AutoCloner

Multiple sequence alignment - TraesCS6A01G388200

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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	TraesCS6A01G388200	chr6A	100.000	2687	0	0	1	2687	604459235	604456549	0.000000e+00	4963.0
1	TraesCS6A01G388200	chr6A	86.121	562	78	0	1120	1681	604573547	604572986	8.230000e-170	606.0
2	TraesCS6A01G388200	chr6A	100.000	30	0	0	770	799	604458390	604458361	3.740000e-04	56.5
3	TraesCS6A01G388200	chr6A	100.000	30	0	0	846	875	604458466	604458437	3.740000e-04	56.5
4	TraesCS6A01G388200	chr6D	94.383	1727	83	6	968	2687	457593208	457591489	0.000000e+00	2639.0
5	TraesCS6A01G388200	chr6D	89.609	972	69	24	1	967	457594195	457593251	0.000000e+00	1206.0
6	TraesCS6A01G388200	chr6D	80.116	689	107	17	997	1664	457585464	457584785	1.120000e-133	486.0
7	TraesCS6A01G388200	chr6D	79.221	231	41	6	78	307	457640500	457640276	1.290000e-33	154.0
8	TraesCS6A01G388200	chr6B	91.212	1320	90	15	1379	2687	696023084	696021780	0.000000e+00	1772.0
9	TraesCS6A01G388200	chr6B	90.306	588	43	8	91	674	696023659	696023082	0.000000e+00	758.0
10	TraesCS6A01G388200	chr6B	81.909	702	107	10	996	1681	696099936	696099239	2.320000e-160	575.0
11	TraesCS6A01G388200	chr2A	84.495	832	124	5	1002	1831	23864362	23865190	0.000000e+00	817.0
12	TraesCS6A01G388200	chr2A	75.890	618	75	42	2079	2662	23827128	23827705	5.740000e-62	248.0
13	TraesCS6A01G388200	chr2A	100.000	32	0	0	895	926	23828241	23828272	2.890000e-05	60.2
14	TraesCS6A01G388200	chr2D	85.432	556	81	0	1117	1672	21642632	21643187	1.790000e-161	579.0
15	TraesCS6A01G388200	chr2D	84.536	582	83	5	1117	1692	21681444	21682024	1.080000e-158	569.0
16	TraesCS6A01G388200	chr2D	84.712	556	85	0	1117	1672	21621125	21621680	8.400000e-155	556.0
17	TraesCS6A01G388200	chr2D	75.425	765	104	49	1949	2677	21618387	21619103	7.270000e-76	294.0
18	TraesCS6A01G388200	chr2D	74.106	587	93	37	1968	2530	21744101	21744652	1.270000e-43	187.0
19	TraesCS6A01G388200	chr2D	73.765	587	91	40	1968	2530	21771836	21772383	3.560000e-39	172.0
20	TraesCS6A01G388200	chr2D	95.000	40	2	0	895	934	21619585	21619624	2.230000e-06	63.9
21	TraesCS6A01G388200	chr2D	95.000	40	2	0	895	934	21642300	21642339	2.230000e-06	63.9
22	TraesCS6A01G388200	chr2B	84.256	578	86	3	1120	1692	34864324	34863747	2.340000e-155	558.0
23	TraesCS6A01G388200	chr2B	95.000	40	2	0	895	934	34864659	34864620	2.230000e-06	63.9

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	TraesCS6A01G388200	chr6A	604456549	604459235	2686	True	1692.000000	4963	100.000000	1	2687	3	chr6A.!!$R2	2686
1	TraesCS6A01G388200	chr6A	604572986	604573547	561	True	606.000000	606	86.121000	1120	1681	1	chr6A.!!$R1	561
2	TraesCS6A01G388200	chr6D	457591489	457594195	2706	True	1922.500000	2639	91.996000	1	2687	2	chr6D.!!$R3	2686
3	TraesCS6A01G388200	chr6D	457584785	457585464	679	True	486.000000	486	80.116000	997	1664	1	chr6D.!!$R1	667
4	TraesCS6A01G388200	chr6B	696021780	696023659	1879	True	1265.000000	1772	90.759000	91	2687	2	chr6B.!!$R2	2596
5	TraesCS6A01G388200	chr6B	696099239	696099936	697	True	575.000000	575	81.909000	996	1681	1	chr6B.!!$R1	685
6	TraesCS6A01G388200	chr2A	23864362	23865190	828	False	817.000000	817	84.495000	1002	1831	1	chr2A.!!$F1	829
7	TraesCS6A01G388200	chr2D	21681444	21682024	580	False	569.000000	569	84.536000	1117	1692	1	chr2D.!!$F1	575
8	TraesCS6A01G388200	chr2D	21642300	21643187	887	False	321.450000	579	90.216000	895	1672	2	chr2D.!!$F5	777
9	TraesCS6A01G388200	chr2D	21618387	21621680	3293	False	304.633333	556	85.045667	895	2677	3	chr2D.!!$F4	1782
10	TraesCS6A01G388200	chr2B	34863747	34864659	912	True	310.950000	558	89.628000	895	1692	2	chr2B.!!$R1	797

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
674	681	0.398239	CAGGCTGGGGAGATCAGAGA	60.398	60.000	6.61	0.0	34.36	3.10	F
1461	3154	2.036346	GGACTTTGTGCATGCCTTCTTT	59.964	45.455	16.68	0.0	0.00	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1549	3242	0.819259	AGCGGCAAGTTCTTGAGCAA	60.819	50.0	23.55	0.0	32.34	3.91	R
2519	4229	5.476599	TGGAGGGACACAAAACATATTCAAG	59.523	40.0	0.00	0.0	0.00	3.02	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
66	67	2.850695	TACCCCAAAACAACACCCTT	57.149	45.000	0.00	0.00	0.00	3.95
86	87	8.778358	CACCCTTCTACATGCTCTAAATTAATC	58.222	37.037	0.00	0.00	0.00	1.75
116	117	5.646360	GCGCATATAATACCCCAAATACACT	59.354	40.000	0.30	0.00	0.00	3.55
124	125	1.074727	CCCCAAATACACTGGACCACA	59.925	52.381	0.00	0.00	35.85	4.17
130	131	5.475220	CCAAATACACTGGACCACAAATACA	59.525	40.000	0.00	0.00	35.85	2.29
155	156	6.692681	ACAAAATTGATTATCGGAAATCAGCG	59.307	34.615	11.46	0.00	44.43	5.18
160	161	3.520290	TTATCGGAAATCAGCGTCAGT	57.480	42.857	0.00	0.00	0.00	3.41
357	362	6.256539	ACGCCGAATATTTCTATGATGCATAG	59.743	38.462	0.00	7.89	43.52	2.23
370	375	9.554395	TCTATGATGCATAGATTAACCGAAAAA	57.446	29.630	11.90	0.00	45.13	1.94
426	431	1.666209	AAAATCTTGATGGGGCGCCG	61.666	55.000	22.54	4.34	0.00	6.46
483	488	9.537192	CCATATACAAACAAAATCTGAATGCAT	57.463	29.630	0.00	0.00	0.00	3.96
562	567	1.990060	TCTTCCCCAAGAGGCTCCG	60.990	63.158	11.71	2.38	33.38	4.63
674	681	0.398239	CAGGCTGGGGAGATCAGAGA	60.398	60.000	6.61	0.00	34.36	3.10
741	748	8.321353	TGATGATTAGCTAGTTTTCTTTCCTCA	58.679	33.333	0.00	0.00	0.00	3.86
759	766	2.634940	CTCACCTTCCTGGAAGAAGACA	59.365	50.000	32.80	13.62	45.08	3.41
766	773	5.104360	CCTTCCTGGAAGAAGACATCCATAA	60.104	44.000	32.80	0.00	45.08	1.90
768	775	5.032846	TCCTGGAAGAAGACATCCATAACT	58.967	41.667	0.00	0.00	41.95	2.24
770	777	6.012508	TCCTGGAAGAAGACATCCATAACTTT	60.013	38.462	0.00	0.00	41.95	2.66
771	778	6.317391	CCTGGAAGAAGACATCCATAACTTTC	59.683	42.308	0.00	0.00	41.95	2.62
773	780	7.405292	TGGAAGAAGACATCCATAACTTTCAT	58.595	34.615	0.00	0.00	38.70	2.57
774	781	7.337689	TGGAAGAAGACATCCATAACTTTCATG	59.662	37.037	0.00	0.00	38.70	3.07
775	782	7.337942	GGAAGAAGACATCCATAACTTTCATGT	59.662	37.037	0.00	0.00	34.46	3.21
776	783	7.856145	AGAAGACATCCATAACTTTCATGTC	57.144	36.000	2.73	2.73	42.45	3.06
777	784	7.397221	AGAAGACATCCATAACTTTCATGTCA	58.603	34.615	11.77	0.00	43.88	3.58
778	785	8.051535	AGAAGACATCCATAACTTTCATGTCAT	58.948	33.333	11.77	1.23	43.88	3.06
781	788	8.489489	AGACATCCATAACTTTCATGTCATACT	58.511	33.333	11.77	0.00	43.88	2.12
799	806	9.448438	TGTCATACTAATTCAATTACAGCTTGT	57.552	29.630	0.00	0.00	0.00	3.16
819	826	9.305925	AGCTTGTTTAATTAATTATCAGCTTGC	57.694	29.630	17.19	15.22	0.00	4.01
820	827	9.086336	GCTTGTTTAATTAATTATCAGCTTGCA	57.914	29.630	8.70	0.00	0.00	4.08
884	908	6.633500	TCAATTACAGCTTGCACTAACTTT	57.367	33.333	0.00	0.00	0.00	2.66
885	909	6.668323	TCAATTACAGCTTGCACTAACTTTC	58.332	36.000	0.00	0.00	0.00	2.62
888	912	4.292977	ACAGCTTGCACTAACTTTCAAC	57.707	40.909	0.00	0.00	0.00	3.18
891	915	5.237344	ACAGCTTGCACTAACTTTCAACTAG	59.763	40.000	0.00	0.00	0.00	2.57
985	2642	6.151144	GCCTATACCCAAATTAAATCGAGCAT	59.849	38.462	0.00	0.00	0.00	3.79
986	2643	7.335924	GCCTATACCCAAATTAAATCGAGCATA	59.664	37.037	0.00	0.00	0.00	3.14
1059	2716	5.102953	TCCAGATAACTCCACCAATCAAG	57.897	43.478	0.00	0.00	0.00	3.02
1079	2748	7.809546	TCAAGAACGATGATAGTGAGATAGT	57.190	36.000	0.00	0.00	0.00	2.12
1086	2755	9.557061	AACGATGATAGTGAGATAGTAGTTACA	57.443	33.333	0.00	0.00	0.00	2.41
1232	2922	2.432628	GTGCGAGACCTCCAACCG	60.433	66.667	0.00	0.00	0.00	4.44
1293	2983	2.037772	GTGCCTCTTCTTCTCCTTCACA	59.962	50.000	0.00	0.00	0.00	3.58
1408	3098	2.505819	AGGCAGGAGTGGAACGATATTT	59.494	45.455	0.00	0.00	45.86	1.40
1411	3101	4.439057	GCAGGAGTGGAACGATATTTACA	58.561	43.478	0.00	0.00	45.86	2.41
1425	3115	7.553334	ACGATATTTACAAGTTTCAGAGGCTA	58.447	34.615	0.00	0.00	0.00	3.93
1446	3139	2.750350	CTCGGGCCACTGGACTTT	59.250	61.111	4.39	0.00	0.00	2.66
1461	3154	2.036346	GGACTTTGTGCATGCCTTCTTT	59.964	45.455	16.68	0.00	0.00	2.52
1511	3204	2.502080	CGACGTCGGACTGCAGAC	60.502	66.667	29.70	15.15	36.11	3.51
1549	3242	2.430367	GCGGGAACACCCAAGAGT	59.570	61.111	6.12	0.00	43.64	3.24
1805	3502	4.329638	TGATGGGGTGGATGTTGTTATT	57.670	40.909	0.00	0.00	0.00	1.40
1811	3508	4.526650	GGGGTGGATGTTGTTATTGTTTCT	59.473	41.667	0.00	0.00	0.00	2.52
1907	3610	0.982673	GTGTGCGTGTGTAGACGATC	59.017	55.000	5.71	0.00	42.10	3.69
1920	3623	1.202582	AGACGATCGGTTTCCTGACAG	59.797	52.381	20.98	0.00	0.00	3.51
1963	3666	4.439305	TCTTGCATCTTGTTTGGCATAC	57.561	40.909	0.75	0.75	35.98	2.39
2169	3872	8.945057	AGAGATTTTCTGCTAAGAAGTCAATTC	58.055	33.333	0.00	0.00	43.27	2.17
2259	3962	9.981114	TCTGCTTTAAGATCGATTGATGTTATA	57.019	29.630	12.15	7.75	39.33	0.98
2344	4053	4.172807	ACCTTACACTTCTTCCATACCCA	58.827	43.478	0.00	0.00	0.00	4.51
2345	4054	4.019591	ACCTTACACTTCTTCCATACCCAC	60.020	45.833	0.00	0.00	0.00	4.61
2346	4055	4.225267	CCTTACACTTCTTCCATACCCACT	59.775	45.833	0.00	0.00	0.00	4.00
2348	4057	4.287766	ACACTTCTTCCATACCCACTTC	57.712	45.455	0.00	0.00	0.00	3.01
2349	4058	3.650942	ACACTTCTTCCATACCCACTTCA	59.349	43.478	0.00	0.00	0.00	3.02
2350	4059	4.289672	ACACTTCTTCCATACCCACTTCAT	59.710	41.667	0.00	0.00	0.00	2.57
2452	4162	6.613153	TGGGATAAACACTTAAATTTGGGG	57.387	37.500	0.00	0.00	0.00	4.96
2519	4229	7.500807	ACTCGATTGTGTAAAACAACAAAAC	57.499	32.000	0.00	0.00	44.97	2.43
2542	4252	5.476945	ACTTGAATATGTTTTGTGTCCCTCC	59.523	40.000	0.00	0.00	0.00	4.30
2636	4346	1.340991	CCACGAGGATCAAACCCCAAT	60.341	52.381	0.00	0.00	36.89	3.16
2666	4376	4.672542	GCGCTTTGATTTCTCATTAGTGCA	60.673	41.667	0.00	0.00	42.96	4.57
2684	4394	5.804639	AGTGCAAGTATTCTTCACATGGTA	58.195	37.500	0.00	0.00	35.86	3.25

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	4.773149	GGTGTTGTTTTGGGGTATTATGGA	59.227	41.667	0.00	0.00	0.00	3.41
86	87	5.276461	TGGGGTATTATATGCGCATAGAG	57.724	43.478	31.57	0.00	0.00	2.43
116	117	6.471233	TCAATTTTGTGTATTTGTGGTCCA	57.529	33.333	0.00	0.00	0.00	4.02
130	131	6.692681	CGCTGATTTCCGATAATCAATTTTGT	59.307	34.615	11.55	0.00	42.29	2.83
155	156	6.341316	TCATGGAAGAATGTTAGCTACTGAC	58.659	40.000	0.00	0.00	0.00	3.51
402	407	3.130340	GCGCCCCATCAAGATTTTCTTTA	59.870	43.478	0.00	0.00	33.78	1.85
404	409	1.478105	GCGCCCCATCAAGATTTTCTT	59.522	47.619	0.00	0.00	37.14	2.52
405	410	1.106285	GCGCCCCATCAAGATTTTCT	58.894	50.000	0.00	0.00	0.00	2.52
406	411	0.103026	GGCGCCCCATCAAGATTTTC	59.897	55.000	18.11	0.00	0.00	2.29
426	431	8.060090	GCATTAACATACACCTTGTTCGTATAC	58.940	37.037	0.00	0.00	38.26	1.47
483	488	4.161565	ACCGTTGAATATGTAGGAGCTTCA	59.838	41.667	0.00	0.00	0.00	3.02
562	567	0.527385	TGCTTGCACCAAAAAGACGC	60.527	50.000	0.00	0.00	0.00	5.19
564	569	1.199624	CGTGCTTGCACCAAAAAGAC	58.800	50.000	18.48	0.00	0.00	3.01
610	617	3.882888	TGAAAACGATGAAGCAGAACCTT	59.117	39.130	0.00	0.00	0.00	3.50
698	705	7.578310	AATCATCAGCTTGTGCATAAGTATT	57.422	32.000	22.26	10.91	42.74	1.89
702	709	5.450171	GCTAATCATCAGCTTGTGCATAAG	58.550	41.667	18.06	18.06	42.74	1.73
741	748	2.573915	GGATGTCTTCTTCCAGGAAGGT	59.426	50.000	26.42	8.23	41.94	3.50
770	777	9.836864	AGCTGTAATTGAATTAGTATGACATGA	57.163	29.630	0.00	0.00	0.00	3.07
773	780	9.448438	ACAAGCTGTAATTGAATTAGTATGACA	57.552	29.630	0.00	0.00	0.00	3.58
793	800	9.305925	GCAAGCTGATAATTAATTAAACAAGCT	57.694	29.630	20.42	20.42	0.00	3.74
794	801	9.086336	TGCAAGCTGATAATTAATTAAACAAGC	57.914	29.630	11.80	15.71	0.00	4.01
801	808	9.104965	ACGTTAGTGCAAGCTGATAATTAATTA	57.895	29.630	10.27	10.27	0.00	1.40
802	809	7.910162	CACGTTAGTGCAAGCTGATAATTAATT	59.090	33.333	5.89	5.89	41.94	1.40
803	810	7.409697	CACGTTAGTGCAAGCTGATAATTAAT	58.590	34.615	0.00	0.00	41.94	1.40
804	811	6.771076	CACGTTAGTGCAAGCTGATAATTAA	58.229	36.000	0.00	0.00	41.94	1.40
806	813	5.221891	CACGTTAGTGCAAGCTGATAATT	57.778	39.130	0.00	0.00	41.94	1.40
807	814	4.864916	CACGTTAGTGCAAGCTGATAAT	57.135	40.909	0.00	0.00	41.94	1.28
884	908	5.623956	ACTCTCTAGCTAGCTCTAGTTGA	57.376	43.478	23.26	14.63	37.78	3.18
885	909	5.820423	TCAACTCTCTAGCTAGCTCTAGTTG	59.180	44.000	31.31	31.31	37.78	3.16
888	912	6.055588	ACTTCAACTCTCTAGCTAGCTCTAG	58.944	44.000	23.26	19.14	37.87	2.43
891	915	4.036380	GGACTTCAACTCTCTAGCTAGCTC	59.964	50.000	23.26	1.01	0.00	4.09
985	2642	8.880244	AGAAGATGCCATGGTATTTATGTACTA	58.120	33.333	17.13	0.00	0.00	1.82
986	2643	7.749666	AGAAGATGCCATGGTATTTATGTACT	58.250	34.615	17.13	4.53	0.00	2.73
999	2656	4.575645	GGAGAAGAAGAAGAAGATGCCATG	59.424	45.833	0.00	0.00	0.00	3.66
1079	2748	0.037697	CACTGCCGTGCCTGTAACTA	60.038	55.000	0.00	0.00	33.82	2.24
1168	2858	2.304092	CAATGCCTGGTATGTGAGCAT	58.696	47.619	0.00	0.00	45.68	3.79
1293	2983	1.474478	CGGTGACTGACTATGCTGTCT	59.526	52.381	0.00	0.00	37.55	3.41
1432	3125	2.564721	GCACAAAGTCCAGTGGCCC	61.565	63.158	3.51	0.00	36.29	5.80
1446	3139	1.164411	CCGTAAAGAAGGCATGCACA	58.836	50.000	21.36	0.00	0.00	4.57
1461	3154	1.004679	GAGGAAAACCACGGCCGTA	60.005	57.895	33.70	0.00	0.00	4.02
1511	3204	2.125512	CGTCCGGGAAGAAGCAGG	60.126	66.667	3.68	0.00	0.00	4.85
1549	3242	0.819259	AGCGGCAAGTTCTTGAGCAA	60.819	50.000	23.55	0.00	32.34	3.91
1769	3466	6.475504	CACCCCATCATATTTACATGCTAGA	58.524	40.000	0.00	0.00	0.00	2.43
1907	3610	1.594293	ACGCACTGTCAGGAAACCG	60.594	57.895	4.53	2.08	0.00	4.44
1963	3666	9.506018	TGACATAATGGAACTATATTGTCATGG	57.494	33.333	0.00	0.00	0.00	3.66
2047	3750	8.452534	CAGCCATGCAAATTTTATTACACATTT	58.547	29.630	0.00	0.00	0.00	2.32
2162	3865	6.494893	TGCTTACATACTTGTGGAATTGAC	57.505	37.500	0.00	0.00	36.53	3.18
2169	3872	5.918608	ACTAGGATGCTTACATACTTGTGG	58.081	41.667	4.85	0.00	45.89	4.17
2452	4162	8.586273	CACATACAATTATTTTTGTGTAGCTGC	58.414	33.333	0.00	0.00	40.00	5.25
2519	4229	5.476599	TGGAGGGACACAAAACATATTCAAG	59.523	40.000	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.