AutoCloner

Multiple sequence alignment - TraesCS6D01G161600

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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	TraesCS6D01G161600	chr6D	100.000	3179	0	0	1	3179	140036523	140039701	0.000000e+00	5871.0
1	TraesCS6D01G161600	chr6B	93.802	2275	62	29	1	2215	239911992	239914247	0.000000e+00	3347.0
2	TraesCS6D01G161600	chr6B	92.056	856	62	4	2212	3062	239914457	239915311	0.000000e+00	1199.0
3	TraesCS6D01G161600	chr6B	90.984	122	7	2	3062	3179	239916798	239916919	9.130000e-36	161.0
4	TraesCS6D01G161600	chr6B	76.636	214	29	12	2557	2751	648698009	648698220	7.260000e-17	99.0
5	TraesCS6D01G161600	chr6A	94.802	1924	45	10	277	2185	183767851	183765968	0.000000e+00	2948.0
6	TraesCS6D01G161600	chr6A	87.991	866	91	9	2212	3066	183765418	183764555	0.000000e+00	1011.0
7	TraesCS6D01G161600	chr6A	83.860	285	15	11	1	285	183768256	183768003	3.170000e-60	243.0
8	TraesCS6D01G161600	chr7D	74.667	600	111	22	2321	2880	180213218	180213816	8.870000e-56	228.0
9	TraesCS6D01G161600	chr7D	78.049	246	43	11	2807	3046	511373673	511373913	9.190000e-31	145.0
10	TraesCS6D01G161600	chr7A	72.658	790	160	38	2296	3041	287883530	287882753	8.930000e-51	211.0
11	TraesCS6D01G161600	chr7A	87.647	170	19	2	1756	1924	564346266	564346098	2.500000e-46	196.0
12	TraesCS6D01G161600	chr7A	78.148	270	49	8	2592	2854	184578076	184578342	2.540000e-36	163.0
13	TraesCS6D01G161600	chr7B	88.235	170	18	2	1756	1924	526883537	526883369	5.380000e-48	202.0
14	TraesCS6D01G161600	chr1D	76.068	234	50	6	2297	2527	124349505	124349735	2.000000e-22	117.0
15	TraesCS6D01G161600	chrUn	79.825	114	20	2	2744	2854	93785700	93785813	2.630000e-11	80.5

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	TraesCS6D01G161600	chr6D	140036523	140039701	3178	False	5871.000000	5871	100.000000	1	3179	1	chr6D.!!$F1	3178
1	TraesCS6D01G161600	chr6B	239911992	239916919	4927	False	1569.000000	3347	92.280667	1	3179	3	chr6B.!!$F2	3178
2	TraesCS6D01G161600	chr6A	183764555	183768256	3701	True	1400.666667	2948	88.884333	1	3066	3	chr6A.!!$R1	3065
3	TraesCS6D01G161600	chr7D	180213218	180213816	598	False	228.000000	228	74.667000	2321	2880	1	chr7D.!!$F1	559
4	TraesCS6D01G161600	chr7A	287882753	287883530	777	True	211.000000	211	72.658000	2296	3041	1	chr7A.!!$R1	745

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
648	852	1.025041	CGTGTCCTCATCGATCTCCA	58.975	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2440	3216	0.804989	GCATAGCAGGCGTTGTTCTT	59.195	50.0	0.0	0.0	0.0	2.52	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
96	97	7.971168	ACAAAATTGTGTGAAAAATAGTCGTGA	59.029	29.630	0.00	0.00	40.49	4.35
136	139	6.374333	ACAACCGCTGTTCATTAATGTAAGAT	59.626	34.615	14.97	0.07	32.99	2.40
348	525	6.520792	GTCGCTAAGACTTTCACTTGTAAA	57.479	37.500	0.00	0.00	46.13	2.01
349	526	7.118422	GTCGCTAAGACTTTCACTTGTAAAT	57.882	36.000	0.00	0.00	46.13	1.40
350	527	7.573627	GTCGCTAAGACTTTCACTTGTAAATT	58.426	34.615	0.00	0.00	46.13	1.82
351	528	7.530861	GTCGCTAAGACTTTCACTTGTAAATTG	59.469	37.037	0.00	0.00	46.13	2.32
352	529	6.797033	CGCTAAGACTTTCACTTGTAAATTGG	59.203	38.462	0.00	0.00	0.00	3.16
387	568	5.077564	ACAAAATCCAACCTAACTTCTCCC	58.922	41.667	0.00	0.00	0.00	4.30
389	570	1.272807	TCCAACCTAACTTCTCCCGG	58.727	55.000	0.00	0.00	0.00	5.73
393	574	3.497227	CCAACCTAACTTCTCCCGGAAAA	60.497	47.826	0.73	0.00	33.07	2.29
394	575	4.139038	CAACCTAACTTCTCCCGGAAAAA	58.861	43.478	0.73	0.00	33.07	1.94
519	718	5.282055	TGGATGTCCTTGCTAATGAGTAG	57.718	43.478	0.09	0.00	36.82	2.57
575	774	2.937433	GCTGGGCAGACTTAACTTCCTC	60.937	54.545	0.00	0.00	0.00	3.71
601	800	3.986572	CCATCAGCTAGATTCATCACGAC	59.013	47.826	0.00	0.00	33.72	4.34
616	815	2.029380	TCACGACACATCCTTGAATCGT	60.029	45.455	0.00	0.00	43.02	3.73
633	837	2.173519	TCGTCCCCTCTTTTATCGTGT	58.826	47.619	0.00	0.00	0.00	4.49
636	840	2.500504	GTCCCCTCTTTTATCGTGTCCT	59.499	50.000	0.00	0.00	0.00	3.85
648	852	1.025041	CGTGTCCTCATCGATCTCCA	58.975	55.000	0.00	0.00	0.00	3.86
741	955	2.593978	CCATGACTCCCTGGGCAG	59.406	66.667	8.22	9.16	0.00	4.85
742	956	1.997311	CCATGACTCCCTGGGCAGA	60.997	63.158	8.22	0.00	0.00	4.26
743	957	1.525923	CATGACTCCCTGGGCAGAG	59.474	63.158	8.22	2.73	36.16	3.35
744	958	1.692042	ATGACTCCCTGGGCAGAGG	60.692	63.158	8.22	0.00	34.27	3.69
745	959	2.284995	GACTCCCTGGGCAGAGGT	60.285	66.667	8.22	1.40	34.27	3.85
746	960	1.920835	GACTCCCTGGGCAGAGGTT	60.921	63.158	8.22	0.00	34.27	3.50
1210	1428	2.284625	AGGAGTGGATGGCGGACA	60.285	61.111	0.00	0.00	0.00	4.02
1869	2111	1.594310	GGAGCTCACCACCTGTCTC	59.406	63.158	17.19	0.00	0.00	3.36
2247	3020	8.538409	AAATTTATTTCAGTTGCCTGTGAATC	57.462	30.769	0.00	0.00	39.82	2.52
2254	3027	1.236616	TTGCCTGTGAATCACGGCTG	61.237	55.000	32.17	17.70	46.11	4.85
2292	3065	5.598416	TCTCTCTTGAAATAGATTCGCCA	57.402	39.130	0.00	0.00	41.18	5.69
2294	3067	5.360999	TCTCTCTTGAAATAGATTCGCCAGA	59.639	40.000	0.00	0.00	41.18	3.86
2412	3188	3.838795	CAGAACGCACGCGCTACC	61.839	66.667	12.02	0.00	44.19	3.18
2440	3216	6.846505	ACCAATAGAGAACATAGGAAGATCCA	59.153	38.462	0.00	0.00	39.61	3.41
2568	3378	1.750399	CCCCAAAGGAGCATCACGG	60.750	63.158	0.00	0.00	38.24	4.94
2615	3439	2.025441	GTCGGCAACAAAGCGCAA	59.975	55.556	11.47	0.00	34.64	4.85
2618	3442	1.588667	CGGCAACAAAGCGCAAAGT	60.589	52.632	11.47	0.53	34.64	2.66
2632	3456	2.604373	CGCAAAGTTTTTGATCGGCAGA	60.604	45.455	5.77	0.00	0.00	4.26
2633	3457	2.982470	GCAAAGTTTTTGATCGGCAGAG	59.018	45.455	5.77	0.00	0.00	3.35
2634	3458	3.304659	GCAAAGTTTTTGATCGGCAGAGA	60.305	43.478	5.77	0.00	0.00	3.10
2880	3710	4.514585	ACACCGCCAACTGCCCAA	62.515	61.111	0.00	0.00	36.24	4.12
2921	3751	3.465966	TGGTAGGAGGAGCAGAGGTAATA	59.534	47.826	0.00	0.00	0.00	0.98
2958	3788	1.911357	ACATCAGCCACTGAGATTGGA	59.089	47.619	3.42	0.00	44.08	3.53
2973	3803	1.508667	TTGGATCAGTGCCCCCATGT	61.509	55.000	0.00	0.00	0.00	3.21
3005	3835	2.283101	GCATGTGTCCCCAGCCAA	60.283	61.111	0.00	0.00	0.00	4.52
3055	3885	3.075005	ACTACCGATGGCTGCCGT	61.075	61.111	14.43	14.43	0.00	5.68
3097	5415	0.534427	ATCAGCGTCGATCTACCCGA	60.534	55.000	0.00	0.00	0.00	5.14
3105	5423	1.065928	GATCTACCCGACGGTGCAG	59.934	63.158	13.94	6.71	44.40	4.41
3128	5446	2.445085	TCACGACCACCACCACCT	60.445	61.111	0.00	0.00	0.00	4.00
3130	5448	2.122989	ACGACCACCACCACCTCT	60.123	61.111	0.00	0.00	0.00	3.69
3131	5449	2.343758	CGACCACCACCACCTCTG	59.656	66.667	0.00	0.00	0.00	3.35
3132	5450	2.750350	GACCACCACCACCTCTGG	59.250	66.667	0.00	0.00	44.26	3.86
3133	5451	3.553095	GACCACCACCACCTCTGGC	62.553	68.421	0.00	0.00	42.08	4.85
3134	5452	4.351054	CCACCACCACCTCTGGCC	62.351	72.222	0.00	0.00	42.08	5.36
3135	5453	4.704833	CACCACCACCTCTGGCCG	62.705	72.222	0.00	0.00	42.08	6.13
3164	5485	4.320844	AGGACAACCTCACTGCCT	57.679	55.556	0.00	0.00	44.13	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.533318	CGAGATAAATGCCCTCGCC	58.467	57.895	0.00	0.00	42.34	5.54
104	105	8.707839	CATTAATGAACAGCGGTTGTAATTTTT	58.292	29.630	10.04	0.00	39.73	1.94
110	111	6.874664	TCTTACATTAATGAACAGCGGTTGTA	59.125	34.615	22.16	0.00	39.73	2.41
111	112	5.703592	TCTTACATTAATGAACAGCGGTTGT	59.296	36.000	22.16	0.00	43.45	3.32
112	113	6.176975	TCTTACATTAATGAACAGCGGTTG	57.823	37.500	22.16	0.00	37.36	3.77
114	115	5.880332	ACATCTTACATTAATGAACAGCGGT	59.120	36.000	22.16	11.28	0.00	5.68
115	116	6.363577	ACATCTTACATTAATGAACAGCGG	57.636	37.500	22.16	10.78	0.00	5.52
116	117	8.673626	AAAACATCTTACATTAATGAACAGCG	57.326	30.769	22.16	8.42	0.00	5.18
197	200	2.814336	CGTCTTCTCCCCCTTCTTTTTG	59.186	50.000	0.00	0.00	0.00	2.44
273	288	7.147976	GCCAAACTGTGAAATAACAAGAATCT	58.852	34.615	0.00	0.00	0.00	2.40
349	526	9.482627	GTTGGATTTTGTTGTGATTATAACCAA	57.517	29.630	0.00	0.00	0.00	3.67
350	527	8.091449	GGTTGGATTTTGTTGTGATTATAACCA	58.909	33.333	0.00	0.00	33.43	3.67
351	528	8.311109	AGGTTGGATTTTGTTGTGATTATAACC	58.689	33.333	0.00	0.00	33.40	2.85
395	576	5.240844	CCGTGAGAAGTTAGGTTGGATTTTT	59.759	40.000	0.00	0.00	0.00	1.94
519	718	0.517316	ACGAATCAACTTGCTTCCGC	59.483	50.000	0.00	0.00	0.00	5.54
575	774	4.863689	GTGATGAATCTAGCTGATGGATCG	59.136	45.833	0.00	0.00	35.21	3.69
601	800	1.210478	AGGGGACGATTCAAGGATGTG	59.790	52.381	0.00	0.00	0.00	3.21
616	815	2.764572	GAGGACACGATAAAAGAGGGGA	59.235	50.000	0.00	0.00	0.00	4.81
741	955	4.456911	TGATCTTGATTTGTGCTCAACCTC	59.543	41.667	0.00	2.44	32.93	3.85
742	956	4.217118	GTGATCTTGATTTGTGCTCAACCT	59.783	41.667	0.00	0.00	32.93	3.50
743	957	4.479619	GTGATCTTGATTTGTGCTCAACC	58.520	43.478	0.00	0.00	32.93	3.77
744	958	4.083855	TCGTGATCTTGATTTGTGCTCAAC	60.084	41.667	0.00	0.00	32.93	3.18
745	959	4.064388	TCGTGATCTTGATTTGTGCTCAA	58.936	39.130	0.00	0.00	0.00	3.02
746	960	3.663025	TCGTGATCTTGATTTGTGCTCA	58.337	40.909	0.00	0.00	0.00	4.26
812	1026	2.034879	TCCTCGTGGGACGTACGTC	61.035	63.158	34.70	34.70	43.14	4.34
813	1027	2.032528	TCCTCGTGGGACGTACGT	59.967	61.111	23.04	23.04	43.14	3.57
1190	1408	3.866582	CCGCCATCCACTCCTCCC	61.867	72.222	0.00	0.00	0.00	4.30
1210	1428	1.140589	CGAGGAAGAGCTGCGACAT	59.859	57.895	0.00	0.00	0.00	3.06
1242	1460	4.096003	CGGCTGTTGGACCCCGAT	62.096	66.667	0.13	0.00	43.20	4.18
2010	2252	2.161012	CACGACGTAGCTAAACTCAGGA	59.839	50.000	0.00	0.00	0.00	3.86
2019	2261	1.789751	CACGGACACGACGTAGCTA	59.210	57.895	0.00	0.00	43.58	3.32
2247	3020	1.725641	TTATGCAAGAGACAGCCGTG	58.274	50.000	0.00	0.00	0.00	4.94
2254	3027	9.539825	TTCAAGAGAGATAATTATGCAAGAGAC	57.460	33.333	1.78	0.00	0.00	3.36
2289	3062	8.756864	GCTATCGCTTTATATATAAAGTCTGGC	58.243	37.037	31.63	26.03	46.78	4.85
2412	3188	7.841282	TCTTCCTATGTTCTCTATTGGTAGG	57.159	40.000	0.00	0.00	0.00	3.18
2440	3216	0.804989	GCATAGCAGGCGTTGTTCTT	59.195	50.000	0.00	0.00	0.00	2.52
2519	3296	1.007387	GTGAAAACCTTGGCAGCGG	60.007	57.895	3.64	3.64	0.00	5.52
2615	3439	2.814336	GGTCTCTGCCGATCAAAAACTT	59.186	45.455	0.00	0.00	0.00	2.66
2618	3442	2.813754	CAAGGTCTCTGCCGATCAAAAA	59.186	45.455	0.00	0.00	0.00	1.94
2632	3456	4.988598	CGTGGTGGCGCAAGGTCT	62.989	66.667	10.83	0.00	38.28	3.85
2633	3457	4.980805	TCGTGGTGGCGCAAGGTC	62.981	66.667	10.83	0.00	38.28	3.85
2634	3458	4.988598	CTCGTGGTGGCGCAAGGT	62.989	66.667	10.83	0.00	38.28	3.50
2880	3710	3.509575	ACCATGGTTTGTGCGTTATGAAT	59.490	39.130	13.00	0.00	0.00	2.57
2958	3788	0.552848	CCTAACATGGGGGCACTGAT	59.447	55.000	0.00	0.00	0.00	2.90
2973	3803	2.731571	ATGCCTCGCCGCTTCCTAA	61.732	57.895	0.00	0.00	0.00	2.69
3055	3885	1.948104	CACAGTCGTGGGTTTCTTCA	58.052	50.000	0.00	0.00	39.64	3.02
3097	5415	1.664649	CGTGACATCACTGCACCGT	60.665	57.895	10.18	0.00	44.34	4.83
3105	5423	0.949105	GGTGGTGGTCGTGACATCAC	60.949	60.000	10.26	10.26	46.54	3.06
3128	5446	2.659063	CCTCATGGACACGGCCAGA	61.659	63.158	2.24	0.00	42.15	3.86
3130	5448	2.606213	TCCTCATGGACACGGCCA	60.606	61.111	2.24	0.00	43.23	5.36
3131	5449	2.187946	CTCCTCATGGACACGGCC	59.812	66.667	0.00	0.00	37.46	6.13
3132	5450	2.187946	CCTCCTCATGGACACGGC	59.812	66.667	0.00	0.00	37.46	5.68
3133	5451	4.034246	TCCTCCTCATGGACACGG	57.966	61.111	0.00	0.00	37.46	4.94

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.