AutoCloner

Multiple sequence alignment - TraesCS6B01G054900

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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	TraesCS6B01G054900	chr6B	100.000	3074	0	0	1	3074	35530270	35527197	0.000000e+00	5677.0
1	TraesCS6B01G054900	chr6B	84.584	1239	186	5	912	2147	27992452	27991216	0.000000e+00	1225.0
2	TraesCS6B01G054900	chr6B	79.364	1541	276	29	682	2198	34341690	34340168	0.000000e+00	1046.0
3	TraesCS6B01G054900	chr6B	80.368	1304	217	24	912	2198	34685368	34684087	0.000000e+00	953.0
4	TraesCS6B01G054900	chr6B	89.801	402	40	1	122	523	708969172	708968772	5.880000e-142	514.0
5	TraesCS6B01G054900	chr6B	82.902	193	28	4	682	873	27992652	27992464	5.270000e-38	169.0
6	TraesCS6B01G054900	chr6B	91.358	81	7	0	1	81	708969248	708969168	9.010000e-21	111.0
7	TraesCS6B01G054900	chr6B	80.851	141	24	2	2444	2581	51336424	51336284	1.170000e-19	108.0
8	TraesCS6B01G054900	chr6D	93.905	2576	120	15	531	3074	20603025	20600455	0.000000e+00	3853.0
9	TraesCS6B01G054900	chr6D	84.286	1470	216	10	685	2147	16242667	16244128	0.000000e+00	1421.0
10	TraesCS6B01G054900	chr6D	79.207	1539	286	24	684	2198	20312487	20310959	0.000000e+00	1038.0
11	TraesCS6B01G054900	chr6D	91.587	523	40	3	1	523	464980147	464979629	0.000000e+00	719.0
12	TraesCS6B01G054900	chr6A	92.053	2479	136	32	531	2978	20522751	20520303	0.000000e+00	3430.0
13	TraesCS6B01G054900	chr6A	83.458	1469	230	9	686	2147	16530997	16532459	0.000000e+00	1354.0
14	TraesCS6B01G054900	chr6A	80.723	1245	218	14	965	2198	20310456	20309223	0.000000e+00	950.0
15	TraesCS6B01G054900	chr6A	90.476	63	1	4	2969	3026	20519035	20518973	9.140000e-11	78.7
16	TraesCS6B01G054900	chrUn	79.402	1539	279	25	682	2198	273854551	273856073	0.000000e+00	1051.0
17	TraesCS6B01G054900	chrUn	91.810	525	37	4	1	523	76462616	76463136	0.000000e+00	726.0
18	TraesCS6B01G054900	chr5A	92.734	523	37	1	1	523	114384878	114384357	0.000000e+00	754.0
19	TraesCS6B01G054900	chr5D	83.333	204	28	5	2442	2642	539019600	539019800	1.880000e-42	183.0
20	TraesCS6B01G054900	chr5B	81.347	193	29	5	2439	2624	8901203	8901395	1.910000e-32	150.0
21	TraesCS6B01G054900	chr1B	83.673	147	23	1	2442	2587	553144914	553144768	1.490000e-28	137.0
22	TraesCS6B01G054900	chr1A	83.673	147	23	1	2442	2587	506545515	506545369	1.490000e-28	137.0
23	TraesCS6B01G054900	chr7A	82.432	148	20	5	2439	2581	439809149	439809295	1.160000e-24	124.0
24	TraesCS6B01G054900	chr7D	96.491	57	2	0	2434	2490	389190473	389190529	9.070000e-16	95.3
25	TraesCS6B01G054900	chr2B	92.424	66	5	0	2207	2272	37776470	37776535	9.070000e-16	95.3
26	TraesCS6B01G054900	chr3B	96.429	56	2	0	2	57	13443629	13443684	3.260000e-15	93.5

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	TraesCS6B01G054900	chr6B	35527197	35530270	3073	True	5677.00	5677	100.0000	1	3074	1	chr6B.!!$R3	3073
1	TraesCS6B01G054900	chr6B	34340168	34341690	1522	True	1046.00	1046	79.3640	682	2198	1	chr6B.!!$R1	1516
2	TraesCS6B01G054900	chr6B	34684087	34685368	1281	True	953.00	953	80.3680	912	2198	1	chr6B.!!$R2	1286
3	TraesCS6B01G054900	chr6B	27991216	27992652	1436	True	697.00	1225	83.7430	682	2147	2	chr6B.!!$R5	1465
4	TraesCS6B01G054900	chr6D	20600455	20603025	2570	True	3853.00	3853	93.9050	531	3074	1	chr6D.!!$R2	2543
5	TraesCS6B01G054900	chr6D	16242667	16244128	1461	False	1421.00	1421	84.2860	685	2147	1	chr6D.!!$F1	1462
6	TraesCS6B01G054900	chr6D	20310959	20312487	1528	True	1038.00	1038	79.2070	684	2198	1	chr6D.!!$R1	1514
7	TraesCS6B01G054900	chr6D	464979629	464980147	518	True	719.00	719	91.5870	1	523	1	chr6D.!!$R3	522
8	TraesCS6B01G054900	chr6A	20518973	20522751	3778	True	1754.35	3430	91.2645	531	3026	2	chr6A.!!$R2	2495
9	TraesCS6B01G054900	chr6A	16530997	16532459	1462	False	1354.00	1354	83.4580	686	2147	1	chr6A.!!$F1	1461
10	TraesCS6B01G054900	chr6A	20309223	20310456	1233	True	950.00	950	80.7230	965	2198	1	chr6A.!!$R1	1233
11	TraesCS6B01G054900	chrUn	273854551	273856073	1522	False	1051.00	1051	79.4020	682	2198	1	chrUn.!!$F2	1516
12	TraesCS6B01G054900	chrUn	76462616	76463136	520	False	726.00	726	91.8100	1	523	1	chrUn.!!$F1	522
13	TraesCS6B01G054900	chr5A	114384357	114384878	521	True	754.00	754	92.7340	1	523	1	chr5A.!!$R1	522

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
525	528	0.599728	GTGCGCTCCATCTCTCCATC	60.600	60.0	9.73	0.0	0.0	3.51	F
1342	1414	0.247736	GTCAGACTGTGGGAAGCGAT	59.752	55.0	1.59	0.0	0.0	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1756	1832	0.961857	TGCAGCAACGCCATCTCATT	60.962	50.000	0.0	0.0	0.0	2.57	R
2498	2583	1.067974	TGTAGTGTGAGACGTTGGGTG	59.932	52.381	0.0	0.0	0.0	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
22	23	5.881637	TTTTTGCGATTGTAAAGCTTCAC	57.118	34.783	0.00	0.00	31.18	3.18
75	76	7.227512	GCTTACATAAGGCTAAGATGTGTTCAT	59.772	37.037	15.92	0.00	35.48	2.57
122	123	1.229658	AGGCTGCCTCCCTAGTTGT	60.230	57.895	17.22	0.00	0.00	3.32
151	152	4.637977	TGCATGACTAACACAGTTCAAACA	59.362	37.500	0.00	0.00	37.72	2.83
185	186	5.630121	TGTGTTATTTCATGTGGTCTTCCT	58.370	37.500	0.00	0.00	34.23	3.36
190	191	3.350219	TTCATGTGGTCTTCCTAAGCC	57.650	47.619	0.00	0.00	34.23	4.35
243	244	3.243535	CGCAGCTGGTGATCTATCAACTA	60.244	47.826	17.12	0.00	44.70	2.24
247	248	6.442952	CAGCTGGTGATCTATCAACTACTAC	58.557	44.000	5.57	0.00	44.70	2.73
264	265	2.593468	TACGCCCTTGAGCATGCTCC	62.593	60.000	37.92	23.86	42.09	4.70
305	308	1.480954	TCCAGGATTGAAGGTAGCGTC	59.519	52.381	0.54	0.54	0.00	5.19
336	339	2.982488	AGTGTGAGTGAAATCCCTTCCT	59.018	45.455	0.00	0.00	32.53	3.36
354	357	3.230976	TCCTGACAAGCAGTGAGTTCTA	58.769	45.455	0.00	0.00	43.33	2.10
362	365	1.896465	GCAGTGAGTTCTACCTCCAGT	59.104	52.381	0.00	0.00	0.00	4.00
363	366	2.300437	GCAGTGAGTTCTACCTCCAGTT	59.700	50.000	0.00	0.00	0.00	3.16
423	426	6.838401	AAATCACCTCTCCCTCAGAATTAT	57.162	37.500	0.00	0.00	0.00	1.28
424	427	7.937700	AAATCACCTCTCCCTCAGAATTATA	57.062	36.000	0.00	0.00	0.00	0.98
476	479	1.361668	CTTCCACGAAGGCACCATCG	61.362	60.000	12.39	12.39	42.62	3.84
479	482	0.953471	CCACGAAGGCACCATCGAAA	60.953	55.000	20.00	0.00	39.98	3.46
490	493	3.003275	GCACCATCGAAAGTTCAGTTTGA	59.997	43.478	0.00	0.00	0.00	2.69
505	508	2.813226	TTTGAACCATCCCTCCGGCG	62.813	60.000	0.00	0.00	0.00	6.46
523	526	2.725312	GGTGCGCTCCATCTCTCCA	61.725	63.158	23.09	0.00	0.00	3.86
524	527	1.445095	GTGCGCTCCATCTCTCCAT	59.555	57.895	9.73	0.00	0.00	3.41
525	528	0.599728	GTGCGCTCCATCTCTCCATC	60.600	60.000	9.73	0.00	0.00	3.51
526	529	1.372748	GCGCTCCATCTCTCCATCG	60.373	63.158	0.00	0.00	0.00	3.84
527	530	1.800283	GCGCTCCATCTCTCCATCGA	61.800	60.000	0.00	0.00	0.00	3.59
528	531	0.887247	CGCTCCATCTCTCCATCGAT	59.113	55.000	0.00	0.00	0.00	3.59
529	532	1.402588	CGCTCCATCTCTCCATCGATG	60.403	57.143	18.76	18.76	37.39	3.84
593	596	7.833285	TTGTTAATTTAGGAAAAGCCTCTGT	57.167	32.000	0.00	0.00	46.97	3.41
599	602	1.891150	AGGAAAAGCCTCTGTGCATTG	59.109	47.619	0.00	0.00	46.97	2.82
654	658	9.109393	GAGTTGAGAATATTTGTACCTTATGCA	57.891	33.333	0.00	0.00	0.00	3.96
661	665	7.880160	ATATTTGTACCTTATGCATGTGTGT	57.120	32.000	10.16	3.92	0.00	3.72
682	686	2.880879	CTCGCGTGCGTGTGCTAT	60.881	61.111	14.47	0.00	43.34	2.97
804	867	7.611213	ACAGTTACTACTAAATTCACCATGC	57.389	36.000	0.00	0.00	31.96	4.06
810	873	3.960571	ACTAAATTCACCATGCAGCTCT	58.039	40.909	0.00	0.00	0.00	4.09
841	904	3.050275	GCGACCTTGCCTGTGGTC	61.050	66.667	0.00	0.00	46.69	4.02
869	932	5.884232	TCTACTACTTCAGCATTTCCGAGTA	59.116	40.000	0.00	0.00	0.00	2.59
883	948	3.565307	TCCGAGTAAACCGGGTATACAT	58.435	45.455	6.32	0.00	46.47	2.29
918	987	7.044181	CCATGCACCACGAGAATTCTATATAT	58.956	38.462	8.25	0.00	0.00	0.86
1330	1402	1.903183	GCTCCAACCTTAGGTCAGACT	59.097	52.381	3.62	0.00	33.12	3.24
1332	1404	2.900546	CTCCAACCTTAGGTCAGACTGT	59.099	50.000	3.62	0.00	33.12	3.55
1342	1414	0.247736	GTCAGACTGTGGGAAGCGAT	59.752	55.000	1.59	0.00	0.00	4.58
1424	1496	2.659897	GCGCATGAGAGGCTACGG	60.660	66.667	0.30	0.00	0.00	4.02
1493	1566	2.031674	GCTTGTTGGGCCTTTGCAGT	62.032	55.000	4.53	0.00	40.13	4.40
1532	1605	3.118261	GGCATCAACTCCATCAGGACTAA	60.118	47.826	0.00	0.00	39.61	2.24
1533	1606	4.517285	GCATCAACTCCATCAGGACTAAA	58.483	43.478	0.00	0.00	39.61	1.85
1729	1805	2.422597	GGAAACATGTCGTCACCATCA	58.577	47.619	0.00	0.00	0.00	3.07
1756	1832	2.791347	TAAAGAGGTGCCGCCAAATA	57.209	45.000	0.00	0.00	40.61	1.40
1947	2023	2.874701	GAGACGCATGCAATACTGGATT	59.125	45.455	19.57	0.00	29.85	3.01
1966	2042	4.102054	GGATTATAAAGAACTCGTGGGGGA	59.898	45.833	0.00	0.00	0.00	4.81
2198	2282	6.254589	CAGTGAACAGCTAGACTTACTATTGC	59.745	42.308	0.00	0.00	0.00	3.56
2200	2284	5.186992	TGAACAGCTAGACTTACTATTGCCA	59.813	40.000	0.00	0.00	0.00	4.92
2404	2488	8.767085	CAAATATGCACAAGTTTGACTTTTCAT	58.233	29.630	8.44	0.00	36.03	2.57
2498	2583	0.618458	TGAGCCATCCAACCACCTAC	59.382	55.000	0.00	0.00	0.00	3.18
2524	2609	4.552355	CAACGTCTCACACTACACCAATA	58.448	43.478	0.00	0.00	0.00	1.90
2677	2763	1.221466	ACTGGATGTTCGTGCACGTG	61.221	55.000	35.74	12.28	40.80	4.49
2750	2841	4.960329	TGTCGTTGTTTGTACAGTTTGAC	58.040	39.130	0.00	2.30	35.28	3.18
2806	2897	1.422977	TAGGTTGCTTGGCCCACTCA	61.423	55.000	0.00	0.00	0.00	3.41
2820	2911	3.547746	CCCACTCACTAGACTCTACTCC	58.452	54.545	0.00	0.00	0.00	3.85
2858	2949	5.627499	AATGAACATCTGCGTGTGTTATT	57.373	34.783	1.13	1.07	38.57	1.40
2860	2951	3.435327	TGAACATCTGCGTGTGTTATTCC	59.565	43.478	1.13	0.00	38.57	3.01
2889	2980	1.455849	CAGCTTCACCTTGGGTCCA	59.544	57.895	0.00	0.00	31.02	4.02
2901	2992	3.777522	CCTTGGGTCCAACTTCTAGAGAT	59.222	47.826	0.00	0.00	0.00	2.75
3030	4403	4.925646	GGTGAATTTTGATGAAGCAGGAAC	59.074	41.667	0.00	0.00	0.00	3.62
3062	4435	2.876091	GCTATGTGCACTGACTTCGTA	58.124	47.619	19.41	0.00	42.31	3.43

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	5.129634	TGGTTGATGAGTGAAGCTTTACAA	58.870	37.500	21.91	11.00	0.00	2.41
22	23	3.875727	CTGTAATGCTCCTGGTTGATGAG	59.124	47.826	0.00	0.00	0.00	2.90
122	123	3.993562	ACTGTGTTAGTCATGCACTTGCA	60.994	43.478	6.33	6.33	46.13	4.08
181	182	3.951563	AACATATGCTGGGCTTAGGAA	57.048	42.857	1.58	0.00	0.00	3.36
185	186	3.799281	GCAAAACATATGCTGGGCTTA	57.201	42.857	1.58	0.00	40.64	3.09
243	244	1.450312	GCATGCTCAAGGGCGTAGT	60.450	57.895	11.37	0.00	34.52	2.73
247	248	3.207669	GGAGCATGCTCAAGGGCG	61.208	66.667	40.37	0.00	44.40	6.13
336	339	2.965831	AGGTAGAACTCACTGCTTGTCA	59.034	45.455	0.00	0.00	0.00	3.58
354	357	3.303135	TGCGAGCGAACTGGAGGT	61.303	61.111	0.00	0.00	0.00	3.85
362	365	0.389687	TGTCATCATGTGCGAGCGAA	60.390	50.000	0.00	0.00	0.00	4.70
363	366	0.389687	TTGTCATCATGTGCGAGCGA	60.390	50.000	0.00	0.00	0.00	4.93
423	426	5.357742	TGAGCTGCTGGTATGATTCTTTA	57.642	39.130	7.01	0.00	0.00	1.85
424	427	4.226427	TGAGCTGCTGGTATGATTCTTT	57.774	40.909	7.01	0.00	0.00	2.52
505	508	2.037620	ATGGAGAGATGGAGCGCACC	62.038	60.000	17.78	17.78	0.00	5.01
599	602	7.088589	TCCTAAGAGTTGCAGAATAAATTGC	57.911	36.000	0.00	0.00	40.67	3.56
654	658	2.280119	ACGCGAGCACACACACAT	60.280	55.556	15.93	0.00	0.00	3.21
774	825	8.718734	GGTGAATTTAGTAGTAACTGTTTGAGG	58.281	37.037	0.00	0.00	36.36	3.86
804	867	4.047822	CGCCACTAGAAGATTTAGAGCTG	58.952	47.826	0.00	0.00	0.00	4.24
810	873	4.755411	CAAGGTCGCCACTAGAAGATTTA	58.245	43.478	0.00	0.00	0.00	1.40
841	904	3.802948	AATGCTGAAGTAGTAGACCGG	57.197	47.619	0.00	0.00	0.00	5.28
889	955	0.327924	TTCTCGTGGTGCATGGGAAT	59.672	50.000	0.00	0.00	35.26	3.01
891	957	0.327924	AATTCTCGTGGTGCATGGGA	59.672	50.000	0.00	0.00	0.00	4.37
918	987	2.170607	GCTATGTAGCTTTGGTCCTCCA	59.829	50.000	4.81	0.00	45.62	3.86
944	1013	2.166907	AGCTATCAGGCTAGTGTGGT	57.833	50.000	0.00	0.00	41.16	4.16
1330	1402	1.675310	CTTGGCATCGCTTCCCACA	60.675	57.895	0.00	0.00	0.00	4.17
1332	1404	1.377202	GTCTTGGCATCGCTTCCCA	60.377	57.895	0.00	0.00	0.00	4.37
1493	1566	2.745698	CCTCCACTGCTGCTGTCA	59.254	61.111	9.34	0.00	0.00	3.58
1532	1605	2.362077	GCAGACAATGACACCAGGTTTT	59.638	45.455	0.00	0.00	0.00	2.43
1533	1606	1.956477	GCAGACAATGACACCAGGTTT	59.044	47.619	0.00	0.00	0.00	3.27
1606	1679	4.322080	TGTACTTGAAGGCCGATGATAG	57.678	45.455	0.00	0.00	0.00	2.08
1729	1805	1.818674	CGGCACCTCTTTAAAGCCATT	59.181	47.619	10.51	0.00	45.47	3.16
1756	1832	0.961857	TGCAGCAACGCCATCTCATT	60.962	50.000	0.00	0.00	0.00	2.57
1872	1948	1.353022	ACCACCGTCATTGTATGGGTT	59.647	47.619	0.00	0.00	34.56	4.11
1947	2023	3.443052	TGTCCCCCACGAGTTCTTTATA	58.557	45.455	0.00	0.00	0.00	0.98
1966	2042	1.202592	GCCGTTTTCACCCCATTTTGT	60.203	47.619	0.00	0.00	0.00	2.83
2175	2259	5.520649	GGCAATAGTAAGTCTAGCTGTTCAC	59.479	44.000	0.00	0.00	31.67	3.18
2198	2282	9.696917	GGAAATTTATGCACCTTATATTCTTGG	57.303	33.333	0.00	0.00	0.00	3.61
2421	2505	6.309389	AGTAGTACTCCCCTAACCAAAATG	57.691	41.667	0.00	0.00	0.00	2.32
2426	2511	9.559496	TTTTTATAAGTAGTACTCCCCTAACCA	57.441	33.333	2.58	0.00	0.00	3.67
2498	2583	1.067974	TGTAGTGTGAGACGTTGGGTG	59.932	52.381	0.00	0.00	0.00	4.61
2651	2737	4.068599	TGCACGAACATCCAGTTTGATAA	58.931	39.130	2.45	0.00	43.16	1.75
2677	2763	8.291032	AGTCTACATTATGTCTAGTAATCGTGC	58.709	37.037	0.00	0.00	0.00	5.34
2806	2897	4.271661	CGAAAAGGGGAGTAGAGTCTAGT	58.728	47.826	7.25	7.25	0.00	2.57
2820	2911	5.708948	TGTTCATTTCATTAGCGAAAAGGG	58.291	37.500	0.00	0.00	38.33	3.95
2858	2949	2.362077	GTGAAGCTGCTTTTTCTTGGGA	59.638	45.455	17.10	0.00	0.00	4.37
2860	2951	2.363359	AGGTGAAGCTGCTTTTTCTTGG	59.637	45.455	17.10	0.00	0.00	3.61
2901	2992	6.905736	ACATATGTGGGGTGTTGTTATATCA	58.094	36.000	7.78	0.00	0.00	2.15
2958	3049	7.176690	CCATTTTAAGTGTTGTAGTTCCCAGAT	59.823	37.037	0.00	0.00	0.00	2.90
3030	4403	1.863454	GCACATAGCATCTCTTGGACG	59.137	52.381	0.00	0.00	44.79	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.