AutoCloner

Multiple sequence alignment - TraesCS4A01G051000

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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	TraesCS4A01G051000	chr4A	100.000	9332	0	0	1	9332	41960682	41951351	0.000000e+00	17234.0
1	TraesCS4A01G051000	chr4A	100.000	33	0	0	4630	4662	119794956	119794924	2.810000e-05	62.1
2	TraesCS4A01G051000	chr4D	96.271	3164	92	10	1471	4627	422246184	422249328	0.000000e+00	5166.0
3	TraesCS4A01G051000	chr4D	94.975	2746	91	15	4679	7406	422249315	422252031	0.000000e+00	4263.0
4	TraesCS4A01G051000	chr4D	92.875	2779	147	27	5095	7847	422513119	422515872	0.000000e+00	3988.0
5	TraesCS4A01G051000	chr4D	95.062	2167	77	11	1471	3615	422504450	422506608	0.000000e+00	3382.0
6	TraesCS4A01G051000	chr4D	94.061	1448	69	10	7897	9332	422515874	422517316	0.000000e+00	2182.0
7	TraesCS4A01G051000	chr4D	91.746	1478	83	16	1	1446	422244265	422245735	0.000000e+00	2017.0
8	TraesCS4A01G051000	chr4D	93.714	1034	40	8	3601	4630	422506624	422507636	0.000000e+00	1526.0
9	TraesCS4A01G051000	chr4D	92.344	1045	63	11	7448	8480	422252031	422253070	0.000000e+00	1471.0
10	TraesCS4A01G051000	chr4D	83.939	1432	158	32	68	1446	422502381	422503793	0.000000e+00	1304.0
11	TraesCS4A01G051000	chr4D	95.050	202	10	0	4871	5072	422512927	422513128	1.510000e-82	318.0
12	TraesCS4A01G051000	chr4D	83.382	343	44	9	8426	8762	422252950	422253285	1.180000e-78	305.0
13	TraesCS4A01G051000	chr4D	91.707	205	8	4	4679	4875	422507620	422507823	9.230000e-70	276.0
14	TraesCS4A01G051000	chr4D	91.304	46	2	2	4617	4662	346123361	346123404	2.810000e-05	62.1
15	TraesCS4A01G051000	chr4B	96.106	2645	83	11	1471	4105	519251044	519253678	0.000000e+00	4296.0
16	TraesCS4A01G051000	chr4B	94.835	2401	99	8	4679	7071	519254224	519256607	0.000000e+00	3723.0
17	TraesCS4A01G051000	chr4B	93.341	2508	127	19	5092	7582	519344129	519346613	0.000000e+00	3670.0
18	TraesCS4A01G051000	chr4B	94.890	1957	72	6	1471	3399	519340424	519342380	0.000000e+00	3035.0
19	TraesCS4A01G051000	chr4B	93.955	1373	65	10	7117	8480	519256598	519257961	0.000000e+00	2060.0
20	TraesCS4A01G051000	chr4B	91.393	1034	40	17	3601	4630	519342769	519343757	0.000000e+00	1371.0
21	TraesCS4A01G051000	chr4B	92.805	820	42	9	7896	8709	519347263	519348071	0.000000e+00	1171.0
22	TraesCS4A01G051000	chr4B	81.518	1423	155	48	71	1446	519338487	519339848	0.000000e+00	1072.0
23	TraesCS4A01G051000	chr4B	92.717	714	22	8	757	1446	519248667	519249374	0.000000e+00	1003.0
24	TraesCS4A01G051000	chr4B	94.118	527	16	3	4104	4630	519253729	519254240	0.000000e+00	787.0
25	TraesCS4A01G051000	chr4B	87.276	613	70	6	141	748	519248100	519248709	0.000000e+00	693.0
26	TraesCS4A01G051000	chr4B	90.962	520	40	5	8818	9331	519354037	519354555	0.000000e+00	693.0
27	TraesCS4A01G051000	chr4B	92.040	402	23	5	4679	5072	519343741	519344141	2.940000e-154	556.0
28	TraesCS4A01G051000	chr4B	92.694	219	8	4	3397	3615	519342541	519342751	9.100000e-80	309.0
29	TraesCS4A01G051000	chr4B	86.861	274	29	6	7580	7848	519346992	519347263	5.480000e-77	300.0
30	TraesCS4A01G051000	chr4B	96.460	113	4	0	8706	8818	519350771	519350883	4.450000e-43	187.0
31	TraesCS4A01G051000	chr4B	79.452	219	28	10	8546	8762	519258061	519258264	1.260000e-28	139.0
32	TraesCS4A01G051000	chr4B	87.611	113	14	0	1	113	519247993	519248105	2.110000e-26	132.0
33	TraesCS4A01G051000	chr5A	78.049	369	66	12	8974	9332	668229305	668229668	1.580000e-52	219.0
34	TraesCS4A01G051000	chr5A	93.023	43	3	0	4631	4673	271053391	271053433	7.820000e-06	63.9
35	TraesCS4A01G051000	chr5A	100.000	32	0	0	4631	4662	346127521	346127490	1.010000e-04	60.2
36	TraesCS4A01G051000	chr5D	77.966	354	48	10	4690	5015	409336211	409335860	2.660000e-45	195.0
37	TraesCS4A01G051000	chr6A	72.941	340	76	13	8980	9309	48197183	48196850	4.610000e-18	104.0
38	TraesCS4A01G051000	chr6A	95.000	40	0	2	4631	4668	504483112	504483073	2.810000e-05	62.1
39	TraesCS4A01G051000	chr7B	90.196	51	3	1	4631	4679	571397908	571397858	2.180000e-06	65.8
40	TraesCS4A01G051000	chr7B	97.222	36	1	0	4632	4667	418738841	418738806	2.810000e-05	62.1
41	TraesCS4A01G051000	chr1A	93.023	43	3	0	4620	4662	114347924	114347966	7.820000e-06	63.9
42	TraesCS4A01G051000	chr3B	93.182	44	0	3	4620	4662	381481201	381481242	2.810000e-05	62.1
43	TraesCS4A01G051000	chr5B	100.000	32	0	0	4631	4662	294094677	294094646	1.010000e-04	60.2
44	TraesCS4A01G051000	chr3A	88.235	51	4	2	4613	4662	528595028	528595077	1.010000e-04	60.2
45	TraesCS4A01G051000	chr7A	94.595	37	0	2	4631	4667	647301458	647301424	1.000000e-03	56.5

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	TraesCS4A01G051000	chr4A	41951351	41960682	9331	True	17234.000000	17234	100.000000	1	9332	1	chr4A.!!$R1	9331
1	TraesCS4A01G051000	chr4D	422244265	422253285	9020	False	2644.400000	5166	91.743600	1	8762	5	chr4D.!!$F2	8761
2	TraesCS4A01G051000	chr4D	422512927	422517316	4389	False	2162.666667	3988	93.995333	4871	9332	3	chr4D.!!$F4	4461
3	TraesCS4A01G051000	chr4D	422502381	422507823	5442	False	1622.000000	3382	91.105500	68	4875	4	chr4D.!!$F3	4807
4	TraesCS4A01G051000	chr4B	519247993	519258264	10271	False	1604.125000	4296	90.758750	1	8762	8	chr4B.!!$F1	8761
5	TraesCS4A01G051000	chr4B	519338487	519354555	16068	False	1236.400000	3670	91.296400	71	9331	10	chr4B.!!$F2	9260

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
751	781	0.037326	TGGATGTTCGGCTCTCACAC	60.037	55.000	0.00	0.00	0.00	3.82	F
1125	1249	0.178990	GGCCTCTGAAGGTGGTGTTT	60.179	55.000	0.00	0.00	45.34	2.83	F
2000	4024	1.133976	GCTTATGGCCTGTCTGGTGAT	60.134	52.381	3.32	0.00	38.35	3.06	F
2700	4725	0.759346	ACCAGAGTCTTTTCCAGCGT	59.241	50.000	0.00	0.00	0.00	5.07	F
2821	4846	1.596603	CACTGTGCAGATGGTTGACA	58.403	50.000	6.17	0.00	0.00	3.58	F
3598	5789	2.627699	ACACATTTGGCCTTTTCGATGT	59.372	40.909	3.32	2.49	0.00	3.06	F
5430	7760	1.003545	GCCATGCAGTACTTGTATGCG	60.004	52.381	13.81	10.16	45.35	4.73	F
5514	7844	0.174845	ACTGTCGCCGCTTGCTTATA	59.825	50.000	0.00	0.00	38.05	0.98	F
6796	9139	1.195115	TGACCTCCCGAGATTCCTTG	58.805	55.000	0.00	0.00	0.00	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2391	4416	0.107066	ATGCATTGTCATCTCCCGCA	60.107	50.000	0.00	0.00	0.00	5.69	R
2700	4725	1.400142	CGTGAAAGTTGCAAGGACACA	59.600	47.619	18.79	7.58	0.00	3.72	R
3218	5245	1.814394	GACTGCATGCAAGGACAATCA	59.186	47.619	22.88	0.00	0.00	2.57	R
4349	6663	3.452627	AGAACACACTGTTTCCAGAGACT	59.547	43.478	0.00	0.00	41.28	3.24	R
4640	6954	3.595190	AGCCTTTAGTCCCAAACAAGT	57.405	42.857	0.00	0.00	0.00	3.16	R
5489	7819	0.025001	CAAGCGGCGACAGTAATTCG	59.975	55.000	12.98	0.00	39.56	3.34	R
7114	9461	0.471022	AGCACCCCCGTTCCAAAAAT	60.471	50.000	0.00	0.00	0.00	1.82	R
7121	9468	0.893727	ATTGTTGAGCACCCCCGTTC	60.894	55.000	0.00	0.00	0.00	3.95	R
8587	11553	2.095415	AGTTTAATCGGCGCAAAGGTTC	60.095	45.455	10.83	0.00	0.00	3.62	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
21	22	2.739704	CGATCGCCAACGTGCACAT	61.740	57.895	18.64	0.00	41.18	3.21
51	52	1.754803	CTACTACCTTGGATGTGGCGA	59.245	52.381	0.00	0.00	0.00	5.54
69	70	0.884704	GACAACGCTTCCTCCTTGCA	60.885	55.000	0.00	0.00	0.00	4.08
276	277	2.716424	TCAAAGTGGGGATGAAGGAGTT	59.284	45.455	0.00	0.00	0.00	3.01
281	282	2.040412	GTGGGGATGAAGGAGTTCAAGT	59.960	50.000	0.00	0.00	45.88	3.16
349	350	1.069090	GTCAACTGTCACCGCCAGA	59.931	57.895	0.00	0.00	34.04	3.86
381	385	4.113815	CGGGGCAGATGGAGGCAA	62.114	66.667	0.00	0.00	0.00	4.52
393	397	1.349688	TGGAGGCAACCGAACAACTAT	59.650	47.619	0.00	0.00	37.17	2.12
404	408	4.643784	ACCGAACAACTATATCCGAAGACT	59.356	41.667	0.00	0.00	0.00	3.24
492	496	1.094785	CCATGCCTAAAAGGTCACCG	58.905	55.000	0.00	0.00	37.80	4.94
493	497	1.094785	CATGCCTAAAAGGTCACCGG	58.905	55.000	0.00	0.00	37.80	5.28
636	643	6.737254	ACATGAATTTCGTCCGTCTTAAAT	57.263	33.333	0.00	0.00	0.00	1.40
638	645	8.259049	ACATGAATTTCGTCCGTCTTAAATTA	57.741	30.769	0.00	0.00	33.03	1.40
639	646	8.173130	ACATGAATTTCGTCCGTCTTAAATTAC	58.827	33.333	0.00	0.00	33.03	1.89
687	695	0.692476	TCTGTGGTTGGATGGTCAGG	59.308	55.000	0.00	0.00	0.00	3.86
692	700	0.984230	GGTTGGATGGTCAGGTCTCA	59.016	55.000	0.00	0.00	0.00	3.27
709	717	2.590575	ACTGTCAACCGCGTTGGG	60.591	61.111	17.28	11.89	42.99	4.12
724	732	3.063045	GCGTTGGGGTTATCTTTACTTCG	59.937	47.826	0.00	0.00	0.00	3.79
730	760	5.188163	TGGGGTTATCTTTACTTCGTCATGA	59.812	40.000	0.00	0.00	0.00	3.07
738	768	6.406370	TCTTTACTTCGTCATGATTGGATGT	58.594	36.000	0.00	8.15	0.00	3.06
749	779	1.936547	GATTGGATGTTCGGCTCTCAC	59.063	52.381	0.00	0.00	0.00	3.51
750	780	0.684535	TTGGATGTTCGGCTCTCACA	59.315	50.000	0.00	0.00	0.00	3.58
751	781	0.037326	TGGATGTTCGGCTCTCACAC	60.037	55.000	0.00	0.00	0.00	3.82
766	801	7.519970	CGGCTCTCACACTGTTTTAAAGTTATT	60.520	37.037	0.00	0.00	0.00	1.40
794	829	0.918983	ATCATGGTTGGATGGTCGGT	59.081	50.000	0.00	0.00	0.00	4.69

Showing 1 to 25 of 194 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	1.448540	GAGGAGGTGGATGTGCACG	60.449	63.158	13.13	0.00	0.00	5.34
21	22	2.024273	CCAAGGTAGTAGAGGAGGTGGA	60.024	54.545	0.00	0.00	0.00	4.02
51	52	1.148273	TGCAAGGAGGAAGCGTTGT	59.852	52.632	0.00	0.00	36.37	3.32
58	59	4.716784	ACTATCATAGTGTGCAAGGAGGAA	59.283	41.667	0.00	0.00	37.69	3.36
69	70	4.022762	CGCCTTCAGCTACTATCATAGTGT	60.023	45.833	7.66	0.00	40.39	3.55
145	146	1.944676	GCCATCGCGGACTTAGTCG	60.945	63.158	6.13	3.35	36.56	4.18
334	335	1.071471	CCTTCTGGCGGTGACAGTT	59.929	57.895	0.00	0.00	40.10	3.16
381	385	4.643784	AGTCTTCGGATATAGTTGTTCGGT	59.356	41.667	0.00	0.00	0.00	4.69
393	397	3.947910	ACAACGGAAAGTCTTCGGATA	57.052	42.857	0.00	0.00	36.15	2.59
404	408	2.421751	TGTCCTTCCAACAACGGAAA	57.578	45.000	0.00	0.00	44.42	3.13
423	427	2.140717	GTCCCTTTCGTCAACATCGTT	58.859	47.619	0.00	0.00	0.00	3.85
609	614	6.737254	AAGACGGACGAAATTCATGTAAAT	57.263	33.333	0.00	0.00	0.00	1.40
638	645	9.725019	TGAATATTCACACTAGTTCAAATGAGT	57.275	29.630	14.23	0.00	31.01	3.41
668	676	0.692476	CCTGACCATCCAACCACAGA	59.308	55.000	0.00	0.00	0.00	3.41
669	677	0.401738	ACCTGACCATCCAACCACAG	59.598	55.000	0.00	0.00	0.00	3.66
687	695	0.874607	AACGCGGTTGACAGTGAGAC	60.875	55.000	12.47	0.00	0.00	3.36
692	700	2.590575	CCCAACGCGGTTGACAGT	60.591	61.111	12.47	0.00	45.28	3.55
724	732	2.289002	GAGCCGAACATCCAATCATGAC	59.711	50.000	0.00	0.00	0.00	3.06
730	760	1.278985	TGTGAGAGCCGAACATCCAAT	59.721	47.619	0.00	0.00	0.00	3.16
738	768	2.325583	AAAACAGTGTGAGAGCCGAA	57.674	45.000	0.00	0.00	0.00	4.30
766	801	6.015918	ACCATCCAACCATGATCAAGTAAAA	58.984	36.000	0.00	0.00	0.00	1.52
774	809	1.134098	ACCGACCATCCAACCATGATC	60.134	52.381	0.00	0.00	0.00	2.92
780	815	0.613777	AGAGAACCGACCATCCAACC	59.386	55.000	0.00	0.00	0.00	3.77
784	819	0.895530	TGACAGAGAACCGACCATCC	59.104	55.000	0.00	0.00	0.00	3.51
794	829	5.677319	ATTCTAATCCGGTTGACAGAGAA	57.323	39.130	0.00	2.95	0.00	2.87

Showing 1 to 25 of 149 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.