AutoCloner

Multiple sequence alignment - TraesCS2D01G183800

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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	TraesCS2D01G183800	chr2D	100.000	3501	0	0	1	3501	129158932	129162432	0.000000e+00	6466
1	TraesCS2D01G183800	chr2D	99.661	295	1	0	3207	3501	129172073	129172367	1.110000e-149	540
2	TraesCS2D01G183800	chr2D	97.403	308	7	1	3194	3501	15758070	15758376	1.110000e-144	523
3	TraesCS2D01G183800	chr2D	92.823	209	9	6	1	206	609381874	609382079	7.350000e-77	298
4	TraesCS2D01G183800	chr2D	98.864	88	1	0	846	933	129159699	129159786	1.300000e-34	158
5	TraesCS2D01G183800	chr2D	98.864	88	1	0	768	855	129159777	129159864	1.300000e-34	158
6	TraesCS2D01G183800	chr2B	93.212	1871	98	9	868	2725	182705794	182707648	0.000000e+00	2724
7	TraesCS2D01G183800	chr2B	94.541	403	22	0	174	576	788187095	788186693	1.070000e-174	623
8	TraesCS2D01G183800	chr2B	97.059	136	3	1	2727	2862	182707878	182708012	9.780000e-56	228
9	TraesCS2D01G183800	chr2A	94.806	1752	70	15	846	2582	136051050	136052795	0.000000e+00	2712
10	TraesCS2D01G183800	chr2A	92.806	278	19	1	578	854	136050859	136051136	5.440000e-108	401
11	TraesCS2D01G183800	chr2A	90.323	155	10	2	2611	2763	136052793	136052944	7.670000e-47	198
12	TraesCS2D01G183800	chr2A	100.000	74	0	0	2789	2862	136052931	136053004	1.690000e-28	137
13	TraesCS2D01G183800	chr4A	96.790	405	13	0	174	578	738866350	738865946	0.000000e+00	676
14	TraesCS2D01G183800	chr5A	95.802	405	17	0	174	578	321019144	321019548	0.000000e+00	654
15	TraesCS2D01G183800	chr5A	88.660	97	11	0	2862	2958	135061063	135061159	6.140000e-23	119
16	TraesCS2D01G183800	chr7A	94.568	405	21	1	174	578	28987854	28988257	2.970000e-175	625
17	TraesCS2D01G183800	chr7A	94.554	404	21	1	174	577	28894283	28894685	1.070000e-174	623
18	TraesCS2D01G183800	chr7A	94.307	404	22	1	174	577	28865382	28865784	4.960000e-173	617
19	TraesCS2D01G183800	chr7A	94.307	404	22	1	174	577	28935359	28935761	4.960000e-173	617
20	TraesCS2D01G183800	chr7A	93.317	404	26	1	174	577	28824253	28824655	2.330000e-166	595
21	TraesCS2D01G183800	chr7B	91.358	405	34	1	174	578	73006416	73006819	1.420000e-153	553
22	TraesCS2D01G183800	chr7B	96.809	188	2	3	1	188	563715224	563715041	9.440000e-81	311
23	TraesCS2D01G183800	chrUn	99.322	295	2	0	3207	3501	225936077	225935783	5.140000e-148	534
24	TraesCS2D01G183800	chrUn	99.322	295	2	0	3207	3501	334232221	334232515	5.140000e-148	534
25	TraesCS2D01G183800	chrUn	99.322	295	2	0	3207	3501	454003203	454003497	5.140000e-148	534
26	TraesCS2D01G183800	chr7D	99.322	295	2	0	3207	3501	89029612	89029318	5.140000e-148	534
27	TraesCS2D01G183800	chr7D	86.930	329	39	4	2882	3208	555178614	555178940	1.990000e-97	366
28	TraesCS2D01G183800	chr7D	95.855	193	5	3	1	190	459401639	459401447	3.390000e-80	309
29	TraesCS2D01G183800	chr7D	90.000	170	15	2	2882	3049	555178408	555178577	5.880000e-53	219
30	TraesCS2D01G183800	chr5D	99.322	295	2	0	3207	3501	312303740	312303446	5.140000e-148	534
31	TraesCS2D01G183800	chr5D	85.227	352	45	5	2862	3208	492607280	492606931	4.300000e-94	355
32	TraesCS2D01G183800	chr5D	95.876	194	5	3	1	192	558547158	558546966	9.440000e-81	311
33	TraesCS2D01G183800	chr3D	99.322	295	2	0	3207	3501	107399693	107399987	5.140000e-148	534
34	TraesCS2D01G183800	chr3D	99.322	295	2	0	3207	3501	108428836	108428542	5.140000e-148	534
35	TraesCS2D01G183800	chr3D	98.343	181	3	0	1	181	474194970	474194790	5.640000e-83	318
36	TraesCS2D01G183800	chr1D	86.610	351	41	4	2861	3208	362605133	362605480	1.970000e-102	383
37	TraesCS2D01G183800	chr1D	97.312	186	3	2	1	185	431001300	431001116	7.290000e-82	315
38	TraesCS2D01G183800	chr1D	96.316	190	4	3	1	189	444976508	444976695	3.390000e-80	309
39	TraesCS2D01G183800	chr6D	97.312	186	3	2	1	184	98211733	98211918	7.290000e-82	315
40	TraesCS2D01G183800	chr4D	94.500	200	6	5	1	196	406018235	406018037	1.580000e-78	303
41	TraesCS2D01G183800	chr4D	92.670	191	13	1	2859	3048	473975828	473976018	1.240000e-69	274
42	TraesCS2D01G183800	chr6B	87.432	183	17	5	2863	3039	4512799	4512617	4.580000e-49	206
43	TraesCS2D01G183800	chr1A	93.103	116	7	1	2864	2978	6422136	6422021	6.010000e-38	169

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	TraesCS2D01G183800	chr2D	129158932	129162432	3500	False	2260.666667	6466	99.242667	1	3501	3	chr2D.!!$F4	3500
1	TraesCS2D01G183800	chr2B	182705794	182708012	2218	False	1476.000000	2724	95.135500	868	2862	2	chr2B.!!$F1	1994
2	TraesCS2D01G183800	chr2A	136050859	136053004	2145	False	862.000000	2712	94.483750	578	2862	4	chr2A.!!$F1	2284
3	TraesCS2D01G183800	chr7D	555178408	555178940	532	False	292.500000	366	88.465000	2882	3208	2	chr7D.!!$F1	326

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
49	50	0.038892	ACGACTACATCAACCGCGTT	60.039	50.0	4.92	0.00	4.84	F
429	430	0.105224	TCTTCGAAGGGCGTGAAACA	59.895	50.0	24.37	41.80	2.83	F
462	463	0.178068	ACAGCCTCGTCAAACACACT	59.822	50.0	0.00	0.00	3.55	F
478	479	0.247736	CACTTTGGGACTCTCTCCGG	59.752	60.0	0.00	40.56	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2020	2045	0.370273	GCTTCGTCATGTACTTGCCG	59.630	55.000	5.90	5.9	0.00	5.69	R
2290	2315	2.125147	ATGGCGACCATGTCCGTG	60.125	61.111	10.09	0.0	43.39	4.94	R
2437	2462	1.248785	CGGGGAAGTCGGTGAAGAGA	61.249	60.000	0.00	0.0	0.00	3.10	R
2527	2552	1.848652	ACCTGTCTGTGGCTACGTAT	58.151	50.000	0.00	0.0	0.00	3.06	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
25	26	3.165559	GATCGGTCGGATCGTGAAG	57.834	57.895	10.85	0.00	42.02	3.02
26	27	0.661552	GATCGGTCGGATCGTGAAGA	59.338	55.000	10.85	0.00	42.02	2.87
27	28	0.381089	ATCGGTCGGATCGTGAAGAC	59.619	55.000	10.85	0.00	0.00	3.01
29	30	1.505353	GGTCGGATCGTGAAGACGT	59.495	57.895	0.00	0.00	46.20	4.34
30	31	0.729116	GGTCGGATCGTGAAGACGTA	59.271	55.000	0.00	0.00	46.20	3.57
31	32	1.530646	GGTCGGATCGTGAAGACGTAC	60.531	57.143	0.00	0.00	46.20	3.67
32	33	0.371301	TCGGATCGTGAAGACGTACG	59.629	55.000	15.01	15.01	46.20	3.67
38	39	2.403259	TCGTGAAGACGTACGACTACA	58.597	47.619	24.41	13.28	46.20	2.74
39	40	2.995939	TCGTGAAGACGTACGACTACAT	59.004	45.455	24.41	6.17	46.20	2.29
40	41	3.061295	TCGTGAAGACGTACGACTACATC	59.939	47.826	24.41	15.62	46.20	3.06
41	42	3.181527	CGTGAAGACGTACGACTACATCA	60.182	47.826	24.41	18.00	42.54	3.07
42	43	4.667415	CGTGAAGACGTACGACTACATCAA	60.667	45.833	24.41	4.49	42.54	2.57
43	44	4.552660	GTGAAGACGTACGACTACATCAAC	59.447	45.833	24.41	11.90	0.00	3.18
44	45	3.754188	AGACGTACGACTACATCAACC	57.246	47.619	24.41	0.00	0.00	3.77
45	46	2.094894	AGACGTACGACTACATCAACCG	59.905	50.000	24.41	0.00	0.00	4.44
46	47	1.186030	CGTACGACTACATCAACCGC	58.814	55.000	10.44	0.00	0.00	5.68
47	48	1.186030	GTACGACTACATCAACCGCG	58.814	55.000	0.00	0.00	0.00	6.46
48	49	0.804364	TACGACTACATCAACCGCGT	59.196	50.000	4.92	0.00	0.00	6.01
49	50	0.038892	ACGACTACATCAACCGCGTT	60.039	50.000	4.92	0.00	0.00	4.84
50	51	0.365523	CGACTACATCAACCGCGTTG	59.634	55.000	4.92	10.14	43.99	4.10
51	52	1.425412	GACTACATCAACCGCGTTGT	58.575	50.000	16.97	9.99	43.23	3.32
52	53	1.126113	GACTACATCAACCGCGTTGTG	59.874	52.381	16.97	15.92	43.23	3.33
53	54	0.179225	CTACATCAACCGCGTTGTGC	60.179	55.000	16.97	0.00	43.23	4.57
54	55	0.601576	TACATCAACCGCGTTGTGCT	60.602	50.000	16.97	6.88	43.23	4.40
55	56	0.601576	ACATCAACCGCGTTGTGCTA	60.602	50.000	16.97	3.28	43.23	3.49

Showing 1 to 25 of 678 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.334779	CGATCCGACCGATCAAGTACC	60.335	57.143	4.93	0.00	46.85	3.34
1	2	1.332997	ACGATCCGACCGATCAAGTAC	59.667	52.381	0.00	0.00	46.85	2.73
2	3	1.332686	CACGATCCGACCGATCAAGTA	59.667	52.381	0.00	0.00	46.85	2.24
3	4	0.100682	CACGATCCGACCGATCAAGT	59.899	55.000	0.00	0.00	46.85	3.16
4	5	0.380733	TCACGATCCGACCGATCAAG	59.619	55.000	0.00	0.00	46.85	3.02
5	6	0.812549	TTCACGATCCGACCGATCAA	59.187	50.000	0.00	0.00	46.85	2.57
6	7	0.380733	CTTCACGATCCGACCGATCA	59.619	55.000	0.00	0.00	46.85	2.92
7	8	0.661552	TCTTCACGATCCGACCGATC	59.338	55.000	0.00	0.00	43.58	3.69
8	9	0.381089	GTCTTCACGATCCGACCGAT	59.619	55.000	0.00	0.00	0.00	4.18
9	10	1.798735	GTCTTCACGATCCGACCGA	59.201	57.895	0.00	0.00	0.00	4.69
10	11	4.379221	GTCTTCACGATCCGACCG	57.621	61.111	0.00	0.00	0.00	4.79
20	21	4.332186	TGATGTAGTCGTACGTCTTCAC	57.668	45.455	19.61	13.19	43.23	3.18
21	22	4.378770	GGTTGATGTAGTCGTACGTCTTCA	60.379	45.833	19.61	19.79	43.23	3.02
22	23	4.094212	GGTTGATGTAGTCGTACGTCTTC	58.906	47.826	19.61	15.02	43.23	2.87
23	24	3.425359	CGGTTGATGTAGTCGTACGTCTT	60.425	47.826	19.61	2.66	43.23	3.01
24	25	2.094894	CGGTTGATGTAGTCGTACGTCT	59.905	50.000	18.54	18.54	43.23	4.18
25	26	2.434761	CGGTTGATGTAGTCGTACGTC	58.565	52.381	16.05	10.06	43.16	4.34
26	27	1.466360	GCGGTTGATGTAGTCGTACGT	60.466	52.381	16.05	0.00	30.95	3.57
27	28	1.186030	GCGGTTGATGTAGTCGTACG	58.814	55.000	9.53	9.53	30.95	3.67
28	29	1.186030	CGCGGTTGATGTAGTCGTAC	58.814	55.000	0.00	0.00	0.00	3.67
29	30	0.804364	ACGCGGTTGATGTAGTCGTA	59.196	50.000	12.47	0.00	0.00	3.43
30	31	0.038892	AACGCGGTTGATGTAGTCGT	60.039	50.000	12.47	0.00	0.00	4.34
31	32	0.365523	CAACGCGGTTGATGTAGTCG	59.634	55.000	12.47	0.00	45.28	4.18
32	33	1.126113	CACAACGCGGTTGATGTAGTC	59.874	52.381	22.26	0.00	45.28	2.59
33	34	1.144969	CACAACGCGGTTGATGTAGT	58.855	50.000	22.26	2.04	45.28	2.73

Showing 1 to 25 of 743 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.