AutoCloner

Multiple sequence alignment - TraesCS1B01G185400

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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	TraesCS1B01G185400	chr1B	100.000	6350	0	0	1	6350	332162064	332155715	0.000000e+00	11727.0
1	TraesCS1B01G185400	chr1B	92.272	867	26	6	5498	6350	390431152	390430313	0.000000e+00	1192.0
2	TraesCS1B01G185400	chr1B	92.378	328	5	6	5500	5813	169943132	169942811	3.490000e-122	449.0
3	TraesCS1B01G185400	chr1B	91.870	246	6	4	5499	5730	332152948	332153193	1.320000e-86	331.0
4	TraesCS1B01G185400	chr1B	90.244	246	9	5	5499	5730	390428945	390429189	2.220000e-79	307.0
5	TraesCS1B01G185400	chr1B	94.118	68	3	1	3891	3958	211322988	211323054	1.130000e-17	102.0
6	TraesCS1B01G185400	chr1B	94.118	68	3	1	3891	3958	319127190	319127256	1.130000e-17	102.0
7	TraesCS1B01G185400	chr1A	92.613	2667	147	24	2791	5429	306641089	306643733	0.000000e+00	3788.0
8	TraesCS1B01G185400	chr1A	91.167	1551	72	16	735	2284	306639201	306640687	0.000000e+00	2045.0
9	TraesCS1B01G185400	chr1A	93.253	667	23	9	16	665	306637343	306638004	0.000000e+00	963.0
10	TraesCS1B01G185400	chr1A	91.617	334	13	5	5495	5813	483640001	483640334	1.260000e-121	448.0
11	TraesCS1B01G185400	chr1A	91.358	243	14	6	2507	2743	306640850	306641091	6.140000e-85	326.0
12	TraesCS1B01G185400	chr1A	95.567	203	8	1	2321	2522	306640690	306640892	2.210000e-84	324.0
13	TraesCS1B01G185400	chr1A	97.222	72	2	0	5428	5499	306643936	306644007	8.650000e-24	122.0
14	TraesCS1B01G185400	chr1D	92.245	2682	141	30	2791	5429	245979356	245982013	0.000000e+00	3738.0
15	TraesCS1B01G185400	chr1D	92.107	2420	100	24	16	2416	245972690	245975037	0.000000e+00	3326.0
16	TraesCS1B01G185400	chr1D	91.667	240	16	3	2507	2743	245979120	245979358	4.750000e-86	329.0
17	TraesCS1B01G185400	chr1D	96.262	107	3	1	2412	2517	245979051	245979157	2.350000e-39	174.0
18	TraesCS1B01G185400	chr1D	100.000	72	0	0	5428	5499	245982210	245982281	3.990000e-27	134.0
19	TraesCS1B01G185400	chr6B	95.732	867	22	5	5498	6350	631946881	631947746	0.000000e+00	1382.0
20	TraesCS1B01G185400	chr6B	85.871	1182	116	30	4266	5412	119128480	119129645	0.000000e+00	1210.0
21	TraesCS1B01G185400	chr6B	86.660	1057	92	18	2591	3642	119126939	119127951	0.000000e+00	1125.0
22	TraesCS1B01G185400	chr6B	85.181	857	81	22	1267	2107	119125894	119126720	0.000000e+00	837.0
23	TraesCS1B01G185400	chr6B	93.950	281	17	0	3609	3889	119127947	119128227	5.880000e-115	425.0
24	TraesCS1B01G185400	chr6B	87.031	293	28	7	962	1254	119125511	119125793	7.940000e-84	322.0
25	TraesCS1B01G185400	chr6B	87.008	254	20	6	3977	4227	119128241	119128484	2.260000e-69	274.0
26	TraesCS1B01G185400	chr6B	91.979	187	11	3	2276	2461	22426960	22427143	6.320000e-65	259.0
27	TraesCS1B01G185400	chr6A	86.468	1175	115	27	4266	5412	63118956	63120114	0.000000e+00	1249.0
28	TraesCS1B01G185400	chr6A	87.996	1058	84	21	2591	3642	63117401	63118421	0.000000e+00	1210.0
29	TraesCS1B01G185400	chr6A	85.000	600	59	20	962	1542	63116697	63117284	1.190000e-161	580.0
30	TraesCS1B01G185400	chr6A	92.883	281	20	0	3609	3889	63118417	63118697	5.930000e-110	409.0
31	TraesCS1B01G185400	chr6D	86.283	1181	112	32	4266	5412	52339429	52340593	0.000000e+00	1238.0
32	TraesCS1B01G185400	chr6D	87.879	1056	85	20	2591	3642	52337884	52338900	0.000000e+00	1201.0
33	TraesCS1B01G185400	chr6D	85.592	1173	121	21	962	2107	52336518	52337669	0.000000e+00	1186.0
34	TraesCS1B01G185400	chr6D	93.238	281	19	0	3609	3889	52338896	52339176	1.270000e-111	414.0
35	TraesCS1B01G185400	chr3B	95.971	546	19	1	5808	6350	250146231	250145686	0.000000e+00	883.0
36	TraesCS1B01G185400	chr3B	92.513	187	10	2	2276	2461	201514117	201514300	1.360000e-66	265.0
37	TraesCS1B01G185400	chr3B	92.513	187	10	2	2276	2461	201515696	201515879	1.360000e-66	265.0
38	TraesCS1B01G185400	chr3B	91.979	187	11	2	2276	2461	201514654	201514837	6.320000e-65	259.0
39	TraesCS1B01G185400	chr3B	92.778	180	10	1	2282	2461	201515173	201515349	2.270000e-64	257.0
40	TraesCS1B01G185400	chr3B	94.118	68	4	0	3891	3958	438545824	438545757	3.130000e-18	104.0
41	TraesCS1B01G185400	chr3D	94.843	543	25	1	5808	6350	171152667	171152128	0.000000e+00	845.0
42	TraesCS1B01G185400	chr3D	87.946	224	12	2	5499	5708	143611218	143611440	3.800000e-62	250.0
43	TraesCS1B01G185400	chr3A	93.923	543	33	0	5808	6350	208737288	208736746	0.000000e+00	821.0
44	TraesCS1B01G185400	chr3A	95.588	68	3	0	3891	3958	215955020	215955087	6.730000e-20	110.0
45	TraesCS1B01G185400	chr5B	93.921	329	6	4	5499	5813	704280064	704279736	9.570000e-133	484.0
46	TraesCS1B01G185400	chr5B	90.909	88	8	0	5727	5814	667839350	667839437	1.120000e-22	119.0
47	TraesCS1B01G185400	chr5B	94.118	68	3	1	3891	3958	347653276	347653342	1.130000e-17	102.0
48	TraesCS1B01G185400	chr4B	93.114	334	8	5	5495	5813	175550662	175550329	5.760000e-130	475.0
49	TraesCS1B01G185400	chr4B	93.248	311	6	5	5499	5795	564199608	564199299	1.620000e-120	444.0
50	TraesCS1B01G185400	chr4B	91.837	245	6	2	5500	5730	564197113	564197357	4.750000e-86	329.0
51	TraesCS1B01G185400	chr4A	91.870	246	6	1	5499	5730	321128521	321128766	1.320000e-86	331.0
52	TraesCS1B01G185400	chr7B	92.513	187	10	2	2276	2461	45215173	45214990	1.360000e-66	265.0
53	TraesCS1B01G185400	chrUn	91.979	187	11	2	2276	2461	445812047	445811864	6.320000e-65	259.0
54	TraesCS1B01G185400	chr2A	84.871	271	20	6	5479	5730	73282790	73282522	2.940000e-63	254.0
55	TraesCS1B01G185400	chr5D	100.000	87	0	0	5727	5813	529257605	529257691	1.830000e-35	161.0
56	TraesCS1B01G185400	chr5D	94.118	68	3	1	3891	3958	284895003	284895069	1.130000e-17	102.0
57	TraesCS1B01G185400	chr2B	95.588	68	3	0	3891	3958	166470833	166470900	6.730000e-20	110.0
58	TraesCS1B01G185400	chr2D	96.296	54	2	0	423	476	6838258	6838205	8.770000e-14	89.8

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	TraesCS1B01G185400	chr1B	332155715	332162064	6349	True	11727.000000	11727	100.000000	1	6350	1	chr1B.!!$R2	6349
1	TraesCS1B01G185400	chr1B	390430313	390431152	839	True	1192.000000	1192	92.272000	5498	6350	1	chr1B.!!$R3	852
2	TraesCS1B01G185400	chr1A	306637343	306644007	6664	False	1261.333333	3788	93.530000	16	5499	6	chr1A.!!$F2	5483
3	TraesCS1B01G185400	chr1D	245972690	245975037	2347	False	3326.000000	3326	92.107000	16	2416	1	chr1D.!!$F1	2400
4	TraesCS1B01G185400	chr1D	245979051	245982281	3230	False	1093.750000	3738	95.043500	2412	5499	4	chr1D.!!$F2	3087
5	TraesCS1B01G185400	chr6B	631946881	631947746	865	False	1382.000000	1382	95.732000	5498	6350	1	chr6B.!!$F2	852
6	TraesCS1B01G185400	chr6B	119125511	119129645	4134	False	698.833333	1210	87.616833	962	5412	6	chr6B.!!$F3	4450
7	TraesCS1B01G185400	chr6A	63116697	63120114	3417	False	862.000000	1249	88.086750	962	5412	4	chr6A.!!$F1	4450
8	TraesCS1B01G185400	chr6D	52336518	52340593	4075	False	1009.750000	1238	88.248000	962	5412	4	chr6D.!!$F1	4450
9	TraesCS1B01G185400	chr3B	250145686	250146231	545	True	883.000000	883	95.971000	5808	6350	1	chr3B.!!$R1	542
10	TraesCS1B01G185400	chr3B	201514117	201515879	1762	False	261.500000	265	92.445750	2276	2461	4	chr3B.!!$F1	185
11	TraesCS1B01G185400	chr3D	171152128	171152667	539	True	845.000000	845	94.843000	5808	6350	1	chr3D.!!$R1	542
12	TraesCS1B01G185400	chr3A	208736746	208737288	542	True	821.000000	821	93.923000	5808	6350	1	chr3A.!!$R1	542

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
341	350	0.603975	GGTCGAAGGAGCAAGCAACT	60.604	55.0	0.00	0.00	40.40	3.16	F
1240	2395	0.399949	TCCCTGTCACCTGTCCACTT	60.400	55.0	0.00	0.00	0.00	3.16	F
1647	2901	0.463620	GCTGGTTTTGGCAGGTTCAA	59.536	50.0	0.00	0.00	0.00	2.69	F
2715	4050	0.984995	GACCCTTCTACAGGCCTGTT	59.015	55.0	41.69	23.39	41.83	3.16	F
4291	5699	0.034756	TGGACATCATTATCCGCCCG	59.965	55.0	0.00	0.00	37.87	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1736	2990	0.323178	CTTGGCACTTGAGGCATCCT	60.323	55.000	0.00	44.02	3.24	R
2887	4236	1.247567	AAGAATTGGTTGGCCTCGTG	58.752	50.000	3.32	35.27	4.35	R
2926	4275	3.737559	AGGACTGCCAACATGGATAAA	57.262	42.857	0.00	40.96	1.40	R
4387	5806	0.179215	GTCAGCGAGGCATCAAAACG	60.179	55.000	0.00	0.00	3.60	R
5959	7629	1.304381	GTGATGGGGCTGGAAAGCA	60.304	57.895	0.00	36.33	3.91	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
54	55	4.155733	CGCCCTATGTGCGTCCCA	62.156	66.667	0.00	0.00	46.59	4.37
62	63	4.314440	GTGCGTCCCACTGCTCCA	62.314	66.667	0.00	0.00	41.35	3.86
236	245	2.192861	CCGGCTGGTTGTTGCAAGA	61.193	57.895	2.29	0.00	0.00	3.02
237	246	1.732917	CGGCTGGTTGTTGCAAGAA	59.267	52.632	4.66	4.66	0.00	2.52
341	350	0.603975	GGTCGAAGGAGCAAGCAACT	60.604	55.000	0.00	0.00	40.40	3.16
644	666	7.064966	TCACAATGATATGTTTAGTGCAGTCAG	59.935	37.037	0.00	0.00	0.00	3.51
650	672	1.135575	GTTTAGTGCAGTCAGCCATGC	60.136	52.381	0.00	0.00	44.83	4.06
719	1854	7.540400	TGTTTCACGTAAAATTAGCAATGATGG	59.460	33.333	0.00	0.00	0.00	3.51
753	1902	7.012704	GCCAATTTCAAGAAGAGCATATCTGTA	59.987	37.037	0.00	0.00	38.67	2.74
803	1952	5.202765	TGGTCATTCCGGTGTATTCTAGTA	58.797	41.667	0.00	0.00	39.52	1.82
831	1980	4.645588	GGAGCACTAGATACTGGTACTTGT	59.354	45.833	0.00	0.00	0.00	3.16
832	1981	5.221087	GGAGCACTAGATACTGGTACTTGTC	60.221	48.000	0.00	0.00	0.00	3.18
852	2001	7.891183	ACTTGTCCAACAATACCCATGTATTAA	59.109	33.333	0.00	0.00	44.06	1.40
924	2073	7.118101	GCATATTTTGCCTTCAGTTTGAAATCA	59.882	33.333	0.00	0.00	46.15	2.57
927	2076	3.225104	TGCCTTCAGTTTGAAATCAGCT	58.775	40.909	0.00	0.00	35.73	4.24
1023	2172	2.112198	GTCATTTCCGCCGCATCCA	61.112	57.895	0.00	0.00	0.00	3.41
1191	2346	1.956170	CTATGGCGCCACATCCGTC	60.956	63.158	35.50	0.00	32.39	4.79
1240	2395	0.399949	TCCCTGTCACCTGTCCACTT	60.400	55.000	0.00	0.00	0.00	3.16
1314	2557	5.523438	AGCTAGCAGAGTTCCTTATGTAC	57.477	43.478	18.83	0.00	0.00	2.90
1358	2603	3.196685	AGGTCTACTGAGATTTGTCTGCC	59.803	47.826	0.00	0.00	33.14	4.85
1505	2758	3.264450	CAGGTTCCTTCCCTCAAGTACAT	59.736	47.826	0.00	0.00	0.00	2.29
1506	2759	4.469945	CAGGTTCCTTCCCTCAAGTACATA	59.530	45.833	0.00	0.00	0.00	2.29
1530	2783	7.602517	ACTCTGCTTGATTAGTTGTACATTC	57.397	36.000	0.00	0.00	0.00	2.67
1545	2798	6.525121	TGTACATTCTCTTTGTTCGAACTG	57.475	37.500	27.32	17.03	0.00	3.16
1546	2799	4.474226	ACATTCTCTTTGTTCGAACTGC	57.526	40.909	27.32	3.51	0.00	4.40

Showing 1 to 25 of 159 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	3.197790	CAGCCCATTCGCGGACAG	61.198	66.667	6.13	0.00	0.00	3.51
8	9	4.776322	CCAGCCCATTCGCGGACA	62.776	66.667	6.13	0.00	0.00	4.02
644	666	1.948145	CTTCTCTGAATCAGGCATGGC	59.052	52.381	12.14	12.14	31.51	4.40
650	672	8.256605	TCTTCATTACTTCTTCTCTGAATCAGG	58.743	37.037	10.71	1.52	31.51	3.86
688	710	8.912787	TTGCTAATTTTACGTGAAACAAGAAA	57.087	26.923	7.74	6.60	35.74	2.52
691	713	8.500837	TCATTGCTAATTTTACGTGAAACAAG	57.499	30.769	7.74	9.29	35.74	3.16
711	1846	8.890124	TGAAATTGGCAATTATACCATCATTG	57.110	30.769	24.58	0.00	35.42	2.82
719	1854	7.975616	TGCTCTTCTTGAAATTGGCAATTATAC	59.024	33.333	24.58	18.17	0.00	1.47
774	1923	2.227194	ACACCGGAATGACCAAAAGAC	58.773	47.619	9.46	0.00	38.90	3.01
803	1952	4.033709	ACCAGTATCTAGTGCTCCACATT	58.966	43.478	0.00	0.00	36.74	2.71
831	1980	9.922477	TTACATTAATACATGGGTATTGTTGGA	57.078	29.630	9.67	2.68	46.84	3.53
832	1981	9.959749	GTTACATTAATACATGGGTATTGTTGG	57.040	33.333	9.67	1.52	46.84	3.77
877	2026	7.599630	ATGCATGGAAATTCACAACATAAAC	57.400	32.000	0.00	0.00	0.00	2.01
924	2073	3.913107	AGCAACCAAGAGGGAGCT	58.087	55.556	0.00	0.00	43.36	4.09
927	2076	0.108585	GTGACAGCAACCAAGAGGGA	59.891	55.000	0.00	0.00	41.15	4.20
1023	2172	3.322466	CCGGGCAGTGGAGGAAGT	61.322	66.667	0.00	0.00	0.00	3.01
1240	2395	5.906113	TGTAAAACACCAAAGAAAGCAGA	57.094	34.783	0.00	0.00	0.00	4.26
1340	2585	2.544685	CGGGCAGACAAATCTCAGTAG	58.455	52.381	0.00	0.00	30.42	2.57
1358	2603	6.726490	ATACCATATGTATTACCTAGGCGG	57.274	41.667	9.30	0.00	36.77	6.13
1493	2744	4.160439	TCAAGCAGAGTATGTACTTGAGGG	59.840	45.833	4.34	0.00	41.20	4.30
1505	2758	8.531982	AGAATGTACAACTAATCAAGCAGAGTA	58.468	33.333	0.00	0.00	0.00	2.59
1506	2759	7.390027	AGAATGTACAACTAATCAAGCAGAGT	58.610	34.615	0.00	0.00	0.00	3.24
1530	2783	2.032549	CACAGGCAGTTCGAACAAAGAG	60.033	50.000	28.78	17.39	0.00	2.85
1545	2798	6.586082	ACGAAAACAATTCATATTTCACAGGC	59.414	34.615	0.00	0.00	32.64	4.85
1546	2799	7.807433	TCACGAAAACAATTCATATTTCACAGG	59.193	33.333	0.00	0.00	32.64	4.00

Showing 1 to 25 of 146 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.