AutoCloner

Multiple sequence alignment - TraesCS3B01G048500

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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	TraesCS3B01G048500	chr3B	100.000	2825	0	0	1	2825	24552268	24549444	0.000000e+00	5217.0
1	TraesCS3B01G048500	chr3B	94.872	1911	96	2	917	2825	416100621	416102531	0.000000e+00	2985.0
2	TraesCS3B01G048500	chr3B	89.255	940	74	14	678	1616	2026565	2027478	0.000000e+00	1151.0
3	TraesCS3B01G048500	chr3B	88.595	491	47	6	674	1157	250973018	250973506	3.130000e-164	588.0
4	TraesCS3B01G048500	chr3B	89.264	326	31	4	63	385	250972500	250972824	3.390000e-109	405.0
5	TraesCS3B01G048500	chr3B	96.053	76	2	1	1	76	24524319	24524245	3.820000e-24	122.0
6	TraesCS3B01G048500	chr7D	94.902	2236	88	6	600	2825	42667451	42669670	0.000000e+00	3474.0
7	TraesCS3B01G048500	chr7D	90.929	893	51	13	678	1561	631828967	631828096	0.000000e+00	1173.0
8	TraesCS3B01G048500	chr7D	94.919	492	23	1	77	568	42666799	42667288	0.000000e+00	769.0
9	TraesCS3B01G048500	chr7B	93.463	2157	116	16	678	2825	290095708	290093568	0.000000e+00	3179.0
10	TraesCS3B01G048500	chr2D	93.352	2151	115	11	681	2825	99342134	99340006	0.000000e+00	3155.0
11	TraesCS3B01G048500	chr5B	97.588	1824	44	0	1002	2825	398162275	398164098	0.000000e+00	3125.0
12	TraesCS3B01G048500	chr5B	96.614	502	16	1	77	577	398161420	398161921	0.000000e+00	832.0
13	TraesCS3B01G048500	chr5B	89.655	493	37	8	82	574	153191401	153190923	1.440000e-172	616.0
14	TraesCS3B01G048500	chr5B	95.522	268	11	1	571	837	398162003	398162270	7.230000e-116	427.0
15	TraesCS3B01G048500	chr1D	96.584	1844	61	2	984	2825	111542320	111544163	0.000000e+00	3055.0
16	TraesCS3B01G048500	chr6A	95.455	1914	82	5	917	2825	64590335	64592248	0.000000e+00	3048.0
17	TraesCS3B01G048500	chr6A	92.041	490	36	2	77	566	616973940	616973454	0.000000e+00	686.0
18	TraesCS3B01G048500	chr2A	94.704	1926	83	7	900	2825	762103309	762101403	0.000000e+00	2974.0
19	TraesCS3B01G048500	chr2A	81.013	316	32	15	674	963	401210114	401210427	2.830000e-55	226.0
20	TraesCS3B01G048500	chr2B	94.715	1911	99	2	917	2825	25160363	25158453	0.000000e+00	2968.0
21	TraesCS3B01G048500	chr2B	88.846	260	27	2	305	564	45592503	45592246	4.540000e-83	318.0
22	TraesCS3B01G048500	chr2B	90.805	87	8	0	600	686	45592079	45591993	1.780000e-22	117.0
23	TraesCS3B01G048500	chr3A	94.505	1911	103	2	917	2825	34549749	34551659	0.000000e+00	2946.0
24	TraesCS3B01G048500	chr5D	92.454	1471	73	14	678	2142	236420961	236419523	0.000000e+00	2067.0
25	TraesCS3B01G048500	chr5D	85.340	191	25	3	674	861	296694002	296694192	7.990000e-46	195.0
26	TraesCS3B01G048500	chr3D	91.786	487	34	4	77	563	574547215	574547695	0.000000e+00	673.0
27	TraesCS3B01G048500	chr3D	90.541	74	5	1	1	74	17122902	17122831	2.320000e-16	97.1
28	TraesCS3B01G048500	chr3D	92.453	53	4	0	600	652	574547863	574547915	3.020000e-10	76.8
29	TraesCS3B01G048500	chr3D	100.000	31	0	0	571	601	574547801	574547831	1.090000e-04	58.4
30	TraesCS3B01G048500	chrUn	88.641	493	47	5	77	567	88015669	88015184	2.420000e-165	592.0
31	TraesCS3B01G048500	chr4B	84.641	599	84	7	683	1273	268560293	268559695	8.720000e-165	590.0
32	TraesCS3B01G048500	chr4B	84.399	391	48	6	182	567	90454818	90454436	3.440000e-99	372.0
33	TraesCS3B01G048500	chr4B	89.333	75	5	3	600	672	90454257	90454184	1.080000e-14	91.6
34	TraesCS3B01G048500	chr5A	87.982	441	43	8	141	578	456279166	456278733	1.940000e-141	512.0
35	TraesCS3B01G048500	chr7A	82.379	227	12	10	77	279	567530738	567530960	3.740000e-39	172.0
36	TraesCS3B01G048500	chr4D	91.667	48	2	2	621	666	225717711	225717758	6.530000e-07	65.8
37	TraesCS3B01G048500	chr1A	91.667	48	2	2	621	666	45886475	45886522	6.530000e-07	65.8
38	TraesCS3B01G048500	chr4A	92.683	41	3	0	626	666	311657660	311657620	3.040000e-05	60.2

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	TraesCS3B01G048500	chr3B	24549444	24552268	2824	True	5217.000000	5217	100.000000	1	2825	1	chr3B.!!$R2	2824
1	TraesCS3B01G048500	chr3B	416100621	416102531	1910	False	2985.000000	2985	94.872000	917	2825	1	chr3B.!!$F2	1908
2	TraesCS3B01G048500	chr3B	2026565	2027478	913	False	1151.000000	1151	89.255000	678	1616	1	chr3B.!!$F1	938
3	TraesCS3B01G048500	chr3B	250972500	250973506	1006	False	496.500000	588	88.929500	63	1157	2	chr3B.!!$F3	1094
4	TraesCS3B01G048500	chr7D	42666799	42669670	2871	False	2121.500000	3474	94.910500	77	2825	2	chr7D.!!$F1	2748
5	TraesCS3B01G048500	chr7D	631828096	631828967	871	True	1173.000000	1173	90.929000	678	1561	1	chr7D.!!$R1	883
6	TraesCS3B01G048500	chr7B	290093568	290095708	2140	True	3179.000000	3179	93.463000	678	2825	1	chr7B.!!$R1	2147
7	TraesCS3B01G048500	chr2D	99340006	99342134	2128	True	3155.000000	3155	93.352000	681	2825	1	chr2D.!!$R1	2144
8	TraesCS3B01G048500	chr5B	398161420	398164098	2678	False	1461.333333	3125	96.574667	77	2825	3	chr5B.!!$F1	2748
9	TraesCS3B01G048500	chr1D	111542320	111544163	1843	False	3055.000000	3055	96.584000	984	2825	1	chr1D.!!$F1	1841
10	TraesCS3B01G048500	chr6A	64590335	64592248	1913	False	3048.000000	3048	95.455000	917	2825	1	chr6A.!!$F1	1908
11	TraesCS3B01G048500	chr2A	762101403	762103309	1906	True	2974.000000	2974	94.704000	900	2825	1	chr2A.!!$R1	1925
12	TraesCS3B01G048500	chr2B	25158453	25160363	1910	True	2968.000000	2968	94.715000	917	2825	1	chr2B.!!$R1	1908
13	TraesCS3B01G048500	chr2B	45591993	45592503	510	True	217.500000	318	89.825500	305	686	2	chr2B.!!$R2	381
14	TraesCS3B01G048500	chr3A	34549749	34551659	1910	False	2946.000000	2946	94.505000	917	2825	1	chr3A.!!$F1	1908
15	TraesCS3B01G048500	chr5D	236419523	236420961	1438	True	2067.000000	2067	92.454000	678	2142	1	chr5D.!!$R1	1464
16	TraesCS3B01G048500	chr3D	574547215	574547915	700	False	269.400000	673	94.746333	77	652	3	chr3D.!!$F1	575
17	TraesCS3B01G048500	chr4B	268559695	268560293	598	True	590.000000	590	84.641000	683	1273	1	chr4B.!!$R1	590
18	TraesCS3B01G048500	chr4B	90454184	90454818	634	True	231.800000	372	86.866000	182	672	2	chr4B.!!$R2	490

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
866	1124	0.741326	GTCTACTGCTCCAGATCGCA	59.259	55.0	0.0	0.0	35.18	5.1	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2305	2581	0.108615	CCTCGACTCGCAACAGGAAT	60.109	55.0	0.0	0.0	0.0	3.01	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
25	26	8.455903	TGGATTGATTCATCTTTCCATCTTAC	57.544	34.615	7.02	0.00	35.28	2.34
26	27	8.277197	TGGATTGATTCATCTTTCCATCTTACT	58.723	33.333	7.02	0.00	35.28	2.24
27	28	9.129532	GGATTGATTCATCTTTCCATCTTACTT	57.870	33.333	0.00	0.00	32.41	2.24
38	39	9.216117	TCTTTCCATCTTACTTTACTTACAAGC	57.784	33.333	0.00	0.00	0.00	4.01
39	40	8.911918	TTTCCATCTTACTTTACTTACAAGCA	57.088	30.769	0.00	0.00	0.00	3.91
40	41	8.911918	TTCCATCTTACTTTACTTACAAGCAA	57.088	30.769	0.00	0.00	0.00	3.91
41	42	8.319143	TCCATCTTACTTTACTTACAAGCAAC	57.681	34.615	0.00	0.00	0.00	4.17
42	43	7.389607	TCCATCTTACTTTACTTACAAGCAACC	59.610	37.037	0.00	0.00	0.00	3.77
43	44	7.174253	CCATCTTACTTTACTTACAAGCAACCA	59.826	37.037	0.00	0.00	0.00	3.67
44	45	8.730680	CATCTTACTTTACTTACAAGCAACCAT	58.269	33.333	0.00	0.00	0.00	3.55
45	46	8.094798	TCTTACTTTACTTACAAGCAACCATG	57.905	34.615	0.00	0.00	0.00	3.66
46	47	5.705609	ACTTTACTTACAAGCAACCATGG	57.294	39.130	11.19	11.19	0.00	3.66
47	48	4.022329	ACTTTACTTACAAGCAACCATGGC	60.022	41.667	13.04	0.00	0.00	4.40
48	49	0.881118	ACTTACAAGCAACCATGGCG	59.119	50.000	13.04	4.23	36.08	5.69
49	50	1.164411	CTTACAAGCAACCATGGCGA	58.836	50.000	13.04	0.00	36.08	5.54
50	51	0.878416	TTACAAGCAACCATGGCGAC	59.122	50.000	13.04	0.23	36.08	5.19
61	62	4.134623	TGGCGACAAGTGGACAAC	57.865	55.556	0.00	0.00	37.44	3.32
62	63	1.525077	TGGCGACAAGTGGACAACC	60.525	57.895	0.00	0.00	37.44	3.77
63	64	1.525077	GGCGACAAGTGGACAACCA	60.525	57.895	0.00	0.00	44.76	3.67
269	275	4.047834	CAACTCGTGCTGCTTCCA	57.952	55.556	0.00	0.00	0.00	3.53
313	319	1.758440	TTGCTCTCTGTTCTGCCGGT	61.758	55.000	1.90	0.00	0.00	5.28
415	495	7.505258	TGTGTTGGATTCTATATCGGATTTCA	58.495	34.615	0.00	0.00	0.00	2.69
450	530	2.669569	GCTGGCCGCTTGTCTTCA	60.670	61.111	11.61	0.00	35.14	3.02
866	1124	0.741326	GTCTACTGCTCCAGATCGCA	59.259	55.000	0.00	0.00	35.18	5.10
910	1168	1.098712	TGTTCGGCTGGCTTTTCGTT	61.099	50.000	0.00	0.00	0.00	3.85
985	1251	5.569355	TGGGTGATCTTTGCTATTCTCAAA	58.431	37.500	0.00	0.00	33.04	2.69
987	1253	6.493115	TGGGTGATCTTTGCTATTCTCAAAAA	59.507	34.615	0.00	0.00	33.60	1.94
1130	1403	1.766496	TCGTCTCTGGGGTGTTCTTTT	59.234	47.619	0.00	0.00	0.00	2.27
1410	1683	2.346766	TGCCTCAGTTTGCTTCTGAA	57.653	45.000	7.28	0.00	40.68	3.02
1569	1843	7.113437	AGTTCTACACTCAGAGTTCTGCTATA	58.887	38.462	0.00	0.00	43.46	1.31
1719	1994	0.317020	GACGTGCTCAGTTGTTTGCC	60.317	55.000	0.00	0.00	0.00	4.52
2025	2300	2.228822	GGAGCGCAATTCTTCTTTTGGA	59.771	45.455	11.47	0.00	0.00	3.53
2191	2466	6.326583	CTGTCTACACAGTCAGGTACATCCT	61.327	48.000	0.00	0.00	45.28	3.24
2367	2643	7.174946	TCCTTTTATGTTCCAGATGTTTCTCAC	59.825	37.037	0.00	0.00	0.00	3.51
2514	2790	3.044809	GCGCTACCGTGATTCTCAA	57.955	52.632	0.00	0.00	36.67	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	9.216117	GCTTGTAAGTAAAGTAAGATGGAAAGA	57.784	33.333	0.00	0.00	0.00	2.52
13	14	8.999431	TGCTTGTAAGTAAAGTAAGATGGAAAG	58.001	33.333	0.00	0.00	0.00	2.62
14	15	8.911918	TGCTTGTAAGTAAAGTAAGATGGAAA	57.088	30.769	0.00	0.00	0.00	3.13
15	16	8.780249	GTTGCTTGTAAGTAAAGTAAGATGGAA	58.220	33.333	0.00	0.00	32.46	3.53
16	17	7.389607	GGTTGCTTGTAAGTAAAGTAAGATGGA	59.610	37.037	0.00	0.00	32.46	3.41
17	18	7.174253	TGGTTGCTTGTAAGTAAAGTAAGATGG	59.826	37.037	0.00	0.00	32.46	3.51
18	19	8.094798	TGGTTGCTTGTAAGTAAAGTAAGATG	57.905	34.615	0.00	0.00	32.46	2.90
19	20	8.730680	CATGGTTGCTTGTAAGTAAAGTAAGAT	58.269	33.333	0.00	0.00	32.46	2.40
20	21	7.174253	CCATGGTTGCTTGTAAGTAAAGTAAGA	59.826	37.037	2.57	0.00	32.46	2.10
21	22	7.305474	CCATGGTTGCTTGTAAGTAAAGTAAG	58.695	38.462	2.57	0.00	32.46	2.34
22	23	6.294286	GCCATGGTTGCTTGTAAGTAAAGTAA	60.294	38.462	14.67	0.00	32.46	2.24
23	24	5.182380	GCCATGGTTGCTTGTAAGTAAAGTA	59.818	40.000	14.67	0.00	32.46	2.24
24	25	4.022329	GCCATGGTTGCTTGTAAGTAAAGT	60.022	41.667	14.67	0.00	32.46	2.66
25	26	4.485163	GCCATGGTTGCTTGTAAGTAAAG	58.515	43.478	14.67	0.00	32.46	1.85
26	27	3.057876	CGCCATGGTTGCTTGTAAGTAAA	60.058	43.478	14.67	0.00	32.46	2.01
27	28	2.486203	CGCCATGGTTGCTTGTAAGTAA	59.514	45.455	14.67	0.00	0.00	2.24
28	29	2.080693	CGCCATGGTTGCTTGTAAGTA	58.919	47.619	14.67	0.00	0.00	2.24
29	30	0.881118	CGCCATGGTTGCTTGTAAGT	59.119	50.000	14.67	0.00	0.00	2.24
30	31	1.135689	GTCGCCATGGTTGCTTGTAAG	60.136	52.381	14.67	0.00	0.00	2.34
31	32	0.878416	GTCGCCATGGTTGCTTGTAA	59.122	50.000	14.67	0.00	0.00	2.41
32	33	0.250510	TGTCGCCATGGTTGCTTGTA	60.251	50.000	14.67	0.00	0.00	2.41
33	34	1.106351	TTGTCGCCATGGTTGCTTGT	61.106	50.000	14.67	0.00	0.00	3.16
34	35	0.387622	CTTGTCGCCATGGTTGCTTG	60.388	55.000	14.67	0.00	0.00	4.01
35	36	0.823356	ACTTGTCGCCATGGTTGCTT	60.823	50.000	14.67	0.00	0.00	3.91
36	37	1.228245	ACTTGTCGCCATGGTTGCT	60.228	52.632	14.67	0.00	0.00	3.91
37	38	1.081242	CACTTGTCGCCATGGTTGC	60.081	57.895	14.67	4.14	0.00	4.17
38	39	0.888736	TCCACTTGTCGCCATGGTTG	60.889	55.000	14.67	6.70	33.67	3.77
39	40	0.889186	GTCCACTTGTCGCCATGGTT	60.889	55.000	14.67	0.00	33.67	3.67
40	41	1.302511	GTCCACTTGTCGCCATGGT	60.303	57.895	14.67	0.00	33.67	3.55
41	42	0.888736	TTGTCCACTTGTCGCCATGG	60.889	55.000	7.63	7.63	0.00	3.66
42	43	0.238289	GTTGTCCACTTGTCGCCATG	59.762	55.000	0.00	0.00	0.00	3.66
43	44	0.889186	GGTTGTCCACTTGTCGCCAT	60.889	55.000	0.00	0.00	0.00	4.40
44	45	1.525077	GGTTGTCCACTTGTCGCCA	60.525	57.895	0.00	0.00	0.00	5.69
45	46	1.507141	CTGGTTGTCCACTTGTCGCC	61.507	60.000	0.00	0.00	39.03	5.54
46	47	0.814010	ACTGGTTGTCCACTTGTCGC	60.814	55.000	0.00	0.00	39.03	5.19
47	48	1.217882	GACTGGTTGTCCACTTGTCG	58.782	55.000	0.00	0.00	39.03	4.35
48	49	2.213499	CTGACTGGTTGTCCACTTGTC	58.787	52.381	0.00	0.00	44.75	3.18
49	50	1.559682	ACTGACTGGTTGTCCACTTGT	59.440	47.619	0.00	0.00	44.75	3.16
50	51	2.332063	ACTGACTGGTTGTCCACTTG	57.668	50.000	0.00	0.00	44.75	3.16
51	52	4.706842	ATTACTGACTGGTTGTCCACTT	57.293	40.909	0.00	0.00	44.75	3.16
52	53	4.706842	AATTACTGACTGGTTGTCCACT	57.293	40.909	0.00	0.00	44.75	4.00
53	54	5.767816	AAAATTACTGACTGGTTGTCCAC	57.232	39.130	0.00	0.00	44.75	4.02
54	55	5.654650	ACAAAAATTACTGACTGGTTGTCCA	59.345	36.000	0.00	0.00	44.75	4.02
55	56	6.144078	ACAAAAATTACTGACTGGTTGTCC	57.856	37.500	0.00	0.00	44.75	4.02
56	57	8.617809	TCTAACAAAAATTACTGACTGGTTGTC	58.382	33.333	0.00	0.00	45.54	3.18
57	58	8.514330	TCTAACAAAAATTACTGACTGGTTGT	57.486	30.769	0.00	0.00	0.00	3.32
58	59	8.621286	ACTCTAACAAAAATTACTGACTGGTTG	58.379	33.333	0.00	0.00	0.00	3.77
59	60	8.747538	ACTCTAACAAAAATTACTGACTGGTT	57.252	30.769	0.00	0.00	0.00	3.67
60	61	8.747538	AACTCTAACAAAAATTACTGACTGGT	57.252	30.769	0.00	0.00	0.00	4.00
269	275	0.674895	GCCGTGCAGAAGATTGGACT	60.675	55.000	0.00	0.00	37.28	3.85
313	319	1.686052	AGGCAAAAGCAAAATCACGGA	59.314	42.857	0.00	0.00	0.00	4.69
415	495	1.290324	CGGCTCAATCGATCGGGAT	59.710	57.895	16.41	0.00	0.00	3.85
886	1144	0.251341	AAAGCCAGCCGAACAAGGAT	60.251	50.000	0.00	0.00	0.00	3.24
910	1168	2.502142	ACCAGCAGCAGATCAATCAA	57.498	45.000	0.00	0.00	0.00	2.57
1106	1376	1.002087	GAACACCCCAGAGACGAATGT	59.998	52.381	0.00	0.00	0.00	2.71
1410	1683	7.125811	TCAAAGACAGTACTGAGGCCTATAAAT	59.874	37.037	29.30	1.64	0.00	1.40
1526	1799	6.865834	AGAACTCATCAATAGTGGAGTCTT	57.134	37.500	3.15	0.00	39.55	3.01
1569	1843	2.437359	GAGTCAAGCTGGCGCCAT	60.437	61.111	32.87	14.47	36.60	4.40
2025	2300	0.959553	TCGAGGAAGAAGCACGAGTT	59.040	50.000	0.00	0.00	0.00	3.01
2191	2466	2.507058	CTCCAGAATCCAGAACCCATGA	59.493	50.000	0.00	0.00	0.00	3.07
2304	2580	1.673033	CCTCGACTCGCAACAGGAATT	60.673	52.381	0.00	0.00	0.00	2.17
2305	2581	0.108615	CCTCGACTCGCAACAGGAAT	60.109	55.000	0.00	0.00	0.00	3.01
2367	2643	2.173669	CATGGTAAGGCGAGGCACG	61.174	63.158	0.00	0.00	45.66	5.34
2514	2790	1.068352	AGTCCAACTCCCAAAGCCCT	61.068	55.000	0.00	0.00	0.00	5.19
2654	2930	2.030451	AGACCACGACGAACTAAAGACC	60.030	50.000	0.00	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.