AutoCloner

Multiple sequence alignment - TraesCS1D01G027200

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	TraesCS1D01G027200	chr1D	100.000	3459	0	0	1	3459	10937478	10934020	0.000000e+00	6388
1	TraesCS1D01G027200	chr1A	95.787	2872	103	10	3	2869	22754508	22757366	0.000000e+00	4617
2	TraesCS1D01G027200	chr1A	97.976	593	7	3	2867	3459	22757407	22757994	0.000000e+00	1024
3	TraesCS1D01G027200	chr1B	90.462	1992	130	24	703	2666	16428592	16426633	0.000000e+00	2571
4	TraesCS1D01G027200	chr1B	88.918	758	60	15	1851	2586	39846899	39846144	0.000000e+00	913
5	TraesCS1D01G027200	chr1B	82.839	472	62	15	2992	3459	16425455	16424999	4.160000e-109	405
6	TraesCS1D01G027200	chr1B	82.590	471	66	12	2992	3459	39828445	39827988	5.380000e-108	401
7	TraesCS1D01G027200	chr1B	81.712	257	34	10	3204	3459	39821768	39821524	5.850000e-48	202
8	TraesCS1D01G027200	chr1B	93.258	89	4	2	617	704	16428834	16428747	2.800000e-26	130
9	TraesCS1D01G027200	chr7B	78.592	1420	251	36	1042	2442	551897374	551898759	0.000000e+00	889
10	TraesCS1D01G027200	chr7B	80.416	914	157	17	1539	2442	551539582	551540483	0.000000e+00	676
11	TraesCS1D01G027200	chr7A	78.125	1440	259	37	1028	2445	593015991	593014586	0.000000e+00	863
12	TraesCS1D01G027200	chr7A	80.735	898	159	10	1552	2442	593376913	593377803	0.000000e+00	688
13	TraesCS1D01G027200	chr7D	78.160	1424	248	41	1042	2442	518573774	518575157	0.000000e+00	848
14	TraesCS1D01G027200	chr7D	80.688	901	160	10	1552	2445	518090549	518089656	0.000000e+00	688
15	TraesCS1D01G027200	chr3A	83.473	714	95	18	4	707	742578030	742577330	0.000000e+00	643
16	TraesCS1D01G027200	chr3A	88.918	379	37	4	211	585	40809902	40810279	2.430000e-126	462
17	TraesCS1D01G027200	chrUn	85.356	519	47	8	1	515	27691978	27692471	8.560000e-141	510
18	TraesCS1D01G027200	chrUn	93.333	90	3	2	620	708	27692500	27692587	2.800000e-26	130
19	TraesCS1D01G027200	chr4D	78.485	330	40	16	383	706	373841796	373842100	1.640000e-43	187
20	TraesCS1D01G027200	chr5A	85.938	128	17	1	2869	2996	676758956	676759082	6.020000e-28	135
21	TraesCS1D01G027200	chr5A	85.271	129	17	2	2868	2995	531690042	531690169	7.790000e-27	132
22	TraesCS1D01G027200	chr6A	89.423	104	11	0	2874	2977	96809458	96809355	7.790000e-27	132
23	TraesCS1D01G027200	chr5B	86.179	123	15	1	569	691	143502094	143502214	7.790000e-27	132
24	TraesCS1D01G027200	chr5B	85.039	127	19	0	2869	2995	182472583	182472457	2.800000e-26	130
25	TraesCS1D01G027200	chr5B	83.846	130	18	2	2868	2995	462328918	462329046	1.690000e-23	121
26	TraesCS1D01G027200	chr2D	88.182	110	13	0	2868	2977	41264071	41264180	7.790000e-27	132
27	TraesCS1D01G027200	chr2B	85.600	125	18	0	2868	2992	796371454	796371578	7.790000e-27	132
28	TraesCS1D01G027200	chr6B	82.812	128	22	0	2868	2995	714045345	714045472	7.840000e-22	115

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	TraesCS1D01G027200	chr1D	10934020	10937478	3458	True	6388.000000	6388	100.0000	1	3459	1	chr1D.!!$R1	3458
1	TraesCS1D01G027200	chr1A	22754508	22757994	3486	False	2820.500000	4617	96.8815	3	3459	2	chr1A.!!$F1	3456
2	TraesCS1D01G027200	chr1B	16424999	16428834	3835	True	1035.333333	2571	88.8530	617	3459	3	chr1B.!!$R4	2842
3	TraesCS1D01G027200	chr1B	39846144	39846899	755	True	913.000000	913	88.9180	1851	2586	1	chr1B.!!$R3	735
4	TraesCS1D01G027200	chr7B	551897374	551898759	1385	False	889.000000	889	78.5920	1042	2442	1	chr7B.!!$F2	1400
5	TraesCS1D01G027200	chr7B	551539582	551540483	901	False	676.000000	676	80.4160	1539	2442	1	chr7B.!!$F1	903
6	TraesCS1D01G027200	chr7A	593014586	593015991	1405	True	863.000000	863	78.1250	1028	2445	1	chr7A.!!$R1	1417
7	TraesCS1D01G027200	chr7A	593376913	593377803	890	False	688.000000	688	80.7350	1552	2442	1	chr7A.!!$F1	890
8	TraesCS1D01G027200	chr7D	518573774	518575157	1383	False	848.000000	848	78.1600	1042	2442	1	chr7D.!!$F1	1400
9	TraesCS1D01G027200	chr7D	518089656	518090549	893	True	688.000000	688	80.6880	1552	2445	1	chr7D.!!$R1	893
10	TraesCS1D01G027200	chr3A	742577330	742578030	700	True	643.000000	643	83.4730	4	707	1	chr3A.!!$R1	703
11	TraesCS1D01G027200	chrUn	27691978	27692587	609	False	320.000000	510	89.3445	1	708	2	chrUn.!!$F1	707

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
753	920	0.472044	TGCAAGGACACCAGCTACAA	59.528	50.0	0.0	0.0	0.0	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2518	2737	3.773418	TTATGGAACGGAGGAAACACA	57.227	42.857	0.0	0.0	0.0	3.72	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
63	65	6.151144	CCAACTAAATAAGTAGCTGGCAACTT	59.849	38.462	8.05	8.05	37.50	2.66
85	87	5.878406	TTGTATGTTGTTCCCAAACCATT	57.122	34.783	0.00	0.00	34.28	3.16
112	114	0.946221	CCTCGGATATTGTGCCTCGC	60.946	60.000	0.00	0.00	0.00	5.03
122	124	2.281484	TGCCTCGCCCAACAAGAC	60.281	61.111	0.00	0.00	0.00	3.01
128	130	1.302033	CGCCCAACAAGACTGCTCT	60.302	57.895	0.00	0.00	0.00	4.09
163	165	4.803426	GGCAGACGCGGGAGACAG	62.803	72.222	12.47	0.00	39.92	3.51
185	187	2.299297	CGAAGAGGAAACTGTGGGTACT	59.701	50.000	0.00	0.00	44.43	2.73
212	214	1.276844	GCGAGCTGTGTTGTGTGTC	59.723	57.895	0.00	0.00	0.00	3.67
241	243	8.428536	GTTTGCGATCTATAGTTGTATGTGATC	58.571	37.037	0.00	0.00	32.40	2.92
361	366	4.820775	TGAGCAGTTCCTCCCTATTCTAT	58.179	43.478	0.00	0.00	0.00	1.98
533	542	9.683069	GAATGTTCCATTATTTTGGTATGCTAG	57.317	33.333	0.00	0.00	38.01	3.42
602	611	1.302832	CACAGTCTTGCTCACCCCC	60.303	63.158	0.00	0.00	0.00	5.40
676	686	7.009174	CGTGCTCAACAAAAGACTACAAATTTT	59.991	33.333	0.00	0.00	0.00	1.82
677	687	8.655970	GTGCTCAACAAAAGACTACAAATTTTT	58.344	29.630	0.00	0.00	0.00	1.94
680	690	9.586435	CTCAACAAAAGACTACAAATTTTTCCT	57.414	29.630	0.00	0.00	0.00	3.36
710	877	4.164294	GCGCGGGTATCTACTAGTTTATG	58.836	47.826	8.83	0.00	0.00	1.90
744	911	1.135972	CAAGTACGCATGCAAGGACAC	60.136	52.381	19.57	5.44	0.00	3.67
746	913	0.953471	GTACGCATGCAAGGACACCA	60.953	55.000	19.57	0.00	0.00	4.17
752	919	0.692476	ATGCAAGGACACCAGCTACA	59.308	50.000	0.00	0.00	0.00	2.74
753	920	0.472044	TGCAAGGACACCAGCTACAA	59.528	50.000	0.00	0.00	0.00	2.41
757	924	3.313526	GCAAGGACACCAGCTACAATATG	59.686	47.826	0.00	0.00	0.00	1.78
787	954	6.075415	CGCTTTGTTTTGTGTTGTATTGAGAG	60.075	38.462	0.00	0.00	0.00	3.20
794	961	8.583765	GTTTTGTGTTGTATTGAGAGTTTTCAC	58.416	33.333	0.00	0.00	0.00	3.18
1472	1647	1.278127	TGTTCAGGTACCAAGCTAGCC	59.722	52.381	15.94	0.00	0.00	3.93
1476	1651	3.380393	TCAGGTACCAAGCTAGCCAATA	58.620	45.455	15.94	0.00	0.00	1.90
1479	1654	3.716872	AGGTACCAAGCTAGCCAATACAT	59.283	43.478	15.94	4.32	0.00	2.29
1480	1655	3.815401	GGTACCAAGCTAGCCAATACATG	59.185	47.826	12.13	0.00	0.00	3.21
1482	1657	3.968265	ACCAAGCTAGCCAATACATGTT	58.032	40.909	12.13	0.00	0.00	2.71
1492	1667	1.917955	CAATACATGTTCGTCGCGTCT	59.082	47.619	2.30	0.00	0.00	4.18
1500	1675	0.596600	TTCGTCGCGTCTGAAGCTTT	60.597	50.000	13.43	0.00	0.00	3.51
1501	1676	0.596600	TCGTCGCGTCTGAAGCTTTT	60.597	50.000	13.43	0.00	0.00	2.27
1502	1677	1.057636	CGTCGCGTCTGAAGCTTTTA	58.942	50.000	13.43	0.00	0.00	1.52
1503	1678	1.654105	CGTCGCGTCTGAAGCTTTTAT	59.346	47.619	13.43	0.00	0.00	1.40
2255	2442	1.675310	CATGCCGGGTTCAAGAGCA	60.675	57.895	2.18	0.00	37.94	4.26
2518	2737	6.433093	TGATGCTATGTATACGTCACCTACAT	59.567	38.462	0.00	13.85	39.00	2.29
2556	2775	6.991938	TCCATAATTCTTCTGGTGGTTTTTG	58.008	36.000	0.00	0.00	0.00	2.44
2724	2990	4.018870	TCACAACAGGGCTGTAATTATGGA	60.019	41.667	0.00	0.00	44.13	3.41
2863	3203	0.842635	ATGGGAGAGATGTCTTGCCC	59.157	55.000	9.20	9.20	38.99	5.36
2931	3730	4.511826	CGGCAAGAATTTATGGAGTACCTC	59.488	45.833	0.00	0.00	37.04	3.85
3288	4391	9.391006	AGCATTCAAATTGAAGCATTTATTGAT	57.609	25.926	22.33	8.88	40.05	2.57
3289	4392	9.997482	GCATTCAAATTGAAGCATTTATTGATT	57.003	25.926	14.10	0.00	40.05	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
85	87	3.466836	CACAATATCCGAGGCTTTGCTA	58.533	45.455	0.00	0.00	0.00	3.49
112	114	2.224523	TGGTTAGAGCAGTCTTGTTGGG	60.225	50.000	0.00	0.00	33.84	4.12
122	124	6.705381	CCTCTTCATATTTCTGGTTAGAGCAG	59.295	42.308	0.90	0.90	44.57	4.24
128	130	6.349300	GTCTGCCTCTTCATATTTCTGGTTA	58.651	40.000	0.00	0.00	0.00	2.85
163	165	0.250338	ACCCACAGTTTCCTCTTCGC	60.250	55.000	0.00	0.00	0.00	4.70
169	171	3.551846	CAAACAGTACCCACAGTTTCCT	58.448	45.455	0.00	0.00	41.01	3.36
212	214	8.906693	CACATACAACTATAGATCGCAAACTAG	58.093	37.037	6.78	0.00	0.00	2.57
533	542	3.758425	TCTAACAAAGCTGTAAACCCCC	58.242	45.455	0.00	0.00	33.45	5.40
585	594	1.062488	AAGGGGGTGAGCAAGACTGT	61.062	55.000	0.00	0.00	0.00	3.55
592	601	1.352622	AAGTGTCAAGGGGGTGAGCA	61.353	55.000	0.00	0.00	0.00	4.26
602	611	3.679389	ACTGGCTATTGGAAGTGTCAAG	58.321	45.455	0.00	0.00	0.00	3.02
650	659	4.530094	TTGTAGTCTTTTGTTGAGCACG	57.470	40.909	0.00	0.00	0.00	5.34
680	690	4.444838	ATACCCGCGCGTTGCTGA	62.445	61.111	29.95	7.80	43.27	4.26
710	877	4.211794	TGCGTACTTGTGTTAGCCTTTAAC	59.788	41.667	0.00	0.00	0.00	2.01
720	887	1.266718	CCTTGCATGCGTACTTGTGTT	59.733	47.619	14.09	0.00	0.00	3.32
727	894	0.953471	TGGTGTCCTTGCATGCGTAC	60.953	55.000	14.09	8.74	0.00	3.67
744	911	3.722147	AGCGAGAACATATTGTAGCTGG	58.278	45.455	0.00	0.00	30.25	4.85
746	913	5.178797	ACAAAGCGAGAACATATTGTAGCT	58.821	37.500	0.00	0.00	31.77	3.32
752	919	6.503524	ACACAAAACAAAGCGAGAACATATT	58.496	32.000	0.00	0.00	0.00	1.28
753	920	6.072112	ACACAAAACAAAGCGAGAACATAT	57.928	33.333	0.00	0.00	0.00	1.78
757	924	3.917985	ACAACACAAAACAAAGCGAGAAC	59.082	39.130	0.00	0.00	0.00	3.01
960	1134	1.903183	AGGTGGGCTGTAGAGAACTTC	59.097	52.381	0.00	0.00	0.00	3.01
1251	1425	3.984186	CTTCCTCCCGGCCTCCTCA	62.984	68.421	0.00	0.00	0.00	3.86
1472	1647	1.917955	AGACGCGACGAACATGTATTG	59.082	47.619	15.93	0.00	0.00	1.90
1476	1651	0.318360	TTCAGACGCGACGAACATGT	60.318	50.000	15.93	0.00	0.00	3.21
1479	1654	2.014554	GCTTCAGACGCGACGAACA	61.015	57.895	15.93	0.00	0.00	3.18
1480	1655	1.276145	AAGCTTCAGACGCGACGAAC	61.276	55.000	15.93	9.61	0.00	3.95
1482	1657	0.596600	AAAAGCTTCAGACGCGACGA	60.597	50.000	15.93	6.03	0.00	4.20
1492	1667	6.206634	CACTTGGTACCTGAATAAAAGCTTCA	59.793	38.462	14.36	0.00	0.00	3.02
1500	1675	4.359434	TGTGCACTTGGTACCTGAATAA	57.641	40.909	19.41	0.00	0.00	1.40
1501	1676	4.260985	CATGTGCACTTGGTACCTGAATA	58.739	43.478	21.78	0.00	31.19	1.75
1502	1677	2.949177	TGTGCACTTGGTACCTGAAT	57.051	45.000	19.41	0.00	0.00	2.57
1503	1678	2.158682	ACATGTGCACTTGGTACCTGAA	60.159	45.455	29.70	0.00	33.27	3.02
2518	2737	3.773418	TTATGGAACGGAGGAAACACA	57.227	42.857	0.00	0.00	0.00	3.72
2841	3181	3.073650	GGGCAAGACATCTCTCCCATTAT	59.926	47.826	11.54	0.00	37.37	1.28
2842	3182	2.439507	GGGCAAGACATCTCTCCCATTA	59.560	50.000	11.54	0.00	37.37	1.90
2845	3185	1.617018	CGGGCAAGACATCTCTCCCA	61.617	60.000	14.99	0.00	37.31	4.37
2863	3203	9.277565	CAATAAAAGAGAATATGTTGGTTCACG	57.722	33.333	0.00	0.00	0.00	4.35
2931	3730	4.744137	GTCTCGAGAATCATGAGTGGAATG	59.256	45.833	18.55	0.00	33.17	2.67
3033	4135	0.240145	ATCGAACTTGCGACGTCTCA	59.760	50.000	14.70	9.42	43.79	3.27

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.