AutoCloner

Multiple sequence alignment - TraesCS4D01G030300

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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	TraesCS4D01G030300	chr4D	100.000	6592	0	0	1	6592	13743321	13749912	0.000000e+00	12174
1	TraesCS4D01G030300	chr4D	98.540	6097	74	5	1	6084	13927548	13933642	0.000000e+00	10752
2	TraesCS4D01G030300	chr4D	98.940	4149	41	3	1	4148	13838073	13842219	0.000000e+00	7415
3	TraesCS4D01G030300	chr4D	97.413	889	12	4	5707	6592	13842296	13843176	0.000000e+00	1504
4	TraesCS4D01G030300	chr4B	97.414	6264	90	28	348	6592	24397835	24404045	0.000000e+00	10604
5	TraesCS4D01G030300	chr4B	98.559	5273	57	4	796	6064	24538466	24543723	0.000000e+00	9299
6	TraesCS4D01G030300	chr4B	98.090	733	13	1	1	732	24537734	24538466	0.000000e+00	1275
7	TraesCS4D01G030300	chr4B	95.146	309	12	1	6026	6331	24543719	24544027	9.940000e-133	484
8	TraesCS4D01G030300	chr4A	97.000	5266	103	17	757	5996	588615092	588620328	0.000000e+00	8798
9	TraesCS4D01G030300	chr4A	86.962	3091	281	53	748	3782	457235397	457238421	0.000000e+00	3363
10	TraesCS4D01G030300	chr4A	92.135	2136	95	27	4154	6249	574157216	574155114	0.000000e+00	2946
11	TraesCS4D01G030300	chr4A	92.652	1946	85	20	4151	6064	457237877	457239796	0.000000e+00	2748
12	TraesCS4D01G030300	chr4A	93.078	1777	76	19	4151	5907	586858590	586860339	0.000000e+00	2556
13	TraesCS4D01G030300	chr4A	92.954	1774	79	18	4154	5907	586919277	586917530	0.000000e+00	2542
14	TraesCS4D01G030300	chr4A	91.935	806	39	13	1	797	586853224	586854012	0.000000e+00	1105
15	TraesCS4D01G030300	chr4A	90.613	767	56	11	1	762	457234627	457235382	0.000000e+00	1003
16	TraesCS4D01G030300	chr4A	88.038	836	77	8	753	1581	586854000	586854819	0.000000e+00	968
17	TraesCS4D01G030300	chr4A	92.246	374	16	7	6226	6592	457239908	457240275	9.800000e-143	518
18	TraesCS4D01G030300	chr4A	91.957	373	17	7	6226	6592	588620431	588620796	1.640000e-140	510
19	TraesCS4D01G030300	chr4A	86.450	369	25	9	5901	6249	586860496	586860859	1.340000e-101	381
20	TraesCS4D01G030300	chr4A	86.450	369	25	9	5901	6249	586917373	586917010	1.340000e-101	381
21	TraesCS4D01G030300	chr4A	93.103	232	11	1	6366	6592	574154950	574154719	1.060000e-87	335
22	TraesCS4D01G030300	chr4A	93.304	224	15	0	6026	6249	457239792	457240015	1.370000e-86	331
23	TraesCS4D01G030300	chr4A	92.241	232	11	4	6366	6592	586861024	586861253	8.250000e-84	322
24	TraesCS4D01G030300	chr4A	93.810	210	13	0	6040	6249	588620329	588620538	3.840000e-82	316
25	TraesCS4D01G030300	chr4A	82.403	233	10	4	6366	6592	586916844	586916637	2.440000e-39	174
26	TraesCS4D01G030300	chr4A	90.840	131	8	2	6252	6379	574155199	574155070	8.790000e-39	172
27	TraesCS4D01G030300	chr4A	90.299	134	9	2	6249	6379	586860771	586860903	8.790000e-39	172
28	TraesCS4D01G030300	chr4A	87.342	158	11	5	6226	6380	586917116	586916965	8.790000e-39	172
29	TraesCS4D01G030300	chr3B	95.638	4333	126	16	1784	6087	454190563	454186265	0.000000e+00	6896
30	TraesCS4D01G030300	chr3B	98.486	3302	46	4	2755	6054	454486799	454483500	0.000000e+00	5818
31	TraesCS4D01G030300	chr3B	94.073	3442	143	32	180	3580	454374988	454371567	0.000000e+00	5169
32	TraesCS4D01G030300	chr3B	96.960	2730	48	4	2787	5515	453994707	453992012	0.000000e+00	4549
33	TraesCS4D01G030300	chr3B	92.980	2977	152	35	1	2935	453997651	453994690	0.000000e+00	4287
34	TraesCS4D01G030300	chr3B	95.564	2525	68	11	3580	6087	454367385	454364888	0.000000e+00	4002
35	TraesCS4D01G030300	chr3B	95.404	2154	51	18	543	2680	454488943	454486822	0.000000e+00	3386
36	TraesCS4D01G030300	chr3B	92.113	1813	100	26	1	1783	454204567	454202768	0.000000e+00	2516
37	TraesCS4D01G030300	chr3B	98.248	856	13	2	1	855	454375854	454375000	0.000000e+00	1496
38	TraesCS4D01G030300	chr3B	97.321	560	11	2	6036	6592	454482959	454482401	0.000000e+00	948
39	TraesCS4D01G030300	chr3B	87.135	171	22	0	5983	6153	454482739	454482569	1.880000e-45	195
40	TraesCS4D01G030300	chr3B	86.275	102	14	0	6413	6514	454482955	454482854	1.940000e-20	111
41	TraesCS4D01G030300	chrUn	100.000	1682	0	0	2262	3943	379573553	379575234	0.000000e+00	3107

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	TraesCS4D01G030300	chr4D	13743321	13749912	6591	False	12174.000000	12174	100.000000	1	6592	1	chr4D.!!$F1	6591
1	TraesCS4D01G030300	chr4D	13927548	13933642	6094	False	10752.000000	10752	98.540000	1	6084	1	chr4D.!!$F2	6083
2	TraesCS4D01G030300	chr4D	13838073	13843176	5103	False	4459.500000	7415	98.176500	1	6592	2	chr4D.!!$F3	6591
3	TraesCS4D01G030300	chr4B	24397835	24404045	6210	False	10604.000000	10604	97.414000	348	6592	1	chr4B.!!$F1	6244
4	TraesCS4D01G030300	chr4B	24537734	24544027	6293	False	3686.000000	9299	97.265000	1	6331	3	chr4B.!!$F2	6330
5	TraesCS4D01G030300	chr4A	588615092	588620796	5704	False	3208.000000	8798	94.255667	757	6592	3	chr4A.!!$F3	5835
6	TraesCS4D01G030300	chr4A	457234627	457240275	5648	False	1592.600000	3363	91.155400	1	6592	5	chr4A.!!$F1	6591
7	TraesCS4D01G030300	chr4A	574154719	574157216	2497	True	1151.000000	2946	92.026000	4154	6592	3	chr4A.!!$R1	2438
8	TraesCS4D01G030300	chr4A	586853224	586861253	8029	False	917.333333	2556	90.340167	1	6592	6	chr4A.!!$F2	6591
9	TraesCS4D01G030300	chr4A	586916637	586919277	2640	True	817.250000	2542	87.287250	4154	6592	4	chr4A.!!$R2	2438
10	TraesCS4D01G030300	chr3B	454186265	454190563	4298	True	6896.000000	6896	95.638000	1784	6087	1	chr3B.!!$R1	4303
11	TraesCS4D01G030300	chr3B	453992012	453997651	5639	True	4418.000000	4549	94.970000	1	5515	2	chr3B.!!$R4	5514
12	TraesCS4D01G030300	chr3B	454364888	454367385	2497	True	4002.000000	4002	95.564000	3580	6087	1	chr3B.!!$R3	2507
13	TraesCS4D01G030300	chr3B	454371567	454375854	4287	True	3332.500000	5169	96.160500	1	3580	2	chr3B.!!$R5	3579
14	TraesCS4D01G030300	chr3B	454202768	454204567	1799	True	2516.000000	2516	92.113000	1	1783	1	chr3B.!!$R2	1782
15	TraesCS4D01G030300	chr3B	454482401	454488943	6542	True	2091.600000	5818	92.924200	543	6592	5	chr3B.!!$R6	6049
16	TraesCS4D01G030300	chrUn	379573553	379575234	1681	False	3107.000000	3107	100.000000	2262	3943	1	chrUn.!!$F1	1681

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
21	22	1.298667	GGGCAGGTCCACGTGTAAT	59.701	57.895	15.65	0.00	36.21	1.89	F
861	1665	1.598130	GTTGCCTCCTCTGTGCGTT	60.598	57.895	0.00	0.00	0.00	4.84	F
1006	1811	0.107508	CTCCTCGGTTGCCATGATGT	60.108	55.000	0.00	0.00	0.00	3.06	F
1255	2060	1.918467	CTGCCCAGATCTGAAGCCCA	61.918	60.000	24.62	10.23	0.00	5.36	F
1272	2077	1.948834	CCCAATGCATTCGCTGACATA	59.051	47.619	9.53	0.00	39.64	2.29	F
1337	2143	2.190578	CATCTGCCCCGAACTCCC	59.809	66.667	0.00	0.00	0.00	4.30	F
4045	7124	2.359850	GCCGTTGCTGGACATCCA	60.360	61.111	0.00	0.00	45.30	3.41	F
5277	9270	6.231211	TCTAGAATTTGAAACACAGGGAGTC	58.769	40.000	0.00	0.00	0.00	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1006	1811	1.544537	CCGGAGTTGGTTGTCATCCAA	60.545	52.381	10.75	10.75	41.84	3.53	R
1957	4886	1.920835	AGTCCTCCTCCCAGTTGCC	60.921	63.158	0.00	0.00	0.00	4.52	R
3306	6385	1.412079	TGGAGCCACTGCAACATTTT	58.588	45.000	0.00	0.00	41.13	1.82	R
4434	8423	0.111253	AAGGGGGTGAAAGCTGACAG	59.889	55.000	0.00	0.00	0.00	3.51	R
4630	8621	3.243177	GGCTAGCTCTCGTGTTTAATTCG	59.757	47.826	15.72	0.00	0.00	3.34	R
5244	9237	6.801862	GTGTTTCAAATTCTAGATTTGTCCCG	59.198	38.462	18.74	3.43	39.36	5.14	R
5397	9390	1.294659	CCAACAACCGCTCTGCTCTC	61.295	60.000	0.00	0.00	0.00	3.20	R
6250	11420	7.360017	CGAGCAATAATGTTTCACTACTGAACA	60.360	37.037	0.00	0.00	36.06	3.18	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
21	22	1.298667	GGGCAGGTCCACGTGTAAT	59.701	57.895	15.65	0.00	36.21	1.89
213	214	8.336080	GTTCGAGTTAAGGGCTGAAATATAAAG	58.664	37.037	0.00	0.00	0.00	1.85
819	1614	2.882761	TGATTGCTATAGTACCGAGCGT	59.117	45.455	0.84	0.00	39.14	5.07
861	1665	1.598130	GTTGCCTCCTCTGTGCGTT	60.598	57.895	0.00	0.00	0.00	4.84
1003	1808	1.918293	ACCTCCTCGGTTGCCATGA	60.918	57.895	0.00	0.00	46.37	3.07
1006	1811	0.107508	CTCCTCGGTTGCCATGATGT	60.108	55.000	0.00	0.00	0.00	3.06
1255	2060	1.918467	CTGCCCAGATCTGAAGCCCA	61.918	60.000	24.62	10.23	0.00	5.36
1272	2077	1.948834	CCCAATGCATTCGCTGACATA	59.051	47.619	9.53	0.00	39.64	2.29
1332	2138	3.460672	GATCGCCATCTGCCCCGAA	62.461	63.158	0.00	0.00	36.24	4.30
1334	2140	4.473520	CGCCATCTGCCCCGAACT	62.474	66.667	0.00	0.00	36.24	3.01
1337	2143	2.190578	CATCTGCCCCGAACTCCC	59.809	66.667	0.00	0.00	0.00	4.30
1957	4886	4.437239	CATTGGCTCTACTTCTGGTAGTG	58.563	47.826	0.00	0.00	45.86	2.74
3306	6385	3.756082	ATGGTTGGCTTATTTGAGGGA	57.244	42.857	0.00	0.00	0.00	4.20
4045	7124	2.359850	GCCGTTGCTGGACATCCA	60.360	61.111	0.00	0.00	45.30	3.41
4434	8423	7.251281	GCACTTATCCCATTCAGTAAAAGTTC	58.749	38.462	0.00	0.00	0.00	3.01
5024	9017	7.446106	ACTGTCCCTATATTTGTACCATTCA	57.554	36.000	0.00	0.00	0.00	2.57
5244	9237	8.268850	TGGCTAAAGATAGAAATGTTTGACTC	57.731	34.615	0.00	0.00	31.53	3.36
5277	9270	6.231211	TCTAGAATTTGAAACACAGGGAGTC	58.769	40.000	0.00	0.00	0.00	3.36
5397	9390	7.047891	TGCTAATGTTAGTACTCCTTTGATGG	58.952	38.462	0.00	0.00	33.32	3.51
5619	9622	5.446143	TTGTTACCGAAATTTGAGTGCAT	57.554	34.783	0.00	0.00	0.00	3.96
5682	9685	1.612676	AAGCCCCGGTACAAAGAAAC	58.387	50.000	0.00	0.00	0.00	2.78
5831	9837	1.279496	TGCTAGCCATGTGAGGTCTT	58.721	50.000	13.29	0.00	0.00	3.01
5836	9842	5.130311	TGCTAGCCATGTGAGGTCTTTATAA	59.870	40.000	13.29	0.00	0.00	0.98
5863	9869	7.698506	AGACTTGCTAAAATAACCCTAAACC	57.301	36.000	0.00	0.00	0.00	3.27
5864	9870	6.662234	AGACTTGCTAAAATAACCCTAAACCC	59.338	38.462	0.00	0.00	0.00	4.11
5866	9872	6.783482	ACTTGCTAAAATAACCCTAAACCCAA	59.217	34.615	0.00	0.00	0.00	4.12
5867	9873	7.456585	ACTTGCTAAAATAACCCTAAACCCAAT	59.543	33.333	0.00	0.00	0.00	3.16
6001	10355	5.701290	GTCCAGTAGTGAAACATTACTGCTT	59.299	40.000	20.83	0.00	46.29	3.91
6046	11026	3.691609	GCATCTTCAAAGTCCACCCTTAG	59.308	47.826	0.00	0.00	0.00	2.18
6244	11414	2.961062	GGCCCTCAAATCACTTGCATAT	59.039	45.455	0.00	0.00	34.76	1.78
6250	11420	6.127535	CCCTCAAATCACTTGCATATGTCTTT	60.128	38.462	4.29	0.00	34.76	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	7.701539	ATTTGCCCTTCGATGCATATATAAA	57.298	32.000	0.00	0.00	37.33	1.40
377	1067	1.125093	AGGGACACACACCGATCCAA	61.125	55.000	0.00	0.00	32.45	3.53
807	1602	2.932614	GACTCTGTAACGCTCGGTACTA	59.067	50.000	16.94	6.11	38.95	1.82
819	1614	3.766691	GCCGGCCCGACTCTGTAA	61.767	66.667	18.11	0.00	0.00	2.41
861	1665	3.762288	CGATATTTATCTCGGGGACTCCA	59.238	47.826	0.00	0.00	34.36	3.86
1006	1811	1.544537	CCGGAGTTGGTTGTCATCCAA	60.545	52.381	10.75	10.75	41.84	3.53
1255	2060	1.949525	GGGTATGTCAGCGAATGCATT	59.050	47.619	12.83	12.83	46.23	3.56
1272	2077	3.897657	TCCGTATAGGAGATCTTGGGT	57.102	47.619	0.00	0.00	45.98	4.51
1295	2100	3.691744	CTGAGCAGGACGAGGTCGC	62.692	68.421	0.00	0.00	44.43	5.19
1314	2119	3.460672	TTCGGGGCAGATGGCGATC	62.461	63.158	0.00	0.00	46.16	3.69
1318	2123	2.514824	GAGTTCGGGGCAGATGGC	60.515	66.667	0.00	0.00	43.74	4.40
1352	2158	3.735181	ACGAAGTAGCGGATGTTCC	57.265	52.632	0.00	0.00	41.94	3.62
1957	4886	1.920835	AGTCCTCCTCCCAGTTGCC	60.921	63.158	0.00	0.00	0.00	4.52
3306	6385	1.412079	TGGAGCCACTGCAACATTTT	58.588	45.000	0.00	0.00	41.13	1.82
4434	8423	0.111253	AAGGGGGTGAAAGCTGACAG	59.889	55.000	0.00	0.00	0.00	3.51
4630	8621	3.243177	GGCTAGCTCTCGTGTTTAATTCG	59.757	47.826	15.72	0.00	0.00	3.34
5244	9237	6.801862	GTGTTTCAAATTCTAGATTTGTCCCG	59.198	38.462	18.74	3.43	39.36	5.14
5277	9270	2.636830	AGTTCTCTTCCATTCCATGCG	58.363	47.619	0.00	0.00	0.00	4.73
5397	9390	1.294659	CCAACAACCGCTCTGCTCTC	61.295	60.000	0.00	0.00	0.00	3.20
5619	9622	4.269183	TGAACTCAAACTTCTTTCCAGCA	58.731	39.130	0.00	0.00	0.00	4.41
5682	9685	6.607004	TGAGGTAGGAAAGACTTCTTAAGG	57.393	41.667	1.85	0.00	34.61	2.69
6001	10355	3.628032	CCTGACTACGAGAGCAAGATACA	59.372	47.826	0.00	0.00	0.00	2.29
6046	11026	3.429135	GGTCCAGACGTAGGAAAGTGATC	60.429	52.174	10.52	0.00	36.80	2.92
6244	11414	7.624360	AATGTTTCACTACTGAACAAAGACA	57.376	32.000	0.00	0.00	36.06	3.41
6250	11420	7.360017	CGAGCAATAATGTTTCACTACTGAACA	60.360	37.037	0.00	0.00	36.06	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.