AutoCloner

Multiple sequence alignment - TraesCS6A01G311900

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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	TraesCS6A01G311900	chr6A	100.000	3128	0	0	1	3128	548109681	548112808	0.000000e+00	5777
1	TraesCS6A01G311900	chr6A	93.814	97	5	1	2722	2818	548112314	548112409	9.040000e-31	145
2	TraesCS6A01G311900	chr6A	93.814	97	5	1	2634	2729	548112402	548112498	9.040000e-31	145
3	TraesCS6A01G311900	chr6D	93.265	2554	82	41	627	3128	401736660	401739175	0.000000e+00	3681
4	TraesCS6A01G311900	chr6D	88.641	537	41	9	1	533	401736015	401736535	1.220000e-178	636
5	TraesCS6A01G311900	chr6D	97.753	89	2	0	2634	2722	401738756	401738844	1.500000e-33	154
6	TraesCS6A01G311900	chr6D	92.784	97	6	1	2722	2818	401738668	401738763	4.210000e-29	139
7	TraesCS6A01G311900	chr6B	92.749	2579	77	34	633	3128	602503768	602506319	0.000000e+00	3626
8	TraesCS6A01G311900	chr6B	88.618	615	46	12	13	625	602503130	602503722	0.000000e+00	726
9	TraesCS6A01G311900	chr6B	93.960	298	15	2	1177	1471	85848898	85849195	6.150000e-122	448
10	TraesCS6A01G311900	chr6B	94.845	97	4	1	2634	2729	602505884	602505980	1.940000e-32	150
11	TraesCS6A01G311900	chr6B	89.076	119	7	6	2700	2818	602505779	602505891	3.250000e-30	143
12	TraesCS6A01G311900	chr4D	95.923	834	29	2	1177	2007	399420202	399419371	0.000000e+00	1347
13	TraesCS6A01G311900	chr1B	92.597	824	41	13	1178	1994	668249327	668250137	0.000000e+00	1166
14	TraesCS6A01G311900	chr1B	95.161	62	3	0	2054	2115	668250135	668250196	7.140000e-17	99
15	TraesCS6A01G311900	chr7D	88.199	966	95	15	1078	2040	159062796	159063745	0.000000e+00	1134
16	TraesCS6A01G311900	chr7A	87.436	971	104	14	1073	2040	159558363	159557408	0.000000e+00	1101
17	TraesCS6A01G311900	chr7B	87.238	956	106	13	1087	2040	119700558	119701499	0.000000e+00	1075
18	TraesCS6A01G311900	chr2B	94.483	145	5	2	1666	1810	196347126	196347267	1.460000e-53	220

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	TraesCS6A01G311900	chr6A	548109681	548112808	3127	False	2022.333333	5777	95.87600	1	3128	3	chr6A.!!$F1	3127
1	TraesCS6A01G311900	chr6D	401736015	401739175	3160	False	1152.500000	3681	93.11075	1	3128	4	chr6D.!!$F1	3127
2	TraesCS6A01G311900	chr6B	602503130	602506319	3189	False	1161.250000	3626	91.32200	13	3128	4	chr6B.!!$F2	3115
3	TraesCS6A01G311900	chr4D	399419371	399420202	831	True	1347.000000	1347	95.92300	1177	2007	1	chr4D.!!$R1	830
4	TraesCS6A01G311900	chr1B	668249327	668250196	869	False	632.500000	1166	93.87900	1178	2115	2	chr1B.!!$F1	937
5	TraesCS6A01G311900	chr7D	159062796	159063745	949	False	1134.000000	1134	88.19900	1078	2040	1	chr7D.!!$F1	962
6	TraesCS6A01G311900	chr7A	159557408	159558363	955	True	1101.000000	1101	87.43600	1073	2040	1	chr7A.!!$R1	967
7	TraesCS6A01G311900	chr7B	119700558	119701499	941	False	1075.000000	1075	87.23800	1087	2040	1	chr7B.!!$F1	953

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
608	633	0.034477	ATCCGACCCCGATTTGCTTT	60.034	50.0	0.0	0.0	38.22	3.51	F
737	827	0.822121	GGGGGCTTTATTGGTAGCGG	60.822	60.0	0.0	0.0	38.28	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1506	1636	1.712977	GCACGTCCGAGTCGAGGTAT	61.713	60.000	15.64	0.0	30.06	2.73	R
2196	2326	2.044555	CAGCTGTGATGGCAGTGGG	61.045	63.158	5.25	0.0	38.65	4.61	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
129	132	6.801539	AATTTGCTTGAGATGTCGTTCTTA	57.198	33.333	0.00	0.00	0.00	2.10
210	213	7.741027	CATTGGTTGCAAGAGATGATACTAT	57.259	36.000	0.00	0.00	0.00	2.12
222	225	9.806448	AAGAGATGATACTATGCTAAGAAGAGA	57.194	33.333	0.00	0.00	0.00	3.10
245	248	9.995003	GAGATAGGATATGTTGAGAAATTGTCT	57.005	33.333	0.00	0.00	40.25	3.41
335	338	8.587608	CCCAACATGCATTACTTATATTCCATT	58.412	33.333	0.00	0.00	0.00	3.16
382	388	5.389520	TGGTAGTATCTCATCTTAGCTGCT	58.610	41.667	7.57	7.57	0.00	4.24
396	402	2.125552	TGCTTCCAGCGGATCACG	60.126	61.111	0.00	0.00	46.26	4.35
398	404	2.202932	CTTCCAGCGGATCACGGG	60.203	66.667	0.00	0.00	44.51	5.28
420	426	4.261867	GGTGGGTAACTTTGGTTGATTGAC	60.262	45.833	0.00	0.00	36.92	3.18
538	544	4.118995	CGCGGCCACATGCATTGT	62.119	61.111	2.24	0.00	43.89	2.71
549	555	3.398406	ACATGCATTGTGTTCTCGTACA	58.602	40.909	0.00	0.00	37.11	2.90
550	556	3.433274	ACATGCATTGTGTTCTCGTACAG	59.567	43.478	0.00	0.00	37.11	2.74
551	557	3.106242	TGCATTGTGTTCTCGTACAGT	57.894	42.857	0.00	0.00	0.00	3.55
552	558	4.245845	TGCATTGTGTTCTCGTACAGTA	57.754	40.909	0.00	0.00	0.00	2.74
553	559	3.985279	TGCATTGTGTTCTCGTACAGTAC	59.015	43.478	0.00	0.00	0.00	2.73
604	629	1.143183	ACGATCCGACCCCGATTTG	59.857	57.895	0.00	0.00	38.22	2.32
608	633	0.034477	ATCCGACCCCGATTTGCTTT	60.034	50.000	0.00	0.00	38.22	3.51
640	719	4.933400	TGAGAATTTCCTACTAAACACGGC	59.067	41.667	0.00	0.00	0.00	5.68
689	768	2.421877	ATTAGCGCGTCATCCCGAGG	62.422	60.000	8.43	0.00	0.00	4.63
737	827	0.822121	GGGGGCTTTATTGGTAGCGG	60.822	60.000	0.00	0.00	38.28	5.52
778	868	3.958147	AGGAAAACAAACCATCGGAGTTT	59.042	39.130	0.00	0.00	37.93	2.66
872	962	1.918800	ACTTCGTTCCCCTCCCCTG	60.919	63.158	0.00	0.00	0.00	4.45
894	984	1.277557	CCAACCCAACCAGAGAGAGAG	59.722	57.143	0.00	0.00	0.00	3.20
895	985	2.251818	CAACCCAACCAGAGAGAGAGA	58.748	52.381	0.00	0.00	0.00	3.10
896	986	2.230130	ACCCAACCAGAGAGAGAGAG	57.770	55.000	0.00	0.00	0.00	3.20
1048	1163	4.643387	GGCTGGTCTTGGTGGCGT	62.643	66.667	0.00	0.00	0.00	5.68
1049	1164	2.594592	GCTGGTCTTGGTGGCGTT	60.595	61.111	0.00	0.00	0.00	4.84
1302	1429	3.302347	CTTCCACTTCCTCGCCGCT	62.302	63.158	0.00	0.00	0.00	5.52
2196	2326	2.121786	CAATTGCCTTGCGATGCATAC	58.878	47.619	4.61	0.00	38.76	2.39
2367	2501	6.148315	TCGGATTGATTCATTATGCTGTGATC	59.852	38.462	0.00	0.00	0.00	2.92
2386	2520	1.000019	CGGAGGTGGTGACTAGGGA	60.000	63.158	0.00	0.00	0.00	4.20
2387	2521	1.038130	CGGAGGTGGTGACTAGGGAG	61.038	65.000	0.00	0.00	0.00	4.30
2388	2522	0.688087	GGAGGTGGTGACTAGGGAGG	60.688	65.000	0.00	0.00	0.00	4.30
2389	2523	0.688087	GAGGTGGTGACTAGGGAGGG	60.688	65.000	0.00	0.00	0.00	4.30
2563	2706	3.881688	CAGGGTGGATCTTATTCTTGCTG	59.118	47.826	0.00	0.00	0.00	4.41
2564	2707	3.782523	AGGGTGGATCTTATTCTTGCTGA	59.217	43.478	0.00	0.00	0.00	4.26
2594	2740	4.955925	ACTCTCTTGTATCTGTCACTCG	57.044	45.455	0.00	0.00	0.00	4.18
2645	2791	9.866655	ATGGCTTAATCTCTTGTTATTTCCATA	57.133	29.630	0.00	0.00	0.00	2.74
2766	2912	2.989166	GTCAATTTTTGCTGTGGCTAGC	59.011	45.455	6.04	6.04	43.95	3.42
2778	2924	1.063174	GTGGCTAGCTTGCTTTGATCG	59.937	52.381	19.45	0.00	0.00	3.69
2865	3012	7.657354	AGGTCCAAATTTATTGCTGTTTTTCTC	59.343	33.333	0.00	0.00	0.00	2.87
2928	3075	3.063588	GCCTTATCTACGCCTGTTTCAAC	59.936	47.826	0.00	0.00	0.00	3.18
2936	3083	1.856802	GCCTGTTTCAACTTTGCCTG	58.143	50.000	0.00	0.00	0.00	4.85
2939	3086	2.159057	CCTGTTTCAACTTTGCCTGCTT	60.159	45.455	0.00	0.00	0.00	3.91
2940	3087	2.861935	CTGTTTCAACTTTGCCTGCTTG	59.138	45.455	0.00	0.00	0.00	4.01
2950	3119	0.401356	TGCCTGCTTGTTCATCCAGA	59.599	50.000	0.00	0.00	0.00	3.86
3000	3172	5.448360	GCCTAATCTGCTGATGTTTCTGTTC	60.448	44.000	6.88	0.00	32.44	3.18
3055	3227	9.630098	CTGCATTGTTGATTATTTAGTTTCAGT	57.370	29.630	0.00	0.00	0.00	3.41
3075	3247	8.479313	TTCAGTATTTGTCTGTCATGTATGTC	57.521	34.615	0.00	0.00	34.86	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
108	110	6.801539	AATAAGAACGACATCTCAAGCAAA	57.198	33.333	0.00	0.00	0.00	3.68
129	132	1.909700	ATGAAGGACGCCACACAAAT	58.090	45.000	0.00	0.00	0.00	2.32
177	180	4.798288	CAACCAATGCTGCCATCG	57.202	55.556	0.00	0.00	0.00	3.84
210	213	8.712228	TCAACATATCCTATCTCTTCTTAGCA	57.288	34.615	0.00	0.00	0.00	3.49
261	264	5.225899	ACGCTTTTCACGTTACTCTTTTT	57.774	34.783	0.00	0.00	41.93	1.94
262	265	4.549489	CGACGCTTTTCACGTTACTCTTTT	60.549	41.667	0.00	0.00	45.24	2.27
263	266	3.060740	CGACGCTTTTCACGTTACTCTTT	60.061	43.478	0.00	0.00	45.24	2.52
264	267	2.470257	CGACGCTTTTCACGTTACTCTT	59.530	45.455	0.00	0.00	45.24	2.85
277	280	4.957266	TCGATGTGACGACGCTTT	57.043	50.000	0.00	0.00	37.37	3.51
382	388	3.000819	ACCCGTGATCCGCTGGAA	61.001	61.111	1.44	0.00	34.34	3.53
396	402	2.368311	TCAACCAAAGTTACCCACCC	57.632	50.000	0.00	0.00	33.27	4.61
398	404	4.583073	AGTCAATCAACCAAAGTTACCCAC	59.417	41.667	0.00	0.00	33.27	4.61
420	426	1.860950	CTGCACGACGGAATGGAATAG	59.139	52.381	0.00	0.00	0.00	1.73
532	538	4.563524	GTACTGTACGAGAACACAATGC	57.436	45.455	1.67	0.00	0.00	3.56
570	595	0.931202	TCGTGCCGCATACGAATACG	60.931	55.000	3.78	0.00	46.29	3.06
595	620	3.401033	AAAAAGGAAAGCAAATCGGGG	57.599	42.857	0.00	0.00	0.00	5.73
625	650	5.664294	TGATTAAGCCGTGTTTAGTAGGA	57.336	39.130	0.00	0.00	0.00	2.94
640	719	4.285342	CGATCGTCATCGCTTGATTAAG	57.715	45.455	7.03	0.00	45.28	1.85
708	798	4.830600	CCAATAAAGCCCCCGTGTTTATAT	59.169	41.667	0.00	0.00	0.00	0.86
709	799	4.208746	CCAATAAAGCCCCCGTGTTTATA	58.791	43.478	0.00	0.00	0.00	0.98
710	800	3.028130	CCAATAAAGCCCCCGTGTTTAT	58.972	45.455	0.00	0.00	0.00	1.40
711	801	2.225066	ACCAATAAAGCCCCCGTGTTTA	60.225	45.455	0.00	0.00	0.00	2.01
712	802	1.262417	CCAATAAAGCCCCCGTGTTT	58.738	50.000	0.00	0.00	0.00	2.83
737	827	1.812571	CTGGGGGCGATTTATATGTGC	59.187	52.381	0.00	0.00	0.00	4.57
810	900	2.041265	TCCTTGGCTCCTCCCTCC	59.959	66.667	0.00	0.00	0.00	4.30
811	901	2.069430	CCTCCTTGGCTCCTCCCTC	61.069	68.421	0.00	0.00	0.00	4.30
812	902	2.041928	CCTCCTTGGCTCCTCCCT	59.958	66.667	0.00	0.00	0.00	4.20
813	903	2.923852	ATCCCTCCTTGGCTCCTCCC	62.924	65.000	0.00	0.00	0.00	4.30
872	962	1.303643	CTCTCTGGTTGGGTTGGGC	60.304	63.158	0.00	0.00	0.00	5.36
894	984	3.471680	GCTCTTCCTCTCTCTCTCTCTC	58.528	54.545	0.00	0.00	0.00	3.20
895	985	2.158900	CGCTCTTCCTCTCTCTCTCTCT	60.159	54.545	0.00	0.00	0.00	3.10
896	986	2.158957	TCGCTCTTCCTCTCTCTCTCTC	60.159	54.545	0.00	0.00	0.00	3.20
1037	1152	1.021202	CAACAAGAACGCCACCAAGA	58.979	50.000	0.00	0.00	0.00	3.02
1038	1153	0.738389	ACAACAAGAACGCCACCAAG	59.262	50.000	0.00	0.00	0.00	3.61
1039	1154	1.135257	CAACAACAAGAACGCCACCAA	60.135	47.619	0.00	0.00	0.00	3.67
1041	1156	0.248866	CCAACAACAAGAACGCCACC	60.249	55.000	0.00	0.00	0.00	4.61
1042	1157	0.869880	GCCAACAACAAGAACGCCAC	60.870	55.000	0.00	0.00	0.00	5.01
1048	1163	0.313672	GATGCGGCCAACAACAAGAA	59.686	50.000	2.24	0.00	0.00	2.52
1049	1164	1.851021	CGATGCGGCCAACAACAAGA	61.851	55.000	2.24	0.00	0.00	3.02
1506	1636	1.712977	GCACGTCCGAGTCGAGGTAT	61.713	60.000	15.64	0.00	30.06	2.73
2196	2326	2.044555	CAGCTGTGATGGCAGTGGG	61.045	63.158	5.25	0.00	38.65	4.61
2367	2501	2.058595	CCCTAGTCACCACCTCCGG	61.059	68.421	0.00	0.00	0.00	5.14
2386	2520	3.915346	AAAGTAATTCCAACACCCCCT	57.085	42.857	0.00	0.00	0.00	4.79
2387	2521	5.105106	CCAATAAAGTAATTCCAACACCCCC	60.105	44.000	0.00	0.00	0.00	5.40
2388	2522	5.482526	ACCAATAAAGTAATTCCAACACCCC	59.517	40.000	0.00	0.00	0.00	4.95
2389	2523	6.394809	CACCAATAAAGTAATTCCAACACCC	58.605	40.000	0.00	0.00	0.00	4.61
2563	2706	7.093992	ACAGATACAAGAGAGTTTAGCACTTC	58.906	38.462	0.00	0.00	35.01	3.01
2564	2707	6.998802	ACAGATACAAGAGAGTTTAGCACTT	58.001	36.000	0.00	0.00	35.01	3.16
2645	2791	6.757947	CAGCAAAAATGGACCATTATCGAAAT	59.242	34.615	20.11	0.00	32.43	2.17
2660	2806	3.184986	GCAAACTAGCCACAGCAAAAATG	59.815	43.478	0.00	0.00	43.56	2.32
2778	2924	1.177401	GAGGCCATTCTGGTTGAACC	58.823	55.000	7.57	7.57	40.46	3.62
2865	3012	3.094572	AGGCAATTCTGGATGAACAAGG	58.905	45.455	0.00	0.00	37.52	3.61
2916	3063	0.385390	AGGCAAAGTTGAAACAGGCG	59.615	50.000	0.00	0.00	0.00	5.52
2918	3065	1.410153	AGCAGGCAAAGTTGAAACAGG	59.590	47.619	0.00	0.00	0.00	4.00
2928	3075	1.614903	TGGATGAACAAGCAGGCAAAG	59.385	47.619	0.00	0.00	0.00	2.77
2936	3083	2.494870	AGGCAATTCTGGATGAACAAGC	59.505	45.455	0.00	0.00	37.52	4.01
2939	3086	3.084039	GACAGGCAATTCTGGATGAACA	58.916	45.455	0.00	0.00	38.98	3.18
2940	3087	3.128242	CAGACAGGCAATTCTGGATGAAC	59.872	47.826	0.00	0.00	38.98	3.18
2950	3119	5.809001	TCTTAGATGAACAGACAGGCAATT	58.191	37.500	0.00	0.00	0.00	2.32
3000	3172	3.685139	TCTGGAAGAACAAGTAGGCAG	57.315	47.619	0.00	0.00	42.31	4.85
3055	3227	8.314021	AGAACAGACATACATGACAGACAAATA	58.686	33.333	0.00	0.00	0.00	1.40
3056	3228	7.164122	AGAACAGACATACATGACAGACAAAT	58.836	34.615	0.00	0.00	0.00	2.32
3057	3229	6.524734	AGAACAGACATACATGACAGACAAA	58.475	36.000	0.00	0.00	0.00	2.83
3066	3238	8.654230	AGCAATTACTAGAACAGACATACATG	57.346	34.615	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.