AutoCloner

Multiple sequence alignment - TraesCS7D01G354400

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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	TraesCS7D01G354400	chr7D	100.000	3470	0	0	1	3470	458355862	458352393	0.000000e+00	6408.0
1	TraesCS7D01G354400	chr7D	87.765	425	37	6	3057	3470	587113366	587112946	1.870000e-132	483.0
2	TraesCS7D01G354400	chr7D	86.842	418	31	5	3055	3470	575307345	575306950	2.460000e-121	446.0
3	TraesCS7D01G354400	chr7D	83.582	402	42	13	2674	3054	587113813	587113415	4.260000e-94	355.0
4	TraesCS7D01G354400	chr7B	93.102	2566	108	24	1	2545	480206985	480204468	0.000000e+00	3694.0
5	TraesCS7D01G354400	chr7B	96.269	134	5	0	2536	2669	480204296	480204163	1.620000e-53	220.0
6	TraesCS7D01G354400	chr7A	91.060	2718	137	43	1	2669	541897834	541900494	0.000000e+00	3576.0
7	TraesCS7D01G354400	chr7A	89.423	416	19	3	3055	3470	38115646	38115256	5.170000e-138	501.0
8	TraesCS7D01G354400	chr7A	90.181	387	29	4	2674	3054	206014510	206014127	2.410000e-136	496.0
9	TraesCS7D01G354400	chr7A	89.567	393	33	3	2674	3060	603520779	603520389	3.110000e-135	492.0
10	TraesCS7D01G354400	chr7A	88.462	416	23	3	3055	3470	603520340	603519950	2.420000e-131	479.0
11	TraesCS7D01G354400	chr7A	92.373	118	7	2	3353	3470	38116058	38115943	2.140000e-37	167.0
12	TraesCS7D01G354400	chr6B	90.700	1957	131	33	746	2667	183611459	183609519	0.000000e+00	2558.0
13	TraesCS7D01G354400	chr6D	90.185	1834	118	28	744	2545	99235505	99233702	0.000000e+00	2333.0
14	TraesCS7D01G354400	chr6D	89.167	120	12	1	433	552	99236853	99236735	7.760000e-32	148.0
15	TraesCS7D01G354400	chr6A	88.280	1843	127	34	746	2545	119595285	119593489	0.000000e+00	2124.0
16	TraesCS7D01G354400	chr2A	89.569	719	63	6	1374	2080	137530266	137529548	0.000000e+00	902.0
17	TraesCS7D01G354400	chr2A	91.295	448	27	3	937	1375	137537786	137537342	4.960000e-168	601.0
18	TraesCS7D01G354400	chr2A	86.176	340	42	4	2674	3011	618999957	618999621	2.550000e-96	363.0
19	TraesCS7D01G354400	chr2A	85.890	326	27	11	2742	3053	521070	521390	2.580000e-86	329.0
20	TraesCS7D01G354400	chr4D	98.784	329	4	0	3142	3470	9594909	9595237	1.390000e-163	586.0
21	TraesCS7D01G354400	chr2D	90.649	385	29	7	3055	3439	591781886	591782263	4.000000e-139	505.0
22	TraesCS7D01G354400	chr2D	89.706	340	32	3	3054	3392	493086104	493085767	6.880000e-117	431.0
23	TraesCS7D01G354400	chr2D	86.822	387	38	6	2674	3054	591781453	591781832	1.490000e-113	420.0
24	TraesCS7D01G354400	chr1B	87.204	422	41	10	3050	3470	29485500	29485091	5.240000e-128	468.0
25	TraesCS7D01G354400	chr1B	85.061	328	41	7	2684	3009	29485924	29485603	9.290000e-86	327.0
26	TraesCS7D01G354400	chr1B	87.037	54	7	0	2081	2134	535908548	535908495	1.040000e-05	62.1
27	TraesCS7D01G354400	chr1B	87.755	49	6	0	2081	2129	535939125	535939077	1.350000e-04	58.4
28	TraesCS7D01G354400	chr1B	87.755	49	6	0	2081	2129	536121819	536121771	1.350000e-04	58.4
29	TraesCS7D01G354400	chr5D	90.801	337	27	3	3055	3389	413064523	413064189	6.830000e-122	448.0
30	TraesCS7D01G354400	chr1D	89.504	343	24	3	3055	3389	83694285	83694623	1.150000e-114	424.0
31	TraesCS7D01G354400	chr1D	87.037	54	7	0	2081	2134	399414145	399414092	1.040000e-05	62.1
32	TraesCS7D01G354400	chr4B	86.471	340	41	4	2674	3011	494024532	494024868	5.470000e-98	368.0
33	TraesCS7D01G354400	chr3A	85.174	344	39	7	2673	3009	155961460	155961122	3.320000e-90	342.0
34	TraesCS7D01G354400	chr3B	82.891	339	48	5	2674	3011	603491524	603491853	2.620000e-76	296.0

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	TraesCS7D01G354400	chr7D	458352393	458355862	3469	True	6408.0	6408	100.0000	1	3470	1	chr7D.!!$R1	3469
1	TraesCS7D01G354400	chr7D	587112946	587113813	867	True	419.0	483	85.6735	2674	3470	2	chr7D.!!$R3	796
2	TraesCS7D01G354400	chr7B	480204163	480206985	2822	True	1957.0	3694	94.6855	1	2669	2	chr7B.!!$R1	2668
3	TraesCS7D01G354400	chr7A	541897834	541900494	2660	False	3576.0	3576	91.0600	1	2669	1	chr7A.!!$F1	2668
4	TraesCS7D01G354400	chr7A	603519950	603520779	829	True	485.5	492	89.0145	2674	3470	2	chr7A.!!$R3	796
5	TraesCS7D01G354400	chr7A	38115256	38116058	802	True	334.0	501	90.8980	3055	3470	2	chr7A.!!$R2	415
6	TraesCS7D01G354400	chr6B	183609519	183611459	1940	True	2558.0	2558	90.7000	746	2667	1	chr6B.!!$R1	1921
7	TraesCS7D01G354400	chr6D	99233702	99236853	3151	True	1240.5	2333	89.6760	433	2545	2	chr6D.!!$R1	2112
8	TraesCS7D01G354400	chr6A	119593489	119595285	1796	True	2124.0	2124	88.2800	746	2545	1	chr6A.!!$R1	1799
9	TraesCS7D01G354400	chr2A	137529548	137530266	718	True	902.0	902	89.5690	1374	2080	1	chr2A.!!$R1	706
10	TraesCS7D01G354400	chr2D	591781453	591782263	810	False	462.5	505	88.7355	2674	3439	2	chr2D.!!$F1	765
11	TraesCS7D01G354400	chr1B	29485091	29485924	833	True	397.5	468	86.1325	2684	3470	2	chr1B.!!$R4	786

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
911	1989	0.532573	ACAGACGATCCGAGCATTGT	59.467	50.000	0.0	0.0	0.00	2.71	F
1503	2624	1.219124	GTCCTGCTTCTCGATGGCA	59.781	57.895	0.0	0.0	34.66	4.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1722	2855	0.182061	AGGCCGATACGTAGTCCTCA	59.818	55.0	0.08	0.0	43.93	3.86	R
3000	4348	0.730840	GCGTATTTTTGGCTAGCGGT	59.269	50.0	9.00	0.0	0.00	5.68	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
55	56	3.074242	ACCACCTTACAATCGGGGTTTTA	59.926	43.478	0.00	0.00	0.00	1.52
56	57	3.692593	CCACCTTACAATCGGGGTTTTAG	59.307	47.826	0.00	0.00	0.00	1.85
57	58	3.128068	CACCTTACAATCGGGGTTTTAGC	59.872	47.826	0.00	0.00	0.00	3.09
135	136	3.125316	GCGTCAGTCCAAATCGAGAAATT	59.875	43.478	0.00	0.00	0.00	1.82
136	137	4.641954	CGTCAGTCCAAATCGAGAAATTG	58.358	43.478	0.00	0.00	0.00	2.32
312	314	2.802667	CGCGAAGATGGCCGTTCAG	61.803	63.158	0.00	0.00	0.00	3.02
334	337	8.630054	TCAGTTGCATATACCCCAAATTATAC	57.370	34.615	0.00	0.00	0.00	1.47
336	339	9.077885	CAGTTGCATATACCCCAAATTATACTT	57.922	33.333	0.00	0.00	0.00	2.24
342	345	9.231297	CATATACCCCAAATTATACTTCAGTGG	57.769	37.037	0.00	0.00	0.00	4.00
503	511	3.194968	AGAGCCATGAAAAGAAGCAATGG	59.805	43.478	0.00	0.00	0.00	3.16
591	639	6.261826	ACTCTGGTAATGAAGCATTGCTATTC	59.738	38.462	12.39	7.49	38.25	1.75
592	640	5.237127	TCTGGTAATGAAGCATTGCTATTCG	59.763	40.000	12.39	0.34	38.25	3.34
594	642	5.764686	TGGTAATGAAGCATTGCTATTCGAT	59.235	36.000	12.39	2.73	38.25	3.59
595	643	6.934083	TGGTAATGAAGCATTGCTATTCGATA	59.066	34.615	12.39	1.82	38.25	2.92
597	645	7.746475	GGTAATGAAGCATTGCTATTCGATAAC	59.254	37.037	12.39	3.96	38.25	1.89
598	646	5.328886	TGAAGCATTGCTATTCGATAACG	57.671	39.130	12.39	0.00	38.25	3.18
599	647	5.047188	TGAAGCATTGCTATTCGATAACGA	58.953	37.500	12.39	0.00	42.00	3.85
656	707	2.570169	CAATGAACCGTTGCTGTTACG	58.430	47.619	0.00	0.00	38.67	3.18
664	715	1.126113	CGTTGCTGTTACGCGATTTCT	59.874	47.619	15.93	0.00	31.73	2.52
696	747	1.819229	AGCTGGATAGACAGGTGCG	59.181	57.895	0.00	0.00	46.46	5.34
719	777	3.995048	CTCAACCTTAACTTTCCGACCTC	59.005	47.826	0.00	0.00	0.00	3.85
733	1734	3.136763	CCGACCTCTAAGACGCTGTATA	58.863	50.000	0.00	0.00	0.00	1.47
866	1938	7.889469	AGCATTGATTCCGCATATCTAAAAAT	58.111	30.769	0.00	0.00	0.00	1.82
868	1940	9.793252	GCATTGATTCCGCATATCTAAAAATAT	57.207	29.630	0.00	0.00	0.00	1.28
911	1989	0.532573	ACAGACGATCCGAGCATTGT	59.467	50.000	0.00	0.00	0.00	2.71
919	1997	2.839486	TCCGAGCATTGTGTTTCTCT	57.161	45.000	0.00	0.00	0.00	3.10
920	1998	3.126001	TCCGAGCATTGTGTTTCTCTT	57.874	42.857	0.00	0.00	0.00	2.85
921	1999	4.265904	TCCGAGCATTGTGTTTCTCTTA	57.734	40.909	0.00	0.00	0.00	2.10
956	2052	3.963428	ACACCTCACCATAGACTTCAC	57.037	47.619	0.00	0.00	0.00	3.18
984	2089	3.813166	ACAAGTCAGAACCAAACCATACG	59.187	43.478	0.00	0.00	0.00	3.06
1503	2624	1.219124	GTCCTGCTTCTCGATGGCA	59.781	57.895	0.00	0.00	34.66	4.92
1722	2855	0.322816	ACAGCTTCGCCATGTTGGAT	60.323	50.000	0.00	0.00	40.96	3.41
2070	3203	3.551322	TGGATCCCCCAGAGGAGT	58.449	61.111	9.90	0.00	40.82	3.85
2343	3476	3.383026	GCAGAAAATGCGAGCGAAA	57.617	47.368	0.00	0.00	46.99	3.46
2423	3556	1.893808	CGTTGCTGAAGCTGGTGGT	60.894	57.895	3.61	0.00	42.66	4.16
2424	3557	1.447317	CGTTGCTGAAGCTGGTGGTT	61.447	55.000	3.61	0.00	42.66	3.67
2466	3608	2.159379	TGACGTCATCAAGGATCACTCG	60.159	50.000	15.76	0.00	33.02	4.18
2480	3625	8.400947	CAAGGATCACTCGTAATCAAATCAATT	58.599	33.333	0.00	0.00	0.00	2.32
2486	3631	3.692101	TCGTAATCAAATCAATTGGCGGT	59.308	39.130	5.42	0.00	39.62	5.68
2553	3885	0.815615	TGTGTATGTGCGGTTGTGCA	60.816	50.000	0.00	0.00	43.95	4.57
2572	3904	1.447838	CCGAGGTGCAAGTGCGTAT	60.448	57.895	0.00	0.00	45.83	3.06
2669	4001	6.971184	CCTGACATTTGCTTTATTTCAGCTAG	59.029	38.462	0.00	0.00	38.19	3.42
2670	4002	6.855836	TGACATTTGCTTTATTTCAGCTAGG	58.144	36.000	0.00	0.00	38.19	3.02
2671	4003	6.658816	TGACATTTGCTTTATTTCAGCTAGGA	59.341	34.615	0.00	0.00	38.19	2.94
2672	4004	7.176515	TGACATTTGCTTTATTTCAGCTAGGAA	59.823	33.333	0.00	0.00	38.19	3.36
2736	4068	5.545063	AATCGAACCCCAAACTTCAAATT	57.455	34.783	0.00	0.00	0.00	1.82
2778	4111	3.892588	ACTCTCAGATCCCGGTCTATTTC	59.107	47.826	0.00	0.00	0.00	2.17
2783	4116	3.134804	CAGATCCCGGTCTATTTCCAACT	59.865	47.826	0.00	0.00	0.00	3.16
2795	4128	7.013369	GGTCTATTTCCAACTTTGAGTGAGTTT	59.987	37.037	0.00	0.00	35.26	2.66
2798	4131	4.229304	TCCAACTTTGAGTGAGTTTCCA	57.771	40.909	0.00	0.00	35.26	3.53
2927	4264	2.717893	GCGCGACGTAAAAAGTCTTCTG	60.718	50.000	12.10	0.00	36.53	3.02
2941	4280	3.437049	AGTCTTCTGTTCATTAAAGCGCC	59.563	43.478	2.29	0.00	0.00	6.53
2989	4337	0.110486	GAACTTGGGACCTGGCTGAA	59.890	55.000	0.00	0.00	0.00	3.02
3000	4348	2.507058	ACCTGGCTGAATTGAGCTCATA	59.493	45.455	19.04	9.12	39.11	2.15
3340	4749	8.642908	TCACGAGTTTAGATAAATGTATGTGG	57.357	34.615	0.00	0.00	0.00	4.17
3341	4750	7.223971	TCACGAGTTTAGATAAATGTATGTGGC	59.776	37.037	0.00	0.00	0.00	5.01
3342	4751	7.011016	CACGAGTTTAGATAAATGTATGTGGCA	59.989	37.037	0.00	0.00	0.00	4.92
3343	4752	7.715249	ACGAGTTTAGATAAATGTATGTGGCAT	59.285	33.333	0.00	0.00	0.00	4.40
3344	4753	8.559536	CGAGTTTAGATAAATGTATGTGGCATT	58.440	33.333	0.00	0.00	38.09	3.56
3406	4869	2.098934	TCAAAAACTGTGCTTGCGACAT	59.901	40.909	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
135	136	4.383850	GCATATGTTTGCAATACACCCA	57.616	40.909	14.04	6.06	42.31	4.51
215	217	1.547820	GCACCTCATGAGAGACAGACA	59.452	52.381	24.62	0.00	44.98	3.41
312	314	9.073475	TGAAGTATAATTTGGGGTATATGCAAC	57.927	33.333	0.00	0.00	0.00	4.17
334	337	3.659786	TGATACAAACGGACCACTGAAG	58.340	45.455	0.00	0.00	0.00	3.02
336	339	3.973206	ATGATACAAACGGACCACTGA	57.027	42.857	0.00	0.00	0.00	3.41
342	345	7.924103	AAGTTGAAAAATGATACAAACGGAC	57.076	32.000	0.00	0.00	0.00	4.79
425	433	2.054687	TGCGTACACCTTTCACGTAG	57.945	50.000	0.00	0.00	37.95	3.51
503	511	0.696501	TTTCTTCCTGCCACCCTACC	59.303	55.000	0.00	0.00	0.00	3.18
591	639	2.347292	GGCAATAGCAACGTCGTTATCG	60.347	50.000	10.86	0.00	44.61	2.92
592	640	2.605818	TGGCAATAGCAACGTCGTTATC	59.394	45.455	10.86	5.90	44.61	1.75
594	642	2.081725	TGGCAATAGCAACGTCGTTA	57.918	45.000	10.86	0.00	44.61	3.18
595	643	1.448985	ATGGCAATAGCAACGTCGTT	58.551	45.000	4.40	4.40	44.61	3.85
597	645	2.596575	CGTTATGGCAATAGCAACGTCG	60.597	50.000	0.00	0.00	44.61	5.12
598	646	2.605818	TCGTTATGGCAATAGCAACGTC	59.394	45.455	15.87	0.00	43.73	4.34
599	647	2.623535	TCGTTATGGCAATAGCAACGT	58.376	42.857	15.87	0.00	43.73	3.99
656	707	7.165483	CAGCTATCTCAAATTTTCAGAAATCGC	59.835	37.037	0.00	2.99	34.44	4.58
664	715	8.267183	TGTCTATCCAGCTATCTCAAATTTTCA	58.733	33.333	0.00	0.00	0.00	2.69
696	747	2.483106	GGTCGGAAAGTTAAGGTTGAGC	59.517	50.000	0.00	0.00	0.00	4.26
719	777	8.483218	CAATCTTGTCAATATACAGCGTCTTAG	58.517	37.037	0.00	0.00	0.00	2.18
763	1825	1.806542	GGTGCATACACTTGTCAGGTG	59.193	52.381	13.19	13.19	46.57	4.00
870	1942	9.636789	TCTGTATCCTTTTGTGCTATACTACTA	57.363	33.333	0.00	0.00	0.00	1.82
871	1943	8.414778	GTCTGTATCCTTTTGTGCTATACTACT	58.585	37.037	0.00	0.00	0.00	2.57
872	1944	7.378995	CGTCTGTATCCTTTTGTGCTATACTAC	59.621	40.741	0.00	0.00	0.00	2.73
887	1965	1.240256	GCTCGGATCGTCTGTATCCT	58.760	55.000	0.00	0.00	40.74	3.24
919	1997	7.178628	GGTGAGGTGTTGAGCTCCTATATATAA	59.821	40.741	12.15	0.00	44.77	0.98
920	1998	6.663953	GGTGAGGTGTTGAGCTCCTATATATA	59.336	42.308	12.15	0.00	44.77	0.86
921	1999	5.482175	GGTGAGGTGTTGAGCTCCTATATAT	59.518	44.000	12.15	0.00	44.77	0.86
956	2052	2.638480	TGGTTCTGACTTGTGAAGGG	57.362	50.000	0.00	0.00	0.00	3.95
1275	2383	3.771160	GACTCCACGCCGGATGGT	61.771	66.667	21.12	6.27	45.19	3.55
1621	2754	4.458829	TGGATCCTCGGCGTCCCT	62.459	66.667	14.23	0.00	0.00	4.20
1623	2756	3.148279	ACTGGATCCTCGGCGTCC	61.148	66.667	14.23	7.10	0.00	4.79
1722	2855	0.182061	AGGCCGATACGTAGTCCTCA	59.818	55.000	0.08	0.00	43.93	3.86
2061	3194	0.459489	GAGCTAGCACACTCCTCTGG	59.541	60.000	18.83	0.00	0.00	3.86
2070	3203	4.082523	GCGGGGTGAGCTAGCACA	62.083	66.667	18.83	14.86	40.52	4.57
2423	3556	1.229496	TAGGTCCCCTGCAGCTCAA	60.229	57.895	8.66	0.00	34.61	3.02
2424	3557	1.990060	GTAGGTCCCCTGCAGCTCA	60.990	63.158	8.66	0.00	36.26	4.26
2466	3608	4.798387	GTCACCGCCAATTGATTTGATTAC	59.202	41.667	7.12	0.00	37.53	1.89
2486	3631	2.463620	CGTCCGTATCGTCCCGTCA	61.464	63.158	0.00	0.00	0.00	4.35
2553	3885	2.167398	ATACGCACTTGCACCTCGGT	62.167	55.000	1.48	0.00	42.21	4.69
2572	3904	1.737236	GCGGCATATCACACAACAGAA	59.263	47.619	0.00	0.00	0.00	3.02
2736	4068	1.375396	CGGTGTGCTGATTTCCGGA	60.375	57.895	0.00	0.00	37.92	5.14
2778	4111	4.981806	TTGGAAACTCACTCAAAGTTGG	57.018	40.909	0.00	0.00	37.06	3.77
2783	4116	3.699038	CCCTGTTTGGAAACTCACTCAAA	59.301	43.478	4.02	0.00	39.59	2.69
2795	4128	1.606994	CGTCGACAATCCCTGTTTGGA	60.607	52.381	17.16	0.00	38.84	3.53
2798	4131	1.508632	CACGTCGACAATCCCTGTTT	58.491	50.000	17.16	0.00	38.84	2.83
2892	4229	1.022451	TCGCGCGCCTTAAGGAAAAT	61.022	50.000	27.95	0.00	37.39	1.82
2903	4240	2.569812	CTTTTTACGTCGCGCGCC	60.570	61.111	27.95	14.67	46.11	6.53
2927	4264	4.789784	TGTTACTTGGCGCTTTAATGAAC	58.210	39.130	7.64	8.18	0.00	3.18
2941	4280	3.847105	GCCCGAGACGTTTTTGTTACTTG	60.847	47.826	0.00	0.00	0.00	3.16
2989	4337	1.001406	GGCTAGCGGTATGAGCTCAAT	59.999	52.381	22.50	11.85	44.79	2.57
3000	4348	0.730840	GCGTATTTTTGGCTAGCGGT	59.269	50.000	9.00	0.00	0.00	5.68
3392	4855	5.633996	TTTTAAAAATGTCGCAAGCACAG	57.366	34.783	0.00	0.00	32.50	3.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.