AutoCloner

Multiple sequence alignment - TraesCS1B01G356400

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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	TraesCS1B01G356400	chr1B	100.000	2549	0	0	1	2549	585422615	585425163	0.000000e+00	4708
1	TraesCS1B01G356400	chr1B	95.777	1989	77	7	567	2549	581717563	581715576	0.000000e+00	3201
2	TraesCS1B01G356400	chr1B	95.514	1984	81	7	569	2549	520844119	520842141	0.000000e+00	3164
3	TraesCS1B01G356400	chr1B	95.386	1994	80	9	562	2549	561526121	561528108	0.000000e+00	3162
4	TraesCS1B01G356400	chr4A	95.567	1985	80	7	569	2549	705529252	705527272	0.000000e+00	3171
5	TraesCS1B01G356400	chr3B	95.523	1988	82	6	567	2549	108092314	108090329	0.000000e+00	3171
6	TraesCS1B01G356400	chr3B	95.375	1989	83	6	568	2549	19701236	19703222	0.000000e+00	3155
7	TraesCS1B01G356400	chr3B	95.043	1997	88	8	558	2549	474243184	474241194	0.000000e+00	3129
8	TraesCS1B01G356400	chr7B	95.416	1985	84	6	568	2549	12494680	12492700	0.000000e+00	3155
9	TraesCS1B01G356400	chr7B	91.419	571	33	2	1	568	440674983	440674426	0.000000e+00	769
10	TraesCS1B01G356400	chr2B	95.178	1991	87	7	563	2549	692955892	692957877	0.000000e+00	3136
11	TraesCS1B01G356400	chr2B	89.394	528	35	6	1	522	112586546	112586034	0.000000e+00	645
12	TraesCS1B01G356400	chr2B	88.760	516	46	8	9	522	306083377	306082872	2.790000e-174	621
13	TraesCS1B01G356400	chr3D	93.217	575	32	2	1	568	486815967	486816541	0.000000e+00	839
14	TraesCS1B01G356400	chr3D	90.767	574	44	4	1	568	494748967	494748397	0.000000e+00	758
15	TraesCS1B01G356400	chr5B	91.769	571	37	3	1	569	585195561	585196123	0.000000e+00	785
16	TraesCS1B01G356400	chr5B	90.570	509	45	3	1	509	645302673	645302168	0.000000e+00	671
17	TraesCS1B01G356400	chr7A	89.455	569	42	9	1	568	274028095	274027544	0.000000e+00	702
18	TraesCS1B01G356400	chr2A	89.676	494	29	2	1	472	141629332	141629825	6.030000e-171	610
19	TraesCS1B01G356400	chr2A	86.125	591	36	7	1	568	463551557	463550990	1.690000e-166	595
20	TraesCS1B01G356400	chr2A	88.739	444	46	3	76	519	290101323	290100884	8.020000e-150	540
21	TraesCS1B01G356400	chr2A	91.594	345	28	1	1	344	157234017	157233673	2.290000e-130	475
22	TraesCS1B01G356400	chr2A	94.656	131	5	2	342	472	497204287	497204415	4.300000e-48	202
23	TraesCS1B01G356400	chr2A	94.958	119	6	0	1	119	359736671	359736789	1.200000e-43	187
24	TraesCS1B01G356400	chr2A	92.784	97	6	1	472	568	578420629	578420534	3.420000e-29	139

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	TraesCS1B01G356400	chr1B	585422615	585425163	2548	False	4708	4708	100.000	1	2549	1	chr1B.!!$F2	2548
1	TraesCS1B01G356400	chr1B	581715576	581717563	1987	True	3201	3201	95.777	567	2549	1	chr1B.!!$R2	1982
2	TraesCS1B01G356400	chr1B	520842141	520844119	1978	True	3164	3164	95.514	569	2549	1	chr1B.!!$R1	1980
3	TraesCS1B01G356400	chr1B	561526121	561528108	1987	False	3162	3162	95.386	562	2549	1	chr1B.!!$F1	1987
4	TraesCS1B01G356400	chr4A	705527272	705529252	1980	True	3171	3171	95.567	569	2549	1	chr4A.!!$R1	1980
5	TraesCS1B01G356400	chr3B	108090329	108092314	1985	True	3171	3171	95.523	567	2549	1	chr3B.!!$R1	1982
6	TraesCS1B01G356400	chr3B	19701236	19703222	1986	False	3155	3155	95.375	568	2549	1	chr3B.!!$F1	1981
7	TraesCS1B01G356400	chr3B	474241194	474243184	1990	True	3129	3129	95.043	558	2549	1	chr3B.!!$R2	1991
8	TraesCS1B01G356400	chr7B	12492700	12494680	1980	True	3155	3155	95.416	568	2549	1	chr7B.!!$R1	1981
9	TraesCS1B01G356400	chr7B	440674426	440674983	557	True	769	769	91.419	1	568	1	chr7B.!!$R2	567
10	TraesCS1B01G356400	chr2B	692955892	692957877	1985	False	3136	3136	95.178	563	2549	1	chr2B.!!$F1	1986
11	TraesCS1B01G356400	chr2B	112586034	112586546	512	True	645	645	89.394	1	522	1	chr2B.!!$R1	521
12	TraesCS1B01G356400	chr2B	306082872	306083377	505	True	621	621	88.760	9	522	1	chr2B.!!$R2	513
13	TraesCS1B01G356400	chr3D	486815967	486816541	574	False	839	839	93.217	1	568	1	chr3D.!!$F1	567
14	TraesCS1B01G356400	chr3D	494748397	494748967	570	True	758	758	90.767	1	568	1	chr3D.!!$R1	567
15	TraesCS1B01G356400	chr5B	585195561	585196123	562	False	785	785	91.769	1	569	1	chr5B.!!$F1	568
16	TraesCS1B01G356400	chr5B	645302168	645302673	505	True	671	671	90.570	1	509	1	chr5B.!!$R1	508
17	TraesCS1B01G356400	chr7A	274027544	274028095	551	True	702	702	89.455	1	568	1	chr7A.!!$R1	567
18	TraesCS1B01G356400	chr2A	463550990	463551557	567	True	595	595	86.125	1	568	1	chr2A.!!$R3	567

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
194	195	0.266152	TTCCATCCTCTCCCTCTCCC	59.734	60.0	0.0	0.0	0.0	4.30	F
1013	1056	0.254178	AGCTCCATGTCTTCCGCAAT	59.746	50.0	0.0	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1048	1095	2.106338	TGAAGACAGGCATCTCCAAACA	59.894	45.455	0.0	0.0	37.29	2.83	R
2520	2586	3.117322	TGGTTGTCATTCAAAAGAGGGGA	60.117	43.478	0.0	0.0	37.81	4.81	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
19	20	4.459089	GAGAGCGGTGGTGGGAGC	62.459	72.222	0.00	0.00	0.00	4.70
176	177	4.065281	CCCGACGACGCTTCCCTT	62.065	66.667	0.64	0.00	38.29	3.95
194	195	0.266152	TTCCATCCTCTCCCTCTCCC	59.734	60.000	0.00	0.00	0.00	4.30
225	226	4.586235	ACAGGGCGGCTGTTTGCT	62.586	61.111	9.56	0.00	42.39	3.91
238	239	3.084039	CTGTTTGCTGCCAAGGAATAGA	58.916	45.455	0.00	0.00	33.29	1.98
247	248	2.158740	GCCAAGGAATAGAAGGGGACTC	60.159	54.545	0.00	0.00	42.68	3.36
267	273	2.070039	CCCCCAGCCCAATAGTCGA	61.070	63.158	0.00	0.00	0.00	4.20
274	280	0.811616	GCCCAATAGTCGAGCAGGTG	60.812	60.000	0.00	0.00	0.00	4.00
374	415	8.909671	GTCTTTTGAATTTCAGATTTGCAGTAG	58.090	33.333	0.00	0.00	0.00	2.57
388	429	4.743057	TGCAGTAGTGAGCATATGAAGT	57.257	40.909	6.97	0.00	35.51	3.01
461	502	7.418337	TCATAGGAGTATAAAAGTGCAGACA	57.582	36.000	0.00	0.00	0.00	3.41
462	503	7.847096	TCATAGGAGTATAAAAGTGCAGACAA	58.153	34.615	0.00	0.00	0.00	3.18
463	504	8.486210	TCATAGGAGTATAAAAGTGCAGACAAT	58.514	33.333	0.00	0.00	0.00	2.71
464	505	6.992063	AGGAGTATAAAAGTGCAGACAATG	57.008	37.500	0.00	0.00	0.00	2.82
465	506	6.476378	AGGAGTATAAAAGTGCAGACAATGT	58.524	36.000	0.00	0.00	0.00	2.71
466	507	6.372659	AGGAGTATAAAAGTGCAGACAATGTG	59.627	38.462	0.00	0.00	0.00	3.21
467	508	6.371548	GGAGTATAAAAGTGCAGACAATGTGA	59.628	38.462	0.00	0.00	0.00	3.58
468	509	7.066284	GGAGTATAAAAGTGCAGACAATGTGAT	59.934	37.037	0.00	0.00	0.00	3.06
469	510	8.340618	AGTATAAAAGTGCAGACAATGTGATT	57.659	30.769	0.00	0.00	0.00	2.57
470	511	8.454106	AGTATAAAAGTGCAGACAATGTGATTC	58.546	33.333	0.00	0.00	0.00	2.52
471	512	5.779529	AAAAGTGCAGACAATGTGATTCT	57.220	34.783	0.00	0.00	0.00	2.40
472	513	5.368256	AAAGTGCAGACAATGTGATTCTC	57.632	39.130	0.00	0.00	0.00	2.87
473	514	4.011966	AGTGCAGACAATGTGATTCTCA	57.988	40.909	0.00	0.00	0.00	3.27
552	593	2.620585	AGAAACTGCAACTTTCAGAGGC	59.379	45.455	15.50	0.00	35.61	4.70
553	594	2.057137	AACTGCAACTTTCAGAGGCA	57.943	45.000	0.00	0.00	35.61	4.75
554	595	1.312815	ACTGCAACTTTCAGAGGCAC	58.687	50.000	0.00	0.00	35.61	5.01
555	596	1.311859	CTGCAACTTTCAGAGGCACA	58.688	50.000	0.00	0.00	33.54	4.57
556	597	1.884579	CTGCAACTTTCAGAGGCACAT	59.115	47.619	0.00	0.00	33.54	3.21
560	601	3.057033	GCAACTTTCAGAGGCACATCATT	60.057	43.478	0.00	0.00	0.00	2.57
565	606	8.627403	CAACTTTCAGAGGCACATCATTTATAT	58.373	33.333	0.00	0.00	0.00	0.86
573	614	7.667219	AGAGGCACATCATTTATATTAGGGTTG	59.333	37.037	0.00	0.00	0.00	3.77
618	659	1.202915	TCCATCTGCTCAGTTTTGCCA	60.203	47.619	0.00	0.00	0.00	4.92
662	703	3.849951	CCCCTAGTCCGTGCGCAT	61.850	66.667	15.91	0.00	0.00	4.73
692	733	0.468226	TGTGAACTTTGGCGTCTCCT	59.532	50.000	0.00	0.00	35.26	3.69
754	795	1.803289	GGCAGAGGCGGTCAATTTC	59.197	57.895	0.00	0.00	42.47	2.17
790	831	4.966787	GTGGCTTGCGGGACCCAA	62.967	66.667	12.15	0.00	0.00	4.12
870	913	1.604693	GGTGACCACGACGACAAAGAT	60.605	52.381	0.00	0.00	0.00	2.40
896	939	1.429148	GCTGACCACGGCGATTAAGG	61.429	60.000	16.62	9.67	38.67	2.69
906	949	0.876342	GCGATTAAGGGAGAGCACGG	60.876	60.000	0.00	0.00	0.00	4.94
924	967	3.771160	CGGCGGTGGGAAGCTAGT	61.771	66.667	0.00	0.00	0.00	2.57
1013	1056	0.254178	AGCTCCATGTCTTCCGCAAT	59.746	50.000	0.00	0.00	0.00	3.56
1051	1098	4.349503	TGCAGAGCCGGGCATGTT	62.350	61.111	23.09	0.00	34.58	2.71
1175	1222	1.772453	GAATGGGGTAAGAATCGGGGA	59.228	52.381	0.00	0.00	0.00	4.81
1860	1914	3.433343	TGTCATGGAAAATGTGCCTCAT	58.567	40.909	0.00	0.00	38.57	2.90
1881	1935	5.615925	ATCTCTGGTAGATGTTTACACCC	57.384	43.478	0.00	0.00	43.62	4.61
2019	2078	4.622456	CGCGTGGGTTTGTGGTGC	62.622	66.667	0.00	0.00	0.00	5.01
2214	2277	2.668212	GCTGCACTGGTAACCGCA	60.668	61.111	0.00	0.00	34.55	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
175	176	0.266152	GGGAGAGGGAGAGGATGGAA	59.734	60.000	0.00	0.00	0.00	3.53
176	177	0.631998	AGGGAGAGGGAGAGGATGGA	60.632	60.000	0.00	0.00	0.00	3.41
194	195	2.001812	CCCTGTGAGACGATGTGAAG	57.998	55.000	0.00	0.00	0.00	3.02
225	226	1.564348	GTCCCCTTCTATTCCTTGGCA	59.436	52.381	0.00	0.00	0.00	4.92
267	273	1.546323	CCTGACAATTCACCACCTGCT	60.546	52.381	0.00	0.00	0.00	4.24
274	280	1.280421	AGCTCCTCCTGACAATTCACC	59.720	52.381	0.00	0.00	0.00	4.02
461	502	6.149142	GCAGTTTCTTCTCTGAGAATCACATT	59.851	38.462	19.61	3.23	42.56	2.71
462	503	5.642919	GCAGTTTCTTCTCTGAGAATCACAT	59.357	40.000	19.61	4.94	42.56	3.21
463	504	4.993584	GCAGTTTCTTCTCTGAGAATCACA	59.006	41.667	19.61	3.12	42.56	3.58
464	505	4.993584	TGCAGTTTCTTCTCTGAGAATCAC	59.006	41.667	19.61	15.39	42.56	3.06
465	506	8.118720	AACTTGCAGTTTCTTCTCTGAGAATCA	61.119	37.037	19.61	7.69	37.86	2.57
466	507	5.700373	ACTTGCAGTTTCTTCTCTGAGAATC	59.300	40.000	19.61	10.93	35.70	2.52
467	508	5.619220	ACTTGCAGTTTCTTCTCTGAGAAT	58.381	37.500	19.61	2.74	35.70	2.40
468	509	5.028549	ACTTGCAGTTTCTTCTCTGAGAA	57.971	39.130	18.40	18.40	34.00	2.87
469	510	4.679373	ACTTGCAGTTTCTTCTCTGAGA	57.321	40.909	2.58	2.58	34.02	3.27
470	511	5.747951	AAACTTGCAGTTTCTTCTCTGAG	57.252	39.130	0.00	0.00	44.47	3.35
471	512	6.823689	ACTAAAACTTGCAGTTTCTTCTCTGA	59.176	34.615	12.60	0.00	46.78	3.27
472	513	7.020914	ACTAAAACTTGCAGTTTCTTCTCTG	57.979	36.000	12.60	0.00	46.78	3.35
473	514	7.631717	AACTAAAACTTGCAGTTTCTTCTCT	57.368	32.000	12.60	2.39	46.78	3.10
510	551	7.566760	TTCTTATCTGAAACTGAACTTGCAA	57.433	32.000	0.00	0.00	0.00	4.08
565	606	4.959839	GGGCAAAAGGATAATCAACCCTAA	59.040	41.667	0.00	0.00	31.84	2.69
573	614	5.067805	CACCACTAAGGGCAAAAGGATAATC	59.932	44.000	0.00	0.00	43.89	1.75
662	703	3.113322	CAAAGTTCACAGAACGAGTCGA	58.887	45.455	21.50	0.00	0.00	4.20
747	788	3.567585	TGCAACGGTCTGAATGAAATTGA	59.432	39.130	0.00	0.00	36.07	2.57
790	831	1.135915	CTATGCTCAACGGCTCTCTGT	59.864	52.381	0.00	0.00	0.00	3.41
860	903	0.039437	AGCGTCGTGATCTTTGTCGT	60.039	50.000	0.00	0.00	0.00	4.34
870	913	4.337060	CCGTGGTCAGCGTCGTGA	62.337	66.667	0.00	0.00	0.00	4.35
891	934	2.577059	CGCCGTGCTCTCCCTTAA	59.423	61.111	0.00	0.00	0.00	1.85
892	935	3.458163	CCGCCGTGCTCTCCCTTA	61.458	66.667	0.00	0.00	0.00	2.69
943	986	0.980231	CCCTCCACAGCTAGCTTCCT	60.980	60.000	16.46	0.00	0.00	3.36
1013	1056	3.311110	GTGAGGTGGCGTGGGAGA	61.311	66.667	0.00	0.00	0.00	3.71
1048	1095	2.106338	TGAAGACAGGCATCTCCAAACA	59.894	45.455	0.00	0.00	37.29	2.83
1051	1098	2.842496	AGATGAAGACAGGCATCTCCAA	59.158	45.455	0.00	0.00	45.99	3.53
1693	1745	8.301730	TGCATTTCATTGATCAAAAGTTTCTC	57.698	30.769	13.09	0.00	0.00	2.87
1860	1914	4.422057	TGGGTGTAAACATCTACCAGAGA	58.578	43.478	0.00	0.00	39.01	3.10
2214	2277	3.152341	CAAACTCTTGCCATCTGTCCTT	58.848	45.455	0.00	0.00	0.00	3.36
2513	2579	5.711976	GTCATTCAAAAGAGGGGATGAGAAA	59.288	40.000	0.00	0.00	0.00	2.52
2520	2586	3.117322	TGGTTGTCATTCAAAAGAGGGGA	60.117	43.478	0.00	0.00	37.81	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.