AutoCloner

Multiple sequence alignment - TraesCS4B01G318400

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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	TraesCS4B01G318400	chr4B	100.000	5773	0	0	1	5773	608965689	608971461	0.000000e+00	10661.0
1	TraesCS4B01G318400	chr4B	92.398	171	12	1	5222	5391	61314274	61314104	5.780000e-60	243.0
2	TraesCS4B01G318400	chr4B	99.153	118	1	0	2939	3056	545037295	545037178	4.530000e-51	213.0
3	TraesCS4B01G318400	chr4B	94.737	133	6	1	3463	3594	20719388	20719256	7.580000e-49	206.0
4	TraesCS4B01G318400	chr4B	93.182	132	9	0	5260	5391	522286018	522285887	1.640000e-45	195.0
5	TraesCS4B01G318400	chr4B	90.909	143	11	2	3468	3609	300811321	300811462	2.120000e-44	191.0
6	TraesCS4B01G318400	chr4B	90.541	148	8	6	3463	3608	425296292	425296149	2.120000e-44	191.0
7	TraesCS4B01G318400	chr4B	90.972	144	7	6	3469	3611	132331055	132331193	7.640000e-44	189.0
8	TraesCS4B01G318400	chr4D	89.851	2020	109	48	1	1982	480878248	480880209	0.000000e+00	2507.0
9	TraesCS4B01G318400	chr4D	93.349	1308	62	13	3593	4891	480881389	480882680	0.000000e+00	1910.0
10	TraesCS4B01G318400	chr4D	93.408	622	32	7	2028	2647	480880197	480880811	0.000000e+00	913.0
11	TraesCS4B01G318400	chr4D	91.697	277	10	3	2678	2941	480880815	480881091	7.060000e-99	372.0
12	TraesCS4B01G318400	chr4D	97.895	190	4	0	3283	3472	480881200	480881389	4.310000e-86	329.0
13	TraesCS4B01G318400	chr4D	80.531	339	21	26	5467	5773	480883323	480883648	9.740000e-53	219.0
14	TraesCS4B01G318400	chr4D	94.643	112	6	0	3055	3166	480881090	480881201	2.140000e-39	174.0
15	TraesCS4B01G318400	chr4D	93.617	47	3	0	5163	5209	480883212	480883258	2.890000e-08	71.3
16	TraesCS4B01G318400	chr5A	88.280	1988	139	57	3	1938	662532394	662530449	0.000000e+00	2294.0
17	TraesCS4B01G318400	chr5A	91.703	1627	92	17	3591	5209	662529164	662527573	0.000000e+00	2217.0
18	TraesCS4B01G318400	chr5A	87.661	932	80	14	2040	2941	662530381	662529455	0.000000e+00	1051.0
19	TraesCS4B01G318400	chr5A	95.789	190	6	1	3281	3470	662529348	662529161	7.270000e-79	305.0
20	TraesCS4B01G318400	chr5A	94.815	135	5	2	3469	3601	652657840	652657706	5.860000e-50	209.0
21	TraesCS4B01G318400	chr5A	90.476	147	10	4	3467	3611	708307783	708307639	2.120000e-44	191.0
22	TraesCS4B01G318400	chr5A	95.327	107	5	0	3055	3161	662529456	662529350	2.770000e-38	171.0
23	TraesCS4B01G318400	chr5A	78.138	247	39	10	1	240	320058493	320058731	6.030000e-30	143.0
24	TraesCS4B01G318400	chr5A	83.117	154	10	6	5489	5641	662527500	662527362	6.070000e-25	126.0
25	TraesCS4B01G318400	chr5A	93.103	58	0	3	5402	5459	662527563	662527510	1.330000e-11	82.4
26	TraesCS4B01G318400	chr3B	89.860	286	12	7	4951	5233	717561137	717560866	9.200000e-93	351.0
27	TraesCS4B01G318400	chr3B	94.340	159	8	1	5236	5393	815182903	815183061	5.780000e-60	243.0
28	TraesCS4B01G318400	chr3B	98.361	122	2	0	2940	3061	667390119	667389998	1.260000e-51	215.0
29	TraesCS4B01G318400	chr3B	82.018	228	19	15	5392	5605	717560871	717560652	2.140000e-39	174.0
30	TraesCS4B01G318400	chr3B	85.057	87	8	3	3198	3284	713874113	713874032	3.710000e-12	84.2
31	TraesCS4B01G318400	chr5B	88.811	286	15	8	4951	5233	42874090	42873819	9.270000e-88	335.0
32	TraesCS4B01G318400	chr5B	99.153	118	1	0	2940	3057	711156068	711155951	4.530000e-51	213.0
33	TraesCS4B01G318400	chr5B	91.837	147	8	4	3468	3611	18077089	18076944	9.810000e-48	202.0
34	TraesCS4B01G318400	chr5B	84.000	225	18	12	5392	5606	42873824	42873608	3.530000e-47	200.0
35	TraesCS4B01G318400	chr5B	92.254	142	9	2	3460	3600	118525764	118525904	3.530000e-47	200.0
36	TraesCS4B01G318400	chr6B	93.567	171	10	1	5224	5393	561695754	561695924	2.670000e-63	254.0
37	TraesCS4B01G318400	chr6B	94.776	134	6	1	2939	3072	164883035	164882903	2.110000e-49	207.0
38	TraesCS4B01G318400	chr6B	93.478	138	7	2	2940	3075	658678568	658678705	2.730000e-48	204.0
39	TraesCS4B01G318400	chr1B	96.129	155	5	1	5236	5389	301635740	301635894	9.600000e-63	252.0
40	TraesCS4B01G318400	chr1B	95.385	130	4	2	3469	3597	50989950	50990078	7.580000e-49	206.0
41	TraesCS4B01G318400	chr1B	82.645	121	21	0	1594	1714	491040849	491040729	2.200000e-19	108.0
42	TraesCS4B01G318400	chr1B	97.436	39	1	0	3165	3203	320588132	320588094	3.730000e-07	67.6
43	TraesCS4B01G318400	chr6A	95.484	155	5	2	5236	5389	531408681	531408834	4.470000e-61	246.0
44	TraesCS4B01G318400	chr6A	92.308	169	10	3	5229	5395	58764721	58764554	2.690000e-58	237.0
45	TraesCS4B01G318400	chr6A	97.561	123	3	0	2937	3059	601207222	601207344	1.630000e-50	211.0
46	TraesCS4B01G318400	chr6A	85.185	81	9	1	3205	3282	607680091	607680171	4.800000e-11	80.5
47	TraesCS4B01G318400	chr3A	95.484	155	6	1	5236	5389	163792625	163792471	4.470000e-61	246.0
48	TraesCS4B01G318400	chr3A	90.476	147	10	4	3467	3611	405828114	405827970	2.120000e-44	191.0
49	TraesCS4B01G318400	chr4A	94.839	155	7	1	5236	5389	710670511	710670665	2.080000e-59	241.0
50	TraesCS4B01G318400	chr4A	92.222	90	7	0	3200	3289	738372227	738372316	1.690000e-25	128.0
51	TraesCS4B01G318400	chr4A	84.524	84	4	6	3202	3285	5817676	5817750	2.230000e-09	75.0
52	TraesCS4B01G318400	chr2B	93.750	160	9	1	5236	5394	504194992	504195151	7.480000e-59	239.0
53	TraesCS4B01G318400	chr2B	95.489	133	3	2	3469	3598	19447944	19447812	5.860000e-50	209.0
54	TraesCS4B01G318400	chr5D	99.167	120	1	0	2939	3058	47283883	47284002	3.500000e-52	217.0
55	TraesCS4B01G318400	chr5D	97.561	123	3	0	2934	3056	462793848	462793970	1.630000e-50	211.0
56	TraesCS4B01G318400	chr3D	94.245	139	4	2	2939	3077	66262961	66262827	5.860000e-50	209.0
57	TraesCS4B01G318400	chr3D	84.783	92	5	2	3200	3282	94644848	94644757	3.710000e-12	84.2
58	TraesCS4B01G318400	chr3D	100.000	28	0	0	212	239	574723828	574723855	1.000000e-02	52.8
59	TraesCS4B01G318400	chr7B	95.420	131	5	1	3466	3595	736367488	736367618	2.110000e-49	207.0
60	TraesCS4B01G318400	chr7B	92.308	143	8	3	3463	3604	227053654	227053794	3.530000e-47	200.0
61	TraesCS4B01G318400	chr7B	90.476	147	12	2	3462	3607	141907369	141907224	5.900000e-45	193.0
62	TraesCS4B01G318400	chr7B	85.542	83	6	4	3200	3282	168752754	168752678	1.330000e-11	82.4
63	TraesCS4B01G318400	chr7B	83.721	86	13	1	1	85	88859967	88859882	4.800000e-11	80.5
64	TraesCS4B01G318400	chr2A	92.857	140	8	2	3463	3600	70030628	70030767	9.810000e-48	202.0
65	TraesCS4B01G318400	chr1D	89.865	148	12	3	3466	3611	384835328	384835474	2.750000e-43	187.0
66	TraesCS4B01G318400	chr1D	86.792	106	13	1	29	134	363057792	363057896	3.650000e-22	117.0
67	TraesCS4B01G318400	chr1D	83.065	124	21	0	1591	1714	366723826	366723949	4.730000e-21	113.0
68	TraesCS4B01G318400	chr1D	88.235	85	9	1	3200	3284	310858581	310858498	3.680000e-17	100.0
69	TraesCS4B01G318400	chr2D	88.816	152	13	4	3461	3611	619720539	619720687	3.550000e-42	183.0
70	TraesCS4B01G318400	chr2D	87.640	89	6	1	3159	3242	584666822	584666910	1.320000e-16	99.0
71	TraesCS4B01G318400	chr1A	83.333	120	20	0	1595	1714	465454634	465454515	1.700000e-20	111.0
72	TraesCS4B01G318400	chr1A	92.308	39	3	0	3162	3200	172566506	172566544	8.080000e-04	56.5
73	TraesCS4B01G318400	chr7D	82.609	115	17	3	19	132	1248611	1248723	1.320000e-16	99.0
74	TraesCS4B01G318400	chr6D	83.146	89	10	5	3200	3287	7460256	7460172	6.200000e-10	76.8

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	TraesCS4B01G318400	chr4B	608965689	608971461	5772	False	10661.000000	10661	100.000000	1	5773	1	chr4B.!!$F3	5772
1	TraesCS4B01G318400	chr4D	480878248	480883648	5400	False	811.912500	2507	91.873875	1	5773	8	chr4D.!!$F1	5772
2	TraesCS4B01G318400	chr5A	662527362	662532394	5032	True	892.342857	2294	90.711429	3	5641	7	chr5A.!!$R3	5638

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
667	702	0.035317	GATACATCTCATGGCGCCCA	59.965	55.0	26.77	12.96	38.19	5.36	F
757	799	0.109342	CTGCTTCTGGGTCCACAGTT	59.891	55.0	0.00	0.00	39.48	3.16	F
785	827	0.163788	CCACGTGTCATTGAACGAGC	59.836	55.0	15.65	0.00	42.32	5.03	F
791	833	0.234625	GTCATTGAACGAGCGCAACA	59.765	50.0	11.47	0.00	0.00	3.33	F
1996	2074	0.247814	GCATCGTGCGAGTTTGATGG	60.248	55.0	0.00	0.00	38.85	3.51	F
2958	3081	0.032813	TACTCCCTCCGTCCGGAAAT	60.033	55.0	5.23	0.00	44.66	2.17	F
2961	3084	0.032813	TCCCTCCGTCCGGAAATACT	60.033	55.0	5.23	0.00	44.66	2.12	F
4612	4747	0.110688	CACTCACATTGTCAACCGCG	60.111	55.0	0.00	0.00	0.00	6.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2376	2480	0.034059	CTGACGAGGTTCTTGTGCCT	59.966	55.000	0.00	37.91	4.75	R
2414	2518	0.968901	TGTACCTGTAGGCACCCTCG	60.969	60.000	0.00	39.32	4.63	R
2665	2770	1.256812	ATAGCACTTGGCAAACCCAC	58.743	50.000	0.00	45.34	4.61	R
2779	2899	8.394121	GTCTTCTAAGAACTAAAATGCTCATGG	58.606	37.037	0.00	36.68	3.66	R
2939	3062	0.032813	ATTTCCGGACGGAGGGAGTA	60.033	55.000	13.64	46.06	2.59	R
4593	4728	0.110688	CGCGGTTGACAATGTGAGTG	60.111	55.000	0.00	0.00	3.51	R
4717	4852	1.538512	GTGCCATTCCCATCATCATCG	59.461	52.381	0.00	0.00	3.84	R
5523	5972	0.036590	ACCAAACCAATGGCAATGGC	59.963	50.000	21.40	44.75	4.40	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
31	32	8.850007	AAAAAGAACTAAAGAGGTAGATCCAC	57.150	34.615	0.00	0.00	39.02	4.02
96	97	0.108186	TCCAATGACGAGCGCTCAAT	60.108	50.000	34.69	23.30	0.00	2.57
99	100	3.005367	TCCAATGACGAGCGCTCAATATA	59.995	43.478	34.69	17.13	0.00	0.86
142	143	4.400884	TCATGCCAAATATAAAACGCCAGT	59.599	37.500	0.00	0.00	0.00	4.00
143	144	4.103365	TGCCAAATATAAAACGCCAGTG	57.897	40.909	0.00	0.00	0.00	3.66
189	202	4.942761	ACCCAATATCCATGTGCAATTC	57.057	40.909	0.00	0.00	0.00	2.17
196	209	8.192774	CCAATATCCATGTGCAATTCATATACC	58.807	37.037	0.00	0.00	0.00	2.73
197	210	8.741841	CAATATCCATGTGCAATTCATATACCA	58.258	33.333	0.00	0.00	0.00	3.25
199	212	5.693961	TCCATGTGCAATTCATATACCACT	58.306	37.500	0.00	0.00	0.00	4.00
200	213	5.532032	TCCATGTGCAATTCATATACCACTG	59.468	40.000	0.00	0.00	0.00	3.66
201	214	4.898829	TGTGCAATTCATATACCACTGC	57.101	40.909	0.00	0.00	0.00	4.40
202	215	4.268359	TGTGCAATTCATATACCACTGCA	58.732	39.130	0.00	0.00	36.06	4.41
219	232	4.907582	CACTGCATAATATCAACGTGCATG	59.092	41.667	3.82	3.82	43.89	4.06
221	234	3.314635	TGCATAATATCAACGTGCATGCA	59.685	39.130	18.46	18.46	43.48	3.96
274	290	4.711355	CACAATCCCATTAATTGACACCCT	59.289	41.667	3.06	0.00	37.51	4.34
275	291	5.890985	CACAATCCCATTAATTGACACCCTA	59.109	40.000	3.06	0.00	37.51	3.53
276	292	6.039717	CACAATCCCATTAATTGACACCCTAG	59.960	42.308	3.06	0.00	37.51	3.02
277	293	4.164843	TCCCATTAATTGACACCCTAGC	57.835	45.455	0.00	0.00	0.00	3.42
278	294	3.525609	TCCCATTAATTGACACCCTAGCA	59.474	43.478	0.00	0.00	0.00	3.49
279	295	3.632145	CCCATTAATTGACACCCTAGCAC	59.368	47.826	0.00	0.00	0.00	4.40
283	301	6.127366	CCATTAATTGACACCCTAGCACATTT	60.127	38.462	0.00	0.00	0.00	2.32
325	345	9.308000	ACATTCTATTCCCAGTAAAAATCAACA	57.692	29.630	0.00	0.00	0.00	3.33
400	421	5.897377	ATTTAGAACAAAAGATCCCACCG	57.103	39.130	0.00	0.00	0.00	4.94
440	462	5.769662	TGGTGATAAAGCACACTCTTTGATT	59.230	36.000	0.33	0.00	40.52	2.57
479	502	7.820648	ACATAGACAACTAGGCAAAAATGAAG	58.179	34.615	0.00	0.00	34.28	3.02

Showing 1 to 25 of 523 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	3.157881	CGGCTGAGATTAGGTGGATCTA	58.842	50.000	0.00	0.00	34.13	1.98
31	32	1.927174	CGTTTGACGGCTGAGATTAGG	59.073	52.381	0.00	0.00	38.08	2.69
40	41	0.034896	ATTGACCTCGTTTGACGGCT	59.965	50.000	0.00	0.00	42.81	5.52
41	42	0.442699	GATTGACCTCGTTTGACGGC	59.557	55.000	0.27	0.00	42.81	5.68
75	76	1.153745	GAGCGCTCGTCATTGGAGT	60.154	57.895	23.61	0.00	34.00	3.85
99	100	7.329226	GGCATGATATTAATTGCAACGCTAAAT	59.671	33.333	0.00	0.19	36.82	1.40
164	177	3.052329	TGCACATGGATATTGGGTAGGA	58.948	45.455	0.00	0.00	0.00	2.94
171	184	8.741841	TGGTATATGAATTGCACATGGATATTG	58.258	33.333	0.00	0.00	0.00	1.90
180	193	4.268359	TGCAGTGGTATATGAATTGCACA	58.732	39.130	0.00	0.00	35.41	4.57
189	202	8.382875	CACGTTGATATTATGCAGTGGTATATG	58.617	37.037	0.00	0.00	0.00	1.78
196	209	4.534794	TGCACGTTGATATTATGCAGTG	57.465	40.909	0.00	0.00	41.18	3.66
200	213	3.665409	GTGCATGCACGTTGATATTATGC	59.335	43.478	33.20	7.24	39.72	3.14
219	232	8.792831	ATACATACTAGTAATTGTGTACGTGC	57.207	34.615	16.17	0.00	0.00	5.34
255	271	4.167892	TGCTAGGGTGTCAATTAATGGGAT	59.832	41.667	0.00	0.00	0.00	3.85
304	322	7.492344	GCCATTGTTGATTTTTACTGGGAATAG	59.508	37.037	0.00	0.00	0.00	1.73
305	323	7.038729	TGCCATTGTTGATTTTTACTGGGAATA	60.039	33.333	0.00	0.00	0.00	1.75
309	327	4.892433	TGCCATTGTTGATTTTTACTGGG	58.108	39.130	0.00	0.00	0.00	4.45
325	345	3.467374	ACGTTCCAAAATGTTGCCATT	57.533	38.095	0.00	0.00	43.14	3.16
400	421	3.554934	TCACCACTTGGATCAATATGGC	58.445	45.455	1.14	0.00	34.69	4.40
440	462	6.318648	AGTTGTCTATGTCTTTTGCTTTGTGA	59.681	34.615	0.00	0.00	0.00	3.58
457	480	6.770785	ACACTTCATTTTTGCCTAGTTGTCTA	59.229	34.615	0.00	0.00	0.00	2.59
479	502	3.242712	CGTGCAATCACCTTTTGAAACAC	59.757	43.478	0.00	0.00	40.04	3.32
484	507	4.517075	TGTTATCGTGCAATCACCTTTTGA	59.483	37.500	0.00	0.00	40.04	2.69
497	520	3.152261	AGTCAGCTAGTGTTATCGTGC	57.848	47.619	0.00	0.00	0.00	5.34
527	550	9.349713	TCAACTTTTGTCAAGGATTATTAGTGT	57.650	29.630	0.00	0.00	0.00	3.55

Showing 1 to 25 of 486 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.