AutoCloner

Multiple sequence alignment - TraesCS3A01G110200

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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	TraesCS3A01G110200	chr3A	100.000	3035	0	0	1	3035	77477134	77474100	0.000000e+00	5605
1	TraesCS3A01G110200	chr3D	94.420	2079	81	13	819	2885	66344886	66342831	0.000000e+00	3164
2	TraesCS3A01G110200	chr3D	96.774	155	5	0	2881	3035	66342797	66342643	3.000000e-65	259
3	TraesCS3A01G110200	chr3B	92.575	2101	97	26	819	2885	109947616	109945541	0.000000e+00	2961
4	TraesCS3A01G110200	chr2B	96.636	773	26	0	1	773	766621617	766622389	0.000000e+00	1284
5	TraesCS3A01G110200	chr1A	96.489	769	26	1	1	768	50526617	50525849	0.000000e+00	1269
6	TraesCS3A01G110200	chr1A	96.354	768	25	3	1	768	523397382	523398146	0.000000e+00	1260
7	TraesCS3A01G110200	chr1A	95.635	756	32	1	12	767	583677743	583676989	0.000000e+00	1212
8	TraesCS3A01G110200	chr1A	94.868	760	34	4	9	768	569477438	569476684	0.000000e+00	1182
9	TraesCS3A01G110200	chr2A	95.926	761	29	1	9	769	39479233	39478475	0.000000e+00	1232
10	TraesCS3A01G110200	chr6A	95.151	763	35	2	9	771	140567073	140567833	0.000000e+00	1203
11	TraesCS3A01G110200	chr1B	94.730	759	38	2	9	767	92344506	92343750	0.000000e+00	1179
12	TraesCS3A01G110200	chr1B	94.730	759	39	1	9	767	300985760	300985003	0.000000e+00	1179

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	TraesCS3A01G110200	chr3A	77474100	77477134	3034	True	5605.0	5605	100.000	1	3035	1	chr3A.!!$R1	3034
1	TraesCS3A01G110200	chr3D	66342643	66344886	2243	True	1711.5	3164	95.597	819	3035	2	chr3D.!!$R1	2216
2	TraesCS3A01G110200	chr3B	109945541	109947616	2075	True	2961.0	2961	92.575	819	2885	1	chr3B.!!$R1	2066
3	TraesCS3A01G110200	chr2B	766621617	766622389	772	False	1284.0	1284	96.636	1	773	1	chr2B.!!$F1	772
4	TraesCS3A01G110200	chr1A	50525849	50526617	768	True	1269.0	1269	96.489	1	768	1	chr1A.!!$R1	767
5	TraesCS3A01G110200	chr1A	523397382	523398146	764	False	1260.0	1260	96.354	1	768	1	chr1A.!!$F1	767
6	TraesCS3A01G110200	chr1A	583676989	583677743	754	True	1212.0	1212	95.635	12	767	1	chr1A.!!$R3	755
7	TraesCS3A01G110200	chr1A	569476684	569477438	754	True	1182.0	1182	94.868	9	768	1	chr1A.!!$R2	759
8	TraesCS3A01G110200	chr2A	39478475	39479233	758	True	1232.0	1232	95.926	9	769	1	chr2A.!!$R1	760
9	TraesCS3A01G110200	chr6A	140567073	140567833	760	False	1203.0	1203	95.151	9	771	1	chr6A.!!$F1	762
10	TraesCS3A01G110200	chr1B	92343750	92344506	756	True	1179.0	1179	94.730	9	767	1	chr1B.!!$R1	758
11	TraesCS3A01G110200	chr1B	300985003	300985760	757	True	1179.0	1179	94.730	9	767	1	chr1B.!!$R2	758

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
986	993	0.102481	TCTCCATTAGCGCGAAGGTC	59.898	55.0	12.1	0.0	0.0	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2035	2042	2.035066	GCCATCTACAAATGATGTGCCC	59.965	50.0	0.0	0.0	43.77	5.36	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
97	98	0.911525	CCACCTCATCCCACCACTCT	60.912	60.000	0.00	0.00	0.00	3.24
166	168	3.437395	GCCCATTAACGTGTATGTGAACA	59.563	43.478	8.74	0.00	0.00	3.18
203	205	1.228306	CCCTCCTCGCGATAGTCCT	60.228	63.158	10.36	0.00	39.35	3.85
366	370	0.453782	GCAAACATTGTACGCGGGTC	60.454	55.000	12.47	1.56	0.00	4.46
528	533	2.485038	GCGTCATCCCGTTTTAAAGGAA	59.515	45.455	0.00	0.00	32.26	3.36
619	625	2.840753	GGGTGTGTCATGGGGTGGT	61.841	63.158	0.00	0.00	0.00	4.16
678	684	2.798847	GTCGACTTTGAGGTTGGTGTAC	59.201	50.000	8.70	0.00	0.00	2.90
691	697	5.100943	GGTTGGTGTACGAGAGAGAAATAC	58.899	45.833	0.00	0.00	0.00	1.89
773	779	6.469322	CACGGGCGTTTTACTAGTATAAAAC	58.531	40.000	18.19	18.19	45.46	2.43
774	780	6.311200	CACGGGCGTTTTACTAGTATAAAACT	59.689	38.462	22.53	8.64	46.18	2.66
775	781	7.487829	CACGGGCGTTTTACTAGTATAAAACTA	59.512	37.037	22.53	0.00	46.18	2.24
776	782	8.032451	ACGGGCGTTTTACTAGTATAAAACTAA	58.968	33.333	22.53	5.08	46.18	2.24
777	783	8.534778	CGGGCGTTTTACTAGTATAAAACTAAG	58.465	37.037	22.53	13.50	46.18	2.18
778	784	9.586435	GGGCGTTTTACTAGTATAAAACTAAGA	57.414	33.333	22.53	0.00	46.18	2.10
792	798	6.642683	AAAACTAAGATACGTCATTGGTCG	57.357	37.500	0.00	1.88	0.00	4.79
793	799	4.978083	ACTAAGATACGTCATTGGTCGT	57.022	40.909	0.00	11.12	41.47	4.34
794	800	6.441093	AACTAAGATACGTCATTGGTCGTA	57.559	37.500	13.82	13.82	43.18	3.43
795	801	5.814783	ACTAAGATACGTCATTGGTCGTAC	58.185	41.667	13.76	9.80	42.17	3.67
796	802	4.978083	AAGATACGTCATTGGTCGTACT	57.022	40.909	13.76	11.17	42.17	2.73
797	803	4.548991	AGATACGTCATTGGTCGTACTC	57.451	45.455	13.76	12.42	42.17	2.59
798	804	4.197750	AGATACGTCATTGGTCGTACTCT	58.802	43.478	13.76	13.69	42.17	3.24
799	805	4.639310	AGATACGTCATTGGTCGTACTCTT	59.361	41.667	13.76	3.11	42.17	2.85
800	806	5.819379	AGATACGTCATTGGTCGTACTCTTA	59.181	40.000	13.76	0.00	42.17	2.10
801	807	4.771590	ACGTCATTGGTCGTACTCTTAA	57.228	40.909	6.15	0.00	37.03	1.85
802	808	5.125100	ACGTCATTGGTCGTACTCTTAAA	57.875	39.130	6.15	0.00	37.03	1.52
803	809	5.531634	ACGTCATTGGTCGTACTCTTAAAA	58.468	37.500	6.15	0.00	37.03	1.52
804	810	5.984926	ACGTCATTGGTCGTACTCTTAAAAA	59.015	36.000	6.15	0.00	37.03	1.94
822	828	2.608640	AAAAACTCGTCGTTCCGGG	58.391	52.632	0.00	0.00	33.90	5.73
833	839	1.448922	CGTTCCGGGCAACTTTCCAA	61.449	55.000	0.00	0.00	0.00	3.53
854	860	1.615424	GGGCCTCCTCTACACCCAA	60.615	63.158	0.84	0.00	40.52	4.12
861	867	0.768622	CCTCTACACCCAACCCAACA	59.231	55.000	0.00	0.00	0.00	3.33
906	913	3.570912	TCAGAGTTTCGTTCCCCTTTT	57.429	42.857	0.00	0.00	0.00	2.27
909	916	2.876550	AGAGTTTCGTTCCCCTTTTTCG	59.123	45.455	0.00	0.00	0.00	3.46
939	946	3.804873	GTCAACTCAGTCACTTTCTCCAC	59.195	47.826	0.00	0.00	0.00	4.02
976	983	5.065218	CCAAACCGTCTCAAATCTCCATTAG	59.935	44.000	0.00	0.00	0.00	1.73
981	988	2.100749	TCTCAAATCTCCATTAGCGCGA	59.899	45.455	12.10	0.00	0.00	5.87
986	993	0.102481	TCTCCATTAGCGCGAAGGTC	59.898	55.000	12.10	0.00	0.00	3.85
1554	1561	2.029844	GGTCAGGTTCAGCAGCGTC	61.030	63.158	0.00	0.00	0.00	5.19
1644	1651	2.043652	GTGCACATGCCCAGGGAT	60.044	61.111	10.89	0.00	41.18	3.85
1648	1655	4.511246	ACATGCCCAGGGATGCCG	62.511	66.667	17.19	0.00	45.87	5.69
1650	1657	4.195334	ATGCCCAGGGATGCCGAC	62.195	66.667	10.89	0.00	0.00	4.79
1725	1732	2.105128	CGGGAGATCCAGTGCGAC	59.895	66.667	0.47	0.00	37.91	5.19
1746	1753	2.664851	TTTGCCGTGAGTGCCGAG	60.665	61.111	0.00	0.00	0.00	4.63
1779	1786	2.691252	ATCCCGGGGTTGACTCCC	60.691	66.667	23.50	0.00	46.31	4.30
1821	1828	2.946762	GTGCTTCGCCACAAGTCC	59.053	61.111	0.00	0.00	35.80	3.85
1900	1907	1.524849	GCGGAGGAAGCCAAGATCC	60.525	63.158	0.00	0.00	35.88	3.36
2035	2042	6.301486	TCCCATATGGATCACAAGATTTGAG	58.699	40.000	24.00	0.28	38.61	3.02
2048	2055	4.730949	AGATTTGAGGGCACATCATTTG	57.269	40.909	0.00	0.00	34.41	2.32
2315	2322	6.282167	TGTTGTAACTCGTCCAACAGAAATA	58.718	36.000	9.70	0.00	42.41	1.40
2323	2332	7.974675	ACTCGTCCAACAGAAATATGTTAATG	58.025	34.615	0.00	0.00	41.41	1.90
2340	2349	7.000575	TGTTAATGCTGTAGAAAACGATAGC	57.999	36.000	0.00	0.00	42.67	2.97
2342	2351	5.470845	AATGCTGTAGAAAACGATAGCAC	57.529	39.130	0.00	0.00	43.03	4.40
2559	2569	2.281276	GGACGTCCCTGCCGTTTT	60.281	61.111	24.75	0.00	38.92	2.43
2560	2570	2.613506	GGACGTCCCTGCCGTTTTG	61.614	63.158	24.75	0.00	38.92	2.44
2614	2624	9.973450	ATGTACTAATCTCTGTTGCTGTAATAG	57.027	33.333	0.00	0.00	0.00	1.73
2616	2626	9.804758	GTACTAATCTCTGTTGCTGTAATAGTT	57.195	33.333	2.58	0.00	0.00	2.24
2737	2779	2.287427	CCGGAGAAATGATCATTGCAGC	60.287	50.000	25.32	17.02	0.00	5.25
2795	2838	6.338146	TGCAGTGTTATCCTGTATGTAAGTC	58.662	40.000	0.00	0.00	32.41	3.01
2800	2843	9.298250	AGTGTTATCCTGTATGTAAGTCGATAT	57.702	33.333	0.00	0.00	0.00	1.63
2951	3038	2.171448	CCTCTCATCCAACCCTACCTTG	59.829	54.545	0.00	0.00	0.00	3.61
2953	3040	3.713764	CTCTCATCCAACCCTACCTTGAT	59.286	47.826	0.00	0.00	0.00	2.57
2970	3057	9.401058	CTACCTTGATCCAAGTAATGATCTTTT	57.599	33.333	0.00	0.00	39.58	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	98	3.078837	GTCAAAGGTGGGCGAAAGATAA	58.921	45.455	0.00	0.00	0.00	1.75
166	168	0.257039	GCAGGTGATGGGAGGATTGT	59.743	55.000	0.00	0.00	0.00	2.71
203	205	4.415332	GGAAGCGCGAGGACGTCA	62.415	66.667	18.91	0.00	41.98	4.35
294	296	2.112691	AGAGGAGTTTGGGGAGAAGAGA	59.887	50.000	0.00	0.00	0.00	3.10
366	370	2.469826	GAACCGGTGAAAGCCAAAAAG	58.530	47.619	8.52	0.00	0.00	2.27
528	533	0.393537	CATTTCTCGCTGGAGCCCTT	60.394	55.000	0.00	0.00	40.26	3.95
557	562	0.882927	CCTTCCGCTCGGTTTTCACA	60.883	55.000	8.28	0.00	36.47	3.58
619	625	7.412563	GCGATCTAGTGTAGCAACATAAAAACA	60.413	37.037	0.00	0.00	38.08	2.83
663	669	2.960384	TCTCTCGTACACCAACCTCAAA	59.040	45.455	0.00	0.00	0.00	2.69
678	684	8.561932	TGATATTGAAACGTATTTCTCTCTCG	57.438	34.615	0.00	0.00	44.02	4.04
773	779	6.018098	AGAGTACGACCAATGACGTATCTTAG	60.018	42.308	13.22	0.00	44.40	2.18
774	780	5.819379	AGAGTACGACCAATGACGTATCTTA	59.181	40.000	13.22	0.00	44.40	2.10
775	781	4.639310	AGAGTACGACCAATGACGTATCTT	59.361	41.667	13.22	5.62	44.40	2.40
776	782	4.197750	AGAGTACGACCAATGACGTATCT	58.802	43.478	13.22	13.01	44.40	1.98
777	783	4.548991	AGAGTACGACCAATGACGTATC	57.451	45.455	13.22	11.66	44.40	2.24
778	784	4.978083	AAGAGTACGACCAATGACGTAT	57.022	40.909	13.22	5.73	44.40	3.06
779	785	5.878332	TTAAGAGTACGACCAATGACGTA	57.122	39.130	8.08	8.08	42.56	3.57
780	786	4.771590	TTAAGAGTACGACCAATGACGT	57.228	40.909	9.70	9.70	44.60	4.34
781	787	6.456447	TTTTTAAGAGTACGACCAATGACG	57.544	37.500	0.00	0.00	35.75	4.35
815	821	0.747852	TTTGGAAAGTTGCCCGGAAC	59.252	50.000	0.73	0.00	0.00	3.62
816	822	1.342819	CATTTGGAAAGTTGCCCGGAA	59.657	47.619	0.73	0.00	0.00	4.30
817	823	0.965439	CATTTGGAAAGTTGCCCGGA	59.035	50.000	0.73	0.00	0.00	5.14
818	824	0.037419	CCATTTGGAAAGTTGCCCGG	60.037	55.000	0.00	0.00	37.39	5.73
819	825	0.037419	CCCATTTGGAAAGTTGCCCG	60.037	55.000	0.00	0.00	37.39	6.13
820	826	0.321564	GCCCATTTGGAAAGTTGCCC	60.322	55.000	0.00	0.00	37.39	5.36
821	827	0.321564	GGCCCATTTGGAAAGTTGCC	60.322	55.000	0.00	0.00	37.39	4.52
822	828	0.686789	AGGCCCATTTGGAAAGTTGC	59.313	50.000	0.00	0.00	37.39	4.17
833	839	0.988678	GGGTGTAGAGGAGGCCCATT	60.989	60.000	0.00	0.00	39.13	3.16
854	860	1.489230	AGGAAGAAACGTCTGTTGGGT	59.511	47.619	0.00	0.00	38.62	4.51
861	867	0.321996	GCTGGGAGGAAGAAACGTCT	59.678	55.000	0.00	0.00	34.72	4.18
906	913	2.362397	ACTGAGTTGACTTGCTCTCGAA	59.638	45.455	0.00	0.00	33.22	3.71
909	916	3.056304	GTGACTGAGTTGACTTGCTCTC	58.944	50.000	0.00	0.00	33.22	3.20
939	946	1.500396	GTTTGGGGCTTCGCGTTAG	59.500	57.895	5.77	6.30	0.00	2.34
1429	1436	2.009774	CTTGACCCACCATTCGATGAC	58.990	52.381	0.00	0.00	0.00	3.06
1648	1655	2.821366	CACCATCTGCGCCCTGTC	60.821	66.667	4.18	0.00	0.00	3.51
1746	1753	2.125106	ATCCTCGCCGCCAAGAAC	60.125	61.111	0.00	0.00	0.00	3.01
2035	2042	2.035066	GCCATCTACAAATGATGTGCCC	59.965	50.000	0.00	0.00	43.77	5.36
2048	2055	2.609459	CGACATCAAGTTGGCCATCTAC	59.391	50.000	16.73	7.38	0.00	2.59
2302	2309	7.538575	ACAGCATTAACATATTTCTGTTGGAC	58.461	34.615	0.00	0.00	39.60	4.02
2315	2322	7.279981	TGCTATCGTTTTCTACAGCATTAACAT	59.720	33.333	0.00	0.00	34.30	2.71
2323	2332	4.389077	AGTTGTGCTATCGTTTTCTACAGC	59.611	41.667	0.00	0.00	0.00	4.40
2614	2624	7.253420	CGTTAATCATTTCAGCATTAGCACAAC	60.253	37.037	0.00	0.00	45.49	3.32
2616	2626	6.257423	CGTTAATCATTTCAGCATTAGCACA	58.743	36.000	0.00	0.00	45.49	4.57
2937	3024	2.352561	TGGATCAAGGTAGGGTTGGA	57.647	50.000	0.00	0.00	0.00	3.53
2944	3031	8.970859	AAAGATCATTACTTGGATCAAGGTAG	57.029	34.615	11.65	0.63	44.81	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.