AutoCloner

Multiple sequence alignment - TraesCS3D01G183000

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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	TraesCS3D01G183000	chr3D	100.000	3497	0	0	1	3497	167762596	167766092	0.000000e+00	6458.0
1	TraesCS3D01G183000	chr3D	78.750	480	78	19	317	778	2630856	2630383	2.040000e-77	300.0
2	TraesCS3D01G183000	chr3D	80.339	295	50	7	487	778	102650286	102650575	2.110000e-52	217.0
3	TraesCS3D01G183000	chr3B	94.068	3523	137	27	1	3497	242867093	242870569	0.000000e+00	5282.0
4	TraesCS3D01G183000	chr3B	79.673	428	64	17	332	753	641707922	641708332	1.590000e-73	287.0
5	TraesCS3D01G183000	chr3B	81.673	251	34	9	281	526	342492635	342492878	7.660000e-47	198.0
6	TraesCS3D01G183000	chr3B	81.119	143	15	9	41	182	130251537	130251406	1.720000e-18	104.0
7	TraesCS3D01G183000	chr3A	95.492	2684	68	22	849	3497	201508113	201505448	0.000000e+00	4237.0
8	TraesCS3D01G183000	chr2D	80.742	431	67	15	369	791	140988730	140989152	4.350000e-84	322.0
9	TraesCS3D01G183000	chr2D	79.535	430	63	18	360	779	476278945	476279359	2.050000e-72	283.0
10	TraesCS3D01G183000	chr7D	79.691	453	77	14	332	777	570832405	570832849	2.620000e-81	313.0
11	TraesCS3D01G183000	chr1D	78.074	488	80	19	271	743	483476823	483477298	2.050000e-72	283.0
12	TraesCS3D01G183000	chr1D	76.699	309	52	12	232	526	473782361	473782663	1.680000e-33	154.0
13	TraesCS3D01G183000	chr7B	79.439	428	65	16	359	777	366825288	366825701	7.390000e-72	281.0
14	TraesCS3D01G183000	chr7B	77.017	409	74	17	332	735	131481561	131481168	2.110000e-52	217.0
15	TraesCS3D01G183000	chr2A	80.186	323	48	13	463	779	82135170	82135482	9.760000e-56	228.0
16	TraesCS3D01G183000	chr2A	75.150	334	55	20	73	399	175466369	175466681	7.880000e-27	132.0
17	TraesCS3D01G183000	chr2A	83.740	123	12	8	63	182	749864430	749864313	3.690000e-20	110.0
18	TraesCS3D01G183000	chr2A	81.081	111	14	5	73	182	13091005	13090901	8.050000e-12	82.4
19	TraesCS3D01G183000	chr2B	81.749	263	40	8	526	782	43164167	43163907	2.730000e-51	213.0
20	TraesCS3D01G183000	chr2B	86.486	111	12	3	73	182	778010612	778010720	6.130000e-23	119.0
21	TraesCS3D01G183000	chr2B	86.364	110	10	5	76	182	205480903	205481010	7.930000e-22	115.0
22	TraesCS3D01G183000	chr2B	85.714	112	11	5	73	182	205532075	205532183	2.850000e-21	113.0
23	TraesCS3D01G183000	chr5D	74.769	432	77	22	112	526	202848181	202847765	7.770000e-37	165.0
24	TraesCS3D01G183000	chr6D	86.667	105	12	2	73	176	42921826	42921929	7.930000e-22	115.0
25	TraesCS3D01G183000	chr5B	76.786	224	35	10	73	291	22531728	22531939	3.690000e-20	110.0

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	TraesCS3D01G183000	chr3D	167762596	167766092	3496	False	6458	6458	100.000	1	3497	1	chr3D.!!$F2	3496
1	TraesCS3D01G183000	chr3B	242867093	242870569	3476	False	5282	5282	94.068	1	3497	1	chr3B.!!$F1	3496
2	TraesCS3D01G183000	chr3A	201505448	201508113	2665	True	4237	4237	95.492	849	3497	1	chr3A.!!$R1	2648

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
330	338	0.182775	ACGGTTGCCTCTGGAAAACT	59.817	50.0	0.0	0.0	0.00	2.66	F
1439	1472	0.249911	GTCACCATCTCGGGGTATGC	60.250	60.0	0.0	0.0	40.26	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1779	1812	1.377690	TCTGCCCCATACCCTCAAAA	58.622	50.0	0.0	0.0	0.0	2.44	R
2615	2661	1.108776	AGGCTCGGTTAGTTCGCATA	58.891	50.0	0.0	0.0	0.0	3.14	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	1.884444	GGTCGTCTTCGCCTTCTCT	59.116	57.895	0.00	0.00	36.96	3.10
21	22	0.522180	GTCGTCTTCGCCTTCTCTGA	59.478	55.000	0.00	0.00	36.96	3.27
27	28	1.270826	CTTCGCCTTCTCTGACACTGA	59.729	52.381	0.00	0.00	0.00	3.41
56	57	2.232298	GAGGTGCCTCTCGGAAGTGG	62.232	65.000	10.80	0.00	39.80	4.00
99	102	2.894387	GCGAGAGACATGGCCTGC	60.894	66.667	3.32	0.00	0.00	4.85
110	113	0.257039	ATGGCCTGCCTCTCGAAAAT	59.743	50.000	9.97	0.00	36.94	1.82
118	121	3.226777	TGCCTCTCGAAAATGGGAAAAA	58.773	40.909	0.00	0.00	0.00	1.94
176	179	1.872237	CGGTTTTGCTTCCGTGAGAGA	60.872	52.381	0.00	0.00	41.58	3.10
227	230	4.111967	AAAAACCATGCCCCTCGG	57.888	55.556	0.00	0.00	0.00	4.63
231	234	0.898326	AAACCATGCCCCTCGGAAAC	60.898	55.000	0.00	0.00	0.00	2.78
285	293	1.658994	ACGGTTTTGCTTTCGTGAGA	58.341	45.000	0.00	0.00	34.40	3.27
330	338	0.182775	ACGGTTGCCTCTGGAAAACT	59.817	50.000	0.00	0.00	0.00	2.66
381	389	3.833706	GCGAGAGGCATGTATTTGC	57.166	52.632	0.00	0.00	42.87	3.68
382	390	1.303309	GCGAGAGGCATGTATTTGCT	58.697	50.000	0.00	0.00	42.38	3.91
384	392	2.286654	GCGAGAGGCATGTATTTGCTTC	60.287	50.000	0.00	0.80	46.00	3.86
448	457	4.976731	GCGTTTCCTTTCTCTTTTCCTTTC	59.023	41.667	0.00	0.00	0.00	2.62
540	549	2.545113	GGAAACGCCTTTTGGAAAGGAC	60.545	50.000	20.57	11.86	44.07	3.85
543	552	2.104170	ACGCCTTTTGGAAAGGACAAA	58.896	42.857	20.57	0.00	44.07	2.83
564	573	4.525912	AAAATGTGCTCCCAATTCTGTC	57.474	40.909	0.00	0.00	0.00	3.51
579	588	6.818142	CCAATTCTGTCTTTTGTCCAGTTTTT	59.182	34.615	0.00	0.00	0.00	1.94
613	622	4.377839	TTTTTCGTCAAACCAATCAGCA	57.622	36.364	0.00	0.00	0.00	4.41
614	623	4.582701	TTTTCGTCAAACCAATCAGCAT	57.417	36.364	0.00	0.00	0.00	3.79
615	624	3.557577	TTCGTCAAACCAATCAGCATG	57.442	42.857	0.00	0.00	37.54	4.06
616	625	1.811965	TCGTCAAACCAATCAGCATGG	59.188	47.619	0.00	0.00	43.84	3.66
617	626	1.135315	CGTCAAACCAATCAGCATGGG	60.135	52.381	0.00	0.00	42.48	4.00
628	637	5.361857	CCAATCAGCATGGGATCTAGTTTTT	59.638	40.000	0.00	0.00	36.16	1.94
636	645	7.936301	AGCATGGGATCTAGTTTTTAAGATCTC	59.064	37.037	11.05	8.38	45.96	2.75
653	662	1.153901	TCGACGCGAGGAATCCAAC	60.154	57.895	15.93	0.00	0.00	3.77
664	673	2.884639	AGGAATCCAACGGTGAAAACAG	59.115	45.455	0.00	0.00	0.00	3.16
668	677	5.221087	GGAATCCAACGGTGAAAACAGTTTA	60.221	40.000	0.00	0.00	0.00	2.01
675	684	7.253950	CCAACGGTGAAAACAGTTTAAGATTTG	60.254	37.037	0.00	0.10	0.00	2.32
683	692	5.418310	ACAGTTTAAGATTTGGACACACG	57.582	39.130	0.00	0.00	0.00	4.49
690	699	9.620660	GTTTAAGATTTGGACACACGATTTAAT	57.379	29.630	0.00	0.00	0.00	1.40
779	789	2.945984	CAGCGTGCCATTTGTCGT	59.054	55.556	0.00	0.00	0.00	4.34
788	798	2.752354	TGCCATTTGTCGTAATTGAGGG	59.248	45.455	0.00	0.00	0.00	4.30
793	803	2.961526	TGTCGTAATTGAGGGAGAGC	57.038	50.000	0.00	0.00	0.00	4.09
795	805	0.744874	TCGTAATTGAGGGAGAGCGG	59.255	55.000	0.00	0.00	0.00	5.52
878	890	2.203567	CGGGCCCAAAGTCCCAAA	60.204	61.111	24.92	0.00	42.75	3.28
1062	1095	0.612174	TCTCCCTCCTCAACCGACTG	60.612	60.000	0.00	0.00	0.00	3.51
1361	1394	1.185618	TACTTCTCCTGTGCCTGCGT	61.186	55.000	0.00	0.00	0.00	5.24
1439	1472	0.249911	GTCACCATCTCGGGGTATGC	60.250	60.000	0.00	0.00	40.26	3.14
1779	1812	4.660938	GCCAAGGCGGTGGAGGTT	62.661	66.667	13.68	0.00	41.65	3.50
2410	2443	9.998106	ATCCTTGCTTACATAAGATACGTAAAT	57.002	29.630	0.00	0.00	35.33	1.40
2429	2462	5.818136	AAATTATTGTGTGAGATCACCGG	57.182	39.130	10.34	0.00	45.88	5.28
2551	2597	2.103432	TGTGTGTGTACGGAAGGTCAAT	59.897	45.455	0.00	0.00	0.00	2.57
2581	2627	3.878778	AGCTGATCCTTGATGGTGTAAC	58.121	45.455	0.00	0.00	37.07	2.50
2629	2675	4.565166	TGTTCTCATTATGCGAACTAACCG	59.435	41.667	22.95	0.00	41.29	4.44
2666	2712	2.169978	GCTACAGGTAAGGGTAAGGGTG	59.830	54.545	0.00	0.00	0.00	4.61
2680	2726	5.063880	GGTAAGGGTGCCATCTATTAACTG	58.936	45.833	0.00	0.00	0.00	3.16
2748	2794	8.814235	CATGGCTTTGAATTTTAGCTAAGAATG	58.186	33.333	6.24	0.00	35.30	2.67
2908	2954	7.751732	TGTTTCAGGATATGTCAAATTTCTCG	58.248	34.615	0.00	0.00	0.00	4.04
3293	3340	8.647796	TGTAGGGACTATATGTACATTGAAAGG	58.352	37.037	14.77	2.10	45.60	3.11

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.741092	GGCCTCGGTTCAGTGTCA	59.259	61.111	0.00	0.00	0.00	3.58
21	22	2.915659	TCGGCCTCGGTTCAGTGT	60.916	61.111	0.00	0.00	36.95	3.55
77	78	1.880340	GCCATGTCTCTCGCGGAAG	60.880	63.158	6.13	4.04	0.00	3.46
135	138	3.214328	GTGCCTCTCACTGAAGGAAAAA	58.786	45.455	10.01	0.00	42.38	1.94
136	139	2.806745	CGTGCCTCTCACTGAAGGAAAA	60.807	50.000	10.01	0.00	43.46	2.29
137	140	1.270305	CGTGCCTCTCACTGAAGGAAA	60.270	52.381	10.01	0.00	43.46	3.13
138	141	0.318441	CGTGCCTCTCACTGAAGGAA	59.682	55.000	10.01	0.00	43.46	3.36
139	142	1.536073	CCGTGCCTCTCACTGAAGGA	61.536	60.000	10.01	0.00	43.46	3.36
140	143	1.079543	CCGTGCCTCTCACTGAAGG	60.080	63.158	3.94	3.94	43.46	3.46
141	144	0.034059	AACCGTGCCTCTCACTGAAG	59.966	55.000	0.00	0.00	43.46	3.02
170	173	3.371063	GGACGGCCGTGTCTCTCA	61.371	66.667	39.65	0.00	38.91	3.27
217	220	0.250989	TTTTCGTTTCCGAGGGGCAT	60.251	50.000	0.00	0.00	45.24	4.40
257	261	4.610680	CGAAAGCAAAACCGTTCCTCTAAG	60.611	45.833	0.00	0.00	0.00	2.18
259	263	2.803956	CGAAAGCAAAACCGTTCCTCTA	59.196	45.455	0.00	0.00	0.00	2.43
260	264	1.602377	CGAAAGCAAAACCGTTCCTCT	59.398	47.619	0.00	0.00	0.00	3.69
262	266	1.064952	CACGAAAGCAAAACCGTTCCT	59.935	47.619	0.00	0.00	32.50	3.36
263	267	1.064357	TCACGAAAGCAAAACCGTTCC	59.936	47.619	0.00	0.00	32.50	3.62
264	268	2.031191	TCTCACGAAAGCAAAACCGTTC	59.969	45.455	0.00	0.00	32.50	3.95
265	269	2.011222	TCTCACGAAAGCAAAACCGTT	58.989	42.857	0.00	0.00	32.50	4.44
267	271	1.069906	CCTCTCACGAAAGCAAAACCG	60.070	52.381	0.00	0.00	0.00	4.44
269	273	1.333619	TGCCTCTCACGAAAGCAAAAC	59.666	47.619	0.00	0.00	0.00	2.43
270	274	1.333619	GTGCCTCTCACGAAAGCAAAA	59.666	47.619	0.00	0.00	35.76	2.44
285	293	4.464008	TCTCACAGAAGAAATTTGTGCCT	58.536	39.130	0.00	0.00	41.41	4.75
424	433	3.551846	AGGAAAAGAGAAAGGAAACGCA	58.448	40.909	0.00	0.00	0.00	5.24
425	434	4.569761	AAGGAAAAGAGAAAGGAAACGC	57.430	40.909	0.00	0.00	0.00	4.84
426	435	5.205565	CGAAAGGAAAAGAGAAAGGAAACG	58.794	41.667	0.00	0.00	0.00	3.60
427	436	5.971792	CACGAAAGGAAAAGAGAAAGGAAAC	59.028	40.000	0.00	0.00	0.00	2.78
428	437	5.883673	TCACGAAAGGAAAAGAGAAAGGAAA	59.116	36.000	0.00	0.00	0.00	3.13
431	440	5.057149	TCTCACGAAAGGAAAAGAGAAAGG	58.943	41.667	0.00	0.00	0.00	3.11
432	441	5.333721	GCTCTCACGAAAGGAAAAGAGAAAG	60.334	44.000	0.00	0.00	32.38	2.62
433	442	4.511826	GCTCTCACGAAAGGAAAAGAGAAA	59.488	41.667	0.00	0.00	32.38	2.52
436	445	2.739379	GGCTCTCACGAAAGGAAAAGAG	59.261	50.000	0.00	0.00	0.00	2.85
438	447	2.224314	GTGGCTCTCACGAAAGGAAAAG	59.776	50.000	0.00	0.00	36.56	2.27
543	552	4.154942	AGACAGAATTGGGAGCACATTTT	58.845	39.130	0.00	0.00	0.00	1.82
592	601	4.377839	TGCTGATTGGTTTGACGAAAAA	57.622	36.364	0.00	0.00	0.00	1.94
593	602	4.297510	CATGCTGATTGGTTTGACGAAAA	58.702	39.130	0.00	0.00	0.00	2.29
594	603	3.305267	CCATGCTGATTGGTTTGACGAAA	60.305	43.478	0.00	0.00	0.00	3.46
598	607	2.170166	TCCCATGCTGATTGGTTTGAC	58.830	47.619	0.00	0.00	31.99	3.18
611	620	7.095439	CGAGATCTTAAAAACTAGATCCCATGC	60.095	40.741	0.00	0.00	45.05	4.06
612	621	8.144478	TCGAGATCTTAAAAACTAGATCCCATG	58.856	37.037	0.00	0.00	45.05	3.66
613	622	8.145122	GTCGAGATCTTAAAAACTAGATCCCAT	58.855	37.037	0.00	0.00	45.05	4.00
614	623	7.490000	GTCGAGATCTTAAAAACTAGATCCCA	58.510	38.462	0.00	0.00	45.05	4.37
615	624	6.637658	CGTCGAGATCTTAAAAACTAGATCCC	59.362	42.308	0.00	0.00	45.05	3.85
616	625	6.142639	GCGTCGAGATCTTAAAAACTAGATCC	59.857	42.308	0.00	1.33	45.05	3.36
617	626	6.129665	CGCGTCGAGATCTTAAAAACTAGATC	60.130	42.308	0.00	0.00	44.54	2.75
636	645	2.505498	CGTTGGATTCCTCGCGTCG	61.505	63.158	5.77	0.00	0.00	5.12
653	662	6.416750	GTCCAAATCTTAAACTGTTTTCACCG	59.583	38.462	11.48	0.00	0.00	4.94
664	673	9.620660	ATTAAATCGTGTGTCCAAATCTTAAAC	57.379	29.630	0.00	0.00	0.00	2.01
668	677	8.786826	TCTATTAAATCGTGTGTCCAAATCTT	57.213	30.769	0.00	0.00	0.00	2.40
727	736	2.554893	TGTCATAACCGGGCAGTTTTTC	59.445	45.455	6.32	0.00	0.00	2.29
728	737	2.588620	TGTCATAACCGGGCAGTTTTT	58.411	42.857	6.32	0.00	0.00	1.94
738	748	2.741517	TGTGCATCACTTGTCATAACCG	59.258	45.455	0.00	0.00	35.11	4.44
739	749	4.665212	CATGTGCATCACTTGTCATAACC	58.335	43.478	0.00	0.00	35.64	2.85
763	773	1.448985	ATTACGACAAATGGCACGCT	58.551	45.000	0.00	0.00	0.00	5.07
779	789	4.503714	AATTTCCGCTCTCCCTCAATTA	57.496	40.909	0.00	0.00	0.00	1.40
788	798	6.422776	TCATTTTCACTAATTTCCGCTCTC	57.577	37.500	0.00	0.00	0.00	3.20
793	803	7.697691	AGCACTATCATTTTCACTAATTTCCG	58.302	34.615	0.00	0.00	0.00	4.30
795	805	9.713740	CAGAGCACTATCATTTTCACTAATTTC	57.286	33.333	0.00	0.00	0.00	2.17
1361	1394	4.435436	CACTGCGTGCGGAGGCTA	62.435	66.667	21.98	8.16	40.82	3.93
1439	1472	2.221299	TCCAGGTTCCCGGACTTGG	61.221	63.158	16.02	16.02	45.37	3.61
1779	1812	1.377690	TCTGCCCCATACCCTCAAAA	58.622	50.000	0.00	0.00	0.00	2.44
2429	2462	6.866480	ACATAACCAATGGATTTCATGTCAC	58.134	36.000	6.16	0.00	40.16	3.67
2551	2597	6.499699	ACCATCAAGGATCAGCTATCTGAATA	59.500	38.462	0.00	0.00	45.94	1.75
2581	2627	7.756395	AATCTCTCATATAACAAGCCAATGG	57.244	36.000	0.00	0.00	0.00	3.16
2583	2629	8.757982	ACAAATCTCTCATATAACAAGCCAAT	57.242	30.769	0.00	0.00	0.00	3.16
2615	2661	1.108776	AGGCTCGGTTAGTTCGCATA	58.891	50.000	0.00	0.00	0.00	3.14
2666	2712	4.061596	GCTCCTGTCAGTTAATAGATGGC	58.938	47.826	0.00	0.00	0.00	4.40
2680	2726	1.908483	CAGGTAAGGGGCTCCTGTC	59.092	63.158	5.46	1.49	44.07	3.51
2908	2954	8.311650	AGTGTATGAGTGAACAAACTATGAAC	57.688	34.615	0.00	0.00	0.00	3.18
3293	3340	4.379918	GCCTAAATTTCCACTTCTGCACTC	60.380	45.833	0.00	0.00	0.00	3.51
3461	3508	4.261801	ACTAAGGAAACAACGATGGGATG	58.738	43.478	0.00	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.