AutoCloner

Multiple sequence alignment - TraesCS5A01G124100

Loading Multiple Alignment...

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	TraesCS5A01G124100	chr5A	100.000	3835	0	0	1	3835	271051381	271047547	0.000000e+00	7083.0
1	TraesCS5A01G124100	chr5A	100.000	484	0	0	4227	4710	271047155	271046672	0.000000e+00	894.0
2	TraesCS5A01G124100	chr5A	76.856	229	31	11	1431	1657	51555520	51555312	4.980000e-20	110.0
3	TraesCS5A01G124100	chr5A	84.286	70	8	3	1436	1504	461484151	461484084	1.090000e-06	65.8
4	TraesCS5A01G124100	chr5D	97.799	3181	53	8	649	3824	209645872	209642704	0.000000e+00	5470.0
5	TraesCS5A01G124100	chr5D	95.008	621	24	5	30	648	209646842	209646227	0.000000e+00	968.0
6	TraesCS5A01G124100	chr5D	94.518	456	17	3	4263	4710	209642358	209641903	0.000000e+00	697.0
7	TraesCS5A01G124100	chr5D	84.962	266	16	12	30	277	182143674	182143933	1.010000e-61	248.0
8	TraesCS5A01G124100	chr5B	97.526	3193	63	9	649	3835	223127093	223123911	0.000000e+00	5445.0
9	TraesCS5A01G124100	chr5B	93.930	626	25	6	30	648	223128065	223127446	0.000000e+00	933.0
10	TraesCS5A01G124100	chr5B	96.099	282	5	1	4227	4502	223123893	223123612	5.560000e-124	455.0
11	TraesCS5A01G124100	chr5B	92.174	230	10	4	4489	4710	223121918	223121689	7.610000e-83	318.0
12	TraesCS5A01G124100	chr5B	95.161	124	6	0	155	278	290449421	290449298	3.720000e-46	196.0
13	TraesCS5A01G124100	chr5B	100.000	33	0	0	1	33	112181741	112181709	1.420000e-05	62.1
14	TraesCS5A01G124100	chr5B	100.000	30	0	0	1	30	567785201	567785230	6.580000e-04	56.5
15	TraesCS5A01G124100	chr5B	96.875	32	1	0	1	32	44864071	44864040	2.000000e-03	54.7
16	TraesCS5A01G124100	chr6A	84.800	250	28	6	30	277	75296723	75296964	4.710000e-60	243.0
17	TraesCS5A01G124100	chr6A	100.000	30	0	0	1	30	169511803	169511832	6.580000e-04	56.5
18	TraesCS5A01G124100	chr4D	84.270	267	18	11	30	278	211045073	211045333	6.090000e-59	239.0
19	TraesCS5A01G124100	chr4D	84.411	263	17	12	33	277	93831888	93831632	2.190000e-58	237.0
20	TraesCS5A01G124100	chr4D	83.835	266	19	12	30	277	362707135	362707394	1.020000e-56	231.0
21	TraesCS5A01G124100	chr4D	96.970	33	1	0	1	33	323550195	323550163	6.580000e-04	56.5
22	TraesCS5A01G124100	chr2D	84.739	249	27	8	30	277	214157797	214158035	6.090000e-59	239.0
23	TraesCS5A01G124100	chr2D	100.000	30	0	0	1	30	337396512	337396483	6.580000e-04	56.5
24	TraesCS5A01G124100	chr1A	83.846	260	28	10	30	282	432976804	432976552	7.880000e-58	235.0
25	TraesCS5A01G124100	chr7B	83.459	266	20	13	35	282	6751265	6751524	4.740000e-55	226.0
26	TraesCS5A01G124100	chr7B	81.893	243	26	9	294	531	711069013	711068784	6.220000e-44	189.0
27	TraesCS5A01G124100	chr2A	95.161	124	6	0	155	278	5671952	5672075	3.720000e-46	196.0
28	TraesCS5A01G124100	chr2A	94.444	36	2	0	1	36	680275869	680275904	6.580000e-04	56.5
29	TraesCS5A01G124100	chr4A	94.444	126	7	0	157	282	143246771	143246896	1.340000e-45	195.0
30	TraesCS5A01G124100	chr1D	80.515	272	25	12	30	282	326478128	326478390	2.890000e-42	183.0
31	TraesCS5A01G124100	chr1D	100.000	31	0	0	1	31	103681552	103681522	1.830000e-04	58.4
32	TraesCS5A01G124100	chr6D	100.000	29	0	0	1	29	178856010	178856038	2.000000e-03	54.7

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	TraesCS5A01G124100	chr5A	271046672	271051381	4709	True	3988.500000	7083	100.00000	1	4710	2	chr5A.!!$R3	4709
1	TraesCS5A01G124100	chr5D	209641903	209646842	4939	True	2378.333333	5470	95.77500	30	4710	3	chr5D.!!$R1	4680
2	TraesCS5A01G124100	chr5B	223121689	223128065	6376	True	1787.750000	5445	94.93225	30	4710	4	chr5B.!!$R4	4680

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	Hairpin	End Stability	Orientation
47	48	0.393537	GCTCTCCACACCTCAATGGG	60.394	60.000	0.00	41.11	4.00	F
1140	1507	0.911053	TGCATGATCCAGCACCTGTA	59.089	50.000	0.00	35.51	2.74	F
1898	2268	1.074405	TCCTTTGCCTTCATCTGCAGT	59.926	47.619	14.67	38.95	4.40	F
3244	3618	1.301244	CAGTGCCGTTGCTCACTCT	60.301	57.895	0.00	41.19	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1898	2268	0.036732	AAGGAAAGTGATGGCTGCGA	59.963	50.000	0.00	0.00	5.10	R
2662	3032	1.276421	GGCTACCAAGACTGCAAGAGA	59.724	52.381	0.00	37.43	3.10	R
3358	3732	2.296945	TATCACCCAATGCCTGGCCC	62.297	60.000	17.53	44.90	5.80	R
4609	6699	2.361104	TTGGCGCAACCTCCCATC	60.361	61.111	10.83	40.22	3.51	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
26	27	3.180417	GACTCTTCGACTCGTAAACGT	57.820	47.619	2.02	0.00	40.80	3.99
27	28	3.549574	GACTCTTCGACTCGTAAACGTT	58.450	45.455	0.00	0.00	40.80	3.99
28	29	3.294943	ACTCTTCGACTCGTAAACGTTG	58.705	45.455	0.00	0.00	40.80	4.10
47	48	0.393537	GCTCTCCACACCTCAATGGG	60.394	60.000	0.00	0.00	41.11	4.00
267	275	1.959899	CTGCTCCGTCGTTGATGCAC	61.960	60.000	0.00	0.00	0.00	4.57
341	349	9.396022	TGGAAATAGAAATGGAGTTACTTCATC	57.604	33.333	6.61	0.00	26.49	2.92
393	401	4.471904	TCAATTGATCAGTTACCGCTCT	57.528	40.909	3.38	0.00	0.00	4.09
394	402	4.433615	TCAATTGATCAGTTACCGCTCTC	58.566	43.478	3.38	0.00	0.00	3.20
395	403	4.160439	TCAATTGATCAGTTACCGCTCTCT	59.840	41.667	3.38	0.00	0.00	3.10
396	404	4.744795	ATTGATCAGTTACCGCTCTCTT	57.255	40.909	0.00	0.00	0.00	2.85
518	529	5.612725	TTGGTCTTTTCCAGCATTCTTTT	57.387	34.783	0.00	0.00	38.80	2.27
536	547	6.044512	TCTTTTCTTCGTAACTGAAGTTGC	57.955	37.500	5.95	3.69	44.53	4.17
579	590	1.379531	TGCTGGTGCATCATGGTGA	59.620	52.632	11.02	0.00	45.31	4.02
609	620	7.973944	GGCATAGAAGTTGGACGAAAATAATTT	59.026	33.333	0.00	0.00	0.00	1.82
924	1291	4.172807	ACAGTACTTTGGGAGTTGGGATA	58.827	43.478	0.00	0.00	39.86	2.59
1140	1507	0.911053	TGCATGATCCAGCACCTGTA	59.089	50.000	0.00	0.00	35.51	2.74
1591	1958	5.589452	TCGGTAGTGGTTTTGTTTTGTACAT	59.411	36.000	0.00	0.00	36.44	2.29
1592	1959	5.683743	CGGTAGTGGTTTTGTTTTGTACATG	59.316	40.000	0.00	0.00	36.44	3.21
1593	1960	6.566141	GGTAGTGGTTTTGTTTTGTACATGT	58.434	36.000	2.69	2.69	36.44	3.21
1652	2022	7.555965	AGCTTGACTTAGGAACAAAACAAATT	58.444	30.769	0.00	0.00	0.00	1.82
1692	2062	4.403734	TGGAGGGAGTATTTGGTTTTGAC	58.596	43.478	0.00	0.00	0.00	3.18
1895	2265	3.518590	CAATTCCTTTGCCTTCATCTGC	58.481	45.455	0.00	0.00	0.00	4.26
1896	2266	2.291209	TTCCTTTGCCTTCATCTGCA	57.709	45.000	0.00	0.00	35.27	4.41
1897	2267	1.830279	TCCTTTGCCTTCATCTGCAG	58.170	50.000	7.63	7.63	38.95	4.41
1898	2268	1.074405	TCCTTTGCCTTCATCTGCAGT	59.926	47.619	14.67	0.00	38.95	4.40
1899	2269	1.471684	CCTTTGCCTTCATCTGCAGTC	59.528	52.381	14.67	0.00	38.95	3.51
1979	2349	4.102524	ACAACCAAAGAGTGATGTAGTCCA	59.897	41.667	0.00	0.00	0.00	4.02
2053	2423	5.713025	ACTGATCATTGTATTTGGTGTTGC	58.287	37.500	0.00	0.00	0.00	4.17
2054	2424	5.243507	ACTGATCATTGTATTTGGTGTTGCA	59.756	36.000	0.00	0.00	0.00	4.08
2068	2438	3.215244	GTGTTGCATCGTTAAACAGTCG	58.785	45.455	0.00	0.00	34.64	4.18
2087	2457	3.823330	GCTCCAGTGCATGCCAGC	61.823	66.667	16.68	10.74	0.00	4.85
2105	2475	5.221224	TGCCAGCCATTTATGCTTAATGTAC	60.221	40.000	0.00	0.00	36.81	2.90
2120	2490	7.541783	TGCTTAATGTACATTCATTGTTTGCTC	59.458	33.333	24.00	3.52	39.87	4.26
2620	2990	3.565307	TGCCATTCTTCTTCCAGTTGTT	58.435	40.909	0.00	0.00	0.00	2.83
2662	3032	5.549619	CCCCTCAGTGGAAGATCCTATATTT	59.450	44.000	0.00	0.00	37.46	1.40
2703	3073	9.032420	GTAGCCTACTTGTTAGTATTCATTGAC	57.968	37.037	0.00	0.00	36.32	3.18
2882	3254	8.919145	TGTACATTGGAAAATTGAGGTAAACTT	58.081	29.630	0.00	0.00	0.00	2.66
2924	3298	7.737972	TCATTTTCCTTTTCGTCTGATTGTA	57.262	32.000	0.00	0.00	0.00	2.41
2925	3299	7.806690	TCATTTTCCTTTTCGTCTGATTGTAG	58.193	34.615	0.00	0.00	0.00	2.74
2927	3301	3.596214	TCCTTTTCGTCTGATTGTAGCC	58.404	45.455	0.00	0.00	0.00	3.93
2928	3302	3.007506	TCCTTTTCGTCTGATTGTAGCCA	59.992	43.478	0.00	0.00	0.00	4.75
2930	3304	4.396166	CCTTTTCGTCTGATTGTAGCCATT	59.604	41.667	0.00	0.00	0.00	3.16
2932	3306	6.093495	CCTTTTCGTCTGATTGTAGCCATTAA	59.907	38.462	0.00	0.00	0.00	1.40
2933	3307	7.201732	CCTTTTCGTCTGATTGTAGCCATTAAT	60.202	37.037	0.00	0.00	0.00	1.40
2934	3308	8.725405	TTTTCGTCTGATTGTAGCCATTAATA	57.275	30.769	0.00	0.00	0.00	0.98
2935	3309	8.902540	TTTCGTCTGATTGTAGCCATTAATAT	57.097	30.769	0.00	0.00	0.00	1.28
2936	3310	8.534333	TTCGTCTGATTGTAGCCATTAATATC	57.466	34.615	0.00	0.00	0.00	1.63
3241	3615	2.607892	GGACAGTGCCGTTGCTCAC	61.608	63.158	0.00	0.00	38.71	3.51
3244	3618	1.301244	CAGTGCCGTTGCTCACTCT	60.301	57.895	0.00	0.00	41.19	3.24
3358	3732	0.988145	TAGGTGGCTCCAGGAATGGG	60.988	60.000	8.51	0.00	39.02	4.00
3514	3888	1.034838	ACTTCCAACTTGTTGCCGCA	61.035	50.000	7.89	0.00	0.00	5.69
3721	4095	4.417506	CTTGCGAATGAAATCATCAGCAA	58.582	39.130	24.06	24.06	46.27	3.91
3723	4097	3.690628	TGCGAATGAAATCATCAGCAAGA	59.309	39.130	17.56	2.26	42.53	3.02
4275	4649	3.273434	TGCTCAGCTGTATCACCATTTC	58.727	45.455	14.67	0.00	0.00	2.17
4475	4856	1.069227	GGTGAATCGTTGGAACACTGC	60.069	52.381	0.00	0.00	39.29	4.40
4497	6587	7.060383	TGCATTCTTGGGAAAATGAGTTAAA	57.940	32.000	0.00	0.00	35.35	1.52
4522	6612	9.628500	AAATTAGGTTCTTAAGATATGGTCACC	57.372	33.333	5.89	8.93	0.00	4.02
4545	6635	0.951558	TTTCCTTGCGGTTCTGCTTC	59.048	50.000	5.23	0.00	35.36	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.294943	CAACGTTTACGAGTCGAAGAGT	58.705	45.455	21.50	9.35	46.63	3.24
8	9	2.088664	GCAACGTTTACGAGTCGAAGAG	59.911	50.000	21.50	8.71	43.02	2.85
9	10	2.046313	GCAACGTTTACGAGTCGAAGA	58.954	47.619	21.50	0.55	43.02	2.87
10	11	2.049228	AGCAACGTTTACGAGTCGAAG	58.951	47.619	21.50	7.64	43.02	3.79
11	12	2.046313	GAGCAACGTTTACGAGTCGAA	58.954	47.619	21.50	6.43	43.02	3.71
12	13	1.265095	AGAGCAACGTTTACGAGTCGA	59.735	47.619	21.50	0.00	43.02	4.20
13	14	1.642843	GAGAGCAACGTTTACGAGTCG	59.357	52.381	11.85	11.85	43.02	4.18
14	15	1.984297	GGAGAGCAACGTTTACGAGTC	59.016	52.381	9.53	0.42	43.02	3.36
15	16	1.338973	TGGAGAGCAACGTTTACGAGT	59.661	47.619	9.53	0.00	43.02	4.18
16	17	1.719780	GTGGAGAGCAACGTTTACGAG	59.280	52.381	9.53	2.51	43.02	4.18
17	18	1.067364	TGTGGAGAGCAACGTTTACGA	59.933	47.619	9.53	0.00	43.02	3.43
18	19	1.191647	GTGTGGAGAGCAACGTTTACG	59.808	52.381	0.00	0.00	46.33	3.18
19	20	1.529865	GGTGTGGAGAGCAACGTTTAC	59.470	52.381	0.00	0.00	0.00	2.01
20	21	1.414919	AGGTGTGGAGAGCAACGTTTA	59.585	47.619	0.00	0.00	0.00	2.01
21	22	0.180406	AGGTGTGGAGAGCAACGTTT	59.820	50.000	0.00	0.00	0.00	3.60
22	23	0.249911	GAGGTGTGGAGAGCAACGTT	60.250	55.000	0.00	0.00	0.00	3.99
23	24	1.367840	GAGGTGTGGAGAGCAACGT	59.632	57.895	0.00	0.00	0.00	3.99
24	25	0.249868	TTGAGGTGTGGAGAGCAACG	60.250	55.000	0.00	0.00	0.00	4.10
25	26	1.808945	CATTGAGGTGTGGAGAGCAAC	59.191	52.381	0.00	0.00	0.00	4.17
26	27	1.271543	CCATTGAGGTGTGGAGAGCAA	60.272	52.381	0.00	0.00	37.72	3.91
27	28	0.325933	CCATTGAGGTGTGGAGAGCA	59.674	55.000	0.00	0.00	37.72	4.26
28	29	0.393537	CCCATTGAGGTGTGGAGAGC	60.394	60.000	0.00	0.00	37.72	4.09
47	48	0.779997	ATGGCCCCTGATTGTATCCC	59.220	55.000	0.00	0.00	0.00	3.85
267	275	3.036431	GGGGGTCAACCAAGTCAAG	57.964	57.895	0.89	0.00	42.91	3.02
290	298	7.716799	ATACAAATTCACAACCATGGTATGT	57.283	32.000	20.12	20.29	0.00	2.29
292	300	7.398618	TCCAATACAAATTCACAACCATGGTAT	59.601	33.333	20.12	6.80	0.00	2.73
341	349	8.954950	ATCTGTTATTTGTCAGTGAGATAAGG	57.045	34.615	0.00	0.00	33.89	2.69
448	458	2.614057	CACAGGGCGTAAGAATCCATTC	59.386	50.000	0.00	0.00	43.02	2.67
461	471	0.035439	ACCCATCTTAACACAGGGCG	60.035	55.000	0.00	0.00	43.47	6.13
536	547	1.923356	AGGGTACAAATGGTGCAAGG	58.077	50.000	0.00	0.00	33.19	3.61
579	590	2.073816	CGTCCAACTTCTATGCCGTTT	58.926	47.619	0.00	0.00	0.00	3.60
732	1097	8.556517	AAATACGTTAAAACTGAAGCTTGTTC	57.443	30.769	2.10	0.00	0.00	3.18
885	1252	8.677148	AAGTACTGTCAACATAAACTGAACAT	57.323	30.769	0.00	0.00	0.00	2.71
955	1322	3.883830	ACAATTGTGCTGAAACACCAA	57.116	38.095	11.07	0.00	39.93	3.67
956	1323	3.883830	AACAATTGTGCTGAAACACCA	57.116	38.095	12.82	0.00	39.93	4.17
1022	1389	3.569491	CCAAAGCCATCCCTTACATCAT	58.431	45.455	0.00	0.00	0.00	2.45
1652	2022	1.901159	CCATCCCAAAATGCAAGTCCA	59.099	47.619	0.00	0.00	0.00	4.02
1692	2062	9.650539	AATATATGAAGCTTCTACTGTGCTATG	57.349	33.333	26.09	0.00	35.85	2.23
1894	2264	1.580845	AAAGTGATGGCTGCGACTGC	61.581	55.000	0.00	0.00	43.20	4.40
1895	2265	0.445436	GAAAGTGATGGCTGCGACTG	59.555	55.000	0.00	0.00	0.00	3.51
1896	2266	0.674895	GGAAAGTGATGGCTGCGACT	60.675	55.000	0.00	0.00	0.00	4.18
1897	2267	0.674895	AGGAAAGTGATGGCTGCGAC	60.675	55.000	0.00	0.00	0.00	5.19
1898	2268	0.036732	AAGGAAAGTGATGGCTGCGA	59.963	50.000	0.00	0.00	0.00	5.10
1899	2269	0.169672	CAAGGAAAGTGATGGCTGCG	59.830	55.000	0.00	0.00	0.00	5.18
2053	2423	2.092211	GGAGCACGACTGTTTAACGATG	59.908	50.000	0.00	0.00	0.00	3.84
2054	2424	2.288579	TGGAGCACGACTGTTTAACGAT	60.289	45.455	0.00	0.00	0.00	3.73
2105	2475	8.767478	AGAAAATAAGGAGCAAACAATGAATG	57.233	30.769	0.00	0.00	0.00	2.67
2120	2490	6.808212	CAGCCATGTACAACAAGAAAATAAGG	59.192	38.462	0.00	0.00	0.00	2.69
2620	2990	5.367352	TGAGGGGTTAGTTGAGAACAAGTTA	59.633	40.000	0.00	0.00	39.86	2.24
2662	3032	1.276421	GGCTACCAAGACTGCAAGAGA	59.724	52.381	0.00	0.00	37.43	3.10
2833	3205	7.564793	ACATGTTGCTTGACCTAGATGTATTA	58.435	34.615	0.00	0.00	0.00	0.98
2903	3277	5.048991	GGCTACAATCAGACGAAAAGGAAAA	60.049	40.000	0.00	0.00	0.00	2.29
2924	3298	7.830848	ATGGGGTAGTAAGATATTAATGGCT	57.169	36.000	0.00	0.00	0.00	4.75
2925	3299	7.339466	CCAATGGGGTAGTAAGATATTAATGGC	59.661	40.741	0.00	0.00	0.00	4.40
3244	3618	2.751259	GCTGCCAAATGACTCATCAAGA	59.249	45.455	0.00	0.00	38.69	3.02
3358	3732	2.296945	TATCACCCAATGCCTGGCCC	62.297	60.000	17.53	0.00	44.90	5.80
3514	3888	3.311486	GCTTCAGCAGTAGACTCTGTT	57.689	47.619	0.00	0.00	41.59	3.16
3697	4071	3.732774	GCTGATGATTTCATTCGCAAGCA	60.733	43.478	8.99	0.00	36.57	3.91
3721	4095	4.890581	AGTCTCTTACATAATCGGTGCTCT	59.109	41.667	0.00	0.00	0.00	4.09
3723	4097	4.202161	CCAGTCTCTTACATAATCGGTGCT	60.202	45.833	0.00	0.00	0.00	4.40
4275	4649	6.753744	AGAAAGCAAGCTGTTAAAAACAAGAG	59.246	34.615	0.00	0.00	41.61	2.85
4396	4770	7.277539	TGAGACAAGGCAAAAATTTGTAACTTG	59.722	33.333	22.96	22.96	43.53	3.16
4497	6587	8.778059	TGGTGACCATATCTTAAGAACCTAATT	58.222	33.333	9.71	0.00	0.00	1.40
4609	6699	2.361104	TTGGCGCAACCTCCCATC	60.361	61.111	10.83	0.00	40.22	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.