AutoCloner

Multiple sequence alignment - TraesCS1A01G432600

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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	TraesCS1A01G432600	chr1A	100.000	5696	0	0	1	5696	584350973	584356668	0.000000e+00	10519.0
1	TraesCS1A01G432600	chr1A	84.298	1019	129	14	2373	3362	584072349	584071333	0.000000e+00	966.0
2	TraesCS1A01G432600	chr1A	84.640	931	127	8	3373	4288	584071136	584070207	0.000000e+00	913.0
3	TraesCS1A01G432600	chr1A	89.407	708	54	3	1220	1906	584073069	584072362	0.000000e+00	872.0
4	TraesCS1A01G432600	chr1A	86.217	341	42	3	886	1222	584073568	584073229	1.170000e-96	364.0
5	TraesCS1A01G432600	chr1D	95.355	5576	166	18	1	5490	486754076	486759644	0.000000e+00	8776.0
6	TraesCS1A01G432600	chr1D	81.964	4042	592	71	991	4934	486400912	486396910	0.000000e+00	3299.0
7	TraesCS1A01G432600	chr1D	86.021	1724	194	13	879	2566	486733369	486735081	0.000000e+00	1805.0
8	TraesCS1A01G432600	chr1D	83.203	2042	263	37	3367	5360	396183155	396181146	0.000000e+00	1797.0
9	TraesCS1A01G432600	chr1D	85.116	1290	164	13	2102	3363	396184646	396183357	0.000000e+00	1293.0
10	TraesCS1A01G432600	chr1D	80.760	1606	248	44	3369	4940	486736133	486737711	0.000000e+00	1197.0
11	TraesCS1A01G432600	chr1D	82.931	1242	173	19	878	2099	396185900	396184678	0.000000e+00	1083.0
12	TraesCS1A01G432600	chr1D	85.860	785	104	4	2581	3363	486735135	486735914	0.000000e+00	828.0
13	TraesCS1A01G432600	chr1D	79.982	1084	147	40	4027	5090	482061858	482060825	0.000000e+00	736.0
14	TraesCS1A01G432600	chr1D	91.667	192	14	1	5503	5692	486759693	486759884	1.220000e-66	265.0
15	TraesCS1A01G432600	chr1D	88.636	176	18	2	5523	5696	396181145	396180970	4.470000e-51	213.0
16	TraesCS1A01G432600	chr1B	82.271	2527	366	46	887	3353	677382827	677380323	0.000000e+00	2109.0
17	TraesCS1A01G432600	chr1B	81.597	1766	243	41	857	2569	677630413	677632149	0.000000e+00	1386.0
18	TraesCS1A01G432600	chr1B	83.333	1368	195	24	3369	4710	677633198	677634558	0.000000e+00	1232.0
19	TraesCS1A01G432600	chr1B	83.902	938	127	13	3373	4288	677380117	677379182	0.000000e+00	874.0
20	TraesCS1A01G432600	chr1B	84.566	784	116	3	2581	3363	677632200	677632979	0.000000e+00	773.0
21	TraesCS1A01G432600	chr1B	77.163	578	93	25	4391	4941	677379112	677378547	3.340000e-77	300.0
22	TraesCS1A01G432600	chr1B	81.818	143	14	11	4795	4933	677634601	677634735	6.030000e-20	110.0
23	TraesCS1A01G432600	chr2A	85.981	1769	217	15	820	2563	750412392	750410630	0.000000e+00	1864.0
24	TraesCS1A01G432600	chr2A	88.195	737	81	3	2629	3362	750410543	750409810	0.000000e+00	874.0
25	TraesCS1A01G432600	chr2A	81.288	652	104	10	3367	4000	750383311	750382660	3.940000e-141	512.0
26	TraesCS1A01G432600	chr4A	74.262	474	104	12	1789	2250	676543678	676544145	3.510000e-42	183.0
27	TraesCS1A01G432600	chr4A	100.000	28	0	0	4614	4641	456852767	456852794	1.000000e-02	52.8
28	TraesCS1A01G432600	chr4A	100.000	28	0	0	4614	4641	574109443	574109470	1.000000e-02	52.8
29	TraesCS1A01G432600	chr4A	100.000	28	0	0	4614	4641	574120991	574121018	1.000000e-02	52.8
30	TraesCS1A01G432600	chr4D	94.286	35	2	0	4607	4641	14651875	14651909	3.000000e-03	54.7
31	TraesCS1A01G432600	chr3B	100.000	28	0	0	4614	4641	452976111	452976084	1.000000e-02	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	TraesCS1A01G432600	chr1A	584350973	584356668	5695	False	10519.000000	10519	100.000000	1	5696	1	chr1A.!!$F1	5695
1	TraesCS1A01G432600	chr1A	584070207	584073568	3361	True	778.750000	966	86.140500	886	4288	4	chr1A.!!$R1	3402
2	TraesCS1A01G432600	chr1D	486754076	486759884	5808	False	4520.500000	8776	93.511000	1	5692	2	chr1D.!!$F2	5691
3	TraesCS1A01G432600	chr1D	486396910	486400912	4002	True	3299.000000	3299	81.964000	991	4934	1	chr1D.!!$R2	3943
4	TraesCS1A01G432600	chr1D	486733369	486737711	4342	False	1276.666667	1805	84.213667	879	4940	3	chr1D.!!$F1	4061
5	TraesCS1A01G432600	chr1D	396180970	396185900	4930	True	1096.500000	1797	84.971500	878	5696	4	chr1D.!!$R3	4818
6	TraesCS1A01G432600	chr1D	482060825	482061858	1033	True	736.000000	736	79.982000	4027	5090	1	chr1D.!!$R1	1063
7	TraesCS1A01G432600	chr1B	677378547	677382827	4280	True	1094.333333	2109	81.112000	887	4941	3	chr1B.!!$R1	4054
8	TraesCS1A01G432600	chr1B	677630413	677634735	4322	False	875.250000	1386	82.828500	857	4933	4	chr1B.!!$F1	4076
9	TraesCS1A01G432600	chr2A	750409810	750412392	2582	True	1369.000000	1864	87.088000	820	3362	2	chr2A.!!$R2	2542
10	TraesCS1A01G432600	chr2A	750382660	750383311	651	True	512.000000	512	81.288000	3367	4000	1	chr2A.!!$R1	633

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
696	724	0.471591	AAATGTTGGGGAGCTTGCCA	60.472	50.000	0.00	0.00	0.0	4.92	F
1800	2070	2.310647	GGGGAATGACCAAAAGGACCTA	59.689	50.000	0.00	0.00	41.2	3.08	F
3018	3360	1.391485	GTGACATGTGCTCGTGATGAC	59.609	52.381	14.62	4.48	34.9	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2591	2930	0.389948	GGACAGTGACGTGATGACCC	60.390	60.0	0.00	0.0	0.00	4.46	R
3473	4034	0.250338	AAGTTTCCCTGTCGGAGCAC	60.250	55.0	0.00	0.0	43.39	4.40	R
4822	5473	0.179127	CGAGCGAGCTCTTCATCCAA	60.179	55.0	20.97	0.0	40.69	3.53	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
149	150	2.368875	GCCTTAGGTCATAGCTAGGCAA	59.631	50.000	13.78	0.00	39.75	4.52
206	230	5.603170	TTCTCCCGTTCTTAATATTCCGT	57.397	39.130	0.00	0.00	0.00	4.69
214	238	6.418956	CGTTCTTAATATTCCGTCATGGTTG	58.581	40.000	0.00	0.00	39.52	3.77
319	343	7.860373	TGTTGTTAAACAATCACAGCAGAATAC	59.140	33.333	0.00	0.00	43.32	1.89
359	383	9.663904	AACGTCAATTTATTCGATCAAATATGG	57.336	29.630	5.46	1.07	0.00	2.74
422	450	7.872483	TCCAATTTAAGAAGTGCAAAGAAATCC	59.128	33.333	0.00	0.00	29.82	3.01
556	584	4.222810	GCCCAAAATCCACTCTACCAATTT	59.777	41.667	0.00	0.00	0.00	1.82
598	626	9.990868	AAATTAGGTCTTTACTTGGATGGTTAT	57.009	29.630	0.00	0.00	0.00	1.89
601	629	7.213178	AGGTCTTTACTTGGATGGTTATCAT	57.787	36.000	0.00	0.00	39.13	2.45
696	724	0.471591	AAATGTTGGGGAGCTTGCCA	60.472	50.000	0.00	0.00	0.00	4.92
703	731	2.401766	GGGAGCTTGCCACGTGATG	61.402	63.158	19.30	1.58	0.00	3.07
721	749	3.052109	TGATGGGAGAGGTGGTACATAGT	60.052	47.826	0.00	0.00	44.52	2.12
726	754	4.217983	GGGAGAGGTGGTACATAGTATTCG	59.782	50.000	0.00	0.00	44.52	3.34
777	805	7.284034	GTCAAAATCATGGATTGGAGACTGTAT	59.716	37.037	0.00	0.00	32.14	2.29
813	841	4.646040	TGCATAACATTTTGGGATGGAGAG	59.354	41.667	0.00	0.00	0.00	3.20
1797	2067	2.604912	AGGGGAATGACCAAAAGGAC	57.395	50.000	0.00	0.00	41.20	3.85
1800	2070	2.310647	GGGGAATGACCAAAAGGACCTA	59.689	50.000	0.00	0.00	41.20	3.08
2112	2412	2.882761	GGTCTATATGCCCCCGAAAAAC	59.117	50.000	0.00	0.00	0.00	2.43
2591	2930	1.942586	GCAAAGCCATTTTCTGCCCAG	60.943	52.381	0.00	0.00	0.00	4.45
3018	3360	1.391485	GTGACATGTGCTCGTGATGAC	59.609	52.381	14.62	4.48	34.90	3.06
3121	3469	3.315470	CGACGTCATGGAGAAGGAAGATA	59.685	47.826	17.16	0.00	0.00	1.98
3473	4034	0.463833	GCAAGGATGTTAGGACCGGG	60.464	60.000	6.32	0.00	0.00	5.73
3724	4294	2.673368	GAGGTTGCTAAACATGTCTCCG	59.327	50.000	0.00	0.00	38.10	4.63
4129	4735	8.988934	CAATAGTACAATATCGCATTACCAAGT	58.011	33.333	0.00	0.00	0.00	3.16
4134	4740	1.151777	ATCGCATTACCAAGTCGGCG	61.152	55.000	0.00	0.00	45.24	6.46
4572	5199	1.495584	GGTTCTGTGCAAGCGACGAA	61.496	55.000	0.00	0.00	0.00	3.85
4603	5230	7.232737	TCACAGAAGTATCACTAAAAGAGGTGA	59.767	37.037	0.00	0.00	44.84	4.02
4790	5441	6.538945	AGTTTGGTTTATTTTGTGGAGTGT	57.461	33.333	0.00	0.00	0.00	3.55
4791	5442	6.941857	AGTTTGGTTTATTTTGTGGAGTGTT	58.058	32.000	0.00	0.00	0.00	3.32
4822	5473	1.704641	GTGGGAAGGGCTTGAAGTTT	58.295	50.000	0.00	0.00	0.00	2.66
4889	5549	5.636965	TCGCAATTCAATTTGGTTGTAATGG	59.363	36.000	13.29	0.02	38.95	3.16
5051	5732	7.648112	GGAATTTTGAACTGACCTGAACTTTAC	59.352	37.037	0.00	0.00	0.00	2.01
5052	5733	6.445357	TTTTGAACTGACCTGAACTTTACC	57.555	37.500	0.00	0.00	0.00	2.85
5098	5781	4.892934	TCAGAATTTTTAACTGTGCCACCT	59.107	37.500	0.00	0.00	33.93	4.00
5106	5789	6.578163	TTTAACTGTGCCACCTTATTTACC	57.422	37.500	0.00	0.00	0.00	2.85
5155	5838	6.712547	ACAAAACAAAACCAAATCAAAGACCA	59.287	30.769	0.00	0.00	0.00	4.02
5182	5865	7.057894	ACAAGGTTTGTTAGATGTAACTCCAA	58.942	34.615	13.36	2.36	42.22	3.53
5231	5915	9.125026	TCTGAGAAGCTTAATTCAGAAACTTTT	57.875	29.630	24.40	0.00	42.08	2.27
5362	6047	7.631007	TCTACAGACTAGAGTTACTGATTGGA	58.369	38.462	0.00	0.00	34.88	3.53
5366	6051	7.337436	ACAGACTAGAGTTACTGATTGGAGTAC	59.663	40.741	0.00	0.00	34.88	2.73
5404	6089	0.743097	GGCTGAAGGGTTGATGCATC	59.257	55.000	20.14	20.14	0.00	3.91
5406	6091	1.019673	CTGAAGGGTTGATGCATCCG	58.980	55.000	23.67	0.34	0.00	4.18
5407	6092	1.031571	TGAAGGGTTGATGCATCCGC	61.032	55.000	23.67	16.46	39.24	5.54
5408	6093	1.728490	GAAGGGTTGATGCATCCGCC	61.728	60.000	23.67	22.49	37.32	6.13
5409	6094	3.585990	GGGTTGATGCATCCGCCG	61.586	66.667	23.67	0.00	37.32	6.46
5410	6095	2.824041	GGTTGATGCATCCGCCGT	60.824	61.111	23.67	0.00	37.32	5.68
5411	6096	2.709475	GTTGATGCATCCGCCGTC	59.291	61.111	23.67	0.00	37.32	4.79
5490	6192	4.803908	CCGCTCTTGCCCCTTCCC	62.804	72.222	0.00	0.00	35.36	3.97
5492	6194	3.342477	GCTCTTGCCCCTTCCCCT	61.342	66.667	0.00	0.00	0.00	4.79
5493	6195	2.679716	CTCTTGCCCCTTCCCCTG	59.320	66.667	0.00	0.00	0.00	4.45
5494	6196	2.121506	TCTTGCCCCTTCCCCTGT	60.122	61.111	0.00	0.00	0.00	4.00
5495	6197	1.778383	TCTTGCCCCTTCCCCTGTT	60.778	57.895	0.00	0.00	0.00	3.16
5496	6198	1.304464	CTTGCCCCTTCCCCTGTTC	60.304	63.158	0.00	0.00	0.00	3.18
5498	6200	4.062032	GCCCCTTCCCCTGTTCCC	62.062	72.222	0.00	0.00	0.00	3.97
5499	6201	3.347590	CCCCTTCCCCTGTTCCCC	61.348	72.222	0.00	0.00	0.00	4.81
5501	6203	2.609610	CCTTCCCCTGTTCCCCGA	60.610	66.667	0.00	0.00	0.00	5.14
5525	6263	4.648762	ACAATAGTCCTCTCCTCATCAGTG	59.351	45.833	0.00	0.00	0.00	3.66
5547	6285	2.481276	CGATGTTCCTGACTCGCCAATA	60.481	50.000	0.00	0.00	0.00	1.90
5550	6288	2.271800	GTTCCTGACTCGCCAATACAG	58.728	52.381	0.00	0.00	0.00	2.74
5599	6339	4.681942	GTGTAGTGTAGCTGTTCTGTTCAG	59.318	45.833	0.00	0.00	36.18	3.02
5681	6421	4.464244	TCTCATACAGGAAGAACACTCCAG	59.536	45.833	0.00	0.00	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	2.869233	CACAGGGAAAAGGTGTGTTG	57.131	50.000	0.00	0.00	37.41	3.33
149	150	1.303317	GCACCCGACCAGGACAAAT	60.303	57.895	0.00	0.00	45.00	2.32
296	320	6.488344	TGGTATTCTGCTGTGATTGTTTAACA	59.512	34.615	0.00	0.00	0.00	2.41
422	450	7.225341	TCACCTCATCGATTATGATTTGAACTG	59.775	37.037	0.00	0.00	43.70	3.16
513	541	2.477863	GCAAAATCCGAACATAGCGCTT	60.478	45.455	18.68	0.00	0.00	4.68
696	724	0.040646	TACCACCTCTCCCATCACGT	59.959	55.000	0.00	0.00	0.00	4.49
703	731	4.217983	CGAATACTATGTACCACCTCTCCC	59.782	50.000	0.00	0.00	0.00	4.30
927	962	9.121517	GCAAGACCAATTCATCAAATATATTCG	57.878	33.333	0.00	0.00	0.00	3.34
1797	2067	4.445699	GCGAAGGCCAGACATAGG	57.554	61.111	5.01	0.00	0.00	2.57
1837	2107	1.153549	GTGTCACATCCTCGAGCCC	60.154	63.158	6.99	0.00	0.00	5.19
2591	2930	0.389948	GGACAGTGACGTGATGACCC	60.390	60.000	0.00	0.00	0.00	4.46
3018	3360	8.230486	AGTAGCGAGTCACAATTTTTAAGAATG	58.770	33.333	0.00	0.00	0.00	2.67
3121	3469	3.255642	AGTTTTGCACCTAATCGCACAAT	59.744	39.130	0.00	0.00	38.00	2.71
3473	4034	0.250338	AAGTTTCCCTGTCGGAGCAC	60.250	55.000	0.00	0.00	43.39	4.40
3577	4138	9.813446	AAAATCTGAATTCCTTGAGCAAATATC	57.187	29.630	2.27	0.00	0.00	1.63
3582	4143	7.094205	GGTCTAAAATCTGAATTCCTTGAGCAA	60.094	37.037	2.27	0.00	0.00	3.91
3970	4570	2.124403	CCTGTCAGCTGGATGGCC	60.124	66.667	15.13	0.00	35.96	5.36
4129	4735	1.624336	ATGGTTAGTATAGGCGCCGA	58.376	50.000	23.20	18.26	0.00	5.54
4134	4740	7.671302	TCTTCAGATGAATGGTTAGTATAGGC	58.329	38.462	0.00	0.00	33.01	3.93
4572	5199	8.097038	TCTTTTAGTGATACTTCTGTGATGCTT	58.903	33.333	0.00	0.00	0.00	3.91
4603	5230	1.781786	ATGTAGGCCTGACACTCGAT	58.218	50.000	17.99	0.00	0.00	3.59
4822	5473	0.179127	CGAGCGAGCTCTTCATCCAA	60.179	55.000	20.97	0.00	40.69	3.53
4889	5549	9.754382	ACAGTTTGCAAATGGATATGATTATTC	57.246	29.630	16.21	0.00	0.00	1.75
5025	5699	5.774498	AGTTCAGGTCAGTTCAAAATTCC	57.226	39.130	0.00	0.00	0.00	3.01
5085	5767	4.255301	CGGTAAATAAGGTGGCACAGTTA	58.745	43.478	20.82	15.96	41.80	2.24
5098	5781	4.456566	GCAGGTGAGGAAAACGGTAAATAA	59.543	41.667	0.00	0.00	0.00	1.40
5106	5789	0.886490	AGCTGCAGGTGAGGAAAACG	60.886	55.000	19.45	0.00	0.00	3.60
5155	5838	8.380099	TGGAGTTACATCTAACAAACCTTGTAT	58.620	33.333	0.00	0.00	44.59	2.29
5182	5865	7.716123	CAGAGAAGGCAAGATAGAATCTGAATT	59.284	37.037	0.00	0.00	40.13	2.17
5231	5915	3.676049	CGAAGCAACCATACAGCTCAGTA	60.676	47.826	0.00	0.00	37.70	2.74
5362	6047	6.183360	GCCGATTGCAACTAGTTTTATGTACT	60.183	38.462	5.07	0.00	40.77	2.73
5366	6051	5.030295	CAGCCGATTGCAACTAGTTTTATG	58.970	41.667	5.07	0.00	44.83	1.90
5404	6089	4.227134	CCTCCAGGATGACGGCGG	62.227	72.222	13.24	0.00	39.69	6.13
5471	6173	4.803908	GAAGGGGCAAGAGCGGGG	62.804	72.222	0.00	0.00	43.41	5.73
5481	6183	4.062032	GGGAACAGGGGAAGGGGC	62.062	72.222	0.00	0.00	0.00	5.80
5493	6195	2.500504	AGAGGACTATTGTTCGGGGAAC	59.499	50.000	1.65	1.65	42.26	3.62
5494	6196	2.764572	GAGAGGACTATTGTTCGGGGAA	59.235	50.000	0.00	0.00	0.00	3.97
5495	6197	2.385803	GAGAGGACTATTGTTCGGGGA	58.614	52.381	0.00	0.00	0.00	4.81
5496	6198	1.413077	GGAGAGGACTATTGTTCGGGG	59.587	57.143	0.00	0.00	0.00	5.73
5498	6200	3.024547	TGAGGAGAGGACTATTGTTCGG	58.975	50.000	0.00	0.00	0.00	4.30
5499	6201	4.339530	TGATGAGGAGAGGACTATTGTTCG	59.660	45.833	0.00	0.00	0.00	3.95
5501	6203	5.128499	CACTGATGAGGAGAGGACTATTGTT	59.872	44.000	0.00	0.00	0.00	2.83
5599	6339	5.540911	TCTGCAATTTGGTCCTGAATTTTC	58.459	37.500	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.