AutoCloner

Multiple sequence alignment - TraesCS7D01G084600

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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	TraesCS7D01G084600	chr7D	100.000	2911	0	0	1	2911	51738097	51735187	0.000000e+00	5376.0
1	TraesCS7D01G084600	chr7A	93.379	2930	143	35	1	2903	54666511	54663606	0.000000e+00	4289.0
2	TraesCS7D01G084600	chr4A	97.304	1966	50	2	1	1964	666116285	666114321	0.000000e+00	3334.0
3	TraesCS7D01G084600	chr4A	89.062	896	69	11	2045	2911	666114291	666113396	0.000000e+00	1085.0
4	TraesCS7D01G084600	chr4A	80.804	224	38	5	2458	2678	302677507	302677286	1.390000e-38	171.0
5	TraesCS7D01G084600	chr4A	73.986	296	56	14	2405	2680	694868213	694867919	1.850000e-17	100.0
6	TraesCS7D01G084600	chr5B	84.818	303	37	5	2408	2702	54387102	54386801	2.190000e-76	296.0
7	TraesCS7D01G084600	chr5B	78.333	300	46	15	2413	2702	259557955	259558245	2.980000e-40	176.0
8	TraesCS7D01G084600	chr1A	81.553	309	34	13	2404	2703	21000647	21000353	1.740000e-57	233.0
9	TraesCS7D01G084600	chr6B	80.068	296	40	8	2410	2704	439409325	439409602	4.920000e-48	202.0
10	TraesCS7D01G084600	chr6D	80.769	260	47	3	2448	2705	325690509	325690251	1.770000e-47	200.0
11	TraesCS7D01G084600	chr2A	86.022	186	18	4	2522	2705	104714610	104714431	2.960000e-45	193.0
12	TraesCS7D01G084600	chr2A	72.917	288	61	9	2409	2680	755767978	755768264	1.860000e-12	84.2
13	TraesCS7D01G084600	chr3A	74.882	211	39	10	2481	2680	17589402	17589195	1.860000e-12	84.2
14	TraesCS7D01G084600	chr3A	73.828	256	37	18	2460	2704	19289291	19289527	1.120000e-09	75.0
15	TraesCS7D01G084600	chr3A	72.881	295	48	22	2408	2680	457686859	457686575	4.020000e-09	73.1
16	TraesCS7D01G084600	chr3A	91.304	46	4	0	2409	2454	40848977	40849022	2.420000e-06	63.9

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	TraesCS7D01G084600	chr7D	51735187	51738097	2910	True	5376.0	5376	100.000	1	2911	1	chr7D.!!$R1	2910
1	TraesCS7D01G084600	chr7A	54663606	54666511	2905	True	4289.0	4289	93.379	1	2903	1	chr7A.!!$R1	2902
2	TraesCS7D01G084600	chr4A	666113396	666116285	2889	True	2209.5	3334	93.183	1	2911	2	chr4A.!!$R3	2910

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
889	890	0.731417	GCTGCATGCATCTTCTTCGT	59.269	50.0	22.97	0.0	42.31	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2033	2036	0.320771	ATCTTTTGCTCGTCGTGCCT	60.321	50.0	15.98	0.0	0.0	4.75	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
26	27	4.576216	AGTCATCCTCGACATCATGTAC	57.424	45.455	0.00	0.00	38.43	2.90
128	129	2.146342	CACGGTCAGCTTTCAACAGAT	58.854	47.619	0.00	0.00	0.00	2.90
505	506	3.065371	GGTTCCATAGGCAAACTGATTCG	59.935	47.826	0.00	0.00	0.00	3.34
543	544	4.769688	TGATGTCAGCCATAACAACCTAG	58.230	43.478	0.00	0.00	32.56	3.02
735	736	1.533625	TTCCTCGGCAGAATGGTTTG	58.466	50.000	0.00	0.00	35.86	2.93
818	819	4.925646	GCAAATCATCAGAAAAAGGACCAC	59.074	41.667	0.00	0.00	0.00	4.16
888	889	1.015109	AGCTGCATGCATCTTCTTCG	58.985	50.000	22.97	7.95	45.94	3.79
889	890	0.731417	GCTGCATGCATCTTCTTCGT	59.269	50.000	22.97	0.00	42.31	3.85
943	944	5.006386	AGAAAGTGCCATTGTAAAGAGAGG	58.994	41.667	0.00	0.00	0.00	3.69
1280	1281	3.034635	GGAGTCTAGCCTCAATCCTGAA	58.965	50.000	2.77	0.00	32.91	3.02
1287	1288	3.771216	AGCCTCAATCCTGAACAACAAT	58.229	40.909	0.00	0.00	0.00	2.71
1303	1304	3.947910	ACAATGACCAAGCAATCCAAG	57.052	42.857	0.00	0.00	0.00	3.61
1371	1372	3.577805	ATTTCCTACCTACACCATGGC	57.422	47.619	13.04	0.00	0.00	4.40
1569	1570	5.752955	CCCAGTGAAAACTGTTGGTTAATTG	59.247	40.000	5.24	0.00	37.12	2.32
1646	1649	1.289109	CTTACACGCCCTTGGTCACG	61.289	60.000	0.00	0.00	0.00	4.35
1938	1941	3.523157	TCCTGATTCCCTGAGTTGCATAA	59.477	43.478	0.00	0.00	0.00	1.90
1940	1943	4.891756	CCTGATTCCCTGAGTTGCATAAAT	59.108	41.667	0.00	0.00	0.00	1.40
1944	1947	5.389859	TTCCCTGAGTTGCATAAATTGTG	57.610	39.130	0.00	0.00	0.00	3.33
1964	1967	6.997239	TGTGGTCACATACTAGTACAGTAG	57.003	41.667	4.31	3.34	43.01	2.57
1965	1968	6.479006	TGTGGTCACATACTAGTACAGTAGT	58.521	40.000	4.31	2.47	43.01	2.73
1966	1969	7.623630	TGTGGTCACATACTAGTACAGTAGTA	58.376	38.462	4.31	6.44	43.01	1.82
1967	1970	7.550551	TGTGGTCACATACTAGTACAGTAGTAC	59.449	40.741	4.31	6.46	43.01	2.73
2000	2003	2.202743	CGGCCGAGCGAATCTTCA	60.203	61.111	24.07	0.00	0.00	3.02
2023	2026	9.453572	TTCAAGTCTTGATGATTAATAAGCTGT	57.546	29.630	15.95	0.00	39.84	4.40
2039	2042	1.933853	GCTGTAAATCAGGTAGGCACG	59.066	52.381	0.00	0.00	43.78	5.34
2040	2043	2.418197	GCTGTAAATCAGGTAGGCACGA	60.418	50.000	0.00	0.00	43.78	4.35
2041	2044	3.187700	CTGTAAATCAGGTAGGCACGAC	58.812	50.000	0.00	0.00	40.23	4.34
2042	2045	2.190981	GTAAATCAGGTAGGCACGACG	58.809	52.381	0.00	0.00	33.81	5.12
2043	2046	0.892755	AAATCAGGTAGGCACGACGA	59.107	50.000	0.00	0.00	33.81	4.20
2100	2103	6.203723	GTCGGAATCAAGAATGAATTCCCTAG	59.796	42.308	2.27	0.00	38.57	3.02
2210	2214	2.023015	TGGCTCTCCCCTTATTCTCTCA	60.023	50.000	0.00	0.00	0.00	3.27
2271	2275	3.259064	CTTCTTTTTATCTCCGACGGCA	58.741	45.455	9.66	0.00	0.00	5.69
2296	2300	2.588439	GCGGGGGTAGGGAAGAAC	59.412	66.667	0.00	0.00	0.00	3.01
2297	2301	2.295602	GCGGGGGTAGGGAAGAACA	61.296	63.158	0.00	0.00	0.00	3.18
2389	2398	0.748005	CCAAGGTCAGCCCAATACGG	60.748	60.000	0.00	0.00	34.66	4.02
2425	2458	1.434188	CACTATACCTGGCCATGGGA	58.566	55.000	17.65	12.89	0.00	4.37
2547	2580	5.163854	CCTGTCGTATTTGCAGTTTAAGGAG	60.164	44.000	0.00	0.00	0.00	3.69
2552	2585	2.200373	TTGCAGTTTAAGGAGGAGGC	57.800	50.000	0.00	0.00	0.00	4.70
2588	2628	1.537202	ACGAGCTTTTTGACTGATGGC	59.463	47.619	0.00	0.00	0.00	4.40
2737	2778	2.510238	CCTGCAGCGAGCCAGTAC	60.510	66.667	8.66	0.00	44.83	2.73
2762	2803	2.132762	CTGGTCCAGTAACAACGTGAC	58.867	52.381	11.09	0.00	0.00	3.67
2763	2804	1.481363	TGGTCCAGTAACAACGTGACA	59.519	47.619	0.00	0.00	0.00	3.58
2766	2807	3.386486	GTCCAGTAACAACGTGACATCA	58.614	45.455	0.00	0.00	0.00	3.07
2783	2824	4.726416	ACATCATCACGCATGTCTTTTTC	58.274	39.130	0.00	0.00	33.66	2.29
2792	2833	6.855914	TCACGCATGTCTTTTTCAACTTTATC	59.144	34.615	0.00	0.00	0.00	1.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	4.307443	TGTACATGATGTCGAGGATGAC	57.693	45.455	0.00	0.00	39.37	3.06
26	27	6.762187	GTGCTATATCTCCATCCATCTGATTG	59.238	42.308	0.00	0.00	0.00	2.67
128	129	0.402504	AGTTACCGCATGAACCCCAA	59.597	50.000	0.00	0.00	0.00	4.12
505	506	3.403038	ACATCAAGTGTTGTCTGTAGGC	58.597	45.455	0.00	0.00	38.01	3.93
543	544	0.548031	TCTGGAGGAATGGCACCATC	59.452	55.000	1.88	0.00	35.31	3.51
631	632	2.893398	GGAGTCCTGCTACCGTGG	59.107	66.667	0.41	0.00	0.00	4.94
735	736	3.182967	CGCAGAGACCTCTATTGTGAAC	58.817	50.000	0.00	0.00	37.98	3.18
818	819	4.766891	ACACCCACTTTTAACATGAGGATG	59.233	41.667	0.00	0.00	35.49	3.51
943	944	2.977808	TCCATATGGAGAAGAGGTCCC	58.022	52.381	20.98	0.00	39.78	4.46
1047	1048	5.310451	TCCACCTTGTAGACATTACCAAAC	58.690	41.667	0.00	0.00	0.00	2.93
1280	1281	2.964464	TGGATTGCTTGGTCATTGTTGT	59.036	40.909	0.00	0.00	0.00	3.32
1287	1288	2.942804	TCAACTTGGATTGCTTGGTCA	58.057	42.857	0.00	0.00	0.00	4.02
1303	1304	3.648339	TGCTCTTTTCTGCCAATCAAC	57.352	42.857	0.00	0.00	0.00	3.18
1371	1372	5.414360	CGATGGATTATAGGTGGATCACAG	58.586	45.833	0.00	0.00	35.86	3.66
1569	1570	4.767409	AGGGATTGTTTTTGAAGGAGCTAC	59.233	41.667	0.00	0.00	0.00	3.58
1646	1649	2.541762	GCTGTAGACATCGCATTTCTCC	59.458	50.000	0.00	0.00	0.00	3.71
1718	1721	1.879796	GCAGCTGCAGGTCTGTTTAGT	60.880	52.381	33.36	0.00	41.59	2.24
1938	1941	7.241042	ACTGTACTAGTATGTGACCACAATT	57.759	36.000	5.75	0.00	38.04	2.32
1940	1943	6.944290	ACTACTGTACTAGTATGTGACCACAA	59.056	38.462	5.75	0.00	41.72	3.33
1964	1967	1.391485	CGAGCATGTTCAGTGCAGTAC	59.609	52.381	10.36	0.00	44.87	2.73
1965	1968	1.672737	CCGAGCATGTTCAGTGCAGTA	60.673	52.381	10.36	0.00	44.87	2.74
1966	1969	0.952497	CCGAGCATGTTCAGTGCAGT	60.952	55.000	10.36	0.00	44.87	4.40
1967	1970	1.792301	CCGAGCATGTTCAGTGCAG	59.208	57.895	10.36	0.00	44.87	4.41
1968	1971	2.327343	GCCGAGCATGTTCAGTGCA	61.327	57.895	10.36	0.00	44.87	4.57
2023	2026	2.093890	TCGTCGTGCCTACCTGATTTA	58.906	47.619	0.00	0.00	0.00	1.40
2028	2031	2.202623	GCTCGTCGTGCCTACCTG	60.203	66.667	8.06	0.00	0.00	4.00
2029	2032	1.812686	TTTGCTCGTCGTGCCTACCT	61.813	55.000	15.98	0.00	0.00	3.08
2033	2036	0.320771	ATCTTTTGCTCGTCGTGCCT	60.321	50.000	15.98	0.00	0.00	4.75
2034	2037	0.517316	AATCTTTTGCTCGTCGTGCC	59.483	50.000	15.98	0.05	0.00	5.01
2035	2038	1.194547	TCAATCTTTTGCTCGTCGTGC	59.805	47.619	12.19	12.19	32.61	5.34
2036	2039	3.410850	CATCAATCTTTTGCTCGTCGTG	58.589	45.455	0.00	0.00	32.61	4.35
2037	2040	2.159653	GCATCAATCTTTTGCTCGTCGT	60.160	45.455	0.00	0.00	33.61	4.34
2038	2041	2.159667	TGCATCAATCTTTTGCTCGTCG	60.160	45.455	0.00	0.00	37.28	5.12
2039	2042	3.476295	TGCATCAATCTTTTGCTCGTC	57.524	42.857	0.00	0.00	37.28	4.20
2040	2043	4.171005	CAATGCATCAATCTTTTGCTCGT	58.829	39.130	0.00	0.00	37.28	4.18
2041	2044	3.000078	GCAATGCATCAATCTTTTGCTCG	60.000	43.478	0.00	0.00	37.28	5.03
2042	2045	3.930229	TGCAATGCATCAATCTTTTGCTC	59.070	39.130	15.92	0.00	37.28	4.26
2043	2046	3.932822	TGCAATGCATCAATCTTTTGCT	58.067	36.364	15.92	0.00	37.28	3.91
2100	2103	2.608090	GGTCGTTATAAGGTGAGCTTGC	59.392	50.000	7.22	0.00	0.00	4.01
2210	2214	4.301027	GATTCGCCGGCCGGAGAT	62.301	66.667	44.46	33.68	43.32	2.75
2296	2300	1.303799	AAATGCTCTGCGGCTGTCTG	61.304	55.000	0.00	0.00	0.00	3.51
2297	2301	0.607489	AAAATGCTCTGCGGCTGTCT	60.607	50.000	0.00	0.00	0.00	3.41
2389	2398	1.034292	GTGGGCTCCCTGCTGAATTC	61.034	60.000	6.50	0.00	42.39	2.17
2405	2414	0.401738	CCCATGGCCAGGTATAGTGG	59.598	60.000	17.55	14.31	38.21	4.00
2406	2415	1.434188	TCCCATGGCCAGGTATAGTG	58.566	55.000	17.55	4.85	0.00	2.74
2407	2416	2.057922	CTTCCCATGGCCAGGTATAGT	58.942	52.381	17.55	0.00	0.00	2.12
2408	2417	1.271597	GCTTCCCATGGCCAGGTATAG	60.272	57.143	17.55	10.70	0.00	1.31
2409	2418	0.771127	GCTTCCCATGGCCAGGTATA	59.229	55.000	17.55	0.00	0.00	1.47
2520	2553	1.019278	ACTGCAAATACGACAGGCCG	61.019	55.000	0.00	0.00	35.70	6.13
2571	2611	1.260544	GGGCCATCAGTCAAAAAGCT	58.739	50.000	4.39	0.00	0.00	3.74
2639	2680	1.068474	CGACACAGAAAACCTAGGCG	58.932	55.000	9.30	0.00	0.00	5.52
2683	2724	1.045407	GTATACCTGGCCATCCGTCA	58.955	55.000	5.51	0.00	34.14	4.35
2762	2803	4.725359	TGAAAAAGACATGCGTGATGATG	58.275	39.130	14.17	0.00	35.80	3.07
2763	2804	5.048504	AGTTGAAAAAGACATGCGTGATGAT	60.049	36.000	14.17	0.00	35.80	2.45
2766	2807	4.836125	AGTTGAAAAAGACATGCGTGAT	57.164	36.364	14.17	0.00	0.00	3.06
2870	2914	9.448438	TTGTATACACTGCATTTACATCTTCTT	57.552	29.630	4.68	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.