AutoCloner

Multiple sequence alignment - TraesCS5A01G499800

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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	TraesCS5A01G499800	chr5A	100.000	2825	0	0	1	2825	666224788	666227612	0.000000e+00	5217
1	TraesCS5A01G499800	chr5A	84.143	391	53	7	2435	2824	707991620	707992002	1.240000e-98	370
2	TraesCS5A01G499800	chr4D	93.190	2144	94	13	719	2825	485379162	485381290	0.000000e+00	3103
3	TraesCS5A01G499800	chr4D	97.399	346	8	1	1	345	485374442	485374787	3.130000e-164	588
4	TraesCS5A01G499800	chr4D	95.062	324	13	3	344	664	485378151	485378474	9.030000e-140	507
5	TraesCS5A01G499800	chr4B	92.346	810	51	4	758	1560	618587517	618588322	0.000000e+00	1142
6	TraesCS5A01G499800	chr4B	84.733	393	51	6	2435	2825	668757324	668757709	4.410000e-103	385
7	TraesCS5A01G499800	chr4B	84.439	392	53	5	2435	2825	668658581	668658965	2.050000e-101	379
8	TraesCS5A01G499800	chr4B	89.474	190	20	0	31	220	618420523	618420712	1.010000e-59	241
9	TraesCS5A01G499800	chr4B	90.104	192	8	2	1607	1787	618588333	618588524	3.640000e-59	239
10	TraesCS5A01G499800	chr4B	89.571	163	12	2	191	348	618586796	618586958	4.770000e-48	202
11	TraesCS5A01G499800	chr4B	89.583	96	7	3	250	343	618420714	618420808	4.940000e-23	119
12	TraesCS5A01G499800	chr3D	79.075	908	145	22	1956	2825	545836261	545835361	1.460000e-162	582
13	TraesCS5A01G499800	chr6B	83.662	557	81	5	2250	2806	164395825	164395279	1.500000e-142	516
14	TraesCS5A01G499800	chr3B	80.137	730	113	21	2112	2825	685933226	685932513	1.500000e-142	516
15	TraesCS5A01G499800	chr3B	75.810	463	74	27	2369	2825	94495898	94496328	1.720000e-47	200
16	TraesCS5A01G499800	chr5B	84.439	392	52	7	2435	2825	704832205	704832588	7.390000e-101	377
17	TraesCS5A01G499800	chr1D	82.201	427	56	12	2366	2781	50706172	50706589	1.610000e-92	350

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	TraesCS5A01G499800	chr5A	666224788	666227612	2824	False	5217.000000	5217	100.000000	1	2825	1	chr5A.!!$F1	2824
1	TraesCS5A01G499800	chr4D	485374442	485381290	6848	False	1399.333333	3103	95.217000	1	2825	3	chr4D.!!$F1	2824
2	TraesCS5A01G499800	chr4B	618586796	618588524	1728	False	527.666667	1142	90.673667	191	1787	3	chr4B.!!$F4	1596
3	TraesCS5A01G499800	chr3D	545835361	545836261	900	True	582.000000	582	79.075000	1956	2825	1	chr3D.!!$R1	869
4	TraesCS5A01G499800	chr6B	164395279	164395825	546	True	516.000000	516	83.662000	2250	2806	1	chr6B.!!$R1	556
5	TraesCS5A01G499800	chr3B	685932513	685933226	713	True	516.000000	516	80.137000	2112	2825	1	chr3B.!!$R1	713

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
958	4976	0.112412	CTCCTCCTCCTCCTCCTAGC	59.888	65.0	0.0	0.0	0.0	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1946	5993	0.178961	AACCCCCTGCCTTTCAAGTC	60.179	55.0	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
44	45	4.697756	CTTGGGTTGGCCTCGCGA	62.698	66.667	9.26	9.26	34.45	5.87
105	106	6.184789	GGTGGGGTAATGATAGAAACAGAAA	58.815	40.000	0.00	0.00	0.00	2.52
171	172	3.096852	TCGCTTGGTCTATCTGGAAAGA	58.903	45.455	0.00	0.00	0.00	2.52
173	174	3.118956	CGCTTGGTCTATCTGGAAAGAGT	60.119	47.826	0.00	0.00	0.00	3.24
211	212	6.060028	TCTGAAGAAAAGTTCGTCCATTTG	57.940	37.500	2.23	0.00	37.37	2.32
384	3755	5.140747	TCTTGAGGACTTTGTAGCTCTTC	57.859	43.478	0.00	0.00	0.00	2.87
398	3769	8.771920	TTGTAGCTCTTCTTCGATAATTCAAA	57.228	30.769	0.00	0.00	0.00	2.69
423	3794	1.379044	CTTGGGCACATCTCCACCC	60.379	63.158	0.00	0.00	43.14	4.61
439	3810	5.045432	TCTCCACCCGGTGAATAGTAATTTT	60.045	40.000	19.81	0.00	35.23	1.82
506	3880	3.451526	CATAGAAGATGCTCAAGTGCGA	58.548	45.455	0.00	0.00	35.36	5.10
652	4028	4.305769	TCCAAACATCTCCAAATTTTGCG	58.694	39.130	3.50	0.00	0.00	4.85
725	4737	5.712917	ACCGATTTTATTGTTGGAGCCTTAA	59.287	36.000	0.00	0.00	0.00	1.85
737	4749	5.235850	TGGAGCCTTAACATCTGTACAAA	57.764	39.130	0.00	0.00	0.00	2.83
738	4750	5.245531	TGGAGCCTTAACATCTGTACAAAG	58.754	41.667	0.00	0.00	0.00	2.77
741	4753	5.003804	AGCCTTAACATCTGTACAAAGTGG	58.996	41.667	0.00	0.00	0.00	4.00
765	4778	3.650950	GGAAGGGCCTGAGGTGCA	61.651	66.667	6.92	0.00	0.00	4.57
820	4833	3.297134	AAAAGAGTCTCAAGCCACCAA	57.703	42.857	1.94	0.00	0.00	3.67
821	4834	3.515602	AAAGAGTCTCAAGCCACCAAT	57.484	42.857	1.94	0.00	0.00	3.16
822	4835	3.515602	AAGAGTCTCAAGCCACCAATT	57.484	42.857	1.94	0.00	0.00	2.32
940	4958	2.959030	GCCACTTTCAGAAAAAGTCCCT	59.041	45.455	0.00	0.00	38.32	4.20
941	4959	3.004839	GCCACTTTCAGAAAAAGTCCCTC	59.995	47.826	0.00	0.00	38.32	4.30
942	4960	3.570125	CCACTTTCAGAAAAAGTCCCTCC	59.430	47.826	0.00	0.00	38.32	4.30
943	4961	4.464947	CACTTTCAGAAAAAGTCCCTCCT	58.535	43.478	0.00	0.00	38.32	3.69
958	4976	0.112412	CTCCTCCTCCTCCTCCTAGC	59.888	65.000	0.00	0.00	0.00	3.42
981	4999	1.866015	ACATCCCTCAACCATCTCGA	58.134	50.000	0.00	0.00	0.00	4.04
1023	5041	1.833630	TCATACCAGACCCTTGAGCTG	59.166	52.381	0.00	0.00	0.00	4.24
1068	5086	7.546250	TCTTAAGAAGGTGTCATTCTTCTCT	57.454	36.000	16.65	11.67	46.13	3.10
1398	5422	0.736325	CCCACGGCGTTCTCTACTTG	60.736	60.000	11.19	0.00	0.00	3.16
1446	5470	0.807667	CTTCCGCAAGCGCTACAGAT	60.808	55.000	12.05	0.00	38.24	2.90
1481	5505	3.133003	CAGTATGTCAAGTACTCTGGGGG	59.867	52.174	0.00	0.00	30.24	5.40
1532	5556	2.510691	CGTCACCGCATACCCACC	60.511	66.667	0.00	0.00	0.00	4.61
1658	5697	0.179140	GCACCGGCAACAATGTATGG	60.179	55.000	0.00	0.00	40.72	2.74
1749	5788	4.003788	CTCCTCGGTGGCGTGGTT	62.004	66.667	0.00	0.00	35.26	3.67
1791	5838	1.068250	GGAGTCTGATGCCGCCTAC	59.932	63.158	0.00	0.00	0.00	3.18
1806	5853	0.108329	CCTACGACGCTGGGTTCAAT	60.108	55.000	0.00	0.00	0.00	2.57
1835	5882	7.447238	TGGGATGAGTTTTTAGTTCTCGAAATT	59.553	33.333	0.00	0.00	0.00	1.82
1874	5921	4.922206	AGGATGTCCTTGCAAATCTGTAA	58.078	39.130	0.00	0.00	46.09	2.41
1882	5929	6.749118	GTCCTTGCAAATCTGTAATGTGAATC	59.251	38.462	0.00	0.00	0.00	2.52
1895	5942	8.093659	TGTAATGTGAATCGAAAATGAGTGAA	57.906	30.769	0.00	0.00	0.00	3.18
1905	5952	6.255215	TCGAAAATGAGTGAACAAAGTGAAC	58.745	36.000	0.00	0.00	0.00	3.18
1914	5961	7.714813	TGAGTGAACAAAGTGAACTCATCATAA	59.285	33.333	9.71	0.00	41.63	1.90
1923	5970	5.032863	GTGAACTCATCATAATGTGCAAGC	58.967	41.667	0.00	0.00	40.97	4.01
2039	6091	4.643387	GGGACGGGTGCTTGTGCT	62.643	66.667	0.00	0.00	40.48	4.40
2167	6246	1.614317	GCTTCAAGGTGCAGGTATGGT	60.614	52.381	0.00	0.00	0.00	3.55
2268	6373	2.281484	GCGGTGCACCTCCTTTCA	60.281	61.111	32.28	0.00	0.00	2.69
2273	6378	1.963515	GGTGCACCTCCTTTCATTGTT	59.036	47.619	29.12	0.00	0.00	2.83
2286	6391	0.604073	CATTGTTGGCATGGTGCTCA	59.396	50.000	1.64	0.00	44.28	4.26
2327	6432	2.604686	TCCGGTGGCTCAGCTCTT	60.605	61.111	0.00	0.00	0.00	2.85
2349	6455	1.064463	GTGGCCTTTCATGGATCTGGA	60.064	52.381	3.32	0.00	0.00	3.86
2378	6484	0.584396	TTGTGTTTGGTCGTCGATGC	59.416	50.000	0.00	0.00	0.00	3.91
2499	6608	4.760047	ATGTGCGGTCGAGGTGGC	62.760	66.667	0.00	0.00	0.00	5.01
2511	6620	4.329545	GGTGGCGTGGGAGCTTGA	62.330	66.667	0.00	0.00	37.29	3.02
2512	6621	2.281484	GTGGCGTGGGAGCTTGAA	60.281	61.111	0.00	0.00	37.29	2.69
2579	6688	0.107410	TGTGGCTGTCGTTGACCTTT	60.107	50.000	0.00	0.00	0.00	3.11
2698	6807	1.370051	GCGCCTTGGTGTCGTTTTC	60.370	57.895	0.00	0.00	0.00	2.29
2727	6836	0.322975	GGGCTTTGTCTCAGAGCTCA	59.677	55.000	17.77	0.00	41.05	4.26
2767	6876	4.639171	GTTTGCGGCGGTTGTGGG	62.639	66.667	9.78	0.00	0.00	4.61
2793	6902	0.661483	GCTTCTGCGGCAACAAAGAC	60.661	55.000	18.23	9.35	0.00	3.01
2806	6915	0.174845	CAAAGACGGTGGGAGCGATA	59.825	55.000	1.68	0.00	42.41	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	4.475747	CCAACCCAAGTAAGGACCCTATTA	59.524	45.833	0.00	0.00	0.00	0.98
105	106	3.593442	TCTTTTGTTGTCCATGAGGGT	57.407	42.857	0.00	0.00	38.11	4.34
171	172	0.471617	AGAGGCTCTGTTGTTGCACT	59.528	50.000	17.96	0.00	0.00	4.40
173	174	0.469494	TCAGAGGCTCTGTTGTTGCA	59.531	50.000	36.22	18.11	44.58	4.08
359	3730	7.344352	AGAAGAGCTACAAAGTCCTCAAGATAT	59.656	37.037	0.00	0.00	0.00	1.63
384	3755	6.253746	CAAGCTCAGGTTTGAATTATCGAAG	58.746	40.000	0.00	0.00	36.04	3.79
398	3769	1.001641	GATGTGCCCAAGCTCAGGT	60.002	57.895	4.06	0.00	45.01	4.00
511	3885	5.104527	TCCTCGAATGTCATTAACCCTGAAT	60.105	40.000	0.00	0.00	0.00	2.57
652	4028	0.307453	TGAACTGTCGCAATGTGCAC	59.693	50.000	10.75	10.75	45.36	4.57
664	4040	8.655970	GCAAAAATGTTAGAAAAACTGAACTGT	58.344	29.630	0.00	0.00	0.00	3.55
695	4097	7.062956	GGCTCCAACAATAAAATCGGTAAAAAG	59.937	37.037	0.00	0.00	0.00	2.27
716	4118	5.122396	CACTTTGTACAGATGTTAAGGCTCC	59.878	44.000	7.45	0.00	0.00	4.70
717	4119	5.122396	CCACTTTGTACAGATGTTAAGGCTC	59.878	44.000	7.45	0.00	0.00	4.70
725	4737	3.403038	GTGCTCCACTTTGTACAGATGT	58.597	45.455	0.00	0.00	0.00	3.06
737	4749	3.322466	CCCTTCCCGTGCTCCACT	61.322	66.667	0.00	0.00	31.34	4.00
741	4753	4.785453	CAGGCCCTTCCCGTGCTC	62.785	72.222	0.00	0.00	34.51	4.26
765	4778	1.003718	GTGGCCTAGCGTTGGTCTT	60.004	57.895	3.32	0.00	0.00	3.01
940	4958	1.365105	GGCTAGGAGGAGGAGGAGGA	61.365	65.000	0.00	0.00	0.00	3.71
941	4959	1.155155	GGCTAGGAGGAGGAGGAGG	59.845	68.421	0.00	0.00	0.00	4.30
942	4960	1.155155	GGGCTAGGAGGAGGAGGAG	59.845	68.421	0.00	0.00	0.00	3.69
943	4961	0.027907	TAGGGCTAGGAGGAGGAGGA	60.028	60.000	0.00	0.00	0.00	3.71
958	4976	2.370189	GAGATGGTTGAGGGATGTAGGG	59.630	54.545	0.00	0.00	0.00	3.53
1023	5041	2.224885	GCTCGCCGAGATCAACGTC	61.225	63.158	20.05	0.00	0.00	4.34
1398	5422	0.320421	TGCCGGTGAACTTGTAGCTC	60.320	55.000	1.90	0.00	0.00	4.09
1446	5470	4.720046	TGACATACTGCCCTTGTTTGTTA	58.280	39.130	0.00	0.00	31.68	2.41
1481	5505	3.194719	GCATTGCCACCTCAGAGC	58.805	61.111	0.00	0.00	0.00	4.09
1532	5556	0.038435	TGAAAATGTGGCATGCGGTG	60.038	50.000	12.44	0.00	0.00	4.94
1574	5598	0.591170	ATACACTGCGTTTGGTGCAC	59.409	50.000	8.80	8.80	37.44	4.57
1749	5788	4.240103	CCGAGCATCATCCCGCCA	62.240	66.667	0.00	0.00	33.17	5.69
1791	5838	0.374758	CATCATTGAACCCAGCGTCG	59.625	55.000	0.00	0.00	0.00	5.12
1800	5847	7.830739	ACTAAAAACTCATCCCATCATTGAAC	58.169	34.615	0.00	0.00	0.00	3.18
1806	5853	5.874810	CGAGAACTAAAAACTCATCCCATCA	59.125	40.000	0.00	0.00	0.00	3.07
1835	5882	4.202398	ACATCCTCCTTATACGTAGTCCGA	60.202	45.833	0.08	0.00	43.93	4.55
1864	5911	9.558648	TCATTTTCGATTCACATTACAGATTTG	57.441	29.630	0.00	0.00	0.00	2.32
1874	5921	6.558771	TGTTCACTCATTTTCGATTCACAT	57.441	33.333	0.00	0.00	0.00	3.21
1882	5929	6.258160	AGTTCACTTTGTTCACTCATTTTCG	58.742	36.000	0.00	0.00	0.00	3.46
1895	5942	6.207221	TGCACATTATGATGAGTTCACTTTGT	59.793	34.615	4.20	0.00	37.11	2.83
1905	5952	4.913335	AAGGCTTGCACATTATGATGAG	57.087	40.909	4.20	0.00	36.73	2.90
1914	5961	5.473066	AAGATACAAAAAGGCTTGCACAT	57.527	34.783	0.00	0.00	0.00	3.21
1946	5993	0.178961	AACCCCCTGCCTTTCAAGTC	60.179	55.000	0.00	0.00	0.00	3.01
2044	6096	2.219458	CATCTTTGCGATGCCAGATCT	58.781	47.619	0.00	0.00	42.75	2.75
2268	6373	0.892755	CTGAGCACCATGCCAACAAT	59.107	50.000	0.00	0.00	46.52	2.71
2273	6378	2.360726	CTGCTGAGCACCATGCCA	60.361	61.111	1.40	0.00	46.52	4.92
2321	6426	0.407139	ATGAAAGGCCACCAAGAGCT	59.593	50.000	5.01	0.00	0.00	4.09
2327	6432	1.002069	AGATCCATGAAAGGCCACCA	58.998	50.000	5.01	0.00	0.00	4.17
2349	6455	1.035139	CCAAACACAAGAGCCAGCTT	58.965	50.000	0.00	0.00	0.00	3.74
2499	6608	1.734465	GTCTTCATTCAAGCTCCCACG	59.266	52.381	0.00	0.00	31.26	4.94
2511	6620	0.250513	GCCGAGACAGGGTCTTCATT	59.749	55.000	0.00	0.00	43.53	2.57
2512	6621	0.616111	AGCCGAGACAGGGTCTTCAT	60.616	55.000	0.00	0.00	43.53	2.57
2579	6688	2.189191	AAAGCAGCGATGCCTCCAGA	62.189	55.000	24.00	0.00	34.90	3.86
2714	6823	0.455005	CGATGCTGAGCTCTGAGACA	59.545	55.000	23.35	12.41	0.00	3.41
2793	6902	2.258591	CCGATATCGCTCCCACCG	59.741	66.667	19.78	0.00	38.18	4.94
2806	6915	3.195002	CATTGCCACGTCGCCGAT	61.195	61.111	1.78	0.00	37.88	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.