AutoCloner

Multiple sequence alignment - TraesCS3B01G277000

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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	TraesCS3B01G277000	chr3B	100.000	4971	0	0	1	4971	447019635	447024605	0.000000e+00	9180.0
1	TraesCS3B01G277000	chr3B	98.010	402	8	0	1	402	4306207	4306608	0.000000e+00	699.0
2	TraesCS3B01G277000	chr3B	84.422	199	22	8	433	627	18242975	18243168	2.360000e-43	187.0
3	TraesCS3B01G277000	chr3D	92.934	3057	145	27	993	4031	347300082	347303085	0.000000e+00	4383.0
4	TraesCS3B01G277000	chr3D	82.105	380	49	11	624	995	347299646	347300014	1.740000e-79	307.0
5	TraesCS3B01G277000	chr3D	82.902	193	27	3	439	627	583468450	583468260	8.560000e-38	169.0
6	TraesCS3B01G277000	chr3A	94.588	1737	80	9	2245	3973	466461101	466462831	0.000000e+00	2675.0
7	TraesCS3B01G277000	chr3A	93.810	1244	51	9	993	2233	466459642	466460862	0.000000e+00	1847.0
8	TraesCS3B01G277000	chr3A	88.652	282	16	6	4032	4300	466463084	466463362	3.710000e-86	329.0
9	TraesCS3B01G277000	chr3A	89.247	186	14	4	4297	4480	466463465	466463646	1.390000e-55	228.0
10	TraesCS3B01G277000	chr3A	88.119	101	8	3	898	995	466459475	466459574	3.140000e-22	117.0
11	TraesCS3B01G277000	chr7D	85.608	938	104	17	2434	3366	44263358	44262447	0.000000e+00	955.0
12	TraesCS3B01G277000	chr7D	83.795	938	120	18	2434	3366	44040878	44039968	0.000000e+00	861.0
13	TraesCS3B01G277000	chr7D	84.301	637	82	11	2734	3366	44118303	44117681	1.530000e-169	606.0
14	TraesCS3B01G277000	chr7D	83.775	641	85	11	2731	3366	44070942	44070316	1.540000e-164	590.0
15	TraesCS3B01G277000	chr7D	84.407	295	34	9	2434	2727	44236965	44236682	3.790000e-71	279.0
16	TraesCS3B01G277000	chr7D	90.909	55	4	1	3395	3448	180245435	180245489	6.900000e-09	73.1
17	TraesCS3B01G277000	chr4A	84.968	938	108	21	2434	3366	655098267	655097358	0.000000e+00	920.0
18	TraesCS3B01G277000	chr4A	84.861	938	110	20	2434	3366	655154769	655153859	0.000000e+00	917.0
19	TraesCS3B01G277000	chr4A	84.861	938	110	20	2434	3366	655212540	655211630	0.000000e+00	917.0
20	TraesCS3B01G277000	chr4A	84.615	936	112	19	2436	3366	655244558	655243650	0.000000e+00	902.0
21	TraesCS3B01G277000	chr4A	84.452	939	112	22	2434	3366	655188610	655187700	0.000000e+00	894.0
22	TraesCS3B01G277000	chr4A	82.609	207	30	4	415	618	491693408	491693205	1.420000e-40	178.0
23	TraesCS3B01G277000	chr2B	98.526	407	5	1	1	406	677044528	677044934	0.000000e+00	717.0
24	TraesCS3B01G277000	chr2B	87.850	107	11	2	4794	4898	236097689	236097583	1.880000e-24	124.0
25	TraesCS3B01G277000	chr2B	85.057	87	9	2	3363	3448	114043888	114043971	8.870000e-13	86.1
26	TraesCS3B01G277000	chr2B	90.909	55	2	3	3404	3457	134244614	134244666	2.480000e-08	71.3
27	TraesCS3B01G277000	chr2B	93.333	45	3	0	4547	4591	273055808	273055764	3.210000e-07	67.6
28	TraesCS3B01G277000	chr2B	100.000	29	0	0	4793	4821	791944427	791944399	3.000000e-03	54.7
29	TraesCS3B01G277000	chr2B	100.000	29	0	0	4793	4821	792027955	792027927	3.000000e-03	54.7
30	TraesCS3B01G277000	chr7A	98.515	404	6	0	1	404	55360793	55361196	0.000000e+00	713.0
31	TraesCS3B01G277000	chr7A	98.272	405	7	0	1	405	653011940	653011536	0.000000e+00	710.0
32	TraesCS3B01G277000	chr7A	84.901	404	47	10	2434	2836	46686089	46685699	3.610000e-106	396.0
33	TraesCS3B01G277000	chr7A	84.406	404	49	10	2434	2836	46632858	46632468	7.810000e-103	385.0
34	TraesCS3B01G277000	chr7A	85.222	203	19	7	426	618	32179808	32180009	1.090000e-46	198.0
35	TraesCS3B01G277000	chr5B	98.020	404	8	0	1	404	692519913	692520316	0.000000e+00	702.0
36	TraesCS3B01G277000	chr5B	84.694	686	82	11	2683	3364	448474340	448475006	0.000000e+00	664.0
37	TraesCS3B01G277000	chr5B	94.286	35	2	0	3414	3448	19440873	19440907	3.000000e-03	54.7
38	TraesCS3B01G277000	chr5A	97.794	408	7	2	1	406	43538433	43538840	0.000000e+00	702.0
39	TraesCS3B01G277000	chr5A	84.932	73	11	0	4655	4727	509996409	509996337	1.920000e-09	75.0
40	TraesCS3B01G277000	chr1B	98.259	402	6	1	1	402	131780898	131781298	0.000000e+00	702.0
41	TraesCS3B01G277000	chr1B	89.773	88	6	3	4794	4878	667540388	667540301	5.260000e-20	110.0
42	TraesCS3B01G277000	chr1B	94.915	59	2	1	4551	4609	253016331	253016274	1.910000e-14	91.6
43	TraesCS3B01G277000	chr1B	84.091	88	13	1	662	748	588847396	588847309	3.190000e-12	84.2
44	TraesCS3B01G277000	chr1B	91.525	59	4	1	4551	4609	123695811	123695754	4.130000e-11	80.5
45	TraesCS3B01G277000	chr1B	100.000	28	0	0	4794	4821	133158785	133158812	9.000000e-03	52.8
46	TraesCS3B01G277000	chr7B	97.257	401	11	0	1	401	477972921	477972521	0.000000e+00	680.0
47	TraesCS3B01G277000	chr7B	85.135	74	9	2	3376	3448	146076118	146076190	1.920000e-09	75.0
48	TraesCS3B01G277000	chr7B	89.474	57	5	1	4551	4607	337157956	337158011	2.480000e-08	71.3
49	TraesCS3B01G277000	chr7B	94.286	35	1	1	3415	3448	552011818	552011852	9.000000e-03	52.8
50	TraesCS3B01G277000	chr4D	96.259	401	15	0	1	401	95817011	95816611	0.000000e+00	658.0
51	TraesCS3B01G277000	chr4D	85.083	181	23	3	440	618	64581315	64581137	1.100000e-41	182.0
52	TraesCS3B01G277000	chr4D	85.593	118	17	0	4793	4910	404689742	404689859	1.880000e-24	124.0
53	TraesCS3B01G277000	chr4D	93.182	44	3	0	4549	4592	468359314	468359271	1.160000e-06	65.8
54	TraesCS3B01G277000	chr4D	100.000	28	0	0	3422	3449	50462529	50462502	9.000000e-03	52.8
55	TraesCS3B01G277000	chr1D	86.243	189	18	7	433	616	452830450	452830265	1.090000e-46	198.0
56	TraesCS3B01G277000	chr1D	84.656	189	25	4	439	627	473397100	473396916	8.500000e-43	185.0
57	TraesCS3B01G277000	chr1A	85.641	195	21	7	439	628	18785913	18786105	1.090000e-46	198.0
58	TraesCS3B01G277000	chr1A	85.641	195	21	7	439	628	18867856	18868048	1.090000e-46	198.0
59	TraesCS3B01G277000	chr1A	85.641	195	21	7	439	628	18950380	18950572	1.090000e-46	198.0
60	TraesCS3B01G277000	chr1A	100.000	29	0	0	3407	3435	583115793	583115821	3.000000e-03	54.7
61	TraesCS3B01G277000	chr1A	100.000	28	0	0	4794	4821	521132399	521132426	9.000000e-03	52.8
62	TraesCS3B01G277000	chr6B	83.246	191	27	4	441	629	101558000	101558187	2.380000e-38	171.0
63	TraesCS3B01G277000	chr6B	93.220	59	3	1	4551	4609	382768398	382768341	8.870000e-13	86.1
64	TraesCS3B01G277000	chr2A	82.653	196	26	6	429	616	765368063	765368258	3.080000e-37	167.0
65	TraesCS3B01G277000	chr2A	95.122	41	2	0	4551	4591	81534125	81534165	1.160000e-06	65.8
66	TraesCS3B01G277000	chr5D	91.463	82	7	0	4794	4875	269202828	269202909	4.070000e-21	113.0
67	TraesCS3B01G277000	chr5D	100.000	28	0	0	4551	4578	29493731	29493758	9.000000e-03	52.8
68	TraesCS3B01G277000	chr6D	94.915	59	2	1	4551	4609	295270411	295270468	1.910000e-14	91.6
69	TraesCS3B01G277000	chr6D	100.000	28	0	0	4794	4821	157811794	157811821	9.000000e-03	52.8
70	TraesCS3B01G277000	chr2D	91.111	45	4	0	4547	4591	234147919	234147875	1.490000e-05	62.1
71	TraesCS3B01G277000	chr2D	100.000	30	0	0	4794	4823	542647336	542647307	6.950000e-04	56.5
72	TraesCS3B01G277000	chr2D	100.000	29	0	0	4793	4821	74765159	74765187	3.000000e-03	54.7
73	TraesCS3B01G277000	chr6A	100.000	29	0	0	4793	4821	461778940	461778912	3.000000e-03	54.7

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	TraesCS3B01G277000	chr3B	447019635	447024605	4970	False	9180.0	9180	100.0000	1	4971	1	chr3B.!!$F3	4970
1	TraesCS3B01G277000	chr3D	347299646	347303085	3439	False	2345.0	4383	87.5195	624	4031	2	chr3D.!!$F1	3407
2	TraesCS3B01G277000	chr3A	466459475	466463646	4171	False	1039.2	2675	90.8832	898	4480	5	chr3A.!!$F1	3582
3	TraesCS3B01G277000	chr7D	44262447	44263358	911	True	955.0	955	85.6080	2434	3366	1	chr7D.!!$R5	932
4	TraesCS3B01G277000	chr7D	44039968	44040878	910	True	861.0	861	83.7950	2434	3366	1	chr7D.!!$R1	932
5	TraesCS3B01G277000	chr7D	44117681	44118303	622	True	606.0	606	84.3010	2734	3366	1	chr7D.!!$R3	632
6	TraesCS3B01G277000	chr7D	44070316	44070942	626	True	590.0	590	83.7750	2731	3366	1	chr7D.!!$R2	635
7	TraesCS3B01G277000	chr4A	655097358	655098267	909	True	920.0	920	84.9680	2434	3366	1	chr4A.!!$R2	932
8	TraesCS3B01G277000	chr4A	655153859	655154769	910	True	917.0	917	84.8610	2434	3366	1	chr4A.!!$R3	932
9	TraesCS3B01G277000	chr4A	655211630	655212540	910	True	917.0	917	84.8610	2434	3366	1	chr4A.!!$R5	932
10	TraesCS3B01G277000	chr4A	655243650	655244558	908	True	902.0	902	84.6150	2436	3366	1	chr4A.!!$R6	930
11	TraesCS3B01G277000	chr4A	655187700	655188610	910	True	894.0	894	84.4520	2434	3366	1	chr4A.!!$R4	932
12	TraesCS3B01G277000	chr5B	448474340	448475006	666	False	664.0	664	84.6940	2683	3364	1	chr5B.!!$F2	681

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
211	212	0.025513	GTGATGACGATGACGCTTGC	59.974	55.000	0.00	0.00	43.96	4.01	F
552	553	0.034059	CCTAACTATGCAGAGGCCGG	59.966	60.000	13.85	0.00	40.13	6.13	F
553	554	0.034059	CTAACTATGCAGAGGCCGGG	59.966	60.000	13.85	0.00	40.13	5.73	F
916	921	0.179040	TCCAACACGGTTCCACTTCC	60.179	55.000	0.00	0.00	35.57	3.46	F
1351	1431	0.179192	CGTCATGTGCCCGATTGTTG	60.179	55.000	0.00	0.00	0.00	3.33	F
1474	1554	1.281867	CCCAAATAGCCACAGACCAGA	59.718	52.381	0.00	0.00	0.00	3.86	F
3342	3677	0.891373	TCTGTAGCCAGCTGTCTGTC	59.109	55.000	13.81	3.98	38.66	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1446	1526	0.991146	TGGCTATTTGGGAGTGCTGA	59.009	50.000	0.00	0.00	4.26	R
1452	1532	1.281867	TGGTCTGTGGCTATTTGGGAG	59.718	52.381	0.00	0.00	4.30	R
1820	1911	1.604915	GACCTCAGCTTCCCCTTCC	59.395	63.158	0.00	0.00	3.46	R
2764	3091	2.187351	AACACACATGCGTGACAAAC	57.813	45.000	20.28	46.80	2.93	R
3297	3632	4.037923	CAGCCAAACTTTGTAAGTGGACAT	59.962	41.667	0.88	41.91	3.06	R
3426	3763	4.847512	TGTACTCCCTCTGACCCAAAATAA	59.152	41.667	0.00	0.00	1.40	R
4910	5579	0.031449	TCGCCGATATCAACGCATGA	59.969	50.000	3.12	43.67	3.07	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	End Stability
17	18	3.536917	TATGGAGGGCACGCTCGG	61.537	66.667	8.42	4.63
25	26	3.482783	GCACGCTCGGCTCAAGTC	61.483	66.667	0.00	3.01
26	27	2.811317	CACGCTCGGCTCAAGTCC	60.811	66.667	0.00	3.85
27	28	2.992114	ACGCTCGGCTCAAGTCCT	60.992	61.111	0.00	3.85
28	29	2.507992	CGCTCGGCTCAAGTCCTG	60.508	66.667	0.00	3.86
29	30	2.817396	GCTCGGCTCAAGTCCTGC	60.817	66.667	0.00	4.85
30	31	2.659016	CTCGGCTCAAGTCCTGCA	59.341	61.111	0.00	4.41
31	32	1.220206	CTCGGCTCAAGTCCTGCAT	59.780	57.895	0.00	3.96
32	33	0.461548	CTCGGCTCAAGTCCTGCATA	59.538	55.000	0.00	3.14
33	34	1.069823	CTCGGCTCAAGTCCTGCATAT	59.930	52.381	0.00	1.78
34	35	1.486310	TCGGCTCAAGTCCTGCATATT	59.514	47.619	0.00	1.28
35	36	2.092968	TCGGCTCAAGTCCTGCATATTT	60.093	45.455	0.00	1.40
36	37	2.289002	CGGCTCAAGTCCTGCATATTTC	59.711	50.000	0.00	2.17
37	38	2.620585	GGCTCAAGTCCTGCATATTTCC	59.379	50.000	0.00	3.13
38	39	2.620585	GCTCAAGTCCTGCATATTTCCC	59.379	50.000	0.00	3.97
39	40	3.686691	GCTCAAGTCCTGCATATTTCCCT	60.687	47.826	0.00	4.20
40	41	4.530875	CTCAAGTCCTGCATATTTCCCTT	58.469	43.478	0.00	3.95
41	42	4.934356	TCAAGTCCTGCATATTTCCCTTT	58.066	39.130	0.00	3.11
42	43	4.949856	TCAAGTCCTGCATATTTCCCTTTC	59.050	41.667	0.00	2.62
43	44	3.545703	AGTCCTGCATATTTCCCTTTCG	58.454	45.455	0.00	3.46
44	45	3.199946	AGTCCTGCATATTTCCCTTTCGA	59.800	43.478	0.00	3.71
45	46	3.945285	GTCCTGCATATTTCCCTTTCGAA	59.055	43.478	0.00	3.71
46	47	4.035675	GTCCTGCATATTTCCCTTTCGAAG	59.964	45.833	0.00	3.79
47	48	3.243201	CCTGCATATTTCCCTTTCGAAGC	60.243	47.826	0.00	3.86
48	49	3.620488	TGCATATTTCCCTTTCGAAGCT	58.380	40.909	0.00	3.74

Showing 1 to 25 of 774 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	3.536917	CCGAGCGTGCCCTCCATA	61.537	66.667	0.00	0.00	2.74
8	9	3.482783	GACTTGAGCCGAGCGTGC	61.483	66.667	0.00	0.00	5.34
9	10	2.811317	GGACTTGAGCCGAGCGTG	60.811	66.667	0.00	0.00	5.34
10	11	2.992114	AGGACTTGAGCCGAGCGT	60.992	61.111	0.00	0.00	5.07
11	12	2.507992	CAGGACTTGAGCCGAGCG	60.508	66.667	0.00	0.00	5.03
12	13	2.817396	GCAGGACTTGAGCCGAGC	60.817	66.667	0.00	0.00	5.03
13	14	0.461548	TATGCAGGACTTGAGCCGAG	59.538	55.000	0.00	0.00	4.63
14	15	1.123077	ATATGCAGGACTTGAGCCGA	58.877	50.000	0.00	0.00	5.54
15	16	1.959042	AATATGCAGGACTTGAGCCG	58.041	50.000	0.00	0.00	5.52
16	17	2.620585	GGAAATATGCAGGACTTGAGCC	59.379	50.000	0.00	0.00	4.70
17	18	2.620585	GGGAAATATGCAGGACTTGAGC	59.379	50.000	0.00	0.00	4.26
18	19	4.162040	AGGGAAATATGCAGGACTTGAG	57.838	45.455	0.00	0.00	3.02
19	20	4.591321	AAGGGAAATATGCAGGACTTGA	57.409	40.909	0.00	0.00	3.02
20	21	4.201950	CGAAAGGGAAATATGCAGGACTTG	60.202	45.833	0.00	0.00	3.16
21	22	3.947834	CGAAAGGGAAATATGCAGGACTT	59.052	43.478	0.00	0.00	3.01
22	23	3.199946	TCGAAAGGGAAATATGCAGGACT	59.800	43.478	0.00	0.00	3.85
23	24	3.541632	TCGAAAGGGAAATATGCAGGAC	58.458	45.455	0.00	0.00	3.85
24	25	3.924114	TCGAAAGGGAAATATGCAGGA	57.076	42.857	0.00	0.00	3.86
25	26	3.243201	GCTTCGAAAGGGAAATATGCAGG	60.243	47.826	0.00	0.00	4.85
26	27	3.629398	AGCTTCGAAAGGGAAATATGCAG	59.371	43.478	0.00	0.00	4.41
27	28	3.620488	AGCTTCGAAAGGGAAATATGCA	58.380	40.909	0.00	0.00	3.96
28	29	3.303395	CGAGCTTCGAAAGGGAAATATGC	60.303	47.826	0.00	43.74	3.14
29	30	3.871594	ACGAGCTTCGAAAGGGAAATATG	59.128	43.478	11.64	43.74	1.78
30	31	4.120589	GACGAGCTTCGAAAGGGAAATAT	58.879	43.478	11.64	43.74	1.28
31	32	3.518590	GACGAGCTTCGAAAGGGAAATA	58.481	45.455	11.64	43.74	1.40

Showing 1 to 25 of 740 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.