AutoCloner

Multiple sequence alignment - TraesCS3A01G504500

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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	TraesCS3A01G504500	chr3A	100.000	2675	0	0	1	2675	726514803	726517477	0.000000e+00	4940.0
1	TraesCS3A01G504500	chr3A	90.246	1179	100	9	585	1752	726457920	726459094	0.000000e+00	1526.0
2	TraesCS3A01G504500	chr3A	84.552	1340	141	43	467	1777	726411270	726409968	0.000000e+00	1267.0
3	TraesCS3A01G504500	chr3A	86.333	439	31	8	99	523	726457491	726457914	4.060000e-123	451.0
4	TraesCS3A01G504500	chr3A	80.870	230	25	12	2186	2401	726862731	726862507	2.130000e-36	163.0
5	TraesCS3A01G504500	chr3D	94.739	2699	73	17	1	2675	595738193	595740846	0.000000e+00	4133.0
6	TraesCS3A01G504500	chr3D	89.847	1507	118	19	265	1752	595704611	595706101	0.000000e+00	1903.0
7	TraesCS3A01G504500	chr3D	88.026	1069	112	10	749	1805	595674232	595675296	0.000000e+00	1251.0
8	TraesCS3A01G504500	chr3D	87.583	1055	112	9	771	1811	595302940	595303989	0.000000e+00	1205.0
9	TraesCS3A01G504500	chr3D	87.684	885	98	7	942	1816	595286611	595285728	0.000000e+00	1020.0
10	TraesCS3A01G504500	chr3D	87.230	556	44	11	219	759	595673542	595674085	2.280000e-170	608.0
11	TraesCS3A01G504500	chr3D	85.135	370	44	7	413	773	595302393	595302760	4.210000e-98	368.0
12	TraesCS3A01G504500	chr3D	82.167	443	42	19	467	881	595287060	595286627	1.970000e-91	346.0
13	TraesCS3A01G504500	chr3D	81.818	429	56	16	222	636	596111698	596111278	9.170000e-90	340.0
14	TraesCS3A01G504500	chr3D	89.247	186	19	1	1981	2166	595304173	595304357	5.760000e-57	231.0
15	TraesCS3A01G504500	chr3D	82.329	249	32	6	1919	2163	595675410	595675650	3.490000e-49	206.0
16	TraesCS3A01G504500	chr3D	92.086	139	11	0	88	226	595301608	595301746	2.100000e-46	196.0
17	TraesCS3A01G504500	chr3D	81.776	214	29	6	2182	2390	596095794	596095586	1.270000e-38	171.0
18	TraesCS3A01G504500	chr3D	83.851	161	23	2	2271	2429	595304770	595304929	1.660000e-32	150.0
19	TraesCS3A01G504500	chr3D	96.000	50	2	0	2626	2675	595305136	595305185	6.140000e-12	82.4
20	TraesCS3A01G504500	chr3D	90.000	50	5	0	854	903	596111122	596111073	6.180000e-07	65.8
21	TraesCS3A01G504500	chr3B	91.006	1223	86	13	448	1655	798686144	798687357	0.000000e+00	1628.0
22	TraesCS3A01G504500	chr3B	92.373	944	67	4	813	1752	798648158	798649100	0.000000e+00	1339.0
23	TraesCS3A01G504500	chr3B	83.733	959	125	11	772	1722	799522163	799521228	0.000000e+00	878.0
24	TraesCS3A01G504500	chr3B	86.248	669	38	23	76	726	798647329	798647961	0.000000e+00	676.0
25	TraesCS3A01G504500	chr3B	87.476	519	23	11	1647	2163	798689772	798690250	6.470000e-156	560.0
26	TraesCS3A01G504500	chr1A	91.250	80	5	1	88	165	37142806	37142885	1.010000e-19	108.0
27	TraesCS3A01G504500	chr1A	90.000	80	6	1	88	165	37009136	37009215	4.710000e-18	102.0

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	TraesCS3A01G504500	chr3A	726514803	726517477	2674	False	4940.000000	4940	100.000000	1	2675	1	chr3A.!!$F1	2674
1	TraesCS3A01G504500	chr3A	726409968	726411270	1302	True	1267.000000	1267	84.552000	467	1777	1	chr3A.!!$R1	1310
2	TraesCS3A01G504500	chr3A	726457491	726459094	1603	False	988.500000	1526	88.289500	99	1752	2	chr3A.!!$F2	1653
3	TraesCS3A01G504500	chr3D	595738193	595740846	2653	False	4133.000000	4133	94.739000	1	2675	1	chr3D.!!$F2	2674
4	TraesCS3A01G504500	chr3D	595704611	595706101	1490	False	1903.000000	1903	89.847000	265	1752	1	chr3D.!!$F1	1487
5	TraesCS3A01G504500	chr3D	595673542	595675650	2108	False	688.333333	1251	85.861667	219	2163	3	chr3D.!!$F4	1944
6	TraesCS3A01G504500	chr3D	595285728	595287060	1332	True	683.000000	1020	84.925500	467	1816	2	chr3D.!!$R2	1349
7	TraesCS3A01G504500	chr3D	595301608	595305185	3577	False	372.066667	1205	88.983667	88	2675	6	chr3D.!!$F3	2587
8	TraesCS3A01G504500	chr3D	596111073	596111698	625	True	202.900000	340	85.909000	222	903	2	chr3D.!!$R3	681
9	TraesCS3A01G504500	chr3B	798686144	798690250	4106	False	1094.000000	1628	89.241000	448	2163	2	chr3B.!!$F2	1715
10	TraesCS3A01G504500	chr3B	798647329	798649100	1771	False	1007.500000	1339	89.310500	76	1752	2	chr3B.!!$F1	1676
11	TraesCS3A01G504500	chr3B	799521228	799522163	935	True	878.000000	878	83.733000	772	1722	1	chr3B.!!$R1	950

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
55	56	1.877637	TTGGTTATGATCGATGCCGG	58.122	50.0	0.54	0.0	36.24	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1969	5527	1.524621	GCGCTGGGTATGCAGACAT	60.525	57.895	14.36	0.0	40.49	3.06	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
54	55	3.961477	TTTTGGTTATGATCGATGCCG	57.039	42.857	0.54	0.00	37.07	5.69
55	56	1.877637	TTGGTTATGATCGATGCCGG	58.122	50.000	0.54	0.00	36.24	6.13
188	189	3.682718	GCCTGTATGCTGTCTGTACCAAT	60.683	47.826	0.00	0.00	0.00	3.16
189	190	4.517285	CCTGTATGCTGTCTGTACCAATT	58.483	43.478	0.00	0.00	0.00	2.32
190	191	4.572389	CCTGTATGCTGTCTGTACCAATTC	59.428	45.833	0.00	0.00	0.00	2.17
191	192	5.420725	TGTATGCTGTCTGTACCAATTCT	57.579	39.130	0.00	0.00	0.00	2.40
192	193	6.406961	CCTGTATGCTGTCTGTACCAATTCTA	60.407	42.308	0.00	0.00	0.00	2.10
193	194	6.338146	TGTATGCTGTCTGTACCAATTCTAC	58.662	40.000	0.00	0.00	0.00	2.59
194	195	4.202245	TGCTGTCTGTACCAATTCTACC	57.798	45.455	0.00	0.00	0.00	3.18
195	196	3.055385	TGCTGTCTGTACCAATTCTACCC	60.055	47.826	0.00	0.00	0.00	3.69
309	650	8.200120	TGCTCTTATCCACATGATACTATATGC	58.800	37.037	0.00	0.00	35.66	3.14
378	720	6.438259	AATTCAGAGCTGATTCAGTGAATG	57.562	37.500	22.93	10.60	35.98	2.67
393	735	2.094417	GTGAATGTTTGCTCGCTACTCC	59.906	50.000	0.00	0.00	0.00	3.85
642	1170	2.607457	CGACGTTTGTTGCTACCCA	58.393	52.632	0.00	0.00	0.00	4.51
809	1707	6.693315	TTGCTCAAAACTTAACTTGCTAGT	57.307	33.333	0.00	0.00	35.68	2.57
822	1858	3.257393	CTTGCTAGTCTTAGTGTGGCAG	58.743	50.000	0.00	0.00	0.00	4.85
840	1876	2.222819	GCAGCTTGTTCTGTATACACGC	60.223	50.000	0.08	0.00	40.04	5.34
919	1977	4.078805	TGGGCTCTCTACTACCTGGAATTA	60.079	45.833	0.00	0.00	0.00	1.40
1065	2129	2.301296	CAAGGTCCACTCATCAGACACT	59.699	50.000	0.00	0.00	31.99	3.55
1176	2241	2.609427	GCATCCAGCATGACTCTACA	57.391	50.000	0.00	0.00	44.79	2.74
1561	2627	0.183731	GAAAGGCACTCCCCCTATGG	59.816	60.000	0.00	0.00	38.49	2.74
1580	2646	1.712977	GAGCAGCGCCTCATCTTTGG	61.713	60.000	2.29	0.00	0.00	3.28
1633	2699	2.930887	GCGGACTACAACATTCAGAGCA	60.931	50.000	0.00	0.00	0.00	4.26
1735	5229	2.025605	TGGAGCCTTCCTTCGAGTAGTA	60.026	50.000	0.00	0.00	44.36	1.82
1786	5295	7.069852	AGTACTGTCCGTTAGTATATATGCG	57.930	40.000	0.00	0.00	33.60	4.73
1806	5315	2.811431	CGCCAGTATTGTTCCTTCACAA	59.189	45.455	0.00	0.00	40.92	3.33
1858	5393	8.139350	TGTCAATGTCTCGAGTAGTTCTTTTTA	58.861	33.333	13.13	0.00	0.00	1.52
1859	5394	8.640291	GTCAATGTCTCGAGTAGTTCTTTTTAG	58.360	37.037	13.13	0.00	0.00	1.85
1860	5395	8.358148	TCAATGTCTCGAGTAGTTCTTTTTAGT	58.642	33.333	13.13	0.00	0.00	2.24
1942	5496	3.730715	GCAGTTTGATTGACCGACAAAAG	59.269	43.478	0.00	0.00	42.03	2.27
1969	5527	8.739972	GCCTCCTTTATTTACTCATTTCTTTCA	58.260	33.333	0.00	0.00	0.00	2.69
1997	5555	2.687700	TACCCAGCGCGGTTAATTTA	57.312	45.000	8.73	0.00	37.34	1.40
2175	5733	6.015940	GGAGTTGAAATCAAGTTGTCCTCAAT	60.016	38.462	14.70	7.94	39.43	2.57
2237	5825	5.454329	GGAGGTGTTAGTTGTATATGACCCC	60.454	48.000	0.00	0.00	0.00	4.95
2238	5826	4.411212	AGGTGTTAGTTGTATATGACCCCC	59.589	45.833	0.00	0.00	0.00	5.40
2244	5832	2.706190	GTTGTATATGACCCCCTCAGCT	59.294	50.000	0.00	0.00	30.20	4.24
2267	5855	0.113776	ATGGAGCATTGGGGGCATAG	59.886	55.000	0.00	0.00	0.00	2.23
2315	6182	0.108041	GATTTGGGGTGGCAGCATTG	60.108	55.000	19.48	0.00	0.00	2.82
2420	6287	0.596082	GCAAGTGGTACAACGCCAAT	59.404	50.000	0.00	0.00	44.16	3.16
2425	6292	2.152830	GTGGTACAACGCCAATGGTTA	58.847	47.619	0.00	0.00	44.16	2.85
2427	6294	1.741145	GGTACAACGCCAATGGTTAGG	59.259	52.381	0.00	0.00	0.00	2.69
2492	6359	6.816640	GGGTTTAGGGATAAAGATTGTTTTGC	59.183	38.462	0.00	0.00	0.00	3.68
2509	6376	6.606768	TGTTTTGCTCAAATTTGAACAAACC	58.393	32.000	33.49	29.47	46.64	3.27
2564	6432	7.333672	GGTGTTAAACATTGTAGGAAGGAGTAG	59.666	40.741	0.00	0.00	0.00	2.57
2565	6433	7.333672	GTGTTAAACATTGTAGGAAGGAGTAGG	59.666	40.741	0.00	0.00	0.00	3.18
2566	6434	7.236019	TGTTAAACATTGTAGGAAGGAGTAGGA	59.764	37.037	0.00	0.00	0.00	2.94
2567	6435	5.678955	AACATTGTAGGAAGGAGTAGGAC	57.321	43.478	0.00	0.00	0.00	3.85
2568	6436	4.949121	ACATTGTAGGAAGGAGTAGGACT	58.051	43.478	0.00	0.00	0.00	3.85
2569	6437	6.088541	ACATTGTAGGAAGGAGTAGGACTA	57.911	41.667	0.00	0.00	0.00	2.59
2596	6464	3.438434	TGCAAAAGGCCAAAAACAGTTTC	59.562	39.130	5.01	0.00	43.89	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	0.756294	ACCGGCATCGATCATAACCA	59.244	50.000	0.00	0.00	39.00	3.67
62	63	6.049955	AGGTATCGATCCTGTTCTCAAAAA	57.950	37.500	0.00	0.00	33.62	1.94
63	64	5.677319	AGGTATCGATCCTGTTCTCAAAA	57.323	39.130	0.00	0.00	33.62	2.44
64	65	5.677319	AAGGTATCGATCCTGTTCTCAAA	57.323	39.130	14.62	0.00	35.27	2.69
65	66	5.677319	AAAGGTATCGATCCTGTTCTCAA	57.323	39.130	14.62	0.00	35.27	3.02
66	67	5.046591	ACAAAAGGTATCGATCCTGTTCTCA	60.047	40.000	14.62	0.00	35.27	3.27
74	75	3.377172	CACCCAACAAAAGGTATCGATCC	59.623	47.826	0.00	3.29	33.52	3.36
188	189	1.990327	GGTTGAGGGGAAAGGGTAGAA	59.010	52.381	0.00	0.00	0.00	2.10
189	190	1.665137	GGTTGAGGGGAAAGGGTAGA	58.335	55.000	0.00	0.00	0.00	2.59
190	191	0.624254	GGGTTGAGGGGAAAGGGTAG	59.376	60.000	0.00	0.00	0.00	3.18
191	192	0.103823	TGGGTTGAGGGGAAAGGGTA	60.104	55.000	0.00	0.00	0.00	3.69
192	193	1.388217	TGGGTTGAGGGGAAAGGGT	60.388	57.895	0.00	0.00	0.00	4.34
193	194	1.384191	CTGGGTTGAGGGGAAAGGG	59.616	63.158	0.00	0.00	0.00	3.95
194	195	1.304464	GCTGGGTTGAGGGGAAAGG	60.304	63.158	0.00	0.00	0.00	3.11
195	196	0.040204	ATGCTGGGTTGAGGGGAAAG	59.960	55.000	0.00	0.00	0.00	2.62
284	614	8.420222	AGCATATAGTATCATGTGGATAAGAGC	58.580	37.037	0.00	0.00	40.11	4.09
309	650	7.377928	CACAAAGACAGCTGATGAAAAGTAAAG	59.622	37.037	23.35	0.00	0.00	1.85
367	709	2.816087	AGCGAGCAAACATTCACTGAAT	59.184	40.909	0.00	0.00	31.86	2.57
378	720	2.742053	TGAATTGGAGTAGCGAGCAAAC	59.258	45.455	0.00	0.00	0.00	2.93
393	735	5.912360	TCTATGTGCGAGCTTATGAATTG	57.088	39.130	0.00	0.00	0.00	2.32
580	1102	9.376075	CCCTATTTGTCTCAGCATATATAGTTG	57.624	37.037	0.00	0.00	0.00	3.16
642	1170	3.129287	CCTGTCAAGTGCAGTTTTTCACT	59.871	43.478	3.38	0.00	44.64	3.41
809	1707	2.104792	AGAACAAGCTGCCACACTAAGA	59.895	45.455	0.00	0.00	0.00	2.10
840	1876	9.190858	GAAGAGAGATGTACTGCATAAATACTG	57.809	37.037	0.00	0.00	38.06	2.74
1065	2129	3.133901	TCTTTGCCTTGACAGTGTACAGA	59.866	43.478	0.00	0.00	0.00	3.41
1176	2241	3.766051	GCATCTTTTCCTGGAGGTCAATT	59.234	43.478	0.00	0.00	36.34	2.32
1561	2627	1.712977	CCAAAGATGAGGCGCTGCTC	61.713	60.000	7.64	7.08	0.00	4.26
1580	2646	3.060615	CCTCCAGCTGCTTGCCAC	61.061	66.667	8.66	0.00	44.23	5.01
1786	5295	5.880332	TCTATTGTGAAGGAACAATACTGGC	59.120	40.000	5.83	0.00	46.41	4.85
1835	5369	8.522178	ACTAAAAAGAACTACTCGAGACATTG	57.478	34.615	21.68	6.41	0.00	2.82
1858	5393	4.171044	ACCCAGGGACTCTTGATAGATACT	59.829	45.833	14.54	0.00	34.60	2.12
1859	5394	4.484912	ACCCAGGGACTCTTGATAGATAC	58.515	47.826	14.54	0.00	34.60	2.24
1860	5395	4.420552	AGACCCAGGGACTCTTGATAGATA	59.579	45.833	14.54	0.00	34.60	1.98
1942	5496	7.646548	AAGAAATGAGTAAATAAAGGAGGCC	57.353	36.000	0.00	0.00	0.00	5.19
1952	5510	8.114331	TGCAGACATGAAAGAAATGAGTAAAT	57.886	30.769	0.00	0.00	0.00	1.40
1969	5527	1.524621	GCGCTGGGTATGCAGACAT	60.525	57.895	14.36	0.00	40.49	3.06
2237	5825	0.763652	ATGCTCCATGGTAGCTGAGG	59.236	55.000	26.29	6.92	40.73	3.86
2238	5826	2.219458	CAATGCTCCATGGTAGCTGAG	58.781	52.381	26.29	12.86	40.73	3.35
2244	5832	1.929745	CCCCCAATGCTCCATGGTA	59.070	57.895	12.58	0.00	0.00	3.25
2284	6150	0.826062	CCCAAATCTCCAATGCCACC	59.174	55.000	0.00	0.00	0.00	4.61
2315	6182	1.616994	CCCATCCACCTTCAAACCCTC	60.617	57.143	0.00	0.00	0.00	4.30
2349	6216	5.105310	CCCCTCCTATAAATACCTCGTCATG	60.105	48.000	0.00	0.00	0.00	3.07
2425	6292	0.395311	CACCAGAGCATTCATGGCCT	60.395	55.000	3.32	0.00	37.64	5.19
2427	6294	0.737219	GACACCAGAGCATTCATGGC	59.263	55.000	0.00	0.00	37.64	4.40
2428	6295	2.014857	CTGACACCAGAGCATTCATGG	58.985	52.381	0.00	0.00	43.02	3.66
2429	6296	2.708051	ACTGACACCAGAGCATTCATG	58.292	47.619	0.00	0.00	43.02	3.07
2430	6297	3.430042	AACTGACACCAGAGCATTCAT	57.570	42.857	0.00	0.00	43.02	2.57
2431	6298	2.936919	AACTGACACCAGAGCATTCA	57.063	45.000	0.00	0.00	43.02	2.57
2432	6299	3.406764	AGAAACTGACACCAGAGCATTC	58.593	45.455	0.00	0.00	43.02	2.67
2433	6300	3.498774	AGAAACTGACACCAGAGCATT	57.501	42.857	0.00	0.00	43.02	3.56
2434	6301	4.833478	ATAGAAACTGACACCAGAGCAT	57.167	40.909	0.00	0.00	43.02	3.79
2435	6302	5.337571	CCTTATAGAAACTGACACCAGAGCA	60.338	44.000	0.00	0.00	43.02	4.26
2492	6359	4.314740	TCCCGGTTTGTTCAAATTTGAG	57.685	40.909	19.64	7.53	38.61	3.02
2509	6376	1.557832	TCACCCCTGAAACTATTCCCG	59.442	52.381	0.00	0.00	34.49	5.14
2564	6432	1.813178	GGCCTTTTGCAAGTCTAGTCC	59.187	52.381	0.00	0.00	43.89	3.85
2565	6433	2.504367	TGGCCTTTTGCAAGTCTAGTC	58.496	47.619	3.32	0.00	43.89	2.59
2566	6434	2.656947	TGGCCTTTTGCAAGTCTAGT	57.343	45.000	3.32	0.00	43.89	2.57
2567	6435	4.320608	TTTTGGCCTTTTGCAAGTCTAG	57.679	40.909	3.32	0.00	43.89	2.43
2568	6436	4.081420	TGTTTTTGGCCTTTTGCAAGTCTA	60.081	37.500	3.32	0.00	43.89	2.59
2569	6437	3.270027	GTTTTTGGCCTTTTGCAAGTCT	58.730	40.909	3.32	0.00	43.89	3.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.