AutoCloner

Multiple sequence alignment - TraesCS4D01G198300

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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	TraesCS4D01G198300	chr4D	100.000	2924	0	0	1	2924	344298578	344295655	0.000000e+00	5400.0
1	TraesCS4D01G198300	chr3D	93.401	2167	92	18	3	2168	133263498	133261382	0.000000e+00	3162.0
2	TraesCS4D01G198300	chr3D	91.685	445	29	6	2477	2921	133260911	133260475	6.930000e-171	610.0
3	TraesCS4D01G198300	chr3D	95.614	228	9	1	2171	2397	133261349	133261122	5.960000e-97	364.0
4	TraesCS4D01G198300	chr6D	89.722	2335	160	39	114	2404	424956097	424953799	0.000000e+00	2909.0
5	TraesCS4D01G198300	chr6D	89.979	1936	160	23	236	2165	227523397	227525304	0.000000e+00	2470.0
6	TraesCS4D01G198300	chr6D	89.087	449	40	6	2477	2921	424953587	424953144	1.530000e-152	549.0
7	TraesCS4D01G198300	chr6D	84.430	456	55	10	2477	2924	227525750	227526197	4.480000e-118	435.0
8	TraesCS4D01G198300	chr6D	89.610	231	19	5	2170	2398	218378804	218378577	3.690000e-74	289.0
9	TraesCS4D01G198300	chr6D	87.281	228	24	5	2173	2397	227525342	227525567	3.740000e-64	255.0
10	TraesCS4D01G198300	chr6D	97.436	39	1	0	1	39	424956149	424956111	1.880000e-07	67.6
11	TraesCS4D01G198300	chr7B	87.549	2289	187	38	235	2475	198616103	198613865	0.000000e+00	2558.0
12	TraesCS4D01G198300	chr7B	93.590	156	10	0	2769	2924	198613883	198613728	1.750000e-57	233.0
13	TraesCS4D01G198300	chr2D	88.211	2197	190	32	235	2395	354684706	354686869	0.000000e+00	2558.0
14	TraesCS4D01G198300	chr2D	93.548	62	4	0	2414	2475	354686862	354686923	3.100000e-15	93.5
15	TraesCS4D01G198300	chr5D	90.041	1938	156	20	235	2165	43331337	43333244	0.000000e+00	2475.0
16	TraesCS4D01G198300	chr5D	86.637	449	51	8	2477	2924	43333717	43334157	3.390000e-134	488.0
17	TraesCS4D01G198300	chr5D	89.177	231	20	5	2171	2398	43333280	43333508	1.720000e-72	283.0
18	TraesCS4D01G198300	chr4A	88.448	1939	183	26	236	2168	460276441	460274538	0.000000e+00	2302.0
19	TraesCS4D01G198300	chr4A	84.444	450	59	9	2477	2924	460274095	460273655	1.610000e-117	433.0
20	TraesCS4D01G198300	chr4A	78.914	313	58	7	2614	2924	499960926	499961232	3.820000e-49	206.0
21	TraesCS4D01G198300	chr3B	86.618	1928	198	31	251	2168	233306207	233304330	0.000000e+00	2076.0
22	TraesCS4D01G198300	chr3B	88.696	230	21	5	2171	2397	233304297	233304070	2.870000e-70	276.0
23	TraesCS4D01G198300	chr4B	86.336	1954	205	40	235	2168	409739262	409737351	0.000000e+00	2073.0
24	TraesCS4D01G198300	chr6B	90.501	1537	126	14	1	1530	252555700	252554177	0.000000e+00	2012.0
25	TraesCS4D01G198300	chr7D	88.379	1394	136	8	778	2165	316752364	316753737	0.000000e+00	1653.0
26	TraesCS4D01G198300	chr7D	78.981	314	56	9	2614	2924	316754163	316754469	3.820000e-49	206.0
27	TraesCS4D01G198300	chr2A	87.348	1399	145	15	778	2165	413480678	413479301	0.000000e+00	1574.0
28	TraesCS4D01G198300	chr2A	86.224	196	23	4	2172	2365	413479264	413479071	2.950000e-50	209.0
29	TraesCS4D01G198300	chr5B	86.860	449	50	7	2477	2924	488989657	488990097	7.280000e-136	494.0
30	TraesCS4D01G198300	chr5B	89.130	230	21	4	2171	2398	488989224	488989451	1.720000e-72	283.0
31	TraesCS4D01G198300	chr5A	85.266	414	57	4	2507	2919	432465364	432464954	9.690000e-115	424.0
32	TraesCS4D01G198300	chr1D	87.629	291	27	8	2477	2766	480345046	480345328	2.170000e-86	329.0
33	TraesCS4D01G198300	chr1B	86.598	291	30	8	2477	2766	668652245	668652527	2.190000e-81	313.0
34	TraesCS4D01G198300	chr1B	85.714	231	28	5	2171	2396	121765504	121765274	3.770000e-59	239.0

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	TraesCS4D01G198300	chr4D	344295655	344298578	2923	True	5400.000000	5400	100.000000	1	2924	1	chr4D.!!$R1	2923
1	TraesCS4D01G198300	chr3D	133260475	133263498	3023	True	1378.666667	3162	93.566667	3	2921	3	chr3D.!!$R1	2918
2	TraesCS4D01G198300	chr6D	424953144	424956149	3005	True	1175.200000	2909	92.081667	1	2921	3	chr6D.!!$R2	2920
3	TraesCS4D01G198300	chr6D	227523397	227526197	2800	False	1053.333333	2470	87.230000	236	2924	3	chr6D.!!$F1	2688
4	TraesCS4D01G198300	chr7B	198613728	198616103	2375	True	1395.500000	2558	90.569500	235	2924	2	chr7B.!!$R1	2689
5	TraesCS4D01G198300	chr2D	354684706	354686923	2217	False	1325.750000	2558	90.879500	235	2475	2	chr2D.!!$F1	2240
6	TraesCS4D01G198300	chr5D	43331337	43334157	2820	False	1082.000000	2475	88.618333	235	2924	3	chr5D.!!$F1	2689
7	TraesCS4D01G198300	chr4A	460273655	460276441	2786	True	1367.500000	2302	86.446000	236	2924	2	chr4A.!!$R1	2688
8	TraesCS4D01G198300	chr3B	233304070	233306207	2137	True	1176.000000	2076	87.657000	251	2397	2	chr3B.!!$R1	2146
9	TraesCS4D01G198300	chr4B	409737351	409739262	1911	True	2073.000000	2073	86.336000	235	2168	1	chr4B.!!$R1	1933
10	TraesCS4D01G198300	chr6B	252554177	252555700	1523	True	2012.000000	2012	90.501000	1	1530	1	chr6B.!!$R1	1529
11	TraesCS4D01G198300	chr7D	316752364	316754469	2105	False	929.500000	1653	83.680000	778	2924	2	chr7D.!!$F1	2146
12	TraesCS4D01G198300	chr2A	413479071	413480678	1607	True	891.500000	1574	86.786000	778	2365	2	chr2A.!!$R1	1587
13	TraesCS4D01G198300	chr5B	488989224	488990097	873	False	388.500000	494	87.995000	2171	2924	2	chr5B.!!$F1	753

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
432	439	0.904649	ATGAGGTCTCCGCAATGACA	59.095	50.0	0.0	0.0	36.81	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2406	2498	0.163788	GATAGCACACACACACACGC	59.836	55.0	0.0	0.0	0.0	5.34	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
52	53	6.947158	TGCCATATCATAACCAATGCATTCTA	59.053	34.615	9.53	1.96	35.38	2.10
73	74	1.891060	GAAGCGAAGTGGTGCTCGTG	61.891	60.000	0.00	0.00	41.46	4.35
147	148	5.292765	TCTGCTCTGACTCTGTTTTGTTAG	58.707	41.667	0.00	0.00	0.00	2.34
195	200	5.248477	ACTGGTGATCCTGTTATGTTACAGT	59.752	40.000	0.00	0.00	43.17	3.55
202	207	6.343716	TCCTGTTATGTTACAGTTTACCGA	57.656	37.500	0.00	0.00	43.17	4.69
249	255	6.767524	TTGTTACAGTTTCTTGTCAATGGT	57.232	33.333	0.00	0.00	32.56	3.55
432	439	0.904649	ATGAGGTCTCCGCAATGACA	59.095	50.000	0.00	0.00	36.81	3.58
546	556	5.353394	TGTGTCAGTTTTCTGGTCTTACT	57.647	39.130	0.00	0.00	46.94	2.24
590	601	6.767524	TTGTAAGTTGTCCTGTTTGAATGT	57.232	33.333	0.00	0.00	0.00	2.71
766	780	7.609918	TCAATATAGCTACTTTGTTTTGCTGGA	59.390	33.333	14.09	0.00	35.47	3.86
799	813	5.769484	TTCTTGTGATACTCTATCGGGTC	57.231	43.478	0.00	0.00	38.02	4.46
921	951	7.509546	AGTTATGCAAGCCTACATACATTACT	58.490	34.615	0.00	0.00	0.00	2.24
922	952	7.442364	AGTTATGCAAGCCTACATACATTACTG	59.558	37.037	0.00	0.00	29.29	2.74
940	970	7.281774	ACATTACTGGACTATCTTTCAAGCATG	59.718	37.037	0.00	0.00	0.00	4.06
1091	1121	8.845227	TCAACATATGTTTGAAAGTAAAGAGCA	58.155	29.630	18.50	0.00	35.83	4.26
1092	1122	9.630098	CAACATATGTTTGAAAGTAAAGAGCAT	57.370	29.630	18.50	0.00	35.83	3.79
1156	1186	7.249858	TGATATGGTCAACAAAATGTTCGATG	58.750	34.615	0.00	0.00	38.77	3.84
1328	1359	6.011122	AGATGGTTTTATCAGGAGCTTCAT	57.989	37.500	0.00	0.00	0.00	2.57
1459	1490	3.618019	GCAATTGGCACTGGATTTCATGT	60.618	43.478	7.72	0.00	43.97	3.21
1871	1909	9.720769	ATTCTCGACTTATCTTTTTAGTTCCAA	57.279	29.630	0.00	0.00	0.00	3.53
1922	1963	1.208259	TTGTAGCTGCGCGACATATG	58.792	50.000	12.10	0.00	42.94	1.78
2148	2202	4.224594	TCCTGAAGCTCTCAATGAGAACAT	59.775	41.667	14.44	2.58	45.39	2.71
2153	2207	4.505808	AGCTCTCAATGAGAACATGTCAG	58.494	43.478	14.44	1.24	45.39	3.51
2159	2213	6.370718	TCTCAATGAGAACATGTCAGTTGATG	59.629	38.462	10.99	0.00	35.59	3.07
2168	2222	5.603596	ACATGTCAGTTGATGCAAAATGTT	58.396	33.333	0.00	0.00	0.00	2.71
2352	2444	1.557269	AAGCAGGAGCCAATCGGACT	61.557	55.000	0.00	0.00	43.56	3.85
2392	2484	9.979270	TTTGTTTTTGTATTGCTAATTTGTGTG	57.021	25.926	0.00	0.00	0.00	3.82
2393	2485	8.709386	TGTTTTTGTATTGCTAATTTGTGTGT	57.291	26.923	0.00	0.00	0.00	3.72
2394	2486	8.598924	TGTTTTTGTATTGCTAATTTGTGTGTG	58.401	29.630	0.00	0.00	0.00	3.82
2395	2487	8.599774	GTTTTTGTATTGCTAATTTGTGTGTGT	58.400	29.630	0.00	0.00	0.00	3.72
2396	2488	7.691430	TTTGTATTGCTAATTTGTGTGTGTG	57.309	32.000	0.00	0.00	0.00	3.82
2397	2489	5.218885	TGTATTGCTAATTTGTGTGTGTGC	58.781	37.500	0.00	0.00	0.00	4.57
2398	2490	2.397777	TGCTAATTTGTGTGTGTGCG	57.602	45.000	0.00	0.00	0.00	5.34
2399	2491	1.673400	TGCTAATTTGTGTGTGTGCGT	59.327	42.857	0.00	0.00	0.00	5.24
2400	2492	2.043411	GCTAATTTGTGTGTGTGCGTG	58.957	47.619	0.00	0.00	0.00	5.34
2401	2493	2.540769	GCTAATTTGTGTGTGTGCGTGT	60.541	45.455	0.00	0.00	0.00	4.49
2402	2494	1.906757	AATTTGTGTGTGTGCGTGTG	58.093	45.000	0.00	0.00	0.00	3.82
2403	2495	0.525242	ATTTGTGTGTGTGCGTGTGC	60.525	50.000	0.00	0.00	43.20	4.57
2475	2569	4.458989	GGCATGATTTCTGTGTGTTTCCTA	59.541	41.667	0.00	0.00	0.00	2.94
2502	2754	7.002879	AGCATATTGTCTTTGCTCATTATCCT	58.997	34.615	0.00	0.00	42.88	3.24
2513	2765	8.635765	TTTGCTCATTATCCTAGTCTGTTTTT	57.364	30.769	0.00	0.00	0.00	1.94
2670	2935	3.504906	ACTGATCATGACCAGCAGTTTTG	59.495	43.478	17.57	0.00	36.49	2.44
2681	2946	2.416547	CAGCAGTTTTGATACTGGACCG	59.583	50.000	5.97	0.00	44.50	4.79
2683	2948	2.356135	CAGTTTTGATACTGGACCGGG	58.644	52.381	6.32	0.00	41.43	5.73
2684	2949	1.280998	AGTTTTGATACTGGACCGGGG	59.719	52.381	6.32	0.00	0.00	5.73
2685	2950	0.621609	TTTTGATACTGGACCGGGGG	59.378	55.000	6.32	0.00	0.00	5.40
2819	3085	2.559698	TTTCTGTCCTGAATTCGGCA	57.440	45.000	8.91	9.90	0.00	5.69
2827	3093	3.632145	GTCCTGAATTCGGCATACCAAAT	59.368	43.478	8.91	0.00	34.57	2.32
2893	3159	4.211164	TGTTGATCAAGCAACTACTTCACG	59.789	41.667	8.80	0.00	46.31	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	0.946221	CGAGCACCACTTCGCTTCTT	60.946	55.000	0.00	0.00	38.99	2.52
195	200	5.880164	TGGATTCAGGTATCATCGGTAAA	57.120	39.130	0.00	0.00	0.00	2.01
202	207	8.418662	CAAAACATTCATGGATTCAGGTATCAT	58.581	33.333	0.00	0.00	0.00	2.45
432	439	6.838382	AGAGAAAAACTAACATACCACCTGT	58.162	36.000	0.00	0.00	0.00	4.00
562	573	9.665719	ATTCAAACAGGACAACTTACAAAAATT	57.334	25.926	0.00	0.00	0.00	1.82
766	780	6.382570	AGAGTATCACAAGAAATGCTAGAGGT	59.617	38.462	0.00	0.00	37.82	3.85
921	951	3.523157	TCCCATGCTTGAAAGATAGTCCA	59.477	43.478	0.22	0.00	0.00	4.02
922	952	4.156455	TCCCATGCTTGAAAGATAGTCC	57.844	45.455	0.22	0.00	0.00	3.85
940	970	8.464404	ACTAAACTTCTTAACAGTTTTGTTCCC	58.536	33.333	11.53	0.00	44.00	3.97
1149	1179	1.745489	GCCACCAGGGACATCGAAC	60.745	63.158	0.00	0.00	40.01	3.95
1251	1282	9.118300	TCTATTTTGTTGATTGGCATTTTGTTT	57.882	25.926	0.00	0.00	0.00	2.83
1459	1490	0.537371	TGACGCTCTGACTCCTCACA	60.537	55.000	0.00	0.00	0.00	3.58
1670	1706	8.890718	CACAGTTGACTGATGATTCTCAATAAT	58.109	33.333	17.42	0.00	46.59	1.28
1877	1916	6.831727	TGCAGTTGAACAAATGATGAAAAG	57.168	33.333	17.03	0.00	38.53	2.27
1922	1963	1.274167	CATTGGCATATGGGGTGCATC	59.726	52.381	4.56	0.00	44.25	3.91
2148	2202	4.804665	CACAACATTTTGCATCAACTGACA	59.195	37.500	0.00	0.00	36.00	3.58
2159	2213	4.967437	TCAACTTTTGCACAACATTTTGC	58.033	34.783	0.00	0.00	36.00	3.68
2168	2222	1.134848	GCCTGGTTCAACTTTTGCACA	60.135	47.619	0.00	0.00	0.00	4.57
2404	2496	2.892542	TAGCACACACACACACGCGT	62.893	55.000	5.58	5.58	0.00	6.01
2405	2497	1.556591	ATAGCACACACACACACGCG	61.557	55.000	3.53	3.53	0.00	6.01
2406	2498	0.163788	GATAGCACACACACACACGC	59.836	55.000	0.00	0.00	0.00	5.34
2407	2499	1.783284	AGATAGCACACACACACACG	58.217	50.000	0.00	0.00	0.00	4.49
2572	2831	5.611796	TTCAGCTGCAAACATTACTACAG	57.388	39.130	9.47	0.00	0.00	2.74
2583	2842	7.452880	AATCTGTAGTAAATTCAGCTGCAAA	57.547	32.000	9.47	0.00	0.00	3.68
2670	2935	0.186873	TACTCCCCCGGTCCAGTATC	59.813	60.000	0.00	0.00	0.00	2.24
2680	2945	1.406887	CCACATCAGTTTACTCCCCCG	60.407	57.143	0.00	0.00	0.00	5.73
2681	2946	1.913419	TCCACATCAGTTTACTCCCCC	59.087	52.381	0.00	0.00	0.00	5.40
2683	2948	3.009143	AGGTTCCACATCAGTTTACTCCC	59.991	47.826	0.00	0.00	0.00	4.30
2684	2949	4.287766	AGGTTCCACATCAGTTTACTCC	57.712	45.455	0.00	0.00	0.00	3.85
2685	2950	5.998363	AGAAAGGTTCCACATCAGTTTACTC	59.002	40.000	0.00	0.00	0.00	2.59
2727	2993	5.105756	GCCAAAAGGACAATTAGCTACATGT	60.106	40.000	2.69	2.69	0.00	3.21
2737	3003	7.069455	ACAAGTTAACTAGCCAAAAGGACAATT	59.931	33.333	8.92	0.00	0.00	2.32
2819	3085	7.456269	TGAACAGGGAAAATTGGTATTTGGTAT	59.544	33.333	0.00	0.00	34.27	2.73
2827	3093	4.746466	ACCATGAACAGGGAAAATTGGTA	58.254	39.130	12.42	0.00	34.59	3.25
2854	3120	6.950842	TGATCAACAGAGTTGGTATTCAGAT	58.049	36.000	9.72	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.