AutoCloner

Multiple sequence alignment - TraesCS6A01G332200

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	TraesCS6A01G332200	chr6A	100.000	3111	0	0	1	3111	564110487	564113597	0.000000e+00	5746
1	TraesCS6A01G332200	chr6A	97.143	525	14	1	1811	2334	564098120	564098644	0.000000e+00	885
2	TraesCS6A01G332200	chr6A	90.196	102	8	2	1784	1884	599642770	599642670	7.000000e-27	132
3	TraesCS6A01G332200	chr3A	94.074	1772	78	5	564	2334	8616236	8617981	0.000000e+00	2665
4	TraesCS6A01G332200	chr3A	95.720	514	22	0	1821	2334	8611926	8612439	0.000000e+00	828
5	TraesCS6A01G332200	chr3A	96.487	427	15	0	1	427	8615688	8616114	0.000000e+00	706
6	TraesCS6A01G332200	chr3A	93.617	141	8	1	442	582	8616251	8616112	3.140000e-50	209
7	TraesCS6A01G332200	chr3A	76.678	283	57	3	843	1125	701183824	701184097	6.950000e-32	148
8	TraesCS6A01G332200	chr1D	93.059	922	60	4	1	921	475616968	475616050	0.000000e+00	1345
9	TraesCS6A01G332200	chr1D	85.370	540	58	13	1129	1662	475610515	475609991	9.820000e-150	540
10	TraesCS6A01G332200	chr1D	93.810	210	8	1	916	1125	475610670	475610466	8.380000e-81	311
11	TraesCS6A01G332200	chr1D	84.762	105	16	0	902	1006	492435425	492435321	4.240000e-19	106
12	TraesCS6A01G332200	chr3B	89.378	932	92	7	1	931	707064315	707065240	0.000000e+00	1166
13	TraesCS6A01G332200	chr3B	85.448	536	59	14	1134	1662	707083621	707084144	9.820000e-150	540
14	TraesCS6A01G332200	chr6D	88.918	776	53	11	2342	3110	420896480	420897229	0.000000e+00	926
15	TraesCS6A01G332200	chr7A	97.661	513	12	0	1822	2334	647867452	647866940	0.000000e+00	881
16	TraesCS6A01G332200	chr7A	91.176	102	8	1	1784	1884	571370182	571370283	1.500000e-28	137
17	TraesCS6A01G332200	chr6B	86.126	728	86	10	2386	3109	634311096	634311812	0.000000e+00	771
18	TraesCS6A01G332200	chr6B	83.451	284	31	14	2075	2356	255204586	255204317	1.850000e-62	250
19	TraesCS6A01G332200	chr4B	89.892	554	49	4	1784	2335	637064804	637065352	0.000000e+00	706
20	TraesCS6A01G332200	chr4B	92.464	491	32	3	1844	2334	637059194	637059679	0.000000e+00	697
21	TraesCS6A01G332200	chr4B	84.015	269	32	9	2075	2341	610788722	610788463	6.660000e-62	248
22	TraesCS6A01G332200	chr4B	83.969	262	31	9	2075	2334	610794419	610794167	1.110000e-59	241
23	TraesCS6A01G332200	chr2B	80.103	387	53	12	746	1125	98414123	98414492	1.840000e-67	267
24	TraesCS6A01G332200	chr5B	78.696	230	34	11	1784	2008	661301875	661301656	4.180000e-29	139
25	TraesCS6A01G332200	chr5B	75.618	283	60	3	843	1125	497460624	497460897	7.000000e-27	132
26	TraesCS6A01G332200	chr4A	80.311	193	30	6	1784	1973	625640057	625640244	4.180000e-29	139
27	TraesCS6A01G332200	chr7B	76.207	290	52	9	843	1128	192374101	192373825	1.500000e-28	137
28	TraesCS6A01G332200	chr5A	90.196	102	8	2	1784	1884	546870486	546870586	7.000000e-27	132

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	TraesCS6A01G332200	chr6A	564110487	564113597	3110	False	5746.000000	5746	100.000	1	3111	1	chr6A.!!$F2	3110
1	TraesCS6A01G332200	chr6A	564098120	564098644	524	False	885.000000	885	97.143	1811	2334	1	chr6A.!!$F1	523
2	TraesCS6A01G332200	chr3A	8611926	8617981	6055	False	1399.666667	2665	95.427	1	2334	3	chr3A.!!$F2	2333
3	TraesCS6A01G332200	chr1D	475616050	475616968	918	True	1345.000000	1345	93.059	1	921	1	chr1D.!!$R1	920
4	TraesCS6A01G332200	chr1D	475609991	475610670	679	True	425.500000	540	89.590	916	1662	2	chr1D.!!$R3	746
5	TraesCS6A01G332200	chr3B	707064315	707065240	925	False	1166.000000	1166	89.378	1	931	1	chr3B.!!$F1	930
6	TraesCS6A01G332200	chr3B	707083621	707084144	523	False	540.000000	540	85.448	1134	1662	1	chr3B.!!$F2	528
7	TraesCS6A01G332200	chr6D	420896480	420897229	749	False	926.000000	926	88.918	2342	3110	1	chr6D.!!$F1	768
8	TraesCS6A01G332200	chr7A	647866940	647867452	512	True	881.000000	881	97.661	1822	2334	1	chr7A.!!$R1	512
9	TraesCS6A01G332200	chr6B	634311096	634311812	716	False	771.000000	771	86.126	2386	3109	1	chr6B.!!$F1	723
10	TraesCS6A01G332200	chr4B	637064804	637065352	548	False	706.000000	706	89.892	1784	2335	1	chr4B.!!$F2	551

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
844	4636	0.041684	CTCCATTTGCCCCCTTTCCT	59.958	55.0	0.0	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2549	6355	0.413832	ACTCTGGCCCTTAGAGGTGA	59.586	55.0	19.73	0.0	44.65	4.02	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
101	3864	9.862371	AATAAAATGACGTAAAATGCACCAATA	57.138	25.926	0.00	0.00	0.00	1.90
178	3941	0.727793	GCAACGTGGTAAACCGCATG	60.728	55.000	12.87	11.18	46.55	4.06
291	4054	9.868277	AACATGAAATTCACACTTCACTAAAAA	57.132	25.926	0.00	0.00	34.52	1.94
382	4145	6.125029	CAGGAAGGTGATCATCATAAAAGGT	58.875	40.000	9.06	0.00	0.00	3.50
491	4281	8.760103	TTAAATCACAATCCACAACATGAATG	57.240	30.769	0.00	0.09	0.00	2.67
690	4481	0.178992	CAAGACAACCTGGGCCTCAA	60.179	55.000	4.53	0.00	0.00	3.02
691	4482	0.779997	AAGACAACCTGGGCCTCAAT	59.220	50.000	4.53	0.00	0.00	2.57
794	4585	3.117372	CGGGATCGTCCGTAGCTT	58.883	61.111	0.00	0.00	44.60	3.74
844	4636	0.041684	CTCCATTTGCCCCCTTTCCT	59.958	55.000	0.00	0.00	0.00	3.36
847	4639	0.977627	CATTTGCCCCCTTTCCTCCC	60.978	60.000	0.00	0.00	0.00	4.30
962	4754	0.955428	TGCAATGGACTGAGTTCCGC	60.955	55.000	0.00	0.00	38.69	5.54
971	4763	3.112709	GAGTTCCGCGCGCTCTTT	61.113	61.111	30.48	10.69	0.00	2.52
1122	4914	2.640989	CGTCCACCAGTTCGTCGA	59.359	61.111	0.00	0.00	0.00	4.20
1123	4915	1.728426	CGTCCACCAGTTCGTCGAC	60.728	63.158	5.18	5.18	0.00	4.20
1124	4916	1.728426	GTCCACCAGTTCGTCGACG	60.728	63.158	31.30	31.30	41.45	5.12
1170	4962	3.186047	GCGCGCGTCCATTAGTGT	61.186	61.111	32.35	0.00	0.00	3.55
1176	4968	0.989890	GCGTCCATTAGTGTGTCGAC	59.010	55.000	9.11	9.11	0.00	4.20
1342	5140	3.681593	TGGTGAAAAATCCTAGGGTTCG	58.318	45.455	8.01	0.00	0.00	3.95
1512	5311	8.055279	TGGCTTAATTAATCCAAGAACAAGAG	57.945	34.615	16.56	0.00	29.32	2.85
1604	5403	9.106070	CATAGGTAATAACTTAAACAGTGGGAC	57.894	37.037	0.00	0.00	35.12	4.46
1606	5405	7.166167	AGGTAATAACTTAAACAGTGGGACAG	58.834	38.462	0.00	0.00	41.80	3.51
1747	5546	4.081807	ACTTAACCGTAAGAACTAGGCCTG	60.082	45.833	17.99	8.18	39.36	4.85
1765	5564	9.640963	CTAGGCCTGTTACTTAATCATATACAC	57.359	37.037	17.99	0.00	0.00	2.90
1793	5592	1.674441	GCCTAATGCGGGGTTCTAAAC	59.326	52.381	0.00	0.00	0.00	2.01
2155	5961	1.406539	GGTCGATAGCCACGGTTTCTA	59.593	52.381	0.00	0.00	33.33	2.10
2169	5975	4.957327	ACGGTTTCTATTAGCCTCTCTTCT	59.043	41.667	0.00	0.00	0.00	2.85
2335	6141	8.573035	TGTTACCTGAGATTAAATTCCAACAAC	58.427	33.333	0.00	0.00	0.00	3.32
2336	6142	8.573035	GTTACCTGAGATTAAATTCCAACAACA	58.427	33.333	0.00	0.00	0.00	3.33
2337	6143	7.595819	ACCTGAGATTAAATTCCAACAACAA	57.404	32.000	0.00	0.00	0.00	2.83
2338	6144	8.193953	ACCTGAGATTAAATTCCAACAACAAT	57.806	30.769	0.00	0.00	0.00	2.71
2339	6145	9.308000	ACCTGAGATTAAATTCCAACAACAATA	57.692	29.630	0.00	0.00	0.00	1.90
2369	6175	4.937015	TCAAATCGAGACATCAAAGATGCA	59.063	37.500	6.90	0.00	0.00	3.96
2383	6189	6.571605	TCAAAGATGCACACAATCAAAAAGA	58.428	32.000	0.00	0.00	0.00	2.52
2386	6192	8.980610	CAAAGATGCACACAATCAAAAAGATTA	58.019	29.630	0.00	0.00	45.06	1.75
2387	6193	9.545105	AAAGATGCACACAATCAAAAAGATTAA	57.455	25.926	0.00	0.00	45.06	1.40
2416	6222	0.251209	GGAAGGGGAAAAACTCGGCT	60.251	55.000	0.00	0.00	0.00	5.52
2462	6268	4.708177	AGCAACAACAACATCTACAGTCT	58.292	39.130	0.00	0.00	0.00	3.24
2508	6314	1.933181	GTTTTTCAAAAGCAGCGCCTT	59.067	42.857	2.29	0.00	0.00	4.35
2549	6355	1.154016	CGCCAGTGTCGTCGAATCT	60.154	57.895	0.00	0.00	0.00	2.40
2554	6360	1.200252	CAGTGTCGTCGAATCTCACCT	59.800	52.381	9.38	0.00	0.00	4.00
2571	6377	2.838202	CACCTCTAAGGGCCAGAGTTTA	59.162	50.000	17.07	1.69	40.58	2.01
2608	6414	7.413510	GAAGAGCACGTCTTAGTAGACTCCG	62.414	52.000	4.05	0.00	46.21	4.63
2627	6433	4.651778	TCCGAGGAAATGTCTTCAACAAT	58.348	39.130	0.00	0.00	42.37	2.71
2633	6439	7.076842	AGGAAATGTCTTCAACAATGATACG	57.923	36.000	0.00	0.00	42.37	3.06
2683	6489	3.821600	ACCACGCATAAACACAACCATTA	59.178	39.130	0.00	0.00	0.00	1.90
2685	6491	4.320567	CCACGCATAAACACAACCATTACA	60.321	41.667	0.00	0.00	0.00	2.41
2694	6500	3.068024	ACACAACCATTACAAGGTGCAAG	59.932	43.478	0.00	0.00	39.86	4.01
2778	6584	0.033366	GTTTGTTGCCATCACCCCAC	59.967	55.000	0.00	0.00	0.00	4.61
2797	6603	1.380246	GATGTTGCATGGAGGGGCA	60.380	57.895	0.00	0.00	38.46	5.36
2816	6622	1.603802	CACACACACACCCTGATCAAC	59.396	52.381	0.00	0.00	0.00	3.18
2845	6651	3.005684	TGAAATCAACTGTTCCATGGCAC	59.994	43.478	6.96	7.35	0.00	5.01
2952	6768	0.933097	CGGAGAGCCAAACATCATCG	59.067	55.000	0.00	0.00	0.00	3.84
3054	6870	3.515316	CTTCGTGGCCGTCACAGGT	62.515	63.158	3.63	0.00	46.36	4.00
3090	6906	2.319841	GCACTGTCGCTGCATCACA	61.320	57.895	0.00	0.00	34.56	3.58
3092	6908	1.643880	CACTGTCGCTGCATCACATA	58.356	50.000	0.00	0.00	0.00	2.29
3110	6926	0.809636	TAATGTCGCCACCATCGCTG	60.810	55.000	0.00	0.00	0.00	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	3864	7.441836	CCTCTTGGGCAAAACTAAAGTTTATT	58.558	34.615	8.45	0.00	46.47	1.40
382	4145	7.816995	GGTGTTGAAGTCATTTTATTAATGGCA	59.183	33.333	0.00	0.00	34.86	4.92
573	4363	5.974751	GCCAAAATTAAAGTTCTTCACGTCA	59.025	36.000	0.00	0.00	0.00	4.35
666	4457	1.843421	CCCAGGTTGTCTTGACCCA	59.157	57.895	0.00	0.00	37.93	4.51
794	4585	2.840066	CGGGCGGCTGTTTTGTTCA	61.840	57.895	10.16	0.00	0.00	3.18
844	4636	1.064758	CACTCCATTCATTTCGGGGGA	60.065	52.381	0.00	0.00	0.00	4.81
847	4639	0.740737	GCCACTCCATTCATTTCGGG	59.259	55.000	0.00	0.00	0.00	5.14
962	4754	4.801221	GCTTGCCGAAAGAGCGCG	62.801	66.667	0.00	0.00	38.24	6.86
1017	4809	1.372582	GCGAAATGCTCATCCAGTCA	58.627	50.000	0.00	0.00	41.73	3.41
1050	4842	1.081242	CGCCTTCATGTTTTGCGCT	60.081	52.632	9.73	0.00	38.69	5.92
1170	4962	2.974489	GAAGGAGCCGTCGTCGACA	61.974	63.158	24.13	0.00	39.71	4.35
1176	4968	4.796231	CACGGGAAGGAGCCGTCG	62.796	72.222	0.00	0.00	38.13	5.12
1283	5075	6.806388	AATGCCCAAATGATGAAAGAAAAC	57.194	33.333	0.00	0.00	0.00	2.43
1342	5140	7.775561	ACTGATAAGTAAATCCCCAATTCAGAC	59.224	37.037	0.00	0.00	0.00	3.51
1515	5314	8.683615	GCTATGGGTTAGTGCTAATTAGTTTTT	58.316	33.333	13.91	1.20	0.00	1.94
1604	5403	9.906660	TTAATGGCTGATGTTTAAAGTTTACTG	57.093	29.630	0.00	0.00	0.00	2.74
1647	5446	4.377021	TGATTGCATGATTACGTCCCTAC	58.623	43.478	0.00	0.00	0.00	3.18
1765	5564	1.247567	CCCGCATTAGGCCTAATTGG	58.752	55.000	31.50	30.94	40.31	3.16
1777	5576	2.304761	TCTCTGTTTAGAACCCCGCATT	59.695	45.455	0.00	0.00	31.21	3.56
1793	5592	7.876582	TGGTATCATGAGCAAGATTAATCTCTG	59.123	37.037	18.19	17.32	35.76	3.35
1905	5705	7.394077	TCCAATAATGATTTCTGCAAGTCAAGA	59.606	33.333	0.00	0.00	32.45	3.02
2155	5961	4.283212	GGATAGCACAGAAGAGAGGCTAAT	59.717	45.833	0.00	0.00	40.12	1.73
2169	5975	7.823745	AAGAAAGAAAGAAAAGGATAGCACA	57.176	32.000	0.00	0.00	0.00	4.57
2335	6141	8.553696	TGATGTCTCGATTTGATGTTGATATTG	58.446	33.333	0.00	0.00	0.00	1.90
2336	6142	8.667076	TGATGTCTCGATTTGATGTTGATATT	57.333	30.769	0.00	0.00	0.00	1.28
2337	6143	8.667076	TTGATGTCTCGATTTGATGTTGATAT	57.333	30.769	0.00	0.00	0.00	1.63
2338	6144	8.491331	TTTGATGTCTCGATTTGATGTTGATA	57.509	30.769	0.00	0.00	0.00	2.15
2339	6145	6.990341	TTGATGTCTCGATTTGATGTTGAT	57.010	33.333	0.00	0.00	0.00	2.57
2340	6146	6.650390	TCTTTGATGTCTCGATTTGATGTTGA	59.350	34.615	0.00	0.00	0.00	3.18
2383	6189	8.504811	TTTTCCCCTTCCTCTTCATTTTTAAT	57.495	30.769	0.00	0.00	0.00	1.40
2386	6192	6.386927	AGTTTTTCCCCTTCCTCTTCATTTTT	59.613	34.615	0.00	0.00	0.00	1.94
2387	6193	5.905331	AGTTTTTCCCCTTCCTCTTCATTTT	59.095	36.000	0.00	0.00	0.00	1.82
2391	6197	3.496160	CGAGTTTTTCCCCTTCCTCTTCA	60.496	47.826	0.00	0.00	0.00	3.02
2416	6222	4.937201	TCTGTTCTAAGTTGTCAGCTGA	57.063	40.909	13.74	13.74	0.00	4.26
2474	6280	7.274904	GCTTTTGAAAAACCTTTTCGTACTTCT	59.725	33.333	7.22	0.00	0.00	2.85
2478	6284	6.635166	TGCTTTTGAAAAACCTTTTCGTAC	57.365	33.333	7.22	0.00	0.00	3.67
2508	6314	2.807967	CTGCACATCGTTTCTTTCCTGA	59.192	45.455	0.00	0.00	0.00	3.86
2549	6355	0.413832	ACTCTGGCCCTTAGAGGTGA	59.586	55.000	19.73	0.00	44.65	4.02
2554	6360	3.200958	ACCTAAACTCTGGCCCTTAGA	57.799	47.619	0.00	0.00	0.00	2.10
2571	6377	2.952310	GTGCTCTTCAAGGTGAAAACCT	59.048	45.455	0.00	0.00	43.04	3.50
2608	6414	7.064609	TCGTATCATTGTTGAAGACATTTCCTC	59.935	37.037	0.00	0.00	38.26	3.71
2610	6416	7.072177	TCGTATCATTGTTGAAGACATTTCC	57.928	36.000	0.00	0.00	38.26	3.13
2627	6433	1.199615	TTGTGGGGAGCATCGTATCA	58.800	50.000	0.00	0.00	34.37	2.15
2633	6439	3.069443	TGTTTTTCTTTGTGGGGAGCATC	59.931	43.478	0.00	0.00	0.00	3.91
2683	6489	2.028203	ACTTTTTGTGCTTGCACCTTGT	60.028	40.909	21.01	10.86	0.00	3.16
2685	6491	2.233431	TGACTTTTTGTGCTTGCACCTT	59.767	40.909	21.01	1.33	0.00	3.50
2694	6500	2.427095	ACCAAGGTCTGACTTTTTGTGC	59.573	45.455	7.85	0.00	0.00	4.57
2778	6584	2.484062	GCCCCTCCATGCAACATCG	61.484	63.158	0.00	0.00	0.00	3.84
2797	6603	1.211703	TGTTGATCAGGGTGTGTGTGT	59.788	47.619	0.00	0.00	0.00	3.72
2845	6651	1.320344	AAGCAGCCTCCATGCATGTG	61.320	55.000	24.58	16.49	46.31	3.21
2942	6758	2.198827	TGAACCTGCCGATGATGTTT	57.801	45.000	0.00	0.00	0.00	2.83
2946	6762	1.278985	TGAGTTGAACCTGCCGATGAT	59.721	47.619	0.00	0.00	0.00	2.45
2952	6768	2.946762	GCGTGAGTTGAACCTGCC	59.053	61.111	0.00	0.00	0.00	4.85
2992	6808	1.802960	GTAATCATGCATCGGCCTCTG	59.197	52.381	0.00	0.00	40.13	3.35
3001	6817	2.849880	GGCACGTTGTAATCATGCAT	57.150	45.000	0.00	0.00	38.05	3.96
3090	6906	0.106708	AGCGATGGTGGCGACATTAT	59.893	50.000	0.00	0.00	46.14	1.28
3092	6908	2.108514	CAGCGATGGTGGCGACATT	61.109	57.895	0.00	0.00	46.14	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.