AutoCloner

Multiple sequence alignment - TraesCS6D01G323200

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	TraesCS6D01G323200	chr6D	100.000	3380	0	0	1	3380	429947106	429943727	0.000000e+00	6242.0
1	TraesCS6D01G323200	chr6D	94.137	2473	106	14	943	3378	429895441	429892971	0.000000e+00	3727.0
2	TraesCS6D01G323200	chr6D	97.185	1421	39	1	943	2363	430365647	430364228	0.000000e+00	2401.0
3	TraesCS6D01G323200	chr6D	95.538	986	23	3	2412	3378	430364220	430363237	0.000000e+00	1557.0
4	TraesCS6D01G323200	chr6D	90.909	308	25	3	2716	3022	430369886	430369581	8.730000e-111	411.0
5	TraesCS6D01G323200	chr6D	90.299	268	26	0	1963	2230	430244999	430245266	5.370000e-93	351.0
6	TraesCS6D01G323200	chr6D	85.455	275	25	6	622	893	429896765	429896503	4.300000e-69	272.0
7	TraesCS6D01G323200	chr6D	82.456	285	24	13	622	902	430365906	430365644	3.390000e-55	226.0
8	TraesCS6D01G323200	chr6D	92.063	63	5	0	3054	3116	199867833	199867895	4.650000e-14	89.8
9	TraesCS6D01G323200	chr6B	89.403	2595	165	42	511	3054	648258620	648256085	0.000000e+00	3168.0
10	TraesCS6D01G323200	chr6B	86.809	235	29	1	3139	3371	523014279	523014513	9.300000e-66	261.0
11	TraesCS6D01G323200	chr6B	85.306	245	34	2	3135	3377	695148719	695148475	5.600000e-63	252.0
12	TraesCS6D01G323200	chr6B	86.331	139	15	4	314	451	504137016	504137151	7.560000e-32	148.0
13	TraesCS6D01G323200	chr5B	90.466	1458	117	13	952	2399	609845674	609844229	0.000000e+00	1903.0
14	TraesCS6D01G323200	chr5B	76.487	706	142	18	1659	2349	489313170	489312474	2.480000e-96	363.0
15	TraesCS6D01G323200	chr5B	83.408	223	18	12	682	900	609845883	609845676	4.450000e-44	189.0
16	TraesCS6D01G323200	chr5B	84.277	159	15	7	2398	2553	609844186	609844035	2.720000e-31	147.0
17	TraesCS6D01G323200	chr7A	94.391	517	24	4	1	514	727694324	727693810	0.000000e+00	789.0
18	TraesCS6D01G323200	chr7A	85.892	241	28	5	3139	3377	29322861	29322625	5.600000e-63	252.0
19	TraesCS6D01G323200	chr7A	81.633	147	15	6	314	451	47350461	47350604	9.910000e-21	111.0
20	TraesCS6D01G323200	chr2A	84.762	525	53	13	1	513	3498521	3499030	5.030000e-138	501.0
21	TraesCS6D01G323200	chr2A	81.277	470	46	25	1	451	511097048	511096602	3.230000e-90	342.0
22	TraesCS6D01G323200	chr2A	86.667	240	28	3	3137	3374	744426004	744425767	2.590000e-66	263.0
23	TraesCS6D01G323200	chr1B	95.420	262	10	2	1	262	664612185	664611926	1.880000e-112	416.0
24	TraesCS6D01G323200	chr1B	97.696	217	5	0	295	511	664611926	664611710	1.150000e-99	374.0
25	TraesCS6D01G323200	chr2B	93.145	248	11	5	148	392	23776603	23776847	3.210000e-95	359.0
26	TraesCS6D01G323200	chr5A	75.847	708	143	22	1659	2349	513869855	513869159	5.400000e-88	335.0
27	TraesCS6D01G323200	chr5A	79.675	492	44	23	44	530	588404351	588403911	1.520000e-78	303.0
28	TraesCS6D01G323200	chr5A	89.706	68	6	1	3054	3120	206684586	206684653	6.010000e-13	86.1
29	TraesCS6D01G323200	chr5D	75.530	707	147	21	1659	2349	407988379	407987683	1.170000e-84	324.0
30	TraesCS6D01G323200	chr5D	87.179	234	28	2	3139	3370	520857861	520857628	7.190000e-67	265.0
31	TraesCS6D01G323200	chr5D	96.364	55	2	0	3055	3109	538010524	538010578	1.290000e-14	91.6
32	TraesCS6D01G323200	chr5D	93.333	60	1	2	3058	3117	266749407	266749351	6.010000e-13	86.1
33	TraesCS6D01G323200	chr4B	86.383	235	30	2	3139	3371	438599662	438599896	4.330000e-64	255.0
34	TraesCS6D01G323200	chr3D	85.714	238	34	0	3141	3378	593914017	593914254	5.600000e-63	252.0
35	TraesCS6D01G323200	chr3D	94.737	57	3	0	3054	3110	452654764	452654820	4.650000e-14	89.8
36	TraesCS6D01G323200	chr4D	83.735	166	26	1	1991	2155	14830597	14830432	4.520000e-34	156.0
37	TraesCS6D01G323200	chr4D	93.333	60	4	0	3058	3117	179707486	179707427	4.650000e-14	89.8
38	TraesCS6D01G323200	chr3A	90.625	64	6	0	3054	3117	650034988	650034925	6.010000e-13	86.1

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	TraesCS6D01G323200	chr6D	429943727	429947106	3379	True	6242.000000	6242	100.000000	1	3380	1	chr6D.!!$R1	3379
1	TraesCS6D01G323200	chr6D	429892971	429896765	3794	True	1999.500000	3727	89.796000	622	3378	2	chr6D.!!$R2	2756
2	TraesCS6D01G323200	chr6D	430363237	430369886	6649	True	1148.750000	2401	91.522000	622	3378	4	chr6D.!!$R3	2756
3	TraesCS6D01G323200	chr6B	648256085	648258620	2535	True	3168.000000	3168	89.403000	511	3054	1	chr6B.!!$R1	2543
4	TraesCS6D01G323200	chr5B	609844035	609845883	1848	True	746.333333	1903	86.050333	682	2553	3	chr5B.!!$R2	1871
5	TraesCS6D01G323200	chr5B	489312474	489313170	696	True	363.000000	363	76.487000	1659	2349	1	chr5B.!!$R1	690
6	TraesCS6D01G323200	chr7A	727693810	727694324	514	True	789.000000	789	94.391000	1	514	1	chr7A.!!$R2	513
7	TraesCS6D01G323200	chr2A	3498521	3499030	509	False	501.000000	501	84.762000	1	513	1	chr2A.!!$F1	512
8	TraesCS6D01G323200	chr5A	513869159	513869855	696	True	335.000000	335	75.847000	1659	2349	1	chr5A.!!$R1	690
9	TraesCS6D01G323200	chr5D	407987683	407988379	696	True	324.000000	324	75.530000	1659	2349	1	chr5D.!!$R2	690

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
577	606	0.464036	TACAATAGACCAGCCAGCCG	59.536	55.0	0.0	0.0	0.0	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2476	6956	2.002586	CCCAAGAATCGTGTAGCACAG	58.997	52.381	0.0	0.0	33.4	3.66	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	84	2.739885	AGCTAGCAAGAGTCACACTG	57.260	50.000	18.83	0.00	0.00	3.66
392	405	2.285977	GTAGAAACGGCAATACAGGGG	58.714	52.381	0.00	0.00	0.00	4.79
394	407	1.663379	GAAACGGCAATACAGGGGCC	61.663	60.000	0.00	0.00	44.27	5.80
397	410	2.834968	GGCAATACAGGGGCCAGC	60.835	66.667	4.39	0.00	46.92	4.85
483	512	3.004002	TCGACTGAGACTTCGCTAAAACA	59.996	43.478	0.00	0.00	35.15	2.83
503	532	3.795101	ACACAGTCGACTGAGTTTTAACG	59.205	43.478	43.55	23.33	43.51	3.18
570	599	7.542477	CGCTTATCTGGTATTACAATAGACCAG	59.458	40.741	12.70	12.70	44.29	4.00
573	602	4.966168	TCTGGTATTACAATAGACCAGCCA	59.034	41.667	13.84	3.88	43.06	4.75
577	606	0.464036	TACAATAGACCAGCCAGCCG	59.536	55.000	0.00	0.00	0.00	5.52
593	630	1.815817	GCCGCCCTCATTTTGGTTGT	61.816	55.000	0.00	0.00	0.00	3.32
612	649	4.395959	TGTGGGAGTATCGAACAATACC	57.604	45.455	0.00	0.00	33.42	2.73
613	650	3.770388	TGTGGGAGTATCGAACAATACCA	59.230	43.478	0.00	0.00	33.42	3.25
614	651	4.407621	TGTGGGAGTATCGAACAATACCAT	59.592	41.667	5.23	0.00	33.42	3.55
615	652	4.989168	GTGGGAGTATCGAACAATACCATC	59.011	45.833	5.23	0.00	33.42	3.51
616	653	4.651962	TGGGAGTATCGAACAATACCATCA	59.348	41.667	0.00	0.00	33.42	3.07
617	654	5.306937	TGGGAGTATCGAACAATACCATCAT	59.693	40.000	0.00	0.00	33.42	2.45
619	656	5.869888	GGAGTATCGAACAATACCATCATCC	59.130	44.000	0.00	0.00	33.42	3.51
620	657	5.470368	AGTATCGAACAATACCATCATCCG	58.530	41.667	0.00	0.00	33.42	4.18
630	3990	6.322969	ACAATACCATCATCCGTAAGTCTACA	59.677	38.462	0.00	0.00	0.00	2.74
662	4022	7.624549	AGAGCTCTGTTTAGGTTTTCATGATA	58.375	34.615	17.42	0.00	0.00	2.15
675	4035	6.710744	GGTTTTCATGATACATACCCTACCTG	59.289	42.308	0.00	0.00	0.00	4.00
735	4104	1.580439	CACGCGTCACTTGAATTTCG	58.420	50.000	9.86	0.00	0.00	3.46
765	4134	4.081030	TCTGACGCCGACGACGAC	62.081	66.667	11.37	4.59	43.93	4.34
818	4187	2.016604	GCTTCCACGTTCATGGCCATA	61.017	52.381	20.30	0.00	39.85	2.74
821	4190	1.280710	TCCACGTTCATGGCCATAGTT	59.719	47.619	20.30	0.00	39.85	2.24
828	4197	1.065491	TCATGGCCATAGTTCGCAACT	60.065	47.619	20.30	6.74	45.40	3.16
868	4240	6.837471	AATGTATTTTAAGGTTGCGGGTTA	57.163	33.333	0.00	0.00	0.00	2.85
870	4242	6.256912	TGTATTTTAAGGTTGCGGGTTAAG	57.743	37.500	0.00	0.00	0.00	1.85
871	4243	3.646611	TTTTAAGGTTGCGGGTTAAGC	57.353	42.857	0.00	0.00	0.00	3.09
881	4253	0.601841	CGGGTTAAGCGGTGTCAAGT	60.602	55.000	4.20	0.00	0.00	3.16
893	4265	5.057149	GCGGTGTCAAGTCCAATCTATAAT	58.943	41.667	0.00	0.00	0.00	1.28
895	4267	6.704493	GCGGTGTCAAGTCCAATCTATAATTA	59.296	38.462	0.00	0.00	0.00	1.40
897	4269	9.273016	CGGTGTCAAGTCCAATCTATAATTATT	57.727	33.333	2.68	0.00	0.00	1.40
989	5397	3.314080	TGCAACACTAGCTAACAAACACC	59.686	43.478	0.00	0.00	0.00	4.16
1010	5418	2.831742	AGCGGCCATGGCAGAATG	60.832	61.111	36.83	21.29	44.11	2.67
1485	5893	0.828762	TCCCCGTCGACAAGGAGAAA	60.829	55.000	20.42	0.29	0.00	2.52
1554	5962	0.903454	TCCCTTCCTTCCTCACGGAC	60.903	60.000	0.00	0.00	39.60	4.79
2350	6779	0.443869	CAACATCGCCGACTTCCTTG	59.556	55.000	0.00	0.00	0.00	3.61
2401	6834	8.877864	TTAAACACTTGTCATGAATAATCCCT	57.122	30.769	0.00	0.00	0.00	4.20
2402	6835	7.781324	AAACACTTGTCATGAATAATCCCTT	57.219	32.000	0.00	0.00	0.00	3.95
2403	6836	6.764308	ACACTTGTCATGAATAATCCCTTG	57.236	37.500	0.00	0.00	0.00	3.61
2405	6838	6.375455	ACACTTGTCATGAATAATCCCTTGTC	59.625	38.462	0.00	0.00	0.00	3.18
2407	6840	6.825721	ACTTGTCATGAATAATCCCTTGTCTC	59.174	38.462	0.00	0.00	0.00	3.36
2408	6841	6.566079	TGTCATGAATAATCCCTTGTCTCT	57.434	37.500	0.00	0.00	0.00	3.10
2409	6842	7.675161	TGTCATGAATAATCCCTTGTCTCTA	57.325	36.000	0.00	0.00	0.00	2.43
2410	6843	7.730084	TGTCATGAATAATCCCTTGTCTCTAG	58.270	38.462	0.00	0.00	0.00	2.43
2476	6956	1.871126	GCCTTTCTGCCTGGCTTGTC	61.871	60.000	21.03	0.00	43.05	3.18
2503	6983	5.353123	TGCTACACGATTCTTGGGAATTTAC	59.647	40.000	0.00	0.00	41.68	2.01
2623	7110	7.947890	TCCATTGAGAACCAATATATTAACCCC	59.052	37.037	0.00	0.00	43.27	4.95
2624	7111	7.950124	CCATTGAGAACCAATATATTAACCCCT	59.050	37.037	0.00	0.00	43.27	4.79
2628	7115	6.849151	AGAACCAATATATTAACCCCTGGAC	58.151	40.000	0.00	0.00	0.00	4.02
2761	7265	4.747540	TGTCGTTGAAAGTGATGATTGG	57.252	40.909	0.00	0.00	0.00	3.16
3170	7676	1.340248	ACAGCCGCGCTATATAAGTGT	59.660	47.619	5.56	0.00	36.40	3.55
3238	7744	1.506262	CAGTGGTGGCGCAATAACC	59.494	57.895	10.83	11.78	34.38	2.85
3239	7745	2.038269	AGTGGTGGCGCAATAACCG	61.038	57.895	10.83	0.00	36.73	4.44
3303	7809	1.208103	CGCGCCGTTTATTTGGTGT	59.792	52.632	0.00	0.00	38.05	4.16
3310	7816	1.400500	CGTTTATTTGGTGTGTCCGCC	60.400	52.381	0.00	0.00	41.91	6.13

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	7.070074	ACTCGAATATGAATTAGTTGGGTCTCT	59.930	37.037	0.00	0.00	0.00	3.10
392	405	3.782244	CTCGCACAAGTCGCTGGC	61.782	66.667	0.00	0.00	0.00	4.85
394	407	4.126390	CGCTCGCACAAGTCGCTG	62.126	66.667	0.00	0.00	0.00	5.18
397	410	2.429236	AGTCGCTCGCACAAGTCG	60.429	61.111	0.00	0.00	0.00	4.18
483	512	2.793232	GCGTTAAAACTCAGTCGACTGT	59.207	45.455	37.21	23.96	44.12	3.55
501	530	6.096987	AGAGATAATACCATTATCGGATGCGT	59.903	38.462	6.49	0.00	36.71	5.24
503	532	9.632807	GATAGAGATAATACCATTATCGGATGC	57.367	37.037	11.38	2.72	36.71	3.91
570	599	3.070576	AAAATGAGGGCGGCTGGC	61.071	61.111	11.40	11.40	42.51	4.85
573	602	1.228862	AACCAAAATGAGGGCGGCT	60.229	52.632	9.56	0.00	0.00	5.52
577	606	0.321346	CCCACAACCAAAATGAGGGC	59.679	55.000	0.00	0.00	40.96	5.19
593	630	4.651962	TGATGGTATTGTTCGATACTCCCA	59.348	41.667	9.26	0.00	33.86	4.37
612	649	5.407502	TGTTGTGTAGACTTACGGATGATG	58.592	41.667	0.00	0.00	32.21	3.07
613	650	5.417894	TCTGTTGTGTAGACTTACGGATGAT	59.582	40.000	4.13	0.00	32.21	2.45
614	651	4.763279	TCTGTTGTGTAGACTTACGGATGA	59.237	41.667	4.13	0.00	32.21	2.92
615	652	5.055642	TCTGTTGTGTAGACTTACGGATG	57.944	43.478	4.13	0.00	32.21	3.51
616	653	5.008331	TCTCTGTTGTGTAGACTTACGGAT	58.992	41.667	7.48	0.00	32.21	4.18
617	654	4.392047	TCTCTGTTGTGTAGACTTACGGA	58.608	43.478	7.01	7.01	32.21	4.69
619	656	4.083217	AGCTCTCTGTTGTGTAGACTTACG	60.083	45.833	0.00	0.00	32.21	3.18
620	657	5.182380	AGAGCTCTCTGTTGTGTAGACTTAC	59.818	44.000	11.45	0.00	38.75	2.34
651	4011	7.280356	ACAGGTAGGGTATGTATCATGAAAAC	58.720	38.462	0.00	1.73	0.00	2.43
662	4022	1.563924	TTGCGACAGGTAGGGTATGT	58.436	50.000	0.00	0.00	0.00	2.29
667	4027	2.800544	CGATTATTTGCGACAGGTAGGG	59.199	50.000	0.00	0.00	0.00	3.53
735	4104	0.450983	CGTCAGACGTAAGGAGGACC	59.549	60.000	15.21	0.00	46.39	4.46
765	4134	1.126113	CAAATGGAGGTTTCGTCGTCG	59.874	52.381	0.00	0.00	38.55	5.12
770	4139	0.958822	GGTGCAAATGGAGGTTTCGT	59.041	50.000	0.00	0.00	0.00	3.85
772	4141	0.958822	ACGGTGCAAATGGAGGTTTC	59.041	50.000	0.00	0.00	0.00	2.78
773	4142	0.673437	CACGGTGCAAATGGAGGTTT	59.327	50.000	0.00	0.00	0.00	3.27
774	4143	1.805428	GCACGGTGCAAATGGAGGTT	61.805	55.000	27.10	0.00	44.26	3.50
776	4145	2.568090	GCACGGTGCAAATGGAGG	59.432	61.111	27.10	0.00	44.26	4.30
818	4187	1.660575	CCGTCGTGAGTTGCGAACT	60.661	57.895	1.82	1.82	46.38	3.01
821	4190	2.050714	GACCGTCGTGAGTTGCGA	60.051	61.111	0.00	0.00	35.89	5.10
828	4197	2.490509	ACATTATCTGTGACCGTCGTGA	59.509	45.455	0.00	0.00	36.48	4.35
861	4233	1.908066	CTTGACACCGCTTAACCCGC	61.908	60.000	0.00	0.00	0.00	6.13
868	4240	1.072331	AGATTGGACTTGACACCGCTT	59.928	47.619	0.00	0.00	0.00	4.68
870	4242	2.380084	TAGATTGGACTTGACACCGC	57.620	50.000	0.00	0.00	0.00	5.68
871	4243	8.833231	ATAATTATAGATTGGACTTGACACCG	57.167	34.615	0.00	0.00	0.00	4.94
907	4279	9.862149	AATAAATTTATAGATTTGACTCCCCGT	57.138	29.630	11.07	0.00	31.96	5.28
940	5332	4.233005	GTGTTCTTCTACGGTTGTACTCC	58.767	47.826	0.00	0.00	0.00	3.85
941	5333	4.678742	GTGTGTTCTTCTACGGTTGTACTC	59.321	45.833	0.00	0.00	0.00	2.59
989	5397	4.124351	CTGCCATGGCCGCTGTTG	62.124	66.667	33.44	10.91	41.09	3.33
1010	5418	1.672356	ACGTGAATGCTGTGCTCCC	60.672	57.895	0.00	0.00	0.00	4.30
2399	6832	9.490379	AAAACACAAATACTACTAGAGACAAGG	57.510	33.333	0.00	0.00	0.00	3.61
2476	6956	2.002586	CCCAAGAATCGTGTAGCACAG	58.997	52.381	0.00	0.00	33.40	3.66
2530	7010	6.038603	CCCAACAACTGTGTCCATGATATAAG	59.961	42.308	0.00	0.00	36.80	1.73
2623	7110	0.449388	GGAGCAAATCAAGCGTCCAG	59.551	55.000	0.00	0.00	37.01	3.86
2624	7111	0.960364	GGGAGCAAATCAAGCGTCCA	60.960	55.000	0.00	0.00	37.01	4.02
2628	7115	1.473677	TCATTGGGAGCAAATCAAGCG	59.526	47.619	0.00	0.00	37.01	4.68
3170	7676	2.706432	CACATATTTGCGGCGCGA	59.294	55.556	28.09	24.12	0.00	5.87
3216	7722	1.836999	TATTGCGCCACCACTGGAGT	61.837	55.000	4.18	0.00	40.55	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.