AutoCloner

Multiple sequence alignment - TraesCS4A01G292000

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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	TraesCS4A01G292000	chr4A	100.000	3485	0	0	1	3485	594729519	594733003	0.000000e+00	6436.0
1	TraesCS4A01G292000	chr4A	88.753	1885	142	33	733	2563	594737402	594739270	0.000000e+00	2242.0
2	TraesCS4A01G292000	chr4A	89.685	1173	74	16	1570	2717	563511581	563510431	0.000000e+00	1452.0
3	TraesCS4A01G292000	chr4A	94.372	924	44	5	2565	3485	594709515	594708597	0.000000e+00	1411.0
4	TraesCS4A01G292000	chr4A	94.283	927	45	5	2562	3485	594739562	594740483	0.000000e+00	1411.0
5	TraesCS4A01G292000	chr4A	91.506	1036	69	11	1544	2563	594710842	594709810	0.000000e+00	1408.0
6	TraesCS4A01G292000	chr4A	98.726	785	7	1	1	782	563513611	563512827	0.000000e+00	1391.0
7	TraesCS4A01G292000	chr4A	95.802	786	17	8	775	1557	563512674	563511902	0.000000e+00	1254.0
8	TraesCS4A01G292000	chr4A	87.544	851	69	22	733	1559	594711696	594710859	0.000000e+00	950.0
9	TraesCS4A01G292000	chr4A	82.684	976	93	36	735	1687	563228650	563227728	0.000000e+00	797.0
10	TraesCS4A01G292000	chr4A	91.016	512	34	7	2976	3485	563510430	563509929	0.000000e+00	680.0
11	TraesCS4A01G292000	chr4A	83.029	383	59	6	2500	2880	563227321	563226943	3.330000e-90	342.0
12	TraesCS4A01G292000	chr4A	87.417	151	15	2	198	348	688603366	688603220	1.660000e-38	171.0
13	TraesCS4A01G292000	chr4D	90.196	2040	138	28	733	2728	8628024	8626003	0.000000e+00	2603.0
14	TraesCS4A01G292000	chr4D	90.847	1169	60	16	540	1701	8598941	8597813	0.000000e+00	1522.0
15	TraesCS4A01G292000	chr4D	91.144	734	45	10	2761	3485	8626005	8625283	0.000000e+00	977.0
16	TraesCS4A01G292000	chr4D	86.054	882	91	17	2558	3431	8596581	8595724	0.000000e+00	918.0
17	TraesCS4A01G292000	chr4D	97.529	526	9	1	1	526	8599447	8598926	0.000000e+00	896.0
18	TraesCS4A01G292000	chr4D	89.474	114	11	1	191	304	509754650	509754762	3.630000e-30	143.0
19	TraesCS4A01G292000	chr4D	85.859	99	0	4	1952	2036	8597645	8597547	3.700000e-15	93.5
20	TraesCS4A01G292000	chr4B	90.081	1351	96	16	733	2061	15926713	15925379	0.000000e+00	1718.0
21	TraesCS4A01G292000	chr4B	91.675	1033	65	11	2462	3485	15925075	15924055	0.000000e+00	1411.0
22	TraesCS4A01G292000	chr4B	92.182	307	19	3	2106	2409	15925385	15925081	2.490000e-116	429.0
23	TraesCS4A01G292000	chr4B	83.206	131	21	1	1819	1948	490665211	490665081	6.110000e-23	119.0
24	TraesCS4A01G292000	chr7D	81.379	145	24	3	1809	1951	426146309	426146452	7.900000e-22	115.0
25	TraesCS4A01G292000	chr3D	82.114	123	21	1	1830	1951	295551467	295551589	1.710000e-18	104.0
26	TraesCS4A01G292000	chr2B	80.916	131	24	1	1822	1951	688430029	688429899	6.150000e-18	102.0
27	TraesCS4A01G292000	chr6D	83.721	86	11	2	2408	2490	10715365	10715450	1.040000e-10	78.7

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	TraesCS4A01G292000	chr4A	594729519	594733003	3484	False	6436.000000	6436	100.000000	1	3485	1	chr4A.!!$F1	3484
1	TraesCS4A01G292000	chr4A	594737402	594740483	3081	False	1826.500000	2242	91.518000	733	3485	2	chr4A.!!$F2	2752
2	TraesCS4A01G292000	chr4A	594708597	594711696	3099	True	1256.333333	1411	91.140667	733	3485	3	chr4A.!!$R4	2752
3	TraesCS4A01G292000	chr4A	563509929	563513611	3682	True	1194.250000	1452	93.807250	1	3485	4	chr4A.!!$R3	3484
4	TraesCS4A01G292000	chr4A	563226943	563228650	1707	True	569.500000	797	82.856500	735	2880	2	chr4A.!!$R2	2145
5	TraesCS4A01G292000	chr4D	8625283	8628024	2741	True	1790.000000	2603	90.670000	733	3485	2	chr4D.!!$R2	2752
6	TraesCS4A01G292000	chr4D	8595724	8599447	3723	True	857.375000	1522	90.072250	1	3431	4	chr4D.!!$R1	3430
7	TraesCS4A01G292000	chr4B	15924055	15926713	2658	True	1186.000000	1718	91.312667	733	3485	3	chr4B.!!$R2	2752

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
953	1120	0.321996	GCCCTAAATAGGCCTCCTCG	59.678	60.0	9.68	0.0	45.16	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2712	4501	0.986019	TATCTTGATGGGGGCGGTGT	60.986	55.0	0.0	0.0	0.0	4.16	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
144	145	4.905429	TCAGCAGAACTAATTTAGCCACA	58.095	39.130	3.28	0.00	0.00	4.17
802	969	5.307196	AGCGACTATATATGTTGTCCCCTTT	59.693	40.000	8.10	0.00	0.00	3.11
953	1120	0.321996	GCCCTAAATAGGCCTCCTCG	59.678	60.000	9.68	0.00	45.16	4.63
1169	1375	3.569194	TGGAAAGTCCAGCTACAACAA	57.431	42.857	0.00	0.00	42.67	2.83
1265	1471	0.961019	TGCCGGAAAGTACGTACTGT	59.039	50.000	28.00	23.39	36.50	3.55
1266	1472	2.158559	TGCCGGAAAGTACGTACTGTA	58.841	47.619	28.00	12.26	36.50	2.74
1267	1473	2.754552	TGCCGGAAAGTACGTACTGTAT	59.245	45.455	28.00	17.26	36.50	2.29
1268	1474	3.944650	TGCCGGAAAGTACGTACTGTATA	59.055	43.478	28.00	9.13	36.50	1.47
1269	1475	4.580167	TGCCGGAAAGTACGTACTGTATAT	59.420	41.667	28.00	9.98	36.50	0.86
1270	1476	5.762711	TGCCGGAAAGTACGTACTGTATATA	59.237	40.000	28.00	10.20	36.50	0.86
1391	1613	2.364448	GGTCGGCTCTCCTCCCTT	60.364	66.667	0.00	0.00	0.00	3.95
1502	1729	4.405680	TGATTAGTTTAGCTAGCTGGAGCA	59.594	41.667	27.68	11.68	45.43	4.26
1529	1756	8.874744	AATTATTTGCATACATGGATCTAGCT	57.125	30.769	0.00	0.00	0.00	3.32
1530	1757	9.964354	AATTATTTGCATACATGGATCTAGCTA	57.036	29.630	0.00	0.00	0.00	3.32
1531	1758	9.610705	ATTATTTGCATACATGGATCTAGCTAG	57.389	33.333	15.01	15.01	0.00	3.42
1532	1759	4.462508	TGCATACATGGATCTAGCTAGC	57.537	45.455	16.35	6.62	0.00	3.42
1562	1829	1.226379	GTGTGTGTGTGTGTGCAGC	60.226	57.895	0.00	0.00	0.00	5.25
1731	2395	0.249398	GCGGGCTTGTCTTTCTAGGA	59.751	55.000	0.00	0.00	0.00	2.94
1788	2462	9.048446	GCGGTTTCCTATACTTTATTTGTCATA	57.952	33.333	0.00	0.00	0.00	2.15
1828	2503	7.330946	GCAATACTTTTTGTATGGGAACTTTCC	59.669	37.037	0.00	0.00	42.35	3.13
1850	2525	6.005823	TCCATCTATTCATCGCCAATCATTT	58.994	36.000	0.00	0.00	0.00	2.32
1907	2584	4.008330	TCGAGACTCGAAAACCATCTAGT	58.992	43.478	24.71	0.00	46.90	2.57
2134	3067	1.741706	GTGTGCATCTTGTGATCCAGG	59.258	52.381	0.00	0.00	0.00	4.45
2210	3145	9.877178	AAGAAGTATAAACTCGATCTCAACATT	57.123	29.630	0.00	0.00	33.75	2.71
2247	3183	1.210478	CCCATCAAGTCGACAATCCCT	59.790	52.381	19.50	0.00	0.00	4.20
2369	3553	2.714250	TCATGTGGGGTAAACACCTCTT	59.286	45.455	2.52	0.00	41.04	2.85
2387	3571	8.778059	ACACCTCTTTGATTAGGGATGTAAATA	58.222	33.333	0.00	0.00	37.18	1.40
2431	3622	7.224297	TCTTCTTAGCTCAACCAAATGTACTT	58.776	34.615	0.00	0.00	0.00	2.24
2550	4001	1.474677	CCCTGATCATCTGCTCACACC	60.475	57.143	0.00	0.00	0.00	4.16
2604	4393	1.359848	CGACCGCTGAAGCATAAACT	58.640	50.000	2.79	0.00	42.21	2.66
2671	4460	7.281100	AGGAGTACAAGTCTTCTTTTTGTCAAG	59.719	37.037	0.00	0.00	36.52	3.02
2682	4471	5.938322	TCTTTTTGTCAAGAACCATATCGC	58.062	37.500	0.00	0.00	29.41	4.58
2712	4501	6.377146	GGATAGCAAAAGAACCCAACATAAGA	59.623	38.462	0.00	0.00	0.00	2.10
2717	4506	3.053831	AGAACCCAACATAAGACACCG	57.946	47.619	0.00	0.00	0.00	4.94
2758	4582	7.126421	TGAGAGGAAAGCTTCTTATTGATACCT	59.874	37.037	0.00	0.00	29.54	3.08
2883	4708	8.283291	GTCACAATAAAAGACCAGAGTTTAGTG	58.717	37.037	0.00	0.00	38.25	2.74
2886	4712	8.837389	ACAATAAAAGACCAGAGTTTAGTGAAC	58.163	33.333	9.11	0.00	36.69	3.18
2944	4771	8.691727	GCGATTGTACATGTACTTAAGATACTG	58.308	37.037	30.69	13.76	37.00	2.74
2986	4815	2.282603	GGTGTGCCGGGGCTTAAA	60.283	61.111	11.55	0.00	42.51	1.52
3036	4868	6.994496	AGGGAGTGAATCAATATATGTGTGTG	59.006	38.462	0.00	0.00	0.00	3.82
3038	4870	7.663081	GGGAGTGAATCAATATATGTGTGTGAT	59.337	37.037	0.00	0.00	0.00	3.06
3091	4923	5.768317	ACGCCCATATGTTAATTTATGTGC	58.232	37.500	1.24	5.54	0.00	4.57
3222	5059	3.140325	ACCTCGGATGAAACACACAAT	57.860	42.857	0.00	0.00	0.00	2.71
3223	5060	4.280436	ACCTCGGATGAAACACACAATA	57.720	40.909	0.00	0.00	0.00	1.90
3224	5061	4.253685	ACCTCGGATGAAACACACAATAG	58.746	43.478	0.00	0.00	0.00	1.73
3240	5077	9.231297	ACACACAATAGTATTAATGAAGCAACT	57.769	29.630	11.48	0.00	0.00	3.16
3269	5106	4.391405	ACAGGCTGGAAAGAAAAACTTG	57.609	40.909	20.34	0.00	38.98	3.16
3275	5112	5.394115	GGCTGGAAAGAAAAACTTGACTCAA	60.394	40.000	0.00	0.00	38.98	3.02
3294	5131	2.816087	CAAGACTGAAGAATGGTGTGGG	59.184	50.000	0.00	0.00	0.00	4.61
3301	5138	4.222336	TGAAGAATGGTGTGGGAAAACAT	58.778	39.130	0.00	0.00	31.49	2.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	9.631639	GGCATGAATTAATTTTTATTTGTACGC	57.368	29.630	1.43	0.00	0.00	4.42
720	726	3.393800	CCGTGAGCAAAATCGATCCTAT	58.606	45.455	0.00	0.00	0.00	2.57
802	969	4.544152	AGGAGGAAAAGGGTCCAATAATCA	59.456	41.667	0.00	0.00	40.48	2.57
953	1120	1.008767	CGGCGAGGTCTAATCGTCC	60.009	63.158	0.00	0.00	41.61	4.79
1169	1375	4.037803	CCTTGATCGTGTCAGATGATCTCT	59.962	45.833	5.65	0.00	44.60	3.10
1270	1476	9.206690	ACAAGCTGTGCTGGTCTATATATATAT	57.793	33.333	10.10	10.10	38.65	0.86
1531	1758	2.910482	CACACACACAAAAGCATATCGC	59.090	45.455	0.00	0.00	42.91	4.58
1532	1759	3.907788	CACACACACACAAAAGCATATCG	59.092	43.478	0.00	0.00	0.00	2.92
1562	1829	2.288457	CCAGCATATCACGGTAGGTCTG	60.288	54.545	0.00	0.00	0.00	3.51
1731	2395	4.255510	ACAGTCTTGGCATTATCCCAAT	57.744	40.909	0.00	0.00	41.23	3.16
1828	2503	8.509690	AGTAAAATGATTGGCGATGAATAGATG	58.490	33.333	0.00	0.00	0.00	2.90
1840	2515	7.812191	TGTGTTCATTGTAGTAAAATGATTGGC	59.188	33.333	15.13	7.99	42.15	4.52
1887	2563	5.312120	TCACTAGATGGTTTTCGAGTCTC	57.688	43.478	0.00	0.00	30.34	3.36
1907	2584	4.325972	TGCTTCAATGCTTGTAGTCATCA	58.674	39.130	0.00	0.00	31.53	3.07
2210	3145	3.740397	GGCTGTGCGCATCTTGCA	61.740	61.111	15.91	5.23	45.36	4.08
2301	3485	1.314730	CAAGTTGTTTACCCCAGCGT	58.685	50.000	0.00	0.00	0.00	5.07
2369	3553	7.942341	GGGTCACATATTTACATCCCTAATCAA	59.058	37.037	0.00	0.00	0.00	2.57
2476	3732	3.454858	TCTCTGGCCCTCTTTAGTTCAT	58.545	45.455	0.00	0.00	0.00	2.57
2521	3972	3.823061	GCAGATGATCAGGGATAGGGGTA	60.823	52.174	0.09	0.00	0.00	3.69
2550	4001	8.555485	GAAGTTGTTCAAACTAGCATGTATGCG	61.555	40.741	10.86	1.28	44.26	4.73
2604	4393	8.563123	TCATTTACGTGTTGGTTCCATAAATA	57.437	30.769	0.00	0.00	0.00	1.40
2635	4424	2.612212	ACTTGTACTCCTTTGCACGTTG	59.388	45.455	0.00	0.00	0.00	4.10
2639	4428	4.381411	AGAAGACTTGTACTCCTTTGCAC	58.619	43.478	0.00	0.00	0.00	4.57
2671	4460	3.929610	GCTATCCAAGAGCGATATGGTTC	59.070	47.826	5.04	0.00	35.66	3.62
2682	4471	4.335416	TGGGTTCTTTTGCTATCCAAGAG	58.665	43.478	0.00	0.00	37.08	2.85
2712	4501	0.986019	TATCTTGATGGGGGCGGTGT	60.986	55.000	0.00	0.00	0.00	4.16
2717	4506	2.026449	CCTCTCATATCTTGATGGGGGC	60.026	54.545	0.00	0.00	32.72	5.80
2758	4582	8.315482	TGCATACTATTTTGACACCTAGTTGTA	58.685	33.333	0.00	0.00	0.00	2.41
2883	4708	9.614792	CCCTAAAGGTGCCTATATATATTGTTC	57.385	37.037	0.00	0.00	0.00	3.18
3036	4868	7.591006	TCACCTCGAAGTAAACATAAACATC	57.409	36.000	0.00	0.00	0.00	3.06
3038	4870	6.074195	CGTTCACCTCGAAGTAAACATAAACA	60.074	38.462	1.28	0.00	33.09	2.83
3091	4923	2.599973	GGTGTGCCGTTATTACACGTAG	59.400	50.000	0.00	0.00	44.17	3.51
3196	5033	1.143183	TTTCATCCGAGGTAGGCGC	59.857	57.895	0.00	0.00	0.00	6.53
3222	5059	6.812998	ACGGCTAGTTGCTTCATTAATACTA	58.187	36.000	0.00	0.00	42.39	1.82
3223	5060	5.671493	ACGGCTAGTTGCTTCATTAATACT	58.329	37.500	0.00	0.00	42.39	2.12
3224	5061	5.986004	ACGGCTAGTTGCTTCATTAATAC	57.014	39.130	0.00	0.00	42.39	1.89
3269	5106	4.450419	CACACCATTCTTCAGTCTTGAGTC	59.550	45.833	0.00	0.00	34.15	3.36
3275	5112	2.338809	TCCCACACCATTCTTCAGTCT	58.661	47.619	0.00	0.00	0.00	3.24
3294	5131	2.613691	CAGAGGGCAATGCATGTTTTC	58.386	47.619	7.79	0.00	0.00	2.29
3301	5138	2.036098	CCACCAGAGGGCAATGCA	59.964	61.111	7.79	0.00	37.90	3.96
3351	5188	4.296621	AGTGGTAGTGGGTTTTGTATCC	57.703	45.455	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.