AutoCloner

Multiple sequence alignment - TraesCS3A01G115000

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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	TraesCS3A01G115000	chr3A	100.000	2915	0	0	1	2915	82745281	82742367	0.000000e+00	5384.0
1	TraesCS3A01G115000	chr3A	81.020	353	57	8	709	1056	80102515	80102862	3.700000e-69	272.0
2	TraesCS3A01G115000	chr3A	75.912	137	26	6	895	1028	138807205	138807337	2.430000e-06	63.9
3	TraesCS3A01G115000	chr3D	96.276	2175	80	1	1	2175	71117056	71114883	0.000000e+00	3567.0
4	TraesCS3A01G115000	chr3D	92.215	745	40	2	2171	2915	71114813	71114087	0.000000e+00	1038.0
5	TraesCS3A01G115000	chr3D	80.980	347	56	8	715	1056	68072258	68071917	1.720000e-67	267.0
6	TraesCS3A01G115000	chr3D	71.739	552	105	36	713	1237	127903768	127904295	1.100000e-19	108.0
7	TraesCS3A01G115000	chr3B	94.434	2174	118	3	1	2174	116391273	116389103	0.000000e+00	3341.0
8	TraesCS3A01G115000	chr3B	94.064	2173	125	4	2	2174	116438737	116436569	0.000000e+00	3295.0
9	TraesCS3A01G115000	chr3B	93.423	745	49	0	2171	2915	116389032	116388288	0.000000e+00	1105.0
10	TraesCS3A01G115000	chr3B	92.081	745	49	3	2171	2915	116436498	116435764	0.000000e+00	1040.0
11	TraesCS3A01G115000	chr3B	81.556	347	55	7	709	1050	113930098	113930440	7.960000e-71	278.0
12	TraesCS3A01G115000	chr3B	81.019	216	26	9	174	382	638328225	638328018	1.080000e-34	158.0
13	TraesCS3A01G115000	chr3B	72.727	319	66	15	713	1028	182203230	182203530	1.440000e-13	87.9
14	TraesCS3A01G115000	chr2D	81.836	501	80	10	174	668	617543428	617543923	7.520000e-111	411.0
15	TraesCS3A01G115000	chr2D	100.000	31	0	0	2588	2618	485591201	485591231	1.130000e-04	58.4
16	TraesCS3A01G115000	chr2D	100.000	31	0	0	2588	2618	485634404	485634434	1.130000e-04	58.4
17	TraesCS3A01G115000	chr1D	78.439	538	109	7	174	708	9665752	9665219	7.730000e-91	344.0
18	TraesCS3A01G115000	chr4D	78.067	538	111	7	174	708	131900895	131901428	1.670000e-87	333.0
19	TraesCS3A01G115000	chr2A	77.506	409	76	6	174	581	769519569	769519176	6.280000e-57	231.0
20	TraesCS3A01G115000	chr2A	83.770	191	28	3	174	364	748291309	748291496	8.300000e-41	178.0
21	TraesCS3A01G115000	chr2A	87.143	70	8	1	640	708	108665265	108665334	8.660000e-11	78.7
22	TraesCS3A01G115000	chr5D	76.445	467	79	20	174	638	249528310	249528747	1.050000e-54	224.0

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	TraesCS3A01G115000	chr3A	82742367	82745281	2914	True	5384.0	5384	100.0000	1	2915	1	chr3A.!!$R1	2914
1	TraesCS3A01G115000	chr3D	71114087	71117056	2969	True	2302.5	3567	94.2455	1	2915	2	chr3D.!!$R2	2914
2	TraesCS3A01G115000	chr3B	116388288	116391273	2985	True	2223.0	3341	93.9285	1	2915	2	chr3B.!!$R2	2914
3	TraesCS3A01G115000	chr3B	116435764	116438737	2973	True	2167.5	3295	93.0725	2	2915	2	chr3B.!!$R3	2913
4	TraesCS3A01G115000	chr1D	9665219	9665752	533	True	344.0	344	78.4390	174	708	1	chr1D.!!$R1	534
5	TraesCS3A01G115000	chr4D	131900895	131901428	533	False	333.0	333	78.0670	174	708	1	chr4D.!!$F1	534

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
538	540	0.163788	CAACGTGACGGAGATTGCAC	59.836	55.0	10.66	0.0	0.0	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2459	2536	0.394938	TCAACACCTTGCGCCTTAGA	59.605	50.0	4.18	0.0	0.0	2.1	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
154	155	3.095299	AGGATGGGAATGGGATAACCT	57.905	47.619	0.00	0.00	41.11	3.50
314	315	3.418684	ACGAGGTGTTAAAATGAGCCT	57.581	42.857	0.00	0.00	0.00	4.58
502	504	4.496341	CCGATAGACTGCATCGCAAAATTT	60.496	41.667	1.12	0.00	43.04	1.82
538	540	0.163788	CAACGTGACGGAGATTGCAC	59.836	55.000	10.66	0.00	0.00	4.57
540	542	2.100631	CGTGACGGAGATTGCACCC	61.101	63.158	0.00	0.00	0.00	4.61
588	590	4.284550	GACCAGGTTGGCCCAGCA	62.285	66.667	8.93	0.00	42.67	4.41
602	604	4.990910	AGCAGGTCACCAGGGGCT	62.991	66.667	0.00	0.00	0.00	5.19
657	659	0.324645	AACATGACCCATTGGCCTCC	60.325	55.000	3.32	0.00	33.59	4.30
871	874	4.330250	AGGCATGCATGTTCATAGATACC	58.670	43.478	26.79	15.15	0.00	2.73
928	931	4.101114	TGTAGCATCCCTCCTAAGAAACA	58.899	43.478	0.00	0.00	0.00	2.83
936	939	6.110411	TCCCTCCTAAGAAACAAACACTAG	57.890	41.667	0.00	0.00	0.00	2.57
954	957	7.411486	ACACTAGCATACCATATACATCTCC	57.589	40.000	0.00	0.00	0.00	3.71
961	964	7.016563	AGCATACCATATACATCTCCACTTTCA	59.983	37.037	0.00	0.00	0.00	2.69
1153	1156	4.074259	CACACCATCAGATTCAACTTGGA	58.926	43.478	0.00	0.00	0.00	3.53
1225	1228	5.975344	CCATCAATCAAAGATTGTTCCATCG	59.025	40.000	16.64	0.88	0.00	3.84
1233	1236	3.206150	AGATTGTTCCATCGTGCCATAC	58.794	45.455	0.00	0.00	0.00	2.39
1244	1247	0.243636	GTGCCATACCAAACCAGTGC	59.756	55.000	0.00	0.00	0.00	4.40
1254	1257	2.684881	CCAAACCAGTGCATCACTATCC	59.315	50.000	0.00	0.00	43.43	2.59
1294	1297	4.261801	GCCTGATGCAAAGTTTACTCCTA	58.738	43.478	0.00	0.00	40.77	2.94
1305	1308	7.526025	GCAAAGTTTACTCCTACAACTAGGGTA	60.526	40.741	0.00	0.00	40.31	3.69
1398	1401	7.272144	AGATTTCCTGTCAAACCCTATTAGT	57.728	36.000	0.00	0.00	0.00	2.24
1425	1428	7.612677	ACTACTTTAGTTCATCGGATCAAAGT	58.387	34.615	0.00	1.39	38.11	2.66
1437	1440	5.348986	TCGGATCAAAGTAGGATCTTTTCG	58.651	41.667	0.00	0.00	40.74	3.46
1557	1560	2.044793	TTGAGATCCCAACCAGGAGT	57.955	50.000	0.00	0.00	39.95	3.85
1601	1604	8.838365	AGTACCGTCACAATTTGTTTGTATTTA	58.162	29.630	0.00	0.00	46.90	1.40
1731	1734	1.611419	CACATCCTCACATGGCCCT	59.389	57.895	0.00	0.00	0.00	5.19
1738	1741	2.053244	CCTCACATGGCCCTAGAGAAT	58.947	52.381	0.00	0.00	0.00	2.40
1924	1927	5.551233	AGCTACAAAGTTGAACTATGAGCA	58.449	37.500	17.78	0.00	0.00	4.26
2141	2144	8.394877	TGGTTATCTGCTATGTTAATCGTTTTG	58.605	33.333	0.00	0.00	0.00	2.44
2178	2255	7.994425	TGAAGTAACCATGCTTTTGAGAATA	57.006	32.000	0.00	0.00	31.06	1.75
2211	2288	6.767524	TTTTGTTTACCTATACCATGGCTG	57.232	37.500	13.04	0.00	0.00	4.85
2283	2360	7.282901	CCCATTGAACTTTCAGAATTGGTTTTT	59.717	33.333	0.00	0.00	38.61	1.94
2363	2440	8.006298	TGCTATTTCCTTGTATTTATGGGTTG	57.994	34.615	0.00	0.00	0.00	3.77
2375	2452	8.807118	TGTATTTATGGGTTGCTCATAACAAAA	58.193	29.630	1.34	0.00	36.97	2.44
2509	2586	4.110072	CCCTCATGATATCCAAGATCCCT	58.890	47.826	0.00	0.00	0.00	4.20
2521	2598	0.769873	AGATCCCTGCTATTGGGCTG	59.230	55.000	0.00	0.00	44.23	4.85
2552	2629	4.922692	TGCAACGCTTGGATAAAGAAAATG	59.077	37.500	0.00	0.00	38.24	2.32
2587	2664	0.976641	AACACCCGAGAGAATGCTCA	59.023	50.000	2.79	0.00	43.81	4.26
2662	2739	9.355215	AGTATAATTTGAGTAGAGTGTTGTTCG	57.645	33.333	0.00	0.00	0.00	3.95
2693	2770	6.243900	AGTGTTGTCCATTCAATTCATCTCT	58.756	36.000	0.00	0.00	0.00	3.10
2772	2849	2.166270	GCAAGTGCACAGCCTCTAC	58.834	57.895	21.04	0.00	41.59	2.59
2793	2870	5.537300	ACAGATATCCTTGCGTGTAGATT	57.463	39.130	0.00	0.00	0.00	2.40
2800	2877	3.994392	TCCTTGCGTGTAGATTGAACTTC	59.006	43.478	0.00	0.00	0.00	3.01
2813	2890	5.888724	AGATTGAACTTCGAGAGATGGACTA	59.111	40.000	2.28	0.00	41.60	2.59
2838	2915	1.682005	CCATTTGCATGACCGGGGT	60.682	57.895	6.32	0.00	31.07	4.95

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	149	1.005924	CCAAGGCCAGGTTCAGGTTAT	59.994	52.381	5.01	0.00	0.00	1.89
150	151	1.153756	CCAAGGCCAGGTTCAGGTT	59.846	57.895	5.01	0.00	0.00	3.50
154	155	2.840753	GGGTCCAAGGCCAGGTTCA	61.841	63.158	5.01	0.00	0.00	3.18
314	315	6.373216	CACTAGTCGGATTCCATTTAAACCAA	59.627	38.462	3.09	0.00	0.00	3.67
446	448	2.150397	AACGCTCGCCTATATGAACC	57.850	50.000	0.00	0.00	0.00	3.62
470	472	6.096036	CGATGCAGTCTATCGGATAATTTCT	58.904	40.000	0.00	0.00	42.63	2.52
502	504	2.270850	GGCATTGTCGTAGGGCCA	59.729	61.111	6.18	0.00	44.01	5.36
538	540	8.625651	CCTTATAGTCTTATATCTCACATCGGG	58.374	40.741	0.00	0.00	0.00	5.14
540	542	9.995957	CACCTTATAGTCTTATATCTCACATCG	57.004	37.037	0.00	0.00	0.00	3.84
581	583	4.729918	CCTGGTGACCTGCTGGGC	62.730	72.222	14.82	12.09	43.36	5.36
602	604	1.133199	AGATTGGGGTCAACAAAGCCA	60.133	47.619	0.00	0.00	38.60	4.75
607	609	4.026744	TCAAACAAGATTGGGGTCAACAA	58.973	39.130	0.00	0.00	35.48	2.83
657	659	4.173256	GTCACTTATCGGCCCAAAAATTG	58.827	43.478	0.00	0.00	0.00	2.32
668	670	2.279252	CGCCGGGTCACTTATCGG	60.279	66.667	2.18	0.00	44.70	4.18
671	673	4.171103	GCCCGCCGGGTCACTTAT	62.171	66.667	25.58	0.00	46.51	1.73
897	900	2.435805	GAGGGATGCTACATGAGGTGAA	59.564	50.000	0.00	0.00	0.00	3.18
928	931	8.314751	GGAGATGTATATGGTATGCTAGTGTTT	58.685	37.037	0.00	0.00	0.00	2.83
936	939	7.161404	TGAAAGTGGAGATGTATATGGTATGC	58.839	38.462	0.00	0.00	0.00	3.14
954	957	8.197439	AACTTTTCTGGAAAGGTATTGAAAGTG	58.803	33.333	12.84	0.00	43.40	3.16
961	964	8.712228	ATCAAGAACTTTTCTGGAAAGGTATT	57.288	30.769	12.84	6.94	45.19	1.89
1153	1156	2.132686	GGTAGGTGGGGTGTTCCATAT	58.867	52.381	0.00	0.00	39.26	1.78
1225	1228	0.243636	GCACTGGTTTGGTATGGCAC	59.756	55.000	0.00	0.00	0.00	5.01
1233	1236	2.684881	GGATAGTGATGCACTGGTTTGG	59.315	50.000	10.15	0.00	45.01	3.28
1244	1247	4.279671	GTGGAGGTAGTGAGGATAGTGATG	59.720	50.000	0.00	0.00	0.00	3.07
1254	1257	1.338200	GGCAACTGTGGAGGTAGTGAG	60.338	57.143	0.00	0.00	0.00	3.51
1305	1308	3.850173	TGGGCTGAGAAGTAAGGGTATTT	59.150	43.478	0.00	0.00	0.00	1.40
1425	1428	4.585162	GGAGACTCCATCGAAAAGATCCTA	59.415	45.833	17.10	0.00	37.52	2.94
1557	1560	6.490040	ACGGTACTAAGTTTACCTTGTAGACA	59.510	38.462	2.95	0.00	37.45	3.41
1614	1617	5.132502	CCCTGCATAATAATTGGTGAGTGA	58.867	41.667	0.00	0.00	0.00	3.41
1632	1635	3.380320	GTGGTATATTTTGTGGACCCTGC	59.620	47.826	0.00	0.00	0.00	4.85
1731	1734	6.778069	CACCCATAGGAGTCTTGTATTCTCTA	59.222	42.308	0.00	0.00	36.73	2.43
1738	1741	4.264487	TGGTACACCCATAGGAGTCTTGTA	60.264	45.833	0.00	0.00	38.72	2.41
1924	1927	3.094572	CTCTGCCTTCATCCATTTTGGT	58.905	45.455	0.00	0.00	39.03	3.67
2141	2144	8.764287	GCATGGTTACTTCATAAATTTAATGGC	58.236	33.333	1.21	0.00	0.00	4.40
2178	2255	7.068226	GGTATAGGTAAACAAAATGTGCTCCAT	59.932	37.037	0.00	0.00	34.36	3.41
2283	2360	4.256920	GCTAGAGAAAGGAGCATGACAAA	58.743	43.478	0.00	0.00	36.20	2.83
2289	2366	5.108187	TGAATTGCTAGAGAAAGGAGCAT	57.892	39.130	0.00	0.00	45.20	3.79
2303	2380	2.991250	ACATAGCCGTCTTGAATTGCT	58.009	42.857	0.00	0.00	36.11	3.91
2363	2440	9.956720	ATGCTCAATAGTAATTTTGTTATGAGC	57.043	29.630	14.97	14.97	42.65	4.26
2401	2478	7.591426	AGTTTGAACAAGCAATCGATAGTTTTC	59.409	33.333	0.00	0.00	37.40	2.29
2459	2536	0.394938	TCAACACCTTGCGCCTTAGA	59.605	50.000	4.18	0.00	0.00	2.10
2509	2586	3.476740	GCTACACAGCCCAATAGCA	57.523	52.632	0.00	0.00	42.37	3.49
2521	2598	0.454957	CCAAGCGTTGCATGCTACAC	60.455	55.000	27.53	20.07	40.06	2.90
2534	2611	6.799512	AGGAATCATTTTCTTTATCCAAGCG	58.200	36.000	0.00	0.00	31.70	4.68
2552	2629	3.879892	GGGTGTTCTATGCAGAAGGAATC	59.120	47.826	0.00	0.00	41.48	2.52
2587	2664	5.708230	GTGGTAATCTCGTGATCTATCTCCT	59.292	44.000	0.00	0.00	31.51	3.69
2662	2739	2.303022	TGAATGGACAACACTCTCCTCC	59.697	50.000	0.00	0.00	0.00	4.30
2764	2841	2.560542	CGCAAGGATATCTGTAGAGGCT	59.439	50.000	2.05	0.00	0.00	4.58
2772	2849	5.532557	TCAATCTACACGCAAGGATATCTG	58.467	41.667	2.05	0.00	46.39	2.90
2793	2870	4.590918	ACTAGTCCATCTCTCGAAGTTCA	58.409	43.478	3.32	0.00	0.00	3.18
2800	2877	2.156098	GGCCTACTAGTCCATCTCTCG	58.844	57.143	0.00	0.00	0.00	4.04
2813	2890	1.686115	GGTCATGCAAATGGGCCTACT	60.686	52.381	4.53	0.00	0.00	2.57
2838	2915	2.254152	ATTCTAGCCACCTCCACTCA	57.746	50.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.