AutoCloner

Multiple sequence alignment - TraesCS4A01G115700

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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	TraesCS4A01G115700	chr4A	100.000	3704	0	0	1	3704	140774690	140770987	0.000000e+00	6841.0
1	TraesCS4A01G115700	chr4A	84.932	73	7	4	3248	3318	484551459	484551529	1.850000e-08	71.3
2	TraesCS4A01G115700	chr1B	91.153	3199	160	51	598	3704	135247139	135243972	0.000000e+00	4226.0
3	TraesCS4A01G115700	chr1B	90.793	391	16	7	1	377	135248047	135247663	4.270000e-139	505.0
4	TraesCS4A01G115700	chr4D	96.065	2033	57	6	683	2708	329300208	329302224	0.000000e+00	3290.0
5	TraesCS4A01G115700	chr4D	79.728	809	96	30	2945	3704	329302681	329303470	1.180000e-144	523.0
6	TraesCS4A01G115700	chr4D	88.689	389	26	9	1	377	329299052	329299434	3.370000e-125	459.0
7	TraesCS4A01G115700	chr4D	90.400	250	9	7	2706	2953	329302262	329302498	7.720000e-82	315.0
8	TraesCS4A01G115700	chr4D	92.593	54	3	1	598	650	329299866	329299919	3.970000e-10	76.8
9	TraesCS4A01G115700	chr4B	90.292	2194	152	38	1549	3704	409249387	409251557	0.000000e+00	2815.0
10	TraesCS4A01G115700	chr4B	92.146	1566	74	17	2	1552	409235952	409237483	0.000000e+00	2165.0
11	TraesCS4A01G115700	chr5A	77.644	331	64	10	1997	2322	327726587	327726912	3.780000e-45	193.0
12	TraesCS4A01G115700	chr6A	75.589	467	61	32	3197	3635	31388935	31389376	8.170000e-42	182.0
13	TraesCS4A01G115700	chr6A	82.979	94	16	0	1530	1623	100653175	100653082	6.590000e-13	86.1
14	TraesCS4A01G115700	chr5D	77.039	331	66	9	1997	2322	229141907	229141582	8.170000e-42	182.0
15	TraesCS4A01G115700	chr5B	77.039	331	66	9	1997	2322	276824293	276824618	8.170000e-42	182.0
16	TraesCS4A01G115700	chr7D	84.906	106	15	1	3540	3645	579540390	579540494	5.060000e-19	106.0
17	TraesCS4A01G115700	chr7D	85.333	75	5	4	3018	3086	469556741	469556815	5.130000e-09	73.1
18	TraesCS4A01G115700	chr3D	75.221	226	48	7	1523	1747	613590366	613590148	2.350000e-17	100.0
19	TraesCS4A01G115700	chr3D	79.798	99	13	7	3226	3322	19877663	19877756	8.590000e-07	65.8
20	TraesCS4A01G115700	chr6B	82.292	96	11	5	3249	3342	554029041	554028950	1.100000e-10	78.7
21	TraesCS4A01G115700	chr2D	73.115	305	47	29	3218	3508	509757221	509757504	3.970000e-10	76.8

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	TraesCS4A01G115700	chr4A	140770987	140774690	3703	True	6841.00	6841	100.000	1	3704	1	chr4A.!!$R1	3703
1	TraesCS4A01G115700	chr1B	135243972	135248047	4075	True	2365.50	4226	90.973	1	3704	2	chr1B.!!$R1	3703
2	TraesCS4A01G115700	chr4D	329299052	329303470	4418	False	932.76	3290	89.495	1	3704	5	chr4D.!!$F1	3703
3	TraesCS4A01G115700	chr4B	409249387	409251557	2170	False	2815.00	2815	90.292	1549	3704	1	chr4B.!!$F2	2155
4	TraesCS4A01G115700	chr4B	409235952	409237483	1531	False	2165.00	2165	92.146	2	1552	1	chr4B.!!$F1	1550

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
559	979	0.172803	ATCCGTACAGCGAAGTGTCC	59.827	55.000	0.0	0.0	44.77	4.02	F
797	1489	1.144936	CTGATCCGGTCCTTCTGGC	59.855	63.158	0.0	0.0	42.13	4.85	F
1274	1972	1.153147	GGGAAGATGAAGACGGCCC	60.153	63.158	0.0	0.0	0.00	5.80	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1409	2110	0.954449	CGCCAGCCAGATGATCATCC	60.954	60.0	28.23	15.5	38.58	3.51	R
2587	3288	0.107312	ACCATCTGCTCATCCAGTGC	60.107	55.0	0.00	0.0	37.26	4.40	R
2981	3924	0.725117	GTTCCATGCGGTACTTTCGG	59.275	55.0	0.00	0.0	30.17	4.30	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
39	40	4.482990	TCCATGCTCTATATGTGGAGTGA	58.517	43.478	4.79	0.00	35.54	3.41
40	41	4.525874	TCCATGCTCTATATGTGGAGTGAG	59.474	45.833	4.79	0.00	35.54	3.51
41	42	4.282957	CCATGCTCTATATGTGGAGTGAGT	59.717	45.833	4.79	0.00	35.54	3.41
42	43	4.926140	TGCTCTATATGTGGAGTGAGTG	57.074	45.455	4.79	0.00	35.54	3.51
99	101	2.203337	TCTGTGGGTGCTTGCACC	60.203	61.111	30.40	30.40	44.27	5.01
117	119	0.811281	CCGTTGGATTCAGCTTTCCC	59.189	55.000	4.98	0.00	0.00	3.97
130	133	1.272490	GCTTTCCCCTTTCCCTTTTCG	59.728	52.381	0.00	0.00	0.00	3.46
134	137	0.965866	CCCCTTTCCCTTTTCGCCTC	60.966	60.000	0.00	0.00	0.00	4.70
180	186	3.829886	ATTCACACGGTATGTTTGCTG	57.170	42.857	0.00	0.00	40.64	4.41
198	204	0.661552	TGCGGAGTACTGATAGCGAC	59.338	55.000	0.00	0.00	0.00	5.19
333	350	7.113658	TCCATAGAGACTAGTTCATCCAAAC	57.886	40.000	0.00	0.00	0.00	2.93
502	705	0.875059	GCAAGGTTCTGAAACTCGGG	59.125	55.000	8.66	3.14	35.61	5.14
532	951	2.941333	CTCCAGTGCGTTGCTGTG	59.059	61.111	0.00	0.00	32.41	3.66
533	952	1.595109	CTCCAGTGCGTTGCTGTGA	60.595	57.895	0.00	0.00	32.41	3.58
534	953	1.835483	CTCCAGTGCGTTGCTGTGAC	61.835	60.000	0.00	0.00	32.41	3.67
535	954	1.889105	CCAGTGCGTTGCTGTGACT	60.889	57.895	0.00	0.00	32.41	3.41
536	955	1.277739	CAGTGCGTTGCTGTGACTG	59.722	57.895	0.00	0.00	0.00	3.51
537	956	1.153369	AGTGCGTTGCTGTGACTGT	60.153	52.632	0.00	0.00	0.00	3.55
559	979	0.172803	ATCCGTACAGCGAAGTGTCC	59.827	55.000	0.00	0.00	44.77	4.02
579	1000	1.191647	CAGTTAGTTTCGACGTGCCAC	59.808	52.381	0.00	0.00	0.00	5.01
650	1073	3.273434	CATCCCTACATGTTCCACTGTG	58.727	50.000	2.30	0.00	0.00	3.66
653	1076	2.079158	CCTACATGTTCCACTGTGCTG	58.921	52.381	2.30	0.00	0.00	4.41
679	1103	9.228949	GCTAGTATCTAAGTAGTGGCAGTATAA	57.771	37.037	5.16	0.00	34.10	0.98
687	1111	7.380423	AAGTAGTGGCAGTATAATTCCTCAT	57.620	36.000	5.16	0.00	0.00	2.90
692	1384	4.536090	TGGCAGTATAATTCCTCATAGGGG	59.464	45.833	0.00	0.00	35.59	4.79
704	1396	5.694995	TCCTCATAGGGGTCATTGAATTTC	58.305	41.667	0.00	0.00	35.59	2.17
754	1446	4.848299	GTCAGTTGCAATTAAGAAAGCTCG	59.152	41.667	0.59	0.00	0.00	5.03
797	1489	1.144936	CTGATCCGGTCCTTCTGGC	59.855	63.158	0.00	0.00	42.13	4.85
806	1498	3.429141	CCTTCTGGCTGTGCTGCG	61.429	66.667	0.00	0.00	0.00	5.18
998	1696	3.795041	CTGGGCAGGGCAGAGAGG	61.795	72.222	0.00	0.00	0.00	3.69
1176	1874	1.292541	GCGGTTCCTCGACTTCCTT	59.707	57.895	0.00	0.00	0.00	3.36
1263	1961	3.782443	GTCACGGCCGGGGAAGAT	61.782	66.667	30.43	0.65	0.00	2.40
1274	1972	1.153147	GGGAAGATGAAGACGGCCC	60.153	63.158	0.00	0.00	0.00	5.80
1668	2369	1.377333	GGTGTACTGCAAGGAGGGC	60.377	63.158	0.00	0.00	39.30	5.19
2439	3140	1.342810	CGACTTCGACGACGATCGA	59.657	57.895	24.34	15.25	46.74	3.59
2611	3312	0.596083	GGATGAGCAGATGGTCGACG	60.596	60.000	9.92	0.00	44.88	5.12
2760	3502	2.546321	CGTGTGCTGTTGCTCGAC	59.454	61.111	0.00	0.00	40.48	4.20
2772	3514	0.029967	TGCTCGACGATCTCATGCTC	59.970	55.000	0.00	0.00	0.00	4.26
2781	3523	0.600057	ATCTCATGCTCTATGCGCGA	59.400	50.000	12.10	0.00	46.63	5.87
2822	3565	4.640789	AACAGAACACCATAAACGCAAA	57.359	36.364	0.00	0.00	0.00	3.68
2830	3573	4.501198	ACACCATAAACGCAAACGAAAAAG	59.499	37.500	0.00	0.00	43.93	2.27
2981	3924	3.364964	CCTCTGAACCGTTGCATTTACAC	60.365	47.826	0.00	0.00	0.00	2.90
3004	3947	1.153353	AAGTACCGCATGGAACGTTG	58.847	50.000	5.00	0.00	39.21	4.10
3033	3976	6.550481	TGATTTGCAAGGCATATCCTATTTGA	59.450	34.615	15.64	0.00	46.94	2.69
3417	4422	5.927954	TGAGCTTTTTCAAAATTGATGGC	57.072	34.783	0.00	0.60	37.00	4.40
3523	4530	4.561735	TTCAAAAGTCCGTGGAATTGTC	57.438	40.909	1.90	0.00	32.53	3.18
3536	4543	5.570206	CGTGGAATTGTCTGAATTCACAATG	59.430	40.000	19.42	5.75	41.42	2.82
3538	4545	6.364165	GTGGAATTGTCTGAATTCACAATGTG	59.636	38.462	19.42	7.12	41.42	3.21
3586	4616	2.086599	TACATGGGCCAGCCAACCAA	62.087	55.000	13.78	0.00	37.89	3.67
3662	4694	1.949525	CTCCGATTTGCAATACCAGGG	59.050	52.381	0.00	0.00	0.00	4.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	6.725834	TCACTCCACATATAGAGCATGGAATA	59.274	38.462	0.00	0.00	38.95	1.75
39	40	4.681978	GGCCGTCGCTGTTCCACT	62.682	66.667	0.00	0.00	34.44	4.00
40	41	4.980805	TGGCCGTCGCTGTTCCAC	62.981	66.667	0.00	0.00	34.44	4.02
41	42	4.015406	ATGGCCGTCGCTGTTCCA	62.015	61.111	0.00	0.00	34.44	3.53
42	43	3.499737	CATGGCCGTCGCTGTTCC	61.500	66.667	0.00	0.00	34.44	3.62
99	101	0.811281	GGGGAAAGCTGAATCCAACG	59.189	55.000	13.66	0.00	37.46	4.10
117	119	0.038310	AGGAGGCGAAAAGGGAAAGG	59.962	55.000	0.00	0.00	0.00	3.11
130	133	0.693049	TGGTGGAGAGAAAAGGAGGC	59.307	55.000	0.00	0.00	0.00	4.70
134	137	4.039603	AGGAAATGGTGGAGAGAAAAGG	57.960	45.455	0.00	0.00	0.00	3.11
180	186	0.384477	CGTCGCTATCAGTACTCCGC	60.384	60.000	0.00	0.00	0.00	5.54
333	350	6.380274	TCTGTTGGTAGAAATAGGGTACTCAG	59.620	42.308	0.00	0.00	0.00	3.35
502	705	0.601311	ACTGGAGCGTCAAGAAGCAC	60.601	55.000	10.43	4.03	38.28	4.40
532	951	0.525668	CGCTGTACGGATGGACAGTC	60.526	60.000	5.68	0.00	44.10	3.51
533	952	0.963856	TCGCTGTACGGATGGACAGT	60.964	55.000	5.68	0.00	44.10	3.55
534	953	0.172578	TTCGCTGTACGGATGGACAG	59.827	55.000	5.68	3.25	44.88	3.51
535	954	0.172578	CTTCGCTGTACGGATGGACA	59.827	55.000	5.68	0.00	43.89	4.02
536	955	0.172803	ACTTCGCTGTACGGATGGAC	59.827	55.000	5.68	0.00	43.89	4.02
537	956	0.172578	CACTTCGCTGTACGGATGGA	59.827	55.000	5.68	0.00	43.89	3.41
559	979	1.191647	GTGGCACGTCGAAACTAACTG	59.808	52.381	0.00	0.00	0.00	3.16
581	1002	2.224113	TGTCTAAAGGACCACGGTGAAC	60.224	50.000	10.28	2.93	43.89	3.18
650	1073	4.278669	TGCCACTACTTAGATACTAGCAGC	59.721	45.833	0.00	0.00	0.00	5.25
653	1076	7.690952	ATACTGCCACTACTTAGATACTAGC	57.309	40.000	0.00	0.00	0.00	3.42
679	1103	5.937492	ATTCAATGACCCCTATGAGGAAT	57.063	39.130	0.00	0.00	37.67	3.01
687	1111	5.631481	GCCTACAGAAATTCAATGACCCCTA	60.631	44.000	0.00	0.00	0.00	3.53
754	1446	3.190878	CCGACTGGCCATTTCTGC	58.809	61.111	5.51	0.00	0.00	4.26
797	1489	4.671549	CAACACGCCGCAGCACAG	62.672	66.667	0.00	0.00	39.83	3.66
806	1498	4.563184	TGTAAAAACAATTGTCAACACGCC	59.437	37.500	12.39	0.00	0.00	5.68
1263	1961	3.379445	GAGTCCGGGCCGTCTTCA	61.379	66.667	26.32	0.00	0.00	3.02
1409	2110	0.954449	CGCCAGCCAGATGATCATCC	60.954	60.000	28.23	15.50	38.58	3.51
1503	2204	2.665185	GACCACTTCTTGCGCCGT	60.665	61.111	4.18	0.00	0.00	5.68
1840	2541	4.208686	CAGGTAGAGGGCGGCGAC	62.209	72.222	12.98	8.16	0.00	5.19
2206	2907	3.238241	GCGGATGTCGTCGTCGTG	61.238	66.667	1.33	0.00	41.72	4.35
2238	2939	3.699894	CAGAGGAGCACGCCCACT	61.700	66.667	0.00	0.00	0.00	4.00
2368	3069	1.375140	CGCAGCTCCAGCAGAAGAA	60.375	57.895	0.48	0.00	45.16	2.52
2587	3288	0.107312	ACCATCTGCTCATCCAGTGC	60.107	55.000	0.00	0.00	37.26	4.40
2611	3312	4.570663	CGACCTCCCCATCGCGAC	62.571	72.222	12.93	0.00	0.00	5.19
2760	3502	0.990616	GCGCATAGAGCATGAGATCG	59.009	55.000	0.30	0.00	46.13	3.69
2772	3514	2.250485	GCAGCCAATCGCGCATAG	59.750	61.111	8.75	0.00	44.76	2.23
2822	3565	3.994931	ATAGTACTGCCCCTTTTTCGT	57.005	42.857	5.39	0.00	0.00	3.85
2830	3573	7.606839	GGAAATCTTTATGTATAGTACTGCCCC	59.393	40.741	5.39	0.00	0.00	5.80
2883	3629	9.777297	TGCATCTGCTTATGTACTGAATAATAA	57.223	29.630	3.53	0.00	42.66	1.40
2884	3630	9.948964	ATGCATCTGCTTATGTACTGAATAATA	57.051	29.630	3.53	0.00	42.66	0.98
2908	3654	1.972872	AGGCGCTCCCAAAGAATATG	58.027	50.000	7.64	0.00	35.39	1.78
2981	3924	0.725117	GTTCCATGCGGTACTTTCGG	59.275	55.000	0.00	0.00	30.17	4.30
3004	3947	2.945447	TATGCCTTGCAAATCACTGC	57.055	45.000	0.00	0.00	43.62	4.40
3393	4398	6.487331	TGCCATCAATTTTGAAAAAGCTCATT	59.513	30.769	0.00	0.00	41.13	2.57
3398	4403	7.933728	AAAATGCCATCAATTTTGAAAAAGC	57.066	28.000	0.00	0.00	41.13	3.51
3480	4487	8.299262	TGAAAAACGTTCATGAACTTGAAAAA	57.701	26.923	30.45	12.87	37.36	1.94
3481	4488	7.875316	TGAAAAACGTTCATGAACTTGAAAA	57.125	28.000	30.45	12.20	37.36	2.29
3504	4511	3.563808	TCAGACAATTCCACGGACTTTTG	59.436	43.478	0.00	0.00	0.00	2.44
3523	4530	7.775397	AAAGGAAAACACATTGTGAATTCAG	57.225	32.000	23.12	0.00	36.96	3.02
3551	4580	4.023622	CCCATGTACACGTTCACATTTGAA	60.024	41.667	8.68	0.00	39.55	2.69
3621	4652	3.127533	GCATTCGGCGCTTCAGGT	61.128	61.111	7.64	0.00	0.00	4.00
3662	4694	1.153765	GGCTTTGGGCTTTGATCGC	60.154	57.895	0.00	0.00	41.46	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.