AutoCloner

Multiple sequence alignment - TraesCS7B01G226200

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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	TraesCS7B01G226200	chr7B	100.000	2429	0	0	1	2429	426832398	426834826	0.000000e+00	4486.0
1	TraesCS7B01G226200	chr7B	91.803	305	25	0	1121	1425	426788806	426789110	2.230000e-115	425.0
2	TraesCS7B01G226200	chr7A	91.770	1774	86	26	638	2387	473807189	473808926	0.000000e+00	2412.0
3	TraesCS7B01G226200	chr7A	92.131	305	24	0	1121	1425	473674543	473674847	4.800000e-117	431.0
4	TraesCS7B01G226200	chr7A	76.220	492	104	10	70	554	676364706	676364221	5.190000e-62	248.0
5	TraesCS7B01G226200	chr7A	81.313	198	27	7	362	552	166724770	166724964	4.180000e-33	152.0
6	TraesCS7B01G226200	chr7A	91.525	59	4	1	1684	1741	63334489	63334547	2.000000e-11	80.5
7	TraesCS7B01G226200	chr7D	95.238	966	37	5	551	1515	412394306	412395263	0.000000e+00	1520.0
8	TraesCS7B01G226200	chr7D	85.201	696	76	18	1739	2428	492211883	492212557	0.000000e+00	689.0
9	TraesCS7B01G226200	chr7D	92.459	305	23	0	1121	1425	412235001	412235305	1.030000e-118	436.0
10	TraesCS7B01G226200	chr7D	96.667	90	3	0	1595	1684	412395476	412395565	1.500000e-32	150.0
11	TraesCS7B01G226200	chr7D	80.000	140	26	2	1742	1880	556322321	556322183	4.270000e-18	102.0
12	TraesCS7B01G226200	chr1B	95.118	553	26	1	1	553	525741802	525742353	0.000000e+00	870.0
13	TraesCS7B01G226200	chr5A	93.923	543	33	0	13	555	433718086	433718628	0.000000e+00	821.0
14	TraesCS7B01G226200	chr2A	92.586	553	40	1	1	553	193873223	193873774	0.000000e+00	793.0
15	TraesCS7B01G226200	chr6D	84.857	700	78	19	1735	2428	439659188	439658511	0.000000e+00	680.0
16	TraesCS7B01G226200	chr2D	84.704	693	79	18	1742	2428	120257157	120257828	0.000000e+00	667.0
17	TraesCS7B01G226200	chr4D	84.195	696	81	21	1739	2428	29026163	29026835	0.000000e+00	649.0
18	TraesCS7B01G226200	chr3B	71.316	509	134	10	52	554	46287472	46286970	1.180000e-23	121.0
19	TraesCS7B01G226200	chr5B	84.483	58	8	1	1685	1741	459457061	459457118	3.370000e-04	56.5

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	TraesCS7B01G226200	chr7B	426832398	426834826	2428	False	4486	4486	100.0000	1	2429	1	chr7B.!!$F2	2428
1	TraesCS7B01G226200	chr7A	473807189	473808926	1737	False	2412	2412	91.7700	638	2387	1	chr7A.!!$F4	1749
2	TraesCS7B01G226200	chr7D	412394306	412395565	1259	False	835	1520	95.9525	551	1684	2	chr7D.!!$F3	1133
3	TraesCS7B01G226200	chr7D	492211883	492212557	674	False	689	689	85.2010	1739	2428	1	chr7D.!!$F2	689
4	TraesCS7B01G226200	chr1B	525741802	525742353	551	False	870	870	95.1180	1	553	1	chr1B.!!$F1	552
5	TraesCS7B01G226200	chr5A	433718086	433718628	542	False	821	821	93.9230	13	555	1	chr5A.!!$F1	542
6	TraesCS7B01G226200	chr2A	193873223	193873774	551	False	793	793	92.5860	1	553	1	chr2A.!!$F1	552
7	TraesCS7B01G226200	chr6D	439658511	439659188	677	True	680	680	84.8570	1735	2428	1	chr6D.!!$R1	693
8	TraesCS7B01G226200	chr2D	120257157	120257828	671	False	667	667	84.7040	1742	2428	1	chr2D.!!$F1	686
9	TraesCS7B01G226200	chr4D	29026163	29026835	672	False	649	649	84.1950	1739	2428	1	chr4D.!!$F1	689

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
878	881	0.107703	TGTTCAGGATAAGCTGGCCG	60.108	55.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2074	2280	0.037232	AGTTCGTTGGCTAGCAGGAC	60.037	55.0	18.24	10.39	0.0	3.85	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
343	344	3.255149	ACCGTGTTCTAGTTGACGAGATT	59.745	43.478	10.41	0.00	33.64	2.40
360	361	6.236409	ACGAGATTCGGAGGATAGTTACATA	58.764	40.000	3.37	0.00	45.59	2.29
370	371	8.047911	CGGAGGATAGTTACATAAGAGGATAGA	58.952	40.741	0.00	0.00	0.00	1.98
544	545	6.794534	AGTAATGAAAATCTCCTTTCACCCT	58.205	36.000	1.12	0.00	45.52	4.34
635	636	2.375174	TGGGAAGATAACACTTGGCACT	59.625	45.455	0.00	0.00	0.00	4.40
645	646	2.203280	TTGGCACTCGGTTGGTGG	60.203	61.111	0.00	0.00	35.47	4.61
667	668	6.767080	TGGAACACGTCACAATATTATTTCG	58.233	36.000	0.00	0.00	0.00	3.46
672	673	8.820628	ACACGTCACAATATTATTTCGAATTG	57.179	30.769	0.00	1.74	35.83	2.32
718	719	2.341846	ATACCCCAAGCATACAACCG	57.658	50.000	0.00	0.00	0.00	4.44
853	856	3.353836	CGCTCCAACCCAACCGTG	61.354	66.667	0.00	0.00	0.00	4.94
875	878	1.656652	CCGTGTTCAGGATAAGCTGG	58.343	55.000	0.00	0.00	0.00	4.85
878	881	0.107703	TGTTCAGGATAAGCTGGCCG	60.108	55.000	0.00	0.00	0.00	6.13
942	945	2.364002	GCTCCAACACTATCCTCTCCTC	59.636	54.545	0.00	0.00	0.00	3.71
1152	1159	0.390124	AGGCGACGTACAAGGTGAAA	59.610	50.000	0.00	0.00	0.00	2.69
1516	1524	7.060383	ACTGTATCAGGATATTGAGGAGTTG	57.940	40.000	1.90	0.00	35.51	3.16
1524	1532	6.037610	CAGGATATTGAGGAGTTGCAAAGTAC	59.962	42.308	0.00	0.00	0.00	2.73
1525	1533	5.880332	GGATATTGAGGAGTTGCAAAGTACA	59.120	40.000	0.00	0.00	30.29	2.90
1526	1534	6.037610	GGATATTGAGGAGTTGCAAAGTACAG	59.962	42.308	0.00	0.00	30.29	2.74
1527	1535	3.838244	TGAGGAGTTGCAAAGTACAGT	57.162	42.857	0.00	0.00	30.29	3.55
1528	1536	4.948341	TGAGGAGTTGCAAAGTACAGTA	57.052	40.909	0.00	0.00	30.29	2.74
1529	1537	4.628074	TGAGGAGTTGCAAAGTACAGTAC	58.372	43.478	0.00	2.05	30.29	2.73
1530	1538	3.650139	AGGAGTTGCAAAGTACAGTACG	58.350	45.455	0.00	0.00	30.29	3.67
1771	1954	4.831107	TGCACTGCTGATACATGAAGTTA	58.169	39.130	0.00	0.00	0.00	2.24
1826	2009	5.857822	AAAATACGGAAAGCTAGTGTCAC	57.142	39.130	0.00	0.00	0.00	3.67
1849	2032	7.607607	TCACAACTTGTCTCAAAGTGCATATAT	59.392	33.333	0.00	0.00	40.28	0.86
1862	2045	8.407832	CAAAGTGCATATATGGTTCAATTCTCA	58.592	33.333	14.51	0.00	0.00	3.27
1892	2075	0.034283	TGTATGCTGCTTCCATGGCA	60.034	50.000	6.96	0.00	39.06	4.92
1904	2087	1.000521	CATGGCATGACAGGGTGGT	60.001	57.895	22.91	0.00	0.00	4.16
1906	2089	1.792757	ATGGCATGACAGGGTGGTGT	61.793	55.000	7.63	0.00	0.00	4.16
1912	2095	3.553095	GACAGGGTGGTGTCAGGCC	62.553	68.421	0.00	0.00	45.34	5.19
1921	2104	3.555324	TGTCAGGCCCGCTGTCAA	61.555	61.111	0.00	0.00	0.00	3.18
1922	2105	2.281484	GTCAGGCCCGCTGTCAAA	60.281	61.111	0.00	0.00	0.00	2.69
1929	2112	0.246635	GCCCGCTGTCAAAGACTAGA	59.753	55.000	0.00	0.00	33.15	2.43
1979	2169	7.524698	GCAGAACACCCCTGAATTAATAACAAA	60.525	37.037	0.00	0.00	33.65	2.83
2070	2276	1.740025	GGTTCTCACTACAAGCATGGC	59.260	52.381	0.00	0.00	0.00	4.40
2071	2277	2.426522	GTTCTCACTACAAGCATGGCA	58.573	47.619	0.00	0.00	0.00	4.92
2072	2278	3.012518	GTTCTCACTACAAGCATGGCAT	58.987	45.455	0.00	0.00	0.00	4.40
2073	2279	2.635714	TCTCACTACAAGCATGGCATG	58.364	47.619	22.99	22.99	33.24	4.06
2074	2280	1.674441	CTCACTACAAGCATGGCATGG	59.326	52.381	27.48	14.27	31.12	3.66
2129	2335	6.420913	TTGTCCATCTAAGATAAGTAGGCC	57.579	41.667	0.00	0.00	0.00	5.19
2139	2345	8.861086	TCTAAGATAAGTAGGCCTATTGTTCTG	58.139	37.037	17.38	7.13	0.00	3.02
2141	2347	6.821388	AGATAAGTAGGCCTATTGTTCTGTG	58.179	40.000	17.38	0.00	0.00	3.66
2158	2364	3.294493	GCACCAACATGCACCCGT	61.294	61.111	0.00	0.00	45.39	5.28
2175	2381	2.159382	CCGTCTTAAATGGGTTGCAGT	58.841	47.619	0.00	0.00	0.00	4.40
2176	2382	2.556622	CCGTCTTAAATGGGTTGCAGTT	59.443	45.455	0.00	0.00	0.00	3.16
2177	2383	3.754323	CCGTCTTAAATGGGTTGCAGTTA	59.246	43.478	0.00	0.00	0.00	2.24
2178	2384	4.379082	CCGTCTTAAATGGGTTGCAGTTAC	60.379	45.833	0.00	0.00	0.00	2.50
2179	2385	4.454504	CGTCTTAAATGGGTTGCAGTTACT	59.545	41.667	0.00	0.00	0.00	2.24
2180	2386	5.616866	CGTCTTAAATGGGTTGCAGTTACTG	60.617	44.000	8.18	8.18	34.12	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
50	51	3.131396	CAGTGTTTAACTTCGTCCAGCT	58.869	45.455	0.00	0.00	36.83	4.24
343	344	6.196918	TCCTCTTATGTAACTATCCTCCGA	57.803	41.667	0.00	0.00	0.00	4.55
610	611	5.417580	GTGCCAAGTGTTATCTTCCCAAATA	59.582	40.000	0.00	0.00	0.00	1.40
613	614	3.153919	GTGCCAAGTGTTATCTTCCCAA	58.846	45.455	0.00	0.00	0.00	4.12
614	615	2.375174	AGTGCCAAGTGTTATCTTCCCA	59.625	45.455	0.00	0.00	0.00	4.37
635	636	1.227321	GACGTGTTCCACCAACCGA	60.227	57.895	0.00	0.00	34.56	4.69
645	646	9.485591	AATTCGAAATAATATTGTGACGTGTTC	57.514	29.630	0.00	0.00	0.00	3.18
718	719	3.127533	GGGTGCATGCGTGGTCTC	61.128	66.667	14.09	0.00	0.00	3.36
796	798	0.976073	GAGTGAAGGGGGATCCGTGA	60.976	60.000	5.45	0.00	41.52	4.35
853	856	1.095807	GCTTATCCTGAACACGGGGC	61.096	60.000	0.00	0.00	0.00	5.80
942	945	1.658673	GTAGGCGGATACTCGGTGG	59.341	63.158	0.00	0.00	0.00	4.61
1152	1159	3.461773	CCCTCCGGCGTGATCAGT	61.462	66.667	6.01	0.00	0.00	3.41
1486	1494	7.233553	TCCTCAATATCCTGATACAGTTCGAAT	59.766	37.037	0.00	0.00	0.00	3.34
1488	1496	6.068670	TCCTCAATATCCTGATACAGTTCGA	58.931	40.000	0.00	0.00	0.00	3.71
1516	1524	8.902040	AGTACTAATTACGTACTGTACTTTGC	57.098	34.615	18.77	0.00	44.20	3.68
1524	1532	7.327761	ACAACAGCAAGTACTAATTACGTACTG	59.672	37.037	19.56	15.94	44.89	2.74
1525	1533	7.327761	CACAACAGCAAGTACTAATTACGTACT	59.672	37.037	15.94	15.94	46.93	2.73
1526	1534	7.411157	CCACAACAGCAAGTACTAATTACGTAC	60.411	40.741	0.00	13.17	37.96	3.67
1527	1535	6.587226	CCACAACAGCAAGTACTAATTACGTA	59.413	38.462	0.00	0.00	35.61	3.57
1528	1536	5.407387	CCACAACAGCAAGTACTAATTACGT	59.593	40.000	0.00	0.00	35.61	3.57
1529	1537	5.407387	ACCACAACAGCAAGTACTAATTACG	59.593	40.000	0.00	0.00	35.61	3.18
1530	1538	6.400727	CGACCACAACAGCAAGTACTAATTAC	60.401	42.308	0.00	0.00	0.00	1.89
1547	1555	2.890311	AGCAATCAAAATCCGACCACAA	59.110	40.909	0.00	0.00	0.00	3.33
1617	1785	6.627087	TGGAGTACAATCTCATCTCCTTTT	57.373	37.500	10.22	0.00	43.34	2.27
1621	1789	5.304101	AGACATGGAGTACAATCTCATCTCC	59.696	44.000	0.00	0.00	43.27	3.71
1771	1954	6.017440	GTGACACCAAACTGTATATGTTGTGT	60.017	38.462	12.82	12.82	37.30	3.72
1782	1965	3.417101	TCAACTTGTGACACCAAACTGT	58.583	40.909	2.45	0.00	0.00	3.55
1826	2009	7.148188	ACCATATATGCACTTTGAGACAAGTTG	60.148	37.037	7.24	0.00	0.00	3.16
1849	2032	6.539826	CACAGCTACATATGAGAATTGAACCA	59.460	38.462	10.38	0.00	0.00	3.67
1862	2045	4.613925	AGCAGCATACACAGCTACATAT	57.386	40.909	0.00	0.00	41.14	1.78
1904	2087	3.113514	TTTGACAGCGGGCCTGACA	62.114	57.895	18.31	3.28	44.64	3.58
1906	2089	2.032528	CTTTGACAGCGGGCCTGA	59.967	61.111	18.31	0.00	44.64	3.86
1912	2095	2.166459	TCCATCTAGTCTTTGACAGCGG	59.834	50.000	0.46	0.00	34.60	5.52
1916	2099	3.196469	CCAGCTCCATCTAGTCTTTGACA	59.804	47.826	0.46	0.00	34.60	3.58
1921	2104	2.038659	GCTCCAGCTCCATCTAGTCTT	58.961	52.381	0.00	0.00	38.21	3.01
1922	2105	1.703411	GCTCCAGCTCCATCTAGTCT	58.297	55.000	0.00	0.00	38.21	3.24
1929	2112	4.521062	GCGTCGCTCCAGCTCCAT	62.521	66.667	10.68	0.00	39.32	3.41
1979	2169	1.822371	GGGTCGGGCATTGTACAAAAT	59.178	47.619	13.23	0.00	0.00	1.82
2070	2276	1.091771	CGTTGGCTAGCAGGACCATG	61.092	60.000	18.24	0.00	32.39	3.66
2071	2277	1.221840	CGTTGGCTAGCAGGACCAT	59.778	57.895	18.24	0.00	32.39	3.55
2072	2278	1.476845	TTCGTTGGCTAGCAGGACCA	61.477	55.000	18.24	1.25	0.00	4.02
2073	2279	1.019805	GTTCGTTGGCTAGCAGGACC	61.020	60.000	18.24	0.00	0.00	4.46
2074	2280	0.037232	AGTTCGTTGGCTAGCAGGAC	60.037	55.000	18.24	10.39	0.00	3.85
2129	2335	4.478699	CATGTTGGTGCACAGAACAATAG	58.521	43.478	27.59	19.48	33.50	1.73
2141	2347	3.267597	GACGGGTGCATGTTGGTGC	62.268	63.158	0.00	0.00	45.25	5.01
2158	2364	5.957842	CAGTAACTGCAACCCATTTAAGA	57.042	39.130	0.00	0.00	0.00	2.10
2181	2387	9.612066	AATAACTAAAATATGGCAAATGGGTTG	57.388	29.630	0.00	0.00	40.50	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.