AutoCloner

Multiple sequence alignment - TraesCS7B01G443900

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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	TraesCS7B01G443900	chr7B	100.000	2326	0	0	572	2897	708529008	708531333	0.000000e+00	4296.0
1	TraesCS7B01G443900	chr7B	85.430	1812	183	50	823	2615	708511444	708513193	0.000000e+00	1808.0
2	TraesCS7B01G443900	chr7B	85.842	1681	174	44	823	2466	708445895	708447548	0.000000e+00	1727.0
3	TraesCS7B01G443900	chr7B	79.973	1493	185	63	892	2319	708552337	708553780	0.000000e+00	996.0
4	TraesCS7B01G443900	chr7B	100.000	307	0	0	1	307	708528437	708528743	4.190000e-158	568.0
5	TraesCS7B01G443900	chr7B	98.701	308	3	1	1	307	72497637	72497330	1.960000e-151	545.0
6	TraesCS7B01G443900	chr7B	94.882	254	13	0	572	825	72497194	72496941	5.820000e-107	398.0
7	TraesCS7B01G443900	chr7D	85.085	1951	193	41	979	2897	615765490	615767374	0.000000e+00	1901.0
8	TraesCS7B01G443900	chr7D	85.418	1351	127	42	823	2140	615559624	615558311	0.000000e+00	1339.0
9	TraesCS7B01G443900	chr7D	80.088	1582	182	71	823	2324	615774719	615776247	0.000000e+00	1053.0
10	TraesCS7B01G443900	chr7D	80.652	491	66	22	2131	2615	615555644	615555177	1.280000e-93	353.0
11	TraesCS7B01G443900	chr7D	80.110	362	56	14	2539	2893	615555213	615554861	3.700000e-64	255.0
12	TraesCS7B01G443900	chr7A	89.722	1333	98	16	823	2135	708318929	708320242	0.000000e+00	1666.0
13	TraesCS7B01G443900	chr7A	80.393	1576	190	78	820	2319	708326318	708327850	0.000000e+00	1088.0
14	TraesCS7B01G443900	chr4B	98.701	308	3	1	1	307	43809253	43809560	1.960000e-151	545.0
15	TraesCS7B01G443900	chr4B	98.701	308	3	1	1	307	326000116	325999809	1.960000e-151	545.0
16	TraesCS7B01G443900	chr4B	98.697	307	3	1	2	307	414229856	414229550	7.060000e-151	544.0
17	TraesCS7B01G443900	chr4B	98.052	308	5	1	1	307	18433834	18434141	4.250000e-148	534.0
18	TraesCS7B01G443900	chr4B	95.257	253	12	0	572	824	414229414	414229162	4.500000e-108	401.0
19	TraesCS7B01G443900	chr4B	94.800	250	13	0	572	821	43809699	43809948	9.730000e-105	390.0
20	TraesCS7B01G443900	chr4B	94.000	250	15	0	572	821	18434274	18434523	2.110000e-101	379.0
21	TraesCS7B01G443900	chr1B	98.377	308	4	1	1	307	507402990	507403297	9.130000e-150	540.0
22	TraesCS7B01G443900	chr5B	98.052	308	5	1	1	307	396072604	396072297	4.250000e-148	534.0
23	TraesCS7B01G443900	chr2B	98.052	308	5	1	1	307	46703721	46703414	4.250000e-148	534.0
24	TraesCS7B01G443900	chr2B	97.727	308	5	2	1	307	56031299	56031605	1.980000e-146	529.0
25	TraesCS7B01G443900	chr2B	94.800	250	13	0	572	821	56031740	56031989	9.730000e-105	390.0
26	TraesCS7B01G443900	chr2B	93.927	247	15	0	572	818	24785530	24785776	9.800000e-100	374.0
27	TraesCS7B01G443900	chr3B	94.800	250	13	0	572	821	116933147	116933396	9.730000e-105	390.0
28	TraesCS7B01G443900	chr3B	93.600	250	16	0	572	821	770022863	770022614	9.800000e-100	374.0
29	TraesCS7B01G443900	chr6B	94.000	250	15	0	572	821	671091601	671091850	2.110000e-101	379.0
30	TraesCS7B01G443900	chr6B	85.855	304	43	0	1025	1328	245985723	245985420	1.000000e-84	324.0
31	TraesCS7B01G443900	chr6D	90.164	61	6	0	2402	2462	324493628	324493688	2.390000e-11	80.5
32	TraesCS7B01G443900	chr3A	78.125	96	14	7	2631	2723	678738072	678738163	1.000000e-03	54.7
33	TraesCS7B01G443900	chr3A	79.310	87	11	7	2640	2723	678828753	678828835	1.000000e-03	54.7
34	TraesCS7B01G443900	chr3D	100.000	28	0	0	2432	2459	438284666	438284639	5.000000e-03	52.8

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	TraesCS7B01G443900	chr7B	708528437	708531333	2896	False	2432.0	4296	100.0000	1	2897	2	chr7B.!!$F4	2896
1	TraesCS7B01G443900	chr7B	708511444	708513193	1749	False	1808.0	1808	85.4300	823	2615	1	chr7B.!!$F2	1792
2	TraesCS7B01G443900	chr7B	708445895	708447548	1653	False	1727.0	1727	85.8420	823	2466	1	chr7B.!!$F1	1643
3	TraesCS7B01G443900	chr7B	708552337	708553780	1443	False	996.0	996	79.9730	892	2319	1	chr7B.!!$F3	1427
4	TraesCS7B01G443900	chr7B	72496941	72497637	696	True	471.5	545	96.7915	1	825	2	chr7B.!!$R1	824
5	TraesCS7B01G443900	chr7D	615765490	615767374	1884	False	1901.0	1901	85.0850	979	2897	1	chr7D.!!$F1	1918
6	TraesCS7B01G443900	chr7D	615774719	615776247	1528	False	1053.0	1053	80.0880	823	2324	1	chr7D.!!$F2	1501
7	TraesCS7B01G443900	chr7D	615554861	615559624	4763	True	649.0	1339	82.0600	823	2893	3	chr7D.!!$R1	2070
8	TraesCS7B01G443900	chr7A	708318929	708320242	1313	False	1666.0	1666	89.7220	823	2135	1	chr7A.!!$F1	1312
9	TraesCS7B01G443900	chr7A	708326318	708327850	1532	False	1088.0	1088	80.3930	820	2319	1	chr7A.!!$F2	1499
10	TraesCS7B01G443900	chr4B	414229162	414229856	694	True	472.5	544	96.9770	2	824	2	chr4B.!!$R2	822
11	TraesCS7B01G443900	chr4B	43809253	43809948	695	False	467.5	545	96.7505	1	821	2	chr4B.!!$F2	820
12	TraesCS7B01G443900	chr4B	18433834	18434523	689	False	456.5	534	96.0260	1	821	2	chr4B.!!$F1	820
13	TraesCS7B01G443900	chr2B	56031299	56031989	690	False	459.5	529	96.2635	1	821	2	chr2B.!!$F2	820

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
956	971	0.747255	CGAGTCAATCGTCTCCCCAT	59.253	55.0	0.0	0.0	46.62	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2188	5119	0.736325	ACGTTACTCTGCATCCACGC	60.736	55.0	0.0	0.0	0.0	5.34	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
737	739	4.664677	GCTGTCGGACGCCACACT	62.665	66.667	11.98	0.00	0.00	3.55
738	740	2.734723	CTGTCGGACGCCACACTG	60.735	66.667	3.34	0.00	0.00	3.66
745	747	1.669440	GACGCCACACTGAAGGGTA	59.331	57.895	0.00	0.00	0.00	3.69
809	811	4.739793	TGATTTGGGTCTCAGGTCAAATT	58.260	39.130	0.00	0.00	39.15	1.82
810	812	5.886609	TGATTTGGGTCTCAGGTCAAATTA	58.113	37.500	0.00	0.00	39.15	1.40
821	823	6.881065	TCTCAGGTCAAATTAGTGATTTCTGG	59.119	38.462	7.35	1.63	35.79	3.86
940	955	1.301716	CACCACCTCCCACAACGAG	60.302	63.158	0.00	0.00	0.00	4.18
955	970	2.189833	CGAGTCAATCGTCTCCCCA	58.810	57.895	0.00	0.00	46.62	4.96
956	971	0.747255	CGAGTCAATCGTCTCCCCAT	59.253	55.000	0.00	0.00	46.62	4.00
957	972	1.954382	CGAGTCAATCGTCTCCCCATA	59.046	52.381	0.00	0.00	46.62	2.74
958	973	2.361119	CGAGTCAATCGTCTCCCCATAA	59.639	50.000	0.00	0.00	46.62	1.90
975	990	3.254960	CATAATCCCATCCCAGTCTCCT	58.745	50.000	0.00	0.00	0.00	3.69
1014	1059	1.444933	ACAAGATGGAGGGGTGTGAA	58.555	50.000	0.00	0.00	0.00	3.18
1314	1359	1.062488	ACCACTGGAACTGCTCCCTT	61.062	55.000	0.71	0.00	44.69	3.95
1637	1760	2.736995	CGCGTTCCACCACGACAT	60.737	61.111	0.00	0.00	43.15	3.06
1642	1765	1.600023	GTTCCACCACGACATTTCCA	58.400	50.000	0.00	0.00	0.00	3.53
1643	1766	1.265905	GTTCCACCACGACATTTCCAC	59.734	52.381	0.00	0.00	0.00	4.02
1649	1772	1.671054	ACGACATTTCCACCAGCCG	60.671	57.895	0.00	0.00	0.00	5.52
1657	1780	3.353836	CCACCAGCCGTTTCCACG	61.354	66.667	0.00	0.00	46.71	4.94
1780	1906	0.456221	GATGATCCGTGACGAGGTGT	59.544	55.000	6.54	0.00	0.00	4.16
1794	1920	1.644509	AGGTGTGCAGGTACATCTCA	58.355	50.000	0.00	0.00	37.46	3.27
2025	2231	7.171653	AGAAAGAAGAACTAGGCAAAGCTAAT	58.828	34.615	0.00	0.00	0.00	1.73
2084	2314	6.491403	AGTGGAAAGAAACTTGCATATGTCTT	59.509	34.615	4.29	1.58	0.00	3.01
2122	2352	6.142798	CACTCATGTCAAATTTGTTTTCCTCG	59.857	38.462	17.47	4.37	0.00	4.63
2177	5100	5.130350	TGAAGTGAAAAATCCCTCGTTCTT	58.870	37.500	0.00	0.00	0.00	2.52
2188	5119	1.394917	CCTCGTTCTTCATTTGAGGCG	59.605	52.381	0.00	0.00	39.74	5.52
2191	5122	0.517316	GTTCTTCATTTGAGGCGCGT	59.483	50.000	8.43	0.27	0.00	6.01
2192	5123	0.516877	TTCTTCATTTGAGGCGCGTG	59.483	50.000	7.63	0.00	0.00	5.34
2206	5137	1.742900	CGCGTGGATGCAGAGTAACG	61.743	60.000	0.00	0.00	34.15	3.18
2324	5266	4.701956	AAGGCGTCCATGTATGAAAAAG	57.298	40.909	0.00	0.00	0.00	2.27
2327	5271	4.396166	AGGCGTCCATGTATGAAAAAGAAG	59.604	41.667	0.00	0.00	0.00	2.85
2331	5275	5.967674	CGTCCATGTATGAAAAAGAAGCATC	59.032	40.000	0.00	0.00	0.00	3.91
2461	5406	5.514914	TCGTGAGTTTGAAAAATGTTCAAGC	59.485	36.000	4.80	4.80	39.30	4.01
2470	5415	6.297582	TGAAAAATGTTCAAGCATTCCCAAT	58.702	32.000	0.00	0.00	38.03	3.16
2472	5417	7.284944	TGAAAAATGTTCAAGCATTCCCAATTT	59.715	29.630	0.00	0.00	38.03	1.82
2473	5418	7.585579	AAAATGTTCAAGCATTCCCAATTTT	57.414	28.000	0.00	0.00	38.03	1.82
2474	5419	7.585579	AAATGTTCAAGCATTCCCAATTTTT	57.414	28.000	0.00	0.00	38.03	1.94
2543	5488	8.552865	TCATGAATTTCAAAGATTGTTTGCAAG	58.447	29.630	2.68	0.00	38.10	4.01
2546	5491	8.389603	TGAATTTCAAAGATTGTTTGCAAGTTC	58.610	29.630	0.00	9.25	38.10	3.01
2547	5492	7.846644	ATTTCAAAGATTGTTTGCAAGTTCA	57.153	28.000	0.00	0.00	38.10	3.18
2666	5652	8.275015	TCACGTGTTTCCATAATATGTTCATT	57.725	30.769	16.51	0.00	0.00	2.57
2769	5757	8.404889	TGTTTGTCAGTTTCAACATATGTTTG	57.595	30.769	18.50	13.59	35.83	2.93
2864	5855	8.707839	CCATTTTTAATAGTGTTCACGCATTTT	58.292	29.630	9.67	0.48	0.00	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
139	140	7.822822	GGATGTGTATTCATATTGGTAGTACCC	59.177	40.741	16.91	0.00	37.50	3.69
172	173	4.018870	ACCCTTGATTTGTTTGGTTTGGTT	60.019	37.500	0.00	0.00	0.00	3.67
174	175	4.149511	ACCCTTGATTTGTTTGGTTTGG	57.850	40.909	0.00	0.00	0.00	3.28
668	670	1.359459	CTTTAAGCGTCGCACCTCCC	61.359	60.000	21.09	0.00	0.00	4.30
682	684	1.074072	TGCAGCGCCCTTCCTTTAA	59.926	52.632	2.29	0.00	0.00	1.52
737	739	4.640771	ATTTCACTCTGCTTACCCTTCA	57.359	40.909	0.00	0.00	0.00	3.02
738	740	5.966742	AAATTTCACTCTGCTTACCCTTC	57.033	39.130	0.00	0.00	0.00	3.46
809	811	1.735700	CGCACGAGCCAGAAATCACTA	60.736	52.381	0.00	0.00	37.52	2.74
810	812	1.016130	CGCACGAGCCAGAAATCACT	61.016	55.000	0.00	0.00	37.52	3.41
923	933	1.755393	GACTCGTTGTGGGAGGTGGT	61.755	60.000	0.00	0.00	35.82	4.16
926	936	1.002087	GATTGACTCGTTGTGGGAGGT	59.998	52.381	0.00	0.00	35.82	3.85
929	939	3.507597	CGATTGACTCGTTGTGGGA	57.492	52.632	0.00	0.00	42.56	4.37
940	955	3.557264	GGGATTATGGGGAGACGATTGAC	60.557	52.174	0.00	0.00	0.00	3.18
951	966	1.355720	GACTGGGATGGGATTATGGGG	59.644	57.143	0.00	0.00	0.00	4.96
952	967	2.307098	GAGACTGGGATGGGATTATGGG	59.693	54.545	0.00	0.00	0.00	4.00
953	968	2.307098	GGAGACTGGGATGGGATTATGG	59.693	54.545	0.00	0.00	0.00	2.74
954	969	3.254960	AGGAGACTGGGATGGGATTATG	58.745	50.000	0.00	0.00	41.13	1.90
955	970	3.663298	AGGAGACTGGGATGGGATTAT	57.337	47.619	0.00	0.00	41.13	1.28
975	990	2.104859	CGAGTCTACGACGGGAGCA	61.105	63.158	0.00	0.00	37.67	4.26
1143	1188	4.189580	AGCTGGTTGCACCACCGT	62.190	61.111	3.17	0.00	44.79	4.83
1275	1320	1.372004	CTTGACGGCGTTGTCGGTA	60.372	57.895	16.19	0.00	41.87	4.02
1393	1438	4.717629	CGTGCTCTCCGGCGTGAA	62.718	66.667	6.01	0.00	34.52	3.18
1476	1569	1.373748	GTAAACCTGTCCGAGCGCA	60.374	57.895	11.47	0.00	0.00	6.09
1478	1571	1.804326	CGGTAAACCTGTCCGAGCG	60.804	63.158	0.00	0.00	46.05	5.03
1637	1760	1.104577	GTGGAAACGGCTGGTGGAAA	61.105	55.000	0.00	0.00	0.00	3.13
1642	1765	2.030562	CTCGTGGAAACGGCTGGT	59.969	61.111	0.00	0.00	0.00	4.00
1643	1766	3.423154	GCTCGTGGAAACGGCTGG	61.423	66.667	0.00	0.00	0.00	4.85
1649	1772	1.737008	GGAGACGGCTCGTGGAAAC	60.737	63.158	13.25	0.00	41.37	2.78
1780	1906	1.257750	ACGCCTGAGATGTACCTGCA	61.258	55.000	0.00	0.00	0.00	4.41
1917	2043	2.202987	GCCATCTGCTCGACCTGG	60.203	66.667	0.00	0.00	36.87	4.45
1942	2082	2.359531	GTCCTAGAGTGATTGGTCGAGG	59.640	54.545	0.00	0.00	37.03	4.63
2025	2231	7.977789	TGTATGTACAGAAAGAAGCAAATCA	57.022	32.000	0.33	0.00	0.00	2.57
2060	2290	6.259550	AGACATATGCAAGTTTCTTTCCAC	57.740	37.500	1.58	0.00	0.00	4.02
2159	5075	6.264292	TCAAATGAAGAACGAGGGATTTTTCA	59.736	34.615	0.00	0.00	0.00	2.69
2177	5100	1.078497	ATCCACGCGCCTCAAATGA	60.078	52.632	5.73	0.00	0.00	2.57
2188	5119	0.736325	ACGTTACTCTGCATCCACGC	60.736	55.000	0.00	0.00	0.00	5.34
2191	5122	2.930887	GCTTGACGTTACTCTGCATCCA	60.931	50.000	0.00	0.00	0.00	3.41
2192	5123	1.661112	GCTTGACGTTACTCTGCATCC	59.339	52.381	0.00	0.00	0.00	3.51
2224	5156	0.878416	GCACATAGGTTTTGGTCGCA	59.122	50.000	0.00	0.00	0.00	5.10
2310	5252	7.977293	TGAATGATGCTTCTTTTTCATACATGG	59.023	33.333	0.00	0.00	0.00	3.66
2438	5383	5.288232	TGCTTGAACATTTTTCAAACTCACG	59.712	36.000	0.15	0.00	37.89	4.35
2493	5438	8.199449	TGAATGCTTCTTGAATTCTCTTGTTTT	58.801	29.630	7.05	0.00	40.59	2.43
2495	5440	7.281040	TGAATGCTTCTTGAATTCTCTTGTT	57.719	32.000	7.05	0.00	40.59	2.83
2496	5441	6.889301	TGAATGCTTCTTGAATTCTCTTGT	57.111	33.333	7.05	0.00	40.59	3.16
2497	5442	7.535997	TCATGAATGCTTCTTGAATTCTCTTG	58.464	34.615	7.05	1.83	40.59	3.02
2498	5443	7.698506	TCATGAATGCTTCTTGAATTCTCTT	57.301	32.000	7.05	0.00	40.59	2.85
2499	5444	7.698506	TTCATGAATGCTTCTTGAATTCTCT	57.301	32.000	3.38	0.00	44.14	3.10
2524	5469	7.664082	TTGAACTTGCAAACAATCTTTGAAA	57.336	28.000	0.00	0.00	34.61	2.69
2563	5508	5.972107	ACTGCATGAACATTTCTTAAGCT	57.028	34.783	0.00	0.00	0.00	3.74
2741	5729	8.801715	ACATATGTTGAAACTGACAAACATTC	57.198	30.769	1.41	0.00	0.00	2.67
2744	5732	8.031864	ACAAACATATGTTGAAACTGACAAACA	58.968	29.630	21.46	0.00	38.44	2.83
2745	5733	8.320295	CACAAACATATGTTGAAACTGACAAAC	58.680	33.333	21.46	0.00	38.44	2.93
2747	5735	7.542890	ACACAAACATATGTTGAAACTGACAA	58.457	30.769	21.46	0.00	38.44	3.18
2748	5736	7.094508	ACACAAACATATGTTGAAACTGACA	57.905	32.000	21.46	0.00	38.44	3.58
2749	5737	7.192913	TGACACAAACATATGTTGAAACTGAC	58.807	34.615	21.46	12.19	38.44	3.51
2835	5826	7.299586	TGCGTGAACACTATTAAAAATGGTAC	58.700	34.615	3.51	0.00	0.00	3.34
2845	5836	9.731819	TTTTGTTAAAATGCGTGAACACTATTA	57.268	25.926	3.51	0.00	31.78	0.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.