AutoCloner

Multiple sequence alignment - TraesCS2D01G164900

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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	TraesCS2D01G164900	chr2D	100.000	3118	0	0	1	3118	109128693	109131810	0.000000e+00	5758.0
1	TraesCS2D01G164900	chr2D	92.271	2122	155	9	998	3118	109031209	109033322	0.000000e+00	3001.0
2	TraesCS2D01G164900	chr2D	90.270	1223	109	10	994	2210	109554725	109555943	0.000000e+00	1591.0
3	TraesCS2D01G164900	chr2D	78.822	798	167	2	1125	1921	28965635	28966431	1.270000e-148	536.0
4	TraesCS2D01G164900	chr2D	73.987	765	175	23	2354	3107	506088812	506089563	3.930000e-74	289.0
5	TraesCS2D01G164900	chr2D	81.757	296	22	16	34	319	109554132	109553859	5.240000e-53	219.0
6	TraesCS2D01G164900	chr2D	87.786	131	9	2	2233	2356	109577446	109577576	2.510000e-31	147.0
7	TraesCS2D01G164900	chr2D	88.506	87	10	0	909	995	498531669	498531755	4.250000e-19	106.0
8	TraesCS2D01G164900	chr2B	89.197	1370	116	13	1004	2356	159098897	159100251	0.000000e+00	1681.0
9	TraesCS2D01G164900	chr2B	93.659	552	34	1	1529	2080	158869145	158869695	0.000000e+00	824.0
10	TraesCS2D01G164900	chr2B	93.657	536	33	1	998	1533	158864070	158864604	0.000000e+00	800.0
11	TraesCS2D01G164900	chr2B	93.709	302	9	8	34	332	158863502	158863208	7.930000e-121	444.0
12	TraesCS2D01G164900	chr2B	86.557	305	12	9	1	301	159098379	159098100	3.020000e-80	309.0
13	TraesCS2D01G164900	chr2B	100.000	32	0	0	1	32	158863557	158863526	3.360000e-05	60.2
14	TraesCS2D01G164900	chr2A	91.101	1090	82	4	998	2081	105407878	105408958	0.000000e+00	1461.0
15	TraesCS2D01G164900	chr2A	86.550	684	91	1	2436	3118	769472079	769471396	0.000000e+00	752.0
16	TraesCS2D01G164900	chr2A	79.000	800	166	2	1125	1923	30865296	30866094	2.110000e-151	545.0
17	TraesCS2D01G164900	chr7D	92.826	683	39	8	333	1006	529432467	529431786	0.000000e+00	981.0
18	TraesCS2D01G164900	chr7D	77.285	766	155	15	1125	1882	48356459	48357213	1.720000e-117	433.0
19	TraesCS2D01G164900	chr5B	91.716	676	44	7	332	1000	166586182	166585512	0.000000e+00	928.0
20	TraesCS2D01G164900	chr5B	90.103	677	43	10	332	1001	166590937	166590278	0.000000e+00	857.0
21	TraesCS2D01G164900	chr3A	84.915	769	113	3	2352	3118	705581792	705581025	0.000000e+00	774.0
22	TraesCS2D01G164900	chr3A	78.325	406	75	12	2718	3116	163189561	163189162	1.860000e-62	250.0
23	TraesCS2D01G164900	chr3A	81.633	245	44	1	998	1242	31962436	31962193	5.270000e-48	202.0
24	TraesCS2D01G164900	chr3A	84.946	93	14	0	909	1001	701141356	701141264	9.210000e-16	95.3
25	TraesCS2D01G164900	chr3A	84.091	88	14	0	909	996	696202506	696202419	5.540000e-13	86.1
26	TraesCS2D01G164900	chr7A	84.383	762	114	4	2358	3118	243485173	243484416	0.000000e+00	743.0
27	TraesCS2D01G164900	chr7B	83.963	767	119	4	2354	3118	587957126	587956362	0.000000e+00	732.0
28	TraesCS2D01G164900	chr3B	80.676	947	162	9	998	1943	39452328	39453254	0.000000e+00	715.0
29	TraesCS2D01G164900	chr3B	88.889	423	47	0	2696	3118	63456486	63456064	3.560000e-144	521.0
30	TraesCS2D01G164900	chr6A	83.175	737	120	4	2383	3118	59791451	59790718	0.000000e+00	671.0
31	TraesCS2D01G164900	chr3D	87.972	424	50	1	2406	2828	3400147	3399724	1.670000e-137	499.0
32	TraesCS2D01G164900	chr3D	73.810	420	83	24	2358	2763	610599612	610600018	1.170000e-29	141.0
33	TraesCS2D01G164900	chrUn	78.117	393	82	3	1506	1896	17076110	17075720	2.400000e-61	246.0
34	TraesCS2D01G164900	chr5D	87.368	95	10	2	909	1002	482763259	482763352	1.180000e-19	108.0
35	TraesCS2D01G164900	chr5D	82.883	111	14	5	2355	2462	458770905	458771013	9.210000e-16	95.3
36	TraesCS2D01G164900	chr4D	87.234	94	12	0	909	1002	366976993	366977086	1.180000e-19	108.0
37	TraesCS2D01G164900	chr4D	77.895	95	19	2	909	1002	486920941	486921034	1.210000e-04	58.4
38	TraesCS2D01G164900	chr4A	82.569	109	17	2	2355	2462	58916414	58916307	9.210000e-16	95.3
39	TraesCS2D01G164900	chr6D	95.000	40	2	0	2369	2408	24368776	24368737	2.600000e-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	TraesCS2D01G164900	chr2D	109128693	109131810	3117	False	5758	5758	100.000	1	3118	1	chr2D.!!$F3	3117
1	TraesCS2D01G164900	chr2D	109031209	109033322	2113	False	3001	3001	92.271	998	3118	1	chr2D.!!$F2	2120
2	TraesCS2D01G164900	chr2D	109554725	109555943	1218	False	1591	1591	90.270	994	2210	1	chr2D.!!$F4	1216
3	TraesCS2D01G164900	chr2D	28965635	28966431	796	False	536	536	78.822	1125	1921	1	chr2D.!!$F1	796
4	TraesCS2D01G164900	chr2D	506088812	506089563	751	False	289	289	73.987	2354	3107	1	chr2D.!!$F7	753
5	TraesCS2D01G164900	chr2B	159098897	159100251	1354	False	1681	1681	89.197	1004	2356	1	chr2B.!!$F3	1352
6	TraesCS2D01G164900	chr2B	158869145	158869695	550	False	824	824	93.659	1529	2080	1	chr2B.!!$F2	551
7	TraesCS2D01G164900	chr2B	158864070	158864604	534	False	800	800	93.657	998	1533	1	chr2B.!!$F1	535
8	TraesCS2D01G164900	chr2A	105407878	105408958	1080	False	1461	1461	91.101	998	2081	1	chr2A.!!$F2	1083
9	TraesCS2D01G164900	chr2A	769471396	769472079	683	True	752	752	86.550	2436	3118	1	chr2A.!!$R1	682
10	TraesCS2D01G164900	chr2A	30865296	30866094	798	False	545	545	79.000	1125	1923	1	chr2A.!!$F1	798
11	TraesCS2D01G164900	chr7D	529431786	529432467	681	True	981	981	92.826	333	1006	1	chr7D.!!$R1	673
12	TraesCS2D01G164900	chr7D	48356459	48357213	754	False	433	433	77.285	1125	1882	1	chr7D.!!$F1	757
13	TraesCS2D01G164900	chr5B	166585512	166586182	670	True	928	928	91.716	332	1000	1	chr5B.!!$R1	668
14	TraesCS2D01G164900	chr5B	166590278	166590937	659	True	857	857	90.103	332	1001	1	chr5B.!!$R2	669
15	TraesCS2D01G164900	chr3A	705581025	705581792	767	True	774	774	84.915	2352	3118	1	chr3A.!!$R5	766
16	TraesCS2D01G164900	chr7A	243484416	243485173	757	True	743	743	84.383	2358	3118	1	chr7A.!!$R1	760
17	TraesCS2D01G164900	chr7B	587956362	587957126	764	True	732	732	83.963	2354	3118	1	chr7B.!!$R1	764
18	TraesCS2D01G164900	chr3B	39452328	39453254	926	False	715	715	80.676	998	1943	1	chr3B.!!$F1	945
19	TraesCS2D01G164900	chr6A	59790718	59791451	733	True	671	671	83.175	2383	3118	1	chr6A.!!$R1	735

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
61	62	0.030773	GTGTGTGAGTGAGACAGCGA	59.969	55.0	0.00	0.0	0.0	4.93	F
222	223	0.036388	GAACTCCAATCTGCCACCGA	60.036	55.0	0.00	0.0	0.0	4.69	F
1504	1520	0.108585	GCCTGAGCCGGATTTGGATA	59.891	55.0	5.05	0.0	0.0	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1754	1770	0.173708	CTCTACCACCTCCTTGTCGC	59.826	60.0	0.00	0.0	0.00	5.19	R
2104	2133	0.166161	GCCTCCGCGAAAAAGAAGTC	59.834	55.0	8.23	0.0	0.00	3.01	R
2462	2511	0.179076	TACGAGGACACGCCGATCTA	60.179	55.0	0.00	0.0	43.43	1.98	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
19	20	2.919666	GATCGGTGGTGTGGATTTTG	57.080	50.000	0.00	0.00	0.00	2.44
20	21	1.472480	GATCGGTGGTGTGGATTTTGG	59.528	52.381	0.00	0.00	0.00	3.28
21	22	0.474614	TCGGTGGTGTGGATTTTGGA	59.525	50.000	0.00	0.00	0.00	3.53
22	23	0.596082	CGGTGGTGTGGATTTTGGAC	59.404	55.000	0.00	0.00	0.00	4.02
23	24	0.596082	GGTGGTGTGGATTTTGGACG	59.404	55.000	0.00	0.00	0.00	4.79
24	25	1.314730	GTGGTGTGGATTTTGGACGT	58.685	50.000	0.00	0.00	0.00	4.34
25	26	1.679153	GTGGTGTGGATTTTGGACGTT	59.321	47.619	0.00	0.00	0.00	3.99
26	27	2.100087	GTGGTGTGGATTTTGGACGTTT	59.900	45.455	0.00	0.00	0.00	3.60
27	28	2.099921	TGGTGTGGATTTTGGACGTTTG	59.900	45.455	0.00	0.00	0.00	2.93
28	29	2.544903	GGTGTGGATTTTGGACGTTTGG	60.545	50.000	0.00	0.00	0.00	3.28
29	30	2.359531	GTGTGGATTTTGGACGTTTGGA	59.640	45.455	0.00	0.00	0.00	3.53
30	31	3.024547	TGTGGATTTTGGACGTTTGGAA	58.975	40.909	0.00	0.00	0.00	3.53
31	32	3.639094	TGTGGATTTTGGACGTTTGGAAT	59.361	39.130	0.00	0.00	0.00	3.01
32	33	4.827835	TGTGGATTTTGGACGTTTGGAATA	59.172	37.500	0.00	0.00	0.00	1.75
33	34	5.478679	TGTGGATTTTGGACGTTTGGAATAT	59.521	36.000	0.00	0.00	0.00	1.28
34	35	5.804979	GTGGATTTTGGACGTTTGGAATATG	59.195	40.000	0.00	0.00	0.00	1.78
35	36	5.478679	TGGATTTTGGACGTTTGGAATATGT	59.521	36.000	0.00	0.00	0.00	2.29
36	37	5.804979	GGATTTTGGACGTTTGGAATATGTG	59.195	40.000	0.00	0.00	0.00	3.21
37	38	5.776173	TTTTGGACGTTTGGAATATGTGT	57.224	34.783	0.00	0.00	0.00	3.72
38	39	4.757799	TTGGACGTTTGGAATATGTGTG	57.242	40.909	0.00	0.00	0.00	3.82
39	40	3.745799	TGGACGTTTGGAATATGTGTGT	58.254	40.909	0.00	0.00	0.00	3.72
40	41	3.500299	TGGACGTTTGGAATATGTGTGTG	59.500	43.478	0.00	0.00	0.00	3.82
41	42	3.500680	GGACGTTTGGAATATGTGTGTGT	59.499	43.478	0.00	0.00	0.00	3.72
42	43	4.463209	GACGTTTGGAATATGTGTGTGTG	58.537	43.478	0.00	0.00	0.00	3.82
43	44	3.880490	ACGTTTGGAATATGTGTGTGTGT	59.120	39.130	0.00	0.00	0.00	3.72

Showing 1 to 25 of 326 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	0.596082	GTCCAAAATCCACACCACCG	59.404	55.000	0.00	0.00	0.00	4.94
5	6	1.314730	ACGTCCAAAATCCACACCAC	58.685	50.000	0.00	0.00	0.00	4.16
7	8	2.544903	CCAAACGTCCAAAATCCACACC	60.545	50.000	0.00	0.00	0.00	4.16
8	9	2.359531	TCCAAACGTCCAAAATCCACAC	59.640	45.455	0.00	0.00	0.00	3.82
10	11	3.719173	TTCCAAACGTCCAAAATCCAC	57.281	42.857	0.00	0.00	0.00	4.02
12	13	5.804979	CACATATTCCAAACGTCCAAAATCC	59.195	40.000	0.00	0.00	0.00	3.01
13	14	6.307800	CACACATATTCCAAACGTCCAAAATC	59.692	38.462	0.00	0.00	0.00	2.17
14	15	6.155827	CACACATATTCCAAACGTCCAAAAT	58.844	36.000	0.00	0.00	0.00	1.82
15	16	5.067936	ACACACATATTCCAAACGTCCAAAA	59.932	36.000	0.00	0.00	0.00	2.44
16	17	4.580995	ACACACATATTCCAAACGTCCAAA	59.419	37.500	0.00	0.00	0.00	3.28
17	18	4.023622	CACACACATATTCCAAACGTCCAA	60.024	41.667	0.00	0.00	0.00	3.53
18	19	3.500299	CACACACATATTCCAAACGTCCA	59.500	43.478	0.00	0.00	0.00	4.02
19	20	3.500680	ACACACACATATTCCAAACGTCC	59.499	43.478	0.00	0.00	0.00	4.79
20	21	4.024387	ACACACACACATATTCCAAACGTC	60.024	41.667	0.00	0.00	0.00	4.34
21	22	3.880490	ACACACACACATATTCCAAACGT	59.120	39.130	0.00	0.00	0.00	3.99
22	23	4.218265	CACACACACACATATTCCAAACG	58.782	43.478	0.00	0.00	0.00	3.60
23	24	4.975502	CACACACACACACATATTCCAAAC	59.024	41.667	0.00	0.00	0.00	2.93
24	25	4.642437	ACACACACACACACATATTCCAAA	59.358	37.500	0.00	0.00	0.00	3.28
25	26	4.036144	CACACACACACACACATATTCCAA	59.964	41.667	0.00	0.00	0.00	3.53
26	27	3.563390	CACACACACACACACATATTCCA	59.437	43.478	0.00	0.00	0.00	3.53
27	28	3.812609	TCACACACACACACACATATTCC	59.187	43.478	0.00	0.00	0.00	3.01
28	29	4.511454	ACTCACACACACACACACATATTC	59.489	41.667	0.00	0.00	0.00	1.75
29	30	4.273235	CACTCACACACACACACACATATT	59.727	41.667	0.00	0.00	0.00	1.28
30	31	3.809279	CACTCACACACACACACACATAT	59.191	43.478	0.00	0.00	0.00	1.78
31	32	3.118956	TCACTCACACACACACACACATA	60.119	43.478	0.00	0.00	0.00	2.29

Showing 1 to 25 of 334 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.