AutoCloner

Multiple sequence alignment - TraesCS7A01G490700

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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	TraesCS7A01G490700	chr7A	100.000	4857	0	0	1	4857	679959921	679955065	0.000000e+00	8970
1	TraesCS7A01G490700	chr7D	95.143	4303	95	27	630	4856	588084066	588079802	0.000000e+00	6684
2	TraesCS7A01G490700	chr7D	92.668	641	28	5	4	635	588084930	588084300	0.000000e+00	905
3	TraesCS7A01G490700	chr7B	94.654	2862	89	14	631	3464	660653534	660650709	0.000000e+00	4379
4	TraesCS7A01G490700	chr7B	88.955	1177	71	28	3517	4651	660650708	660649549	0.000000e+00	1399
5	TraesCS7A01G490700	chr7B	90.337	652	34	12	1	635	660654407	660653768	0.000000e+00	828
6	TraesCS7A01G490700	chr7B	89.738	458	24	13	3955	4395	660645999	660645548	9.130000e-157	564
7	TraesCS7A01G490700	chr7B	92.821	195	8	4	4463	4651	660645463	660645269	1.330000e-70	278
8	TraesCS7A01G490700	chr7B	92.308	195	9	4	4463	4651	660644623	660644429	6.190000e-69	272
9	TraesCS7A01G490700	chr7B	93.151	146	4	2	4256	4395	660644853	660644708	4.930000e-50	209
10	TraesCS7A01G490700	chr7B	94.565	92	5	0	3777	3868	660646090	660645999	5.070000e-30	143
11	TraesCS7A01G490700	chr7B	88.000	100	10	2	135	233	427310185	427310283	3.070000e-22	117
12	TraesCS7A01G490700	chr2D	91.667	156	12	1	2752	2906	512769191	512769346	1.060000e-51	215
13	TraesCS7A01G490700	chr5A	92.617	149	10	1	2753	2900	303399813	303399961	3.810000e-51	213
14	TraesCS7A01G490700	chr6B	91.503	153	13	0	2752	2904	233039377	233039225	1.370000e-50	211
15	TraesCS7A01G490700	chr1D	90.968	155	12	2	2746	2899	7349862	7349709	1.770000e-49	207
16	TraesCS7A01G490700	chr1D	87.156	109	9	2	138	244	14482518	14482413	8.540000e-23	119
17	TraesCS7A01G490700	chr1D	83.871	124	15	2	122	243	14482398	14482518	3.970000e-21	113
18	TraesCS7A01G490700	chr3D	77.561	410	46	27	1974	2371	513389130	513389505	6.370000e-49	206
19	TraesCS7A01G490700	chr2B	90.446	157	13	1	2752	2906	602996299	602996455	6.370000e-49	206
20	TraesCS7A01G490700	chr5B	90.000	160	12	4	2745	2901	288327648	288327806	2.290000e-48	204
21	TraesCS7A01G490700	chr4B	89.091	165	14	4	2743	2904	78607930	78607767	8.240000e-48	202
22	TraesCS7A01G490700	chr4B	86.916	107	10	4	140	245	576747805	576747908	3.070000e-22	117
23	TraesCS7A01G490700	chr1A	81.463	205	18	4	2277	2473	113536500	113536692	3.030000e-32	150
24	TraesCS7A01G490700	chr1A	87.156	109	9	2	138	244	15435269	15435374	8.540000e-23	119
25	TraesCS7A01G490700	chr4A	86.207	116	11	4	132	246	11585483	11585372	2.370000e-23	121
26	TraesCS7A01G490700	chr3B	84.615	117	10	5	134	244	556503413	556503299	5.140000e-20	110

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	TraesCS7A01G490700	chr7A	679955065	679959921	4856	True	8970.0	8970	100.000000	1	4857	1	chr7A.!!$R1	4856
1	TraesCS7A01G490700	chr7D	588079802	588084930	5128	True	3794.5	6684	93.905500	4	4856	2	chr7D.!!$R1	4852
2	TraesCS7A01G490700	chr7B	660644429	660654407	9978	True	1009.0	4379	92.066125	1	4651	8	chr7B.!!$R1	4650

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
91	99	1.003118	AGTTGGCCTTGTTATCAGCGA	59.997	47.619	3.32	0.00	4.93	F
380	391	1.140312	AGCCTTGGTGAGTTTCCTCA	58.860	50.000	0.00	45.44	3.86	F
690	949	1.386533	TACTTCGCCGGTCTTCTAGG	58.613	55.000	1.90	0.00	3.02	F
696	955	2.158769	TCGCCGGTCTTCTAGGTACATA	60.159	50.000	1.90	0.00	2.29	F
2545	2823	1.227999	TGCAGTTGTCACTAAGGCGC	61.228	55.000	0.00	0.00	6.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1146	1406	2.034305	CGTCCTCCTCCGTTTATACAGG	59.966	54.545	0.00	0.00	4.00	R
1241	1501	3.063997	CGCATTTCCATCTGTTGTACTCC	59.936	47.826	0.00	0.00	3.85	R
2545	2823	1.593196	TGCTGGTTTTCTTGTCCTCG	58.407	50.000	0.00	0.00	4.63	R
2661	2939	4.446371	GGACCAATCCATAACTGACAGAG	58.554	47.826	10.08	45.47	3.35	R
4144	4462	1.004044	CAAGGAGACATTGCTGGGAGT	59.996	52.381	0.00	0.00	3.85	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
91	99	1.003118	AGTTGGCCTTGTTATCAGCGA	59.997	47.619	3.32	0.00	0.00	4.93
174	182	7.067615	TGCCAAAATAAGTGTCTCAACTTTGTA	59.932	33.333	0.00	0.00	40.77	2.41
215	225	7.730364	ATTGTACTGAAGTTACTGAAGTTGG	57.270	36.000	5.68	0.00	0.00	3.77
229	239	6.126409	ACTGAAGTTGGGACACTTATTTTGA	58.874	36.000	0.00	0.00	39.29	2.69
239	249	4.911390	ACACTTATTTTGAGACAGAGGGG	58.089	43.478	0.00	0.00	0.00	4.79
256	266	1.671979	GGGGTATAAAGGAACCACGC	58.328	55.000	0.00	0.00	37.51	5.34
281	292	7.567952	GCGGTAACAAAATAAAAACATGACACC	60.568	37.037	0.00	0.00	0.00	4.16
380	391	1.140312	AGCCTTGGTGAGTTTCCTCA	58.860	50.000	0.00	0.00	45.44	3.86
396	407	2.105134	TCCTCACCGGTTGTGTTATGTT	59.895	45.455	2.97	0.00	45.61	2.71
520	531	5.261216	TGGAAATCCAATGTCTCTTTACCC	58.739	41.667	0.00	0.00	44.35	3.69
550	570	2.930012	TATACACTGAGGCGCGTGCG	62.930	60.000	15.81	10.36	44.10	5.34
588	608	6.599356	AATTGGTAAGGCTTTTACGGATTT	57.401	33.333	4.45	0.00	0.00	2.17
593	613	5.064834	GGTAAGGCTTTTACGGATTTGAGAG	59.935	44.000	4.45	0.00	0.00	3.20
643	902	4.104102	TCAAGGGGCTTTTCTCTTTGTCTA	59.896	41.667	0.00	0.00	0.00	2.59
690	949	1.386533	TACTTCGCCGGTCTTCTAGG	58.613	55.000	1.90	0.00	0.00	3.02
696	955	2.158769	TCGCCGGTCTTCTAGGTACATA	60.159	50.000	1.90	0.00	0.00	2.29
820	1080	3.909086	GAAGAGCTTGTGGGGCGCT	62.909	63.158	7.64	0.00	41.24	5.92
844	1104	4.526650	GCAGGAGGGAAGGTTTCAAATTTA	59.473	41.667	0.00	0.00	0.00	1.40
1146	1406	5.127845	TCCTACTTCAGAAGATGATCACCAC	59.872	44.000	17.56	0.00	37.89	4.16
1147	1407	4.213564	ACTTCAGAAGATGATCACCACC	57.786	45.455	17.56	0.00	37.89	4.61
1241	1501	5.446473	GGAGTACAAACAGAAATGCGATCAG	60.446	44.000	0.00	0.00	0.00	2.90
1313	1573	4.340617	ACTTTTGAAGATATTTCGCCCCA	58.659	39.130	0.00	0.00	0.00	4.96
1415	1693	3.006967	ACCGCAGAAGCTTCTAAGAGAAA	59.993	43.478	28.02	0.00	39.10	2.52
1449	1727	3.056749	ACTCATCGGTGTCACTTTCTACC	60.057	47.826	2.35	0.00	0.00	3.18
2188	2466	3.390967	TGTTGGTCCAGTCAAGATTCTCA	59.609	43.478	0.00	0.00	0.00	3.27
2382	2660	3.441222	TGCAGCAGTGATGACTATTTTGG	59.559	43.478	13.68	0.00	0.00	3.28
2502	2780	6.098124	TCCTTATTGGTTATTTTCAGCCATGG	59.902	38.462	7.63	7.63	37.07	3.66
2545	2823	1.227999	TGCAGTTGTCACTAAGGCGC	61.228	55.000	0.00	0.00	0.00	6.53
2661	2939	6.434340	AGGTCACCCTAATTTCTTTCAATGTC	59.566	38.462	0.00	0.00	40.19	3.06
2910	3188	5.702349	AGGAACGGAGGTAATATCGTTAG	57.298	43.478	0.00	0.00	44.30	2.34
2919	3197	7.553334	GGAGGTAATATCGTTAGGATATGCAA	58.447	38.462	8.00	0.00	45.53	4.08
3066	3344	8.234546	CGCAGGTTTGTTTCTGTTATATAGTTT	58.765	33.333	0.00	0.00	33.81	2.66
3323	3610	7.448469	ACTCTGTAATAGTTTTTGCACCATTCT	59.552	33.333	0.00	0.00	0.00	2.40
3391	3678	4.538490	TGTCCATTGTAGGAATTGGGTACT	59.462	41.667	0.00	0.00	39.92	2.73
3675	3964	2.890945	ACAAACATTCCAGCTACCAACC	59.109	45.455	0.00	0.00	0.00	3.77
3729	4018	2.466846	AGAAAACCAAACACAGGCCTT	58.533	42.857	0.00	0.00	0.00	4.35
3884	4198	1.754803	ACAACCGTCAGAAGTGAGTCA	59.245	47.619	0.00	0.00	31.53	3.41
3894	4208	3.754850	CAGAAGTGAGTCATGCATTTCCA	59.245	43.478	0.00	0.00	33.89	3.53
4040	4354	3.260100	CCAGTCCCAGCCCCAGTT	61.260	66.667	0.00	0.00	0.00	3.16
4135	4453	2.100631	GGTGTCGCCTCCGAACATG	61.101	63.158	0.00	0.00	46.34	3.21
4205	4524	1.405821	CAGGTCGAGGATTAGAAGCGT	59.594	52.381	0.00	0.00	0.00	5.07
4399	4730	4.665734	GCATCACATTTGTTTGTTTTTCGC	59.334	37.500	0.00	0.00	0.00	4.70
4415	4746	3.755965	TTCGCGTGAATTATTGCATGT	57.244	38.095	7.45	0.00	0.00	3.21
4419	4750	2.029107	CGTGAATTATTGCATGTCGCG	58.971	47.619	0.00	0.00	46.97	5.87
4577	4910	2.578495	CTTGAAACGCTCATCAGTTGC	58.422	47.619	0.00	0.00	32.78	4.17
4581	4914	1.580845	AACGCTCATCAGTTGCCAGC	61.581	55.000	0.00	0.00	0.00	4.85
4583	4916	2.037136	GCTCATCAGTTGCCAGCGT	61.037	57.895	0.00	0.00	0.00	5.07
4585	4918	2.177531	CATCAGTTGCCAGCGTGC	59.822	61.111	0.00	0.00	0.00	5.34
4607	4940	4.142600	GCATCAGGATCGTTTACTGCTTTT	60.143	41.667	0.00	0.00	32.42	2.27
4617	4950	5.531659	TCGTTTACTGCTTTTCCAATGGTTA	59.468	36.000	0.00	0.00	0.00	2.85
4633	4967	5.607119	ATGGTTAGTCGCAGTTTTAGTTG	57.393	39.130	0.00	0.00	0.00	3.16
4664	4998	4.526262	TGTTGAATTGAATTGTTCCGGGAT	59.474	37.500	0.00	0.00	0.00	3.85
4752	9462	6.096001	AGTCCCAAATGAAGATGCAGATTTAC	59.904	38.462	0.00	0.00	0.00	2.01
4835	9605	8.669394	CCGTTAGTAGAGGCAAAAATAAAAAG	57.331	34.615	0.00	0.00	0.00	2.27
4856	9628	5.276868	AAAGAATTTTCGTGTCTGTCAGACG	60.277	40.000	24.45	16.16	41.39	4.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	99	4.345859	TTGACTCCAACACCTTACGATT	57.654	40.909	0.00	0.00	0.00	3.34
191	199	6.710744	CCCAACTTCAGTAACTTCAGTACAAT	59.289	38.462	0.00	0.00	0.00	2.71
204	212	7.284074	TCAAAATAAGTGTCCCAACTTCAGTA	58.716	34.615	0.00	0.00	40.77	2.74
206	214	6.486657	TCTCAAAATAAGTGTCCCAACTTCAG	59.513	38.462	0.00	0.00	40.77	3.02
208	216	6.262273	TGTCTCAAAATAAGTGTCCCAACTTC	59.738	38.462	0.00	0.00	40.77	3.01
215	225	4.938226	CCCTCTGTCTCAAAATAAGTGTCC	59.062	45.833	0.00	0.00	0.00	4.02
229	239	4.038633	GTTCCTTTATACCCCCTCTGTCT	58.961	47.826	0.00	0.00	0.00	3.41
239	249	1.292992	CCGCGTGGTTCCTTTATACC	58.707	55.000	6.91	0.00	34.93	2.73
256	266	7.435488	TGGTGTCATGTTTTTATTTTGTTACCG	59.565	33.333	0.00	0.00	0.00	4.02
281	292	0.987294	ACAACCCCTCTCATGACCTG	59.013	55.000	0.00	0.00	0.00	4.00
346	357	1.079750	GGCTTCGTCAGTGTCTCCC	60.080	63.158	0.00	0.00	0.00	4.30
380	391	6.636562	TTAAATCAACATAACACAACCGGT	57.363	33.333	0.00	0.00	0.00	5.28
381	392	6.034470	GCATTAAATCAACATAACACAACCGG	59.966	38.462	0.00	0.00	0.00	5.28
396	407	1.562008	TCCTCCCGGTGCATTAAATCA	59.438	47.619	0.00	0.00	0.00	2.57
520	531	7.456253	GCGCCTCAGTGTATAATAAATATGTG	58.544	38.462	0.00	0.00	0.00	3.21
550	570	6.812160	CCTTACCAATTATGCGGATACTACTC	59.188	42.308	0.00	0.00	0.00	2.59
643	902	8.900781	CCATAACAAGAGAGATCAATTTGATGT	58.099	33.333	16.41	12.48	37.20	3.06
666	925	0.611714	AAGACCGGCGAAGTAACCAT	59.388	50.000	9.30	0.00	0.00	3.55
696	955	5.650266	TCACAACATTTTGACTTGGTACACT	59.350	36.000	0.00	0.00	35.37	3.55
820	1080	0.850100	TTGAAACCTTCCCTCCTGCA	59.150	50.000	0.00	0.00	0.00	4.41
844	1104	8.322905	ACTTCAAATATCCTTGGGCATAAAAT	57.677	30.769	0.00	0.00	0.00	1.82
1146	1406	2.034305	CGTCCTCCTCCGTTTATACAGG	59.966	54.545	0.00	0.00	0.00	4.00
1147	1407	2.034305	CCGTCCTCCTCCGTTTATACAG	59.966	54.545	0.00	0.00	0.00	2.74
1241	1501	3.063997	CGCATTTCCATCTGTTGTACTCC	59.936	47.826	0.00	0.00	0.00	3.85
1415	1693	4.827284	ACACCGATGAGTTTTTCCAAGAAT	59.173	37.500	0.00	0.00	0.00	2.40
1449	1727	6.102663	GGATATTGACTTCCTATCATCCACG	58.897	44.000	0.00	0.00	0.00	4.94
1919	2197	5.945191	TGAGTTTCATATGGTTCAGCATTCA	59.055	36.000	2.13	0.00	0.00	2.57
2382	2660	2.351157	GCATCAAGTTCAGCAGGTTCAC	60.351	50.000	0.00	0.00	0.00	3.18
2545	2823	1.593196	TGCTGGTTTTCTTGTCCTCG	58.407	50.000	0.00	0.00	0.00	4.63
2661	2939	4.446371	GGACCAATCCATAACTGACAGAG	58.554	47.826	10.08	0.00	45.47	3.35
2910	3188	7.599998	GGGTAATGAAAACATGATTGCATATCC	59.400	37.037	9.45	13.19	32.27	2.59
2919	3197	4.655186	CCCATGGGGTAATGAAAACATGAT	59.345	41.667	24.53	0.00	38.25	2.45
3349	3636	4.314121	GACAGGATAATCCAGATGTCAGC	58.686	47.826	0.00	0.00	38.43	4.26
3501	3788	6.071728	ACTGCTTATCATGCAAAGTAAGCTTT	60.072	34.615	26.51	17.20	45.63	3.51
3502	3789	5.416952	ACTGCTTATCATGCAAAGTAAGCTT	59.583	36.000	26.51	3.48	45.63	3.74
3503	3790	4.946157	ACTGCTTATCATGCAAAGTAAGCT	59.054	37.500	26.51	14.24	45.63	3.74
3504	3791	5.240713	ACTGCTTATCATGCAAAGTAAGC	57.759	39.130	22.88	22.88	45.64	3.09
3505	3792	7.081526	AGAACTGCTTATCATGCAAAGTAAG	57.918	36.000	0.00	0.53	40.13	2.34
3506	3793	7.307694	CAAGAACTGCTTATCATGCAAAGTAA	58.692	34.615	0.00	0.00	40.13	2.24
3640	3929	8.592105	TGGAATGTTTGTTTCAAATCATCTTC	57.408	30.769	0.00	2.44	0.00	2.87
3641	3930	7.172019	GCTGGAATGTTTGTTTCAAATCATCTT	59.828	33.333	0.00	0.00	0.00	2.40
3745	4034	3.123621	CAGTGGAGCAAAACTATGACGAC	59.876	47.826	0.00	0.00	0.00	4.34
3826	4140	3.762288	TCTGCTTATAACTGTCCAGACGT	59.238	43.478	0.40	0.00	0.00	4.34
3862	4176	3.243301	TGACTCACTTCTGACGGTTGTAC	60.243	47.826	0.00	0.00	0.00	2.90
3884	4198	5.133221	GGTAGGTTGTATCTGGAAATGCAT	58.867	41.667	0.00	0.00	0.00	3.96
3894	4208	5.186198	GCTGAATGTTGGTAGGTTGTATCT	58.814	41.667	0.00	0.00	0.00	1.98
4017	4331	4.101448	GGCTGGGACTGGTGCGAT	62.101	66.667	0.00	0.00	0.00	4.58
4040	4354	1.688735	CATCATACAGCGAAGGAGGGA	59.311	52.381	0.00	0.00	0.00	4.20
4135	4453	4.833390	ACATTGCTGGGAGTTAGAACTAC	58.167	43.478	0.00	0.00	39.88	2.73
4143	4461	1.366319	AGGAGACATTGCTGGGAGTT	58.634	50.000	0.00	0.00	0.00	3.01
4144	4462	1.004044	CAAGGAGACATTGCTGGGAGT	59.996	52.381	0.00	0.00	0.00	3.85
4186	4505	1.405821	CACGCTTCTAATCCTCGACCT	59.594	52.381	0.00	0.00	0.00	3.85
4336	4663	7.451501	TTCAATCAGTGCATCAATAAACTCA	57.548	32.000	0.00	0.00	0.00	3.41
4399	4730	2.029107	CGCGACATGCAATAATTCACG	58.971	47.619	0.00	0.00	46.97	4.35
4419	4750	5.929415	AGATTCTTCTCCTTTTCGACAAGTC	59.071	40.000	10.27	0.00	0.00	3.01
4566	4899	1.792301	CACGCTGGCAACTGATGAG	59.208	57.895	0.00	0.00	37.83	2.90
4577	4910	2.242572	CGATCCTGATGCACGCTGG	61.243	63.158	7.71	7.71	0.00	4.85
4581	4914	2.282555	CAGTAAACGATCCTGATGCACG	59.717	50.000	0.00	0.00	0.00	5.34
4583	4916	2.093500	AGCAGTAAACGATCCTGATGCA	60.093	45.455	0.00	0.00	34.93	3.96
4585	4918	5.447818	GGAAAAGCAGTAAACGATCCTGATG	60.448	44.000	0.00	0.00	0.00	3.07
4607	4940	2.851263	AACTGCGACTAACCATTGGA	57.149	45.000	10.37	0.00	0.00	3.53
4617	4950	7.012044	ACAAGATTAACAACTAAAACTGCGACT	59.988	33.333	0.00	0.00	0.00	4.18
4752	9462	8.913656	CGTCTAAAAGACTTTCTTACCTACAAG	58.086	37.037	0.00	0.00	42.92	3.16
4829	9599	8.120465	GTCTGACAGACACGAAAATTCTTTTTA	58.880	33.333	27.15	0.00	44.45	1.52
4832	9602	5.276868	CGTCTGACAGACACGAAAATTCTTT	60.277	40.000	29.99	0.00	45.30	2.52
4835	9605	4.041240	CGTCTGACAGACACGAAAATTC	57.959	45.455	29.99	4.63	45.30	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.