AutoCloner

Multiple sequence alignment - TraesCS1D01G209500

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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	TraesCS1D01G209500	chr1D	100.000	2789	0	0	1	2789	295440546	295443334	0.000000e+00	5151.0
1	TraesCS1D01G209500	chr1B	93.872	2774	111	20	4	2744	396969825	396972572	0.000000e+00	4126.0
2	TraesCS1D01G209500	chr1A	97.040	1588	41	4	743	2328	368745654	368747237	0.000000e+00	2667.0
3	TraesCS1D01G209500	chr1A	87.299	748	63	14	1	743	368744346	368745066	0.000000e+00	826.0
4	TraesCS1D01G209500	chr1A	91.566	249	13	4	2544	2789	368747384	368747627	1.240000e-88	337.0
5	TraesCS1D01G209500	chr6A	92.929	99	6	1	2353	2451	599809026	599808929	2.900000e-30	143.0
6	TraesCS1D01G209500	chr3B	90.909	99	9	0	2353	2451	256253710	256253808	1.740000e-27	134.0
7	TraesCS1D01G209500	chr2B	90.909	99	9	0	2354	2452	7566750	7566848	1.740000e-27	134.0
8	TraesCS1D01G209500	chr2B	85.000	60	5	4	2491	2546	563028185	563028126	1.080000e-04	58.4
9	TraesCS1D01G209500	chr5B	90.816	98	9	0	2354	2451	316712701	316712604	6.270000e-27	132.0
10	TraesCS1D01G209500	chr5B	90.099	101	9	1	2354	2453	352488619	352488719	2.250000e-26	130.0
11	TraesCS1D01G209500	chr5B	89.320	103	10	1	2353	2454	321130428	321130326	8.110000e-26	128.0
12	TraesCS1D01G209500	chr5B	88.235	102	9	3	2351	2450	296853889	296853989	4.880000e-23	119.0
13	TraesCS1D01G209500	chr5D	90.000	100	10	0	2351	2450	51073283	51073382	2.250000e-26	130.0
14	TraesCS1D01G209500	chr3A	93.617	47	3	0	2495	2541	136532880	136532926	1.390000e-08	71.3
15	TraesCS1D01G209500	chr5A	93.333	45	3	0	2496	2540	46587582	46587538	1.790000e-07	67.6
16	TraesCS1D01G209500	chrUn	92.857	42	3	0	2490	2531	43095510	43095551	8.340000e-06	62.1
17	TraesCS1D01G209500	chrUn	92.857	42	3	0	2490	2531	43259048	43259007	8.340000e-06	62.1
18	TraesCS1D01G209500	chrUn	92.857	42	3	0	2490	2531	262842366	262842407	8.340000e-06	62.1
19	TraesCS1D01G209500	chr2D	97.222	36	1	0	2502	2537	7074400	7074435	8.340000e-06	62.1

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	TraesCS1D01G209500	chr1D	295440546	295443334	2788	False	5151.000000	5151	100.000000	1	2789	1	chr1D.!!$F1	2788
1	TraesCS1D01G209500	chr1B	396969825	396972572	2747	False	4126.000000	4126	93.872000	4	2744	1	chr1B.!!$F1	2740
2	TraesCS1D01G209500	chr1A	368744346	368747627	3281	False	1276.666667	2667	91.968333	1	2789	3	chr1A.!!$F1	2788

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
723	731	0.596082	AAAACGTGAAATCCGGCAGG	59.404	50.0	0.0	0.0	39.46	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2438	3057	0.537653	GGTTCCACTACTCCCTCTGC	59.462	60.0	0.0	0.0	0.0	4.26	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
41	42	3.402628	TCTCAACTCTACTTTGGGCAC	57.597	47.619	0.00	0.00	0.00	5.01
44	45	2.629137	TCAACTCTACTTTGGGCACGTA	59.371	45.455	0.00	0.00	0.00	3.57
51	52	3.688694	ACTTTGGGCACGTACAATAGA	57.311	42.857	0.00	0.00	0.00	1.98
56	57	2.764010	TGGGCACGTACAATAGAGTGAT	59.236	45.455	0.00	0.00	36.79	3.06
78	79	9.973450	GTGATATCAGTTGTATGTAAGAGATGT	57.027	33.333	5.42	0.00	0.00	3.06
103	104	6.070995	TCACATAGAAATTTAGACGAGGTGGT	60.071	38.462	0.00	0.00	0.00	4.16
118	119	4.501571	CGAGGTGGTTGAAAGAGAAAGAGA	60.502	45.833	0.00	0.00	0.00	3.10
119	120	5.368989	GAGGTGGTTGAAAGAGAAAGAGAA	58.631	41.667	0.00	0.00	0.00	2.87
210	211	3.153369	TGGATGGTGCATGTAGTTTGT	57.847	42.857	0.00	0.00	0.00	2.83
280	281	3.737032	TGTATGTGTTGTCGAAGGTGA	57.263	42.857	0.00	0.00	0.00	4.02
291	292	3.056179	TGTCGAAGGTGATGTCTATGCAA	60.056	43.478	0.00	0.00	0.00	4.08
300	301	7.382110	AGGTGATGTCTATGCAAGATATGTAC	58.618	38.462	11.03	9.81	36.28	2.90
340	341	4.867608	CCTAAGAGCAACTTTAGCAGAGAC	59.132	45.833	1.81	0.00	39.72	3.36
341	342	4.342862	AAGAGCAACTTTAGCAGAGACA	57.657	40.909	0.00	0.00	34.94	3.41
344	345	2.104792	AGCAACTTTAGCAGAGACACCA	59.895	45.455	0.00	0.00	0.00	4.17
357	358	4.885907	CAGAGACACCATAATGAGCCAATT	59.114	41.667	0.00	0.00	0.00	2.32
359	360	3.382546	AGACACCATAATGAGCCAATTGC	59.617	43.478	0.00	0.00	41.71	3.56
379	380	4.129380	TGCCATCATAACTGTCAGTATGC	58.871	43.478	5.77	4.01	34.76	3.14
395	396	9.267084	TGTCAGTATGCGATGCTAAATAAATAA	57.733	29.630	0.00	0.00	34.76	1.40
416	417	4.475763	AGACATTCTAGCATAGTCGTCG	57.524	45.455	0.00	0.00	40.38	5.12
422	423	4.790810	TCTAGCATAGTCGTCGTACTTG	57.209	45.455	3.29	3.95	40.38	3.16
423	424	2.190325	AGCATAGTCGTCGTACTTGC	57.810	50.000	15.39	15.39	35.53	4.01
434	435	5.034797	TCGTCGTACTTGCTAGAATCATTG	58.965	41.667	1.04	0.00	0.00	2.82
440	441	6.019479	CGTACTTGCTAGAATCATTGTCCTTC	60.019	42.308	1.04	0.00	0.00	3.46
452	453	4.166725	TCATTGTCCTTCATATCTGGCCTT	59.833	41.667	3.32	0.00	0.00	4.35
453	454	4.591321	TTGTCCTTCATATCTGGCCTTT	57.409	40.909	3.32	0.00	0.00	3.11
454	455	4.591321	TGTCCTTCATATCTGGCCTTTT	57.409	40.909	3.32	0.00	0.00	2.27
463	464	6.489603	TCATATCTGGCCTTTTAACCTTCAA	58.510	36.000	3.32	0.00	0.00	2.69
471	472	9.283768	CTGGCCTTTTAACCTTCAAATTTAAAT	57.716	29.630	3.32	0.00	0.00	1.40
506	507	4.216257	ACTCCATATGAAAGTTGTGTGTGC	59.784	41.667	3.65	0.00	0.00	4.57
537	538	8.798975	AGAGAACTTCACATAATCCCCTTATA	57.201	34.615	0.00	0.00	0.00	0.98
551	552	2.109834	CCCTTATATGGGGATGCCACAA	59.890	50.000	14.76	0.00	41.83	3.33
558	559	1.076841	TGGGGATGCCACAAAGATTGA	59.923	47.619	5.30	0.00	31.87	2.57
703	711	9.270640	CAAAATTGGTAATTTCAGACATTTCCA	57.729	29.630	4.02	4.02	40.05	3.53
716	724	6.695278	TCAGACATTTCCAAAAACGTGAAATC	59.305	34.615	7.59	0.99	36.77	2.17
723	731	0.596082	AAAACGTGAAATCCGGCAGG	59.404	50.000	0.00	0.00	39.46	4.85
760	1357	2.161609	CCAGTGCATTTCCCTTTACGAC	59.838	50.000	0.00	0.00	0.00	4.34
761	1358	2.073816	AGTGCATTTCCCTTTACGACG	58.926	47.619	0.00	0.00	0.00	5.12
762	1359	2.070783	GTGCATTTCCCTTTACGACGA	58.929	47.619	0.00	0.00	0.00	4.20
1873	2477	6.432607	TTTGATTGTCTGAATGAGATGAGC	57.567	37.500	0.00	0.00	31.63	4.26
1944	2548	6.986231	AGTTGTAATTTTGAGCCCTGAAAAAG	59.014	34.615	0.00	0.00	30.14	2.27
2111	2716	7.175467	TGTTGTGATAACTAAGAGACCGACTAA	59.825	37.037	0.00	0.00	0.00	2.24
2241	2846	0.827089	TGCCCATGTTGGTGTCCTTG	60.827	55.000	0.00	0.00	35.17	3.61
2273	2879	3.763897	ACTTCCGAAATTCCCTTCAATGG	59.236	43.478	0.00	0.00	0.00	3.16
2293	2899	1.734465	GTGTACTGCATTGCTGGTCTC	59.266	52.381	18.21	8.72	0.00	3.36
2366	2984	6.585695	TTGTATGATATACTTCCTCCGTCC	57.414	41.667	0.00	0.00	0.00	4.79
2384	3003	4.700213	CCGTCCCAAAATAAGTGTCTCAAT	59.300	41.667	0.00	0.00	0.00	2.57
2389	3008	9.010029	GTCCCAAAATAAGTGTCTCAATCTTAA	57.990	33.333	0.00	0.00	0.00	1.85
2425	3044	7.537649	GCACTAAAGTTAATACAAAGTTGAGGC	59.462	37.037	0.00	0.00	28.07	4.70
2438	3057	4.871933	AGTTGAGGCACTTATTTTTGGG	57.128	40.909	0.00	0.00	41.55	4.12
2440	3059	2.603021	TGAGGCACTTATTTTTGGGCA	58.397	42.857	0.00	0.00	41.55	5.36
2445	3064	2.094026	GCACTTATTTTTGGGCAGAGGG	60.094	50.000	0.00	0.00	0.00	4.30
2452	3071	0.984230	TTTGGGCAGAGGGAGTAGTG	59.016	55.000	0.00	0.00	0.00	2.74
2761	3445	5.061179	GGGTAACTAGTGAGCAAAAGTTGA	58.939	41.667	11.57	0.00	34.23	3.18
2766	3450	6.942532	ACTAGTGAGCAAAAGTTGAATTGA	57.057	33.333	0.00	0.00	0.00	2.57
2767	3451	6.963796	ACTAGTGAGCAAAAGTTGAATTGAG	58.036	36.000	0.00	0.00	0.00	3.02
2782	3466	9.401058	AGTTGAATTGAGTTCTCTATTATTGGG	57.599	33.333	8.83	0.00	37.72	4.12
2783	3467	9.396022	GTTGAATTGAGTTCTCTATTATTGGGA	57.604	33.333	8.83	0.00	37.72	4.37

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	3.859443	AGTAGAGTTGAGATTGCAGCAG	58.141	45.455	0.00	0.00	0.00	4.24
56	57	8.966868	TGTGACATCTCTTACATACAACTGATA	58.033	33.333	0.00	0.00	0.00	2.15
77	78	6.255887	CCACCTCGTCTAAATTTCTATGTGAC	59.744	42.308	0.00	0.00	0.00	3.67
78	79	6.070995	ACCACCTCGTCTAAATTTCTATGTGA	60.071	38.462	0.00	0.00	0.00	3.58
95	96	3.728845	TCTTTCTCTTTCAACCACCTCG	58.271	45.455	0.00	0.00	0.00	4.63
150	151	9.513906	TCACTATTTGTAAGATGTCCATCAAAA	57.486	29.630	9.76	5.37	40.22	2.44
151	152	9.685276	ATCACTATTTGTAAGATGTCCATCAAA	57.315	29.630	9.76	2.90	40.22	2.69
152	153	9.685276	AATCACTATTTGTAAGATGTCCATCAA	57.315	29.630	9.76	0.00	40.22	2.57
153	154	9.685276	AAATCACTATTTGTAAGATGTCCATCA	57.315	29.630	9.76	0.00	35.85	3.07
280	281	7.308450	ACCAGTACATATCTTGCATAGACAT	57.692	36.000	0.00	0.00	35.19	3.06
300	301	5.790593	TCTTAGGCAAGTTTGTACTACCAG	58.209	41.667	0.00	0.00	34.62	4.00
340	341	2.431419	TGGCAATTGGCTCATTATGGTG	59.569	45.455	29.53	0.00	44.01	4.17
341	342	2.749600	TGGCAATTGGCTCATTATGGT	58.250	42.857	29.53	0.00	44.01	3.55
344	345	6.495872	AGTTATGATGGCAATTGGCTCATTAT	59.504	34.615	31.73	22.89	44.01	1.28
357	358	4.129380	GCATACTGACAGTTATGATGGCA	58.871	43.478	14.50	0.00	33.68	4.92
359	360	4.620982	TCGCATACTGACAGTTATGATGG	58.379	43.478	14.50	5.96	0.00	3.51
395	396	3.878103	ACGACGACTATGCTAGAATGTCT	59.122	43.478	0.00	0.00	0.00	3.41
416	417	6.818644	TGAAGGACAATGATTCTAGCAAGTAC	59.181	38.462	0.00	0.00	0.00	2.73
422	423	7.333921	CCAGATATGAAGGACAATGATTCTAGC	59.666	40.741	0.00	0.00	0.00	3.42
423	424	7.333921	GCCAGATATGAAGGACAATGATTCTAG	59.666	40.741	0.00	0.00	0.00	2.43
434	435	5.299531	GGTTAAAAGGCCAGATATGAAGGAC	59.700	44.000	5.01	0.00	0.00	3.85
440	441	6.773976	TTGAAGGTTAAAAGGCCAGATATG	57.226	37.500	5.01	0.00	0.00	1.78
471	472	8.637986	ACTTTCATATGGAGTGCACTTTAAAAA	58.362	29.630	22.65	13.46	0.00	1.94
476	477	5.536161	ACAACTTTCATATGGAGTGCACTTT	59.464	36.000	22.65	11.68	0.00	2.66
486	487	3.255395	TGGCACACACAACTTTCATATGG	59.745	43.478	2.13	0.00	0.00	2.74
546	547	5.244626	ACATCTTTTCCCTCAATCTTTGTGG	59.755	40.000	2.16	2.16	42.47	4.17
551	552	6.131972	TGAGACATCTTTTCCCTCAATCTT	57.868	37.500	0.00	0.00	31.72	2.40
558	559	4.020218	TCGACAATGAGACATCTTTTCCCT	60.020	41.667	0.00	0.00	0.00	4.20
591	592	4.784838	TCATATTGGCTGCCTCCATACTAT	59.215	41.667	21.03	0.26	35.77	2.12
703	711	1.000717	CCTGCCGGATTTCACGTTTTT	60.001	47.619	5.05	0.00	0.00	1.94
760	1357	2.226437	CCAGGAAAGTGTGTGGAAATCG	59.774	50.000	0.00	0.00	31.04	3.34
761	1358	2.558359	CCCAGGAAAGTGTGTGGAAATC	59.442	50.000	0.00	0.00	31.04	2.17
762	1359	2.597455	CCCAGGAAAGTGTGTGGAAAT	58.403	47.619	0.00	0.00	31.04	2.17
1045	1648	2.926242	GGTCGGGGTGTGGAGGAA	60.926	66.667	0.00	0.00	0.00	3.36
1101	1704	4.324991	GCGAACGGGGAGGTGGTT	62.325	66.667	0.00	0.00	0.00	3.67
1873	2477	1.624479	ATGCTGCAGAGAGTCCCCAG	61.624	60.000	20.43	0.00	0.00	4.45
2038	2642	4.408182	AATCTACAGCACCCAGTGATAC	57.592	45.455	0.00	0.00	35.23	2.24
2241	2846	5.278022	GGGAATTTCGGAAGTTCATGATAGC	60.278	44.000	22.28	7.59	0.00	2.97
2273	2879	1.734465	GAGACCAGCAATGCAGTACAC	59.266	52.381	8.35	0.00	0.00	2.90
2293	2899	4.267214	CAGTCTGTCGCAAGTTCATGATAG	59.733	45.833	0.00	0.00	39.48	2.08
2357	2975	2.640826	ACACTTATTTTGGGACGGAGGA	59.359	45.455	0.00	0.00	0.00	3.71
2418	3037	3.244044	TGCCCAAAAATAAGTGCCTCAAC	60.244	43.478	0.00	0.00	0.00	3.18
2425	3044	3.430453	TCCCTCTGCCCAAAAATAAGTG	58.570	45.455	0.00	0.00	0.00	3.16
2435	3054	1.306141	CCACTACTCCCTCTGCCCA	60.306	63.158	0.00	0.00	0.00	5.36
2438	3057	0.537653	GGTTCCACTACTCCCTCTGC	59.462	60.000	0.00	0.00	0.00	4.26
2440	3059	2.950990	ATGGTTCCACTACTCCCTCT	57.049	50.000	0.00	0.00	0.00	3.69
2445	3064	9.502091	TGCAAATAATATATGGTTCCACTACTC	57.498	33.333	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.