AutoCloner

Multiple sequence alignment - TraesCS4A01G322700

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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	TraesCS4A01G322700	chr4A	100.000	4187	0	0	1	4187	610639193	610643379	0.000000e+00	7733.0
1	TraesCS4A01G322700	chr4A	98.632	2266	27	3	456	2718	611204141	611201877	0.000000e+00	4010.0
2	TraesCS4A01G322700	chr4A	85.964	1489	182	15	1088	2564	610706856	610708329	0.000000e+00	1567.0
3	TraesCS4A01G322700	chr4A	86.789	1196	138	8	1371	2564	611073200	611072023	0.000000e+00	1315.0
4	TraesCS4A01G322700	chr4A	81.125	1653	285	23	1060	2703	610818320	610816686	0.000000e+00	1299.0
5	TraesCS4A01G322700	chr4A	94.083	676	32	3	3512	4187	611196085	611195418	0.000000e+00	1020.0
6	TraesCS4A01G322700	chr4A	92.710	535	33	4	2718	3250	611201764	611201234	0.000000e+00	767.0
7	TraesCS4A01G322700	chr4A	91.242	491	24	6	955	1435	611024995	611025476	0.000000e+00	651.0
8	TraesCS4A01G322700	chr4A	80.000	275	35	11	752	1009	610706542	610706813	7.150000e-43	185.0
9	TraesCS4A01G322700	chr5B	94.707	2664	82	17	80	2718	704825488	704822859	0.000000e+00	4084.0
10	TraesCS4A01G322700	chr5B	91.134	2301	116	35	456	2718	704478545	704480795	0.000000e+00	3038.0
11	TraesCS4A01G322700	chr5B	94.776	1474	66	4	2718	4187	704822729	704821263	0.000000e+00	2285.0
12	TraesCS4A01G322700	chr5B	86.568	1489	174	13	1088	2564	704760634	704759160	0.000000e+00	1618.0
13	TraesCS4A01G322700	chr5B	83.432	1521	211	25	1080	2564	704498304	704499819	0.000000e+00	1375.0
14	TraesCS4A01G322700	chr5B	82.457	1522	245	16	1098	2602	704723271	704724787	0.000000e+00	1312.0
15	TraesCS4A01G322700	chr5B	95.562	676	24	1	3512	4187	704482176	704482845	0.000000e+00	1077.0
16	TraesCS4A01G322700	chr5B	97.175	531	12	1	2718	3248	704480916	704481443	0.000000e+00	894.0
17	TraesCS4A01G322700	chr5B	92.067	479	25	5	955	1423	704722592	704723067	0.000000e+00	662.0
18	TraesCS4A01G322700	chr5B	97.436	39	1	0	1	39	704825864	704825826	2.700000e-07	67.6

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	TraesCS4A01G322700	chr4A	610639193	610643379	4186	False	7733.000000	7733	100.000000	1	4187	1	chr4A.!!$F1	4186
1	TraesCS4A01G322700	chr4A	611201234	611204141	2907	True	2388.500000	4010	95.671000	456	3250	2	chr4A.!!$R4	2794
2	TraesCS4A01G322700	chr4A	611072023	611073200	1177	True	1315.000000	1315	86.789000	1371	2564	1	chr4A.!!$R2	1193
3	TraesCS4A01G322700	chr4A	610816686	610818320	1634	True	1299.000000	1299	81.125000	1060	2703	1	chr4A.!!$R1	1643
4	TraesCS4A01G322700	chr4A	611195418	611196085	667	True	1020.000000	1020	94.083000	3512	4187	1	chr4A.!!$R3	675
5	TraesCS4A01G322700	chr4A	610706542	610708329	1787	False	876.000000	1567	82.982000	752	2564	2	chr4A.!!$F3	1812
6	TraesCS4A01G322700	chr5B	704821263	704825864	4601	True	2145.533333	4084	95.639667	1	4187	3	chr5B.!!$R2	4186
7	TraesCS4A01G322700	chr5B	704478545	704482845	4300	False	1669.666667	3038	94.623667	456	4187	3	chr5B.!!$F2	3731
8	TraesCS4A01G322700	chr5B	704759160	704760634	1474	True	1618.000000	1618	86.568000	1088	2564	1	chr5B.!!$R1	1476
9	TraesCS4A01G322700	chr5B	704498304	704499819	1515	False	1375.000000	1375	83.432000	1080	2564	1	chr5B.!!$F1	1484
10	TraesCS4A01G322700	chr5B	704722592	704724787	2195	False	987.000000	1312	87.262000	955	2602	2	chr5B.!!$F3	1647

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
336	634	0.027848	GTCTCCTCGTTCCGATCGTC	59.972	60.000	15.09	3.37	34.61	4.20	F
337	635	1.011019	CTCCTCGTTCCGATCGTCG	60.011	63.158	15.09	15.03	40.07	5.12	F
2143	3082	0.179004	TTCCATGCCGTGAACCTTGT	60.179	50.000	0.00	0.00	0.00	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self end TH	End Stability	Orientation
2143	3082	4.082190	CCACTCCTCTGTATTCGAAAGTCA	60.082	45.833	1.03	3.41	R
2841	3936	7.654022	ACAACCAAAAATAAAGTGAGAAGGA	57.346	32.000	0.00	3.36	R
4061	5678	0.599466	CGAGTGATGATGCTGCCGAT	60.599	55.000	0.00	4.18	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
51	52	3.510388	TCGCGAGAGAGACAATGATTT	57.490	42.857	3.71	0.00	34.08	2.17
52	53	3.849911	TCGCGAGAGAGACAATGATTTT	58.150	40.909	3.71	0.00	34.08	1.82
53	54	3.859961	TCGCGAGAGAGACAATGATTTTC	59.140	43.478	3.71	0.00	34.08	2.29
54	55	3.862267	CGCGAGAGAGACAATGATTTTCT	59.138	43.478	0.00	0.00	0.00	2.52
55	56	4.026968	CGCGAGAGAGACAATGATTTTCTC	60.027	45.833	12.24	12.24	36.76	2.87
60	61	5.109500	AGAGACAATGATTTTCTCTCCCC	57.891	43.478	16.00	0.00	41.96	4.81
61	62	4.080072	AGAGACAATGATTTTCTCTCCCCC	60.080	45.833	16.00	0.00	41.96	5.40
119	417	2.352617	CCATGGAAAACACGTGGATTGG	60.353	50.000	21.57	12.15	45.78	3.16
129	427	0.958382	CGTGGATTGGGGCGAGAAAA	60.958	55.000	0.00	0.00	0.00	2.29
228	526	2.519780	GCTCGGATCTCGGGAGGT	60.520	66.667	7.54	0.00	43.26	3.85
292	590	1.354337	CTGTTCCGCGACACCATGAG	61.354	60.000	8.23	0.00	0.00	2.90
329	627	2.493907	AAGCGCAGTCTCCTCGTTCC	62.494	60.000	11.47	0.00	0.00	3.62
330	628	2.202492	CGCAGTCTCCTCGTTCCG	60.202	66.667	0.00	0.00	0.00	4.30
331	629	2.687805	CGCAGTCTCCTCGTTCCGA	61.688	63.158	0.00	0.00	0.00	4.55
332	630	1.810532	GCAGTCTCCTCGTTCCGAT	59.189	57.895	0.00	0.00	34.61	4.18
333	631	0.248702	GCAGTCTCCTCGTTCCGATC	60.249	60.000	0.00	0.00	34.61	3.69
334	632	0.028242	CAGTCTCCTCGTTCCGATCG	59.972	60.000	8.51	8.51	34.61	3.69
335	633	0.392729	AGTCTCCTCGTTCCGATCGT	60.393	55.000	15.09	0.00	34.61	3.73
336	634	0.027848	GTCTCCTCGTTCCGATCGTC	59.972	60.000	15.09	3.37	34.61	4.20
337	635	1.011019	CTCCTCGTTCCGATCGTCG	60.011	63.158	15.09	15.03	40.07	5.12
378	676	2.040679	GTTGAAACCCTAACCCTAGCCA	59.959	50.000	0.00	0.00	0.00	4.75
427	725	2.809299	GCCACTCGGAAGTTTGTAAGGT	60.809	50.000	0.00	0.00	31.71	3.50
1011	1361	3.010027	TGCAGTTCAGAATGGGGAACATA	59.990	43.478	7.20	0.00	44.46	2.29
2143	3082	0.179004	TTCCATGCCGTGAACCTTGT	60.179	50.000	0.00	0.00	0.00	3.16
2630	3584	5.500234	ACATTATAGCTTCTGTCAAGGCAA	58.500	37.500	0.00	0.00	0.00	4.52
2853	3948	7.605691	CAGATTAGTCACAATCCTTCTCACTTT	59.394	37.037	0.00	0.00	35.85	2.66
2948	4043	1.063806	CTTTCGGAGCGTCTGTTCAG	58.936	55.000	0.00	0.00	0.00	3.02
3045	4140	1.607178	TGCCCCTGCATTGGAGTTG	60.607	57.895	4.39	0.00	44.23	3.16
3093	4191	3.009723	TCCAATAGAAGGCTTTCGCAAG	58.990	45.455	0.00	0.00	38.38	4.01
3165	4263	8.773645	CATCTTAAAGGAAAAATTTCACCCAAC	58.226	33.333	8.06	0.00	38.92	3.77
3190	4288	5.245075	TGCACCTTGATTTTACTTTAAGGGG	59.755	40.000	0.00	0.00	43.24	4.79
3576	5193	6.271488	AGCACTGCAGCTATTTTTGATTTA	57.729	33.333	15.27	0.00	44.50	1.40
3618	5235	6.389830	TCTGAATGTTATGCAAAACACACT	57.610	33.333	0.00	0.00	41.89	3.55
3688	5305	9.757227	CTCAAAATTTGGTGTAAATCCAACTAA	57.243	29.630	5.83	0.00	43.45	2.24
3789	5406	6.040504	ACATGAACATGAATGAATGCAGCTAT	59.959	34.615	19.56	0.00	41.20	2.97
3802	5419	7.674120	TGAATGCAGCTATGAATATACTCAGT	58.326	34.615	0.00	0.00	0.00	3.41
3869	5486	2.881352	CCTCGGCGAAAGAGCGAC	60.881	66.667	12.13	0.00	38.18	5.19
3881	5498	4.406173	AGCGACGGACGTGCTCTG	62.406	66.667	5.27	0.00	44.60	3.35
3883	5500	3.733960	CGACGGACGTGCTCTGGA	61.734	66.667	5.27	0.00	37.22	3.86
3884	5501	2.649034	GACGGACGTGCTCTGGAA	59.351	61.111	5.27	0.00	0.00	3.53
3891	5508	2.027625	CGTGCTCTGGAACCGGAAC	61.028	63.158	9.46	0.32	0.00	3.62
3892	5509	1.070786	GTGCTCTGGAACCGGAACA	59.929	57.895	9.46	2.42	0.00	3.18
3959	5576	1.667830	CGGCACATCGACAACCACT	60.668	57.895	0.00	0.00	0.00	4.00
3970	5587	0.458669	ACAACCACTGTCGACGTCTT	59.541	50.000	14.70	3.24	29.87	3.01
4061	5678	0.322456	CCTCGGAATCAACCTTGCCA	60.322	55.000	0.00	0.00	0.00	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	1.623542	GCCTCCACCCATACCGACTT	61.624	60.000	0.00	0.00	0.00	3.01
39	40	4.203226	GGGGGAGAGAAAATCATTGTCTC	58.797	47.826	9.38	9.38	38.46	3.36
40	41	4.242336	GGGGGAGAGAAAATCATTGTCT	57.758	45.455	0.00	0.00	0.00	3.41
66	67	3.706373	CTCAGGACGTGGGGGTGG	61.706	72.222	0.00	0.00	0.00	4.61
67	68	2.603473	TCTCAGGACGTGGGGGTG	60.603	66.667	0.00	0.00	0.00	4.61
68	69	2.603776	GTCTCAGGACGTGGGGGT	60.604	66.667	0.00	0.00	32.47	4.95
76	77	3.254892	GAAAGAATCCACGTCTCAGGAC	58.745	50.000	0.00	0.00	36.60	3.85
77	78	3.594603	GAAAGAATCCACGTCTCAGGA	57.405	47.619	0.00	0.00	38.50	3.86
119	417	1.485066	TCATCTAGGGTTTTCTCGCCC	59.515	52.381	0.00	0.00	45.16	6.13
214	512	3.130227	GGAACCTCCCGAGATCCG	58.870	66.667	0.00	0.00	38.18	4.18
228	526	0.323629	CTCGTTTGGTAGCCAGGGAA	59.676	55.000	0.00	0.00	33.81	3.97
292	590	3.424170	CGCTTTCTCTTCTTGCTAGTTGC	60.424	47.826	0.00	0.00	43.25	4.17
303	601	1.067213	AGGAGACTGCGCTTTCTCTTC	60.067	52.381	27.24	17.22	41.13	2.87
329	627	0.797249	GTGGTGAACTCCGACGATCG	60.797	60.000	14.88	14.88	40.07	3.69
330	628	0.458025	GGTGGTGAACTCCGACGATC	60.458	60.000	0.00	0.00	0.00	3.69
331	629	1.183030	TGGTGGTGAACTCCGACGAT	61.183	55.000	0.00	0.00	35.46	3.73
332	630	1.829096	TGGTGGTGAACTCCGACGA	60.829	57.895	0.00	0.00	35.46	4.20
333	631	1.663702	GTGGTGGTGAACTCCGACG	60.664	63.158	0.00	0.00	35.46	5.12
334	632	1.301479	GGTGGTGGTGAACTCCGAC	60.301	63.158	0.00	0.00	35.46	4.79
335	633	2.513259	GGGTGGTGGTGAACTCCGA	61.513	63.158	0.00	0.00	35.46	4.55
336	634	2.032071	GGGTGGTGGTGAACTCCG	59.968	66.667	0.00	0.00	35.46	4.63
337	635	2.154074	AGGGGTGGTGGTGAACTCC	61.154	63.158	0.00	0.00	37.18	3.85
338	636	1.073199	CAGGGGTGGTGGTGAACTC	59.927	63.158	0.00	0.00	0.00	3.01
339	637	2.460853	CCAGGGGTGGTGGTGAACT	61.461	63.158	0.00	0.00	0.00	3.01
340	638	2.115266	CCAGGGGTGGTGGTGAAC	59.885	66.667	0.00	0.00	0.00	3.18
378	676	1.399744	TAGGTGATCGGCAAGCGGAT	61.400	55.000	13.91	13.91	38.44	4.18
1011	1361	2.158623	TGTTCCAAGCATGAAGGTGAGT	60.159	45.455	0.00	0.00	0.00	3.41
1090	1452	0.320421	TCAAACTGACGGCCTGCTAC	60.320	55.000	0.00	0.00	0.00	3.58
2143	3082	4.082190	CCACTCCTCTGTATTCGAAAGTCA	60.082	45.833	0.00	1.03	0.00	3.41
2841	3936	7.654022	ACAACCAAAAATAAAGTGAGAAGGA	57.346	32.000	0.00	0.00	0.00	3.36
2948	4043	0.815734	ATGCAGGCTCTTCATGTTGC	59.184	50.000	0.00	0.00	0.00	4.17
3093	4191	5.712152	AGTCAACATCCAATTCTTTGTCC	57.288	39.130	0.00	0.00	0.00	4.02
3165	4263	6.389906	CCCTTAAAGTAAAATCAAGGTGCAG	58.610	40.000	0.00	0.00	35.08	4.41
3190	4288	9.924650	CTATACATCCCTACACCAACTAATAAC	57.075	37.037	0.00	0.00	0.00	1.89
3272	4370	8.671384	AACTAGTCACAAAGCACAAGTAAATA	57.329	30.769	0.00	0.00	0.00	1.40
3576	5193	5.916318	TCAGAAATCATTGCCAACAAAAGT	58.084	33.333	0.00	0.00	39.77	2.66
3618	5235	1.071228	AGAGTGACAGATGCAGCAACA	59.929	47.619	4.07	0.00	0.00	3.33
3789	5406	7.382488	GCGCTCTTCATTTACTGAGTATATTCA	59.618	37.037	0.00	0.00	34.68	2.57
3802	5419	2.363788	ACACTCGCGCTCTTCATTTA	57.636	45.000	5.56	0.00	0.00	1.40
3869	5486	2.432628	GGTTCCAGAGCACGTCCG	60.433	66.667	0.00	0.00	0.00	4.79
3872	5489	2.504274	TTCCGGTTCCAGAGCACGT	61.504	57.895	0.00	0.00	0.00	4.49
3879	5496	2.027561	TCCTTATGTGTTCCGGTTCCAG	60.028	50.000	0.00	0.00	0.00	3.86
3880	5497	1.979308	TCCTTATGTGTTCCGGTTCCA	59.021	47.619	0.00	0.00	0.00	3.53
3881	5498	2.773993	TCCTTATGTGTTCCGGTTCC	57.226	50.000	0.00	0.00	0.00	3.62
3882	5499	3.606687	ACATCCTTATGTGTTCCGGTTC	58.393	45.455	0.00	0.00	44.79	3.62
3883	5500	3.713826	ACATCCTTATGTGTTCCGGTT	57.286	42.857	0.00	0.00	44.79	4.44
3884	5501	3.244770	ACAACATCCTTATGTGTTCCGGT	60.245	43.478	0.00	0.00	45.79	5.28
3891	5508	7.281549	TCTCATCATCAACAACATCCTTATGTG	59.718	37.037	0.00	0.00	45.79	3.21
3953	5570	0.742505	TCAAGACGTCGACAGTGGTT	59.257	50.000	17.16	7.46	0.00	3.67
4061	5678	0.599466	CGAGTGATGATGCTGCCGAT	60.599	55.000	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.