AutoCloner

Multiple sequence alignment - TraesCS4A01G003000

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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	TraesCS4A01G003000	chr4A	100.000	3131	0	0	1	3131	2618993	2622123	0.000000e+00	5782
1	TraesCS4A01G003000	chr7A	96.865	3158	54	12	1	3131	619255223	619252084	0.000000e+00	5241
2	TraesCS4A01G003000	chr2A	95.783	3130	51	22	60	3129	724110539	724107431	0.000000e+00	4974
3	TraesCS4A01G003000	chr2A	89.706	136	4	1	1	136	187940488	187940613	6.950000e-37	165
4	TraesCS4A01G003000	chrUn	96.236	2843	65	10	308	3131	69802951	69800132	0.000000e+00	4619
5	TraesCS4A01G003000	chr6D	96.601	1412	33	6	1721	3131	292688383	292686986	0.000000e+00	2327
6	TraesCS4A01G003000	chr6D	94.236	746	13	6	998	1726	292711642	292710910	0.000000e+00	1112
7	TraesCS4A01G003000	chr6D	95.259	696	20	3	308	1001	292716045	292715361	0.000000e+00	1090
8	TraesCS4A01G003000	chr6D	92.769	484	32	3	710	1192	25484166	25483685	0.000000e+00	697
9	TraesCS4A01G003000	chr6D	85.903	227	26	3	2776	3001	46845673	46845452	1.450000e-58	237
10	TraesCS4A01G003000	chr6D	80.808	297	46	7	2776	3067	46626278	46625988	4.060000e-54	222
11	TraesCS4A01G003000	chr5A	93.363	889	41	4	308	1193	568570794	568571667	0.000000e+00	1299
12	TraesCS4A01G003000	chr5A	93.237	695	27	5	1193	1870	568571704	568572395	0.000000e+00	1005
13	TraesCS4A01G003000	chr5A	89.706	136	3	2	1	136	680338072	680338196	2.500000e-36	163
14	TraesCS4A01G003000	chr3A	95.072	690	17	2	1193	1865	31814759	31815448	0.000000e+00	1070
15	TraesCS4A01G003000	chr3A	95.413	327	14	1	869	1194	31814397	31814723	1.290000e-143	520
16	TraesCS4A01G003000	chr1B	93.669	695	24	5	1193	1870	643260340	643259649	0.000000e+00	1022
17	TraesCS4A01G003000	chr1B	91.799	695	24	6	1193	1870	550237914	550237236	0.000000e+00	937
18	TraesCS4A01G003000	chr1B	97.600	250	6	0	734	983	643260998	643260749	2.230000e-116	429
19	TraesCS4A01G003000	chr1B	96.698	212	7	0	982	1193	643260588	643260377	1.380000e-93	353
20	TraesCS4A01G003000	chr6B	91.643	694	25	6	1194	1870	563878652	563877975	0.000000e+00	929
21	TraesCS4A01G003000	chr6B	91.079	695	29	7	1193	1870	563913821	563913143	0.000000e+00	909
22	TraesCS4A01G003000	chr6B	93.857	586	34	2	1885	2469	72318969	72318385	0.000000e+00	881
23	TraesCS4A01G003000	chr6B	93.697	587	34	3	1885	2469	72316176	72315591	0.000000e+00	876
24	TraesCS4A01G003000	chr6B	93.697	587	34	3	1885	2469	72321763	72321178	0.000000e+00	876
25	TraesCS4A01G003000	chr6B	93.697	587	34	3	1885	2469	72324563	72323978	0.000000e+00	876
26	TraesCS4A01G003000	chr6B	94.340	212	10	1	2493	2702	53636666	53636877	1.080000e-84	324
27	TraesCS4A01G003000	chr7B	93.898	590	34	2	1881	2469	703575664	703576252	0.000000e+00	889
28	TraesCS4A01G003000	chr3D	94.603	315	6	2	2	308	19412660	19412349	7.860000e-131	477
29	TraesCS4A01G003000	chr5D	94.304	316	8	3	1	308	370304075	370303762	2.830000e-130	475
30	TraesCS4A01G003000	chr7D	94.286	315	6	2	2	308	31376317	31376007	3.660000e-129	472
31	TraesCS4A01G003000	chr7D	92.727	220	16	0	2504	2723	495142122	495142341	5.040000e-83	318
32	TraesCS4A01G003000	chr4D	92.069	290	20	3	2475	2761	494791799	494791510	3.760000e-109	405
33	TraesCS4A01G003000	chr2B	96.296	243	4	4	6	244	741450969	741451210	8.140000e-106	394
34	TraesCS4A01G003000	chr4B	92.857	266	16	2	2499	2761	577024784	577024519	1.760000e-102	383
35	TraesCS4A01G003000	chr1D	95.455	242	3	1	75	308	423888940	423888699	2.280000e-101	379
36	TraesCS4A01G003000	chr3B	94.262	244	4	1	1	244	792102508	792102275	6.380000e-97	364
37	TraesCS4A01G003000	chr3B	93.852	244	5	1	1	244	792139942	792139709	2.970000e-95	359
38	TraesCS4A01G003000	chr3B	93.724	239	4	2	6	244	351293221	351293448	6.430000e-92	348
39	TraesCS4A01G003000	chr3B	93.033	244	3	2	1	244	792177976	792177747	8.310000e-91	344
40	TraesCS4A01G003000	chr3B	97.183	71	1	1	238	308	792102075	792102006	5.490000e-23	119
41	TraesCS4A01G003000	chr3B	97.183	71	1	1	238	308	792177548	792177479	5.490000e-23	119
42	TraesCS4A01G003000	chr1A	89.823	226	19	4	2488	2709	7692903	7692678	1.420000e-73	287
43	TraesCS4A01G003000	chr5B	97.183	71	1	1	238	308	43243944	43244013	5.490000e-23	119

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	TraesCS4A01G003000	chr4A	2618993	2622123	3130	False	5782.000000	5782	100.0000	1	3131	1	chr4A.!!$F1	3130
1	TraesCS4A01G003000	chr7A	619252084	619255223	3139	True	5241.000000	5241	96.8650	1	3131	1	chr7A.!!$R1	3130
2	TraesCS4A01G003000	chr2A	724107431	724110539	3108	True	4974.000000	4974	95.7830	60	3129	1	chr2A.!!$R1	3069
3	TraesCS4A01G003000	chrUn	69800132	69802951	2819	True	4619.000000	4619	96.2360	308	3131	1	chrUn.!!$R1	2823
4	TraesCS4A01G003000	chr6D	292686986	292688383	1397	True	2327.000000	2327	96.6010	1721	3131	1	chr6D.!!$R4	1410
5	TraesCS4A01G003000	chr6D	292710910	292716045	5135	True	1101.000000	1112	94.7475	308	1726	2	chr6D.!!$R5	1418
6	TraesCS4A01G003000	chr5A	568570794	568572395	1601	False	1152.000000	1299	93.3000	308	1870	2	chr5A.!!$F2	1562
7	TraesCS4A01G003000	chr3A	31814397	31815448	1051	False	795.000000	1070	95.2425	869	1865	2	chr3A.!!$F1	996
8	TraesCS4A01G003000	chr1B	550237236	550237914	678	True	937.000000	937	91.7990	1193	1870	1	chr1B.!!$R1	677
9	TraesCS4A01G003000	chr1B	643259649	643260998	1349	True	601.333333	1022	95.9890	734	1870	3	chr1B.!!$R2	1136
10	TraesCS4A01G003000	chr6B	563877975	563878652	677	True	929.000000	929	91.6430	1194	1870	1	chr6B.!!$R1	676
11	TraesCS4A01G003000	chr6B	563913143	563913821	678	True	909.000000	909	91.0790	1193	1870	1	chr6B.!!$R2	677
12	TraesCS4A01G003000	chr6B	72315591	72324563	8972	True	877.250000	881	93.7370	1885	2469	4	chr6B.!!$R3	584
13	TraesCS4A01G003000	chr7B	703575664	703576252	588	False	889.000000	889	93.8980	1881	2469	1	chr7B.!!$F1	588
14	TraesCS4A01G003000	chr3B	792102006	792102508	502	True	241.500000	364	95.7225	1	308	2	chr3B.!!$R2	307

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
690	899	0.621571	TTGATGGAGAGAGGGGGTGG	60.622	60.000	0.0	0.0	0.0	4.61	F
691	900	1.768077	GATGGAGAGAGGGGGTGGG	60.768	68.421	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2020	11772	0.977395	CTCCTTCCTTCCTGGTCGTT	59.023	55.000	0.0	0.0	37.07	3.85	R
2493	13411	1.010793	AGAGAGAGAGAGGGAGGGAGA	59.989	57.143	0.0	0.0	0.00	3.71	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
40	41	2.615773	CTCCCTCCTCCTACCCCC	59.384	72.222	0.00	0.00	0.00	5.40
250	456	2.873797	CCTTGCTTGGCTAGGGTTC	58.126	57.895	11.14	0.00	45.20	3.62
437	646	1.710013	TGCAAGATTCCTCGAACGAC	58.290	50.000	0.00	0.00	0.00	4.34
465	674	7.993821	TTGTTGCATTTCTTATTTTGTTCGA	57.006	28.000	0.00	0.00	0.00	3.71
489	698	1.290009	GCGAGTTTGGCATTGGCTT	59.710	52.632	11.84	0.00	40.87	4.35
649	858	5.481824	TGGCATTGTAATCAAACCACCATTA	59.518	36.000	0.00	0.00	38.24	1.90
688	897	2.059756	TTTTGATGGAGAGAGGGGGT	57.940	50.000	0.00	0.00	0.00	4.95
689	898	1.289160	TTTGATGGAGAGAGGGGGTG	58.711	55.000	0.00	0.00	0.00	4.61
690	899	0.621571	TTGATGGAGAGAGGGGGTGG	60.622	60.000	0.00	0.00	0.00	4.61
691	900	1.768077	GATGGAGAGAGGGGGTGGG	60.768	68.421	0.00	0.00	0.00	4.61
692	901	3.353689	ATGGAGAGAGGGGGTGGGG	62.354	68.421	0.00	0.00	0.00	4.96
693	902	4.825679	GGAGAGAGGGGGTGGGGG	62.826	77.778	0.00	0.00	0.00	5.40
1104	5198	4.974645	TGATGGAACTTGGTCTACTGTT	57.025	40.909	0.00	0.00	0.00	3.16
1408	5556	4.027437	AGAGATCTGGGAGTTGTACTTCC	58.973	47.826	0.00	0.00	44.55	3.46
1462	5610	7.270151	GTGTTTGTTTACAATTGGCAAGTTTTG	59.730	33.333	10.83	8.26	35.55	2.44
1482	5630	4.986054	TGGGCTTTTACTGTCTTTAGGA	57.014	40.909	0.00	0.00	0.00	2.94
2020	11772	2.054021	TCCACAAGGACCAAGATGACA	58.946	47.619	0.00	0.00	39.61	3.58
2107	11859	2.537143	GACCACAACCTCCCTCTCTAA	58.463	52.381	0.00	0.00	0.00	2.10
2111	11863	4.354087	ACCACAACCTCCCTCTCTAAAATT	59.646	41.667	0.00	0.00	0.00	1.82
2112	11864	5.550403	ACCACAACCTCCCTCTCTAAAATTA	59.450	40.000	0.00	0.00	0.00	1.40
2113	11865	6.217693	ACCACAACCTCCCTCTCTAAAATTAT	59.782	38.462	0.00	0.00	0.00	1.28
2114	11866	6.768381	CCACAACCTCCCTCTCTAAAATTATC	59.232	42.308	0.00	0.00	0.00	1.75
2238	12014	0.174389	ACTCTGCATCTGCTACGTGG	59.826	55.000	0.00	0.00	42.66	4.94
2492	13410	5.249393	AGACATATCTCTCTCTCTCTCTCCC	59.751	48.000	0.00	0.00	0.00	4.30
2493	13411	5.165652	ACATATCTCTCTCTCTCTCTCCCT	58.834	45.833	0.00	0.00	0.00	4.20
2494	13412	5.249393	ACATATCTCTCTCTCTCTCTCCCTC	59.751	48.000	0.00	0.00	0.00	4.30
2495	13413	3.421394	TCTCTCTCTCTCTCTCCCTCT	57.579	52.381	0.00	0.00	0.00	3.69
2496	13414	3.309296	TCTCTCTCTCTCTCTCCCTCTC	58.691	54.545	0.00	0.00	0.00	3.20
2497	13415	2.370189	CTCTCTCTCTCTCTCCCTCTCC	59.630	59.091	0.00	0.00	0.00	3.71
2498	13416	1.421646	CTCTCTCTCTCTCCCTCTCCC	59.578	61.905	0.00	0.00	0.00	4.30
2499	13417	1.010793	TCTCTCTCTCTCCCTCTCCCT	59.989	57.143	0.00	0.00	0.00	4.20
2828	13750	0.743688	CAGTCGGAGTAGCAGCTGAT	59.256	55.000	20.43	15.46	0.00	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	43	4.722700	CAGGTTCAGCGGGGTGGG	62.723	72.222	0.00	0.00	0.00	4.61
43	44	4.722700	CCAGGTTCAGCGGGGTGG	62.723	72.222	0.00	0.00	0.00	4.61
50	51	1.376553	GGAGCTCACCAGGTTCAGC	60.377	63.158	17.19	11.30	0.00	4.26
250	456	6.263392	TCACTACAATCCTAGAGAAAGATCCG	59.737	42.308	0.00	0.00	0.00	4.18
421	629	4.814771	ACAAAAAGTCGTTCGAGGAATCTT	59.185	37.500	0.00	0.00	0.00	2.40
465	674	1.252904	AATGCCAAACTCGCAGCCAT	61.253	50.000	0.00	0.00	40.15	4.40
526	735	7.393515	GGATTAACCCAGACTAACAAACAGATT	59.606	37.037	0.00	0.00	0.00	2.40
649	858	1.904287	TCGCCAACCAAACAGCTAAT	58.096	45.000	0.00	0.00	0.00	1.73
839	1048	4.657436	ACTCCTTGACCGCTAATTAGAG	57.343	45.455	16.85	12.82	0.00	2.43
1104	5198	3.966979	TGCTTTATGGCTCTGAATTCCA	58.033	40.909	2.27	0.00	0.00	3.53
1408	5556	4.787563	GCAAGACACATCACAACAGAAGTG	60.788	45.833	0.00	0.00	41.55	3.16
1482	5630	8.863872	AACTGTAAAAAGTATTGCTAGGATGT	57.136	30.769	0.00	0.00	0.00	3.06
1636	5786	7.256286	TGATCCTAGAAAGTACGACTAAAAGC	58.744	38.462	0.00	0.00	0.00	3.51
1797	5948	1.065491	AGCAGTCACATGGCCGATTAA	60.065	47.619	0.00	0.00	0.00	1.40
1883	6035	1.585297	TCATGAGCACACACACACAG	58.415	50.000	0.00	0.00	0.00	3.66
2020	11772	0.977395	CTCCTTCCTTCCTGGTCGTT	59.023	55.000	0.00	0.00	37.07	3.85
2436	12212	4.089361	AGTTAGATTTTTGGGAGGCCTTG	58.911	43.478	6.77	0.00	0.00	3.61
2492	13410	1.421646	GAGAGAGAGAGGGAGGGAGAG	59.578	61.905	0.00	0.00	0.00	3.20
2493	13411	1.010793	AGAGAGAGAGAGGGAGGGAGA	59.989	57.143	0.00	0.00	0.00	3.71
2494	13412	1.421646	GAGAGAGAGAGAGGGAGGGAG	59.578	61.905	0.00	0.00	0.00	4.30
2495	13413	1.010793	AGAGAGAGAGAGAGGGAGGGA	59.989	57.143	0.00	0.00	0.00	4.20
2496	13414	1.421646	GAGAGAGAGAGAGAGGGAGGG	59.578	61.905	0.00	0.00	0.00	4.30
2497	13415	2.370189	GAGAGAGAGAGAGAGAGGGAGG	59.630	59.091	0.00	0.00	0.00	4.30
2498	13416	2.370189	GGAGAGAGAGAGAGAGAGGGAG	59.630	59.091	0.00	0.00	0.00	4.30
2499	13417	2.293519	TGGAGAGAGAGAGAGAGAGGGA	60.294	54.545	0.00	0.00	0.00	4.20
2828	13750	1.535028	CGGTGTTCTGCAAATGCTACA	59.465	47.619	6.97	5.84	42.66	2.74
2891	13813	3.939939	TCTGCGTGCTCCTTGCCA	61.940	61.111	0.00	0.00	42.00	4.92
2996	13918	2.026641	CGGTATAAAGAGGGGTCGTCA	58.973	52.381	0.00	0.00	0.00	4.35
3001	13923	1.767088	GCCTTCGGTATAAAGAGGGGT	59.233	52.381	8.35	0.00	34.60	4.95
3030	13952	0.320683	TCAATAGCGTGTGCAGCACT	60.321	50.000	25.83	8.64	45.57	4.40
3063	13985	3.230134	AGCTTCTCCTAGAATCGCAGAT	58.770	45.455	0.00	0.00	45.12	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.