AutoCloner

Multiple sequence alignment - TraesCS2B01G131500

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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	TraesCS2B01G131500	chr2B	100.000	3804	0	0	1	3804	98293487	98297290	0.000000e+00	7025.0
1	TraesCS2B01G131500	chr2B	100.000	3046	0	0	4000	7045	98297486	98300531	0.000000e+00	5626.0
2	TraesCS2B01G131500	chr2B	88.482	191	19	3	2171	2358	98295612	98295802	1.980000e-55	228.0
3	TraesCS2B01G131500	chr2B	88.482	191	19	3	2126	2316	98295657	98295844	1.980000e-55	228.0
4	TraesCS2B01G131500	chr2B	80.435	276	50	3	6566	6838	790374604	790374330	2.580000e-49	207.0
5	TraesCS2B01G131500	chr2B	83.851	161	23	3	6884	7043	120187440	120187598	4.400000e-32	150.0
6	TraesCS2B01G131500	chr2B	95.890	73	3	0	6836	6908	98300282	98300354	1.240000e-22	119.0
7	TraesCS2B01G131500	chr2D	92.443	3864	184	40	1	3804	62591212	62595027	0.000000e+00	5419.0
8	TraesCS2B01G131500	chr2D	92.323	1511	67	20	4251	5740	62595214	62596696	0.000000e+00	2102.0
9	TraesCS2B01G131500	chr2D	89.878	573	21	13	5765	6320	62596694	62597246	0.000000e+00	702.0
10	TraesCS2B01G131500	chr2D	87.435	191	21	3	2171	2358	62593309	62593499	4.280000e-52	217.0
11	TraesCS2B01G131500	chr2D	84.242	165	24	2	6880	7043	429043325	429043162	7.310000e-35	159.0
12	TraesCS2B01G131500	chr2D	83.929	168	21	6	6876	7040	513025582	513025746	9.460000e-34	156.0
13	TraesCS2B01G131500	chr2D	90.217	92	7	2	6324	6415	62599381	62599470	1.240000e-22	119.0
14	TraesCS2B01G131500	chr2D	97.436	39	1	0	6840	6878	289156826	289156864	4.560000e-07	67.6
15	TraesCS2B01G131500	chr2D	94.737	38	2	0	6841	6878	32344290	32344327	7.630000e-05	60.2
16	TraesCS2B01G131500	chr2A	92.917	1906	82	16	4033	5897	63691673	63693566	0.000000e+00	2723.0
17	TraesCS2B01G131500	chr2A	94.041	1460	69	11	2171	3617	63689991	63691445	0.000000e+00	2198.0
18	TraesCS2B01G131500	chr2A	88.024	1645	101	33	1	1593	63688032	63689632	0.000000e+00	1858.0
19	TraesCS2B01G131500	chr2A	92.153	548	39	4	1778	2325	63689644	63690187	0.000000e+00	771.0
20	TraesCS2B01G131500	chr2A	98.140	215	4	0	5896	6110	63693672	63693886	6.670000e-100	375.0
21	TraesCS2B01G131500	chr2A	91.943	211	14	2	6115	6323	63693980	63694189	6.910000e-75	292.0
22	TraesCS2B01G131500	chr2A	82.671	277	42	4	6566	6838	553049697	553049423	2.540000e-59	241.0
23	TraesCS2B01G131500	chr2A	86.585	164	8	4	3642	3804	63691509	63691659	1.220000e-37	169.0
24	TraesCS2B01G131500	chr2A	87.671	146	15	3	2216	2358	63689991	63690136	4.370000e-37	167.0
25	TraesCS2B01G131500	chr4A	83.067	626	85	19	2993	3605	712964334	712963717	3.710000e-152	549.0
26	TraesCS2B01G131500	chr4A	85.714	182	21	4	3413	3593	712957728	712957551	3.360000e-43	187.0
27	TraesCS2B01G131500	chr7A	86.266	466	55	9	3155	3617	20400124	20399665	1.360000e-136	497.0
28	TraesCS2B01G131500	chr7A	88.406	69	8	0	1947	2015	20401211	20401143	4.530000e-12	84.2
29	TraesCS2B01G131500	chr7A	90.698	43	4	0	6836	6878	475591768	475591810	2.740000e-04	58.4
30	TraesCS2B01G131500	chr3A	83.273	275	44	1	6566	6838	158163338	158163612	1.170000e-62	252.0
31	TraesCS2B01G131500	chr3A	79.783	277	48	7	6566	6838	643213390	643213662	2.010000e-45	195.0
32	TraesCS2B01G131500	chr3A	97.619	42	1	0	6837	6878	25386097	25386138	9.800000e-09	73.1
33	TraesCS2B01G131500	chr6D	81.091	275	50	1	6566	6838	82194214	82193940	1.190000e-52	219.0
34	TraesCS2B01G131500	chr6D	83.815	173	22	6	6876	7045	323008495	323008664	7.310000e-35	159.0
35	TraesCS2B01G131500	chr6D	83.636	165	25	2	6880	7043	144144459	144144296	3.400000e-33	154.0
36	TraesCS2B01G131500	chr5B	81.203	266	48	2	6567	6830	163258190	163258455	5.540000e-51	213.0
37	TraesCS2B01G131500	chr1B	81.679	262	42	5	6571	6828	110121262	110121521	5.540000e-51	213.0
38	TraesCS2B01G131500	chr1B	73.923	418	76	19	6446	6834	668508009	668508422	3.430000e-28	137.0
39	TraesCS2B01G131500	chr1B	100.000	28	0	0	194	221	596325900	596325927	1.300000e-02	52.8
40	TraesCS2B01G131500	chr5A	76.322	435	77	12	6425	6835	305560600	305561032	7.160000e-50	209.0
41	TraesCS2B01G131500	chr5A	96.970	33	1	0	6836	6868	596037474	596037442	1.000000e-03	56.5
42	TraesCS2B01G131500	chr3B	82.041	245	41	2	6596	6838	202379376	202379619	9.260000e-49	206.0
43	TraesCS2B01G131500	chr3B	75.935	428	82	18	6426	6835	666805303	666805727	4.310000e-47	200.0
44	TraesCS2B01G131500	chr3B	80.090	221	42	1	6618	6836	78654846	78655066	5.650000e-36	163.0
45	TraesCS2B01G131500	chr7D	80.072	276	51	3	6566	6838	41930009	41930283	1.200000e-47	202.0
46	TraesCS2B01G131500	chr7D	96.970	33	0	1	6841	6873	46885706	46885737	4.000000e-03	54.7
47	TraesCS2B01G131500	chr5D	75.223	448	69	22	6424	6838	227735857	227736295	2.610000e-39	174.0
48	TraesCS2B01G131500	chr5D	84.146	164	24	2	6881	7043	92120444	92120606	2.630000e-34	158.0
49	TraesCS2B01G131500	chr3D	84.146	164	24	2	6881	7043	407210053	407209891	2.630000e-34	158.0
50	TraesCS2B01G131500	chr3D	100.000	28	0	0	194	221	480955140	480955113	1.300000e-02	52.8
51	TraesCS2B01G131500	chr1D	84.146	164	24	2	6881	7043	290704703	290704541	2.630000e-34	158.0
52	TraesCS2B01G131500	chr4B	82.840	169	25	4	6876	7042	575046183	575046349	1.580000e-31	148.0
53	TraesCS2B01G131500	chr7B	92.857	42	3	0	6837	6878	428043727	428043768	2.120000e-05	62.1
54	TraesCS2B01G131500	chr4D	93.023	43	2	1	6836	6878	477407910	477407869	2.120000e-05	62.1

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	TraesCS2B01G131500	chr2B	98293487	98300531	7044	False	2645.200	7025	94.57080	1	7045	5	chr2B.!!$F2	7044
1	TraesCS2B01G131500	chr2D	62591212	62599470	8258	False	1711.800	5419	90.45920	1	6415	5	chr2D.!!$F4	6414
2	TraesCS2B01G131500	chr2A	63688032	63694189	6157	False	1069.125	2723	91.43425	1	6323	8	chr2A.!!$F1	6322
3	TraesCS2B01G131500	chr4A	712963717	712964334	617	True	549.000	549	83.06700	2993	3605	1	chr4A.!!$R2	612
4	TraesCS2B01G131500	chr7A	20399665	20401211	1546	True	290.600	497	87.33600	1947	3617	2	chr7A.!!$R1	1670

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
885	900	0.164217	GTCTATCGTAGCTCTCGCGG	59.836	60.000	6.13	0.00	42.32	6.46	F
1793	1851	0.035317	TTGCTGATGTGCGGTCTCTT	59.965	50.000	0.00	0.00	35.36	2.85	F
2521	2601	0.465460	TGCGCAGAGGGTTGAAGTTT	60.465	50.000	5.66	0.00	0.00	2.66	F
3618	3895	0.394762	TGATTGCTGGATGGTCTGGC	60.395	55.000	0.00	0.00	0.00	4.85	F
3638	3924	0.685097	TAGGGCAAAACGCTGAGACT	59.315	50.000	0.00	0.00	42.48	3.24	F
5194	5532	1.003349	CCATGGGAAAGGCATTTGCAA	59.997	47.619	17.08	6.26	44.36	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2132	2199	0.184692	TGTTGGTTCATCAGTGGGCA	59.815	50.000	0.00	0.00	0.00	5.36	R
3286	3562	0.251354	AGCAGCCGAAGACATCATGT	59.749	50.000	0.00	0.00	0.00	3.21	R
4131	4458	0.172352	GCCTCTCTGTTCCGTCTCTG	59.828	60.000	0.00	0.00	0.00	3.35	R
5197	5535	0.443869	GCTCATCGACAAATGCGTGT	59.556	50.000	0.00	0.00	0.00	4.49	R
5531	5877	1.270732	GCTGCCTGGGATACTGATCAG	60.271	57.143	21.37	21.37	33.27	2.90	R
6643	9348	0.034896	GGACGAAGACAAGGCCAAGA	59.965	55.000	5.01	0.00	35.06	3.02	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
273	277	4.456222	TGTTCAGGTGTTTCAGAAAAACGA	59.544	37.500	9.70	0.81	33.05	3.85
328	335	9.128107	AGATTAAACAACGTTTGCATAATTGAG	57.872	29.630	0.00	0.00	29.95	3.02
487	496	8.701908	ATAGGATTCATAAAATGCATGTGACT	57.298	30.769	0.00	0.00	0.00	3.41
542	552	9.894783	TTTCATGGCATTTCAAAAATGTTTATG	57.105	25.926	12.53	13.03	0.00	1.90
737	751	9.903682	TGATTTTTGAAAAACAATCTGCAAAAA	57.096	22.222	5.08	0.00	44.27	1.94
740	754	7.446001	TTTGAAAAACAATCTGCAAAAACCT	57.554	28.000	0.00	0.00	38.36	3.50
741	755	7.446001	TTGAAAAACAATCTGCAAAAACCTT	57.554	28.000	0.00	0.00	33.18	3.50
885	900	0.164217	GTCTATCGTAGCTCTCGCGG	59.836	60.000	6.13	0.00	42.32	6.46
1010	1029	4.101448	ACACCAGATGGCCTCCGC	62.101	66.667	3.32	0.00	39.32	5.54
1032	1051	4.662961	GGCAAGCCCAACGCCAAC	62.663	66.667	0.00	0.00	45.52	3.77
1033	1052	3.910490	GCAAGCCCAACGCCAACA	61.910	61.111	0.00	0.00	38.78	3.33
1226	1248	0.704076	TTCCCTTGCCTGCACCTAAT	59.296	50.000	0.00	0.00	0.00	1.73
1234	1256	1.336125	GCCTGCACCTAATTGATCTGC	59.664	52.381	0.00	0.00	0.00	4.26
1244	1269	0.465097	ATTGATCTGCTCCCTTGCCG	60.465	55.000	0.00	0.00	0.00	5.69
1331	1381	7.334574	GCTTCGTGCGAGATCTTAATAATTA	57.665	36.000	0.00	0.00	0.00	1.40
1332	1382	7.221287	GCTTCGTGCGAGATCTTAATAATTAC	58.779	38.462	0.00	0.00	0.00	1.89
1334	1384	8.503486	TTCGTGCGAGATCTTAATAATTACTC	57.497	34.615	0.00	0.00	0.00	2.59
1335	1385	7.645402	TCGTGCGAGATCTTAATAATTACTCA	58.355	34.615	0.00	0.00	0.00	3.41
1336	1386	8.297426	TCGTGCGAGATCTTAATAATTACTCAT	58.703	33.333	0.00	0.00	0.00	2.90
1385	1435	1.206831	GTTCCGCTTCAAGTTCGGC	59.793	57.895	0.00	0.00	42.65	5.54
1396	1446	1.084370	AAGTTCGGCGATAGTGCTGC	61.084	55.000	11.76	0.00	41.12	5.25
1505	1562	5.252969	TGTGATGCCTGATTGAAATTAGC	57.747	39.130	0.00	0.00	0.00	3.09
1520	1577	1.844771	TTAGCAACACAGCTGCAGCG	61.845	55.000	31.78	26.80	46.11	5.18
1569	1626	3.318839	TGTGCTTGGGACTTTGAATCTTG	59.681	43.478	0.00	0.00	0.00	3.02
1619	1676	8.408233	TCCTAGTGTACCCTCTCTCTATATCTA	58.592	40.741	0.00	0.00	0.00	1.98

Showing 1 to 25 of 660 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	43	1.349357	GGGGGAGCTATGATTCACCTC	59.651	57.143	0.00	0.00	37.07	3.85
238	242	9.442047	TGAAACACCTGAACATTTTAAAACATT	57.558	25.926	1.97	0.48	0.00	2.71
241	245	8.696410	TCTGAAACACCTGAACATTTTAAAAC	57.304	30.769	1.97	0.00	0.00	2.43
256	260	4.274950	TGAGGATCGTTTTTCTGAAACACC	59.725	41.667	12.39	6.23	38.61	4.16
461	470	9.797642	AGTCACATGCATTTTATGAATCCTATA	57.202	29.630	0.00	0.00	0.00	1.31
498	507	9.815936	GCCATGAAAATAGTTTTGAAAGAAATG	57.184	29.630	0.00	0.00	31.94	2.32
499	508	9.558396	TGCCATGAAAATAGTTTTGAAAGAAAT	57.442	25.926	0.00	0.00	31.94	2.17
500	509	8.954950	TGCCATGAAAATAGTTTTGAAAGAAA	57.045	26.923	0.00	0.00	31.94	2.52
502	511	9.558396	AAATGCCATGAAAATAGTTTTGAAAGA	57.442	25.926	0.00	0.00	31.94	2.52
707	719	8.509690	TGCAGATTGTTTTTCAAAAATCAACAA	58.490	25.926	11.77	9.09	38.63	2.83
719	733	9.833182	TTAAAAGGTTTTTGCAGATTGTTTTTC	57.167	25.926	0.00	0.00	0.00	2.29
885	900	1.894282	GGGGCTATTTCTCGCCTGC	60.894	63.158	0.00	0.00	45.57	4.85
992	1011	2.187946	CGGAGGCCATCTGGTGTC	59.812	66.667	5.01	0.00	37.57	3.67
1016	1035	3.910490	TGTTGGCGTTGGGCTTGC	61.910	61.111	0.00	0.00	42.94	4.01
1017	1036	2.027460	GTGTTGGCGTTGGGCTTG	59.973	61.111	0.00	0.00	42.94	4.01
1018	1037	3.223589	GGTGTTGGCGTTGGGCTT	61.224	61.111	0.00	0.00	42.94	4.35
1173	1192	1.456518	CAGGAGGGAGATCGCCTCA	60.457	63.158	15.63	0.00	43.76	3.86
1226	1248	1.078214	CGGCAAGGGAGCAGATCAA	60.078	57.895	0.00	0.00	35.83	2.57
1396	1446	4.486090	ACTACAGTGAACACAAGATAGCG	58.514	43.478	7.68	0.00	0.00	4.26
1490	1547	4.860907	GCTGTGTTGCTAATTTCAATCAGG	59.139	41.667	17.95	8.65	33.41	3.86
1546	1603	3.565307	AGATTCAAAGTCCCAAGCACAA	58.435	40.909	0.00	0.00	0.00	3.33
1569	1626	8.468399	GGAACTGTATATAACCTAGATAGTGGC	58.532	40.741	0.00	0.00	0.00	5.01
1603	1660	9.618890	CAGAGAAAGATAGATATAGAGAGAGGG	57.381	40.741	0.00	0.00	0.00	4.30
1619	1676	6.939163	ACTACATGTCTTTTGCAGAGAAAGAT	59.061	34.615	13.64	2.90	42.95	2.40
1702	1759	1.774110	ACACAGGGCACAATGAAACA	58.226	45.000	0.00	0.00	0.00	2.83

Showing 1 to 25 of 609 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.