AutoCloner

Multiple sequence alignment - TraesCS3B01G316100

Loading Multiple Alignment...

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	TraesCS3B01G316100	chr3B	100.000	2659	0	0	1	2659	507500088	507497430	0.000000e+00	4911
1	TraesCS3B01G316100	chr3A	93.665	1910	83	11	758	2659	510831578	510829699	0.000000e+00	2822
2	TraesCS3B01G316100	chr3A	89.683	126	10	2	601	726	510831696	510831574	9.850000e-35	158
3	TraesCS3B01G316100	chr3D	89.339	1135	61	17	601	1698	390414657	390413546	0.000000e+00	1371
4	TraesCS3B01G316100	chr3D	91.010	990	39	14	1691	2659	390413165	390412205	0.000000e+00	1290
5	TraesCS3B01G316100	chr7B	89.867	602	58	3	1	600	115565526	115564926	0.000000e+00	771
6	TraesCS3B01G316100	chr7B	88.538	602	66	3	1	600	614477069	614477669	0.000000e+00	726
7	TraesCS3B01G316100	chr7B	88.519	601	66	3	1	600	614533125	614533723	0.000000e+00	725
8	TraesCS3B01G316100	chr4B	89.701	602	58	4	1	600	603763560	603762961	0.000000e+00	765
9	TraesCS3B01G316100	chr5B	89.535	602	51	8	1	600	704493457	704492866	0.000000e+00	752
10	TraesCS3B01G316100	chr5B	89.537	583	54	6	1	582	704784473	704785049	0.000000e+00	732
11	TraesCS3B01G316100	chr6B	89.221	603	61	4	1	600	132888475	132887874	0.000000e+00	750
12	TraesCS3B01G316100	chr6B	88.742	604	64	4	1	602	502267024	502267625	0.000000e+00	736
13	TraesCS3B01G316100	chr4A	88.889	603	57	8	1	600	611096724	611097319	0.000000e+00	734

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	TraesCS3B01G316100	chr3B	507497430	507500088	2658	True	4911.0	4911	100.0000	1	2659	1	chr3B.!!$R1	2658
1	TraesCS3B01G316100	chr3A	510829699	510831696	1997	True	1490.0	2822	91.6740	601	2659	2	chr3A.!!$R1	2058
2	TraesCS3B01G316100	chr3D	390412205	390414657	2452	True	1330.5	1371	90.1745	601	2659	2	chr3D.!!$R1	2058
3	TraesCS3B01G316100	chr7B	115564926	115565526	600	True	771.0	771	89.8670	1	600	1	chr7B.!!$R1	599
4	TraesCS3B01G316100	chr7B	614477069	614477669	600	False	726.0	726	88.5380	1	600	1	chr7B.!!$F1	599
5	TraesCS3B01G316100	chr7B	614533125	614533723	598	False	725.0	725	88.5190	1	600	1	chr7B.!!$F2	599
6	TraesCS3B01G316100	chr4B	603762961	603763560	599	True	765.0	765	89.7010	1	600	1	chr4B.!!$R1	599
7	TraesCS3B01G316100	chr5B	704492866	704493457	591	True	752.0	752	89.5350	1	600	1	chr5B.!!$R1	599
8	TraesCS3B01G316100	chr5B	704784473	704785049	576	False	732.0	732	89.5370	1	582	1	chr5B.!!$F1	581
9	TraesCS3B01G316100	chr6B	132887874	132888475	601	True	750.0	750	89.2210	1	600	1	chr6B.!!$R1	599
10	TraesCS3B01G316100	chr6B	502267024	502267625	601	False	736.0	736	88.7420	1	602	1	chr6B.!!$F1	601
11	TraesCS3B01G316100	chr4A	611096724	611097319	595	False	734.0	734	88.8890	1	600	1	chr4A.!!$F1	599

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
506	510	0.371301	GTTTCCGTATCCGTTTCCGC	59.629	55.0	0.0	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1679	1727	0.330604	AGGTCGTAGTGGTAGCAGGA	59.669	55.0	0.0	0.0	0.0	3.86	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
54	55	4.866682	TGGAAATTTGCAAAACGGAAAC	57.133	36.364	17.19	4.04	37.80	2.78
116	118	1.953686	CGGTGTTTTCCAGTGGAACAT	59.046	47.619	24.52	0.00	41.87	2.71
117	119	2.287547	CGGTGTTTTCCAGTGGAACATG	60.288	50.000	24.52	13.09	41.87	3.21
226	229	7.559486	ACACAATGAGTAGAATGAGCAGAATA	58.441	34.615	0.00	0.00	0.00	1.75
230	233	9.491675	CAATGAGTAGAATGAGCAGAATAGATT	57.508	33.333	0.00	0.00	0.00	2.40
239	242	8.632906	AATGAGCAGAATAGATTATTTGAGGG	57.367	34.615	0.00	0.00	0.00	4.30
341	344	8.702163	GTTGCTAGCACAACCATATTATTTTT	57.298	30.769	19.17	0.00	43.34	1.94
460	463	4.824479	TTCCATGTCTGCTCTGTATTCA	57.176	40.909	0.00	0.00	0.00	2.57
506	510	0.371301	GTTTCCGTATCCGTTTCCGC	59.629	55.000	0.00	0.00	0.00	5.54
611	618	7.225931	CCATTTTCATCCCTAATTGCAGATTTG	59.774	37.037	0.00	0.00	0.00	2.32
677	684	4.457257	AGCCGAAAATCCTTGAAAGAGAAG	59.543	41.667	0.00	0.00	0.00	2.85
678	685	4.455877	GCCGAAAATCCTTGAAAGAGAAGA	59.544	41.667	0.00	0.00	0.00	2.87
679	686	5.124617	GCCGAAAATCCTTGAAAGAGAAGAT	59.875	40.000	0.00	0.00	0.00	2.40
692	702	6.310467	TGAAAGAGAAGATGTGCGTGTTATAC	59.690	38.462	0.00	0.00	0.00	1.47
828	838	8.660373	CCTGAAGTAATAAGCTAAGTTTCAGTG	58.340	37.037	17.12	9.81	38.89	3.66
832	842	8.622948	AGTAATAAGCTAAGTTTCAGTGCTTT	57.377	30.769	3.89	0.00	42.81	3.51
845	858	5.342806	TCAGTGCTTTCATTAACGAGTTG	57.657	39.130	0.00	0.00	0.00	3.16
881	894	7.073342	AGTAAAATCGAGATTTGTAACTGGC	57.927	36.000	11.31	0.00	40.57	4.85
882	895	6.879458	AGTAAAATCGAGATTTGTAACTGGCT	59.121	34.615	11.31	0.00	40.57	4.75
883	896	8.038944	AGTAAAATCGAGATTTGTAACTGGCTA	58.961	33.333	11.31	0.00	40.57	3.93
884	897	7.865706	AAAATCGAGATTTGTAACTGGCTAT	57.134	32.000	11.31	0.00	40.57	2.97
885	898	7.484035	AAATCGAGATTTGTAACTGGCTATC	57.516	36.000	9.96	0.00	39.36	2.08
886	899	5.592104	TCGAGATTTGTAACTGGCTATCA	57.408	39.130	0.00	0.00	0.00	2.15
887	900	7.225538	AAATCGAGATTTGTAACTGGCTATCAG	59.774	37.037	9.96	0.00	42.64	2.90
920	933	3.937814	TGGCCATATATAAGCAACGGAG	58.062	45.455	0.00	0.00	0.00	4.63
947	960	2.639347	ACACATCACCTGAACCAGATCA	59.361	45.455	0.00	0.00	32.44	2.92
1023	1036	1.128188	AGACCGCTCCCTCCACTTTT	61.128	55.000	0.00	0.00	0.00	2.27
1048	1061	1.617263	CCCTTCTCCTCGTCCTCTTCA	60.617	57.143	0.00	0.00	0.00	3.02
1060	1073	2.693074	GTCCTCTTCATCCTCTCCTCAC	59.307	54.545	0.00	0.00	0.00	3.51
1061	1074	2.038659	CCTCTTCATCCTCTCCTCACC	58.961	57.143	0.00	0.00	0.00	4.02
1062	1075	2.038659	CTCTTCATCCTCTCCTCACCC	58.961	57.143	0.00	0.00	0.00	4.61
1063	1076	0.749649	CTTCATCCTCTCCTCACCCG	59.250	60.000	0.00	0.00	0.00	5.28
1064	1077	1.330655	TTCATCCTCTCCTCACCCGC	61.331	60.000	0.00	0.00	0.00	6.13
1065	1078	2.444895	ATCCTCTCCTCACCCGCC	60.445	66.667	0.00	0.00	0.00	6.13
1135	1148	2.053277	GTCCTCCTCGTCTCACCCC	61.053	68.421	0.00	0.00	0.00	4.95
1215	1234	3.257375	TGTACATAGTCTTTGTCAGCCGT	59.743	43.478	0.00	0.00	0.00	5.68
1216	1235	4.460034	TGTACATAGTCTTTGTCAGCCGTA	59.540	41.667	0.00	0.00	0.00	4.02
1344	1363	5.706369	GCATAGTATCCGTCCTTCTCTTAGA	59.294	44.000	0.00	0.00	0.00	2.10
1379	1398	2.748461	TTGTTGTTTCTACAGCACGC	57.252	45.000	0.00	0.00	43.86	5.34
1445	1464	2.494445	CGGCGAGGCTCACATGTA	59.506	61.111	15.95	0.00	0.00	2.29
1476	1495	2.096594	GTTAGCAAGTGAGCGCGC	59.903	61.111	26.66	26.66	40.15	6.86
1479	1498	2.220615	TTAGCAAGTGAGCGCGCCTA	62.221	55.000	30.33	17.03	40.15	3.93
1487	1506	0.666274	TGAGCGCGCCTAATTATCCG	60.666	55.000	30.33	0.00	0.00	4.18
1528	1547	1.881973	GCATTCAGAAAGCTGGTGTCA	59.118	47.619	3.01	0.00	42.53	3.58
1621	1669	2.163010	AGACGTACTATGTGGACAACGG	59.837	50.000	6.66	0.00	34.81	4.44
1678	1726	7.084486	GTCTGAAGATCAAATGTTTACCCAAC	58.916	38.462	0.00	0.00	35.71	3.77
1679	1727	7.004086	TCTGAAGATCAAATGTTTACCCAACT	58.996	34.615	0.00	0.00	36.21	3.16
1680	1728	7.174946	TCTGAAGATCAAATGTTTACCCAACTC	59.825	37.037	0.00	0.00	36.21	3.01
1687	1735	3.412237	TGTTTACCCAACTCCTGCTAC	57.588	47.619	0.00	0.00	36.21	3.58
1719	2155	6.299141	ACCTGAAACATGTCACTATGAAGTT	58.701	36.000	0.00	0.00	31.97	2.66
1739	2175	2.126502	GGGCGATTTGTTGCACCG	60.127	61.111	0.00	0.00	0.00	4.94
1760	2196	6.643770	CACCGACTGTTAAGTTTGTACTGTAT	59.356	38.462	0.00	0.00	36.52	2.29
1761	2197	6.643770	ACCGACTGTTAAGTTTGTACTGTATG	59.356	38.462	0.00	0.00	36.52	2.39
1762	2198	6.643770	CCGACTGTTAAGTTTGTACTGTATGT	59.356	38.462	0.00	0.00	36.52	2.29
1763	2199	7.809331	CCGACTGTTAAGTTTGTACTGTATGTA	59.191	37.037	0.00	0.00	36.52	2.29
1795	2238	4.829064	AAGAACGCTTGCAAGTTCATAA	57.171	36.364	26.55	0.00	46.54	1.90
1981	2442	5.649782	TTTCAGCAATTTCCTCTGATTCC	57.350	39.130	0.00	0.00	36.81	3.01
2057	2518	1.954382	GGTGGGTTGAGGTTGAAGAAC	59.046	52.381	0.00	0.00	0.00	3.01
2184	2648	8.905702	CAATAATTTGACAACTAGAAACACAGC	58.094	33.333	0.00	0.00	34.60	4.40
2623	3088	0.603065	GGTTGTCCATGCAAGGAACC	59.397	55.000	13.20	13.91	39.92	3.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	93	1.675552	CACTGGAAAACACCGTTCCT	58.324	50.000	4.92	0.00	44.24	3.36
107	109	1.541147	CCATTTCACGCATGTTCCACT	59.459	47.619	0.00	0.00	0.00	4.00
175	178	3.054287	TGTGTGTTCTTTGGTAGTTGGGA	60.054	43.478	0.00	0.00	0.00	4.37
226	229	6.954102	AGTAAAAGTTGGCCCTCAAATAATCT	59.046	34.615	0.00	0.00	37.08	2.40
230	233	5.947566	GGTAGTAAAAGTTGGCCCTCAAATA	59.052	40.000	0.00	0.00	37.08	1.40
239	242	4.277423	ACATGTGTGGTAGTAAAAGTTGGC	59.723	41.667	0.00	0.00	0.00	4.52
323	326	9.801873	ATGACTACAAAAATAATATGGTTGTGC	57.198	29.630	10.38	3.64	34.43	4.57
391	394	9.807921	AACTTAAAACCTCCTTGAATCATAGAA	57.192	29.630	0.00	0.00	0.00	2.10
460	463	8.638629	AATACTACTAGAAACAGACACAGAGT	57.361	34.615	0.00	0.00	0.00	3.24
506	510	4.533222	AGCAAAAACGAATACAGAAACCG	58.467	39.130	0.00	0.00	0.00	4.44
611	618	2.040679	TGTGGTAGGCTAAAAGGAACCC	59.959	50.000	0.00	0.00	0.00	4.11
692	702	2.556287	GCAAGACGTTTGGCCTCG	59.444	61.111	3.32	9.18	0.00	4.63
741	751	0.550914	AGAGGTGTCTTTTGGGTGCA	59.449	50.000	0.00	0.00	0.00	4.57
828	838	5.057646	GCGTTTACAACTCGTTAATGAAAGC	59.942	40.000	0.00	0.00	0.00	3.51
832	842	4.983538	TGAGCGTTTACAACTCGTTAATGA	59.016	37.500	0.00	0.00	32.98	2.57
845	858	6.814343	TCTCGATTTTACTTTGAGCGTTTAC	58.186	36.000	0.00	0.00	0.00	2.01
855	868	8.021396	GCCAGTTACAAATCTCGATTTTACTTT	58.979	33.333	2.28	0.00	38.84	2.66
864	877	5.592054	CTGATAGCCAGTTACAAATCTCGA	58.408	41.667	0.00	0.00	38.10	4.04
881	894	3.007398	GGCCAAGGGTGATAGACTGATAG	59.993	52.174	0.00	0.00	0.00	2.08
882	895	2.972713	GGCCAAGGGTGATAGACTGATA	59.027	50.000	0.00	0.00	0.00	2.15
883	896	1.771255	GGCCAAGGGTGATAGACTGAT	59.229	52.381	0.00	0.00	0.00	2.90
884	897	1.204146	GGCCAAGGGTGATAGACTGA	58.796	55.000	0.00	0.00	0.00	3.41
885	898	0.911769	TGGCCAAGGGTGATAGACTG	59.088	55.000	0.61	0.00	0.00	3.51
886	899	1.898863	ATGGCCAAGGGTGATAGACT	58.101	50.000	10.96	0.00	0.00	3.24
887	900	5.700402	ATATATGGCCAAGGGTGATAGAC	57.300	43.478	10.96	0.00	0.00	2.59
888	901	6.126768	GCTTATATATGGCCAAGGGTGATAGA	60.127	42.308	10.96	0.00	0.00	1.98
920	933	1.537202	GTTCAGGTGATGTGTGAAGCC	59.463	52.381	0.00	0.00	30.94	4.35
1023	1036	0.898789	GGACGAGGAGAAGGGACACA	60.899	60.000	0.00	0.00	0.00	3.72
1048	1061	2.444895	GGCGGGTGAGGAGAGGAT	60.445	66.667	0.00	0.00	0.00	3.24
1215	1234	3.056393	CCACGGAGTCAATGTAACCAGTA	60.056	47.826	0.00	0.00	41.61	2.74
1216	1235	2.289444	CCACGGAGTCAATGTAACCAGT	60.289	50.000	0.00	0.00	41.61	4.00
1267	1286	1.420138	AGTCACAACCAACCTTCCGAT	59.580	47.619	0.00	0.00	0.00	4.18
1323	1342	7.075851	TCATCTAAGAGAAGGACGGATACTA	57.924	40.000	0.00	0.00	0.00	1.82
1326	1345	5.644206	CGATCATCTAAGAGAAGGACGGATA	59.356	44.000	0.00	0.00	0.00	2.59
1344	1363	8.084073	AGAAACAACAAAAATGTCATCGATCAT	58.916	29.630	0.00	0.00	0.00	2.45
1379	1398	4.009015	GGCCTTCTTTGCCTCCTG	57.991	61.111	0.00	0.00	45.70	3.86
1445	1464	1.003118	TGCTAACTGGTCCGCTTGATT	59.997	47.619	0.00	0.00	0.00	2.57
1476	1495	4.515567	GGAGAAACTTGGCGGATAATTAGG	59.484	45.833	0.00	0.00	0.00	2.69
1479	1498	3.288092	GGGAGAAACTTGGCGGATAATT	58.712	45.455	0.00	0.00	0.00	1.40
1487	1506	2.467566	TCTAACGGGAGAAACTTGGC	57.532	50.000	0.00	0.00	0.00	4.52
1528	1547	2.024918	CTGAGCCACACGCAAAACT	58.975	52.632	0.00	0.00	41.38	2.66
1554	1602	2.031012	CCCTGCACGAGTCAAGCA	59.969	61.111	6.36	6.36	36.72	3.91
1563	1611	4.785453	GCCCTCCTTCCCTGCACG	62.785	72.222	0.00	0.00	0.00	5.34
1678	1726	0.739561	GGTCGTAGTGGTAGCAGGAG	59.260	60.000	0.00	0.00	0.00	3.69
1679	1727	0.330604	AGGTCGTAGTGGTAGCAGGA	59.669	55.000	0.00	0.00	0.00	3.86
1680	1728	0.456221	CAGGTCGTAGTGGTAGCAGG	59.544	60.000	0.00	0.00	0.00	4.85
1687	1735	2.993899	GACATGTTTCAGGTCGTAGTGG	59.006	50.000	0.00	0.00	35.55	4.00
1719	2155	1.523154	GGTGCAACAAATCGCCCAGA	61.523	55.000	0.00	0.00	39.98	3.86
1774	2210	4.036262	TGTTATGAACTTGCAAGCGTTCTT	59.964	37.500	26.27	21.18	40.04	2.52
1776	2212	3.884169	TGTTATGAACTTGCAAGCGTTC	58.116	40.909	26.27	22.31	39.85	3.95
1885	2344	5.304357	GCATAAAATTGTATACAGGGCCCTT	59.696	40.000	26.10	16.65	0.00	3.95
1928	2388	8.118976	ACTGTGATTCAAACAAATCAGATCAT	57.881	30.769	0.00	0.00	44.18	2.45
2002	2463	2.279120	CATCGCCGCCTCTCACTC	60.279	66.667	0.00	0.00	0.00	3.51
2024	2485	3.536917	CCACCATAGCTCCGCCGA	61.537	66.667	0.00	0.00	0.00	5.54
2057	2518	1.225745	GTCAATTTGGCTCGTCGCG	60.226	57.895	0.00	0.00	40.44	5.87
2214	2678	7.908827	TTATTGTGGTTTTCTTATAGCGACA	57.091	32.000	0.00	0.00	0.00	4.35
2247	2711	3.181506	GCATAGAGTTGGCACACTTAAGC	60.182	47.826	1.29	0.00	39.29	3.09
2623	3088	3.770040	TGGGACGTCCTGGCATCG	61.770	66.667	32.52	0.00	36.20	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.