AutoCloner

Multiple sequence alignment - TraesCS6A01G411300

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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	TraesCS6A01G411300	chr6A	100.000	3917	0	0	1	3917	613927129	613931045	0.000000e+00	7234.0
1	TraesCS6A01G411300	chr6D	94.430	3914	179	18	34	3917	467815389	467811485	0.000000e+00	5984.0
2	TraesCS6A01G411300	chr6D	74.598	1929	404	45	406	2287	467787350	467785461	0.000000e+00	769.0
3	TraesCS6A01G411300	chr6D	79.577	284	56	2	2594	2876	467832547	467832829	6.640000e-48	202.0
4	TraesCS6A01G411300	chr6B	91.025	2986	208	36	34	2999	713114836	713117781	0.000000e+00	3975.0
5	TraesCS6A01G411300	chr6B	91.483	2853	187	20	102	2922	713067666	713064838	0.000000e+00	3871.0
6	TraesCS6A01G411300	chr6B	94.751	762	22	5	3092	3852	713118255	713118999	0.000000e+00	1170.0
7	TraesCS6A01G411300	chr6B	73.999	1973	425	53	373	2297	713720369	713722301	0.000000e+00	721.0
8	TraesCS6A01G411300	chr6B	93.258	267	14	2	3223	3485	713063668	713063402	1.320000e-104	390.0
9	TraesCS6A01G411300	chr6B	77.394	376	78	6	2512	2885	713723519	713723889	2.370000e-52	217.0
10	TraesCS6A01G411300	chr6B	96.386	83	3	0	3001	3083	713117931	713118013	1.900000e-28	137.0
11	TraesCS6A01G411300	chr6B	97.674	43	1	0	3001	3043	713064662	713064620	1.510000e-09	75.0
12	TraesCS6A01G411300	chr6B	94.872	39	2	0	2961	2999	713064839	713064801	1.180000e-05	62.1
13	TraesCS6A01G411300	chr6B	100.000	28	0	0	3806	3833	713119012	713119039	7.000000e-03	52.8
14	TraesCS6A01G411300	chr5A	75.571	1928	385	46	406	2287	482354919	482356806	0.000000e+00	872.0
15	TraesCS6A01G411300	chr5A	74.478	1916	405	47	406	2275	482369003	482370880	0.000000e+00	752.0
16	TraesCS6A01G411300	chr3B	78.013	1278	249	25	422	1691	737767234	737765981	0.000000e+00	774.0
17	TraesCS6A01G411300	chr3B	78.829	222	45	2	2067	2287	737765599	737765379	8.770000e-32	148.0
18	TraesCS6A01G411300	chr3B	83.230	161	15	6	31	179	569597010	569597170	1.900000e-28	137.0
19	TraesCS6A01G411300	chr3D	76.015	1551	315	43	412	1946	554956807	554958316	0.000000e+00	750.0
20	TraesCS6A01G411300	chrUn	77.212	373	75	8	2507	2877	248490368	248490732	3.970000e-50	209.0
21	TraesCS6A01G411300	chrUn	83.871	155	15	5	34	179	21461956	21461803	5.280000e-29	139.0
22	TraesCS6A01G411300	chr7D	76.149	348	75	7	2526	2872	631281259	631281599	4.020000e-40	176.0
23	TraesCS6A01G411300	chr7D	85.106	141	11	3	34	165	292419102	292419241	6.830000e-28	135.0
24	TraesCS6A01G411300	chr7D	77.934	213	45	2	2667	2878	631235709	631235920	8.830000e-27	132.0
25	TraesCS6A01G411300	chr2D	86.508	126	15	2	2876	2999	87754558	87754433	1.900000e-28	137.0
26	TraesCS6A01G411300	chr1B	83.230	161	15	6	31	179	632751828	632751988	1.900000e-28	137.0
27	TraesCS6A01G411300	chr4B	81.290	155	19	6	34	179	4349973	4350126	2.470000e-22	117.0
28	TraesCS6A01G411300	chr7A	77.551	196	40	4	2685	2878	6168692	6168885	8.890000e-22	115.0
29	TraesCS6A01G411300	chr7A	76.585	205	45	3	2085	2287	729279140	729278937	4.140000e-20	110.0
30	TraesCS6A01G411300	chr7B	76.961	204	44	3	2085	2287	739395663	739395462	3.200000e-21	113.0
31	TraesCS6A01G411300	chr5D	97.826	46	1	0	3041	3086	3034231	3034186	3.240000e-11	80.5
32	TraesCS6A01G411300	chr5D	95.000	40	2	0	2887	2926	538767173	538767212	3.270000e-06	63.9
33	TraesCS6A01G411300	chr5B	95.000	40	2	0	2887	2926	680338658	680338697	3.270000e-06	63.9
34	TraesCS6A01G411300	chr4A	95.000	40	2	0	2887	2926	629915607	629915568	3.270000e-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	TraesCS6A01G411300	chr6A	613927129	613931045	3916	False	7234.000	7234	100.00000	1	3917	1	chr6A.!!$F1	3916
1	TraesCS6A01G411300	chr6D	467811485	467815389	3904	True	5984.000	5984	94.43000	34	3917	1	chr6D.!!$R2	3883
2	TraesCS6A01G411300	chr6D	467785461	467787350	1889	True	769.000	769	74.59800	406	2287	1	chr6D.!!$R1	1881
3	TraesCS6A01G411300	chr6B	713114836	713119039	4203	False	1333.700	3975	95.54050	34	3852	4	chr6B.!!$F1	3818
4	TraesCS6A01G411300	chr6B	713063402	713067666	4264	True	1099.525	3871	94.32175	102	3485	4	chr6B.!!$R1	3383
5	TraesCS6A01G411300	chr6B	713720369	713723889	3520	False	469.000	721	75.69650	373	2885	2	chr6B.!!$F2	2512
6	TraesCS6A01G411300	chr5A	482354919	482356806	1887	False	872.000	872	75.57100	406	2287	1	chr5A.!!$F1	1881
7	TraesCS6A01G411300	chr5A	482369003	482370880	1877	False	752.000	752	74.47800	406	2275	1	chr5A.!!$F2	1869
8	TraesCS6A01G411300	chr3B	737765379	737767234	1855	True	461.000	774	78.42100	422	2287	2	chr3B.!!$R1	1865
9	TraesCS6A01G411300	chr3D	554956807	554958316	1509	False	750.000	750	76.01500	412	1946	1	chr3D.!!$F1	1534

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
556	626	0.629058	ACAACCACCTCAAACCCACT	59.371	50.0	0.0	0.0	0.00	4.00	F
2215	2342	0.682209	CTGCACTTCCTTGGGGGATG	60.682	60.0	0.0	0.0	44.66	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2287	2414	1.000283	CTGAGTTTCCGAGCTGTGAGT	60.000	52.381	0.0	0.0	0.00	3.41	R
3573	5786	1.585517	CCATTTGTGCATGGCGTCA	59.414	52.632	0.0	0.0	37.51	4.35	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
28	29	4.767255	GCACCAGCTCCACGGAGG	62.767	72.222	14.86	1.87	42.19	4.30
35	36	1.442148	GCTCCACGGAGGTACATCC	59.558	63.158	16.70	16.70	42.19	3.51
89	97	3.392882	CACTTGCATTTTCTTTGGGTCC	58.607	45.455	0.00	0.00	0.00	4.46
131	139	4.402474	TCGAGTCCATGATTTCTTCTGCTA	59.598	41.667	0.00	0.00	0.00	3.49
136	144	4.225942	TCCATGATTTCTTCTGCTACAGGT	59.774	41.667	0.00	0.00	31.51	4.00
161	169	1.512230	CATTGGCACCATCCCAACG	59.488	57.895	0.00	0.00	44.48	4.10
169	177	2.166254	GCACCATCCCAACGAAATTGAT	59.834	45.455	0.00	0.00	41.23	2.57
189	224	2.023673	TGTGCCAAGTTCTTCAAGGTG	58.976	47.619	0.00	0.00	0.00	4.00
195	241	4.762251	GCCAAGTTCTTCAAGGTGACTAAT	59.238	41.667	0.00	0.00	42.68	1.73
196	242	5.938125	GCCAAGTTCTTCAAGGTGACTAATA	59.062	40.000	0.00	0.00	42.68	0.98
197	243	6.430000	GCCAAGTTCTTCAAGGTGACTAATAA	59.570	38.462	0.00	0.00	42.68	1.40
198	244	7.361286	GCCAAGTTCTTCAAGGTGACTAATAAG	60.361	40.741	0.00	0.00	42.68	1.73
200	246	8.499162	CAAGTTCTTCAAGGTGACTAATAAGTG	58.501	37.037	0.00	0.00	42.68	3.16
213	260	9.326413	GTGACTAATAAGTGCATTATACCTTGT	57.674	33.333	0.00	0.00	35.56	3.16
249	303	9.814899	AGTCTCTGTTTTTATACATCTGATGAG	57.185	33.333	23.59	7.62	0.00	2.90
250	304	9.593134	GTCTCTGTTTTTATACATCTGATGAGT	57.407	33.333	23.59	13.27	0.00	3.41
266	320	2.778299	TGAGTAACAGCCCAATGTGAC	58.222	47.619	0.00	0.00	35.10	3.67
273	327	3.614092	ACAGCCCAATGTGACTCTAATG	58.386	45.455	0.00	0.00	30.46	1.90
333	390	6.073980	TGACGTTACTGAAAATACAACTGCTC	60.074	38.462	0.00	0.00	0.00	4.26
365	422	2.822561	CAGAAGAAAAAGGAGAAGGGGC	59.177	50.000	0.00	0.00	0.00	5.80
369	426	1.003233	GAAAAAGGAGAAGGGGCGAGA	59.997	52.381	0.00	0.00	0.00	4.04
398	455	1.279271	GATGTCCCCACAGCTAACACT	59.721	52.381	0.00	0.00	35.92	3.55
510	567	2.505364	GATGCTTGGGCCAGGGTCTT	62.505	60.000	18.18	0.00	37.74	3.01
556	626	0.629058	ACAACCACCTCAAACCCACT	59.371	50.000	0.00	0.00	0.00	4.00
596	669	3.153919	TGTTCAAGGGAAAGTGTATGGC	58.846	45.455	0.00	0.00	34.13	4.40
707	780	2.041350	AGGAGTTGGGAAGACGACTCTA	59.959	50.000	11.99	0.00	46.53	2.43
730	803	6.834959	AGCTCAACTTGTATACAATGATCG	57.165	37.500	18.35	9.18	35.02	3.69
822	895	9.213799	GAGTCACAAGAGAGATGTTAGATTTTT	57.786	33.333	0.00	0.00	0.00	1.94
993	1066	4.384547	CCGTTTAAGCCTAACAATGCAAAC	59.615	41.667	0.00	0.00	0.00	2.93
1522	1598	3.955524	TGGTAAACCTGGGTTTCTTCA	57.044	42.857	19.36	13.50	43.95	3.02
1728	1825	7.120923	TGGGAATATACTTGGTAGTGAGAAC	57.879	40.000	0.00	0.00	35.78	3.01
2002	2114	4.511454	TGTATGATAATTCTGCTGTTCGGC	59.489	41.667	0.00	0.00	0.00	5.54
2215	2342	0.682209	CTGCACTTCCTTGGGGGATG	60.682	60.000	0.00	0.00	44.66	3.51
2216	2343	1.380380	GCACTTCCTTGGGGGATGG	60.380	63.158	0.00	0.00	44.66	3.51
2287	2414	4.274950	GGGTGTTTGATCTGTTCGAGAAAA	59.725	41.667	0.00	0.00	33.12	2.29
2323	3414	2.753452	ACTCAGCTGAAGCCATTGAATG	59.247	45.455	18.85	3.74	43.38	2.67
2445	3539	6.314400	GGCATTTGAATGTATGCAAAACATCT	59.686	34.615	15.95	8.47	46.91	2.90
2644	3816	0.036022	GCTTCTGCTCCACAAGTCCT	59.964	55.000	0.00	0.00	36.03	3.85
2730	3902	4.860802	TCCTGCCCTCAAGATATTGAAA	57.139	40.909	4.06	0.00	0.00	2.69
3124	5333	6.867662	AAGGTATTCTTCTGCCATTTATCG	57.132	37.500	0.00	0.00	0.00	2.92
3303	5513	2.497138	TCATGCTGTCAAGTTGGTGAG	58.503	47.619	2.34	0.00	0.00	3.51
3308	5518	3.070878	TGCTGTCAAGTTGGTGAGTATGA	59.929	43.478	2.34	0.00	0.00	2.15
3397	5610	7.318141	TGCTTCCATGTACAAGTTACTACTAC	58.682	38.462	0.00	0.00	33.17	2.73
3535	5748	3.002246	GTGTTCTGCTGATCGTTCACAAA	59.998	43.478	0.00	0.00	0.00	2.83
3573	5786	1.886542	GTCCAAAAACTCCCTTGCGAT	59.113	47.619	0.00	0.00	0.00	4.58
3627	5840	0.833834	ATAGGCCCGGACAGATGGAG	60.834	60.000	0.73	0.00	0.00	3.86
3668	5881	2.795231	ATCAGGATGGTCAGTGGTTG	57.205	50.000	0.00	0.00	36.16	3.77
3669	5882	1.728323	TCAGGATGGTCAGTGGTTGA	58.272	50.000	0.00	0.00	36.16	3.18
3744	5957	1.186917	ATCGACCCACCGGTACACAA	61.187	55.000	6.87	0.00	44.88	3.33
3854	6067	1.415289	TGTGAACAATGGCAATGGCAA	59.585	42.857	14.81	0.00	42.43	4.52
3893	6106	5.683876	AGGTGTGTTGCTCATACTAGAAT	57.316	39.130	0.00	0.00	38.08	2.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.985456	GCTGGTGCTGTAGGCTCT	59.015	61.111	0.00	0.00	42.39	4.09
11	12	4.767255	CCTCCGTGGAGCTGGTGC	62.767	72.222	10.53	0.00	40.69	5.01
12	13	1.982395	TACCTCCGTGGAGCTGGTG	60.982	63.158	10.53	0.00	40.69	4.17
13	14	1.982938	GTACCTCCGTGGAGCTGGT	60.983	63.158	10.53	6.94	40.69	4.00
14	15	1.330655	ATGTACCTCCGTGGAGCTGG	61.331	60.000	10.53	0.73	40.69	4.85
15	16	0.103208	GATGTACCTCCGTGGAGCTG	59.897	60.000	10.53	0.66	40.69	4.24
16	17	1.043673	GGATGTACCTCCGTGGAGCT	61.044	60.000	10.53	0.00	40.69	4.09
17	18	1.442148	GGATGTACCTCCGTGGAGC	59.558	63.158	10.53	0.00	40.69	4.70
24	25	0.179081	GCTTGGACGGATGTACCTCC	60.179	60.000	7.10	7.10	36.88	4.30
25	26	0.535335	TGCTTGGACGGATGTACCTC	59.465	55.000	0.00	0.00	36.31	3.85
26	27	0.249398	GTGCTTGGACGGATGTACCT	59.751	55.000	0.00	0.00	36.31	3.08
27	28	1.082117	CGTGCTTGGACGGATGTACC	61.082	60.000	6.77	0.00	35.65	3.34
28	29	1.693083	GCGTGCTTGGACGGATGTAC	61.693	60.000	15.66	0.00	39.81	2.90
29	30	1.447140	GCGTGCTTGGACGGATGTA	60.447	57.895	15.66	0.00	39.81	2.29
30	31	2.742372	GCGTGCTTGGACGGATGT	60.742	61.111	15.66	0.00	39.81	3.06
31	32	3.499737	GGCGTGCTTGGACGGATG	61.500	66.667	15.66	0.00	39.81	3.51
32	33	4.015406	TGGCGTGCTTGGACGGAT	62.015	61.111	15.66	0.00	39.81	4.18
33	34	4.980805	GTGGCGTGCTTGGACGGA	62.981	66.667	15.66	0.00	39.81	4.69
35	36	4.988598	AGGTGGCGTGCTTGGACG	62.989	66.667	10.19	10.19	42.42	4.79
36	37	3.357079	CAGGTGGCGTGCTTGGAC	61.357	66.667	0.00	0.00	0.00	4.02
37	38	2.902423	AAACAGGTGGCGTGCTTGGA	62.902	55.000	0.00	0.00	0.00	3.53
38	39	2.489275	AAACAGGTGGCGTGCTTGG	61.489	57.895	0.00	0.00	0.00	3.61
89	97	4.188462	TCGAAATTAGTATGGTGGTGCTG	58.812	43.478	0.00	0.00	0.00	4.41
131	139	1.683365	GCCAATGCCATGGACCTGT	60.683	57.895	18.40	0.00	43.54	4.00
136	144	1.001888	ATGGTGCCAATGCCATGGA	59.998	52.632	18.40	0.31	43.25	3.41
161	169	5.531634	TGAAGAACTTGGCACATCAATTTC	58.468	37.500	0.00	0.00	39.30	2.17
169	177	2.023673	CACCTTGAAGAACTTGGCACA	58.976	47.619	0.00	0.00	0.00	4.57
246	300	2.371841	AGTCACATTGGGCTGTTACTCA	59.628	45.455	0.00	0.00	29.75	3.41
247	301	3.003480	GAGTCACATTGGGCTGTTACTC	58.997	50.000	4.57	4.57	40.92	2.59
249	303	3.059352	AGAGTCACATTGGGCTGTTAC	57.941	47.619	0.00	0.00	0.00	2.50
250	304	4.901197	TTAGAGTCACATTGGGCTGTTA	57.099	40.909	0.00	0.00	0.00	2.41
273	327	0.609662	AAATGTGCAGTGGATTGGCC	59.390	50.000	0.00	0.00	37.10	5.36
343	400	3.498661	GCCCCTTCTCCTTTTTCTTCTGA	60.499	47.826	0.00	0.00	0.00	3.27
365	422	2.939103	GGGGACATCTGTTGAATTCTCG	59.061	50.000	7.05	0.00	0.00	4.04
369	426	3.424703	CTGTGGGGACATCTGTTGAATT	58.575	45.455	0.00	0.00	46.14	2.17
510	567	1.073025	AGCGATTTGGACCTGCACA	59.927	52.632	0.00	0.00	0.00	4.57
556	626	1.488705	AAGACTTGATGTGCCCCGGA	61.489	55.000	0.73	0.00	0.00	5.14
596	669	2.995258	GCAACTCTTCTCTTCAGCTCTG	59.005	50.000	0.00	0.00	0.00	3.35
707	780	6.573434	TCGATCATTGTATACAAGTTGAGCT	58.427	36.000	24.24	12.54	39.47	4.09
730	803	5.942826	AGGTCAAATTGACTCTCCAAATCTC	59.057	40.000	23.30	4.61	46.19	2.75
993	1066	0.249031	TCACGAGTATCATGCTGCCG	60.249	55.000	0.00	0.00	33.17	5.69
1206	1279	0.179018	ACAGTGTCCCTGCAGTTTCC	60.179	55.000	13.81	0.00	45.68	3.13
1522	1598	6.333416	GGAGTTCTTTTCTTTCAACTTGCTT	58.667	36.000	0.00	0.00	0.00	3.91
1757	1854	4.661222	TGTCCTCAATTTTGCCACTGATA	58.339	39.130	0.00	0.00	0.00	2.15
2002	2114	5.585390	CAAGGCAAGGAAAGTAGCATTATG	58.415	41.667	0.00	0.00	29.19	1.90
2215	2342	4.405036	CAGTACCCTTAAACTAGAGACCCC	59.595	50.000	0.00	0.00	0.00	4.95
2216	2343	4.405036	CCAGTACCCTTAAACTAGAGACCC	59.595	50.000	0.00	0.00	0.00	4.46
2287	2414	1.000283	CTGAGTTTCCGAGCTGTGAGT	60.000	52.381	0.00	0.00	0.00	3.41
2310	2437	3.243002	GCTGTAGAGCATTCAATGGCTTC	60.243	47.826	7.06	0.00	45.46	3.86
2323	3414	1.297664	CAGGAATGCAGCTGTAGAGC	58.702	55.000	16.64	3.08	46.64	4.09
2445	3539	7.221450	CCTTCCCTGATATACCACGAAAAATA	58.779	38.462	0.00	0.00	0.00	1.40
2644	3816	1.608590	GCCAAACACTAGCTCTTGCAA	59.391	47.619	0.00	0.00	42.74	4.08
3124	5333	3.320826	ACAACTGCTTACAATTCCAACCC	59.679	43.478	0.00	0.00	0.00	4.11
3397	5610	3.474600	CTTGGTTGATATGGCAGAGAGG	58.525	50.000	0.00	0.00	0.00	3.69
3535	5748	2.290577	GGACTGGCTTCTTCTGGTCAAT	60.291	50.000	0.00	0.00	0.00	2.57
3573	5786	1.585517	CCATTTGTGCATGGCGTCA	59.414	52.632	0.00	0.00	37.51	4.35
3627	5840	6.919662	TGATTTCTGAAGAAGCAAATGTGAAC	59.080	34.615	0.00	0.00	35.21	3.18
3744	5957	5.954153	ATGACAGATGGAGATGAGAGTTT	57.046	39.130	0.00	0.00	0.00	2.66
3854	6067	3.456277	ACACCTTTGAACTCCTCAGAACT	59.544	43.478	0.00	0.00	34.81	3.01
3893	6106	2.088104	ATCGGAGGGAGCAGTTCATA	57.912	50.000	0.00	0.00	0.00	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.