AutoCloner

Multiple sequence alignment - TraesCS4B01G302200

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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	TraesCS4B01G302200	chr4B	100.000	3392	0	0	1	3392	588789623	588786232	0.000000e+00	6264.0
1	TraesCS4B01G302200	chr4B	79.439	1391	244	35	995	2364	588693931	588692562	0.000000e+00	946.0
2	TraesCS4B01G302200	chr4B	80.519	154	27	3	3231	3383	671133387	671133236	7.690000e-22	115.0
3	TraesCS4B01G302200	chr4D	93.632	1696	79	20	816	2494	469074189	469072506	0.000000e+00	2507.0
4	TraesCS4B01G302200	chr4D	81.809	940	150	14	1431	2364	468899385	468898461	0.000000e+00	769.0
5	TraesCS4B01G302200	chr4D	80.717	949	161	13	1429	2371	468862699	468861767	0.000000e+00	719.0
6	TraesCS4B01G302200	chr4D	84.713	628	33	22	7	608	469075722	469075132	1.370000e-158	569.0
7	TraesCS4B01G302200	chr4D	88.316	291	10	6	452	734	469074462	469074188	9.080000e-86	327.0
8	TraesCS4B01G302200	chr4A	92.389	1708	87	18	816	2494	2637748	2636055	0.000000e+00	2394.0
9	TraesCS4B01G302200	chr4A	80.720	944	163	12	1433	2371	2775105	2776034	0.000000e+00	717.0
10	TraesCS4B01G302200	chr4A	80.252	952	159	17	1433	2371	2555799	2554864	0.000000e+00	689.0
11	TraesCS4B01G302200	chr4A	84.404	436	34	12	160	590	2638524	2638118	6.820000e-107	398.0
12	TraesCS4B01G302200	chr4A	99.160	119	1	0	2639	2757	150130415	150130533	7.370000e-52	215.0
13	TraesCS4B01G302200	chr4A	97.561	123	3	0	2639	2761	178478747	178478869	9.540000e-51	211.0
14	TraesCS4B01G302200	chr4A	82.000	150	16	9	3240	3384	742547296	742547153	2.140000e-22	117.0
15	TraesCS4B01G302200	chr2D	90.010	981	86	3	1415	2392	636355196	636356167	0.000000e+00	1258.0
16	TraesCS4B01G302200	chr2D	91.944	360	28	1	988	1347	636354744	636355102	1.400000e-138	503.0
17	TraesCS4B01G302200	chr2D	98.347	121	2	0	2639	2759	299720620	299720500	2.650000e-51	213.0
18	TraesCS4B01G302200	chr7A	81.144	944	171	6	1432	2370	101433562	101434503	0.000000e+00	750.0
19	TraesCS4B01G302200	chr7A	81.402	328	59	2	992	1318	101432997	101433323	2.010000e-67	267.0
20	TraesCS4B01G302200	chr7A	98.361	122	2	0	2639	2760	466311144	466311265	7.370000e-52	215.0
21	TraesCS4B01G302200	chr1D	98.374	123	2	0	2639	2761	270901003	270900881	2.050000e-52	217.0
22	TraesCS4B01G302200	chr1D	79.195	149	17	10	3239	3381	405387918	405388058	1.300000e-14	91.6
23	TraesCS4B01G302200	chr6D	98.361	122	2	0	2639	2760	345490303	345490424	7.370000e-52	215.0
24	TraesCS4B01G302200	chr3D	98.361	122	2	0	2639	2760	359257840	359257719	7.370000e-52	215.0
25	TraesCS4B01G302200	chr5A	97.561	123	3	0	2638	2760	577784192	577784070	9.540000e-51	211.0
26	TraesCS4B01G302200	chr5A	81.928	83	8	6	36	115	516808439	516808361	2.830000e-06	63.9
27	TraesCS4B01G302200	chr5A	83.824	68	8	2	3232	3299	481935028	481934964	1.020000e-05	62.1
28	TraesCS4B01G302200	chr3B	97.561	123	3	0	2638	2760	699701565	699701443	9.540000e-51	211.0
29	TraesCS4B01G302200	chr2A	78.405	301	63	2	1001	1300	767986311	767986012	9.600000e-46	195.0
30	TraesCS4B01G302200	chr2A	78.378	148	25	6	3239	3384	565322745	565322603	4.660000e-14	89.8
31	TraesCS4B01G302200	chr2B	79.004	281	59	0	995	1275	787533946	787533666	3.450000e-45	193.0
32	TraesCS4B01G302200	chrUn	78.292	281	61	0	1001	1281	31626412	31626132	7.480000e-42	182.0
33	TraesCS4B01G302200	chr7D	82.653	98	17	0	2775	2872	190144059	190144156	1.680000e-13	87.9
34	TraesCS4B01G302200	chr7D	80.612	98	17	2	2775	2871	549931190	549931094	1.310000e-09	75.0
35	TraesCS4B01G302200	chr7D	100.000	32	0	0	2833	2864	53628149	53628180	3.660000e-05	60.2

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	TraesCS4B01G302200	chr4B	588786232	588789623	3391	True	6264.000000	6264	100.0000	1	3392	1	chr4B.!!$R2	3391
1	TraesCS4B01G302200	chr4B	588692562	588693931	1369	True	946.000000	946	79.4390	995	2364	1	chr4B.!!$R1	1369
2	TraesCS4B01G302200	chr4D	469072506	469075722	3216	True	1134.333333	2507	88.8870	7	2494	3	chr4D.!!$R3	2487
3	TraesCS4B01G302200	chr4D	468898461	468899385	924	True	769.000000	769	81.8090	1431	2364	1	chr4D.!!$R2	933
4	TraesCS4B01G302200	chr4D	468861767	468862699	932	True	719.000000	719	80.7170	1429	2371	1	chr4D.!!$R1	942
5	TraesCS4B01G302200	chr4A	2636055	2638524	2469	True	1396.000000	2394	88.3965	160	2494	2	chr4A.!!$R3	2334
6	TraesCS4B01G302200	chr4A	2775105	2776034	929	False	717.000000	717	80.7200	1433	2371	1	chr4A.!!$F1	938
7	TraesCS4B01G302200	chr4A	2554864	2555799	935	True	689.000000	689	80.2520	1433	2371	1	chr4A.!!$R1	938
8	TraesCS4B01G302200	chr2D	636354744	636356167	1423	False	880.500000	1258	90.9770	988	2392	2	chr2D.!!$F1	1404
9	TraesCS4B01G302200	chr7A	101432997	101434503	1506	False	508.500000	750	81.2730	992	2370	2	chr7A.!!$F2	1378

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
388	392	0.029834	GCGTGCAATGGGCTAGATTG	59.970	55.0	0.0	0.0	45.15	2.67	F
954	2071	0.096976	CGTGCAAAATGGAGGCTACG	59.903	55.0	0.0	0.0	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1878	3137	0.827925	TCACCTGCGTGAACTCCTCT	60.828	55.0	0.0	0.0	46.09	3.69	R
2547	3811	0.031314	AGAGATAGGATGTGTGCGCG	59.969	55.0	0.0	0.0	0.00	6.86	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)

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	2.611225	TGTGTGTGTGTGTGCTGATA	57.389	45.000	0.00	0.00	0.00	2.15
36	37	3.252944	TGTGTGTGTGCTGATATTGGTTG	59.747	43.478	0.00	0.00	0.00	3.77
44	45	3.129113	TGCTGATATTGGTTGTGTGCATC	59.871	43.478	0.00	0.00	0.00	3.91
45	46	3.379372	GCTGATATTGGTTGTGTGCATCT	59.621	43.478	0.00	0.00	0.00	2.90
48	49	6.404623	GCTGATATTGGTTGTGTGCATCTTAA	60.405	38.462	0.00	0.00	0.00	1.85
49	50	7.643569	TGATATTGGTTGTGTGCATCTTAAT	57.356	32.000	0.00	0.00	0.00	1.40
62	63	5.578727	GTGCATCTTAATTATAGAGAGGCCG	59.421	44.000	15.83	0.00	44.12	6.13
63	64	5.480422	TGCATCTTAATTATAGAGAGGCCGA	59.520	40.000	15.83	0.90	44.12	5.54
64	65	6.039616	GCATCTTAATTATAGAGAGGCCGAG	58.960	44.000	9.97	0.00	40.28	4.63
65	66	6.350612	GCATCTTAATTATAGAGAGGCCGAGT	60.351	42.308	9.97	0.00	40.28	4.18
66	67	6.576662	TCTTAATTATAGAGAGGCCGAGTG	57.423	41.667	0.00	0.00	0.00	3.51
67	68	6.069331	TCTTAATTATAGAGAGGCCGAGTGT	58.931	40.000	0.00	0.00	0.00	3.55
71	72	1.595993	TAGAGAGGCCGAGTGTGTGC	61.596	60.000	0.00	0.00	0.00	4.57
76	77	1.136305	GAGGCCGAGTGTGTGCTTATA	59.864	52.381	0.00	0.00	0.00	0.98
79	80	2.943033	GGCCGAGTGTGTGCTTATAATT	59.057	45.455	0.00	0.00	0.00	1.40
273	274	0.321122	CAGCCTCGCTTCCTTTGACT	60.321	55.000	0.00	0.00	36.40	3.41
303	307	3.315749	GTCCCTCAGGTACGACAGAATAG	59.684	52.174	0.00	0.00	0.00	1.73
330	334	4.119862	TCTACGGATCTGCATGTTAAAGC	58.880	43.478	0.00	0.00	0.00	3.51
331	335	2.710377	ACGGATCTGCATGTTAAAGCA	58.290	42.857	0.00	0.00	39.25	3.91
332	336	3.081061	ACGGATCTGCATGTTAAAGCAA	58.919	40.909	0.00	0.00	40.73	3.91
333	337	3.127548	ACGGATCTGCATGTTAAAGCAAG	59.872	43.478	0.00	0.00	40.73	4.01
334	338	3.488047	CGGATCTGCATGTTAAAGCAAGG	60.488	47.826	0.00	0.00	40.73	3.61
360	364	1.232119	CCTGTTACCACGAAACACCC	58.768	55.000	0.00	0.00	33.45	4.61
361	365	1.475392	CCTGTTACCACGAAACACCCA	60.475	52.381	0.00	0.00	33.45	4.51
381	385	3.876198	CCGTAGCGTGCAATGGGC	61.876	66.667	0.00	0.00	45.13	5.36

Showing 1 to 25 of 705 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	2.294512	TCAGCACACACACACACAAAAA	59.705	40.909	0.00	0.00	0.00	1.94
7	8	1.882623	TCAGCACACACACACACAAAA	59.117	42.857	0.00	0.00	0.00	2.44
8	9	1.528129	TCAGCACACACACACACAAA	58.472	45.000	0.00	0.00	0.00	2.83
9	10	1.748950	ATCAGCACACACACACACAA	58.251	45.000	0.00	0.00	0.00	3.33
10	11	2.611225	TATCAGCACACACACACACA	57.389	45.000	0.00	0.00	0.00	3.72
11	12	3.365264	CCAATATCAGCACACACACACAC	60.365	47.826	0.00	0.00	0.00	3.82
12	13	2.813172	CCAATATCAGCACACACACACA	59.187	45.455	0.00	0.00	0.00	3.72
13	14	2.813754	ACCAATATCAGCACACACACAC	59.186	45.455	0.00	0.00	0.00	3.82
24	25	5.571784	AAGATGCACACAACCAATATCAG	57.428	39.130	0.00	0.00	0.00	2.90
29	30	9.407380	TCTATAATTAAGATGCACACAACCAAT	57.593	29.630	0.00	0.00	0.00	3.16
36	37	6.370166	GGCCTCTCTATAATTAAGATGCACAC	59.630	42.308	12.23	0.00	33.82	3.82
44	45	6.153067	CACACTCGGCCTCTCTATAATTAAG	58.847	44.000	0.00	0.00	0.00	1.85
45	46	5.597182	ACACACTCGGCCTCTCTATAATTAA	59.403	40.000	0.00	0.00	0.00	1.40
48	49	3.319405	CACACACTCGGCCTCTCTATAAT	59.681	47.826	0.00	0.00	0.00	1.28
49	50	2.688446	CACACACTCGGCCTCTCTATAA	59.312	50.000	0.00	0.00	0.00	0.98
53	54	2.936912	GCACACACTCGGCCTCTCT	61.937	63.158	0.00	0.00	0.00	3.10
54	55	2.433318	GCACACACTCGGCCTCTC	60.433	66.667	0.00	0.00	0.00	3.20
149	150	0.472044	GTGCCCACCCATTGGTTTTT	59.528	50.000	1.20	0.00	44.75	1.94
273	274	1.913951	TACCTGAGGGACGGCGACTA	61.914	60.000	16.62	0.00	36.25	2.59
303	307	2.101582	ACATGCAGATCCGTAGAACTCC	59.898	50.000	0.00	0.00	0.00	3.85
330	334	0.322546	GGTAACAGGGGTGCTCCTTG	60.323	60.000	4.53	6.04	46.90	3.61
331	335	0.770557	TGGTAACAGGGGTGCTCCTT	60.771	55.000	4.53	0.00	46.17	3.36
332	336	1.151899	TGGTAACAGGGGTGCTCCT	60.152	57.895	4.53	0.00	46.17	3.69
333	337	3.490851	TGGTAACAGGGGTGCTCC	58.509	61.111	0.00	0.00	46.17	4.70
371	375	2.057137	TCCAATCTAGCCCATTGCAC	57.943	50.000	0.00	0.00	44.83	4.57

Showing 1 to 25 of 727 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.