AutoCloner

Multiple sequence alignment - TraesCS4D01G128100

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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	TraesCS4D01G128100	chr4D	100.000	2462	0	0	1	2462	112198403	112195942	0.000000e+00	4547.0
1	TraesCS4D01G128100	chr4A	93.972	1742	74	11	725	2445	464988832	464990563	0.000000e+00	2606.0
2	TraesCS4D01G128100	chr4A	89.446	379	33	5	1	379	515702223	515701852	2.870000e-129	472.0
3	TraesCS4D01G128100	chr4B	95.312	960	35	8	1494	2445	172776766	172775809	0.000000e+00	1515.0
4	TraesCS4D01G128100	chr4B	95.405	370	11	4	1142	1507	172783195	172782828	3.530000e-163	584.0
5	TraesCS4D01G128100	chr4B	95.392	217	10	0	725	941	172790019	172789803	1.810000e-91	346.0
6	TraesCS4D01G128100	chr4B	100.000	65	0	0	988	1052	172789806	172789742	1.200000e-23	121.0
7	TraesCS4D01G128100	chr4B	98.462	65	1	0	1082	1146	172789740	172789676	5.560000e-22	115.0
8	TraesCS4D01G128100	chr6D	90.976	676	53	2	1	669	390724974	390725648	0.000000e+00	904.0
9	TraesCS4D01G128100	chr6D	92.000	325	19	1	404	721	14898367	14898043	1.340000e-122	449.0
10	TraesCS4D01G128100	chr6D	95.290	276	13	0	1	276	14898645	14898370	2.910000e-119	438.0
11	TraesCS4D01G128100	chr6A	89.808	677	60	3	1	669	537003566	537004241	0.000000e+00	859.0
12	TraesCS4D01G128100	chr6A	87.209	258	30	3	472	729	536981271	536981017	8.610000e-75	291.0
13	TraesCS4D01G128100	chr6A	85.542	83	12	0	341	423	6743962	6743880	1.210000e-13	87.9
14	TraesCS4D01G128100	chr5B	90.877	570	37	5	168	729	207581091	207580529	0.000000e+00	750.0
15	TraesCS4D01G128100	chr5B	92.045	88	7	0	1	88	207581403	207581316	9.240000e-25	124.0
16	TraesCS4D01G128100	chr6B	89.871	543	48	1	121	656	583726536	583725994	0.000000e+00	691.0
17	TraesCS4D01G128100	chr6B	84.726	694	65	14	1	686	38762499	38763159	0.000000e+00	656.0
18	TraesCS4D01G128100	chr1D	83.082	331	42	9	1121	1447	413294081	413293761	3.100000e-74	289.0
19	TraesCS4D01G128100	chr2A	81.564	179	30	3	235	412	710461615	710461439	7.100000e-31	145.0
20	TraesCS4D01G128100	chr3A	78.261	207	33	11	1205	1405	699521509	699521709	3.320000e-24	122.0
21	TraesCS4D01G128100	chr3D	78.836	189	31	9	1205	1390	565037855	565038037	4.300000e-23	119.0
22	TraesCS4D01G128100	chr3B	78.836	189	31	9	1205	1390	753174119	753173937	4.300000e-23	119.0
23	TraesCS4D01G128100	chr5A	81.301	123	22	1	601	722	598261646	598261524	5.600000e-17	99.0

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	TraesCS4D01G128100	chr4D	112195942	112198403	2461	True	4547.0	4547	100.000	1	2462	1	chr4D.!!$R1	2461
1	TraesCS4D01G128100	chr4A	464988832	464990563	1731	False	2606.0	2606	93.972	725	2445	1	chr4A.!!$F1	1720
2	TraesCS4D01G128100	chr4B	172775809	172776766	957	True	1515.0	1515	95.312	1494	2445	1	chr4B.!!$R1	951
3	TraesCS4D01G128100	chr6D	390724974	390725648	674	False	904.0	904	90.976	1	669	1	chr6D.!!$F1	668
4	TraesCS4D01G128100	chr6D	14898043	14898645	602	True	443.5	449	93.645	1	721	2	chr6D.!!$R1	720
5	TraesCS4D01G128100	chr6A	537003566	537004241	675	False	859.0	859	89.808	1	669	1	chr6A.!!$F1	668
6	TraesCS4D01G128100	chr5B	207580529	207581403	874	True	437.0	750	91.461	1	729	2	chr5B.!!$R1	728
7	TraesCS4D01G128100	chr6B	583725994	583726536	542	True	691.0	691	89.871	121	656	1	chr6B.!!$R1	535
8	TraesCS4D01G128100	chr6B	38762499	38763159	660	False	656.0	656	84.726	1	686	1	chr6B.!!$F1	685

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
876	1032	0.109735	TGTGACGCTTACTCGCTCTG	60.11	55.0	0.0	0.0	0.0	3.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2044	2213	0.904865	TGCAGTCGAGGGTGGAGAAT	60.905	55.0	0.0	0.0	0.0	2.4	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
139	140	0.981943	CCTCGTTCTTAACCCCCAGT	59.018	55.000	0.00	0.00	0.00	4.00
267	414	1.298340	CGCCACCATACAGGAACCA	59.702	57.895	0.00	0.00	41.22	3.67
339	486	6.754193	AGAAACGAGACAAAGAAGAGAAGAT	58.246	36.000	0.00	0.00	0.00	2.40
379	526	2.906388	TTCACCCGGACGTCGACA	60.906	61.111	17.16	0.00	42.43	4.35
401	548	1.454111	CGGGTCGTCCATCTCCTCT	60.454	63.158	0.04	0.00	34.36	3.69
503	657	3.119495	GCGGCCACAAATAGACAAGATTT	60.119	43.478	2.24	0.00	0.00	2.17
541	697	2.679132	AAAGTCGCTCACGTGTCGCT	62.679	55.000	22.89	19.44	41.18	4.93
556	712	1.206072	CGCTCTGAAACAGTGCAGC	59.794	57.895	20.16	11.67	46.98	5.25
576	732	0.613572	TCGCTGACAGTGGACCCATA	60.614	55.000	15.79	0.00	0.00	2.74
598	754	2.307309	GCCGAATACGCATGCGCTA	61.307	57.895	38.15	27.53	44.19	4.26
611	767	0.243907	TGCGCTAGAACAGAGTGACC	59.756	55.000	9.73	0.00	0.00	4.02
672	828	8.942338	AAACGTATTATCAAAGATCTAGCACA	57.058	30.769	0.00	0.00	0.00	4.57
693	849	3.773860	AAACTGCACATTCGACACAAA	57.226	38.095	0.00	0.00	0.00	2.83
721	877	5.531659	AGTGACTACCAGTGATATTACCTCG	59.468	44.000	0.00	0.00	0.00	4.63
741	897	6.599638	ACCTCGATAATTTTCTTTCAAGAGGG	59.400	38.462	14.82	0.00	44.06	4.30
798	954	6.073222	ACGAACTAACACTGCCAAATTTAGAG	60.073	38.462	0.00	0.00	0.00	2.43
804	960	6.655078	ACACTGCCAAATTTAGAGACAAAT	57.345	33.333	0.00	0.00	0.00	2.32
822	978	1.945387	ATCAAGATGATCAGCGCGTT	58.055	45.000	8.43	0.00	29.59	4.84
861	1017	3.608662	GTCCCCGTGTCCGTGTGA	61.609	66.667	0.00	0.00	0.00	3.58
876	1032	0.109735	TGTGACGCTTACTCGCTCTG	60.110	55.000	0.00	0.00	0.00	3.35
880	1036	1.309499	ACGCTTACTCGCTCTGCTCT	61.309	55.000	0.00	0.00	0.00	4.09
912	1068	2.086869	GGCATTTCAGCTCAACTGCTA	58.913	47.619	12.21	0.00	46.76	3.49
960	1116	2.057503	AATTCTCGCATCGATCCTCG	57.942	50.000	0.00	0.00	42.10	4.63
1043	1199	2.125269	AGTGCCCGAATACGTGCC	60.125	61.111	0.00	0.00	41.75	5.01
1202	1358	1.593750	CAGACGAGGCCATAGCTGC	60.594	63.158	5.01	0.00	39.73	5.25
1242	1398	1.454111	CGAGATGAGGGAGGACGGT	60.454	63.158	0.00	0.00	0.00	4.83
1266	1422	1.079750	GGTGTGCCTCGAGGACTTC	60.080	63.158	35.69	21.89	37.39	3.01
1277	1433	4.452733	GGACTTCGAGGGTGGCGG	62.453	72.222	0.00	0.00	0.00	6.13
1326	1482	3.730761	CACTGCTTCCACCAGCGC	61.731	66.667	0.00	0.00	43.37	5.92
1344	1500	1.522092	CTGCATCTTCCGGTGGCTA	59.478	57.895	0.00	0.00	0.00	3.93
1345	1501	0.107456	CTGCATCTTCCGGTGGCTAT	59.893	55.000	0.00	0.00	0.00	2.97
1346	1502	0.106708	TGCATCTTCCGGTGGCTATC	59.893	55.000	0.00	0.00	0.00	2.08
1410	1566	3.518998	GACGAGCAGCGCCTCCTA	61.519	66.667	2.29	0.00	46.04	2.94
1472	1636	6.088085	GCTGAAACCAACTGACGATTAATTTG	59.912	38.462	0.00	0.00	0.00	2.32
1525	1689	2.009774	GGATCAACATGGACTGGTTCG	58.990	52.381	0.00	0.00	0.00	3.95
1527	1691	0.036164	TCAACATGGACTGGTTCGGG	59.964	55.000	0.00	0.00	0.00	5.14
1537	1701	3.219198	GGTTCGGGGCCATGATGC	61.219	66.667	4.39	0.00	0.00	3.91
1636	1804	2.414559	GCGCGTTACACACTAGACCTAA	60.415	50.000	8.43	0.00	0.00	2.69
1719	1888	2.412847	CCAGAGAACCAAAATTCGTCGC	60.413	50.000	0.00	0.00	33.57	5.19
1732	1901	3.094058	GTCGCGCCATCGATCTCG	61.094	66.667	0.00	10.48	40.84	4.04
1745	1914	2.159558	TCGATCTCGGACAGAAAGAACG	60.160	50.000	0.00	0.00	40.29	3.95
1813	1982	1.071605	GAAGTGATCACTGCACGTCC	58.928	55.000	28.52	8.67	41.58	4.79
2002	2171	1.298667	CCGAAATTCTCCCGTGGGT	59.701	57.895	4.53	0.00	36.47	4.51
2099	2274	1.806542	TCGCTTTCCTGCAAAGATCAC	59.193	47.619	0.71	0.00	44.02	3.06
2142	2317	5.075858	AGATTCTTCAGCTGAGAGAAGTG	57.924	43.478	28.71	13.80	41.46	3.16
2174	2351	3.215975	TGGTAGTTGGTTTGTAAGCACC	58.784	45.455	0.00	0.00	38.84	5.01
2189	2366	0.517316	GCACCGCTTAGTTGTTCAGG	59.483	55.000	0.00	0.00	0.00	3.86
2257	2434	8.966868	TGATTTACCTTTTCTAAAATGCCTAGG	58.033	33.333	3.67	3.67	0.00	3.02
2428	2610	4.141711	ACTGTAACAGCAAAGAAGGAGACA	60.142	41.667	0.00	0.00	34.37	3.41
2445	2627	7.163001	AGGAGACAATTTTTCAGGCTATTTC	57.837	36.000	0.00	0.00	0.00	2.17
2446	2628	6.153510	AGGAGACAATTTTTCAGGCTATTTCC	59.846	38.462	0.00	0.00	0.00	3.13
2447	2629	6.286240	AGACAATTTTTCAGGCTATTTCCC	57.714	37.500	0.00	0.00	0.00	3.97
2448	2630	5.779771	AGACAATTTTTCAGGCTATTTCCCA	59.220	36.000	0.00	0.00	0.00	4.37
2449	2631	6.041423	ACAATTTTTCAGGCTATTTCCCAG	57.959	37.500	0.00	0.00	0.00	4.45
2450	2632	5.779771	ACAATTTTTCAGGCTATTTCCCAGA	59.220	36.000	0.00	0.00	0.00	3.86
2451	2633	6.071165	ACAATTTTTCAGGCTATTTCCCAGAG	60.071	38.462	0.00	0.00	0.00	3.35
2452	2634	4.657814	TTTTCAGGCTATTTCCCAGAGT	57.342	40.909	0.00	0.00	0.00	3.24
2453	2635	5.772393	TTTTCAGGCTATTTCCCAGAGTA	57.228	39.130	0.00	0.00	0.00	2.59
2454	2636	5.359194	TTTCAGGCTATTTCCCAGAGTAG	57.641	43.478	0.00	0.00	0.00	2.57
2455	2637	3.995636	TCAGGCTATTTCCCAGAGTAGT	58.004	45.455	0.00	0.00	0.00	2.73
2456	2638	3.706594	TCAGGCTATTTCCCAGAGTAGTG	59.293	47.826	0.00	0.00	0.00	2.74
2457	2639	3.452627	CAGGCTATTTCCCAGAGTAGTGT	59.547	47.826	0.00	0.00	0.00	3.55
2458	2640	4.080863	CAGGCTATTTCCCAGAGTAGTGTT	60.081	45.833	0.00	0.00	0.00	3.32
2459	2641	5.128827	CAGGCTATTTCCCAGAGTAGTGTTA	59.871	44.000	0.00	0.00	0.00	2.41
2460	2642	5.724854	AGGCTATTTCCCAGAGTAGTGTTAA	59.275	40.000	0.00	0.00	0.00	2.01
2461	2643	6.214819	AGGCTATTTCCCAGAGTAGTGTTAAA	59.785	38.462	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	3.724374	TGTTCAGTAAGGTTGGAGTTCG	58.276	45.455	0.00	0.00	0.00	3.95
19	20	6.775142	TGATCAATTTGTTCAGTAAGGTTGGA	59.225	34.615	6.14	0.00	0.00	3.53
45	46	2.860735	ACAGATTCGCTAAGATGTTCGC	59.139	45.455	0.00	0.00	0.00	4.70
139	140	4.411927	TGGCAATTCAAGCTAGGGTTTTA	58.588	39.130	0.00	0.00	0.00	1.52
208	355	6.735678	TTCACGTATGCATTGTGAGTAAAT	57.264	33.333	24.56	0.00	42.93	1.40
267	414	0.396811	GCCGCCTATCACCAAGGTAT	59.603	55.000	0.00	0.00	36.43	2.73
276	423	1.277842	TCTTTTCTGTGCCGCCTATCA	59.722	47.619	0.00	0.00	0.00	2.15
339	486	1.958579	AGCGCCGTCATATGGTTAGTA	59.041	47.619	2.29	0.00	0.00	1.82
530	686	0.101579	TGTTTCAGAGCGACACGTGA	59.898	50.000	25.01	0.00	0.00	4.35
541	697	1.224069	GCGAGCTGCACTGTTTCAGA	61.224	55.000	1.02	0.00	45.45	3.27
556	712	1.892819	ATGGGTCCACTGTCAGCGAG	61.893	60.000	0.00	0.00	0.00	5.03
576	732	1.648720	GCATGCGTATTCGGCATGT	59.351	52.632	22.90	0.00	44.64	3.21
598	754	4.866508	TCAAATACGGTCACTCTGTTCT	57.133	40.909	0.00	0.00	36.91	3.01
611	767	8.568732	ACAACTTGTTATTTGGTTCAAATACG	57.431	30.769	11.28	5.27	43.24	3.06
656	812	5.474532	TGCAGTTTTGTGCTAGATCTTTGAT	59.525	36.000	0.00	0.00	44.32	2.57
672	828	3.773860	TTGTGTCGAATGTGCAGTTTT	57.226	38.095	0.00	0.00	0.00	2.43
693	849	9.435570	AGGTAATATCACTGGTAGTCACTAAAT	57.564	33.333	0.00	0.00	0.00	1.40
721	877	6.437477	ACCACCCCTCTTGAAAGAAAATTATC	59.563	38.462	0.00	0.00	34.03	1.75
733	889	0.613853	CTCGGTACCACCCCTCTTGA	60.614	60.000	13.54	0.00	33.75	3.02
737	893	0.901580	TGTTCTCGGTACCACCCCTC	60.902	60.000	13.54	0.00	33.75	4.30
741	897	1.822990	TGATCTGTTCTCGGTACCACC	59.177	52.381	13.54	0.00	34.05	4.61
798	954	3.615614	GCGCTGATCATCTTGATTTGTC	58.384	45.455	0.00	0.00	37.20	3.18
804	960	2.193447	GTAACGCGCTGATCATCTTGA	58.807	47.619	5.73	0.00	0.00	3.02
822	978	2.339418	CGGGCACGTAACAATCTTGTA	58.661	47.619	0.00	0.00	36.37	2.41
852	1008	1.063951	CGAGTAAGCGTCACACGGAC	61.064	60.000	0.00	0.00	42.82	4.79
856	1012	0.109689	AGAGCGAGTAAGCGTCACAC	60.110	55.000	0.00	0.00	43.00	3.82
861	1017	1.137825	GAGCAGAGCGAGTAAGCGT	59.862	57.895	0.00	0.00	43.00	5.07
876	1032	4.625800	CCACTTGGCCACTAGAGC	57.374	61.111	3.88	0.00	0.00	4.09
912	1068	5.073311	AGCGCTCATGGATTATATACGTT	57.927	39.130	2.64	0.00	0.00	3.99
1052	1208	3.672295	CTGTGAGCCTCGAAGCCCC	62.672	68.421	1.47	0.00	0.00	5.80
1083	1239	1.153349	GAAGAAGGCCCCGCTAGTG	60.153	63.158	0.00	0.00	0.00	2.74
1221	1377	2.123251	TCCTCCCTCATCTCGCCC	60.123	66.667	0.00	0.00	0.00	6.13
1277	1433	2.811317	CCCTGAGCTTGTCGTCGC	60.811	66.667	0.00	0.00	0.00	5.19
1326	1482	0.107456	ATAGCCACCGGAAGATGCAG	59.893	55.000	9.46	0.00	0.00	4.41
1439	1595	3.469863	TTGGTTTCAGCTCGGGCGT	62.470	57.895	0.00	0.00	44.37	5.68
1490	1654	9.740239	CCATGTTGATCCTTAATTTGTCAATAG	57.260	33.333	0.00	0.00	32.19	1.73
1525	1689	1.549203	ATAAATCGCATCATGGCCCC	58.451	50.000	0.00	0.00	0.00	5.80
1527	1691	5.627499	TCTTAATAAATCGCATCATGGCC	57.373	39.130	0.00	0.00	0.00	5.36
1636	1804	5.105853	TCCTCCTTTCCTTAACTGGGTAAT	58.894	41.667	0.00	0.00	0.00	1.89
1719	1888	1.371022	CTGTCCGAGATCGATGGCG	60.371	63.158	0.54	6.05	43.02	5.69
1732	1901	3.399330	TGTTGGATCGTTCTTTCTGTCC	58.601	45.455	0.00	0.00	0.00	4.02
1813	1982	1.561643	TCTACAGGGCCTTCACTGAG	58.438	55.000	1.32	6.75	38.09	3.35
2044	2213	0.904865	TGCAGTCGAGGGTGGAGAAT	60.905	55.000	0.00	0.00	0.00	2.40
2099	2274	4.756642	TCTTCCAAGTCTTACAACATGCTG	59.243	41.667	0.00	0.00	0.00	4.41
2110	2285	5.002516	CAGCTGAAGAATCTTCCAAGTCTT	58.997	41.667	19.16	0.92	33.07	3.01
2142	2317	6.039382	ACAAACCAACTACCAACTGAAAGATC	59.961	38.462	0.00	0.00	37.43	2.75
2199	2376	5.560953	GCACTTCTTCAGTTGAACATGGTAC	60.561	44.000	0.00	0.00	30.92	3.34
2318	2495	1.553248	TGTACCTGCTCGCTACCATTT	59.447	47.619	0.00	0.00	0.00	2.32
2330	2512	1.064017	TCCCCATTCCAATGTACCTGC	60.064	52.381	0.00	0.00	34.60	4.85
2428	2610	6.019108	ACTCTGGGAAATAGCCTGAAAAATT	58.981	36.000	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.