AutoCloner

Multiple sequence alignment - TraesCS7B01G458900

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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	TraesCS7B01G458900	chr7B	100.000	3276	0	0	1	3276	716998372	717001647	0.000000e+00	6050.0
1	TraesCS7B01G458900	chr7B	92.123	914	60	6	4	914	716480378	716479474	0.000000e+00	1279.0
2	TraesCS7B01G458900	chr7B	86.344	1179	108	22	2116	3276	716465798	716464655	0.000000e+00	1236.0
3	TraesCS7B01G458900	chr7B	85.178	1039	111	26	1661	2693	716315412	716314411	0.000000e+00	1026.0
4	TraesCS7B01G458900	chr7B	87.779	851	78	9	1073	1901	716467049	716466203	0.000000e+00	972.0
5	TraesCS7B01G458900	chr7B	85.681	866	103	10	783	1633	716316388	716315529	0.000000e+00	893.0
6	TraesCS7B01G458900	chr7B	81.934	786	92	24	881	1631	716370481	716369711	1.290000e-173	619.0
7	TraesCS7B01G458900	chr7B	79.548	841	122	31	1675	2502	716369509	716368706	3.690000e-154	555.0
8	TraesCS7B01G458900	chr7B	78.611	907	134	38	2011	2885	716307360	716306482	2.220000e-151	545.0
9	TraesCS7B01G458900	chr7B	90.559	286	25	1	460	745	716316679	716316396	8.580000e-101	377.0
10	TraesCS7B01G458900	chr7B	84.672	274	31	3	1657	1929	716307675	716307412	2.510000e-66	263.0
11	TraesCS7B01G458900	chr7B	92.517	147	11	0	2700	2846	716314434	716314288	9.210000e-51	211.0
12	TraesCS7B01G458900	chr7B	97.701	87	2	0	2958	3044	716313215	716313129	2.040000e-32	150.0
13	TraesCS7B01G458900	chr7B	92.784	97	5	2	919	1015	716475445	716475351	4.410000e-29	139.0
14	TraesCS7B01G458900	chr7B	79.775	178	31	4	652	824	623520401	623520224	1.230000e-24	124.0
15	TraesCS7B01G458900	chr7B	78.333	180	32	5	652	824	623502526	623502347	3.460000e-20	110.0
16	TraesCS7B01G458900	chr7B	77.041	196	23	14	3085	3276	716313129	716312952	3.480000e-15	93.5
17	TraesCS7B01G458900	chr7D	93.337	2041	108	14	834	2846	620142711	620144751	0.000000e+00	2990.0
18	TraesCS7B01G458900	chr7D	89.788	989	74	11	4	983	620114697	620115667	0.000000e+00	1242.0
19	TraesCS7B01G458900	chr7D	87.153	973	85	11	973	1912	620116077	620117042	0.000000e+00	1068.0
20	TraesCS7B01G458900	chr7D	94.286	665	32	3	2188	2846	620144895	620145559	0.000000e+00	1013.0
21	TraesCS7B01G458900	chr7D	80.652	889	136	22	1978	2850	620198497	620199365	0.000000e+00	656.0
22	TraesCS7B01G458900	chr7D	87.238	572	61	5	1978	2548	620117073	620117633	2.760000e-180	641.0
23	TraesCS7B01G458900	chr7D	87.059	510	59	4	1125	1633	620085664	620086167	1.320000e-158	569.0
24	TraesCS7B01G458900	chr7D	84.795	513	71	5	1121	1631	620197568	620198075	2.920000e-140	508.0
25	TraesCS7B01G458900	chr7D	89.848	394	14	2	2904	3276	620146025	620146413	1.770000e-132	483.0
26	TraesCS7B01G458900	chr7D	92.344	209	13	1	106	311	620137820	620138028	8.890000e-76	294.0
27	TraesCS7B01G458900	chr7D	87.783	221	19	1	1676	1896	620198151	620198363	5.430000e-63	252.0
28	TraesCS7B01G458900	chr7D	89.222	167	17	1	2113	2278	638418519	638418685	1.190000e-49	207.0
29	TraesCS7B01G458900	chr7A	86.935	1240	120	20	699	1912	714823632	714822409	0.000000e+00	1354.0
30	TraesCS7B01G458900	chr7A	88.714	700	53	15	6	700	714825610	714824932	0.000000e+00	832.0
31	TraesCS7B01G458900	chr7A	87.248	596	60	7	1998	2589	714822367	714821784	0.000000e+00	665.0
32	TraesCS7B01G458900	chr7A	90.234	512	37	8	4	508	714844843	714844338	0.000000e+00	656.0
33	TraesCS7B01G458900	chr7A	82.955	704	97	11	1174	1856	714759659	714758958	6.010000e-172	614.0
34	TraesCS7B01G458900	chr7A	85.714	581	44	22	2613	3163	714989289	714988718	7.880000e-161	577.0
35	TraesCS7B01G458900	chr7A	80.357	672	65	32	2639	3267	714821788	714821141	6.450000e-122	448.0
36	TraesCS7B01G458900	chr7A	87.209	86	6	2	3191	3276	714988665	714988585	3.480000e-15	93.5
37	TraesCS7B01G458900	chrUn	89.956	677	60	6	955	1630	466806588	466807257	0.000000e+00	867.0
38	TraesCS7B01G458900	chrUn	91.561	628	36	10	1	620	461239290	461239908	0.000000e+00	850.0
39	TraesCS7B01G458900	chrUn	89.474	152	15	1	794	945	461239969	461240119	1.200000e-44	191.0
40	TraesCS7B01G458900	chr6D	92.955	511	30	3	2342	2846	107534913	107535423	0.000000e+00	739.0
41	TraesCS7B01G458900	chr2D	88.623	167	18	1	2113	2278	379110579	379110413	5.540000e-48	202.0
42	TraesCS7B01G458900	chr2D	80.233	172	27	6	657	822	45090119	45090289	4.440000e-24	122.0
43	TraesCS7B01G458900	chr1D	81.560	141	21	4	686	824	349546140	349546003	9.610000e-21	111.0
44	TraesCS7B01G458900	chr4B	79.730	148	18	7	686	822	636609409	636609263	2.690000e-16	97.1
45	TraesCS7B01G458900	chr4A	77.108	166	31	7	659	821	585540961	585541122	4.500000e-14	89.8
46	TraesCS7B01G458900	chr5D	82.353	102	15	3	723	822	355218852	355218952	5.820000e-13	86.1

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	TraesCS7B01G458900	chr7B	716998372	717001647	3275	False	6050.000000	6050	100.000000	1	3276	1	chr7B.!!$F1	3275
1	TraesCS7B01G458900	chr7B	716479474	716480378	904	True	1279.000000	1279	92.123000	4	914	1	chr7B.!!$R4	910
2	TraesCS7B01G458900	chr7B	716464655	716467049	2394	True	1104.000000	1236	87.061500	1073	3276	2	chr7B.!!$R8	2203
3	TraesCS7B01G458900	chr7B	716368706	716370481	1775	True	587.000000	619	80.741000	881	2502	2	chr7B.!!$R7	1621
4	TraesCS7B01G458900	chr7B	716312952	716316679	3727	True	458.416667	1026	88.112833	460	3276	6	chr7B.!!$R6	2816
5	TraesCS7B01G458900	chr7B	716306482	716307675	1193	True	404.000000	545	81.641500	1657	2885	2	chr7B.!!$R5	1228
6	TraesCS7B01G458900	chr7D	620142711	620146413	3702	False	1495.333333	2990	92.490333	834	3276	3	chr7D.!!$F5	2442
7	TraesCS7B01G458900	chr7D	620114697	620117633	2936	False	983.666667	1242	88.059667	4	2548	3	chr7D.!!$F4	2544
8	TraesCS7B01G458900	chr7D	620085664	620086167	503	False	569.000000	569	87.059000	1125	1633	1	chr7D.!!$F1	508
9	TraesCS7B01G458900	chr7D	620197568	620199365	1797	False	472.000000	656	84.410000	1121	2850	3	chr7D.!!$F6	1729
10	TraesCS7B01G458900	chr7A	714821141	714825610	4469	True	824.750000	1354	85.813500	6	3267	4	chr7A.!!$R3	3261
11	TraesCS7B01G458900	chr7A	714844338	714844843	505	True	656.000000	656	90.234000	4	508	1	chr7A.!!$R2	504
12	TraesCS7B01G458900	chr7A	714758958	714759659	701	True	614.000000	614	82.955000	1174	1856	1	chr7A.!!$R1	682
13	TraesCS7B01G458900	chr7A	714988585	714989289	704	True	335.250000	577	86.461500	2613	3276	2	chr7A.!!$R4	663
14	TraesCS7B01G458900	chrUn	466806588	466807257	669	False	867.000000	867	89.956000	955	1630	1	chrUn.!!$F1	675
15	TraesCS7B01G458900	chrUn	461239290	461240119	829	False	520.500000	850	90.517500	1	945	2	chrUn.!!$F2	944
16	TraesCS7B01G458900	chr6D	107534913	107535423	510	False	739.000000	739	92.955000	2342	2846	1	chr6D.!!$F1	504

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
27	29	0.099436	GGTCAAAGATCGCACATGGC	59.901	55.0	0.0	0.0	39.9	4.40	F
670	683	0.609662	TAAACGGTGTGGCTAGGTCC	59.390	55.0	0.0	0.0	0.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1669	3633	0.183014	AGGCTCTAGCTGCATGCAAT	59.817	50.0	22.88	15.59	45.94	3.56	R
2493	4844	0.177604	CTGCCAAGGCCAACAAACAA	59.822	50.0	5.01	0.00	41.09	2.83	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
27	29	0.099436	GGTCAAAGATCGCACATGGC	59.901	55.000	0.00	0.00	39.90	4.40
30	32	1.033746	CAAAGATCGCACATGGCCCT	61.034	55.000	0.00	0.00	40.31	5.19
43	45	3.263937	ACATGGCCCTTTTATTTGCACAT	59.736	39.130	0.00	0.00	0.00	3.21
64	67	7.170828	GCACATAGTTCATATTTGATACCGTGA	59.829	37.037	0.00	0.00	0.00	4.35
99	102	1.880027	GGACACAGTTGGCTTTACAGG	59.120	52.381	0.00	0.00	0.00	4.00
119	122	1.490910	GGGCTTAATAGGACCTGCACT	59.509	52.381	3.53	0.00	0.00	4.40
132	135	3.679389	ACCTGCACTAATGAAAGTCTGG	58.321	45.455	0.00	0.00	0.00	3.86
140	143	6.752815	GCACTAATGAAAGTCTGGTCTAGTAC	59.247	42.308	0.00	0.00	0.00	2.73
151	154	3.909430	TGGTCTAGTACTGTTGAAAGCG	58.091	45.455	5.39	0.00	0.00	4.68
214	220	2.229784	ACGTGTCCTAGTTTTCTACGGG	59.770	50.000	0.00	0.00	33.04	5.28
533	546	7.302350	TGTCAATCCTATAATCAACGTTGTG	57.698	36.000	26.47	13.85	0.00	3.33
612	625	6.430451	CATGAAAACTACACAAGGAACAGAC	58.570	40.000	0.00	0.00	0.00	3.51
670	683	0.609662	TAAACGGTGTGGCTAGGTCC	59.390	55.000	0.00	0.00	0.00	4.46
675	688	1.296715	GTGTGGCTAGGTCCCAGTG	59.703	63.158	0.00	0.00	31.89	3.66
678	691	0.983378	GTGGCTAGGTCCCAGTGGAT	60.983	60.000	11.95	0.00	44.28	3.41
791	2105	7.745620	TGAATATAGCATCGACTGAGACTTA	57.254	36.000	0.00	0.00	0.00	2.24
849	2164	4.399004	TTTTTGAAACCCACATGTGAGG	57.601	40.909	27.46	25.32	0.00	3.86
884	2209	7.664758	CGGATGGATATAGATGAGAATGCATA	58.335	38.462	0.00	0.00	31.54	3.14
935	2260	2.450699	TACCCCCACCAACCTGCA	60.451	61.111	0.00	0.00	0.00	4.41
996	2747	2.354510	CGATCAACACACAACACAAGGT	59.645	45.455	0.00	0.00	0.00	3.50
1046	2797	3.412408	GGTCTGGGCCCTCCTTCC	61.412	72.222	25.70	14.22	36.20	3.46
1172	2978	3.400505	CGAGTACGTACATCTCTTGCA	57.599	47.619	26.55	0.00	34.56	4.08
1348	3154	1.134280	CACCTTGGCTACCTCATCCAG	60.134	57.143	0.00	0.00	0.00	3.86
1451	3257	4.525487	TGTGGATCAACGGTACTCTTTACT	59.475	41.667	0.00	0.00	0.00	2.24
1549	3355	1.888436	TTCACCTCAGCGCCGAGAAT	61.888	55.000	22.14	6.87	34.79	2.40
1582	3388	3.511540	TGATCGGCCTCCTCTACAATATG	59.488	47.826	0.00	0.00	0.00	1.78
1588	3394	2.975489	CCTCCTCTACAATATGGGCAGT	59.025	50.000	0.00	0.00	0.00	4.40
1633	3566	3.162666	ACATACGTCTCTCCAACTCCAA	58.837	45.455	0.00	0.00	0.00	3.53
1669	3633	1.181786	GCCGGATTTGAACCAATCCA	58.818	50.000	5.05	0.00	32.91	3.41
1756	3728	0.620700	GTGGTAGATCCCTGGGTGGT	60.621	60.000	13.56	0.00	34.77	4.16
1771	3743	4.554036	GGTGAGGGGAGATGGCGC	62.554	72.222	0.00	0.00	0.00	6.53
1796	3768	0.032416	ACTACCGGTACATGGGCTCT	60.032	55.000	11.16	0.00	0.00	4.09
1809	3781	4.057428	GCTCTCTCACCACGCCGT	62.057	66.667	0.00	0.00	0.00	5.68
1811	3783	3.343788	CTCTCTCACCACGCCGTCC	62.344	68.421	0.00	0.00	0.00	4.79
1875	3847	6.103997	CCTACCTCGCTAAGTTGTTAATGAA	58.896	40.000	0.00	0.00	0.00	2.57
1925	4143	5.059404	TGCTAACTTGCAAGAAATTAGCC	57.941	39.130	34.36	24.64	44.58	3.93
1930	4148	3.127030	ACTTGCAAGAAATTAGCCTACGC	59.873	43.478	32.50	0.00	0.00	4.42
1959	4178	7.120726	CGGATTTACAAAGTTATGGTCCTCTTT	59.879	37.037	0.00	0.00	0.00	2.52
1961	4180	9.232473	GATTTACAAAGTTATGGTCCTCTTTCT	57.768	33.333	0.00	0.00	0.00	2.52
1975	4194	4.113354	CCTCTTTCTACTAACCGCATGAC	58.887	47.826	0.00	0.00	0.00	3.06
2090	4384	4.247258	ACGCTGTCCATGACGTAATTAAA	58.753	39.130	0.00	0.00	36.91	1.52
2158	4483	9.900710	AAAGTGCATATATTTGTTCGTTTGTAA	57.099	25.926	0.00	0.00	0.00	2.41
2245	4573	1.288188	TCTGCCCTGATGATGACCAA	58.712	50.000	0.00	0.00	0.00	3.67
2512	4864	0.177604	TTGTTTGTTGGCCTTGGCAG	59.822	50.000	14.04	0.00	39.75	4.85
2575	4937	7.009265	ACGTGTCGTTGTTGATATCTTCAATAG	59.991	37.037	3.98	7.92	41.04	1.73
2651	5017	2.622546	TTCCAATAAAAAGCGCGTCC	57.377	45.000	8.43	0.00	0.00	4.79
2799	5178	6.372103	TCCAGTGTTTCGTTCTTTTCAGTTTA	59.628	34.615	0.00	0.00	0.00	2.01
2897	6498	7.166851	ACCACACTATATAGACGTGCTACTAT	58.833	38.462	16.79	0.00	32.69	2.12
2985	7146	9.378504	AGTCTTGACTCTTATCATGAATAGGAT	57.621	33.333	0.00	0.00	35.30	3.24
3137	7309	2.043992	CCCGTGGGTTATACCAGATGA	58.956	52.381	0.00	0.00	42.20	2.92
3163	7335	2.331805	CGAGCATCTCCCGTACGG	59.668	66.667	27.68	27.68	0.00	4.02
3165	7337	2.758327	AGCATCTCCCGTACGGCA	60.758	61.111	29.15	14.43	0.00	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	45	8.002984	TCACTCACGGTATCAAATATGAACTA	57.997	34.615	0.00	0.00	39.49	2.24
55	57	4.371855	TGAAGACATCACTCACGGTATC	57.628	45.455	0.00	0.00	31.50	2.24
79	82	1.880027	CCTGTAAAGCCAACTGTGTCC	59.120	52.381	0.00	0.00	0.00	4.02
80	83	1.880027	CCCTGTAAAGCCAACTGTGTC	59.120	52.381	0.00	0.00	0.00	3.67
99	102	1.490910	AGTGCAGGTCCTATTAAGCCC	59.509	52.381	0.00	0.00	0.00	5.19
119	122	8.304596	CAACAGTACTAGACCAGACTTTCATTA	58.695	37.037	0.00	0.00	0.00	1.90
132	135	4.167268	CTCCGCTTTCAACAGTACTAGAC	58.833	47.826	0.00	0.00	0.00	2.59
151	154	0.813821	GCATCAAGGACCAAAGCTCC	59.186	55.000	0.00	0.00	0.00	4.70
214	220	1.153289	AGCAGGCACGGATCACATC	60.153	57.895	0.00	0.00	0.00	3.06
533	546	0.743097	GGACTGAAATGCTCATGGCC	59.257	55.000	0.00	0.00	40.92	5.36
670	683	5.773176	ACCTGGTTAAGTTTTAATCCACTGG	59.227	40.000	0.00	0.00	0.00	4.00
675	688	8.859236	ACTTAGACCTGGTTAAGTTTTAATCC	57.141	34.615	19.65	0.00	36.90	3.01
678	691	9.683870	TTTGACTTAGACCTGGTTAAGTTTTAA	57.316	29.630	23.14	18.22	39.52	1.52
735	2049	8.055181	TCTTGCATGGAGATCTAGGTAATTTTT	58.945	33.333	0.00	0.00	0.00	1.94
849	2164	0.033504	TATCCATCCGCTCGGCTTTC	59.966	55.000	2.96	0.00	34.68	2.62
884	2209	3.618690	ATTTCCTCGTGAAGCTAGCTT	57.381	42.857	29.71	29.71	39.23	3.74
935	2260	1.972588	AGCTGGGTTATCCAAGAGGT	58.027	50.000	0.00	0.00	46.51	3.85
1046	2797	2.099431	GCTGAGAAGTGCAGGAGCG	61.099	63.158	0.00	0.00	46.23	5.03
1170	2976	4.490661	GACTCATCGTCTGCATGCATGC	62.491	54.545	38.71	38.71	42.50	4.06
1171	2977	1.260825	GACTCATCGTCTGCATGCATG	59.739	52.381	22.97	22.70	39.61	4.06
1172	2978	1.579698	GACTCATCGTCTGCATGCAT	58.420	50.000	22.97	2.13	39.61	3.96
1333	3139	2.072487	GGCCTGGATGAGGTAGCCA	61.072	63.158	0.00	0.00	44.07	4.75
1582	3388	1.749258	GAAATGGTCCGGACTGCCC	60.749	63.158	32.52	17.84	0.00	5.36
1641	3583	0.329931	TCAAATCCGGCCTGGCTTAA	59.670	50.000	19.68	4.23	37.80	1.85
1642	3584	0.329931	TTCAAATCCGGCCTGGCTTA	59.670	50.000	19.68	4.59	37.80	3.09
1669	3633	0.183014	AGGCTCTAGCTGCATGCAAT	59.817	50.000	22.88	15.59	45.94	3.56
1756	3728	3.473647	CTGCGCCATCTCCCCTCA	61.474	66.667	4.18	0.00	0.00	3.86
1771	3743	1.340248	CCATGTACCGGTAGTAGGCTG	59.660	57.143	16.41	6.32	0.00	4.85
1796	3768	3.680786	CAGGACGGCGTGGTGAGA	61.681	66.667	21.19	0.00	0.00	3.27
1811	3783	3.432051	GATGACCCCCTCGTCGCAG	62.432	68.421	0.00	0.00	35.40	5.18
1863	3835	7.513371	TGGTCGGTAAAATTCATTAACAACT	57.487	32.000	0.00	0.00	0.00	3.16
1875	3847	8.269317	TCAAGGTCTAAATATGGTCGGTAAAAT	58.731	33.333	0.00	0.00	0.00	1.82
1925	4143	2.997986	ACTTTGTAAATCCGGTGCGTAG	59.002	45.455	0.00	0.00	0.00	3.51
1930	4148	5.163693	GGACCATAACTTTGTAAATCCGGTG	60.164	44.000	0.00	0.00	0.00	4.94
1959	4178	4.705507	AGAGAAAGTCATGCGGTTAGTAGA	59.294	41.667	0.00	0.00	0.00	2.59
1961	4180	6.320418	TGATAGAGAAAGTCATGCGGTTAGTA	59.680	38.462	0.00	0.00	0.00	1.82
2111	4430	5.989551	TTGCTTTCTTGAAAAAGATTGGC	57.010	34.783	0.75	0.00	38.30	4.52
2150	4470	3.071479	AGCCCTACACACATTACAAACG	58.929	45.455	0.00	0.00	0.00	3.60
2158	4483	3.264193	TCATCTCAAAGCCCTACACACAT	59.736	43.478	0.00	0.00	0.00	3.21
2245	4573	1.560923	CAGCAGCGTAATAGCGTTCT	58.439	50.000	0.00	0.00	43.00	3.01
2493	4844	0.177604	CTGCCAAGGCCAACAAACAA	59.822	50.000	5.01	0.00	41.09	2.83
2634	5000	2.159448	TGATGGACGCGCTTTTTATTGG	60.159	45.455	5.73	0.00	0.00	3.16
2710	5084	3.889538	AGATTGGATCTGATGTGCAATGG	59.110	43.478	3.21	0.00	37.68	3.16
2813	5192	8.462016	GCACACTTTCTTGAAGGACAATAATAT	58.538	33.333	0.00	0.00	39.79	1.28
2897	6498	2.445682	AAGCCAACAACAACTGGGTA	57.554	45.000	0.00	0.00	42.54	3.69
3122	7294	4.202357	TGTGCATCTCATCTGGTATAACCC	60.202	45.833	0.00	0.00	37.50	4.11
3163	7335	0.179215	CCGAAAACTGAGCACGATGC	60.179	55.000	0.00	0.00	45.46	3.91
3165	7337	1.878953	AACCGAAAACTGAGCACGAT	58.121	45.000	0.00	0.00	0.00	3.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.