AutoCloner

Multiple sequence alignment - TraesCS6D01G287800

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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	TraesCS6D01G287800	chr6D	100.000	4392	0	0	1	4392	397081345	397085736	0.000000e+00	8111.0
1	TraesCS6D01G287800	chr6A	92.489	3395	113	56	785	4130	543394615	543397916	0.000000e+00	4726.0
2	TraesCS6D01G287800	chr6A	83.942	137	4	6	554	674	543394418	543394552	9.980000e-22	115.0
3	TraesCS6D01G287800	chr6B	94.044	3022	86	33	948	3935	593711879	593714840	0.000000e+00	4497.0
4	TraesCS6D01G287800	chr6B	88.024	835	42	24	145	956	593711049	593711848	0.000000e+00	935.0
5	TraesCS6D01G287800	chr6B	86.070	201	9	6	3919	4100	593714863	593715063	9.640000e-47	198.0
6	TraesCS6D01G287800	chr6B	86.726	113	6	2	4116	4219	593716065	593716177	2.780000e-22	117.0
7	TraesCS6D01G287800	chr6B	97.561	41	1	0	1675	1715	142988907	142988867	2.190000e-08	71.3
8	TraesCS6D01G287800	chr7B	88.503	1122	96	20	993	2095	109702389	109703496	0.000000e+00	1327.0
9	TraesCS6D01G287800	chr7B	87.352	253	32	0	1000	1252	664106997	664107249	1.550000e-74	291.0
10	TraesCS6D01G287800	chr7B	84.490	245	26	3	2246	2490	109703638	109703870	9.500000e-57	231.0
11	TraesCS6D01G287800	chr7B	89.820	167	17	0	2792	2958	109704173	109704339	9.570000e-52	215.0
12	TraesCS6D01G287800	chr7B	94.309	123	7	0	2368	2490	664108620	664108742	5.800000e-44	189.0
13	TraesCS6D01G287800	chr7B	98.837	86	1	0	3158	3243	109704632	109704717	2.120000e-33	154.0
14	TraesCS6D01G287800	chr7D	88.403	1121	99	18	993	2095	146862913	146864020	0.000000e+00	1321.0
15	TraesCS6D01G287800	chr7D	83.209	268	30	6	2246	2512	146864162	146864415	9.500000e-57	231.0
16	TraesCS6D01G287800	chr7D	78.919	370	48	23	2597	2958	146864488	146864835	1.590000e-54	224.0
17	TraesCS6D01G287800	chr7D	94.309	123	7	0	2368	2490	589514301	589514423	5.800000e-44	189.0
18	TraesCS6D01G287800	chr7D	98.837	86	1	0	3158	3243	146865133	146865218	2.120000e-33	154.0
19	TraesCS6D01G287800	chr7A	88.068	1123	102	17	993	2095	148415099	148416209	0.000000e+00	1303.0
20	TraesCS6D01G287800	chr7A	76.944	733	105	39	2246	2958	148416357	148417045	4.180000e-95	359.0
21	TraesCS6D01G287800	chr7A	93.496	123	8	0	2368	2490	681013349	681013227	2.700000e-42	183.0
22	TraesCS6D01G287800	chr7A	98.837	86	1	0	3158	3243	148417339	148417424	2.120000e-33	154.0
23	TraesCS6D01G287800	chr7A	93.243	74	5	0	3321	3394	148417554	148417627	4.640000e-20	110.0
24	TraesCS6D01G287800	chr7A	97.561	41	1	0	1675	1715	637052827	637052787	2.190000e-08	71.3
25	TraesCS6D01G287800	chr4D	81.518	817	125	24	1001	1798	109469594	109470403	0.000000e+00	649.0
26	TraesCS6D01G287800	chr4A	81.341	820	127	22	1001	1801	466941639	466940827	1.030000e-180	643.0
27	TraesCS6D01G287800	chr4B	81.273	817	127	23	1001	1798	170927034	170927843	4.790000e-179	638.0
28	TraesCS6D01G287800	chr3A	90.152	132	13	0	2370	2501	432041807	432041938	5.840000e-39	172.0
29	TraesCS6D01G287800	chr5B	97.561	41	1	0	1675	1715	447194713	447194753	2.190000e-08	71.3
30	TraesCS6D01G287800	chr1B	97.561	41	1	0	1675	1715	269297763	269297723	2.190000e-08	71.3

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	TraesCS6D01G287800	chr6D	397081345	397085736	4391	False	8111.00	8111	100.0000	1	4392	1	chr6D.!!$F1	4391
1	TraesCS6D01G287800	chr6A	543394418	543397916	3498	False	2420.50	4726	88.2155	554	4130	2	chr6A.!!$F1	3576
2	TraesCS6D01G287800	chr6B	593711049	593716177	5128	False	1436.75	4497	88.7160	145	4219	4	chr6B.!!$F1	4074
3	TraesCS6D01G287800	chr7B	109702389	109704717	2328	False	481.75	1327	90.4125	993	3243	4	chr7B.!!$F1	2250
4	TraesCS6D01G287800	chr7B	664106997	664108742	1745	False	240.00	291	90.8305	1000	2490	2	chr7B.!!$F2	1490
5	TraesCS6D01G287800	chr7D	146862913	146865218	2305	False	482.50	1321	87.3420	993	3243	4	chr7D.!!$F2	2250
6	TraesCS6D01G287800	chr7A	148415099	148417627	2528	False	481.50	1303	89.2730	993	3394	4	chr7A.!!$F1	2401
7	TraesCS6D01G287800	chr4D	109469594	109470403	809	False	649.00	649	81.5180	1001	1798	1	chr4D.!!$F1	797
8	TraesCS6D01G287800	chr4A	466940827	466941639	812	True	643.00	643	81.3410	1001	1801	1	chr4A.!!$R1	800
9	TraesCS6D01G287800	chr4B	170927034	170927843	809	False	638.00	638	81.2730	1001	1798	1	chr4B.!!$F1	797

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
19	20	0.120377	TCACCACCCCAGGTAGGATT	59.880	55.000	8.61	0.00	40.77	3.01	F
21	22	0.120377	ACCACCCCAGGTAGGATTGA	59.880	55.000	8.61	0.00	40.98	2.57	F
938	982	0.320247	CGCAAAGAGTGAGCTGAGGT	60.320	55.000	0.00	0.00	0.00	3.85	F
946	991	1.842920	TGAGCTGAGGTCCAAGCCA	60.843	57.895	9.40	7.87	0.00	4.75	F
2344	2721	1.969589	GGCGGACCCGAACAACAAT	60.970	57.895	13.24	0.00	42.83	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1485	1604	2.741092	GTGTCGGGGAACTGCTCA	59.259	61.111	36.33	4.26	R
1557	1679	3.989698	CTCGATGGCGTTGCTCCGT	62.990	63.158	38.98	4.69	R
2517	2951	0.373716	GATTGGTTGGTTAGCGAGCG	59.626	55.000	0.00	5.03	R
2520	2954	0.391927	CCGGATTGGTTGGTTAGCGA	60.392	55.000	0.00	4.93	R
4275	5979	0.041982	GAGAAGACCAGAGGGAGGGT	59.958	60.000	40.96	4.34	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	3.289408	TCACCACCCCAGGTAGGA	58.711	61.111	8.61	0.00	40.77	2.94
18	19	1.794688	TCACCACCCCAGGTAGGAT	59.205	57.895	8.61	0.00	40.77	3.24
19	20	0.120377	TCACCACCCCAGGTAGGATT	59.880	55.000	8.61	0.00	40.77	3.01
20	21	0.255890	CACCACCCCAGGTAGGATTG	59.744	60.000	8.61	0.00	40.77	2.67
21	22	0.120377	ACCACCCCAGGTAGGATTGA	59.880	55.000	8.61	0.00	40.98	2.57
22	23	1.275002	ACCACCCCAGGTAGGATTGAT	60.275	52.381	8.61	0.00	40.98	2.57
23	24	1.852965	CCACCCCAGGTAGGATTGATT	59.147	52.381	0.00	0.00	41.22	2.57
24	25	2.244769	CCACCCCAGGTAGGATTGATTT	59.755	50.000	0.00	0.00	41.22	2.17
25	26	3.461831	CCACCCCAGGTAGGATTGATTTA	59.538	47.826	0.00	0.00	41.22	1.40
26	27	4.079443	CCACCCCAGGTAGGATTGATTTAA	60.079	45.833	0.00	0.00	41.22	1.52
27	28	5.515106	CACCCCAGGTAGGATTGATTTAAA	58.485	41.667	0.00	0.00	41.22	1.52
28	29	5.955355	CACCCCAGGTAGGATTGATTTAAAA	59.045	40.000	0.00	0.00	41.22	1.52
29	30	6.096846	CACCCCAGGTAGGATTGATTTAAAAG	59.903	42.308	0.00	0.00	41.22	2.27
30	31	5.069119	CCCCAGGTAGGATTGATTTAAAAGC	59.931	44.000	0.00	0.00	41.22	3.51
31	32	5.656416	CCCAGGTAGGATTGATTTAAAAGCA	59.344	40.000	0.00	0.00	41.22	3.91
32	33	6.324770	CCCAGGTAGGATTGATTTAAAAGCAT	59.675	38.462	0.00	0.00	41.22	3.79
33	34	7.428826	CCAGGTAGGATTGATTTAAAAGCATC	58.571	38.462	0.00	0.00	41.22	3.91
34	35	7.428826	CAGGTAGGATTGATTTAAAAGCATCC	58.571	38.462	12.10	12.10	0.00	3.51
35	36	6.551227	AGGTAGGATTGATTTAAAAGCATCCC	59.449	38.462	14.76	9.90	30.13	3.85
36	37	5.520376	AGGATTGATTTAAAAGCATCCCG	57.480	39.130	14.76	0.00	30.13	5.14
37	38	4.342092	AGGATTGATTTAAAAGCATCCCGG	59.658	41.667	14.76	0.00	30.13	5.73
38	39	4.099419	GGATTGATTTAAAAGCATCCCGGT	59.901	41.667	0.00	0.00	0.00	5.28
39	40	5.395214	GGATTGATTTAAAAGCATCCCGGTT	60.395	40.000	0.00	0.00	36.73	4.44
41	42	5.066968	TGATTTAAAAGCATCCCGGTTTC	57.933	39.130	0.00	0.00	44.42	2.78
42	43	4.524714	TGATTTAAAAGCATCCCGGTTTCA	59.475	37.500	0.00	0.00	44.42	2.69

Showing 1 to 25 of 258 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.255890	CAATCCTACCTGGGGTGGTG	59.744	60.000	0.00	0.00	41.05	4.17
2	3	0.120377	TCAATCCTACCTGGGGTGGT	59.880	55.000	0.00	0.00	43.66	4.16
4	5	3.669939	AAATCAATCCTACCTGGGGTG	57.330	47.619	0.00	0.00	36.19	4.61
5	6	5.806955	TTTAAATCAATCCTACCTGGGGT	57.193	39.130	0.00	0.00	40.16	4.95
6	7	5.069119	GCTTTTAAATCAATCCTACCTGGGG	59.931	44.000	0.00	0.00	36.20	4.96
7	8	5.656416	TGCTTTTAAATCAATCCTACCTGGG	59.344	40.000	0.00	0.00	36.20	4.45
8	9	6.773976	TGCTTTTAAATCAATCCTACCTGG	57.226	37.500	0.00	0.00	37.10	4.45
9	10	7.428826	GGATGCTTTTAAATCAATCCTACCTG	58.571	38.462	12.82	0.00	0.00	4.00
10	11	6.551227	GGGATGCTTTTAAATCAATCCTACCT	59.449	38.462	16.83	0.00	0.00	3.08
11	12	6.515035	CGGGATGCTTTTAAATCAATCCTACC	60.515	42.308	16.83	0.00	0.00	3.18
12	13	6.438763	CGGGATGCTTTTAAATCAATCCTAC	58.561	40.000	16.83	6.62	0.00	3.18
13	14	5.534654	CCGGGATGCTTTTAAATCAATCCTA	59.465	40.000	16.83	0.00	0.00	2.94
14	15	4.342092	CCGGGATGCTTTTAAATCAATCCT	59.658	41.667	16.83	0.00	0.00	3.24
15	16	4.099419	ACCGGGATGCTTTTAAATCAATCC	59.901	41.667	6.32	12.11	0.00	3.01
16	17	5.262588	ACCGGGATGCTTTTAAATCAATC	57.737	39.130	6.32	0.00	0.00	2.67
17	18	5.675684	AACCGGGATGCTTTTAAATCAAT	57.324	34.783	6.32	0.00	0.00	2.57
18	19	5.011125	TGAAACCGGGATGCTTTTAAATCAA	59.989	36.000	6.32	0.00	0.00	2.57
19	20	4.524714	TGAAACCGGGATGCTTTTAAATCA	59.475	37.500	6.32	0.00	0.00	2.57
20	21	5.066968	TGAAACCGGGATGCTTTTAAATC	57.933	39.130	6.32	0.00	0.00	2.17
21	22	5.675684	ATGAAACCGGGATGCTTTTAAAT	57.324	34.783	6.32	0.00	0.00	1.40
22	23	6.783708	ATATGAAACCGGGATGCTTTTAAA	57.216	33.333	6.32	0.00	0.00	1.52
23	24	6.605594	AGAATATGAAACCGGGATGCTTTTAA	59.394	34.615	6.32	0.00	0.00	1.52
24	25	6.126409	AGAATATGAAACCGGGATGCTTTTA	58.874	36.000	6.32	0.00	0.00	1.52
25	26	4.956075	AGAATATGAAACCGGGATGCTTTT	59.044	37.500	6.32	0.00	0.00	2.27
26	27	4.536765	AGAATATGAAACCGGGATGCTTT	58.463	39.130	6.32	0.00	0.00	3.51

Showing 1 to 25 of 271 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.