AutoCloner

Multiple sequence alignment - TraesCS6A01G266200

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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	TraesCS6A01G266200	chr6A	100.000	1969	0	0	1	1969	491034570	491032602	0.000000e+00	3637.0
1	TraesCS6A01G266200	chr6A	100.000	1264	0	0	2205	3468	491032366	491031103	0.000000e+00	2335.0
2	TraesCS6A01G266200	chr6A	100.000	28	0	0	3294	3321	79706333	79706306	6.000000e-03	52.8
3	TraesCS6A01G266200	chr1A	96.721	1647	30	3	29	1662	61029050	61027415	0.000000e+00	2721.0
4	TraesCS6A01G266200	chr1A	95.800	500	19	2	2205	2704	61026327	61025830	0.000000e+00	806.0
5	TraesCS6A01G266200	chr1A	99.310	145	1	0	1666	1810	61027080	61026936	2.650000e-66	263.0
6	TraesCS6A01G266200	chr1A	97.980	99	2	0	1813	1911	61026739	61026641	4.600000e-39	172.0
7	TraesCS6A01G266200	chr1A	100.000	27	0	0	1905	1931	61026633	61026607	2.200000e-02	51.0
8	TraesCS6A01G266200	chr5A	98.822	1188	14	0	1	1188	650682204	650683391	0.000000e+00	2117.0
9	TraesCS6A01G266200	chr5A	96.267	509	17	2	2205	2713	650684950	650685456	0.000000e+00	833.0
10	TraesCS6A01G266200	chr5A	93.750	432	15	1	1243	1662	650683390	650683821	3.770000e-179	638.0
11	TraesCS6A01G266200	chr5A	84.758	433	51	9	2273	2704	13089205	13089623	1.490000e-113	420.0
12	TraesCS6A01G266200	chr5A	99.310	145	1	0	1666	1810	650684091	650684235	2.650000e-66	263.0
13	TraesCS6A01G266200	chr5A	91.379	174	1	5	1810	1969	650684429	650684602	3.480000e-55	226.0
14	TraesCS6A01G266200	chr5A	91.241	137	12	0	2211	2347	13089096	13089232	1.640000e-43	187.0
15	TraesCS6A01G266200	chr4A	97.573	989	12	2	1	988	589665549	589666526	0.000000e+00	1683.0
16	TraesCS6A01G266200	chr4A	95.865	653	12	2	1025	1662	589666514	589667166	0.000000e+00	1042.0
17	TraesCS6A01G266200	chr4A	96.352	466	13	3	2240	2705	589668518	589668979	0.000000e+00	763.0
18	TraesCS6A01G266200	chr4A	98.621	145	2	0	1666	1810	589667626	589667770	1.230000e-64	257.0
19	TraesCS6A01G266200	chr4A	90.244	164	2	1	1810	1959	589667963	589668126	5.870000e-48	202.0
20	TraesCS6A01G266200	chr4A	77.640	161	24	12	3166	3318	713501735	713501579	1.710000e-13	87.9
21	TraesCS6A01G266200	chr4A	96.875	32	1	0	1376	1407	598588767	598588736	2.000000e-03	54.7
22	TraesCS6A01G266200	chr1B	91.388	778	59	5	569	1343	13517301	13516529	0.000000e+00	1059.0
23	TraesCS6A01G266200	chr1B	92.837	363	23	2	1118	1478	9637647	9638008	1.100000e-144	523.0
24	TraesCS6A01G266200	chr1B	90.184	326	18	6	2384	2708	9639721	9640033	2.490000e-111	412.0
25	TraesCS6A01G266200	chr1B	88.963	299	27	5	1	295	9637355	9637651	7.070000e-97	364.0
26	TraesCS6A01G266200	chr1B	92.437	238	18	0	2205	2442	9639482	9639719	1.190000e-89	340.0
27	TraesCS6A01G266200	chr1B	82.081	346	41	11	2374	2715	403202001	403201673	3.410000e-70	276.0
28	TraesCS6A01G266200	chr1B	90.206	194	5	3	1482	1663	9638302	9638493	1.240000e-59	241.0
29	TraesCS6A01G266200	chr1B	86.782	174	9	5	1810	1969	9639171	9639344	7.650000e-42	182.0
30	TraesCS6A01G266200	chr1B	82.836	134	18	5	1	132	9637127	9637257	7.870000e-22	115.0
31	TraesCS6A01G266200	chr1B	88.298	94	11	0	1	94	9637326	9637419	2.830000e-21	113.0
32	TraesCS6A01G266200	chr1B	76.510	149	26	9	3174	3316	189702628	189702483	4.800000e-09	73.1
33	TraesCS6A01G266200	chr6D	89.111	551	49	10	2926	3468	351955137	351955684	0.000000e+00	675.0
34	TraesCS6A01G266200	chr6D	94.611	167	9	0	2704	2870	351954825	351954991	3.430000e-65	259.0
35	TraesCS6A01G266200	chr2B	84.393	519	40	11	2210	2705	788172894	788172394	4.050000e-129	472.0
36	TraesCS6A01G266200	chr7A	86.499	437	39	11	2273	2705	28837409	28837829	2.440000e-126	462.0
37	TraesCS6A01G266200	chr7A	85.484	434	49	8	2273	2705	28800819	28801239	1.140000e-119	440.0
38	TraesCS6A01G266200	chr7A	90.972	144	11	2	2205	2347	28907371	28907513	3.530000e-45	193.0
39	TraesCS6A01G266200	chr7A	90.972	144	11	2	2205	2347	28948464	28948606	3.530000e-45	193.0
40	TraesCS6A01G266200	chr7A	89.583	144	13	2	2205	2347	28878472	28878614	7.650000e-42	182.0
41	TraesCS6A01G266200	chrUn	86.493	422	43	8	2285	2705	326966736	326966328	5.280000e-123	451.0
42	TraesCS6A01G266200	chrUn	85.484	434	49	8	2273	2705	284058338	284058758	1.140000e-119	440.0
43	TraesCS6A01G266200	chrUn	86.019	422	45	8	2285	2705	284066938	284066530	1.140000e-119	440.0
44	TraesCS6A01G266200	chr3B	91.667	144	10	2	2205	2347	60385548	60385406	7.590000e-47	198.0
45	TraesCS6A01G266200	chr3B	74.847	163	30	9	3161	3316	667721769	667721611	2.890000e-06	63.9
46	TraesCS6A01G266200	chr7D	82.946	129	17	5	6	132	574811134	574811009	1.020000e-20	111.0
47	TraesCS6A01G266200	chr7D	82.171	129	18	5	6	132	557953303	557953428	4.730000e-19	106.0
48	TraesCS6A01G266200	chr4B	84.211	114	16	2	1	113	650588134	650588022	3.660000e-20	110.0
49	TraesCS6A01G266200	chr4B	96.970	33	1	0	2944	2976	68000666	68000698	4.840000e-04	56.5
50	TraesCS6A01G266200	chr4D	79.195	149	25	6	8	153	85834044	85834189	7.920000e-17	99.0
51	TraesCS6A01G266200	chr4D	75.362	207	35	7	1	193	85834095	85834299	6.170000e-13	86.1
52	TraesCS6A01G266200	chr3D	77.124	153	25	10	3170	3317	545812851	545812998	2.870000e-11	80.5

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	TraesCS6A01G266200	chr6A	491031103	491034570	3467	True	2986.00	3637	100.000000	1	3468	2	chr6A.!!$R2	3467
1	TraesCS6A01G266200	chr1A	61025830	61029050	3220	True	802.60	2721	97.962200	29	2704	5	chr1A.!!$R1	2675
2	TraesCS6A01G266200	chr5A	650682204	650685456	3252	False	815.40	2117	95.905600	1	2713	5	chr5A.!!$F2	2712
3	TraesCS6A01G266200	chr5A	13089096	13089623	527	False	303.50	420	87.999500	2211	2704	2	chr5A.!!$F1	493
4	TraesCS6A01G266200	chr4A	589665549	589668979	3430	False	789.40	1683	95.731000	1	2705	5	chr4A.!!$F1	2704
5	TraesCS6A01G266200	chr1B	13516529	13517301	772	True	1059.00	1059	91.388000	569	1343	1	chr1B.!!$R1	774
6	TraesCS6A01G266200	chr1B	9637127	9640033	2906	False	286.25	523	89.067875	1	2708	8	chr1B.!!$F1	2707
7	TraesCS6A01G266200	chr6D	351954825	351955684	859	False	467.00	675	91.861000	2704	3468	2	chr6D.!!$F1	764
8	TraesCS6A01G266200	chr2B	788172394	788172894	500	True	472.00	472	84.393000	2210	2705	1	chr2B.!!$R1	495

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
697	929	0.97401	AAGGCCAGCATCACCAATGG	60.974	55.0	5.01	0.0	35.77	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2472	3916	0.613853	TTCGTCTCAACCCCCGATCT	60.614	55.0	0.0	0.0	0.0	2.75	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
519	750	3.423539	ACTGTAACATCAGTGCACCAT	57.576	42.857	14.63	2.73	45.40	3.55
697	929	0.974010	AAGGCCAGCATCACCAATGG	60.974	55.000	5.01	0.00	35.77	3.16
794	1027	1.081892	ACGTCTAGCAGCAGCAAATG	58.918	50.000	3.17	0.00	45.49	2.32
926	1159	2.307098	GGCTGGGGATAGCACTATTCAT	59.693	50.000	0.00	0.00	45.46	2.57
950	1183	3.756082	ACCATCCCAACCACATGTTAT	57.244	42.857	0.00	0.00	34.69	1.89
1344	1579	2.257371	GCGCGGTAGACACAGTCA	59.743	61.111	8.83	0.00	34.60	3.41
1527	2057	2.041216	GGAAAGGTGGGGTTCAGTACAT	59.959	50.000	0.00	0.00	0.00	2.29
1662	2204	9.809096	TTAACTACAAAATGAAGCACAATCAAA	57.191	25.926	0.00	0.00	0.00	2.69
1663	2205	7.935338	ACTACAAAATGAAGCACAATCAAAG	57.065	32.000	0.00	0.00	0.00	2.77
1664	2206	6.925165	ACTACAAAATGAAGCACAATCAAAGG	59.075	34.615	0.00	0.00	0.00	3.11
1767	2772	4.884247	AGATATCCGTAAAACTGCCTAGC	58.116	43.478	0.00	0.00	0.00	3.42
1811	3010	4.920640	ATACGACATTCCGATTCTGTCT	57.079	40.909	0.00	0.00	37.68	3.41
2472	3916	1.499438	AGTGGATCGGGGATGAGACTA	59.501	52.381	0.00	0.00	0.00	2.59
2500	3944	4.573607	GGGGGTTGAGACGAATAAACATAC	59.426	45.833	0.00	0.00	0.00	2.39
2583	4027	5.426185	TCCCACTAAAATTATGTACCGGTCT	59.574	40.000	12.40	0.00	0.00	3.85
2708	4152	7.655732	GCCAATCACCTTAACAGTTGTAAAAAT	59.344	33.333	0.00	0.00	0.00	1.82
2768	4212	3.492337	TGTAAAATGAGGGTGGTTGGTC	58.508	45.455	0.00	0.00	0.00	4.02
2770	4214	0.251165	AAATGAGGGTGGTTGGTCGG	60.251	55.000	0.00	0.00	0.00	4.79
2781	4225	0.233848	GTTGGTCGGTTACTGCAACG	59.766	55.000	0.00	0.00	38.09	4.10
2823	4267	2.429250	CCGGTTTGAATCCCAAATACCC	59.571	50.000	0.00	0.00	45.48	3.69
2827	4271	5.265989	GGTTTGAATCCCAAATACCCTACA	58.734	41.667	0.00	0.00	45.48	2.74
2864	4308	5.534407	GCGGGTTAAAATCAGAAGGAAAAA	58.466	37.500	0.00	0.00	0.00	1.94
2885	4329	4.839668	AAGATACTGTAGATGAGTCGGC	57.160	45.455	0.00	0.00	0.00	5.54
2886	4330	3.150767	AGATACTGTAGATGAGTCGGCC	58.849	50.000	0.00	0.00	0.00	6.13
2887	4331	1.688772	TACTGTAGATGAGTCGGCCC	58.311	55.000	0.00	0.00	0.00	5.80
2888	4332	0.324368	ACTGTAGATGAGTCGGCCCA	60.324	55.000	0.00	0.00	0.00	5.36
2889	4333	0.387202	CTGTAGATGAGTCGGCCCAG	59.613	60.000	0.00	0.00	0.00	4.45
2896	4340	4.711949	AGTCGGCCCAGCTTGCAG	62.712	66.667	0.00	3.35	0.00	4.41
2904	4348	2.360852	CAGCTTGCAGGAGGGGTG	60.361	66.667	0.00	0.00	0.00	4.61
2905	4349	2.856000	AGCTTGCAGGAGGGGTGT	60.856	61.111	0.00	0.00	0.00	4.16
2906	4350	2.674380	GCTTGCAGGAGGGGTGTG	60.674	66.667	0.00	0.00	0.00	3.82
2907	4351	2.674380	CTTGCAGGAGGGGTGTGC	60.674	66.667	0.00	0.00	37.73	4.57
2961	4509	4.320928	CCTCTCGCTCGCTAGCCG	62.321	72.222	9.66	7.37	46.68	5.52
2973	4521	1.498166	CTAGCCGCCTACTCGATCG	59.502	63.158	9.36	9.36	0.00	3.69
2986	4534	0.745486	TCGATCGTTGACTCCCGCTA	60.745	55.000	15.94	0.00	0.00	4.26
3070	4618	6.619801	AAGAAACTTACAGGTTTGCTACAG	57.380	37.500	0.00	0.00	39.20	2.74
3117	4665	1.202348	GGCCGGATTTTGAGTTCAAGG	59.798	52.381	5.05	0.00	37.15	3.61
3118	4666	2.159382	GCCGGATTTTGAGTTCAAGGA	58.841	47.619	5.05	0.00	37.15	3.36
3121	4669	4.321974	GCCGGATTTTGAGTTCAAGGATTT	60.322	41.667	5.05	0.00	37.15	2.17
3122	4670	5.163513	CCGGATTTTGAGTTCAAGGATTTG	58.836	41.667	0.00	0.00	37.15	2.32
3259	4809	8.945481	TCACAAATTTGAAGAATGTTCATTGT	57.055	26.923	24.64	5.20	32.55	2.71
3269	4819	9.650539	TGAAGAATGTTCATTGTTTTTGAAGAA	57.349	25.926	8.81	0.00	33.95	2.52
3336	4888	9.090692	AGTTCATTTTTCACAAAACTTCATCTG	57.909	29.630	0.00	0.00	34.63	2.90
3408	4963	7.518731	TCACCAATTTTGAAGAAAAAGTTCG	57.481	32.000	0.00	0.00	41.00	3.95
3412	4967	6.237701	CCAATTTTGAAGAAAAAGTTCGCGAA	60.238	34.615	19.38	19.38	41.00	4.70
3415	4970	7.972623	TTTTGAAGAAAAAGTTCGCGAATTA	57.027	28.000	26.23	0.00	38.90	1.40
3416	4971	7.972623	TTTGAAGAAAAAGTTCGCGAATTAA	57.027	28.000	26.23	6.38	38.90	1.40
3424	4979	7.743520	AAAAGTTCGCGAATTAAAAAGTTCA	57.256	28.000	26.23	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	192	3.104512	AGATCGATACTTGTGGGTCCAA	58.895	45.455	0.00	0.00	0.00	3.53
519	750	9.756571	TTTATGCCTAGGTTGTAAATTTCCTAA	57.243	29.630	11.31	0.00	33.03	2.69
697	929	8.874816	GTTTGATTGTATGTCCTCTCTTACTTC	58.125	37.037	0.00	0.00	0.00	3.01
926	1159	2.647299	ACATGTGGTTGGGATGGTTAGA	59.353	45.455	0.00	0.00	0.00	2.10
950	1183	2.293170	TCAAATTGTTGGCACGTCTGA	58.707	42.857	0.00	0.00	35.29	3.27
1066	1299	1.895798	AGTCTCCTTCGTGCATGAAGA	59.104	47.619	38.51	26.15	46.64	2.87
1331	1566	1.166129	TCGAGCTGACTGTGTCTACC	58.834	55.000	0.00	0.00	33.15	3.18
1628	2170	7.461107	GCTTCATTTTGTAGTTAATGACGCTA	58.539	34.615	14.95	0.00	45.24	4.26
1662	2204	3.443681	CAGAACCTTTGTGTTGTGAACCT	59.556	43.478	0.00	0.00	40.80	3.50
1663	2205	3.442273	TCAGAACCTTTGTGTTGTGAACC	59.558	43.478	1.79	0.00	43.14	3.62
1664	2206	4.695217	TCAGAACCTTTGTGTTGTGAAC	57.305	40.909	1.79	0.00	43.14	3.18
1767	2772	4.566004	TCCTTAAACTGGACGTTGATGAG	58.434	43.478	0.00	0.00	35.61	2.90
2268	3593	2.378634	CCTTCCTTGCCGGATCCCT	61.379	63.158	5.05	0.00	42.70	4.20
2472	3916	0.613853	TTCGTCTCAACCCCCGATCT	60.614	55.000	0.00	0.00	0.00	2.75
2500	3944	2.330231	TTGAAAATTTCCGCTCGCAG	57.670	45.000	3.00	0.00	0.00	5.18
2611	4055	5.987953	GGAGTTACGAGGAGTTACAAAACTT	59.012	40.000	0.00	0.00	46.09	2.66
2740	4184	7.257722	CAACCACCCTCATTTTACATGATTAC	58.742	38.462	0.00	0.00	0.00	1.89
2768	4212	2.796031	TCAAAGTACGTTGCAGTAACCG	59.204	45.455	15.67	0.00	35.84	4.44
2770	4214	4.271776	AGGTTCAAAGTACGTTGCAGTAAC	59.728	41.667	15.67	13.76	35.90	2.50
2781	4225	3.059120	GGCGACTTCAAGGTTCAAAGTAC	60.059	47.826	0.00	0.00	33.54	2.73
2823	4267	3.974401	CCCGCGAAAAATTATGCATGTAG	59.026	43.478	8.23	0.00	0.00	2.74
2827	4271	3.518634	AACCCGCGAAAAATTATGCAT	57.481	38.095	8.23	3.79	0.00	3.96
2864	4308	3.570550	GGCCGACTCATCTACAGTATCTT	59.429	47.826	0.00	0.00	0.00	2.40
2870	4314	0.387202	CTGGGCCGACTCATCTACAG	59.613	60.000	0.00	0.00	0.00	2.74
2871	4315	1.676678	GCTGGGCCGACTCATCTACA	61.677	60.000	0.00	0.00	0.00	2.74
2872	4316	1.068250	GCTGGGCCGACTCATCTAC	59.932	63.158	0.00	0.00	0.00	2.59
2873	4317	0.687757	AAGCTGGGCCGACTCATCTA	60.688	55.000	0.00	0.00	0.00	1.98
2875	4319	1.817099	CAAGCTGGGCCGACTCATC	60.817	63.158	0.00	0.00	0.00	2.92
2876	4320	2.270205	CAAGCTGGGCCGACTCAT	59.730	61.111	0.00	0.00	0.00	2.90
2877	4321	4.704833	GCAAGCTGGGCCGACTCA	62.705	66.667	0.00	0.00	0.00	3.41
2878	4322	4.704833	TGCAAGCTGGGCCGACTC	62.705	66.667	8.04	0.00	0.00	3.36
2879	4323	4.711949	CTGCAAGCTGGGCCGACT	62.712	66.667	8.04	0.00	0.00	4.18
2885	4329	4.437587	CCCCTCCTGCAAGCTGGG	62.438	72.222	16.48	10.85	42.30	4.45
2886	4330	3.655211	ACCCCTCCTGCAAGCTGG	61.655	66.667	11.30	11.30	36.53	4.85
2887	4331	2.360852	CACCCCTCCTGCAAGCTG	60.361	66.667	0.00	0.00	0.00	4.24
2888	4332	2.856000	ACACCCCTCCTGCAAGCT	60.856	61.111	0.00	0.00	0.00	3.74
2889	4333	2.674380	CACACCCCTCCTGCAAGC	60.674	66.667	0.00	0.00	0.00	4.01
2905	4349	4.841617	TTGTGGGCAAACGGGGCA	62.842	61.111	0.00	0.00	34.52	5.36
2906	4350	4.293648	GTTGTGGGCAAACGGGGC	62.294	66.667	0.00	0.00	36.22	5.80
2907	4351	3.972276	CGTTGTGGGCAAACGGGG	61.972	66.667	10.38	0.00	36.22	5.73
2909	4353	2.330041	GACGTTGTGGGCAAACGG	59.670	61.111	18.98	6.03	36.22	4.44
2911	4355	2.331019	AAGCGACGTTGTGGGCAAAC	62.331	55.000	4.37	0.00	36.22	2.93
2912	4356	2.115911	AAGCGACGTTGTGGGCAAA	61.116	52.632	4.37	0.00	36.22	3.68
2913	4357	2.515057	AAGCGACGTTGTGGGCAA	60.515	55.556	4.37	0.00	0.00	4.52
2915	4359	4.683334	GCAAGCGACGTTGTGGGC	62.683	66.667	4.37	1.96	0.00	5.36
2961	4509	1.268640	GGAGTCAACGATCGAGTAGGC	60.269	57.143	24.34	9.58	0.00	3.93
2973	4521	1.751924	AGTGATCTAGCGGGAGTCAAC	59.248	52.381	0.00	0.00	0.00	3.18
3054	4602	6.259167	CAGTACAAACTGTAGCAAACCTGTAA	59.741	38.462	0.00	0.00	46.76	2.41
3096	4644	1.202348	CTTGAACTCAAAATCCGGCCC	59.798	52.381	0.00	0.00	35.15	5.80
3100	4648	6.012658	TCAAATCCTTGAACTCAAAATCCG	57.987	37.500	0.00	0.00	38.65	4.18
3138	4686	7.307396	TCAAACGTTGAAGATTTGTTTTGCAAA	60.307	29.630	8.05	8.05	42.79	3.68
3141	4689	6.088719	TCAAACGTTGAAGATTTGTTTTGC	57.911	33.333	0.00	0.00	36.59	3.68
3184	4732	7.784633	TTCAAAATGGTTGAACTTTTCATCC	57.215	32.000	8.50	8.50	45.56	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.