AutoCloner

Multiple sequence alignment - TraesCS7A01G550800

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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	TraesCS7A01G550800	chr7A	100.000	2819	0	0	1	2819	724459540	724456722	0.000000e+00	5206
1	TraesCS7A01G550800	chr7A	84.111	1372	141	30	414	1711	726047929	726049297	0.000000e+00	1254
2	TraesCS7A01G550800	chr7A	88.168	879	96	4	838	1711	726130471	726131346	0.000000e+00	1040
3	TraesCS7A01G550800	chr7A	88.168	879	96	4	838	1711	726261337	726262212	0.000000e+00	1040
4	TraesCS7A01G550800	chr7A	87.628	881	98	6	838	1711	726331737	726332613	0.000000e+00	1013
5	TraesCS7A01G550800	chr7A	86.879	282	36	1	1696	1977	724505500	724505220	5.860000e-82	315
6	TraesCS7A01G550800	chr7A	83.333	210	20	5	147	346	726260683	726260887	2.230000e-41	180
7	TraesCS7A01G550800	chr7A	82.857	210	21	5	147	346	726331079	726331283	1.040000e-39	174
8	TraesCS7A01G550800	chr7A	94.737	76	4	0	1696	1771	726049313	726049388	4.930000e-23	119
9	TraesCS7A01G550800	chr7D	95.392	1736	53	11	1	1711	628647519	628649252	0.000000e+00	2737
10	TraesCS7A01G550800	chr7D	93.028	961	63	3	377	1335	628622350	628623308	0.000000e+00	1400
11	TraesCS7A01G550800	chr7D	93.820	712	43	1	2108	2819	628649650	628650360	0.000000e+00	1070
12	TraesCS7A01G550800	chr7D	86.458	864	112	3	838	1697	628641287	628642149	0.000000e+00	942
13	TraesCS7A01G550800	chr7D	97.423	388	10	0	1697	2084	628649269	628649656	0.000000e+00	662
14	TraesCS7A01G550800	chr7B	84.660	1369	137	31	415	1711	732743039	732744406	0.000000e+00	1297
15	TraesCS7A01G550800	chr7B	92.105	76	6	0	1696	1771	732744422	732744497	1.070000e-19	108
16	TraesCS7A01G550800	chrUn	88.168	879	96	4	838	1711	335106377	335107252	0.000000e+00	1040
17	TraesCS7A01G550800	chrUn	83.333	210	20	5	147	346	335105723	335105927	2.230000e-41	180
18	TraesCS7A01G550800	chr1D	76.066	305	59	10	1281	1580	23001456	23001161	2.260000e-31	147
19	TraesCS7A01G550800	chr1D	80.110	181	34	2	1518	1697	22894261	22894082	1.760000e-27	134

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	TraesCS7A01G550800	chr7A	724456722	724459540	2818	True	5206.000000	5206	100.0000	1	2819	1	chr7A.!!$R1	2818
1	TraesCS7A01G550800	chr7A	726130471	726131346	875	False	1040.000000	1040	88.1680	838	1711	1	chr7A.!!$F1	873
2	TraesCS7A01G550800	chr7A	726047929	726049388	1459	False	686.500000	1254	89.4240	414	1771	2	chr7A.!!$F2	1357
3	TraesCS7A01G550800	chr7A	726260683	726262212	1529	False	610.000000	1040	85.7505	147	1711	2	chr7A.!!$F3	1564
4	TraesCS7A01G550800	chr7A	726331079	726332613	1534	False	593.500000	1013	85.2425	147	1711	2	chr7A.!!$F4	1564
5	TraesCS7A01G550800	chr7D	628647519	628650360	2841	False	1489.666667	2737	95.5450	1	2819	3	chr7D.!!$F3	2818
6	TraesCS7A01G550800	chr7D	628622350	628623308	958	False	1400.000000	1400	93.0280	377	1335	1	chr7D.!!$F1	958
7	TraesCS7A01G550800	chr7D	628641287	628642149	862	False	942.000000	942	86.4580	838	1697	1	chr7D.!!$F2	859
8	TraesCS7A01G550800	chr7B	732743039	732744497	1458	False	702.500000	1297	88.3825	415	1771	2	chr7B.!!$F1	1356
9	TraesCS7A01G550800	chrUn	335105723	335107252	1529	False	610.000000	1040	85.7505	147	1711	2	chrUn.!!$F1	1564

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
680	739	1.754803	CCAGGCCGAGTAGTGTATTGA	59.245	52.381	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2125	2273	0.169009	GAGCCAGATCGTTGCCAAAC	59.831	55.0	1.29	0.0	0.0	2.93	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
23	24	3.503748	CGAGAAGGCAAGTTTTCAATCCT	59.496	43.478	0.00	0.00	0.00	3.24
27	28	7.360113	AGAAGGCAAGTTTTCAATCCTTTAA	57.640	32.000	0.00	0.00	34.40	1.52
31	32	7.334858	AGGCAAGTTTTCAATCCTTTAAAACA	58.665	30.769	11.23	0.00	42.69	2.83
39	40	5.583495	TCAATCCTTTAAAACACAACCACG	58.417	37.500	0.00	0.00	0.00	4.94
67	68	2.039084	AGCAGGAACAAACTACCCAGAG	59.961	50.000	0.00	0.00	0.00	3.35
83	84	3.320541	CCCAGAGCGAGAAATACTGATCT	59.679	47.826	0.00	0.00	0.00	2.75
84	85	4.545610	CCAGAGCGAGAAATACTGATCTC	58.454	47.826	0.00	0.00	38.94	2.75
248	249	5.639506	CCGTTATTCAATCCATAGCTGGTAG	59.360	44.000	0.00	0.00	43.61	3.18
627	666	2.689471	TGTGATGCAACTCTTGTTTGCT	59.311	40.909	8.41	0.00	33.52	3.91
661	719	4.142038	AGTTTGGTCCATAACTTGTGTCC	58.858	43.478	11.48	0.00	30.72	4.02
680	739	1.754803	CCAGGCCGAGTAGTGTATTGA	59.245	52.381	0.00	0.00	0.00	2.57
740	817	8.612619	GGACTGGTACATACATTTCTGTTATTG	58.387	37.037	0.00	0.00	38.20	1.90
742	819	8.946085	ACTGGTACATACATTTCTGTTATTGTG	58.054	33.333	0.00	0.00	38.20	3.33
1321	1437	7.619050	TGCAGATCTTCTAGAGTCAAAAGAAT	58.381	34.615	0.00	0.00	31.98	2.40
1330	1446	1.202879	AGTCAAAAGAATGGGCGGACA	60.203	47.619	0.00	0.00	0.00	4.02
1354	1470	1.151668	CTTCTGCGTCCAAGGTGAAG	58.848	55.000	0.00	0.00	0.00	3.02
1441	1557	1.672881	CAATGATGGAGAAAGACGGGC	59.327	52.381	0.00	0.00	0.00	6.13
1446	1562	1.153147	GGAGAAAGACGGGCCATCC	60.153	63.158	4.39	0.00	0.00	3.51
1527	1645	1.683385	GACTGCTTGGTGCTTCCTTTT	59.317	47.619	0.80	0.00	43.37	2.27
1594	1712	1.439228	GAGGCTGCTGATCGCTACA	59.561	57.895	0.00	0.00	40.11	2.74
1874	2022	5.649395	ACTGATACATCACACCTTTCCATTG	59.351	40.000	0.00	0.00	32.50	2.82
1931	2079	7.300320	TGTTCATCATTTCTGTCGAATTTGAG	58.700	34.615	0.00	0.00	30.22	3.02
1940	2088	8.744008	TTTCTGTCGAATTTGAGTTACTCTAG	57.256	34.615	13.86	0.00	0.00	2.43
2022	2170	6.822667	ATAAACTGCAAGAATGACATGTGA	57.177	33.333	1.15	0.00	37.43	3.58
2036	2184	6.474819	TGACATGTGATTAAACTAACACGG	57.525	37.500	1.15	0.00	36.25	4.94
2065	2213	5.243730	CCTATCTTCCCTTTTTCTGCAAACA	59.756	40.000	0.00	0.00	0.00	2.83
2077	2225	8.668510	TTTTTCTGCAAACAAATATTTAGGCA	57.331	26.923	0.00	7.54	0.00	4.75
2078	2226	7.650834	TTTCTGCAAACAAATATTTAGGCAC	57.349	32.000	0.00	0.00	0.00	5.01
2079	2227	6.338214	TCTGCAAACAAATATTTAGGCACA	57.662	33.333	0.00	0.00	0.00	4.57
2080	2228	6.934056	TCTGCAAACAAATATTTAGGCACAT	58.066	32.000	0.00	0.00	0.00	3.21
2081	2229	6.812656	TCTGCAAACAAATATTTAGGCACATG	59.187	34.615	0.00	0.00	0.00	3.21
2082	2230	6.462500	TGCAAACAAATATTTAGGCACATGT	58.538	32.000	0.00	0.00	0.00	3.21
2083	2231	7.606349	TGCAAACAAATATTTAGGCACATGTA	58.394	30.769	0.00	0.00	0.00	2.29
2084	2232	7.758980	TGCAAACAAATATTTAGGCACATGTAG	59.241	33.333	0.00	0.00	0.00	2.74
2085	2233	7.973388	GCAAACAAATATTTAGGCACATGTAGA	59.027	33.333	0.00	0.00	0.00	2.59
2086	2234	9.853555	CAAACAAATATTTAGGCACATGTAGAA	57.146	29.630	0.00	0.00	0.00	2.10
2095	2243	8.837788	TTTAGGCACATGTAGAATATGAGATG	57.162	34.615	0.00	0.00	0.00	2.90
2096	2244	6.676990	AGGCACATGTAGAATATGAGATGA	57.323	37.500	0.00	0.00	0.00	2.92
2097	2245	7.255199	AGGCACATGTAGAATATGAGATGAT	57.745	36.000	0.00	0.00	0.00	2.45
2098	2246	7.687388	AGGCACATGTAGAATATGAGATGATT	58.313	34.615	0.00	0.00	0.00	2.57
2099	2247	8.162085	AGGCACATGTAGAATATGAGATGATTT	58.838	33.333	0.00	0.00	0.00	2.17
2100	2248	9.440773	GGCACATGTAGAATATGAGATGATTTA	57.559	33.333	0.00	0.00	0.00	1.40
2125	2273	5.173312	CAGATTACACGTATCTTAAGGTGCG	59.827	44.000	22.45	22.45	38.50	5.34
2196	2344	2.571206	GCTAAACGCGAAAACTCTTGG	58.429	47.619	15.93	0.00	0.00	3.61
2281	2429	1.294780	AGGAACTCGCAGAAGCTGG	59.705	57.895	0.00	0.00	39.10	4.85
2289	2437	1.018226	CGCAGAAGCTGGAGAGTTGG	61.018	60.000	0.00	0.00	39.10	3.77
2300	2448	2.104792	TGGAGAGTTGGAGTTTGAGTGG	59.895	50.000	0.00	0.00	0.00	4.00
2346	2494	5.168569	CAAGTGATATCGTGTGTACCAGTT	58.831	41.667	0.00	0.00	0.00	3.16
2407	2555	8.956426	CAAGACTTGCTTAAATGGGACTAAATA	58.044	33.333	1.43	0.00	34.31	1.40
2429	2577	0.038599	TGACCAGCTGAATGTGCCAT	59.961	50.000	17.39	0.00	0.00	4.40
2435	2583	1.171308	GCTGAATGTGCCATCAGTGT	58.829	50.000	4.87	0.00	43.91	3.55
2443	2591	6.038492	TGAATGTGCCATCAGTGTTATATGTG	59.962	38.462	0.00	0.00	0.00	3.21
2458	2606	0.179032	ATGTGTTTGTGGCCGACTCA	60.179	50.000	0.00	1.99	0.00	3.41
2462	2610	1.153066	TTTGTGGCCGACTCAAGCA	60.153	52.632	0.00	0.00	34.42	3.91
2469	2617	1.228124	CCGACTCAAGCAACCCCAA	60.228	57.895	0.00	0.00	0.00	4.12
2479	2627	1.303643	CAACCCCAACCAGAGGCTC	60.304	63.158	6.34	6.34	0.00	4.70
2503	2651	3.561725	CCTGCCGAATAGATTTCAACTCC	59.438	47.826	0.00	0.00	0.00	3.85
2508	2656	5.694910	GCCGAATAGATTTCAACTCCGATTA	59.305	40.000	0.00	0.00	0.00	1.75
2529	2677	7.923344	CGATTATTTCAGAGAGGAGAAGCTAAA	59.077	37.037	0.00	0.00	0.00	1.85
2530	2678	9.260002	GATTATTTCAGAGAGGAGAAGCTAAAG	57.740	37.037	0.00	0.00	0.00	1.85
2533	2681	5.850557	TCAGAGAGGAGAAGCTAAAGATG	57.149	43.478	0.00	0.00	0.00	2.90
2552	2700	1.066502	TGGAATTTGCCGTCGATGAGA	60.067	47.619	6.11	0.00	0.00	3.27
2574	2722	0.251341	TTTTTGGCTGGGGAGAGCTC	60.251	55.000	5.27	5.27	39.11	4.09
2587	2735	4.602340	GGAGAGCTCCCGTTAATAATCA	57.398	45.455	10.93	0.00	43.94	2.57
2639	2787	5.426689	ACAATACAGCCAAGAGATTCTCA	57.573	39.130	15.83	0.00	32.06	3.27
2640	2788	5.809001	ACAATACAGCCAAGAGATTCTCAA	58.191	37.500	15.83	0.00	32.06	3.02
2641	2789	6.240894	ACAATACAGCCAAGAGATTCTCAAA	58.759	36.000	15.83	0.00	32.06	2.69
2669	2817	7.649533	AAAAATGCATCCAAGATGAGATACA	57.350	32.000	8.74	0.00	0.00	2.29
2705	2853	8.676401	TGTTGGTGAATGTGAACAATGATATAG	58.324	33.333	0.00	0.00	0.00	1.31

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	3.570926	TGTGCGTGGTTGTGTTTTAAA	57.429	38.095	0.00	0.00	0.00	1.52
27	28	2.542824	GCTAATGTGCGTGGTTGTGTTT	60.543	45.455	0.00	0.00	0.00	2.83
31	32	0.874390	CTGCTAATGTGCGTGGTTGT	59.126	50.000	0.00	0.00	35.36	3.32
39	40	3.923017	AGTTTGTTCCTGCTAATGTGC	57.077	42.857	0.00	0.00	0.00	4.57
67	68	4.463209	CGAGAGAGATCAGTATTTCTCGC	58.537	47.826	8.91	5.68	44.36	5.03
83	84	1.749634	GGTAGCCAACTTAGCGAGAGA	59.250	52.381	0.00	0.00	34.64	3.10
84	85	1.751924	AGGTAGCCAACTTAGCGAGAG	59.248	52.381	0.00	0.00	34.64	3.20
248	249	6.576185	ACTAGTCTCTACTGTCTACTGCTAC	58.424	44.000	0.00	0.00	36.36	3.58
417	450	3.334583	ACTGAACAGCCATTCGTACAT	57.665	42.857	1.46	0.00	0.00	2.29
430	463	4.792068	AGAAGACCAATTCCAACTGAACA	58.208	39.130	0.00	0.00	35.31	3.18
484	517	1.006337	CTGCTATGGCGCTCCTCTC	60.006	63.158	7.64	0.00	42.25	3.20
627	666	1.228124	CCAAACTCACCTTCCCGCA	60.228	57.895	0.00	0.00	0.00	5.69
661	719	2.165641	TGTCAATACACTACTCGGCCTG	59.834	50.000	0.00	0.00	0.00	4.85
680	739	8.321353	TGACTCAATTATTGTAGGATGAACTGT	58.679	33.333	4.77	0.00	0.00	3.55
759	839	6.317140	CCACACAAGATCTAATTAGCACACAT	59.683	38.462	7.67	0.00	0.00	3.21
880	987	3.169908	GGGACCTTAGAAAATTGCCCAA	58.830	45.455	0.00	0.00	34.47	4.12
1035	1142	2.965831	TCCTGGGGAGATCAAACGATAG	59.034	50.000	0.00	0.00	46.19	2.08
1321	1437	1.918293	AGAAGGTCATGTCCGCCCA	60.918	57.895	3.20	0.00	0.00	5.36
1330	1446	0.036010	CCTTGGACGCAGAAGGTCAT	60.036	55.000	0.00	0.00	35.01	3.06
1441	1557	2.882927	TCTTCCACGATTACGGATGG	57.117	50.000	0.00	0.00	44.46	3.51
1446	1562	6.362551	CAGGTAACATATCTTCCACGATTACG	59.637	42.308	0.00	0.00	42.57	3.18
1527	1645	1.341852	TCCTCGTCATCAAAACCGTCA	59.658	47.619	0.00	0.00	0.00	4.35
1594	1712	8.362639	ACATATGAGCTTCAACTTTTCAATTGT	58.637	29.630	10.38	0.00	0.00	2.71
1725	1873	1.486310	TCATAGTCTTGGCTCGCCATT	59.514	47.619	12.00	1.22	46.64	3.16
1922	2070	7.313646	TCTTGGACTAGAGTAACTCAAATTCG	58.686	38.462	0.00	0.00	32.06	3.34
1940	2088	9.438291	CACGAATTGATACATTATTTCTTGGAC	57.562	33.333	0.00	0.00	0.00	4.02
2022	2170	2.040679	AGGGGTGCCGTGTTAGTTTAAT	59.959	45.455	0.00	0.00	0.00	1.40
2036	2184	2.828661	AAAAGGGAAGATAGGGGTGC	57.171	50.000	0.00	0.00	0.00	5.01
2089	2237	9.678941	GATACGTGTAATCTGTAAATCATCTCA	57.321	33.333	0.00	0.00	0.00	3.27
2090	2238	9.900710	AGATACGTGTAATCTGTAAATCATCTC	57.099	33.333	0.00	0.00	0.00	2.75
2097	2245	9.577110	CACCTTAAGATACGTGTAATCTGTAAA	57.423	33.333	3.36	0.00	0.00	2.01
2098	2246	7.703621	GCACCTTAAGATACGTGTAATCTGTAA	59.296	37.037	3.36	0.90	0.00	2.41
2099	2247	7.198390	GCACCTTAAGATACGTGTAATCTGTA	58.802	38.462	3.36	0.00	0.00	2.74
2100	2248	6.040878	GCACCTTAAGATACGTGTAATCTGT	58.959	40.000	3.36	0.00	0.00	3.41
2101	2249	5.173312	CGCACCTTAAGATACGTGTAATCTG	59.827	44.000	3.36	0.00	0.00	2.90
2102	2250	5.163581	ACGCACCTTAAGATACGTGTAATCT	60.164	40.000	3.36	0.00	31.71	2.40
2103	2251	5.039333	ACGCACCTTAAGATACGTGTAATC	58.961	41.667	3.36	0.00	31.71	1.75
2104	2252	5.002464	ACGCACCTTAAGATACGTGTAAT	57.998	39.130	3.36	0.00	31.71	1.89
2105	2253	4.439305	ACGCACCTTAAGATACGTGTAA	57.561	40.909	3.36	0.00	31.71	2.41
2106	2254	4.439305	AACGCACCTTAAGATACGTGTA	57.561	40.909	14.46	0.00	33.48	2.90
2125	2273	0.169009	GAGCCAGATCGTTGCCAAAC	59.831	55.000	1.29	0.00	0.00	2.93
2136	2284	3.222855	CGGAGCTCGGAGCCAGAT	61.223	66.667	25.49	7.82	43.77	2.90
2178	2326	3.460103	ACTCCAAGAGTTTTCGCGTTTA	58.540	40.909	5.77	0.00	40.28	2.01
2196	2344	0.957888	GGCAGCCAGGAGTTCAACTC	60.958	60.000	9.27	9.27	44.32	3.01
2281	2429	3.477210	ACCACTCAAACTCCAACTCTC	57.523	47.619	0.00	0.00	0.00	3.20
2289	2437	4.893424	TTGCTGTAAACCACTCAAACTC	57.107	40.909	0.00	0.00	0.00	3.01
2346	2494	4.742201	GGGAGACAAGCGCTGCGA	62.742	66.667	28.07	0.00	0.00	5.10
2395	2543	4.910304	AGCTGGTCAGATATTTAGTCCCAT	59.090	41.667	1.65	0.00	0.00	4.00
2407	2555	1.681166	GGCACATTCAGCTGGTCAGAT	60.681	52.381	15.13	0.00	0.00	2.90
2429	2577	4.457603	GGCCACAAACACATATAACACTGA	59.542	41.667	0.00	0.00	0.00	3.41
2435	2583	3.936453	GAGTCGGCCACAAACACATATAA	59.064	43.478	2.24	0.00	0.00	0.98
2443	2591	1.282875	GCTTGAGTCGGCCACAAAC	59.717	57.895	2.24	0.00	0.00	2.93
2458	2606	1.153756	CCTCTGGTTGGGGTTGCTT	59.846	57.895	0.00	0.00	0.00	3.91
2462	2610	1.464198	AGAGCCTCTGGTTGGGGTT	60.464	57.895	0.00	0.00	33.12	4.11
2479	2627	4.446371	AGTTGAAATCTATTCGGCAGGAG	58.554	43.478	0.00	0.00	0.00	3.69
2503	2651	5.841810	AGCTTCTCCTCTCTGAAATAATCG	58.158	41.667	0.00	0.00	0.00	3.34
2508	2656	6.865834	TCTTTAGCTTCTCCTCTCTGAAAT	57.134	37.500	0.00	0.00	0.00	2.17
2529	2677	1.942657	CATCGACGGCAAATTCCATCT	59.057	47.619	0.00	0.00	0.00	2.90
2530	2678	1.939934	TCATCGACGGCAAATTCCATC	59.060	47.619	0.00	0.00	0.00	3.51
2533	2681	1.651987	TCTCATCGACGGCAAATTCC	58.348	50.000	0.00	0.00	0.00	3.01
2613	2761	6.893583	AGAATCTCTTGGCTGTATTGTATGT	58.106	36.000	0.00	0.00	0.00	2.29
2649	2797	6.215023	ACCTATGTATCTCATCTTGGATGCAT	59.785	38.462	0.00	0.00	43.69	3.96
2651	2799	6.047511	ACCTATGTATCTCATCTTGGATGC	57.952	41.667	2.95	0.00	37.91	3.91
2669	2817	6.480763	TCACATTCACCAACAACATACCTAT	58.519	36.000	0.00	0.00	0.00	2.57
2756	2904	4.557205	CCTGTTCTATACTGGGCGATAAC	58.443	47.826	0.00	0.00	41.00	1.89
2758	2906	2.561419	GCCTGTTCTATACTGGGCGATA	59.439	50.000	0.00	0.00	43.93	2.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.