AutoCloner

Multiple sequence alignment - TraesCS6D01G295000

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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	TraesCS6D01G295000	chr6D	100.000	2773	0	0	1	2773	406104210	406106982	0.000000e+00	5121.0
1	TraesCS6D01G295000	chr6D	93.571	140	9	0	120	259	406001659	406001798	2.800000e-50	209.0
2	TraesCS6D01G295000	chr6A	91.284	2811	141	45	1	2773	552483650	552486394	0.000000e+00	3738.0
3	TraesCS6D01G295000	chr6B	93.290	1073	47	12	944	2004	609925110	609926169	0.000000e+00	1559.0
4	TraesCS6D01G295000	chr6B	90.216	971	39	27	7	959	609924164	609925096	0.000000e+00	1216.0
5	TraesCS6D01G295000	chr6B	91.024	713	59	4	1996	2706	609926554	609927263	0.000000e+00	957.0
6	TraesCS6D01G295000	chr6B	90.909	44	4	0	2618	2661	374029677	374029720	2.980000e-05	60.2
7	TraesCS6D01G295000	chr6B	90.909	44	4	0	2618	2661	651612831	651612788	2.980000e-05	60.2
8	TraesCS6D01G295000	chr6B	85.455	55	8	0	2616	2670	527033744	527033690	1.070000e-04	58.4
9	TraesCS6D01G295000	chr5A	83.764	271	40	2	2260	2529	367787588	367787321	1.270000e-63	254.0
10	TraesCS6D01G295000	chr2B	80.851	282	53	1	2315	2595	450448841	450448560	1.290000e-53	220.0
11	TraesCS6D01G295000	chr1A	77.745	337	67	6	2254	2586	360454592	360454260	1.680000e-47	200.0
12	TraesCS6D01G295000	chr1A	80.272	147	25	4	2468	2612	281648336	281648192	1.050000e-19	108.0
13	TraesCS6D01G295000	chr2A	79.208	303	39	12	2307	2608	114567110	114566831	3.650000e-44	189.0
14	TraesCS6D01G295000	chr3A	82.292	192	29	2	2314	2500	702600110	702599919	7.950000e-36	161.0
15	TraesCS6D01G295000	chr3A	86.765	68	9	0	2047	2114	696700001	696699934	2.960000e-10	76.8
16	TraesCS6D01G295000	chr1D	80.368	163	30	2	2451	2612	218891751	218891590	3.750000e-24	122.0
17	TraesCS6D01G295000	chr1D	84.211	57	8	1	2618	2674	383804980	383805035	1.000000e-03	54.7
18	TraesCS6D01G295000	chr3D	75.812	277	45	6	2337	2612	82366786	82366531	1.350000e-23	121.0
19	TraesCS6D01G295000	chr3D	74.729	277	47	8	2309	2583	340435361	340435106	4.890000e-18	102.0
20	TraesCS6D01G295000	chr2D	78.882	161	31	3	2425	2583	317599834	317599993	3.780000e-19	106.0
21	TraesCS6D01G295000	chr2D	84.211	57	8	1	2618	2674	454934956	454935011	1.000000e-03	54.7
22	TraesCS6D01G295000	chr3B	76.440	191	40	5	2425	2612	24520846	24520658	6.320000e-17	99.0
23	TraesCS6D01G295000	chr1B	75.694	144	21	7	2107	2236	648791443	648791300	2.980000e-05	60.2
24	TraesCS6D01G295000	chr5D	90.244	41	4	0	2610	2650	424562344	424562384	1.000000e-03	54.7
25	TraesCS6D01G295000	chr4B	87.500	48	4	2	2618	2664	370691290	370691244	1.000000e-03	54.7

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	TraesCS6D01G295000	chr6D	406104210	406106982	2772	False	5121	5121	100.000	1	2773	1	chr6D.!!$F2	2772
1	TraesCS6D01G295000	chr6A	552483650	552486394	2744	False	3738	3738	91.284	1	2773	1	chr6A.!!$F1	2772
2	TraesCS6D01G295000	chr6B	609924164	609927263	3099	False	1244	1559	91.510	7	2706	3	chr6B.!!$F2	2699

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
964	1031	0.174617	AGCTAGCGCCTGAGAGAAAC	59.825	55.0	9.55	0.0	36.6	2.78	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2654	3134	0.035343	GTTAAGGACCACTCCAGCCC	60.035	60.0	0.0	0.0	39.39	5.19	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
70	71	1.269102	ACAAACTGTGTCGAGTCTCGG	60.269	52.381	21.63	8.05	40.88	4.63
172	173	3.118408	TCTCCATGTGAAGGGGTAAATCG	60.118	47.826	0.00	0.00	0.00	3.34
191	192	2.736682	GATTCCACAACGCCGTCGG	61.737	63.158	6.99	6.99	40.69	4.79
192	193	4.973055	TTCCACAACGCCGTCGGG	62.973	66.667	14.38	5.79	40.69	5.14
259	264	0.597568	TTCACTTTGGCCGATTGCTG	59.402	50.000	0.00	0.00	40.92	4.41
294	305	3.004315	TGAAAAGAAGCCGCACCTAAAAG	59.996	43.478	0.00	0.00	0.00	2.27
331	342	2.480419	CCTCAAAGCTACAAAGGTGTCG	59.520	50.000	0.00	0.00	39.30	4.35
333	344	1.069227	CAAAGCTACAAAGGTGTCGCC	60.069	52.381	0.00	0.00	45.26	5.54
334	345	0.949105	AAGCTACAAAGGTGTCGCCG	60.949	55.000	0.00	0.00	45.26	6.46
335	346	2.388232	GCTACAAAGGTGTCGCCGG	61.388	63.158	0.00	0.00	39.84	6.13
368	379	0.839853	ATCTCCTAGCAGGGCATCCC	60.840	60.000	0.00	0.00	45.90	3.85
455	475	4.216687	TGACCACCCGCAAATTTTAACTAG	59.783	41.667	0.00	0.00	0.00	2.57
458	478	5.181811	ACCACCCGCAAATTTTAACTAGTAC	59.818	40.000	0.00	0.00	0.00	2.73
490	513	5.362263	GTGTAGTCTAGTCCTCTAGTGGAG	58.638	50.000	13.84	3.26	42.88	3.86
497	520	3.897239	AGTCCTCTAGTGGAGTCAGATG	58.103	50.000	13.84	0.00	40.30	2.90
498	521	3.268334	AGTCCTCTAGTGGAGTCAGATGT	59.732	47.826	13.84	0.00	40.30	3.06
539	563	8.822652	AAAGCATTTTCTGTTAGAAGAATTGG	57.177	30.769	0.00	0.00	31.62	3.16
542	566	9.077885	AGCATTTTCTGTTAGAAGAATTGGTAA	57.922	29.630	0.00	0.00	35.37	2.85
561	585	4.991687	GGTAATGAAAAGATCGAGCTAGGG	59.008	45.833	2.34	0.00	0.00	3.53
562	586	4.762289	AATGAAAAGATCGAGCTAGGGT	57.238	40.909	2.34	0.00	0.00	4.34
563	587	5.871396	AATGAAAAGATCGAGCTAGGGTA	57.129	39.130	2.34	0.00	0.00	3.69
605	629	9.188588	GCTGATCACCAAATGTTTATGAATATG	57.811	33.333	0.00	0.00	0.00	1.78
618	642	7.658167	TGTTTATGAATATGTACATACACGGGG	59.342	37.037	17.69	0.00	39.30	5.73
625	649	1.396607	TACATACACGGGGCGATGCT	61.397	55.000	0.00	0.00	0.00	3.79
630	654	2.203070	ACGGGGCGATGCTGATTC	60.203	61.111	0.00	0.00	0.00	2.52

Showing 1 to 25 of 88 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	5.346281	GGATCATGTATACTTGCTTAGACGC	59.654	44.000	12.71	0.00	0.00	5.19
62	63	1.149148	GTTTCAAGGTGCCGAGACTC	58.851	55.000	0.00	0.00	0.00	3.36
70	71	0.305313	TTGCGTACGTTTCAAGGTGC	59.695	50.000	17.90	0.00	0.00	5.01
172	173	2.736682	CGACGGCGTTGTGGAATCC	61.737	63.158	16.19	0.00	0.00	3.01
259	264	7.624344	GCGGCTTCTTTTCACATGATATATACC	60.624	40.741	0.00	0.00	0.00	2.73
331	342	3.782046	AGATACGCATATATCAACCGGC	58.218	45.455	0.00	0.00	34.50	6.13
333	344	5.250235	AGGAGATACGCATATATCAACCG	57.750	43.478	0.00	0.00	36.38	4.44
334	345	6.183360	TGCTAGGAGATACGCATATATCAACC	60.183	42.308	0.00	3.30	34.50	3.77
335	346	6.796426	TGCTAGGAGATACGCATATATCAAC	58.204	40.000	0.00	0.00	34.50	3.18
368	379	4.201871	TGCACTTCACCTGTTCTTTTTACG	60.202	41.667	0.00	0.00	0.00	3.18
455	475	6.580416	GGACTAGACTACACGACTTTTTGTAC	59.420	42.308	0.00	0.00	0.00	2.90
458	478	5.770417	AGGACTAGACTACACGACTTTTTG	58.230	41.667	0.00	0.00	0.00	2.44
539	563	5.602628	ACCCTAGCTCGATCTTTTCATTAC	58.397	41.667	0.00	0.00	0.00	1.89
542	566	4.896482	ACTACCCTAGCTCGATCTTTTCAT	59.104	41.667	0.00	0.00	0.00	2.57
544	568	4.922471	ACTACCCTAGCTCGATCTTTTC	57.078	45.455	0.00	0.00	0.00	2.29
561	585	6.752351	TGATCAGCTCGTCTAATTTGAACTAC	59.248	38.462	0.00	0.00	0.00	2.73
562	586	6.752351	GTGATCAGCTCGTCTAATTTGAACTA	59.248	38.462	0.00	0.00	0.00	2.24
563	587	5.578727	GTGATCAGCTCGTCTAATTTGAACT	59.421	40.000	0.00	0.00	0.00	3.01
605	629	1.219522	GCATCGCCCCGTGTATGTAC	61.220	60.000	0.00	0.00	0.00	2.90
606	630	1.068417	GCATCGCCCCGTGTATGTA	59.932	57.895	0.00	0.00	0.00	2.29
607	631	2.203015	GCATCGCCCCGTGTATGT	60.203	61.111	0.00	0.00	0.00	2.29
608	632	2.108976	AGCATCGCCCCGTGTATG	59.891	61.111	0.00	0.00	0.00	2.39
614	638	3.341043	CGAATCAGCATCGCCCCG	61.341	66.667	0.00	0.00	33.07	5.73
618	642	0.305617	TTGCATCGAATCAGCATCGC	59.694	50.000	6.13	0.00	40.04	4.58
625	649	5.427378	TGAAAGGACTATTGCATCGAATCA	58.573	37.500	0.00	0.00	0.00	2.57

Showing 1 to 25 of 82 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.