400	chr5D	81.250	144	18	5	182	319	219223102	219223242	9.650000e-20	108.0
21	TraesCS7D01G303400	chr5A	77.197	421	77	15	1	412	567109482	567109892	7.100000e-56	228.0
22	TraesCS7D01G303400	chr5A	81.181	271	41	7	147	413	292735583	292735847	2.570000e-50	209.0
23	TraesCS7D01G303400	chr1D	84.100	239	28	7	2178	2416	331188798	331189026	3.300000e-54	222.0
24	TraesCS7D01G303400	chr1B	80.192	313	47	10	2183	2491	112191826	112192127	1.190000e-53	220.0
25	TraesCS7D01G303400	chr2D	81.273	267	46	4	2183	2447	73591148	73590884	1.990000e-51	213.0
26	TraesCS7D01G303400	chr5B	79.323	266	44	8	150	411	238563902	238563644	2.610000e-40	176.0
27	TraesCS7D01G303400	chr5B	77.061	279	43	11	147	411	241857871	241858142	9.520000e-30	141.0
28	TraesCS7D01G303400	chr5B	96.875	32	1	0	1629	1660	35821510	35821479	1.000000e-03	54.7
29	TraesCS7D01G303400	chr4D	75.954	262	47	13	1917	2172	16240310	16240059	1.240000e-23	121.0
30	TraesCS7D01G303400	chr6D	88.889	81	3	6	335	413	112822493	112822569	7.520000e-16	95.3
31	TraesCS7D01G303400	chr2B	88.462	78	6	2	342	419	373270097	373270171	9.720000e-15	91.6
32	TraesCS7D01G303400	chr2B	85.366	82	10	2	336	415	647590234	647590153	1.630000e-12	84.2
33	TraesCS7D01G303400	chr2B	100.000	30	0	0	2044	2073	10983843	10983814	3.550000e-04	56.5

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	TraesCS7D01G303400	chr7D	383973089	383975640	2551	True	1087.8	4713	96.5932	1	2552	5	chr7D.!!$R2	2551
1	TraesCS7D01G303400	chr7A	432693210	432695719	2509	True	953.0	4017	96.2118	3	2508	5	chr7A.!!$R2	2505
2	TraesCS7D01G303400	chr7B	378389117	378391542	2425	True	840.0	3489	94.0926	1	2463	5	chr7B.!!$R3	2462

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
178	181	0.259065	TCGGCTCCTCCTCACATACT	59.741	55.0	0.0	0.0	0.0	2.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1909	1915	0.605589	GCCAAGAGGTACAAAGGCGT	60.606	55.0	0.0	0.0	37.19	5.68	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
30	32	3.089284	GGGACAACAACATTCCCTTAGG	58.911	50.000	0.00	0.00	45.14	2.69
75	77	4.365514	TGGATTCCAGTTTGCACTTCTA	57.634	40.909	0.00	0.00	0.00	2.10
178	181	0.259065	TCGGCTCCTCCTCACATACT	59.741	55.000	0.00	0.00	0.00	2.12
246	249	0.540923	AGCAAAGCAAACCAAAGCCA	59.459	45.000	0.00	0.00	0.00	4.75
696	700	9.117183	CCAATTGTCCATATATATGTCATCAGG	57.883	37.037	19.11	14.23	31.82	3.86
793	797	5.012458	ACATATATGTCATCAGTGGAGTGGG	59.988	44.000	12.75	0.00	35.87	4.61
971	975	1.139308	CAGCTCAGAGCCTCAGACG	59.861	63.158	19.40	0.00	43.77	4.18
1658	1662	1.243902	TCAATGCGGACCCTCAAAAC	58.756	50.000	0.00	0.00	0.00	2.43
1668	1672	0.604511	CCCTCAAAACGCCCGTAACT	60.605	55.000	0.00	0.00	0.00	2.24
1672	1676	2.015587	TCAAAACGCCCGTAACTGTTT	58.984	42.857	0.00	0.00	36.17	2.83
1674	1678	1.666054	AAACGCCCGTAACTGTTTGA	58.334	45.000	0.00	0.00	33.59	2.69
1677	1681	1.223187	CGCCCGTAACTGTTTGAAGT	58.777	50.000	0.00	0.00	0.00	3.01
1689	1693	0.756294	TTTGAAGTGAGCAGTCGGGA	59.244	50.000	0.00	0.00	0.00	5.14
1720	1724	4.101430	TGTCATCCAATGCAGTAGCTCATA	59.899	41.667	0.00	0.00	42.74	2.15
1721	1725	5.059161	GTCATCCAATGCAGTAGCTCATAA	58.941	41.667	0.00	0.00	42.74	1.90
1727	1731	4.970860	ATGCAGTAGCTCATAAGTCCAT	57.029	40.909	0.00	0.00	42.74	3.41
1768	1772	1.173043	TTACCGCAAATTGGAGGCAG	58.827	50.000	1.90	0.00	0.00	4.85
1771	1775	1.135315	CGCAAATTGGAGGCAGACG	59.865	57.895	0.00	0.00	0.00	4.18
1826	1830	0.323629	GTTGGAATCCGACACCTCCA	59.676	55.000	14.64	0.00	37.82	3.86
1861	1865	2.583143	CCTTCCGGTCCACTTTTCTTT	58.417	47.619	0.00	0.00	0.00	2.52
1879	1885	0.905809	TTCACTACCTTGCCCGCCTA	60.906	55.000	0.00	0.00	0.00	3.93
1884	1890	0.694196	TACCTTGCCCGCCTACTTTT	59.306	50.000	0.00	0.00	0.00	2.27
1890	1896	0.738975	GCCCGCCTACTTTTCATTCC	59.261	55.000	0.00	0.00	0.00	3.01
1909	1915	1.185618	CCACCCTCCTTGTCTGACGA	61.186	60.000	2.98	0.00	0.00	4.20
1925	1931	0.677842	ACGACGCCTTTGTACCTCTT	59.322	50.000	0.00	0.00	0.00	2.85
1931	1937	1.545651	GCCTTTGTACCTCTTGGCTGT	60.546	52.381	0.00	0.00	37.58	4.40
1941	1947	4.680237	TTGGCTGTCTCCCACGCG	62.680	66.667	3.53	3.53	30.65	6.01
1991	1997	3.927555	CCTGTCGGCCTTTGACTAA	57.072	52.632	0.00	0.00	37.26	2.24
2044	2050	1.605992	CATCCTCAGCCTTCCTGCA	59.394	57.895	0.00	0.00	41.50	4.41
2046	2052	1.633915	ATCCTCAGCCTTCCTGCAGG	61.634	60.000	27.87	27.87	41.50	4.85
2047	2053	2.600729	CCTCAGCCTTCCTGCAGGT	61.601	63.158	31.58	10.06	41.50	4.00
2257	2264	2.123897	GGGCAACAGTGTGTGGGT	60.124	61.111	0.00	0.00	39.74	4.51
2286	2296	7.697291	ACTTGTTTCGATTCTAACTCGAGTATC	59.303	37.037	20.39	16.36	45.00	2.24
2467	2479	5.372343	AAGAAGGAAAAACAAGGGCAAAT	57.628	34.783	0.00	0.00	0.00	2.32
2491	2503	1.678970	GGTGACAGGGTTGGATGGC	60.679	63.158	0.00	0.00	0.00	4.40
2508	2520	1.673808	GGCCGACTCCAGTATCCGTT	61.674	60.000	0.00	0.00	0.00	4.44
2509	2521	1.027357	GCCGACTCCAGTATCCGTTA	58.973	55.000	0.00	0.00	0.00	3.18
2510	2522	1.001597	GCCGACTCCAGTATCCGTTAG	60.002	57.143	0.00	0.00	0.00	2.34
2511	2523	2.295885	CCGACTCCAGTATCCGTTAGT	58.704	52.381	0.00	0.00	0.00	2.24
2512	2524	2.033049	CCGACTCCAGTATCCGTTAGTG	59.967	54.545	0.00	0.00	0.00	2.74
2513	2525	2.681848	CGACTCCAGTATCCGTTAGTGT	59.318	50.000	0.00	0.00	30.40	3.55
2514	2526	3.487042	CGACTCCAGTATCCGTTAGTGTG	60.487	52.174	0.00	0.00	30.40	3.82
2515	2527	3.428532	ACTCCAGTATCCGTTAGTGTGT	58.571	45.455	0.00	0.00	30.40	3.72
2516	2528	3.830755	ACTCCAGTATCCGTTAGTGTGTT	59.169	43.478	0.00	0.00	30.40	3.32
2517	2529	4.282703	ACTCCAGTATCCGTTAGTGTGTTT	59.717	41.667	0.00	0.00	30.40	2.83
2518	2530	4.562082	TCCAGTATCCGTTAGTGTGTTTG	58.438	43.478	0.00	0.00	30.40	2.93
2519	2531	4.039488	TCCAGTATCCGTTAGTGTGTTTGT	59.961	41.667	0.00	0.00	30.40	2.83
2520	2532	4.753107	CCAGTATCCGTTAGTGTGTTTGTT	59.247	41.667	0.00	0.00	30.40	2.83
2521	2533	5.237779	CCAGTATCCGTTAGTGTGTTTGTTT	59.762	40.000	0.00	0.00	30.40	2.83
2522	2534	6.238538	CCAGTATCCGTTAGTGTGTTTGTTTT	60.239	38.462	0.00	0.00	30.40	2.43
2523	2535	6.631238	CAGTATCCGTTAGTGTGTTTGTTTTG	59.369	38.462	0.00	0.00	0.00	2.44
2524	2536	5.821516	ATCCGTTAGTGTGTTTGTTTTGA	57.178	34.783	0.00	0.00	0.00	2.69
2525	2537	5.821516	TCCGTTAGTGTGTTTGTTTTGAT	57.178	34.783	0.00	0.00	0.00	2.57
2526	2538	5.574082	TCCGTTAGTGTGTTTGTTTTGATG	58.426	37.500	0.00	0.00	0.00	3.07
2527	2539	5.354513	TCCGTTAGTGTGTTTGTTTTGATGA	59.645	36.000	0.00	0.00	0.00	2.92
2528	2540	6.038825	TCCGTTAGTGTGTTTGTTTTGATGAT	59.961	34.615	0.00	0.00	0.00	2.45
2529	2541	7.226918	TCCGTTAGTGTGTTTGTTTTGATGATA	59.773	33.333	0.00	0.00	0.00	2.15
2530	2542	8.020819	CCGTTAGTGTGTTTGTTTTGATGATAT	58.979	33.333	0.00	0.00	0.00	1.63
2537	2549	9.636879	TGTGTTTGTTTTGATGATATATGTTGG	57.363	29.630	0.00	0.00	0.00	3.77
2538	2550	9.853555	GTGTTTGTTTTGATGATATATGTTGGA	57.146	29.630	0.00	0.00	0.00	3.53
2543	2555	9.631257	TGTTTTGATGATATATGTTGGAGATGT	57.369	29.630	0.00	0.00	0.00	3.06
2547	2559	9.716531	TTGATGATATATGTTGGAGATGTCTTC	57.283	33.333	0.00	0.00	0.00	2.87
2548	2560	8.873144	TGATGATATATGTTGGAGATGTCTTCA	58.127	33.333	0.00	0.00	30.23	3.02
2549	2561	9.887629	GATGATATATGTTGGAGATGTCTTCAT	57.112	33.333	0.00	0.00	36.95	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	58	4.757149	AGTGTAGAAGTGCAAACTGGAATC	59.243	41.667	0.00	0.00	0.00	2.52
75	77	3.156293	TGCAATATCTTGTGGCAAGTGT	58.844	40.909	8.48	2.85	34.69	3.55
146	149	3.108376	AGGAGCCGACCTAAAGATCTTT	58.892	45.455	23.53	23.53	38.65	2.52
155	158	1.076923	GTGAGGAGGAGCCGACCTA	60.077	63.158	7.95	0.00	43.43	3.08
178	181	4.704540	CCTGTAAGTAATGCATCCAACCAA	59.295	41.667	0.00	0.00	0.00	3.67
246	249	5.750352	TCTACCCAAGTACGAATCCTTTT	57.250	39.130	0.00	0.00	0.00	2.27
362	365	9.620660	AACAATTGTTCTACGGTATTTTCATTC	57.379	29.630	18.13	0.00	31.64	2.67
480	484	9.716507	GATTTTATGCAAAACATCGTACTACAT	57.283	29.630	0.00	0.00	40.38	2.29
696	700	0.035439	TCTCGCCATTTTCCACTCCC	60.035	55.000	0.00	0.00	0.00	4.30
767	771	6.239402	CCACTCCACTGATGACATATATGTGA	60.239	42.308	22.93	15.35	41.95	3.58
793	797	6.422100	TGTGCTCATTAATCTCTCGCTATTTC	59.578	38.462	0.00	0.00	0.00	2.17
971	975	3.505680	TGTGTTATGGGAGATGTGTTTGC	59.494	43.478	0.00	0.00	0.00	3.68
1631	1635	0.749454	GGTCCGCATTGAAGATGCCT	60.749	55.000	5.51	0.00	41.71	4.75
1658	1662	1.070175	CACTTCAAACAGTTACGGGCG	60.070	52.381	0.00	0.00	0.00	6.13
1668	1672	1.581934	CCGACTGCTCACTTCAAACA	58.418	50.000	0.00	0.00	0.00	2.83
1672	1676	1.112916	TGTCCCGACTGCTCACTTCA	61.113	55.000	0.00	0.00	0.00	3.02
1674	1678	1.557099	TATGTCCCGACTGCTCACTT	58.443	50.000	0.00	0.00	0.00	3.16
1677	1681	3.270027	CAAATTATGTCCCGACTGCTCA	58.730	45.455	0.00	0.00	0.00	4.26
1689	1693	7.682741	GCTACTGCATTGGATGACAAATTATGT	60.683	37.037	0.00	0.00	43.46	2.29
1745	1749	2.165437	GCCTCCAATTTGCGGTAATTCA	59.835	45.455	0.00	0.00	0.00	2.57
1786	1790	4.459089	GCAGCGGTCCAGACTCCC	62.459	72.222	0.00	0.00	0.00	4.30
1826	1830	2.558380	GAAGGGGATTTGAGCGGGCT	62.558	60.000	0.00	0.00	0.00	5.19
1861	1865	1.305465	TAGGCGGGCAAGGTAGTGA	60.305	57.895	3.78	0.00	0.00	3.41
1879	1885	2.073776	AGGAGGGTGGGAATGAAAAGT	58.926	47.619	0.00	0.00	0.00	2.66
1884	1890	0.991920	GACAAGGAGGGTGGGAATGA	59.008	55.000	0.00	0.00	0.00	2.57
1890	1896	1.185618	TCGTCAGACAAGGAGGGTGG	61.186	60.000	0.41	0.00	0.00	4.61
1909	1915	0.605589	GCCAAGAGGTACAAAGGCGT	60.606	55.000	0.00	0.00	37.19	5.68
1941	1947	2.888863	CTGCAGAGGTCCGAGGAC	59.111	66.667	8.42	13.61	43.87	3.85
1979	1985	2.450609	TGACGTCTTAGTCAAAGGCC	57.549	50.000	17.92	0.00	46.81	5.19
1991	1997	1.078528	TCCTGGGTGGATGACGTCT	59.921	57.895	17.92	1.84	40.56	4.18
2257	2264	4.921515	CGAGTTAGAATCGAAACAAGTCCA	59.078	41.667	0.00	0.00	42.76	4.02
2286	2296	6.257423	TGATTCATCCATTCGAAATTCAACG	58.743	36.000	0.00	0.00	0.00	4.10
2287	2297	8.464770	TTTGATTCATCCATTCGAAATTCAAC	57.535	30.769	0.00	0.00	0.00	3.18
2288	2298	9.486497	TTTTTGATTCATCCATTCGAAATTCAA	57.514	25.926	0.00	0.47	0.00	2.69
2424	2436	6.025280	TCTTTTAAGTCGCAACACTCAAAAC	58.975	36.000	0.00	0.00	0.00	2.43
2467	2479	2.128535	TCCAACCCTGTCACCTAAACA	58.871	47.619	0.00	0.00	0.00	2.83
2491	2503	2.033049	CACTAACGGATACTGGAGTCGG	59.967	54.545	0.00	0.00	0.00	4.79
2511	2523	9.636879	CCAACATATATCATCAAAACAAACACA	57.363	29.630	0.00	0.00	0.00	3.72
2512	2524	9.853555	TCCAACATATATCATCAAAACAAACAC	57.146	29.630	0.00	0.00	0.00	3.32
2517	2529	9.631257	ACATCTCCAACATATATCATCAAAACA	57.369	29.630	0.00	0.00	0.00	2.83
2521	2533	9.716531	GAAGACATCTCCAACATATATCATCAA	57.283	33.333	0.00	0.00	0.00	2.57
2522	2534	8.873144	TGAAGACATCTCCAACATATATCATCA	58.127	33.333	0.00	0.00	0.00	3.07
2523	2535	9.887629	ATGAAGACATCTCCAACATATATCATC	57.112	33.333	0.00	0.00	29.98	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.