AutoCloner

Multiple sequence alignment - TraesCS7A01G468200

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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	TraesCS7A01G468200	chr7A	100.000	1674	0	0	1	1674	664372928	664371255	0.000000e+00	3092.0
1	TraesCS7A01G468200	chr7A	88.260	954	82	20	730	1672	664415248	664414314	0.000000e+00	1114.0
2	TraesCS7A01G468200	chr7A	80.260	846	111	40	712	1539	664999523	665000330	9.090000e-164	586.0
3	TraesCS7A01G468200	chr7A	100.000	243	0	0	2043	2285	664370886	664370644	1.240000e-122	449.0
4	TraesCS7A01G468200	chr7A	100.000	28	0	0	2258	2285	26175613	26175586	4.000000e-03	52.8
5	TraesCS7A01G468200	chr7D	90.693	967	57	18	730	1672	574764437	574763480	0.000000e+00	1256.0
6	TraesCS7A01G468200	chr7D	89.205	843	58	14	712	1539	574774438	574773614	0.000000e+00	1022.0
7	TraesCS7A01G468200	chr7D	83.582	871	76	38	712	1547	575441325	575442163	0.000000e+00	754.0
8	TraesCS7A01G468200	chr7D	82.597	770	89	31	784	1534	575408159	575408902	2.480000e-179	638.0
9	TraesCS7A01G468200	chr7D	88.095	168	14	2	2097	2264	574763379	574763218	6.440000e-46	195.0
10	TraesCS7A01G468200	chr7B	88.809	974	76	18	728	1672	634580077	634579108	0.000000e+00	1164.0
11	TraesCS7A01G468200	chr7B	84.642	879	83	30	792	1645	634647580	634646729	0.000000e+00	828.0
12	TraesCS7A01G468200	chr7B	80.906	817	103	32	732	1534	636940119	636940896	1.510000e-166	595.0
13	TraesCS7A01G468200	chr7B	89.706	68	4	3	712	777	634647642	634647576	1.450000e-12	84.2
14	TraesCS7A01G468200	chr6A	95.342	730	29	5	2	729	584974020	584973294	0.000000e+00	1155.0
15	TraesCS7A01G468200	chr6A	94.650	729	35	4	2	729	14488676	14487951	0.000000e+00	1127.0
16	TraesCS7A01G468200	chr6A	94.635	727	36	3	2	727	6615602	6616326	0.000000e+00	1123.0
17	TraesCS7A01G468200	chr1A	95.192	728	31	4	2	727	504402912	504403637	0.000000e+00	1147.0
18	TraesCS7A01G468200	chr1A	94.513	729	38	2	2	729	9714187	9714914	0.000000e+00	1123.0
19	TraesCS7A01G468200	chr1A	94.360	727	39	2	2	727	552497573	552498298	0.000000e+00	1114.0
20	TraesCS7A01G468200	chr1A	94.360	727	37	4	2	727	505486139	505486862	0.000000e+00	1112.0
21	TraesCS7A01G468200	chr2A	95.034	725	33	3	2	724	507163061	507162338	0.000000e+00	1136.0
22	TraesCS7A01G468200	chr2A	100.000	28	0	0	2258	2285	662908009	662908036	4.000000e-03	52.8
23	TraesCS7A01G468200	chr3A	94.759	725	35	3	2	725	708643758	708644480	0.000000e+00	1125.0
24	TraesCS7A01G468200	chr3A	79.787	188	28	8	2080	2262	701762979	701763161	6.630000e-26	128.0
25	TraesCS7A01G468200	chr4D	86.772	189	21	4	2074	2260	88148203	88148017	8.270000e-50	207.0
26	TraesCS7A01G468200	chr4B	85.492	193	25	3	2071	2261	124922801	124922610	4.980000e-47	198.0
27	TraesCS7A01G468200	chr4A	85.052	194	24	5	2071	2260	501128834	501128642	2.320000e-45	193.0
28	TraesCS7A01G468200	chr4A	81.250	192	35	1	2069	2260	4247973	4248163	1.090000e-33	154.0
29	TraesCS7A01G468200	chr4A	78.788	198	35	7	2069	2260	601046236	601046432	2.380000e-25	126.0
30	TraesCS7A01G468200	chr5A	86.275	153	20	1	2071	2223	634499655	634499504	5.050000e-37	165.0
31	TraesCS7A01G468200	chr5B	81.176	170	20	9	2071	2234	637447741	637447578	2.380000e-25	126.0
32	TraesCS7A01G468200	chr5B	96.875	32	0	1	2254	2285	313387626	313387596	4.000000e-03	52.8
33	TraesCS7A01G468200	chr1B	100.000	29	0	0	2257	2285	411862407	411862435	1.000000e-03	54.7
34	TraesCS7A01G468200	chr6D	100.000	28	0	0	2258	2285	328107880	328107853	4.000000e-03	52.8
35	TraesCS7A01G468200	chr6B	96.875	32	0	1	2255	2285	119969457	119969488	4.000000e-03	52.8
36	TraesCS7A01G468200	chr3B	96.774	31	1	0	2255	2285	514649444	514649474	4.000000e-03	52.8
37	TraesCS7A01G468200	chr2B	100.000	28	0	0	2258	2285	244699126	244699153	4.000000e-03	52.8

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	TraesCS7A01G468200	chr7A	664370644	664372928	2284	True	1770.5	3092	100.000	1	2285	2	chr7A.!!$R3	2284
1	TraesCS7A01G468200	chr7A	664414314	664415248	934	True	1114.0	1114	88.260	730	1672	1	chr7A.!!$R2	942
2	TraesCS7A01G468200	chr7A	664999523	665000330	807	False	586.0	586	80.260	712	1539	1	chr7A.!!$F1	827
3	TraesCS7A01G468200	chr7D	574773614	574774438	824	True	1022.0	1022	89.205	712	1539	1	chr7D.!!$R1	827
4	TraesCS7A01G468200	chr7D	575441325	575442163	838	False	754.0	754	83.582	712	1547	1	chr7D.!!$F2	835
5	TraesCS7A01G468200	chr7D	574763218	574764437	1219	True	725.5	1256	89.394	730	2264	2	chr7D.!!$R2	1534
6	TraesCS7A01G468200	chr7D	575408159	575408902	743	False	638.0	638	82.597	784	1534	1	chr7D.!!$F1	750
7	TraesCS7A01G468200	chr7B	634579108	634580077	969	True	1164.0	1164	88.809	728	1672	1	chr7B.!!$R1	944
8	TraesCS7A01G468200	chr7B	636940119	636940896	777	False	595.0	595	80.906	732	1534	1	chr7B.!!$F1	802
9	TraesCS7A01G468200	chr7B	634646729	634647642	913	True	456.1	828	87.174	712	1645	2	chr7B.!!$R2	933
10	TraesCS7A01G468200	chr6A	584973294	584974020	726	True	1155.0	1155	95.342	2	729	1	chr6A.!!$R2	727
11	TraesCS7A01G468200	chr6A	14487951	14488676	725	True	1127.0	1127	94.650	2	729	1	chr6A.!!$R1	727
12	TraesCS7A01G468200	chr6A	6615602	6616326	724	False	1123.0	1123	94.635	2	727	1	chr6A.!!$F1	725
13	TraesCS7A01G468200	chr1A	504402912	504403637	725	False	1147.0	1147	95.192	2	727	1	chr1A.!!$F2	725
14	TraesCS7A01G468200	chr1A	9714187	9714914	727	False	1123.0	1123	94.513	2	729	1	chr1A.!!$F1	727
15	TraesCS7A01G468200	chr1A	552497573	552498298	725	False	1114.0	1114	94.360	2	727	1	chr1A.!!$F4	725
16	TraesCS7A01G468200	chr1A	505486139	505486862	723	False	1112.0	1112	94.360	2	727	1	chr1A.!!$F3	725
17	TraesCS7A01G468200	chr2A	507162338	507163061	723	True	1136.0	1136	95.034	2	724	1	chr2A.!!$R1	722
18	TraesCS7A01G468200	chr3A	708643758	708644480	722	False	1125.0	1125	94.759	2	725	1	chr3A.!!$F2	723

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
209	211	0.456995	GCTCTTCTTCCTGGACGTCG	60.457	60.0	9.92	0.0	0.0	5.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1330	1471	0.400213	ACCCAGAAAGTCAATCGCCA	59.6	50.0	0.0	0.0	0.0	5.69	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
103	105	0.463116	AGACGTTGCCGGTTCTTTGT	60.463	50.000	1.90	0.00	38.78	2.83
110	112	2.096248	TGCCGGTTCTTTGTTTTCACT	58.904	42.857	1.90	0.00	0.00	3.41
153	155	0.516877	CCGCGTCTTTTCATTGCTCA	59.483	50.000	4.92	0.00	0.00	4.26
209	211	0.456995	GCTCTTCTTCCTGGACGTCG	60.457	60.000	9.92	0.00	0.00	5.12
398	400	0.726827	CGAAGCGCTGCTATTTTCCA	59.273	50.000	12.58	0.00	38.25	3.53
491	494	4.373116	GGGTGCGAGGCGAGTTGA	62.373	66.667	0.00	0.00	0.00	3.18
515	518	4.649674	GGGAAGAAAACCTTGACTTTTCCT	59.350	41.667	0.00	0.00	38.05	3.36
692	697	2.049156	GCCGAAAAAGTGGCCTGC	60.049	61.111	3.32	0.00	45.73	4.85
777	813	4.019231	ACAGTAAACCTTCCATTCCTCTCC	60.019	45.833	0.00	0.00	0.00	3.71
778	814	3.523972	AGTAAACCTTCCATTCCTCTCCC	59.476	47.826	0.00	0.00	0.00	4.30
779	815	2.367947	AACCTTCCATTCCTCTCCCT	57.632	50.000	0.00	0.00	0.00	4.20
780	816	3.508952	AACCTTCCATTCCTCTCCCTA	57.491	47.619	0.00	0.00	0.00	3.53
781	817	2.765502	ACCTTCCATTCCTCTCCCTAC	58.234	52.381	0.00	0.00	0.00	3.18
782	818	2.050918	CCTTCCATTCCTCTCCCTACC	58.949	57.143	0.00	0.00	0.00	3.18
787	823	0.858369	ATTCCTCTCCCTACCCGCTA	59.142	55.000	0.00	0.00	0.00	4.26
963	1075	8.145767	AGCTAGCTATATACCTACACTATCTCG	58.854	40.741	17.69	0.00	0.00	4.04
985	1097	0.628781	CGTGATCAGTTCGTTCGTCG	59.371	55.000	0.00	0.00	41.41	5.12
1015	1127	1.137675	CGACAATGAGGGAGCTGATCA	59.862	52.381	0.00	0.00	0.00	2.92
1031	1143	2.590391	ATCAGGCGGCTGAGCTTCTG	62.590	60.000	39.29	15.28	36.73	3.02
1330	1471	3.196469	TCAATCAAGCAGATCGAACCTCT	59.804	43.478	0.00	0.00	35.39	3.69
1331	1472	2.662006	TCAAGCAGATCGAACCTCTG	57.338	50.000	9.67	9.67	42.47	3.35
1332	1473	1.205655	TCAAGCAGATCGAACCTCTGG	59.794	52.381	14.63	1.09	40.40	3.86
1349	1494	0.400213	TGGCGATTGACTTTCTGGGT	59.600	50.000	0.00	0.00	0.00	4.51
1350	1495	1.626321	TGGCGATTGACTTTCTGGGTA	59.374	47.619	0.00	0.00	0.00	3.69
1373	1518	0.176680	TTGAGGAGCGATTCTCTGGC	59.823	55.000	10.90	0.00	41.60	4.85
1379	1534	2.520904	GCGATTCTCTGGCGCTGTC	61.521	63.158	7.64	0.00	46.53	3.51
1479	1642	3.130164	TGCCATATGTATTGTGCGCTTTT	59.870	39.130	9.73	0.00	0.00	2.27
1549	1717	8.524870	ACAAGTGAAACAATTGATTATTCAGC	57.475	30.769	13.59	10.71	41.15	4.26
1576	1746	7.027874	ACATTTGTCCTTTCTAATCCTGGTA	57.972	36.000	0.00	0.00	0.00	3.25
1579	1749	8.971073	CATTTGTCCTTTCTAATCCTGGTAAAT	58.029	33.333	0.00	0.00	0.00	1.40
1653	1828	7.011482	AGTGAGAAATTATTTAGTGGACGCATC	59.989	37.037	0.00	0.00	0.00	3.91
1662	1837	2.973945	AGTGGACGCATCTTTACTTCC	58.026	47.619	0.00	0.00	0.00	3.46
1672	1847	5.179045	CATCTTTACTTCCCATGATGCAC	57.821	43.478	0.00	0.00	0.00	4.57
2084	2259	9.415544	ACAAAATAAGAAGACAAATCTTGATGC	57.584	29.630	0.00	0.00	45.60	3.91
2085	2260	9.414295	CAAAATAAGAAGACAAATCTTGATGCA	57.586	29.630	0.00	0.00	45.60	3.96
2086	2261	9.985730	AAAATAAGAAGACAAATCTTGATGCAA	57.014	25.926	0.00	0.00	45.60	4.08
2087	2262	9.985730	AAATAAGAAGACAAATCTTGATGCAAA	57.014	25.926	0.00	0.00	45.60	3.68
2088	2263	9.635520	AATAAGAAGACAAATCTTGATGCAAAG	57.364	29.630	0.00	0.00	45.60	2.77
2089	2264	5.467705	AGAAGACAAATCTTGATGCAAAGC	58.532	37.500	0.00	0.00	45.60	3.51
2090	2265	4.859304	AGACAAATCTTGATGCAAAGCA	57.141	36.364	0.00	0.00	44.86	3.91
2091	2266	5.204409	AGACAAATCTTGATGCAAAGCAA	57.796	34.783	0.00	0.00	43.62	3.91
2092	2267	5.603596	AGACAAATCTTGATGCAAAGCAAA	58.396	33.333	0.00	0.00	43.62	3.68
2093	2268	6.228258	AGACAAATCTTGATGCAAAGCAAAT	58.772	32.000	0.00	0.00	43.62	2.32
2094	2269	7.380536	AGACAAATCTTGATGCAAAGCAAATA	58.619	30.769	0.00	0.00	43.62	1.40
2095	2270	7.544566	AGACAAATCTTGATGCAAAGCAAATAG	59.455	33.333	0.00	0.00	43.62	1.73
2141	2316	7.338449	TGGTTGTAAAGTATAGATTTTCCAGCC	59.662	37.037	0.00	0.00	0.00	4.85
2158	2333	8.415950	TTTCCAGCCATTTCTTAAACTTATGA	57.584	30.769	0.00	0.00	0.00	2.15
2159	2334	8.415950	TTCCAGCCATTTCTTAAACTTATGAA	57.584	30.769	0.00	0.00	0.00	2.57
2160	2335	8.415950	TCCAGCCATTTCTTAAACTTATGAAA	57.584	30.769	10.98	10.98	39.52	2.69
2161	2336	9.034800	TCCAGCCATTTCTTAAACTTATGAAAT	57.965	29.630	13.53	13.53	42.93	2.17
2194	2369	8.219546	TGCGAATGATTAATCCACTTTATTGA	57.780	30.769	12.90	0.00	0.00	2.57
2206	2381	7.531857	TCCACTTTATTGAGTTGCCAAATAA	57.468	32.000	0.00	0.00	0.00	1.40
2262	2437	8.952278	TCGCCATGAAGTTATTGTTATTTACTT	58.048	29.630	0.00	0.00	0.00	2.24
2263	2438	9.221775	CGCCATGAAGTTATTGTTATTTACTTC	57.778	33.333	0.00	0.00	43.00	3.01
2264	2439	9.516314	GCCATGAAGTTATTGTTATTTACTTCC	57.484	33.333	0.00	0.00	42.38	3.46
2284	2459	8.753497	ACTTCCTCCATTCCTAAATATTTGTC	57.247	34.615	11.05	0.00	0.00	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	91	2.494073	AGTGAAAACAAAGAACCGGCAA	59.506	40.909	0.00	0.00	0.00	4.52
240	242	1.118838	CGGATGAGGAGGAAGAGCTT	58.881	55.000	0.00	0.00	0.00	3.74
398	400	1.270907	CTAGATAGCCATTCCCCGCT	58.729	55.000	0.00	0.00	39.17	5.52
444	446	1.893137	TCGGCCACCACTAGCTATATG	59.107	52.381	2.24	0.00	0.00	1.78
489	492	4.519906	AAGTCAAGGTTTTCTTCCCTCA	57.480	40.909	0.00	0.00	32.41	3.86
491	494	4.649674	GGAAAAGTCAAGGTTTTCTTCCCT	59.350	41.667	7.92	0.00	41.63	4.20
515	518	3.625897	CTGGCCCACACCGACAGA	61.626	66.667	0.00	0.00	0.00	3.41
712	717	0.621571	TGGTTAGGGCATCTCCAGCT	60.622	55.000	0.00	0.00	36.21	4.24
777	813	2.304761	AGAGAGAGAGATAGCGGGTAGG	59.695	54.545	0.00	0.00	0.00	3.18
778	814	3.260884	AGAGAGAGAGAGATAGCGGGTAG	59.739	52.174	0.00	0.00	0.00	3.18
779	815	3.244582	AGAGAGAGAGAGATAGCGGGTA	58.755	50.000	0.00	0.00	0.00	3.69
780	816	2.038557	GAGAGAGAGAGAGATAGCGGGT	59.961	54.545	0.00	0.00	0.00	5.28
781	817	2.303022	AGAGAGAGAGAGAGATAGCGGG	59.697	54.545	0.00	0.00	0.00	6.13
782	818	3.006859	TGAGAGAGAGAGAGAGATAGCGG	59.993	52.174	0.00	0.00	0.00	5.52
787	823	3.523157	TGTGGTGAGAGAGAGAGAGAGAT	59.477	47.826	0.00	0.00	0.00	2.75
963	1075	2.578495	ACGAACGAACTGATCACGTAC	58.422	47.619	9.89	0.00	39.31	3.67
985	1097	2.009774	CCTCATTGTCGGTTGATCACC	58.990	52.381	0.00	0.00	43.16	4.02
999	1111	0.473326	GCCTGATCAGCTCCCTCATT	59.527	55.000	17.76	0.00	0.00	2.57
1015	1127	4.093291	CCAGAAGCTCAGCCGCCT	62.093	66.667	0.00	0.00	0.00	5.52
1264	1397	0.608640	CAGTAGTTCTTGGAGGCGGT	59.391	55.000	0.00	0.00	0.00	5.68
1330	1471	0.400213	ACCCAGAAAGTCAATCGCCA	59.600	50.000	0.00	0.00	0.00	5.69
1331	1472	2.396590	TACCCAGAAAGTCAATCGCC	57.603	50.000	0.00	0.00	0.00	5.54
1332	1473	4.694339	AGTATACCCAGAAAGTCAATCGC	58.306	43.478	0.00	0.00	0.00	4.58
1349	1494	4.520874	CCAGAGAATCGCTCCTCAAGTATA	59.479	45.833	0.00	0.00	45.10	1.47
1350	1495	3.320541	CCAGAGAATCGCTCCTCAAGTAT	59.679	47.826	0.00	0.00	45.10	2.12
1373	1518	1.465387	AGAGTCAACTAGTCGACAGCG	59.535	52.381	19.50	7.75	34.48	5.18
1379	1534	1.133407	GGCAGGAGAGTCAACTAGTCG	59.867	57.143	0.00	0.00	32.30	4.18
1547	1715	7.284034	CAGGATTAGAAAGGACAAATGTATGCT	59.716	37.037	0.00	0.00	0.00	3.79
1549	1717	7.557719	ACCAGGATTAGAAAGGACAAATGTATG	59.442	37.037	0.00	0.00	0.00	2.39
1552	1720	5.892348	ACCAGGATTAGAAAGGACAAATGT	58.108	37.500	0.00	0.00	0.00	2.71
1594	1765	7.784470	AAAGCCCAAAAATGTACCAATACTA	57.216	32.000	0.00	0.00	32.00	1.82
1596	1767	7.737972	AAAAAGCCCAAAAATGTACCAATAC	57.262	32.000	0.00	0.00	0.00	1.89
1639	1813	4.933400	GGAAGTAAAGATGCGTCCACTAAA	59.067	41.667	1.23	0.00	39.11	1.85
2062	2237	9.635520	CTTTGCATCAAGATTTGTCTTCTTATT	57.364	29.630	0.00	0.00	32.27	1.40
2069	2244	4.859304	TGCTTTGCATCAAGATTTGTCT	57.141	36.364	2.23	0.00	31.71	3.41
2075	2250	6.519679	TGTCTATTTGCTTTGCATCAAGAT	57.480	33.333	2.23	1.44	38.76	2.40
2076	2251	5.963176	TGTCTATTTGCTTTGCATCAAGA	57.037	34.783	2.23	0.00	38.76	3.02
2077	2252	7.410800	TTTTGTCTATTTGCTTTGCATCAAG	57.589	32.000	0.00	0.00	38.76	3.02
2078	2253	7.966246	ATTTTGTCTATTTGCTTTGCATCAA	57.034	28.000	0.00	0.00	38.76	2.57
2079	2254	9.142515	CTTATTTTGTCTATTTGCTTTGCATCA	57.857	29.630	0.00	0.00	38.76	3.07
2080	2255	9.357652	TCTTATTTTGTCTATTTGCTTTGCATC	57.642	29.630	0.00	0.00	38.76	3.91
2081	2256	9.880157	ATCTTATTTTGTCTATTTGCTTTGCAT	57.120	25.926	0.00	0.00	38.76	3.96
2082	2257	9.709495	AATCTTATTTTGTCTATTTGCTTTGCA	57.291	25.926	0.00	0.00	36.47	4.08
2173	2348	9.807649	GCAACTCAATAAAGTGGATTAATCATT	57.192	29.630	17.07	8.55	0.00	2.57
2184	2359	9.474920	TCTTTTATTTGGCAACTCAATAAAGTG	57.525	29.630	0.00	5.44	40.42	3.16
2185	2360	9.696917	CTCTTTTATTTGGCAACTCAATAAAGT	57.303	29.630	0.00	0.00	40.42	2.66
2189	2364	9.859427	CAATCTCTTTTATTTGGCAACTCAATA	57.141	29.630	0.00	0.00	37.61	1.90
2194	2369	8.587608	TCAATCAATCTCTTTTATTTGGCAACT	58.412	29.630	0.00	0.00	37.61	3.16
2237	2412	9.221775	GAAGTAAATAACAATAACTTCATGGCG	57.778	33.333	8.27	0.00	43.45	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.