AutoCloner

Multiple sequence alignment - TraesCS7D01G454800

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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	TraesCS7D01G454800	chr7D	100.000	2212	0	0	920	3131	573898027	573900238	0.000000e+00	4085.0
1	TraesCS7D01G454800	chr7D	100.000	627	0	0	1	627	573897108	573897734	0.000000e+00	1158.0
2	TraesCS7D01G454800	chr7D	100.000	30	0	0	1783	1812	573905557	573905586	4.360000e-04	56.5
3	TraesCS7D01G454800	chr7B	95.029	1569	49	13	923	2486	632684643	632686187	0.000000e+00	2438.0
4	TraesCS7D01G454800	chr7B	95.777	663	18	3	2472	3131	632687492	632688147	0.000000e+00	1061.0
5	TraesCS7D01G454800	chr7B	94.469	452	16	5	161	606	632684129	632684577	0.000000e+00	688.0
6	TraesCS7D01G454800	chr7B	95.706	163	7	0	1	163	632683905	632684067	2.390000e-66	263.0
7	TraesCS7D01G454800	chr7B	90.000	120	10	2	1585	1703	19975506	19975388	1.500000e-33	154.0
8	TraesCS7D01G454800	chr7B	93.548	62	4	0	16	77	336643887	336643826	3.320000e-15	93.5
9	TraesCS7D01G454800	chr7B	77.160	162	22	8	1815	1962	20034661	20034501	2.590000e-11	80.5
10	TraesCS7D01G454800	chr7B	92.453	53	4	0	1910	1962	632946037	632945985	3.350000e-10	76.8
11	TraesCS7D01G454800	chr7B	100.000	30	0	0	1783	1812	632688538	632688567	4.360000e-04	56.5
12	TraesCS7D01G454800	chr1D	86.246	1425	92	39	930	2283	395559611	395558220	0.000000e+00	1450.0
13	TraesCS7D01G454800	chr1D	82.822	652	70	19	2278	2915	395558195	395557572	2.120000e-151	545.0
14	TraesCS7D01G454800	chr1D	90.610	213	19	1	2920	3131	395557533	395557321	6.610000e-72	281.0
15	TraesCS7D01G454800	chr1A	86.071	1400	108	43	930	2283	489601219	489599861	0.000000e+00	1424.0
16	TraesCS7D01G454800	chr1B	87.873	1138	60	29	928	2004	526348921	526347801	0.000000e+00	1266.0
17	TraesCS7D01G454800	chr1B	81.748	652	67	24	2276	2915	526347269	526346658	6.030000e-137	497.0
18	TraesCS7D01G454800	chr1B	89.623	212	19	1	2920	3131	526346619	526346411	1.850000e-67	267.0
19	TraesCS7D01G454800	chr1B	78.808	302	29	15	2006	2283	526347582	526347292	1.490000e-38	171.0
20	TraesCS7D01G454800	chr1B	92.308	65	5	0	16	80	664312604	664312668	3.320000e-15	93.5
21	TraesCS7D01G454800	chr3B	82.565	889	109	26	956	1812	733628624	733629498	0.000000e+00	741.0
22	TraesCS7D01G454800	chr3B	83.942	822	69	26	921	1701	733574002	733574801	0.000000e+00	728.0
23	TraesCS7D01G454800	chr3B	92.424	66	5	0	16	81	377684204	377684269	9.240000e-16	95.3
24	TraesCS7D01G454800	chr3B	93.548	62	4	0	16	77	190380521	190380582	3.320000e-15	93.5
25	TraesCS7D01G454800	chr3B	92.593	54	3	1	1907	1959	733575023	733575076	3.350000e-10	76.8
26	TraesCS7D01G454800	chr3B	100.000	30	0	0	1783	1812	733574870	733574899	4.360000e-04	56.5
27	TraesCS7D01G454800	chr3A	84.483	754	93	16	956	1704	689111919	689112653	0.000000e+00	723.0
28	TraesCS7D01G454800	chr3A	75.272	368	40	33	1866	2189	689074148	689074508	9.110000e-26	128.0
29	TraesCS7D01G454800	chr3D	83.912	777	89	21	956	1703	552782381	552783150	0.000000e+00	710.0
30	TraesCS7D01G454800	chr3D	81.373	510	76	15	920	1417	552755119	552755621	6.290000e-107	398.0
31	TraesCS7D01G454800	chr3D	88.028	142	15	1	2484	2625	37496066	37496205	1.930000e-37	167.0
32	TraesCS7D01G454800	chr3D	93.651	63	4	0	17	79	481582074	481582136	9.240000e-16	95.3
33	TraesCS7D01G454800	chr3D	100.000	30	0	0	1783	1812	552783231	552783260	4.360000e-04	56.5
34	TraesCS7D01G454800	chr2D	75.915	710	108	26	1007	1665	489009828	489009131	3.920000e-79	305.0
35	TraesCS7D01G454800	chr2D	88.235	204	17	2	1507	1703	488872720	488872923	1.450000e-58	237.0
36	TraesCS7D01G454800	chr2D	82.394	142	23	2	1527	1667	50747788	50747928	4.240000e-24	122.0
37	TraesCS7D01G454800	chr2D	77.108	166	21	14	2520	2670	488993780	488993617	2.590000e-11	80.5
38	TraesCS7D01G454800	chr2D	83.529	85	9	5	1866	1949	488994478	488994398	1.200000e-09	75.0
39	TraesCS7D01G454800	chr4A	89.340	197	17	3	2484	2679	706852546	706852353	8.670000e-61	244.0
40	TraesCS7D01G454800	chr4A	95.312	64	3	0	16	79	608276409	608276472	5.520000e-18	102.0
41	TraesCS7D01G454800	chr4D	88.500	200	20	2	2481	2679	131266749	131266946	4.040000e-59	239.0
42	TraesCS7D01G454800	chr5D	86.935	199	20	5	2484	2679	333382210	333382015	5.260000e-53	219.0
43	TraesCS7D01G454800	chr2B	96.491	57	2	0	24	80	111421756	111421700	9.240000e-16	95.3
44	TraesCS7D01G454800	chr5B	93.548	62	4	0	18	79	412264887	412264826	3.320000e-15	93.5
45	TraesCS7D01G454800	chr2A	81.250	128	12	10	2537	2653	619559892	619560018	3.320000e-15	93.5

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	TraesCS7D01G454800	chr7D	573897108	573900238	3130	False	2621.500000	4085	100.000000	1	3131	2	chr7D.!!$F2	3130
1	TraesCS7D01G454800	chr7B	632683905	632688567	4662	False	901.300000	2438	96.196200	1	3131	5	chr7B.!!$F1	3130
2	TraesCS7D01G454800	chr1D	395557321	395559611	2290	True	758.666667	1450	86.559333	930	3131	3	chr1D.!!$R1	2201
3	TraesCS7D01G454800	chr1A	489599861	489601219	1358	True	1424.000000	1424	86.071000	930	2283	1	chr1A.!!$R1	1353
4	TraesCS7D01G454800	chr1B	526346411	526348921	2510	True	550.250000	1266	84.513000	928	3131	4	chr1B.!!$R1	2203
5	TraesCS7D01G454800	chr3B	733628624	733629498	874	False	741.000000	741	82.565000	956	1812	1	chr3B.!!$F3	856
6	TraesCS7D01G454800	chr3B	733574002	733575076	1074	False	287.100000	728	92.178333	921	1959	3	chr3B.!!$F4	1038
7	TraesCS7D01G454800	chr3A	689111919	689112653	734	False	723.000000	723	84.483000	956	1704	1	chr3A.!!$F2	748
8	TraesCS7D01G454800	chr3D	552755119	552755621	502	False	398.000000	398	81.373000	920	1417	1	chr3D.!!$F3	497
9	TraesCS7D01G454800	chr3D	552782381	552783260	879	False	383.250000	710	91.956000	956	1812	2	chr3D.!!$F4	856
10	TraesCS7D01G454800	chr2D	489009131	489009828	697	True	305.000000	305	75.915000	1007	1665	1	chr2D.!!$R1	658

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
621	741	0.038251	TGCTACAAGTCCTCACAGCG	60.038	55.0	0.0	0.0	0.0	5.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2210	2822	2.457366	AGGAGTACAAGAAAGTGGCG	57.543	50.0	0.0	0.0	0.0	5.69	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
24	25	3.254903	GGGTTGGTATTTTGTGACTGGAC	59.745	47.826	0.00	0.00	0.00	4.02
58	59	3.694535	GTATGAGACGGATATAGGGCG	57.305	52.381	0.00	0.00	0.00	6.13
97	98	9.959721	TGCTCTTAGAATTTTATAGGAAACTGT	57.040	29.630	0.00	0.00	43.88	3.55
173	238	9.029243	TGTGTTTAATCATCAAACAACAATGAC	57.971	29.630	2.48	0.00	44.90	3.06
238	303	8.506168	TCATCATCAAGTTTGGATTACTTACC	57.494	34.615	0.00	0.00	34.22	2.85
263	328	2.433604	AGAGTCACATGGTATGGCTCTG	59.566	50.000	15.83	0.00	36.96	3.35
320	385	1.067974	GCGTAAAACAAAACAGCCCCT	59.932	47.619	0.00	0.00	0.00	4.79
321	386	2.293955	GCGTAAAACAAAACAGCCCCTA	59.706	45.455	0.00	0.00	0.00	3.53
330	395	6.260700	ACAAAACAGCCCCTATATGACATA	57.739	37.500	0.00	0.00	0.00	2.29
343	408	9.480861	CCCTATATGACATAAAGAGTGGAGATA	57.519	37.037	0.00	0.00	0.00	1.98
443	511	1.985473	ACAGCTTGCTTGGAATCACA	58.015	45.000	0.00	0.00	0.00	3.58
454	522	5.182950	TGCTTGGAATCACATGTTTTCGTAT	59.817	36.000	0.00	0.00	0.00	3.06
464	532	7.297391	TCACATGTTTTCGTATGTTGATTCTG	58.703	34.615	0.00	0.00	35.46	3.02
473	541	5.580691	TCGTATGTTGATTCTGTTGATGGAC	59.419	40.000	0.00	0.00	0.00	4.02
616	736	0.610174	CTGGCTGCTACAAGTCCTCA	59.390	55.000	0.00	0.00	0.00	3.86
621	741	0.038251	TGCTACAAGTCCTCACAGCG	60.038	55.000	0.00	0.00	0.00	5.18
622	742	0.243907	GCTACAAGTCCTCACAGCGA	59.756	55.000	0.00	0.00	0.00	4.93
623	743	1.734047	GCTACAAGTCCTCACAGCGAG	60.734	57.143	0.00	0.00	41.89	5.03
624	744	1.813178	CTACAAGTCCTCACAGCGAGA	59.187	52.381	0.00	0.00	45.45	4.04
625	745	0.600557	ACAAGTCCTCACAGCGAGAG	59.399	55.000	0.00	0.00	45.45	3.20
626	746	0.884514	CAAGTCCTCACAGCGAGAGA	59.115	55.000	4.92	0.00	45.45	3.10
1136	1294	2.185350	CAAGCTCGGGCAGATCGT	59.815	61.111	11.40	0.00	41.70	3.73
1499	1713	3.515286	GGCCGATCTGTCCGACGA	61.515	66.667	0.00	0.00	0.00	4.20
2059	2654	7.214381	AGTAGTAGTGTAATGTTGAACTGCAA	58.786	34.615	0.00	0.00	0.00	4.08
2078	2673	3.430929	GCAACTTATCTGTGGGACGATCT	60.431	47.826	0.00	0.00	0.00	2.75
2096	2691	2.838736	TCTAATCGAATTGCAGGAGCC	58.161	47.619	0.00	0.00	41.13	4.70
2149	2761	5.739752	TGCTTCTTGTTCATGGATAATCG	57.260	39.130	0.00	0.00	0.00	3.34
2210	2822	6.917477	TGCTTTAATCATGACAAAGTTGTGAC	59.083	34.615	22.98	12.11	42.43	3.67
2224	2836	2.605837	TGTGACGCCACTTTCTTGTA	57.394	45.000	2.85	0.00	43.55	2.41
2226	2838	2.159014	TGTGACGCCACTTTCTTGTACT	60.159	45.455	2.85	0.00	43.55	2.73
2227	2839	2.475487	GTGACGCCACTTTCTTGTACTC	59.525	50.000	0.00	0.00	40.10	2.59
2228	2840	2.067013	GACGCCACTTTCTTGTACTCC	58.933	52.381	0.00	0.00	0.00	3.85
2230	2842	2.895404	ACGCCACTTTCTTGTACTCCTA	59.105	45.455	0.00	0.00	0.00	2.94
2232	2844	3.263261	GCCACTTTCTTGTACTCCTAGC	58.737	50.000	0.00	0.00	0.00	3.42
2233	2845	3.055747	GCCACTTTCTTGTACTCCTAGCT	60.056	47.826	0.00	0.00	0.00	3.32
2234	2846	4.159879	GCCACTTTCTTGTACTCCTAGCTA	59.840	45.833	0.00	0.00	0.00	3.32
2235	2847	5.680151	GCCACTTTCTTGTACTCCTAGCTAG	60.680	48.000	14.20	14.20	0.00	3.42
2331	3011	6.318648	TCTTTGTAATCATCCTACATGTTGGC	59.681	38.462	20.09	6.24	0.00	4.52
2350	3031	1.210478	GCTATCTGGGACTGGAAGCAA	59.790	52.381	0.00	0.00	37.60	3.91
2352	3033	3.686691	GCTATCTGGGACTGGAAGCAATT	60.687	47.826	0.00	0.00	37.60	2.32
2422	3103	8.189119	TGCCTTGTGTTCTTTTTATCCTTTAT	57.811	30.769	0.00	0.00	0.00	1.40
2703	4712	0.957395	CAACCCAATCGAGCTGCAGT	60.957	55.000	16.64	1.59	0.00	4.40
2704	4713	0.250901	AACCCAATCGAGCTGCAGTT	60.251	50.000	16.64	9.79	0.00	3.16
2705	4714	0.250901	ACCCAATCGAGCTGCAGTTT	60.251	50.000	16.64	3.84	0.00	2.66
2706	4715	0.449388	CCCAATCGAGCTGCAGTTTC	59.551	55.000	16.64	12.45	0.00	2.78
2707	4716	1.159285	CCAATCGAGCTGCAGTTTCA	58.841	50.000	16.64	0.00	0.00	2.69
2708	4717	1.536766	CCAATCGAGCTGCAGTTTCAA	59.463	47.619	16.64	0.00	0.00	2.69
2709	4718	2.578495	CAATCGAGCTGCAGTTTCAAC	58.422	47.619	16.64	0.00	0.00	3.18
2770	4789	5.543405	TGTTCAATCATTTTTCTGGGATGGT	59.457	36.000	0.00	0.00	0.00	3.55
2882	4901	0.175760	GTTCTGCATGGCGTAGGAGA	59.824	55.000	0.00	0.00	0.00	3.71
2891	4912	5.048713	TGCATGGCGTAGGAGATATATATCG	60.049	44.000	15.48	6.09	37.76	2.92
2917	4938	7.068103	GGGTATGGTTGTGAATTGTGATAATCA	59.932	37.037	0.00	0.00	0.00	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	1.982938	AGTCGGGCGCCCTATATCC	60.983	63.158	41.01	19.83	0.00	2.59
58	59	4.740235	GAGCATCTACAGTCGGGC	57.260	61.111	0.00	0.00	0.00	6.13
183	248	2.827921	GGAGCAAGGACATGACCAATTT	59.172	45.455	16.63	0.00	0.00	1.82
187	252	1.067295	AAGGAGCAAGGACATGACCA	58.933	50.000	16.63	0.00	0.00	4.02
191	256	4.326504	AAACAAAAGGAGCAAGGACATG	57.673	40.909	0.00	0.00	0.00	3.21
195	260	4.648762	TGATGAAAACAAAAGGAGCAAGGA	59.351	37.500	0.00	0.00	0.00	3.36
238	303	2.814269	CCATACCATGTGACTCTCGTG	58.186	52.381	0.00	0.00	0.00	4.35
258	323	1.009829	CGGTATGACCAAAGCAGAGC	58.990	55.000	0.00	0.00	38.47	4.09
263	328	4.625311	CCAAAATTTCGGTATGACCAAAGC	59.375	41.667	0.00	0.00	38.47	3.51
407	475	6.128849	GCAAGCTGTAATTAATGTTGTTGTGG	60.129	38.462	0.00	0.00	0.00	4.17
443	511	7.870826	TCAACAGAATCAACATACGAAAACAT	58.129	30.769	0.00	0.00	0.00	2.71
454	522	4.937620	GCTAGTCCATCAACAGAATCAACA	59.062	41.667	0.00	0.00	0.00	3.33
464	532	2.668457	CTCAACACGCTAGTCCATCAAC	59.332	50.000	0.00	0.00	0.00	3.18
473	541	4.903638	TTTCGAAATCTCAACACGCTAG	57.096	40.909	6.47	0.00	0.00	3.42
596	667	0.742635	GAGGACTTGTAGCAGCCAGC	60.743	60.000	0.00	0.00	46.19	4.85
599	670	0.321671	TGTGAGGACTTGTAGCAGCC	59.678	55.000	0.00	0.00	0.00	4.85
606	677	0.600557	CTCTCGCTGTGAGGACTTGT	59.399	55.000	17.44	0.00	45.32	3.16
1136	1294	1.572085	GACCGTGAAGACGTCCGAGA	61.572	60.000	13.01	0.00	44.54	4.04
1477	1682	2.990479	GGACAGATCGGCCTTGGT	59.010	61.111	0.00	0.00	0.00	3.67
2031	2622	8.808529	GCAGTTCAACATTACACTACTACTATG	58.191	37.037	0.00	0.00	0.00	2.23
2033	2624	7.888424	TGCAGTTCAACATTACACTACTACTA	58.112	34.615	0.00	0.00	0.00	1.82
2034	2625	6.755206	TGCAGTTCAACATTACACTACTACT	58.245	36.000	0.00	0.00	0.00	2.57
2059	2654	6.334102	GATTAGATCGTCCCACAGATAAGT	57.666	41.667	0.00	0.00	0.00	2.24
2078	2673	2.708216	TGGCTCCTGCAATTCGATTA	57.292	45.000	0.00	0.00	41.91	1.75
2149	2761	5.955496	GCAATTTTGTCATGCAATTCGATTC	59.045	36.000	0.00	0.00	39.81	2.52
2210	2822	2.457366	AGGAGTACAAGAAAGTGGCG	57.543	50.000	0.00	0.00	0.00	5.69
2227	2839	6.191315	TCTTGCTATCCTAATCCTAGCTAGG	58.809	44.000	30.94	30.94	45.02	3.02
2228	2840	7.779798	AGATCTTGCTATCCTAATCCTAGCTAG	59.220	40.741	14.20	14.20	40.42	3.42
2230	2842	6.502138	AGATCTTGCTATCCTAATCCTAGCT	58.498	40.000	0.00	0.00	38.89	3.32
2232	2844	8.593945	AAGAGATCTTGCTATCCTAATCCTAG	57.406	38.462	0.00	0.00	34.38	3.02
2234	2846	8.964533	TTAAGAGATCTTGCTATCCTAATCCT	57.035	34.615	5.34	0.00	37.40	3.24
2235	2847	9.598517	CATTAAGAGATCTTGCTATCCTAATCC	57.401	37.037	5.34	0.00	37.40	3.01
2238	2850	7.390027	GCCATTAAGAGATCTTGCTATCCTAA	58.610	38.462	5.34	0.00	37.40	2.69
2331	3011	3.853355	ATTGCTTCCAGTCCCAGATAG	57.147	47.619	0.00	0.00	0.00	2.08
2422	3103	5.326900	GGGGTTTTTACCTGAACCTCATTA	58.673	41.667	5.37	0.00	44.23	1.90
2703	4712	4.998671	TCACATGCCTTGAAAGTTGAAA	57.001	36.364	0.00	0.00	0.00	2.69
2704	4713	4.998671	TTCACATGCCTTGAAAGTTGAA	57.001	36.364	0.00	0.00	29.89	2.69
2705	4714	4.998671	TTTCACATGCCTTGAAAGTTGA	57.001	36.364	6.00	0.00	37.91	3.18
2706	4715	6.423862	CAATTTTCACATGCCTTGAAAGTTG	58.576	36.000	20.73	20.73	45.81	3.16
2707	4716	5.528320	CCAATTTTCACATGCCTTGAAAGTT	59.472	36.000	10.39	10.39	42.44	2.66
2708	4717	5.058490	CCAATTTTCACATGCCTTGAAAGT	58.942	37.500	9.21	5.20	42.44	2.66
2709	4718	4.453136	CCCAATTTTCACATGCCTTGAAAG	59.547	41.667	9.21	1.10	42.44	2.62
2846	4865	7.144722	TGCAGAACAAGATTAACGAATGAAT	57.855	32.000	0.00	0.00	0.00	2.57
2882	4901	9.613428	CAATTCACAACCATACCCGATATATAT	57.387	33.333	0.00	0.00	0.00	0.86
2891	4912	6.767524	TTATCACAATTCACAACCATACCC	57.232	37.500	0.00	0.00	0.00	3.69
2917	4938	4.844349	AACAACCAGCATATGTAGGACT	57.156	40.909	18.61	6.05	0.00	3.85
2968	5023	3.165071	ACTAAACATGCTGGAAAAGGGG	58.835	45.455	0.00	0.00	0.00	4.79
3090	5146	8.060020	TCAATTTGATTTGATTGTTCACGAAC	57.940	30.769	2.89	2.89	35.09	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.