AutoCloner

Multiple sequence alignment - TraesCS6A01G388100

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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	TraesCS6A01G388100	chr6A	100.000	2690	0	0	1	2690	604447343	604444654	0.000000e+00	4968
1	TraesCS6A01G388100	chr6A	85.681	859	101	14	845	1688	604537341	604538192	0.000000e+00	885
2	TraesCS6A01G388100	chr6A	83.865	564	82	4	1138	1692	604573547	604572984	1.830000e-146	529
3	TraesCS6A01G388100	chr6A	82.301	565	89	8	1138	1692	604455781	604455218	1.870000e-131	479
4	TraesCS6A01G388100	chr6D	95.065	1074	48	2	860	1933	457585601	457584533	0.000000e+00	1685
5	TraesCS6A01G388100	chr6D	85.748	849	105	10	845	1688	457629897	457630734	0.000000e+00	883
6	TraesCS6A01G388100	chr6D	93.783	563	31	3	1957	2518	457584463	457583904	0.000000e+00	843
7	TraesCS6A01G388100	chr6D	83.422	567	88	3	1116	1676	457593078	457592512	3.070000e-144	521
8	TraesCS6A01G388100	chr6B	92.606	1082	70	6	860	1933	696015996	696014917	0.000000e+00	1546
9	TraesCS6A01G388100	chr6B	92.662	695	48	3	137	829	43244118	43243425	0.000000e+00	998
10	TraesCS6A01G388100	chr6B	92.247	632	45	4	2061	2690	696014714	696014085	0.000000e+00	893
11	TraesCS6A01G388100	chr6B	86.059	746	94	5	941	1686	696079832	696080567	0.000000e+00	793
12	TraesCS6A01G388100	chr6B	81.092	714	102	16	997	1692	696099935	696099237	8.470000e-150	540
13	TraesCS6A01G388100	chr6B	91.129	124	6	4	1957	2075	696014851	696014728	2.140000e-36	163
14	TraesCS6A01G388100	chr5B	94.391	838	42	5	1	834	446410376	446411212	0.000000e+00	1282
15	TraesCS6A01G388100	chr5B	88.462	832	92	4	1	829	394008025	394008855	0.000000e+00	1002
16	TraesCS6A01G388100	chr7B	94.344	831	45	2	1	829	443325068	443325898	0.000000e+00	1273
17	TraesCS6A01G388100	chr3D	92.883	829	57	2	1	828	284850227	284849400	0.000000e+00	1203
18	TraesCS6A01G388100	chr5A	92.188	832	64	1	1	831	635563130	635563961	0.000000e+00	1175
19	TraesCS6A01G388100	chr3B	89.157	830	87	3	1	828	816087059	816087887	0.000000e+00	1031
20	TraesCS6A01G388100	chr2B	88.341	832	93	4	1	829	245813211	245812381	0.000000e+00	996
21	TraesCS6A01G388100	chr1B	87.995	833	95	5	1	829	288443726	288442895	0.000000e+00	979

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	TraesCS6A01G388100	chr6A	604444654	604447343	2689	True	4968.000000	4968	100.000	1	2690	1	chr6A.!!$R1	2689
1	TraesCS6A01G388100	chr6A	604537341	604538192	851	False	885.000000	885	85.681	845	1688	1	chr6A.!!$F1	843
2	TraesCS6A01G388100	chr6A	604572984	604573547	563	True	529.000000	529	83.865	1138	1692	1	chr6A.!!$R3	554
3	TraesCS6A01G388100	chr6A	604455218	604455781	563	True	479.000000	479	82.301	1138	1692	1	chr6A.!!$R2	554
4	TraesCS6A01G388100	chr6D	457583904	457585601	1697	True	1264.000000	1685	94.424	860	2518	2	chr6D.!!$R2	1658
5	TraesCS6A01G388100	chr6D	457629897	457630734	837	False	883.000000	883	85.748	845	1688	1	chr6D.!!$F1	843
6	TraesCS6A01G388100	chr6D	457592512	457593078	566	True	521.000000	521	83.422	1116	1676	1	chr6D.!!$R1	560
7	TraesCS6A01G388100	chr6B	43243425	43244118	693	True	998.000000	998	92.662	137	829	1	chr6B.!!$R1	692
8	TraesCS6A01G388100	chr6B	696014085	696015996	1911	True	867.333333	1546	91.994	860	2690	3	chr6B.!!$R3	1830
9	TraesCS6A01G388100	chr6B	696079832	696080567	735	False	793.000000	793	86.059	941	1686	1	chr6B.!!$F1	745
10	TraesCS6A01G388100	chr6B	696099237	696099935	698	True	540.000000	540	81.092	997	1692	1	chr6B.!!$R2	695
11	TraesCS6A01G388100	chr5B	446410376	446411212	836	False	1282.000000	1282	94.391	1	834	1	chr5B.!!$F2	833
12	TraesCS6A01G388100	chr5B	394008025	394008855	830	False	1002.000000	1002	88.462	1	829	1	chr5B.!!$F1	828
13	TraesCS6A01G388100	chr7B	443325068	443325898	830	False	1273.000000	1273	94.344	1	829	1	chr7B.!!$F1	828
14	TraesCS6A01G388100	chr3D	284849400	284850227	827	True	1203.000000	1203	92.883	1	828	1	chr3D.!!$R1	827
15	TraesCS6A01G388100	chr5A	635563130	635563961	831	False	1175.000000	1175	92.188	1	831	1	chr5A.!!$F1	830
16	TraesCS6A01G388100	chr3B	816087059	816087887	828	False	1031.000000	1031	89.157	1	828	1	chr3B.!!$F1	827
17	TraesCS6A01G388100	chr2B	245812381	245813211	830	True	996.000000	996	88.341	1	829	1	chr2B.!!$R1	828
18	TraesCS6A01G388100	chr1B	288442895	288443726	831	True	979.000000	979	87.995	1	829	1	chr1B.!!$R1	828

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
94	96	0.671472	CTCAACTGCATCCACGCTCA	60.671	55.0	0.0	0.0	0.0	4.26	F
1051	1076	0.969894	GATCCAGATACCTCCACCGG	59.030	60.0	0.0	0.0	0.0	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1212	1243	1.303317	GCCGTGGTTGGTGAAGGAT	60.303	57.895	0.00	0.0	0.0	3.24	R
2424	2556	0.319083	TAAAGGAGCGGCAACTTCGA	59.681	50.000	1.45	0.0	0.0	3.71	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
69	71	3.126000	GCTAGTGCTTGGTTTGATCTCAC	59.874	47.826	0.00	0.00	36.03	3.51
78	80	2.303022	GGTTTGATCTCACACTCCCTCA	59.697	50.000	0.00	0.00	0.00	3.86
94	96	0.671472	CTCAACTGCATCCACGCTCA	60.671	55.000	0.00	0.00	0.00	4.26
121	123	4.675671	GCCAGAGATATACTATGTGGCGAC	60.676	50.000	6.20	0.00	39.00	5.19
230	232	2.743928	GAGACCCAACAGCCGCTG	60.744	66.667	19.08	19.08	37.52	5.18
316	318	3.882326	CATGGATGGAGGCCGCCT	61.882	66.667	27.03	13.16	36.03	5.52
512	514	2.020720	TCTTTGCAAAACTTCGAGGCA	58.979	42.857	13.84	0.00	0.00	4.75
517	519	3.342719	TGCAAAACTTCGAGGCATATCA	58.657	40.909	0.00	0.00	0.00	2.15
643	645	8.634475	AGCTTAGTTGTGATTTTTCTGTTTTC	57.366	30.769	0.00	0.00	0.00	2.29
811	814	7.067494	ACACTTTTGTTGAATAAAGCTCTCTGT	59.933	33.333	0.00	0.00	35.31	3.41
990	1012	1.078708	CACGCCCATACCGAGGTTT	60.079	57.895	0.00	0.00	0.00	3.27
1051	1076	0.969894	GATCCAGATACCTCCACCGG	59.030	60.000	0.00	0.00	0.00	5.28
1479	1519	2.262915	CACTCCTTCTTCGCGGCT	59.737	61.111	6.13	0.00	0.00	5.52
1717	1760	5.759273	TGTTTCATGGCTTGGATTTTTCTTG	59.241	36.000	0.09	0.00	0.00	3.02
1906	1957	9.843874	GAACGAAAGGTAAATTTGAAATTGAAC	57.156	29.630	3.62	0.00	0.00	3.18
1933	1984	3.505386	ACCATGGAACCAAAGCATGTTA	58.495	40.909	21.47	0.00	0.00	2.41
1934	1985	3.900601	ACCATGGAACCAAAGCATGTTAA	59.099	39.130	21.47	0.00	0.00	2.01
1936	1987	4.931002	CCATGGAACCAAAGCATGTTAAAG	59.069	41.667	5.56	0.00	0.00	1.85
1938	1989	4.942852	TGGAACCAAAGCATGTTAAAGTG	58.057	39.130	0.00	0.00	0.00	3.16
1939	1990	4.646945	TGGAACCAAAGCATGTTAAAGTGA	59.353	37.500	0.00	0.00	0.00	3.41
1940	1991	5.127845	TGGAACCAAAGCATGTTAAAGTGAA	59.872	36.000	0.00	0.00	0.00	3.18
1941	1992	6.045955	GGAACCAAAGCATGTTAAAGTGAAA	58.954	36.000	0.00	0.00	0.00	2.69
1943	1994	5.971763	ACCAAAGCATGTTAAAGTGAAACA	58.028	33.333	0.00	0.00	41.43	2.83
1944	1995	6.581712	ACCAAAGCATGTTAAAGTGAAACAT	58.418	32.000	0.00	0.00	45.97	2.71
1946	1997	7.867403	ACCAAAGCATGTTAAAGTGAAACATAG	59.133	33.333	1.46	0.00	43.84	2.23
1947	1998	7.867403	CCAAAGCATGTTAAAGTGAAACATAGT	59.133	33.333	1.46	0.00	43.84	2.12
1948	1999	9.891828	CAAAGCATGTTAAAGTGAAACATAGTA	57.108	29.630	1.46	0.00	43.84	1.82
2130	2262	1.391157	TTGGGCTGAAACCACTGTGC	61.391	55.000	1.29	0.00	37.82	4.57
2143	2275	0.969149	ACTGTGCGTCTTCTGGATCA	59.031	50.000	0.00	0.00	0.00	2.92
2148	2280	1.067565	TGCGTCTTCTGGATCACTGAC	60.068	52.381	0.00	0.00	0.00	3.51
2176	2308	5.438761	ACCTTCGACTCATTTCCTTTTTG	57.561	39.130	0.00	0.00	0.00	2.44
2178	2310	5.215160	CCTTCGACTCATTTCCTTTTTGTG	58.785	41.667	0.00	0.00	0.00	3.33
2180	2312	5.168526	TCGACTCATTTCCTTTTTGTGTG	57.831	39.130	0.00	0.00	0.00	3.82
2184	2316	4.081752	ACTCATTTCCTTTTTGTGTGTGCA	60.082	37.500	0.00	0.00	0.00	4.57
2220	2352	9.911788	AAGATACAAGATAACAACCATCATTCT	57.088	29.630	0.00	0.00	0.00	2.40
2230	2362	3.004752	ACCATCATTCTAACTGCCACC	57.995	47.619	0.00	0.00	0.00	4.61
2449	2581	2.027192	AGTTGCCGCTCCTTTATCAGAA	60.027	45.455	0.00	0.00	0.00	3.02
2460	2592	2.871096	TTATCAGAACCGGCCAAACT	57.129	45.000	0.00	0.00	0.00	2.66
2463	2595	2.642154	TCAGAACCGGCCAAACTTTA	57.358	45.000	0.00	0.00	0.00	1.85
2473	2605	3.312421	CGGCCAAACTTTATCGATGACAT	59.688	43.478	8.54	0.00	0.00	3.06
2490	2622	8.642432	TCGATGACATCCAGAAAGTCTTAATAT	58.358	33.333	9.87	0.00	33.56	1.28
2493	2625	7.337938	TGACATCCAGAAAGTCTTAATATGCA	58.662	34.615	0.00	0.00	33.56	3.96
2499	2631	4.829492	AGAAAGTCTTAATATGCATGCCCC	59.171	41.667	16.68	0.00	0.00	5.80
2500	2632	3.160679	AGTCTTAATATGCATGCCCCC	57.839	47.619	16.68	0.00	0.00	5.40
2522	2654	4.083431	CCAAAGATCAGTGCTCAAGAGTTG	60.083	45.833	0.00	0.00	0.00	3.16
2527	2659	1.206072	GTGCTCAAGAGTTGCAGCG	59.794	57.895	0.00	0.00	37.39	5.18
2540	2672	2.434884	CAGCGGTCGCCAACTGAT	60.435	61.111	11.95	0.00	43.17	2.90
2565	2697	2.057922	AGAGTGTGACACCAAATCCCT	58.942	47.619	12.81	0.00	34.49	4.20
2586	2718	4.473199	CTTCATCTTGCACACACAATCAG	58.527	43.478	0.00	0.00	0.00	2.90
2610	2743	1.351017	CCTAAACTCAGCACCCCAAGA	59.649	52.381	0.00	0.00	0.00	3.02
2616	2749	1.672356	CAGCACCCCAAGAAGACGG	60.672	63.158	0.00	0.00	0.00	4.79
2644	2777	5.643421	ATTTAGCCAGAGTTCCATCATCT	57.357	39.130	0.00	0.00	0.00	2.90
2646	2779	2.761809	AGCCAGAGTTCCATCATCTCT	58.238	47.619	0.00	0.00	38.83	3.10
2647	2780	3.921104	AGCCAGAGTTCCATCATCTCTA	58.079	45.455	0.00	0.00	36.88	2.43
2649	2782	3.244044	GCCAGAGTTCCATCATCTCTACC	60.244	52.174	0.00	0.00	36.88	3.18
2678	2811	6.072452	ACAAAACTCGAGGAGGATTGAAATTC	60.072	38.462	18.41	0.00	34.93	2.17
2687	2820	4.201822	GGAGGATTGAAATTCGAAAGACCG	60.202	45.833	0.00	0.00	41.84	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	71	0.325933	TGGATGCAGTTGAGGGAGTG	59.674	55.000	0.00	0.00	0.00	3.51
78	80	1.028330	CCATGAGCGTGGATGCAGTT	61.028	55.000	2.49	0.00	42.02	3.16
94	96	4.718774	CCACATAGTATATCTCTGGCCCAT	59.281	45.833	0.00	0.00	0.00	4.00
121	123	1.067283	CGATCTTCATCCCTGATCCGG	60.067	57.143	0.00	0.00	34.70	5.14
171	173	3.451894	GGTTGCGGGAATGCCAGG	61.452	66.667	0.00	0.00	35.15	4.45
230	232	1.252215	GCCTCCCGGGTAGATCTAGC	61.252	65.000	22.86	21.30	37.43	3.42
231	233	0.612453	GGCCTCCCGGGTAGATCTAG	60.612	65.000	22.86	8.41	37.43	2.43
288	290	1.484653	TCCATCCATGACCTGGTAACG	59.515	52.381	0.00	0.00	46.08	3.18
316	318	7.862274	AGATATCTTGGTCATACCTGATTCA	57.138	36.000	0.00	0.00	39.58	2.57
517	519	5.188555	ACAGTCAGTCTCCATTATCACATGT	59.811	40.000	0.00	0.00	0.00	3.21
643	645	5.408299	TGACCTGTTTACATGTTGAATCTCG	59.592	40.000	2.30	0.00	0.00	4.04
842	846	2.279582	TGAGCGTTGCTTAGTCTAGC	57.720	50.000	0.00	0.00	39.88	3.42
843	847	3.549471	CACATGAGCGTTGCTTAGTCTAG	59.451	47.826	0.00	0.00	39.88	2.43
873	881	5.959594	TCCATTGATGATTCCAAAGTCCAAT	59.040	36.000	0.00	0.00	0.00	3.16
990	1012	4.634012	AGAAGTTGCCATTGTAGGTACA	57.366	40.909	0.00	0.00	0.00	2.90
1212	1243	1.303317	GCCGTGGTTGGTGAAGGAT	60.303	57.895	0.00	0.00	0.00	3.24
1328	1362	2.358267	CCGTAGTAGAGCTTTCCGTCAT	59.642	50.000	0.00	0.00	0.00	3.06
1446	1486	3.923864	TGCACGAAGTCCAGCGGT	61.924	61.111	0.00	0.00	41.61	5.68
1717	1760	8.996988	TCGATGTTGTACATTGTCTTAAAAAC	57.003	30.769	0.00	0.00	39.27	2.43
1872	1923	9.887406	TCAAATTTACCTTTCGTTCTTCATAAC	57.113	29.630	0.00	0.00	0.00	1.89
1906	1957	4.133820	TGCTTTGGTTCCATGGTATATCG	58.866	43.478	12.58	0.00	0.00	2.92
1968	2065	5.946377	ACAAAACAAATAACCCCTGCAAAAA	59.054	32.000	0.00	0.00	0.00	1.94
1975	2072	9.907229	TTTTAATGAACAAAACAAATAACCCCT	57.093	25.926	0.00	0.00	0.00	4.79
2026	2130	5.935789	GTGTTTTCTACAAGCCACTATGGTA	59.064	40.000	0.00	0.00	38.02	3.25
2075	2207	2.565391	TCATGCGTCTCTTTCCCTGTTA	59.435	45.455	0.00	0.00	0.00	2.41
2130	2262	3.303881	TTGTCAGTGATCCAGAAGACG	57.696	47.619	0.00	0.00	0.00	4.18
2143	2275	3.132289	TGAGTCGAAGGTTCTTTGTCAGT	59.868	43.478	0.00	0.00	0.00	3.41
2148	2280	4.757149	AGGAAATGAGTCGAAGGTTCTTTG	59.243	41.667	0.00	0.00	0.00	2.77
2176	2308	7.312154	TGTATCTTTGGAAAATATGCACACAC	58.688	34.615	0.00	0.00	0.00	3.82
2178	2310	8.243426	TCTTGTATCTTTGGAAAATATGCACAC	58.757	33.333	0.00	0.00	0.00	3.82
2220	2352	3.806949	AGAGGAATTTGGTGGCAGTTA	57.193	42.857	0.00	0.00	0.00	2.24
2230	2362	5.818136	TTCCTTTGCGATAGAGGAATTTG	57.182	39.130	1.94	0.00	42.90	2.32
2282	2414	3.378427	GGTCCTTCTCGCAAAAATAGCAT	59.622	43.478	0.00	0.00	0.00	3.79
2424	2556	0.319083	TAAAGGAGCGGCAACTTCGA	59.681	50.000	1.45	0.00	0.00	3.71
2449	2581	2.014128	CATCGATAAAGTTTGGCCGGT	58.986	47.619	1.90	0.00	0.00	5.28
2460	2592	6.878317	AGACTTTCTGGATGTCATCGATAAA	58.122	36.000	6.74	7.33	35.47	1.40
2463	2595	5.350504	AAGACTTTCTGGATGTCATCGAT	57.649	39.130	6.74	0.00	35.47	3.59
2473	2605	5.532406	GGCATGCATATTAAGACTTTCTGGA	59.468	40.000	21.36	0.00	0.00	3.86
2490	2622	0.685131	CTGATCTTTGGGGGCATGCA	60.685	55.000	21.36	0.00	0.00	3.96
2493	2625	0.685458	GCACTGATCTTTGGGGGCAT	60.685	55.000	0.00	0.00	0.00	4.40
2499	2631	3.672808	ACTCTTGAGCACTGATCTTTGG	58.327	45.455	0.00	0.00	0.00	3.28
2500	2632	4.613167	GCAACTCTTGAGCACTGATCTTTG	60.613	45.833	0.00	0.00	0.00	2.77
2527	2659	0.798776	CTTCACATCAGTTGGCGACC	59.201	55.000	0.00	0.00	0.00	4.79
2540	2672	3.342377	TTTGGTGTCACACTCTTCACA	57.658	42.857	8.12	0.00	34.40	3.58
2565	2697	4.136051	TCTGATTGTGTGTGCAAGATGAA	58.864	39.130	0.00	0.00	0.00	2.57
2586	2718	2.160205	GGGGTGCTGAGTTTAGGTTTC	58.840	52.381	0.00	0.00	0.00	2.78
2610	2743	1.751437	GGCTAAATTCCTGCCGTCTT	58.249	50.000	0.00	0.00	37.11	3.01
2616	2749	2.685388	GGAACTCTGGCTAAATTCCTGC	59.315	50.000	0.00	0.00	36.65	4.85
2634	2767	3.459828	TGTTGGGGTAGAGATGATGGAA	58.540	45.455	0.00	0.00	0.00	3.53
2644	2777	2.038033	CCTCGAGTTTTGTTGGGGTAGA	59.962	50.000	12.31	0.00	0.00	2.59
2646	2779	2.038033	CTCCTCGAGTTTTGTTGGGGTA	59.962	50.000	12.31	0.00	0.00	3.69
2647	2780	0.841289	TCCTCGAGTTTTGTTGGGGT	59.159	50.000	12.31	0.00	0.00	4.95
2649	2782	1.071699	TCCTCCTCGAGTTTTGTTGGG	59.928	52.381	12.31	1.86	0.00	4.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.