AutoCloner

Multiple sequence alignment - TraesCS3B01G258400

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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	TraesCS3B01G258400	chr3B	100.000	2699	0	0	1	2699	416136956	416134258	0.000000e+00	4985.0
1	TraesCS3B01G258400	chr3A	93.973	2721	122	19	1	2699	423670665	423673365	0.000000e+00	4078.0
2	TraesCS3B01G258400	chr3D	92.150	2242	90	31	479	2699	305621663	305623839	0.000000e+00	3086.0
3	TraesCS3B01G258400	chr3D	90.529	454	41	2	1	454	305596994	305597445	1.380000e-167	599.0
4	TraesCS3B01G258400	chr1B	85.143	175	24	2	1459	1632	667750247	667750420	7.680000e-41	178.0
5	TraesCS3B01G258400	chr1A	82.857	175	28	2	1459	1632	575808295	575808468	3.600000e-34	156.0
6	TraesCS3B01G258400	chr1A	97.222	36	1	0	1229	1264	75256103	75256068	8.070000e-06	62.1
7	TraesCS3B01G258400	chr1D	82.286	175	29	2	1459	1632	479540795	479540968	1.670000e-32	150.0
8	TraesCS3B01G258400	chr1D	97.222	36	1	0	1229	1264	74929947	74929912	8.070000e-06	62.1
9	TraesCS3B01G258400	chr5A	78.035	173	34	4	1462	1632	459775648	459775478	3.680000e-19	106.0
10	TraesCS3B01G258400	chr5A	76.404	178	30	11	1461	1632	443289629	443289800	4.790000e-13	86.1
11	TraesCS3B01G258400	chr2D	73.898	295	61	10	46	331	353290151	353290438	1.320000e-18	104.0
12	TraesCS3B01G258400	chr2D	79.433	141	26	1	1128	1268	388481930	388481793	2.210000e-16	97.1
13	TraesCS3B01G258400	chr4D	77.457	173	35	4	1462	1632	61852304	61852474	1.710000e-17	100.0
14	TraesCS3B01G258400	chr2A	79.433	141	26	1	1128	1268	524953218	524953081	2.210000e-16	97.1
15	TraesCS3B01G258400	chr6B	78.621	145	21	6	1136	1272	539195662	539195520	1.330000e-13	87.9
16	TraesCS3B01G258400	chr6A	78.873	142	20	6	1136	1269	499955058	499955197	1.330000e-13	87.9
17	TraesCS3B01G258400	chr6D	77.931	145	22	6	1136	1272	357592515	357592373	6.190000e-12	82.4
18	TraesCS3B01G258400	chr5D	74.302	179	32	12	1461	1632	342175360	342175531	2.240000e-06	63.9

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	TraesCS3B01G258400	chr3B	416134258	416136956	2698	True	4985	4985	100.000	1	2699	1	chr3B.!!$R1	2698
1	TraesCS3B01G258400	chr3A	423670665	423673365	2700	False	4078	4078	93.973	1	2699	1	chr3A.!!$F1	2698
2	TraesCS3B01G258400	chr3D	305621663	305623839	2176	False	3086	3086	92.150	479	2699	1	chr3D.!!$F2	2220

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
191	192	0.037447	GATAGAAGGGCTCCATGGGC	59.963	60.0	13.02	14.08	0.0	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2165	2200	0.403271	AATCCAGTTGCTGTCAGGCT	59.597	50.0	1.14	0.0	0.0	4.58	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
58	59	1.282653	CCTCCCCCTTCCTTCTTCCC	61.283	65.000	0.00	0.00	0.00	3.97
60	61	1.009675	CTCCCCCTTCCTTCTTCCCTA	59.990	57.143	0.00	0.00	0.00	3.53
67	68	3.783082	CCTTCCTTCTTCCCTATCTTGGT	59.217	47.826	0.00	0.00	0.00	3.67
96	97	2.158564	CCATGGTGGATATGGTCTTGCT	60.159	50.000	2.57	0.00	40.96	3.91
100	101	2.368439	GTGGATATGGTCTTGCTGCAA	58.632	47.619	15.16	15.16	0.00	4.08
113	114	0.038892	GCTGCAACAATGGAGGTGTG	60.039	55.000	0.00	0.00	44.51	3.82
121	122	1.000843	CAATGGAGGTGTGACGACTCA	59.999	52.381	8.29	0.00	32.98	3.41
135	136	6.127338	TGTGACGACTCATGGAAGATAGATTT	60.127	38.462	0.00	0.00	0.00	2.17
166	167	2.572284	GCGACTAGCGTTGGAGGT	59.428	61.111	8.08	0.00	43.41	3.85
177	178	4.726583	AGCGTTGGAGGTGTATAGATAGA	58.273	43.478	0.00	0.00	0.00	1.98
181	182	5.047943	CGTTGGAGGTGTATAGATAGAAGGG	60.048	48.000	0.00	0.00	0.00	3.95
187	188	5.026790	GGTGTATAGATAGAAGGGCTCCAT	58.973	45.833	0.00	0.00	0.00	3.41
188	189	5.105146	GGTGTATAGATAGAAGGGCTCCATG	60.105	48.000	0.00	0.00	0.00	3.66
191	192	0.037447	GATAGAAGGGCTCCATGGGC	59.963	60.000	13.02	14.08	0.00	5.36
228	229	3.397618	TGACTTCTCCCCTTTGATCCAAA	59.602	43.478	0.00	0.00	0.00	3.28
243	244	4.346418	TGATCCAAAGATTCTAGAGGAGCC	59.654	45.833	8.68	2.09	30.92	4.70
260	261	1.172812	GCCCAATCCTCGCCCAATAC	61.173	60.000	0.00	0.00	0.00	1.89
263	264	1.543429	CCAATCCTCGCCCAATACCTC	60.543	57.143	0.00	0.00	0.00	3.85
276	277	4.385310	CCCAATACCTCCCTTGGTTTCTAG	60.385	50.000	0.00	0.00	40.28	2.43
284	285	2.973945	CCTTGGTTTCTAGGGAACTCG	58.026	52.381	8.97	0.00	43.67	4.18
295	296	5.021458	TCTAGGGAACTCGTAGGAACAAAT	58.979	41.667	0.00	0.00	43.67	2.32
296	297	6.189859	TCTAGGGAACTCGTAGGAACAAATA	58.810	40.000	0.00	0.00	43.67	1.40
301	302	6.289064	GGAACTCGTAGGAACAAATATGGAT	58.711	40.000	0.00	0.00	0.00	3.41
302	303	7.439381	GGAACTCGTAGGAACAAATATGGATA	58.561	38.462	0.00	0.00	0.00	2.59
332	333	8.647796	TCGGTGAATAATCATAGAAGTTATGGT	58.352	33.333	0.00	0.00	38.01	3.55
342	343	8.648557	TCATAGAAGTTATGGTTGATTCTTCG	57.351	34.615	0.00	0.00	37.12	3.79
344	345	5.805728	AGAAGTTATGGTTGATTCTTCGGT	58.194	37.500	0.00	0.00	37.12	4.69
355	356	4.148838	TGATTCTTCGGTCAAAAATGGGT	58.851	39.130	0.00	0.00	0.00	4.51
364	365	2.093711	GTCAAAAATGGGTGGTATGCCC	60.094	50.000	0.00	0.00	46.26	5.36
387	388	4.647964	GTGCATGGTCGTAAAATACACAG	58.352	43.478	0.00	0.00	0.00	3.66
391	392	6.150307	TGCATGGTCGTAAAATACACAGAAAT	59.850	34.615	0.00	0.00	0.00	2.17
431	433	8.789881	TGGTGAACATTTCTTTTAAATACACG	57.210	30.769	0.00	0.00	0.00	4.49
432	434	7.863375	TGGTGAACATTTCTTTTAAATACACGG	59.137	33.333	0.00	0.00	0.00	4.94
458	460	8.398665	GTGATCTTTTCTTAACATATGGTGACC	58.601	37.037	2.68	0.00	0.00	4.02
477	479	8.498575	TGGTGACCATTTATCTAAATACATGGA	58.501	33.333	14.48	0.00	43.84	3.41
540	542	9.619316	TGAATTTTTGTAAAGATATGGTGAACG	57.381	29.630	0.00	0.00	0.00	3.95
541	543	9.834628	GAATTTTTGTAAAGATATGGTGAACGA	57.165	29.630	0.00	0.00	0.00	3.85
546	548	9.834628	TTTGTAAAGATATGGTGAACGATTTTC	57.165	29.630	0.00	0.00	0.00	2.29
734	738	2.528041	AAAAGAAAGCCGACGAGTCT	57.472	45.000	0.00	0.00	0.00	3.24
1726	1751	3.181474	GCAGGAGACAGGTTCCATAGTAC	60.181	52.174	0.00	0.00	37.18	2.73
1727	1752	4.023980	CAGGAGACAGGTTCCATAGTACA	58.976	47.826	0.00	0.00	37.18	2.90
2068	2102	9.995003	TTAAAATTAAAGAAACCATGAGCACAT	57.005	25.926	0.00	0.00	37.19	3.21
2087	2121	6.016527	AGCACATTCATTCTGATAATCGCAAT	60.017	34.615	0.00	0.00	0.00	3.56
2103	2138	3.123453	TCGCAATCGATGTCAAAAGAGTG	59.877	43.478	0.00	0.00	40.21	3.51
2139	2174	5.109662	TGATTTTGCGTTTACCGAATCAA	57.890	34.783	0.00	0.00	35.57	2.57
2145	2180	3.175929	GCGTTTACCGAATCAAAATGGG	58.824	45.455	0.00	0.00	39.56	4.00
2165	2200	2.280119	GCCGAGGCATGCGACATA	60.280	61.111	12.44	0.00	41.49	2.29
2328	2363	2.284625	ACCATGGTGCGAGGGAGA	60.285	61.111	18.99	0.00	0.00	3.71
2387	2422	5.288804	TCAAGATAACAGGCAAGCAAAAAC	58.711	37.500	0.00	0.00	0.00	2.43
2393	2428	1.860326	CAGGCAAGCAAAAACGAAAGG	59.140	47.619	0.00	0.00	0.00	3.11
2646	2681	8.820933	CGAATAGAAAGTGCTATCAGAAATTCA	58.179	33.333	0.00	0.00	30.95	2.57
2648	2683	9.678260	AATAGAAAGTGCTATCAGAAATTCACT	57.322	29.630	0.00	0.00	36.46	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	3.067645	AGATAGGGAAGAAGGAAGGGG	57.932	52.381	0.00	0.00	0.00	4.79
44	45	3.137360	CCAAGATAGGGAAGAAGGAAGGG	59.863	52.174	0.00	0.00	0.00	3.95
58	59	3.072184	CCATGGAGGAAGGACCAAGATAG	59.928	52.174	5.56	0.00	41.22	2.08
60	61	1.849039	CCATGGAGGAAGGACCAAGAT	59.151	52.381	5.56	0.00	41.22	2.40
96	97	1.317613	GTCACACCTCCATTGTTGCA	58.682	50.000	0.00	0.00	0.00	4.08
100	101	1.000955	GAGTCGTCACACCTCCATTGT	59.999	52.381	0.00	0.00	0.00	2.71
113	114	6.507900	TCAAATCTATCTTCCATGAGTCGTC	58.492	40.000	0.00	0.00	0.00	4.20
121	122	6.885376	GCATCCATCTCAAATCTATCTTCCAT	59.115	38.462	0.00	0.00	0.00	3.41
135	136	3.153781	TCGCCGGCATCCATCTCA	61.154	61.111	28.98	0.00	0.00	3.27
166	167	5.026121	CCATGGAGCCCTTCTATCTATACA	58.974	45.833	5.56	0.00	0.00	2.29
181	182	1.063183	ATAGAGAAGGCCCATGGAGC	58.937	55.000	15.22	14.96	0.00	4.70
187	188	1.770658	CACATCCATAGAGAAGGCCCA	59.229	52.381	0.00	0.00	0.00	5.36
188	189	2.050144	TCACATCCATAGAGAAGGCCC	58.950	52.381	0.00	0.00	0.00	5.80
191	192	5.221422	GGAGAAGTCACATCCATAGAGAAGG	60.221	48.000	0.00	0.00	33.08	3.46
228	229	3.116395	AGGATTGGGCTCCTCTAGAATCT	60.116	47.826	0.00	0.00	42.12	2.40
243	244	0.474184	AGGTATTGGGCGAGGATTGG	59.526	55.000	0.00	0.00	0.00	3.16
250	251	1.632018	CCAAGGGAGGTATTGGGCGA	61.632	60.000	0.00	0.00	41.92	5.54
276	277	4.814771	CCATATTTGTTCCTACGAGTTCCC	59.185	45.833	0.00	0.00	0.00	3.97
279	280	9.675464	TTTTATCCATATTTGTTCCTACGAGTT	57.325	29.630	0.00	0.00	0.00	3.01
284	285	9.063615	ACCGATTTTATCCATATTTGTTCCTAC	57.936	33.333	0.00	0.00	0.00	3.18
307	308	8.833231	ACCATAACTTCTATGATTATTCACCG	57.167	34.615	0.00	0.00	33.85	4.94
321	322	5.805728	ACCGAAGAATCAACCATAACTTCT	58.194	37.500	0.00	0.00	33.84	2.85
322	323	5.642063	TGACCGAAGAATCAACCATAACTTC	59.358	40.000	0.00	0.00	0.00	3.01
332	333	4.586841	ACCCATTTTTGACCGAAGAATCAA	59.413	37.500	0.00	0.00	32.14	2.57
339	340	2.074729	ACCACCCATTTTTGACCGAA	57.925	45.000	0.00	0.00	0.00	4.30
342	343	2.093711	GGCATACCACCCATTTTTGACC	60.094	50.000	0.00	0.00	35.26	4.02
364	365	3.123790	TGTGTATTTTACGACCATGCACG	59.876	43.478	0.00	7.92	36.59	5.34
406	407	7.863375	CCGTGTATTTAAAAGAAATGTTCACCA	59.137	33.333	0.00	0.00	0.00	4.17
407	408	7.863877	ACCGTGTATTTAAAAGAAATGTTCACC	59.136	33.333	0.00	0.00	0.00	4.02
413	414	9.840427	AAGATCACCGTGTATTTAAAAGAAATG	57.160	29.630	0.00	0.00	0.00	2.32
418	419	9.893305	AAGAAAAGATCACCGTGTATTTAAAAG	57.107	29.630	0.00	0.00	0.00	2.27
431	433	8.398665	GTCACCATATGTTAAGAAAAGATCACC	58.601	37.037	1.24	0.00	0.00	4.02
432	434	8.398665	GGTCACCATATGTTAAGAAAAGATCAC	58.601	37.037	1.24	0.00	0.00	3.06
722	726	2.358369	TCGTCAGACTCGTCGGCT	60.358	61.111	0.00	0.00	34.09	5.52
794	798	1.188219	AGCCGGAGAAAGAGTCTGCA	61.188	55.000	5.05	0.00	44.71	4.41
826	830	0.606130	TGGTCGGGCGCGTCTATATA	60.606	55.000	23.19	0.00	0.00	0.86
1010	1020	3.756783	CCCCGTCCTCCTCTCCCT	61.757	72.222	0.00	0.00	0.00	4.20
1726	1751	1.153549	GGAGCGTTGCCTCCTACTG	60.154	63.158	1.07	0.00	46.39	2.74
1727	1752	3.300013	GGAGCGTTGCCTCCTACT	58.700	61.111	1.07	0.00	46.39	2.57
2087	2121	5.869344	CCAATAGACACTCTTTTGACATCGA	59.131	40.000	4.55	0.00	37.54	3.59
2094	2128	6.430925	TCAACCATCCAATAGACACTCTTTTG	59.569	38.462	0.00	0.00	35.91	2.44
2095	2129	6.542821	TCAACCATCCAATAGACACTCTTTT	58.457	36.000	0.00	0.00	0.00	2.27
2103	2138	5.036737	CGCAAAATCAACCATCCAATAGAC	58.963	41.667	0.00	0.00	0.00	2.59
2159	2194	1.002366	GTTGCTGTCAGGCTATGTCG	58.998	55.000	1.14	0.00	0.00	4.35
2160	2195	2.005451	CAGTTGCTGTCAGGCTATGTC	58.995	52.381	1.14	0.00	0.00	3.06
2161	2196	1.339438	CCAGTTGCTGTCAGGCTATGT	60.339	52.381	1.14	0.00	0.00	2.29
2162	2197	1.065926	TCCAGTTGCTGTCAGGCTATG	60.066	52.381	1.14	0.00	0.00	2.23
2163	2198	1.279496	TCCAGTTGCTGTCAGGCTAT	58.721	50.000	1.14	0.00	0.00	2.97
2164	2199	1.279496	ATCCAGTTGCTGTCAGGCTA	58.721	50.000	1.14	0.00	0.00	3.93
2165	2200	0.403271	AATCCAGTTGCTGTCAGGCT	59.597	50.000	1.14	0.00	0.00	4.58
2169	2204	4.769688	CTGGTATAATCCAGTTGCTGTCA	58.230	43.478	4.75	0.00	46.92	3.58
2328	2363	2.676748	TGGCATCCTTGTCAACCTTTT	58.323	42.857	0.00	0.00	33.65	2.27
2387	2422	5.466728	TCTCAAGATGTTGAAGTTCCTTTCG	59.533	40.000	6.75	0.00	42.27	3.46
2521	2556	9.479549	AATGTCCAAATCTTCACTTATATGGTT	57.520	29.630	0.00	0.00	0.00	3.67
2558	2593	2.488937	AGGGCCGTTACATTTTAAACCG	59.511	45.455	0.00	0.00	0.00	4.44
2646	2681	3.323979	ACCTTGTTCTTATGGTCGACAGT	59.676	43.478	18.91	7.54	0.00	3.55
2648	2683	4.525487	AGTACCTTGTTCTTATGGTCGACA	59.475	41.667	18.91	3.91	34.33	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.