AutoCloner

Multiple sequence alignment - TraesCS4A01G466900

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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	TraesCS4A01G466900	chr4A	100.000	2558	0	0	1	2558	729545465	729542908	0.000000e+00	4724
1	TraesCS4A01G466900	chr4A	93.746	1695	100	3	870	2558	180270746	180269052	0.000000e+00	2538
2	TraesCS4A01G466900	chr4A	93.166	878	55	3	1	874	180271777	180270901	0.000000e+00	1284
3	TraesCS4A01G466900	chr6A	94.690	1695	84	3	870	2558	15385999	15384305	0.000000e+00	2627
4	TraesCS4A01G466900	chr6A	94.761	878	40	4	1	874	15387026	15386151	0.000000e+00	1362
5	TraesCS4A01G466900	chr7A	94.507	1693	89	2	870	2558	610462683	610460991	0.000000e+00	2608
6	TraesCS4A01G466900	chr7A	94.419	878	44	3	1	874	610463709	610462833	0.000000e+00	1345
7	TraesCS4A01G466900	chr3B	92.959	1477	96	4	1085	2558	607809354	607807883	0.000000e+00	2145
8	TraesCS4A01G466900	chr3B	94.762	821	38	3	58	874	607810641	607809822	0.000000e+00	1273
9	TraesCS4A01G466900	chr3B	76.244	1246	249	38	1069	2295	766341338	766342555	3.620000e-173	617
10	TraesCS4A01G466900	chr3B	85.714	448	54	5	66	505	534161061	534161506	4.990000e-127	464
11	TraesCS4A01G466900	chr3B	93.636	220	11	1	870	1086	607809667	607809448	2.450000e-85	326
12	TraesCS4A01G466900	chr3B	90.909	55	5	0	1	55	607810966	607810912	9.820000e-10	75
13	TraesCS4A01G466900	chr7D	94.172	1287	75	0	1272	2558	194638625	194639911	0.000000e+00	1962
14	TraesCS4A01G466900	chr7D	93.508	878	51	4	1	874	194637257	194638132	0.000000e+00	1301
15	TraesCS4A01G466900	chr7D	93.948	347	18	1	870	1213	194638282	194638628	2.920000e-144	521
16	TraesCS4A01G466900	chr3A	93.781	804	44	4	1	799	584382061	584382863	0.000000e+00	1203
17	TraesCS4A01G466900	chr5A	93.647	787	45	3	1	783	567266983	567267768	0.000000e+00	1171

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	TraesCS4A01G466900	chr4A	729542908	729545465	2557	True	4724.000000	4724	100.0000	1	2558	1	chr4A.!!$R1	2557
1	TraesCS4A01G466900	chr4A	180269052	180271777	2725	True	1911.000000	2538	93.4560	1	2558	2	chr4A.!!$R2	2557
2	TraesCS4A01G466900	chr6A	15384305	15387026	2721	True	1994.500000	2627	94.7255	1	2558	2	chr6A.!!$R1	2557
3	TraesCS4A01G466900	chr7A	610460991	610463709	2718	True	1976.500000	2608	94.4630	1	2558	2	chr7A.!!$R1	2557
4	TraesCS4A01G466900	chr3B	607807883	607810966	3083	True	954.750000	2145	93.0665	1	2558	4	chr3B.!!$R1	2557
5	TraesCS4A01G466900	chr3B	766341338	766342555	1217	False	617.000000	617	76.2440	1069	2295	1	chr3B.!!$F2	1226
6	TraesCS4A01G466900	chr7D	194637257	194639911	2654	False	1261.333333	1962	93.8760	1	2558	3	chr7D.!!$F1	2557
7	TraesCS4A01G466900	chr3A	584382061	584382863	802	False	1203.000000	1203	93.7810	1	799	1	chr3A.!!$F1	798
8	TraesCS4A01G466900	chr5A	567266983	567267768	785	False	1171.000000	1171	93.6470	1	783	1	chr5A.!!$F1	782

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
76	345	0.320697	CCCCTTTCTTTCCTCGACGT	59.679	55.0	0.0	0.0	0.0	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1917	2469	0.976641	TGAGCAGTCCAACCACCTAG	59.023	55.0	0.0	0.0	0.0	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
33	34	2.035632	GATCCAACATCGGACCTCTCT	58.964	52.381	0.00	0.00	38.07	3.10
42	43	1.448922	CGGACCTCTCTAAGCTCCGG	61.449	65.000	0.00	0.00	45.66	5.14
46	47	2.833582	TCTCTAAGCTCCGGCCCG	60.834	66.667	0.00	0.00	39.73	6.13
76	345	0.320697	CCCCTTTCTTTCCTCGACGT	59.679	55.000	0.00	0.00	0.00	4.34
161	433	4.081031	TCCTCTTCTTCTCGTGCTCTAGTA	60.081	45.833	0.00	0.00	0.00	1.82
187	459	4.873827	CGGATTTATCGTTTCCTTTCTCCA	59.126	41.667	0.00	0.00	0.00	3.86
213	485	4.138290	TGGAAGATTCAAGCGTTTTGGTA	58.862	39.130	2.69	0.00	0.00	3.25
217	489	6.349363	GGAAGATTCAAGCGTTTTGGTAGAAT	60.349	38.462	0.00	0.00	0.00	2.40
249	521	1.187087	AGGGCTTCAGACTTAGTCGG	58.813	55.000	6.73	6.44	37.67	4.79
283	555	2.642311	TGGGTACTGTTCATGGATGTGT	59.358	45.455	0.00	0.00	0.00	3.72
364	636	4.759693	GTCATACTGTGATTTGTTGTCCCA	59.240	41.667	0.00	0.00	39.48	4.37
530	802	7.658261	TGCTCATATTGTATGGTACTGTACTC	58.342	38.462	16.79	8.35	0.00	2.59
557	829	6.701340	TCACTGTAAATCTGATGCTTACTGT	58.299	36.000	14.13	14.13	37.86	3.55
590	863	3.839051	TTTTGTGCCCTTTTGTTTTGC	57.161	38.095	0.00	0.00	0.00	3.68
661	934	1.317431	TGAGTCATGCATGCCCTTGC	61.317	55.000	22.25	9.29	43.07	4.01
697	970	8.435430	GGCTGCTTGTTATTTAAAGAACAATTC	58.565	33.333	30.69	25.50	45.55	2.17
728	1001	6.240894	ACAGTTTCTTGTGGATCACATATGT	58.759	36.000	1.41	1.41	44.16	2.29
736	1009	6.048732	TGTGGATCACATATGTTGTACTGT	57.951	37.500	5.37	0.00	39.62	3.55
879	1329	1.953686	GTGAGGCTGGTTGTTTTGCTA	59.046	47.619	0.00	0.00	0.00	3.49
899	1349	8.654230	TTGCTAAGAGTAATTTCATGAGCTAG	57.346	34.615	0.00	0.00	0.00	3.42
901	1351	7.069950	TGCTAAGAGTAATTTCATGAGCTAGGA	59.930	37.037	0.00	0.00	0.00	2.94
1022	1474	0.678048	GCTCGTCTTCCTTTGGCCAT	60.678	55.000	6.09	0.00	0.00	4.40
1028	1483	2.686915	GTCTTCCTTTGGCCATGAGATG	59.313	50.000	6.09	6.13	0.00	2.90
1031	1486	1.918262	TCCTTTGGCCATGAGATGTCT	59.082	47.619	6.09	0.00	0.00	3.41
1032	1487	2.309755	TCCTTTGGCCATGAGATGTCTT	59.690	45.455	6.09	0.00	0.00	3.01
1035	1490	0.178767	TGGCCATGAGATGTCTTCGG	59.821	55.000	0.00	0.00	0.00	4.30
1169	1719	9.369672	GAGGATTAGAAATAGGGAACTTAGAGA	57.630	37.037	0.00	0.00	43.67	3.10
1243	1793	1.471119	TCGTATGGACAGGAGGACAC	58.529	55.000	0.00	0.00	0.00	3.67
1299	1849	1.840635	GGTCTAGAGGGCACAAGGAAT	59.159	52.381	0.00	0.00	0.00	3.01
1397	1947	6.702329	AGTTCTTTTATCGAAGTGGTGAGAT	58.298	36.000	0.00	0.00	0.00	2.75
1435	1985	4.156556	TCAATAGATGTTTGCTGGCTGTTC	59.843	41.667	0.00	0.00	0.00	3.18
1446	1996	0.251033	TGGCTGTTCTGAAGCTGCAT	60.251	50.000	0.00	0.00	40.64	3.96
1476	2026	7.497773	ACTACTTAAGAAACCAGAGCCTATT	57.502	36.000	10.09	0.00	0.00	1.73
1477	2027	7.919151	ACTACTTAAGAAACCAGAGCCTATTT	58.081	34.615	10.09	0.00	0.00	1.40
1483	2033	2.693267	ACCAGAGCCTATTTCCGAAC	57.307	50.000	0.00	0.00	0.00	3.95
1490	2040	3.290710	AGCCTATTTCCGAACATTGCAT	58.709	40.909	0.00	0.00	0.00	3.96
1696	2248	2.399580	GAGGTATAGGTCAAGGCTGGT	58.600	52.381	0.00	0.00	0.00	4.00
1716	2268	6.418819	GCTGGTTGATATTGATACAAATGTGC	59.581	38.462	0.00	0.00	0.00	4.57
1790	2342	1.083806	GTTCTGCGCATGATGGTCGA	61.084	55.000	12.24	0.00	0.00	4.20
1814	2366	6.212955	AGTTCTTAGAGATGCTATTTCGAGC	58.787	40.000	0.00	0.00	43.16	5.03
1916	2468	4.101119	CCTTATCGAGGTCAAAGGTACCAT	59.899	45.833	15.94	0.00	40.95	3.55
1917	2469	3.821421	ATCGAGGTCAAAGGTACCATC	57.179	47.619	15.94	0.00	39.64	3.51
1934	2486	1.556911	CATCTAGGTGGTTGGACTGCT	59.443	52.381	0.00	0.00	0.00	4.24
1946	2498	1.515521	GGACTGCTCAAAACCCACCG	61.516	60.000	0.00	0.00	0.00	4.94
1979	2531	8.248945	GCAGAGGAATATTTTAATATGCTGCAT	58.751	33.333	20.18	20.18	39.54	3.96
2021	2573	4.630644	TGAGAGATGCTTTGGAAGACTT	57.369	40.909	0.00	0.00	0.00	3.01
2029	2583	3.137544	TGCTTTGGAAGACTTAAGGGTCA	59.862	43.478	7.53	0.00	38.57	4.02
2035	2589	2.715763	AGACTTAAGGGTCAGTGGGA	57.284	50.000	7.53	0.00	38.57	4.37
2036	2590	2.986050	AGACTTAAGGGTCAGTGGGAA	58.014	47.619	7.53	0.00	38.57	3.97
2051	2605	2.488153	GTGGGAAATTTTGAGGTCTCCG	59.512	50.000	0.00	0.00	0.00	4.63
2102	2656	4.456911	CGGATTATAATGGCATGTGCTCTT	59.543	41.667	0.00	2.02	41.70	2.85
2192	2746	2.834638	ACATGGAAATCTTGGAGGGG	57.165	50.000	0.00	0.00	0.00	4.79
2198	2752	2.515853	GGAAATCTTGGAGGGGGAGAAT	59.484	50.000	0.00	0.00	0.00	2.40
2244	2798	9.597170	CTCATATATCAACATCTAATGAGTGGG	57.403	37.037	0.00	0.00	0.00	4.61
2253	2807	7.961326	ACATCTAATGAGTGGGCTAATTTTT	57.039	32.000	0.00	0.00	28.95	1.94
2319	2873	4.850680	AGGTCACTAAGGTTTGTGTTTCA	58.149	39.130	4.58	0.00	35.79	2.69
2418	2972	9.859427	CTTGTTCATTTTGTATGTATGGACAAT	57.141	29.630	8.21	0.00	43.29	2.71
2489	3047	3.334691	GACAACAATGGAGGACGATGAA	58.665	45.455	0.00	0.00	0.00	2.57
2501	3059	3.195610	AGGACGATGAACTAGTCAATGCA	59.804	43.478	0.00	0.00	40.50	3.96
2510	3068	6.567959	TGAACTAGTCAATGCACTCTATGAG	58.432	40.000	0.00	0.00	31.51	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	34	2.998480	TGTTCGGGCCGGAGCTTA	60.998	61.111	27.98	1.38	39.73	3.09
56	325	0.391263	CGTCGAGGAAAGAAAGGGGG	60.391	60.000	0.00	0.00	0.00	5.40
76	345	1.910580	GCCGATCCAGGGAAGGTTCA	61.911	60.000	12.73	0.00	0.00	3.18
161	433	3.639672	AAGGAAACGATAAATCCGGGT	57.360	42.857	0.00	0.00	38.31	5.28
187	459	5.464168	CAAAACGCTTGAATCTTCCAGATT	58.536	37.500	0.00	0.00	46.84	2.40
199	471	5.761234	AGTACAATTCTACCAAAACGCTTGA	59.239	36.000	0.00	0.00	0.00	3.02
213	485	4.104831	AGCCCTAACCAGAGTACAATTCT	58.895	43.478	0.00	0.00	0.00	2.40
217	489	3.244582	TGAAGCCCTAACCAGAGTACAA	58.755	45.455	0.00	0.00	0.00	2.41
249	521	2.749621	CAGTACCCAAATCTCAACTGGC	59.250	50.000	0.00	0.00	32.60	4.85
283	555	6.899089	TCCCTCAAAATATTCTAGTCATGCA	58.101	36.000	0.00	0.00	0.00	3.96
292	564	7.124750	CCACCAAAGAATCCCTCAAAATATTCT	59.875	37.037	0.00	0.00	39.70	2.40
364	636	4.082125	GGATCTGACCACCTCATTTGTTT	58.918	43.478	0.00	0.00	0.00	2.83
519	791	6.814506	TTTACAGTGAGAGAGTACAGTACC	57.185	41.667	7.13	0.00	0.00	3.34
530	802	7.222417	CAGTAAGCATCAGATTTACAGTGAGAG	59.778	40.741	0.00	0.00	31.38	3.20
590	863	7.201750	GCTATTCTCTTATAGTATCACCCTCGG	60.202	44.444	0.00	0.00	31.96	4.63
661	934	0.908198	ACAAGCAGCCTCTTCCCTAG	59.092	55.000	0.00	0.00	0.00	3.02
697	970	5.869344	TGATCCACAAGAAACTGTAGAATCG	59.131	40.000	0.00	0.00	0.00	3.34
728	1001	2.475818	CACAACAGCGGTACAGTACAA	58.524	47.619	12.89	0.00	0.00	2.41
736	1009	2.345991	GAGGCCACAACAGCGGTA	59.654	61.111	5.01	0.00	0.00	4.02
762	1035	7.719633	ACAAACTAAAACAGGATACATCACACT	59.280	33.333	0.00	0.00	41.41	3.55
845	1118	1.149174	CTCACCACAGGGCAAGTGT	59.851	57.895	7.60	0.00	37.90	3.55
1022	1474	4.826274	AAATTCCTCCGAAGACATCTCA	57.174	40.909	0.00	0.00	0.00	3.27
1028	1483	5.819825	AAATGCTAAATTCCTCCGAAGAC	57.180	39.130	0.00	0.00	0.00	3.01
1031	1486	5.996644	TCCTAAATGCTAAATTCCTCCGAA	58.003	37.500	0.00	0.00	0.00	4.30
1032	1487	5.623956	TCCTAAATGCTAAATTCCTCCGA	57.376	39.130	0.00	0.00	0.00	4.55
1158	1708	2.726832	AGTGTGCGTCTCTAAGTTCC	57.273	50.000	0.00	0.00	0.00	3.62
1299	1849	4.483950	CCACTATCTCTTCCAGGGATGTA	58.516	47.826	0.00	0.00	0.00	2.29
1305	1855	3.300388	TGTAGCCACTATCTCTTCCAGG	58.700	50.000	0.00	0.00	0.00	4.45
1418	1968	1.881973	TCAGAACAGCCAGCAAACATC	59.118	47.619	0.00	0.00	0.00	3.06
1435	1985	5.269505	AGTAGTAGGTTATGCAGCTTCAG	57.730	43.478	0.00	0.00	34.13	3.02
1446	1996	7.093596	GGCTCTGGTTTCTTAAGTAGTAGGTTA	60.094	40.741	1.63	0.00	0.00	2.85
1476	2026	6.951062	TTATTATCCATGCAATGTTCGGAA	57.049	33.333	0.00	0.00	44.81	4.30
1477	2027	7.369607	CAATTATTATCCATGCAATGTTCGGA	58.630	34.615	0.00	0.00	44.81	4.55
1522	2072	9.907576	CGACACTAAAATTTTCATGTAGAGATC	57.092	33.333	16.07	6.71	0.00	2.75
1607	2159	5.743636	ATGCACCCAAACAATTCTACAAT	57.256	34.783	0.00	0.00	0.00	2.71
1696	2248	8.839343	CACCTAGCACATTTGTATCAATATCAA	58.161	33.333	0.00	0.00	0.00	2.57
1790	2342	6.040391	AGCTCGAAATAGCATCTCTAAGAACT	59.960	38.462	0.00	0.00	45.30	3.01
1814	2366	1.679032	GGGACTCGAAACCCATCCAAG	60.679	57.143	18.17	0.00	44.96	3.61
1841	2393	3.246226	CAGCATCGACAAGGTAGTATTGC	59.754	47.826	0.00	0.00	0.00	3.56
1916	2468	1.267121	GAGCAGTCCAACCACCTAGA	58.733	55.000	0.00	0.00	0.00	2.43
1917	2469	0.976641	TGAGCAGTCCAACCACCTAG	59.023	55.000	0.00	0.00	0.00	3.02
1934	2486	3.283684	CTGCGCGGTGGGTTTTGA	61.284	61.111	8.83	0.00	0.00	2.69
2021	2573	5.068215	TCAAAATTTCCCACTGACCCTTA	57.932	39.130	0.00	0.00	0.00	2.69
2029	2583	3.767711	GGAGACCTCAAAATTTCCCACT	58.232	45.455	0.00	0.00	0.00	4.00
2035	2589	7.703058	AAATATGACGGAGACCTCAAAATTT	57.297	32.000	0.00	0.00	0.00	1.82
2036	2590	7.148069	GGAAAATATGACGGAGACCTCAAAATT	60.148	37.037	0.00	0.00	0.00	1.82
2192	2746	8.348507	GTGATAAATTCAGGTTCATCATTCTCC	58.651	37.037	0.00	0.00	34.17	3.71
2253	2807	5.488919	ACATCCCTTGAGAAAGAGTATTCCA	59.511	40.000	0.00	0.00	0.00	3.53
2319	2873	4.492494	TGTACATCTGCAATCATCCACT	57.508	40.909	0.00	0.00	0.00	4.00
2397	2951	9.859152	TCCATATTGTCCATACATACAAAATGA	57.141	29.630	0.00	0.00	38.95	2.57
2407	2961	6.933514	TGAGCTATCCATATTGTCCATACA	57.066	37.500	0.00	0.00	0.00	2.29
2418	2972	4.191544	GTGCAACACTTGAGCTATCCATA	58.808	43.478	0.00	0.00	36.32	2.74
2489	3047	4.648762	AGCTCATAGAGTGCATTGACTAGT	59.351	41.667	0.00	0.00	39.15	2.57
2501	3059	4.040217	GGATCCAATGACAGCTCATAGAGT	59.960	45.833	6.95	0.00	35.96	3.24
2510	3068	1.679680	CACCATGGATCCAATGACAGC	59.320	52.381	20.67	0.00	0.00	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.