AutoCloner

Multiple sequence alignment - TraesCS7D01G309100

Loading Multiple Alignment...

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	TraesCS7D01G309100	chr7D	100.000	7901	0	0	1	7901	392254658	392262558	0.000000e+00	14591.0
1	TraesCS7D01G309100	chr7D	87.651	413	39	3	3169	3571	573109241	573109651	3.340000e-128	470.0
2	TraesCS7D01G309100	chr7D	95.804	143	6	0	2872	3014	517335599	517335741	1.710000e-56	231.0
3	TraesCS7D01G309100	chr7D	91.720	157	6	3	6	155	511939884	511940040	2.230000e-50	211.0
4	TraesCS7D01G309100	chr7D	93.590	78	5	0	3085	3162	566960715	566960792	5.010000e-22	117.0
5	TraesCS7D01G309100	chr7A	97.707	4449	66	14	3146	7565	443957892	443962333	0.000000e+00	7618.0
6	TraesCS7D01G309100	chr7A	98.483	2702	35	4	178	2875	443954978	443957677	0.000000e+00	4758.0
7	TraesCS7D01G309100	chr7A	98.198	111	2	0	3016	3126	443957675	443957785	2.250000e-45	195.0
8	TraesCS7D01G309100	chr7B	92.947	4381	173	45	3574	7901	388591306	388595603	0.000000e+00	6253.0
9	TraesCS7D01G309100	chr7B	97.083	2708	56	12	179	2875	388588528	388591223	0.000000e+00	4542.0
10	TraesCS7D01G309100	chr7B	85.000	420	50	4	3167	3576	570462366	570461950	1.590000e-111	414.0
11	TraesCS7D01G309100	chr7B	84.185	411	54	2	3167	3568	64495156	64495564	9.610000e-104	388.0
12	TraesCS7D01G309100	chr7B	91.463	164	7	5	1	157	662648614	662648451	1.330000e-52	219.0
13	TraesCS7D01G309100	chr7B	98.649	74	1	0	3016	3089	388591221	388591294	1.790000e-26	132.0
14	TraesCS7D01G309100	chr7B	88.235	85	10	0	5564	5648	388593156	388593240	1.400000e-17	102.0
15	TraesCS7D01G309100	chr7B	88.312	77	9	0	6471	6547	734775873	734775797	8.440000e-15	93.5
16	TraesCS7D01G309100	chr1D	87.019	416	39	8	3171	3576	308461992	308462402	9.350000e-124	455.0
17	TraesCS7D01G309100	chr1D	90.909	165	6	5	1	156	257424770	257424606	6.210000e-51	213.0
18	TraesCS7D01G309100	chr1D	90.625	160	8	3	2	154	433907865	433907706	1.040000e-48	206.0
19	TraesCS7D01G309100	chr4B	84.964	419	51	3	3168	3577	33626159	33625744	1.590000e-111	414.0
20	TraesCS7D01G309100	chr4B	97.315	149	4	0	2872	3020	398790178	398790326	3.660000e-63	254.0
21	TraesCS7D01G309100	chr2A	85.194	412	46	6	3172	3571	584516390	584516798	7.380000e-110	409.0
22	TraesCS7D01G309100	chr2A	96.429	140	4	1	2875	3014	70056865	70056727	6.170000e-56	230.0
23	TraesCS7D01G309100	chr2A	85.075	67	8	2	3413	3478	34320536	34320471	5.120000e-07	67.6
24	TraesCS7D01G309100	chr2A	92.105	38	2	1	3541	3577	367647793	367647830	1.400000e-02	52.8
25	TraesCS7D01G309100	chr5D	84.010	419	49	10	3170	3575	490931122	490931535	3.460000e-103	387.0
26	TraesCS7D01G309100	chr5D	96.622	148	5	0	2875	3022	37189328	37189181	6.120000e-61	246.0
27	TraesCS7D01G309100	chr5D	89.091	165	10	4	2	158	135516805	135516969	1.740000e-46	198.0
28	TraesCS7D01G309100	chr5D	82.424	165	26	2	3413	3577	112344543	112344382	2.970000e-29	141.0
29	TraesCS7D01G309100	chr4D	84.772	394	42	8	3153	3536	496612670	496613055	5.790000e-101	379.0
30	TraesCS7D01G309100	chr4D	97.987	149	3	0	2870	3018	14942055	14941907	7.870000e-65	259.0
31	TraesCS7D01G309100	chr4D	91.195	159	7	3	2	153	73211779	73211937	8.030000e-50	209.0
32	TraesCS7D01G309100	chr5A	79.717	424	63	7	3171	3577	115247325	115246908	1.300000e-72	285.0
33	TraesCS7D01G309100	chr2D	98.582	141	2	0	2875	3015	135316972	135317112	4.730000e-62	250.0
34	TraesCS7D01G309100	chr2D	92.157	153	7	1	6	153	367987382	367987230	2.230000e-50	211.0
35	TraesCS7D01G309100	chr2D	96.000	75	3	0	3086	3160	376701261	376701187	1.080000e-23	122.0
36	TraesCS7D01G309100	chr2D	94.595	74	4	0	3087	3160	8495904	8495977	1.800000e-21	115.0
37	TraesCS7D01G309100	chr2D	76.364	165	31	6	3413	3574	32180899	32180740	1.830000e-11	82.4
38	TraesCS7D01G309100	chr2D	100.000	28	0	0	3550	3577	15851809	15851782	1.400000e-02	52.8
39	TraesCS7D01G309100	chr2D	92.105	38	2	1	3541	3577	296362677	296362714	1.400000e-02	52.8
40	TraesCS7D01G309100	chr4A	97.203	143	2	2	2873	3014	36371016	36371157	2.850000e-59	241.0
41	TraesCS7D01G309100	chr4A	100.000	29	0	0	3550	3578	78321376	78321348	4.000000e-03	54.7
42	TraesCS7D01G309100	chr5B	98.519	135	2	0	2872	3006	2580306	2580440	1.020000e-58	239.0
43	TraesCS7D01G309100	chr5B	91.720	157	7	2	1	151	448291704	448291548	6.210000e-51	213.0
44	TraesCS7D01G309100	chr1A	94.595	148	8	0	2871	3018	547944618	547944471	6.170000e-56	230.0
45	TraesCS7D01G309100	chr1A	91.083	157	6	4	6	154	232089198	232089042	1.040000e-48	206.0
46	TraesCS7D01G309100	chr6B	76.540	341	48	21	3212	3525	85789528	85789193	2.950000e-34	158.0
47	TraesCS7D01G309100	chr6B	89.888	89	6	2	3085	3170	553057203	553057115	2.330000e-20	111.0
48	TraesCS7D01G309100	chr3D	94.872	78	4	0	3085	3162	555598244	555598321	1.080000e-23	122.0
49	TraesCS7D01G309100	chrUn	94.667	75	4	0	3086	3160	31324798	31324872	5.010000e-22	117.0
50	TraesCS7D01G309100	chr6D	93.421	76	4	1	3085	3159	368365284	368365359	2.330000e-20	111.0
51	TraesCS7D01G309100	chr6A	93.421	76	4	1	3085	3159	509279057	509279132	2.330000e-20	111.0
52	TraesCS7D01G309100	chr2B	92.105	38	2	1	3541	3577	366019067	366019030	1.400000e-02	52.8

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	TraesCS7D01G309100	chr7D	392254658	392262558	7900	False	14591.000000	14591	100.000000	1	7901	1	chr7D.!!$F1	7900
1	TraesCS7D01G309100	chr7A	443954978	443962333	7355	False	4190.333333	7618	98.129333	178	7565	3	chr7A.!!$F1	7387
2	TraesCS7D01G309100	chr7B	388588528	388595603	7075	False	2757.250000	6253	94.228500	179	7901	4	chr7B.!!$F2	7722

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
75	76	0.033228	CAAATGCAAAACTGGGCGGA	59.967	50.000	0.00	0.00	0.00	5.54	F
76	77	0.033366	AAATGCAAAACTGGGCGGAC	59.967	50.000	0.00	0.00	0.00	4.79	F
152	153	0.321298	GCCCGTTGGAGTTGCTCTAA	60.321	55.000	0.00	0.00	0.00	2.10	F
339	340	1.007336	CCTATAATCGCACCGTCCGC	61.007	60.000	0.00	0.00	0.00	5.54	F
1188	1196	1.711060	CCGGATTTAATGTGCCGCGT	61.711	55.000	4.92	0.00	42.29	6.01	F
2900	2912	0.102663	GTTCGGAATCTCTCCCGTCC	59.897	60.000	0.00	0.00	45.48	4.79	F
2951	2963	0.036732	TTGAGCTGCTCCGTGGAAAT	59.963	50.000	25.61	0.00	0.00	2.17	F
2955	2967	0.378610	GCTGCTCCGTGGAAATAAGC	59.621	55.000	0.00	0.00	0.00	3.09	F
2970	2982	0.673644	TAAGCTGCAGTTTCCTCCGC	60.674	55.000	19.79	0.00	0.00	5.54	F
3363	3462	1.002857	AGTGGGGAGAAATGAAGGGG	58.997	55.000	0.00	0.00	0.00	4.79	F
3634	3734	1.065854	ACTCGCCTTGCTAGCAATCTT	60.066	47.619	29.40	9.11	35.20	2.40	F
5248	5357	1.757731	TGTTTGGCTGGCACAAGCT	60.758	52.632	2.29	0.00	38.70	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1188	1196	0.179234	TCGGCAACTCAAAGACCACA	59.821	50.000	0.00	0.00	0.00	4.17	R
1357	1365	3.452264	AGCTTCCCATCCTTTTTATTGCC	59.548	43.478	0.00	0.00	0.00	4.52	R
2261	2269	6.727231	TGTAGGGTTTCCAGACTGATTTACTA	59.273	38.462	3.32	0.00	34.83	1.82	R
2703	2714	9.787435	TGGTAACAGTTAAGTCAAGATACAAAT	57.213	29.630	0.00	0.00	46.17	2.32	R
2932	2944	0.036732	ATTTCCACGGAGCAGCTCAA	59.963	50.000	24.09	8.81	31.08	3.02	R
5064	5172	3.858503	GCAAGAGCTGGTTTGGCTTAAAG	60.859	47.826	0.00	0.00	40.40	1.85	R
5248	5357	7.093068	TGCTCAGATTGTCTATAGTTTGGGTTA	60.093	37.037	0.00	0.00	0.00	2.85	R
5544	5653	2.943036	ACACAGTCCGGGTTGTAATT	57.057	45.000	0.00	0.00	0.00	1.40	R
5555	5664	1.541588	GGCTCCATTTGAACACAGTCC	59.458	52.381	0.00	0.00	0.00	3.85	R
5801	5910	2.159393	GCAAAGCCAATCGATAAGCACA	60.159	45.455	18.60	0.00	0.00	4.57	R
5968	6077	2.671396	AGACCGCATAAAAGTACAAGCG	59.329	45.455	0.00	0.00	44.24	4.68	R
7712	7853	1.338337	AGATCACTGACGCCTATTCCG	59.662	52.381	0.00	0.00	0.00	4.30	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
36	37	2.408835	CATGAAATGGGTCGGCGC	59.591	61.111	0.00	0.00	41.79	6.53
37	38	3.202001	ATGAAATGGGTCGGCGCG	61.202	61.111	0.00	0.00	0.00	6.86
38	39	3.969250	ATGAAATGGGTCGGCGCGT	62.969	57.895	8.43	0.00	0.00	6.01
39	40	3.428282	GAAATGGGTCGGCGCGTT	61.428	61.111	8.43	5.61	38.23	4.84
40	41	3.661025	GAAATGGGTCGGCGCGTTG	62.661	63.158	12.62	0.00	36.96	4.10
60	61	3.434319	CGCGCTGCTGACCCAAAT	61.434	61.111	5.56	0.00	0.00	2.32
61	62	2.180017	GCGCTGCTGACCCAAATG	59.820	61.111	0.00	0.00	0.00	2.32
62	63	2.180017	CGCTGCTGACCCAAATGC	59.820	61.111	0.00	0.00	0.00	3.56
63	64	2.628696	CGCTGCTGACCCAAATGCA	61.629	57.895	0.00	0.00	0.00	3.96
64	65	1.667151	GCTGCTGACCCAAATGCAA	59.333	52.632	0.00	0.00	34.90	4.08
65	66	0.033781	GCTGCTGACCCAAATGCAAA	59.966	50.000	0.00	0.00	34.90	3.68
66	67	1.540797	GCTGCTGACCCAAATGCAAAA	60.541	47.619	0.00	0.00	34.90	2.44
67	68	2.137523	CTGCTGACCCAAATGCAAAAC	58.862	47.619	0.00	0.00	34.90	2.43
68	69	1.761784	TGCTGACCCAAATGCAAAACT	59.238	42.857	0.00	0.00	32.12	2.66
69	70	2.137523	GCTGACCCAAATGCAAAACTG	58.862	47.619	0.00	0.00	0.00	3.16
70	71	2.758009	CTGACCCAAATGCAAAACTGG	58.242	47.619	0.00	0.00	0.00	4.00
72	73	2.931246	CCCAAATGCAAAACTGGGC	58.069	52.632	11.50	0.00	42.10	5.36
73	74	0.950071	CCCAAATGCAAAACTGGGCG	60.950	55.000	11.50	0.00	42.10	6.13
74	75	0.950071	CCAAATGCAAAACTGGGCGG	60.950	55.000	0.00	0.00	0.00	6.13
75	76	0.033228	CAAATGCAAAACTGGGCGGA	59.967	50.000	0.00	0.00	0.00	5.54
76	77	0.033366	AAATGCAAAACTGGGCGGAC	59.967	50.000	0.00	0.00	0.00	4.79
77	78	2.141122	AATGCAAAACTGGGCGGACG	62.141	55.000	0.00	0.00	0.00	4.79
78	79	4.700365	GCAAAACTGGGCGGACGC	62.700	66.667	8.39	8.39	41.06	5.19
104	105	3.047877	CGGCCGACCCAAACAGAC	61.048	66.667	24.07	0.00	0.00	3.51
105	106	2.112297	GGCCGACCCAAACAGACA	59.888	61.111	0.00	0.00	0.00	3.41

Showing 1 to 25 of 230 entries

Previous1 2 3 4 5…10Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
2	3	8.867935	CCATTTCATGTACGCATTCAATTTAAA	58.132	29.630	0.00	31.99	1.52
3	4	7.490725	CCCATTTCATGTACGCATTCAATTTAA	59.509	33.333	0.00	31.99	1.52
4	5	6.977502	CCCATTTCATGTACGCATTCAATTTA	59.022	34.615	0.00	31.99	1.40
5	6	5.811613	CCCATTTCATGTACGCATTCAATTT	59.188	36.000	0.00	31.99	1.82
6	7	5.105392	ACCCATTTCATGTACGCATTCAATT	60.105	36.000	0.00	31.99	2.32
7	8	4.402155	ACCCATTTCATGTACGCATTCAAT	59.598	37.500	0.00	31.99	2.57
8	9	3.761218	ACCCATTTCATGTACGCATTCAA	59.239	39.130	0.00	31.99	2.69
9	10	3.351740	ACCCATTTCATGTACGCATTCA	58.648	40.909	0.00	31.99	2.57
10	11	3.546020	CGACCCATTTCATGTACGCATTC	60.546	47.826	0.00	31.99	2.67
11	12	2.354510	CGACCCATTTCATGTACGCATT	59.645	45.455	0.00	31.99	3.56
12	13	1.939934	CGACCCATTTCATGTACGCAT	59.060	47.619	0.00	35.32	4.73
13	14	1.364721	CGACCCATTTCATGTACGCA	58.635	50.000	0.00	0.00	5.24
14	15	0.655733	CCGACCCATTTCATGTACGC	59.344	55.000	0.00	0.00	4.42
15	16	0.655733	GCCGACCCATTTCATGTACG	59.344	55.000	0.00	0.00	3.67
16	17	0.655733	CGCCGACCCATTTCATGTAC	59.344	55.000	0.00	0.00	2.90
17	18	1.092921	GCGCCGACCCATTTCATGTA	61.093	55.000	0.00	0.00	2.29
18	19	2.406616	GCGCCGACCCATTTCATGT	61.407	57.895	0.00	0.00	3.21
19	20	2.408835	GCGCCGACCCATTTCATG	59.591	61.111	0.00	0.00	3.07
20	21	3.202001	CGCGCCGACCCATTTCAT	61.202	61.111	0.00	0.00	2.57
21	22	4.690719	ACGCGCCGACCCATTTCA	62.691	61.111	5.73	0.00	2.69
22	23	3.428282	AACGCGCCGACCCATTTC	61.428	61.111	5.73	0.00	2.17
23	24	3.732892	CAACGCGCCGACCCATTT	61.733	61.111	5.73	0.00	2.32
43	44	3.434319	ATTTGGGTCAGCAGCGCG	61.434	61.111	0.00	0.00	6.86
44	45	2.180017	CATTTGGGTCAGCAGCGC	59.820	61.111	0.00	0.00	5.92
45	46	2.144833	TTGCATTTGGGTCAGCAGCG	62.145	55.000	0.00	38.35	5.18

Showing 1 to 25 of 242 entries

Previous1 2 3 4 5…10Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.