AutoCloner

Multiple sequence alignment - TraesCS6B01G034800

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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	TraesCS6B01G034800	chr6B	100.000	3043	0	0	1	3043	20836463	20833421	0.000000e+00	5620.0
1	TraesCS6B01G034800	chr6B	91.325	2951	220	19	2	2923	20933017	20930074	0.000000e+00	3999.0
2	TraesCS6B01G034800	chr6B	88.570	2791	272	31	2	2765	20701268	20698498	0.000000e+00	3343.0
3	TraesCS6B01G034800	chr6B	85.905	2994	329	57	12	2951	20962570	20959616	0.000000e+00	3105.0
4	TraesCS6B01G034800	chr6B	90.982	2118	174	12	906	3014	20879353	20877244	0.000000e+00	2837.0
5	TraesCS6B01G034800	chr6B	86.893	412	41	7	2	402	20880229	20879820	1.660000e-122	449.0
6	TraesCS6B01G034800	chr6B	91.156	294	25	1	2751	3043	20698485	20698192	6.110000e-107	398.0
7	TraesCS6B01G034800	chr6D	90.976	2859	214	22	127	2951	11071565	11068717	0.000000e+00	3810.0
8	TraesCS6B01G034800	chr6D	85.099	2973	374	44	1	2923	20761521	20758568	0.000000e+00	2972.0
9	TraesCS6B01G034800	chr6D	90.566	53	1	1	1	49	11072114	11072062	1.960000e-07	67.6
10	TraesCS6B01G034800	chr3A	78.738	1632	302	35	1052	2668	21006624	21008225	0.000000e+00	1050.0
11	TraesCS6B01G034800	chr7B	77.177	1516	299	34	1059	2547	666511982	666510487	0.000000e+00	839.0
12	TraesCS6B01G034800	chr7B	76.225	816	163	25	1059	1855	666506855	666506052	1.310000e-108	403.0
13	TraesCS6B01G034800	chr7D	78.663	778	149	13	1362	2132	575596200	575596967	4.530000e-138	501.0

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	TraesCS6B01G034800	chr6B	20833421	20836463	3042	True	5620.0	5620	100.0000	1	3043	1	chr6B.!!$R1	3042
1	TraesCS6B01G034800	chr6B	20930074	20933017	2943	True	3999.0	3999	91.3250	2	2923	1	chr6B.!!$R2	2921
2	TraesCS6B01G034800	chr6B	20959616	20962570	2954	True	3105.0	3105	85.9050	12	2951	1	chr6B.!!$R3	2939
3	TraesCS6B01G034800	chr6B	20698192	20701268	3076	True	1870.5	3343	89.8630	2	3043	2	chr6B.!!$R4	3041
4	TraesCS6B01G034800	chr6B	20877244	20880229	2985	True	1643.0	2837	88.9375	2	3014	2	chr6B.!!$R5	3012
5	TraesCS6B01G034800	chr6D	20758568	20761521	2953	True	2972.0	2972	85.0990	1	2923	1	chr6D.!!$R1	2922
6	TraesCS6B01G034800	chr6D	11068717	11072114	3397	True	1938.8	3810	90.7710	1	2951	2	chr6D.!!$R2	2950
7	TraesCS6B01G034800	chr3A	21006624	21008225	1601	False	1050.0	1050	78.7380	1052	2668	1	chr3A.!!$F1	1616
8	TraesCS6B01G034800	chr7B	666506052	666511982	5930	True	621.0	839	76.7010	1059	2547	2	chr7B.!!$R1	1488
9	TraesCS6B01G034800	chr7D	575596200	575596967	767	False	501.0	501	78.6630	1362	2132	1	chr7D.!!$F1	770

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
457	902	0.788391	CGGTGCGAGTACCAAAAGAC	59.212	55.0	10.77	0.0	40.89	3.01	F
459	904	0.788391	GTGCGAGTACCAAAAGACGG	59.212	55.0	0.00	0.0	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1791	2335	2.038295	CCCAGGACAAGATAGAGATGCC	59.962	54.545	0.0	0.0	0.0	4.40	R
2217	2761	2.851195	TGTTGCTTCCTCCAGAACTTC	58.149	47.619	0.0	0.0	0.0	3.01	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
55	63	9.706529	AAAGCTCTAATTCCCTTGAATAGAATT	57.293	29.630	7.44	7.44	40.34	2.17
68	76	7.116805	CCTTGAATAGAATTTGAGTGTTTTGGC	59.883	37.037	0.00	0.00	0.00	4.52
79	87	3.153919	AGTGTTTTGGCCGTGACATTAT	58.846	40.909	7.95	0.00	0.00	1.28
80	88	4.328536	AGTGTTTTGGCCGTGACATTATA	58.671	39.130	7.95	0.00	0.00	0.98
99	131	7.070821	ACATTATACGTTGGGATCTTTAGGAGT	59.929	37.037	0.00	0.00	0.00	3.85
100	132	5.952347	ATACGTTGGGATCTTTAGGAGTT	57.048	39.130	0.00	0.00	0.00	3.01
109	143	6.180472	GGGATCTTTAGGAGTTTTGATCACA	58.820	40.000	0.00	0.00	35.25	3.58
172	604	9.810545	GAGAGGTAATATTAAGATAGATGCACC	57.189	37.037	0.00	0.00	0.00	5.01
185	618	3.016736	AGATGCACCGACCTTTTTATGG	58.983	45.455	0.00	0.00	0.00	2.74
245	678	3.713764	CTCTAGATGGTGTGGGGAAATCT	59.286	47.826	0.00	0.00	0.00	2.40
301	734	4.583907	TGTTCAGCAAGGATGTCATTTCAA	59.416	37.500	0.00	0.00	0.00	2.69
318	751	8.124199	GTCATTTCAACTCAATTGCACAAATTT	58.876	29.630	0.00	0.00	36.28	1.82
349	782	1.004745	GCCCTCCAGTTTCCTCATGAA	59.995	52.381	0.00	0.00	0.00	2.57
434	879	6.786967	ACAACTTATATGACGAAGGGTACT	57.213	37.500	0.00	0.00	0.00	2.73
437	882	7.548075	ACAACTTATATGACGAAGGGTACTTTG	59.452	37.037	0.00	0.00	42.71	2.77
451	896	1.666553	CTTTGCGGTGCGAGTACCA	60.667	57.895	10.77	0.00	40.89	3.25
457	902	0.788391	CGGTGCGAGTACCAAAAGAC	59.212	55.000	10.77	0.00	40.89	3.01
458	903	0.788391	GGTGCGAGTACCAAAAGACG	59.212	55.000	5.48	0.00	40.54	4.18
459	904	0.788391	GTGCGAGTACCAAAAGACGG	59.212	55.000	0.00	0.00	0.00	4.79
461	906	1.612950	TGCGAGTACCAAAAGACGGTA	59.387	47.619	0.00	0.00	37.99	4.02
462	907	2.231964	TGCGAGTACCAAAAGACGGTAT	59.768	45.455	0.00	0.00	41.00	2.73
474	919	6.874134	CCAAAAGACGGTATCCTCTATATTGG	59.126	42.308	0.00	0.00	0.00	3.16
476	921	4.673968	AGACGGTATCCTCTATATTGGCA	58.326	43.478	0.00	0.00	0.00	4.92
483	928	3.928754	TCCTCTATATTGGCACTGAGGT	58.071	45.455	15.28	0.00	41.14	3.85
599	1044	1.963515	GCTTGGGTGTCAACTCCAAAT	59.036	47.619	3.86	0.00	36.67	2.32
601	1046	1.993956	TGGGTGTCAACTCCAAATGG	58.006	50.000	3.86	0.00	0.00	3.16
645	1090	1.891919	GTGTGGCAGGCTTTGACGA	60.892	57.895	0.00	0.00	37.78	4.20
682	1164	2.603075	ATGGGTGCAAAGGTACACAT	57.397	45.000	0.00	0.00	46.83	3.21
692	1174	4.635765	GCAAAGGTACACATTGCATCTCTA	59.364	41.667	18.78	0.00	46.57	2.43
774	1287	3.508762	TCGCATACCTTTTCGAGAAGTC	58.491	45.455	14.01	0.00	0.00	3.01
887	1415	5.530915	TGCACATGGTATCCTGTAAATAAGC	59.469	40.000	0.00	0.00	0.00	3.09
1492	2035	9.778741	TGACAACACTAAGATTTTCTCACTATT	57.221	29.630	0.00	0.00	0.00	1.73
1672	2216	2.596851	TTGCAGTCCTCTCCCAGGC	61.597	63.158	0.00	0.00	43.08	4.85
1674	2218	3.028921	GCAGTCCTCTCCCAGGCAG	62.029	68.421	0.00	0.00	43.08	4.85
1791	2335	4.679373	ATCCTTCATGCTAGTACCACTG	57.321	45.455	0.00	0.00	0.00	3.66
2059	2603	7.064253	GGAATATTAGCACACGGGTATATTGAC	59.936	40.741	8.01	0.00	0.00	3.18
2108	2652	9.573166	TTTGGTGTAGTACTTGTAGAGTTACTA	57.427	33.333	0.00	0.00	39.86	1.82
2199	2743	2.834549	GAGATGAGGGAGAAACCACTCA	59.165	50.000	0.00	0.00	44.08	3.41
2202	2746	2.338809	TGAGGGAGAAACCACTCACAT	58.661	47.619	0.00	0.00	42.16	3.21
2217	2761	7.717568	ACCACTCACATAAATAGTAGCTACTG	58.282	38.462	32.21	19.25	37.10	2.74
2402	2946	6.112927	ACAAATGAATACATGCAACCCTTT	57.887	33.333	0.00	0.00	36.79	3.11
2438	2982	2.996621	CCAAGACACTCTTCCGATGTTC	59.003	50.000	0.00	0.00	33.78	3.18
2559	3107	0.172803	ACGCTAGTCCATCGTGTTCC	59.827	55.000	0.00	0.00	34.92	3.62
2568	3117	4.345257	AGTCCATCGTGTTCCTAGCATTAT	59.655	41.667	0.00	0.00	0.00	1.28
2621	3170	3.123621	GCTATATCATTTGCGTCCTTCGG	59.876	47.826	0.00	0.00	40.26	4.30
2802	3391	6.855836	TGTGAATTGTAGCATCTGATTTTCC	58.144	36.000	0.00	0.00	0.00	3.13
2804	3393	7.828717	TGTGAATTGTAGCATCTGATTTTCCTA	59.171	33.333	0.00	0.00	0.00	2.94
2875	5911	8.630054	AGTAATGTATTTTACTTGGAGTTGCA	57.370	30.769	0.00	0.00	38.90	4.08
2920	6633	3.314913	TGTATTAATGCAATGCCACTCCG	59.685	43.478	1.53	0.00	0.00	4.63
2972	6685	5.503634	TCGGACATCATCATGGGATATTT	57.496	39.130	0.00	0.00	33.82	1.40
2997	6710	7.874940	TCATAAAATTTCCTTATGATGCTCCG	58.125	34.615	6.88	0.00	39.63	4.63
3024	6737	5.356470	GGAACTCTTGAGGATTGAAAGGATG	59.644	44.000	2.55	0.00	0.00	3.51
3039	6752	3.515602	AGGATGCATCAACCCTAATCC	57.484	47.619	27.25	8.27	34.94	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	62	1.133407	GTCACGGCCAAAACACTCAAA	59.867	47.619	2.24	0.00	0.00	2.69
55	63	0.736053	GTCACGGCCAAAACACTCAA	59.264	50.000	2.24	0.00	0.00	3.02
68	76	3.167921	TCCCAACGTATAATGTCACGG	57.832	47.619	0.00	0.00	42.35	4.94
79	87	5.750352	AAACTCCTAAAGATCCCAACGTA	57.250	39.130	0.00	0.00	0.00	3.57
80	88	4.635699	AAACTCCTAAAGATCCCAACGT	57.364	40.909	0.00	0.00	0.00	3.99
99	131	7.094248	CCAATACAAGAGGTCATGTGATCAAAA	60.094	37.037	0.00	0.00	0.00	2.44
100	132	6.375174	CCAATACAAGAGGTCATGTGATCAAA	59.625	38.462	0.00	0.00	0.00	2.69
109	143	4.028131	TCGTACCCAATACAAGAGGTCAT	58.972	43.478	0.00	0.00	32.79	3.06
161	593	5.049405	CCATAAAAAGGTCGGTGCATCTATC	60.049	44.000	0.00	0.00	0.00	2.08
172	604	4.270008	ACCCTGATTCCATAAAAAGGTCG	58.730	43.478	0.00	0.00	0.00	4.79
185	618	3.576982	TGTATCGGATGGTACCCTGATTC	59.423	47.826	15.27	11.75	0.00	2.52
245	678	3.270960	AGGCCAAATGGGAAAGGTACATA	59.729	43.478	5.01	0.00	40.01	2.29
301	734	6.539464	ACATTGACAAATTTGTGCAATTGAGT	59.461	30.769	27.85	21.81	42.43	3.41
318	751	0.325933	CTGGAGGGCAGACATTGACA	59.674	55.000	0.00	0.00	36.08	3.58
349	782	7.802117	ACTTTACATAAGTGCCTGTACCATAT	58.198	34.615	0.00	0.00	0.00	1.78
434	879	0.814410	TTTGGTACTCGCACCGCAAA	60.814	50.000	0.00	0.00	41.88	3.68
437	882	0.947180	TCTTTTGGTACTCGCACCGC	60.947	55.000	0.00	0.00	41.88	5.68
451	896	6.042781	TGCCAATATAGAGGATACCGTCTTTT	59.957	38.462	0.00	0.00	38.38	2.27
457	902	4.462834	TCAGTGCCAATATAGAGGATACCG	59.537	45.833	0.00	0.00	37.17	4.02
458	903	5.105146	CCTCAGTGCCAATATAGAGGATACC	60.105	48.000	0.00	0.00	44.12	2.73
459	904	5.482175	ACCTCAGTGCCAATATAGAGGATAC	59.518	44.000	12.76	1.80	44.12	2.24
461	906	4.497516	ACCTCAGTGCCAATATAGAGGAT	58.502	43.478	12.76	0.00	44.12	3.24
462	907	3.928754	ACCTCAGTGCCAATATAGAGGA	58.071	45.455	12.76	0.00	44.12	3.71
474	919	3.581755	TGTCGTATTACAACCTCAGTGC	58.418	45.455	0.00	0.00	0.00	4.40
476	921	3.257375	TGCTGTCGTATTACAACCTCAGT	59.743	43.478	0.00	0.00	0.00	3.41
483	928	2.300723	ACCCACTGCTGTCGTATTACAA	59.699	45.455	0.00	0.00	0.00	2.41
534	979	2.832129	GCATATCCGGTCCTATTCTCCA	59.168	50.000	0.00	0.00	0.00	3.86
599	1044	4.011023	CAACGGTAACCAACATATTCCCA	58.989	43.478	0.00	0.00	0.00	4.37
601	1046	3.440872	TGCAACGGTAACCAACATATTCC	59.559	43.478	0.00	0.00	0.00	3.01
645	1090	6.409704	CACCCATTCACGATATATGGATTCT	58.590	40.000	1.28	0.00	41.05	2.40
660	1105	2.235016	GTGTACCTTTGCACCCATTCA	58.765	47.619	0.00	0.00	32.46	2.57
714	1225	4.098501	GGCATTTCCCTAACAAAGAGATGG	59.901	45.833	0.00	0.00	0.00	3.51
821	1344	3.735591	AGCTTGAGCATGTTTTTGCATT	58.264	36.364	5.70	0.00	45.23	3.56
874	1400	9.727859	TTGTGTATAAACAGCTTATTTACAGGA	57.272	29.630	0.00	0.00	35.91	3.86
1672	2216	3.643159	TCACGATATTCCGGTGATCTG	57.357	47.619	0.00	4.25	0.00	2.90
1674	2218	2.731976	GCTTCACGATATTCCGGTGATC	59.268	50.000	0.00	2.04	0.00	2.92
1791	2335	2.038295	CCCAGGACAAGATAGAGATGCC	59.962	54.545	0.00	0.00	0.00	4.40
1795	2339	4.542906	TCATCCCAGGACAAGATAGAGA	57.457	45.455	0.00	0.00	0.00	3.10
2042	2586	3.123804	CTCAGTCAATATACCCGTGTGC	58.876	50.000	0.00	0.00	0.00	4.57
2059	2603	9.299963	CAAAACTATAGACATCACTCTTCTCAG	57.700	37.037	6.78	0.00	0.00	3.35
2108	2652	6.779860	TGTAAAAATAGGCTTCTTCCTGAGT	58.220	36.000	0.00	0.00	37.01	3.41
2202	2746	8.818622	TCCAGAACTTCAGTAGCTACTATTTA	57.181	34.615	25.63	9.37	34.13	1.40
2217	2761	2.851195	TGTTGCTTCCTCCAGAACTTC	58.149	47.619	0.00	0.00	0.00	3.01
2402	2946	4.097286	GTGTCTTGGCTTTGTCCACTTAAA	59.903	41.667	0.00	0.00	35.50	1.52
2438	2982	5.695816	GTCTACTATACCACTCGGAGTAGTG	59.304	48.000	17.68	9.17	45.33	2.74
2478	3022	3.732212	AGCAATTTTGGTTCCTTTGAGC	58.268	40.909	0.00	0.00	34.89	4.26
2559	3107	8.268850	AGTAGACAACCAAACAATAATGCTAG	57.731	34.615	0.00	0.00	0.00	3.42
2568	3117	8.410141	CAATAGGAAAAGTAGACAACCAAACAA	58.590	33.333	0.00	0.00	0.00	2.83
2621	3170	7.013178	GTGTAGAGTATACTTTACCCTCTCCAC	59.987	44.444	23.68	13.50	33.80	4.02
2668	3217	5.512404	CCAATCTGGATAGTATAAACCGCCA	60.512	44.000	0.00	0.00	40.96	5.69
2719	3268	9.195411	ACATCTGTAGCACAATTACAATTTTTG	57.805	29.630	0.00	0.00	31.17	2.44
2920	6633	9.699703	CTAGAACAAGATACCCTAATTAGAAGC	57.300	37.037	14.28	2.28	0.00	3.86
2972	6685	7.040478	CCGGAGCATCATAAGGAAATTTTATGA	60.040	37.037	11.58	11.58	46.04	2.15
2982	6695	1.133167	TCCTCCGGAGCATCATAAGGA	60.133	52.381	26.87	12.61	36.25	3.36
2991	6704	0.541998	TCAAGAGTTCCTCCGGAGCA	60.542	55.000	26.87	9.03	35.33	4.26
2997	6710	4.559862	TTCAATCCTCAAGAGTTCCTCC	57.440	45.455	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.