AutoCloner

Multiple sequence alignment - TraesCS4B01G059200

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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	TraesCS4B01G059200	chr4B	100.000	2654	0	0	1	2654	50402460	50405113	0.000000e+00	4902.0
1	TraesCS4B01G059200	chr5B	96.341	2624	91	3	35	2654	399785581	399782959	0.000000e+00	4309.0
2	TraesCS4B01G059200	chr5B	97.826	46	1	0	35	80	633666144	633666189	2.190000e-11	80.5
3	TraesCS4B01G059200	chr1B	95.172	2009	93	2	646	2654	532540657	532542661	0.000000e+00	3169.0
4	TraesCS4B01G059200	chr1B	93.802	484	28	2	168	650	532531581	532532063	0.000000e+00	726.0
5	TraesCS4B01G059200	chr1B	82.432	370	43	17	35	398	73363927	73363574	1.190000e-78	303.0
6	TraesCS4B01G059200	chr1B	81.941	371	43	19	35	398	73316290	73315937	2.580000e-75	292.0
7	TraesCS4B01G059200	chr1B	78.338	337	38	20	634	966	628627045	628627350	4.510000e-43	185.0
8	TraesCS4B01G059200	chr1B	84.615	104	13	3	31	132	55003021	55002919	1.680000e-17	100.0
9	TraesCS4B01G059200	chr3B	94.499	1836	95	4	35	1867	23138491	23136659	0.000000e+00	2826.0
10	TraesCS4B01G059200	chr3B	97.143	175	5	0	2480	2654	23136655	23136481	2.000000e-76	296.0
11	TraesCS4B01G059200	chr3B	86.316	190	20	3	438	625	280436689	280436874	4.480000e-48	202.0
12	TraesCS4B01G059200	chr3B	78.571	350	39	20	622	966	187556984	187557302	5.790000e-47	198.0
13	TraesCS4B01G059200	chr3B	89.922	129	13	0	1132	1260	823095849	823095977	1.630000e-37	167.0
14	TraesCS4B01G059200	chr6B	94.928	1459	69	3	31	1484	37929623	37931081	0.000000e+00	2279.0
15	TraesCS4B01G059200	chr6B	95.674	1179	50	1	1477	2654	37931230	37932408	0.000000e+00	1893.0
16	TraesCS4B01G059200	chr6B	95.918	49	2	0	31	79	664691913	664691865	2.190000e-11	80.5
17	TraesCS4B01G059200	chr2B	89.695	1310	94	8	431	1703	14601382	14600077	0.000000e+00	1633.0
18	TraesCS4B01G059200	chr2B	86.597	955	59	19	1722	2654	14599558	14598651	0.000000e+00	990.0
19	TraesCS4B01G059200	chr2B	80.732	519	59	15	1215	1703	693044264	693043757	1.500000e-97	366.0
20	TraesCS4B01G059200	chr2B	80.539	519	60	16	1215	1703	456700083	456699576	6.980000e-96	361.0
21	TraesCS4B01G059200	chr2B	84.409	372	41	6	1343	1703	119633739	119633374	1.510000e-92	350.0
22	TraesCS4B01G059200	chr2B	85.654	237	26	5	2181	2409	119632890	119632654	2.640000e-60	243.0
23	TraesCS4B01G059200	chr2B	86.207	87	11	1	32	117	90289211	90289297	2.810000e-15	93.5
24	TraesCS4B01G059200	chr7B	90.779	629	36	7	2034	2654	84060088	84060702	0.000000e+00	821.0
25	TraesCS4B01G059200	chr7B	78.600	500	56	24	2181	2629	197406195	197405696	1.560000e-72	283.0
26	TraesCS4B01G059200	chr7B	79.641	334	36	10	636	966	682274309	682274613	7.440000e-51	211.0
27	TraesCS4B01G059200	chr7B	86.310	168	23	0	1132	1299	613871231	613871398	1.620000e-42	183.0
28	TraesCS4B01G059200	chr7B	87.402	127	16	0	1168	1294	404038166	404038292	2.130000e-31	147.0
29	TraesCS4B01G059200	chr7B	94.000	50	3	0	31	80	336476777	336476826	2.830000e-10	76.8
30	TraesCS4B01G059200	chr1D	84.864	403	29	10	35	431	257318372	257317996	6.930000e-101	377.0
31	TraesCS4B01G059200	chr1D	80.204	490	47	23	2181	2629	163499727	163500207	3.300000e-84	322.0
32	TraesCS4B01G059200	chr2D	84.450	373	39	8	1343	1703	77383234	77382869	1.510000e-92	350.0
33	TraesCS4B01G059200	chr2A	80.855	491	46	24	2181	2629	465363526	465363042	2.530000e-90	342.0
34	TraesCS4B01G059200	chr2A	87.395	238	20	7	2181	2409	78561562	78561798	5.630000e-67	265.0
35	TraesCS4B01G059200	chr4A	82.630	403	46	16	35	431	708396639	708396255	4.230000e-88	335.0
36	TraesCS4B01G059200	chr4A	96.000	50	2	0	35	84	675185921	675185872	6.090000e-12	82.4
37	TraesCS4B01G059200	chr4D	82.116	397	43	17	35	425	78864658	78865032	5.510000e-82	315.0
38	TraesCS4B01G059200	chr4D	80.397	403	46	17	2181	2555	456260643	456260246	2.600000e-70	276.0
39	TraesCS4B01G059200	chrUn	82.162	370	44	17	35	398	357027320	357026967	5.550000e-77	298.0
40	TraesCS4B01G059200	chrUn	87.006	177	23	0	1111	1287	32340396	32340220	1.610000e-47	200.0
41	TraesCS4B01G059200	chrUn	87.324	142	14	3	424	565	79335106	79335243	2.730000e-35	159.0
42	TraesCS4B01G059200	chrUn	87.037	108	11	2	862	966	85467706	85467813	4.640000e-23	119.0
43	TraesCS4B01G059200	chr6D	85.570	298	18	5	135	431	463217161	463216888	3.340000e-74	289.0
44	TraesCS4B01G059200	chr6D	88.718	195	17	4	431	625	110656276	110656465	1.590000e-57	233.0
45	TraesCS4B01G059200	chr6D	82.784	273	30	14	1731	1997	464100561	464100822	7.390000e-56	228.0
46	TraesCS4B01G059200	chr6D	81.119	286	39	8	1752	2029	464228959	464229237	5.750000e-52	215.0
47	TraesCS4B01G059200	chr1A	85.787	197	25	2	424	620	224081400	224081593	3.460000e-49	206.0

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	TraesCS4B01G059200	chr4B	50402460	50405113	2653	False	4902.0	4902	100.0000	1	2654	1	chr4B.!!$F1	2653
1	TraesCS4B01G059200	chr5B	399782959	399785581	2622	True	4309.0	4309	96.3410	35	2654	1	chr5B.!!$R1	2619
2	TraesCS4B01G059200	chr1B	532540657	532542661	2004	False	3169.0	3169	95.1720	646	2654	1	chr1B.!!$F2	2008
3	TraesCS4B01G059200	chr3B	23136481	23138491	2010	True	1561.0	2826	95.8210	35	2654	2	chr3B.!!$R1	2619
4	TraesCS4B01G059200	chr6B	37929623	37932408	2785	False	2086.0	2279	95.3010	31	2654	2	chr6B.!!$F1	2623
5	TraesCS4B01G059200	chr2B	14598651	14601382	2731	True	1311.5	1633	88.1460	431	2654	2	chr2B.!!$R3	2223
6	TraesCS4B01G059200	chr2B	693043757	693044264	507	True	366.0	366	80.7320	1215	1703	1	chr2B.!!$R2	488
7	TraesCS4B01G059200	chr2B	456699576	456700083	507	True	361.0	361	80.5390	1215	1703	1	chr2B.!!$R1	488
8	TraesCS4B01G059200	chr2B	119632654	119633739	1085	True	296.5	350	85.0315	1343	2409	2	chr2B.!!$R4	1066
9	TraesCS4B01G059200	chr7B	84060088	84060702	614	False	821.0	821	90.7790	2034	2654	1	chr7B.!!$F1	620

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	Hairpin	End Stability	Orientation
26	27	0.114168	AGCAGTTGGCCCATTGGTAA	59.886	50.0	1.92	46.50	2.85	F
227	232	0.393077	AGGGTCACGTCAGTTTCCTG	59.607	55.0	0.00	40.25	3.86	F
1309	1348	1.001282	AAGTACTCCTCCTCCTCGGT	58.999	55.0	0.00	0.00	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1415	1460	0.036388	CCACAAGTACATCCCAGCGT	60.036	55.000	0.00	0.00	5.07	R
1578	1791	0.416231	ACCAGGAGCCCTTGTACCTA	59.584	55.000	0.00	27.08	3.08	R
2341	3123	1.302033	CCCGAGCTGCAAGTTGAGT	60.302	57.895	7.16	35.30	3.41	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
17	18	3.188786	CGTCGCTAGCAGTTGGCC	61.189	66.667	16.45	0.00	46.50	5.36
18	19	2.820037	GTCGCTAGCAGTTGGCCC	60.820	66.667	16.45	0.00	46.50	5.80
19	20	3.318384	TCGCTAGCAGTTGGCCCA	61.318	61.111	16.45	0.00	46.50	5.36
20	21	2.124570	CGCTAGCAGTTGGCCCAT	60.125	61.111	16.45	0.00	46.50	4.00
21	22	1.750399	CGCTAGCAGTTGGCCCATT	60.750	57.895	16.45	0.00	46.50	3.16
22	23	1.811860	GCTAGCAGTTGGCCCATTG	59.188	57.895	10.63	0.00	46.50	2.82
23	24	1.669999	GCTAGCAGTTGGCCCATTGG	61.670	60.000	10.63	0.00	46.50	3.16
24	25	0.323725	CTAGCAGTTGGCCCATTGGT	60.324	55.000	9.04	9.04	46.50	3.67
25	26	0.995803	TAGCAGTTGGCCCATTGGTA	59.004	50.000	7.09	7.09	46.50	3.25
26	27	0.114168	AGCAGTTGGCCCATTGGTAA	59.886	50.000	1.92	0.00	46.50	2.85
27	28	0.532115	GCAGTTGGCCCATTGGTAAG	59.468	55.000	0.00	0.00	36.11	2.34
28	29	0.532115	CAGTTGGCCCATTGGTAAGC	59.468	55.000	0.00	0.00	0.00	3.09
29	30	0.965363	AGTTGGCCCATTGGTAAGCG	60.965	55.000	0.00	0.00	0.00	4.68
30	31	0.963355	GTTGGCCCATTGGTAAGCGA	60.963	55.000	0.00	0.00	0.00	4.93
31	32	0.963355	TTGGCCCATTGGTAAGCGAC	60.963	55.000	0.00	0.00	0.00	5.19
32	33	1.377987	GGCCCATTGGTAAGCGACA	60.378	57.895	1.20	0.00	0.00	4.35
33	34	1.654023	GGCCCATTGGTAAGCGACAC	61.654	60.000	1.20	0.00	0.00	3.67
227	232	0.393077	AGGGTCACGTCAGTTTCCTG	59.607	55.000	0.00	0.00	40.25	3.86
354	360	2.202892	GAAGATGGGTCCGGTCGC	60.203	66.667	8.80	8.80	0.00	5.19
425	431	7.256119	CCTCCACTGCTGTTGTAGATCTATAAT	60.256	40.741	14.18	0.00	0.00	1.28
454	460	1.062002	CACTGTTTGAGCGACACGTTT	59.938	47.619	0.00	0.00	0.00	3.60
565	571	1.264288	CCAGTTCACGTGAGCTTTTCC	59.736	52.381	29.44	8.46	33.18	3.13
583	589	6.094186	GCTTTTCCGATGGTCTTCTAGATTTT	59.906	38.462	0.00	0.00	0.00	1.82
801	825	2.849646	GCCGCCCCCTATCCTCTT	60.850	66.667	0.00	0.00	0.00	2.85
874	898	2.435059	GCGTCAGGCCCTCTGTTC	60.435	66.667	0.00	0.00	43.76	3.18
900	925	2.490148	CGAGGCCGAGATGGTAGCA	61.490	63.158	0.00	0.00	41.21	3.49
1001	1026	1.153168	CGTTGAAGGATGGGGCGAT	60.153	57.895	0.00	0.00	0.00	4.58
1032	1057	1.333619	GACTCTTGGAAAAGCAACGCA	59.666	47.619	0.00	0.00	0.00	5.24
1213	1239	1.153745	GACGCCGATGTTGAGCTCT	60.154	57.895	16.19	0.00	0.00	4.09
1309	1348	1.001282	AAGTACTCCTCCTCCTCGGT	58.999	55.000	0.00	0.00	0.00	4.69
1401	1446	4.704833	ATCTGGCAGTGGCGCGTT	62.705	61.111	15.27	0.00	42.47	4.84
1436	1481	1.134401	CGCTGGGATGTACTTGTGGAT	60.134	52.381	0.00	0.00	0.00	3.41
1605	1818	0.846427	AGGGCTCCTGGTCCATGAAA	60.846	55.000	0.00	0.00	43.45	2.69
1677	1897	3.075005	GAGTGGCACTCCGGGCTA	61.075	66.667	32.55	0.00	39.28	3.93
1846	2599	3.998672	GTCCCACGCCTTCACCGA	61.999	66.667	0.00	0.00	0.00	4.69
1852	2605	2.355363	CGCCTTCACCGACGACAA	60.355	61.111	0.00	0.00	0.00	3.18
2012	2765	4.643334	TGGACTACATGATGTACGTAGCTT	59.357	41.667	0.23	0.00	36.84	3.74
2016	2769	7.092137	ACTACATGATGTACGTAGCTTTGTA	57.908	36.000	0.23	0.81	36.84	2.41
2172	2946	3.508845	AAACACTGCCACTACCATTCT	57.491	42.857	0.00	0.00	0.00	2.40
2341	3123	1.115467	GCAAGCACTAGGAGCTCCTA	58.885	55.000	35.03	35.03	46.48	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.188786	GGCCAACTGCTAGCGACG	61.189	66.667	10.77	3.54	40.92	5.12
1	2	2.820037	GGGCCAACTGCTAGCGAC	60.820	66.667	10.77	0.00	40.92	5.19
2	3	2.196997	AATGGGCCAACTGCTAGCGA	62.197	55.000	11.89	0.00	40.92	4.93
3	4	1.750399	AATGGGCCAACTGCTAGCG	60.750	57.895	11.89	7.61	40.92	4.26
4	5	1.669999	CCAATGGGCCAACTGCTAGC	61.670	60.000	11.89	8.10	40.92	3.42
5	6	0.323725	ACCAATGGGCCAACTGCTAG	60.324	55.000	11.89	1.31	40.92	3.42
6	7	0.995803	TACCAATGGGCCAACTGCTA	59.004	50.000	11.89	0.00	40.92	3.49
7	8	0.114168	TTACCAATGGGCCAACTGCT	59.886	50.000	11.89	0.78	40.92	4.24
8	9	0.532115	CTTACCAATGGGCCAACTGC	59.468	55.000	11.89	0.00	37.90	4.40
9	10	0.532115	GCTTACCAATGGGCCAACTG	59.468	55.000	11.89	11.42	37.90	3.16
10	11	0.965363	CGCTTACCAATGGGCCAACT	60.965	55.000	11.89	0.00	37.90	3.16
11	12	0.963355	TCGCTTACCAATGGGCCAAC	60.963	55.000	11.89	0.00	37.90	3.77
12	13	0.963355	GTCGCTTACCAATGGGCCAA	60.963	55.000	11.89	0.00	37.90	4.52
13	14	1.377987	GTCGCTTACCAATGGGCCA	60.378	57.895	9.61	9.61	37.90	5.36
14	15	1.377987	TGTCGCTTACCAATGGGCC	60.378	57.895	3.55	0.00	37.90	5.80
15	16	0.958382	TGTGTCGCTTACCAATGGGC	60.958	55.000	3.55	0.00	37.90	5.36
16	17	0.802494	GTGTGTCGCTTACCAATGGG	59.198	55.000	3.55	0.00	41.29	4.00
17	18	1.808411	AGTGTGTCGCTTACCAATGG	58.192	50.000	0.00	0.00	0.00	3.16
18	19	4.242475	TCTTAGTGTGTCGCTTACCAATG	58.758	43.478	0.00	0.00	0.00	2.82
19	20	4.530710	TCTTAGTGTGTCGCTTACCAAT	57.469	40.909	0.00	0.00	0.00	3.16
20	21	4.325028	TTCTTAGTGTGTCGCTTACCAA	57.675	40.909	0.00	0.00	0.00	3.67
21	22	4.530710	ATTCTTAGTGTGTCGCTTACCA	57.469	40.909	0.00	0.00	0.00	3.25
22	23	5.648572	AGTATTCTTAGTGTGTCGCTTACC	58.351	41.667	0.00	0.00	0.00	2.85
23	24	6.911511	CCTAGTATTCTTAGTGTGTCGCTTAC	59.088	42.308	0.00	0.00	0.00	2.34
24	25	6.459298	GCCTAGTATTCTTAGTGTGTCGCTTA	60.459	42.308	0.00	0.00	0.00	3.09
25	26	5.679127	GCCTAGTATTCTTAGTGTGTCGCTT	60.679	44.000	0.00	0.00	0.00	4.68
26	27	4.202030	GCCTAGTATTCTTAGTGTGTCGCT	60.202	45.833	0.00	0.00	0.00	4.93
27	28	4.043073	GCCTAGTATTCTTAGTGTGTCGC	58.957	47.826	0.00	0.00	0.00	5.19
28	29	4.499357	GGGCCTAGTATTCTTAGTGTGTCG	60.499	50.000	0.84	0.00	0.00	4.35
29	30	4.499357	CGGGCCTAGTATTCTTAGTGTGTC	60.499	50.000	0.84	0.00	0.00	3.67
30	31	3.383825	CGGGCCTAGTATTCTTAGTGTGT	59.616	47.826	0.84	0.00	0.00	3.72
31	32	3.383825	ACGGGCCTAGTATTCTTAGTGTG	59.616	47.826	0.84	0.00	0.00	3.82
32	33	3.639952	ACGGGCCTAGTATTCTTAGTGT	58.360	45.455	0.84	0.00	0.00	3.55
33	34	5.278858	CCTTACGGGCCTAGTATTCTTAGTG	60.279	48.000	0.84	0.00	0.00	2.74
84	85	6.556874	TCATTTTCTCAGGGGTGGTAATTTTT	59.443	34.615	0.00	0.00	0.00	1.94
86	87	5.480422	GTCATTTTCTCAGGGGTGGTAATTT	59.520	40.000	0.00	0.00	0.00	1.82
87	88	5.016831	GTCATTTTCTCAGGGGTGGTAATT	58.983	41.667	0.00	0.00	0.00	1.40
88	89	4.044065	TGTCATTTTCTCAGGGGTGGTAAT	59.956	41.667	0.00	0.00	0.00	1.89
227	232	2.755650	AGGAAACTGACGTGACATGAC	58.244	47.619	0.00	0.00	41.13	3.06
354	360	5.527511	TTTCTAGAGAGAAGTACGTGTCG	57.472	43.478	0.00	0.00	42.66	4.35
425	431	2.869801	CGCTCAAACAGTGTAGGACAAA	59.130	45.455	0.00	0.00	0.00	2.83
435	441	1.365699	AAACGTGTCGCTCAAACAGT	58.634	45.000	0.00	0.00	0.00	3.55
454	460	3.554960	GGATGTACTGCACACACAGAGAA	60.555	47.826	0.00	0.00	40.86	2.87
521	527	3.316868	CCAAGACATATGCATGCATCACA	59.683	43.478	35.35	19.80	37.82	3.58
565	571	3.491267	GCGGAAAATCTAGAAGACCATCG	59.509	47.826	0.00	0.00	0.00	3.84
583	589	3.204119	CCATGCAGCAATCGCGGA	61.204	61.111	6.13	0.00	45.49	5.54
786	810	0.682292	GAGAAAGAGGATAGGGGGCG	59.318	60.000	0.00	0.00	0.00	6.13
794	818	2.820787	CGCCCGTATAGAGAAAGAGGAT	59.179	50.000	0.00	0.00	0.00	3.24
801	825	2.333938	GCGCGCCCGTATAGAGAA	59.666	61.111	23.24	0.00	36.67	2.87
1001	1026	1.215382	CAAGAGTCCGACGGCATCA	59.785	57.895	9.66	0.00	0.00	3.07
1032	1057	2.977178	CGTGCTCTTCCTCTGCCT	59.023	61.111	0.00	0.00	0.00	4.75
1337	1382	1.137825	CTCGACGAACTCCTGGCTC	59.862	63.158	0.00	0.00	0.00	4.70
1415	1460	0.036388	CCACAAGTACATCCCAGCGT	60.036	55.000	0.00	0.00	0.00	5.07
1436	1481	1.304299	TCGTACATCCACCCGTCCA	60.304	57.895	0.00	0.00	0.00	4.02
1578	1791	0.416231	ACCAGGAGCCCTTGTACCTA	59.584	55.000	0.00	0.00	27.08	3.08
1605	1818	0.531090	TGTCGTTGCCGTGCTTAAGT	60.531	50.000	4.02	0.00	35.01	2.24
1846	2599	3.512680	GAGATGAATCGGAAGTTGTCGT	58.487	45.455	0.00	0.00	0.00	4.34
1852	2605	2.472029	AGGTGGAGATGAATCGGAAGT	58.528	47.619	0.00	0.00	0.00	3.01
1952	2705	2.302260	TCGGTGAATTTGGTTTGCAGA	58.698	42.857	0.00	0.00	0.00	4.26
2012	2765	5.367945	ACTCCAGGTTCAGAAACTTACAA	57.632	39.130	0.00	0.00	35.61	2.41
2016	2769	4.236527	ACAACTCCAGGTTCAGAAACTT	57.763	40.909	0.00	0.00	35.74	2.66
2258	3039	1.600636	CACCCACTTGGCGATGTGT	60.601	57.895	12.61	0.00	37.83	3.72
2341	3123	1.302033	CCCGAGCTGCAAGTTGAGT	60.302	57.895	7.16	0.00	35.30	3.41
2508	3290	2.191128	AGGCTTCCAGATGAACACAC	57.809	50.000	0.00	0.00	0.00	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.