AutoCloner

Multiple sequence alignment - TraesCS3A01G522000

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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	TraesCS3A01G522000	chr3A	100.000	3460	0	0	1	3460	738251833	738248374	0.000000e+00	6390
1	TraesCS3A01G522000	chr3A	82.106	1073	158	19	763	1823	738307745	738306695	0.000000e+00	887
2	TraesCS3A01G522000	chr3A	81.454	949	142	19	881	1822	738694135	738693214	0.000000e+00	747
3	TraesCS3A01G522000	chr3A	79.460	852	146	23	981	1822	738679855	738679023	8.330000e-161	577
4	TraesCS3A01G522000	chr3A	78.799	849	158	16	981	1822	738600889	738600056	5.050000e-153	551
5	TraesCS3A01G522000	chr3A	90.455	220	21	0	338	557	738505098	738504879	1.210000e-74	291
6	TraesCS3A01G522000	chr3A	90.455	220	21	0	338	557	738601431	738601212	1.210000e-74	291
7	TraesCS3A01G522000	chr3A	90.455	220	21	0	338	557	738680397	738680178	1.210000e-74	291
8	TraesCS3A01G522000	chr5A	74.804	1532	312	53	887	2383	624725967	624724475	1.050000e-174	623
9	TraesCS3A01G522000	chr5A	75.258	291	59	12	2864	3146	672845296	672845581	3.630000e-25	126
10	TraesCS3A01G522000	chr3D	78.094	1018	177	25	830	1822	606000187	606001183	1.370000e-168	603
11	TraesCS3A01G522000	chr3D	74.390	1640	299	90	595	2201	605971085	605972636	1.070000e-164	590
12	TraesCS3A01G522000	chr3D	79.408	879	146	25	757	1614	605953035	605953899	3.850000e-164	588
13	TraesCS3A01G522000	chr3D	88.856	341	29	4	549	881	605589910	605590249	8.940000e-111	411
14	TraesCS3A01G522000	chr3D	86.885	305	29	9	578	881	605952667	605952961	7.160000e-87	331
15	TraesCS3A01G522000	chr3D	86.722	241	23	3	565	797	605901298	605901537	3.430000e-65	259
16	TraesCS3A01G522000	chr3D	86.634	202	22	4	578	777	605997840	605998038	5.810000e-53	219
17	TraesCS3A01G522000	chr3D	78.698	338	63	3	901	1231	605590315	605590650	2.090000e-52	217
18	TraesCS3A01G522000	chr3D	91.743	109	3	1	336	438	605996246	605996354	2.780000e-31	147
19	TraesCS3A01G522000	chr3D	87.356	87	10	1	32	117	605970950	605971036	7.900000e-17	99
20	TraesCS3A01G522000	chrUn	79.034	849	156	16	981	1822	344271898	344271065	2.330000e-156	562
21	TraesCS3A01G522000	chrUn	91.469	211	18	0	338	548	339064369	339064579	1.210000e-74	291
22	TraesCS3A01G522000	chrUn	90.455	220	21	0	338	557	344272440	344272221	1.210000e-74	291
23	TraesCS3A01G522000	chrUn	96.809	94	3	0	2662	2755	42327347	42327254	1.290000e-34	158
24	TraesCS3A01G522000	chrUn	96.809	94	3	0	2662	2755	367633409	367633316	1.290000e-34	158
25	TraesCS3A01G522000	chr5D	77.628	818	161	14	887	1691	500140284	500139476	8.690000e-131	477
26	TraesCS3A01G522000	chr5D	77.119	826	157	21	888	1703	500135274	500134471	1.890000e-122	449
27	TraesCS3A01G522000	chr5D	81.720	186	27	6	2863	3044	519659983	519660165	7.740000e-32	148
28	TraesCS3A01G522000	chr5D	93.902	82	5	0	2657	2738	500133791	500133710	1.300000e-24	124
29	TraesCS3A01G522000	chr1A	95.181	249	12	0	2405	2653	95106130	95106378	9.000000e-106	394
30	TraesCS3A01G522000	chr1A	80.791	177	27	6	2864	3036	12388676	12388503	7.790000e-27	132
31	TraesCS3A01G522000	chr7A	91.949	236	17	2	2411	2645	542300063	542300297	2.570000e-86	329
32	TraesCS3A01G522000	chr7A	83.333	186	28	3	2864	3047	608392822	608393006	5.940000e-38	169
33	TraesCS3A01G522000	chr7A	80.928	194	34	3	2864	3055	608684122	608684314	2.150000e-32	150
34	TraesCS3A01G522000	chr4B	89.954	219	20	2	2428	2645	493197499	493197716	7.310000e-72	281
35	TraesCS3A01G522000	chr6D	93.103	174	12	0	2476	2649	103526322	103526495	4.430000e-64	255
36	TraesCS3A01G522000	chr7B	79.667	300	49	9	2857	3148	4006989	4007284	4.530000e-49	206
37	TraesCS3A01G522000	chr3B	96.774	93	3	0	2662	2754	816172581	816172489	4.620000e-34	156
38	TraesCS3A01G522000	chr3B	71.826	575	133	18	1825	2380	816155379	816154815	1.670000e-28	137
39	TraesCS3A01G522000	chr2B	79.227	207	37	6	2865	3067	191755609	191755405	4.660000e-29	139
40	TraesCS3A01G522000	chr1D	82.390	159	27	1	2864	3021	418233182	418233024	1.670000e-28	137
41	TraesCS3A01G522000	chr4A	81.065	169	30	2	2866	3033	390963706	390963873	2.170000e-27	134
42	TraesCS3A01G522000	chr5B	91.209	91	8	0	2654	2744	621478640	621478550	1.300000e-24	124

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	TraesCS3A01G522000	chr3A	738248374	738251833	3459	True	6390.0	6390	100.000000	1	3460	1	chr3A.!!$R1	3459
1	TraesCS3A01G522000	chr3A	738306695	738307745	1050	True	887.0	887	82.106000	763	1823	1	chr3A.!!$R2	1060
2	TraesCS3A01G522000	chr3A	738693214	738694135	921	True	747.0	747	81.454000	881	1822	1	chr3A.!!$R4	941
3	TraesCS3A01G522000	chr3A	738679023	738680397	1374	True	434.0	577	84.957500	338	1822	2	chr3A.!!$R6	1484
4	TraesCS3A01G522000	chr3A	738600056	738601431	1375	True	421.0	551	84.627000	338	1822	2	chr3A.!!$R5	1484
5	TraesCS3A01G522000	chr5A	624724475	624725967	1492	True	623.0	623	74.804000	887	2383	1	chr5A.!!$R1	1496
6	TraesCS3A01G522000	chr3D	605952667	605953899	1232	False	459.5	588	83.146500	578	1614	2	chr3D.!!$F3	1036
7	TraesCS3A01G522000	chr3D	605970950	605972636	1686	False	344.5	590	80.873000	32	2201	2	chr3D.!!$F4	2169
8	TraesCS3A01G522000	chr3D	605996246	606001183	4937	False	323.0	603	85.490333	336	1822	3	chr3D.!!$F5	1486
9	TraesCS3A01G522000	chr3D	605589910	605590650	740	False	314.0	411	83.777000	549	1231	2	chr3D.!!$F2	682
10	TraesCS3A01G522000	chrUn	344271065	344272440	1375	True	426.5	562	84.744500	338	1822	2	chrUn.!!$R3	1484
11	TraesCS3A01G522000	chr5D	500139476	500140284	808	True	477.0	477	77.628000	887	1691	1	chr5D.!!$R1	804
12	TraesCS3A01G522000	chr5D	500133710	500135274	1564	True	286.5	449	85.510500	888	2738	2	chr5D.!!$R2	1850

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
272	274	0.100146	CACCGCGTAGGAGGTAAGTC	59.900	60.0	10.63	0.0	45.34	3.01	F
1828	5652	0.034337	TGACAGTACAACCGGAAGCC	59.966	55.0	9.46	0.0	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2266	6113	0.107312	CACAGAGGAGAATGGCCCAG	60.107	60.0	0.0	0.0	0.0	4.45	R
3392	7239	0.030369	GTCTACGTAGCCACCCGATG	59.970	60.0	18.0	0.0	0.0	3.84	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
21	22	0.912486	ACATCAGGTAGGTTGCCTCC	59.088	55.000	0.00	0.00	34.61	4.30
22	23	0.911769	CATCAGGTAGGTTGCCTCCA	59.088	55.000	0.00	0.00	34.61	3.86
23	24	1.492176	CATCAGGTAGGTTGCCTCCAT	59.508	52.381	0.00	0.00	34.61	3.41
24	25	1.204146	TCAGGTAGGTTGCCTCCATC	58.796	55.000	0.00	0.00	34.61	3.51
25	26	0.911769	CAGGTAGGTTGCCTCCATCA	59.088	55.000	0.00	0.00	34.61	3.07
26	27	1.134280	CAGGTAGGTTGCCTCCATCAG	60.134	57.143	0.00	0.00	34.61	2.90
27	28	0.181350	GGTAGGTTGCCTCCATCAGG	59.819	60.000	0.00	0.00	46.82	3.86
28	29	0.912486	GTAGGTTGCCTCCATCAGGT	59.088	55.000	0.00	0.00	45.61	4.00
29	30	1.134371	GTAGGTTGCCTCCATCAGGTC	60.134	57.143	0.00	0.00	45.61	3.85
30	31	0.548682	AGGTTGCCTCCATCAGGTCT	60.549	55.000	0.00	0.00	45.61	3.85
39	40	1.056700	CCATCAGGTCTAGGTGGGGG	61.057	65.000	0.00	0.00	0.00	5.40
46	47	1.995626	TCTAGGTGGGGGCTGAAGC	60.996	63.158	0.00	0.00	41.14	3.86
72	74	1.671054	CCGACCGCCATTGTTGACT	60.671	57.895	0.00	0.00	0.00	3.41
73	75	1.234615	CCGACCGCCATTGTTGACTT	61.235	55.000	0.00	0.00	0.00	3.01
103	105	2.288334	GCATTCACAACAGGTTGCATGA	60.288	45.455	11.84	6.71	44.03	3.07
106	108	5.680408	GCATTCACAACAGGTTGCATGATAT	60.680	40.000	11.84	4.26	44.03	1.63
113	115	3.817084	ACAGGTTGCATGATATGATTCCG	59.183	43.478	0.00	0.00	0.00	4.30
114	116	2.816087	AGGTTGCATGATATGATTCCGC	59.184	45.455	0.00	0.00	0.00	5.54
115	117	2.413239	GGTTGCATGATATGATTCCGCG	60.413	50.000	0.00	0.00	0.00	6.46
116	118	2.168326	TGCATGATATGATTCCGCGT	57.832	45.000	4.92	0.00	0.00	6.01
117	119	2.493035	TGCATGATATGATTCCGCGTT	58.507	42.857	4.92	0.00	0.00	4.84
118	120	2.480037	TGCATGATATGATTCCGCGTTC	59.520	45.455	4.92	0.00	0.00	3.95
119	121	2.738846	GCATGATATGATTCCGCGTTCT	59.261	45.455	4.92	0.00	0.00	3.01
120	122	3.181526	GCATGATATGATTCCGCGTTCTC	60.182	47.826	4.92	0.00	0.00	2.87
121	123	3.026630	TGATATGATTCCGCGTTCTCC	57.973	47.619	4.92	0.00	0.00	3.71

Showing 1 to 25 of 875 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	0.912486	GGAGGCAACCTACCTGATGT	59.088	55.000	0.00	0.00	37.77	3.06
3	4	0.911769	TGGAGGCAACCTACCTGATG	59.088	55.000	0.00	0.00	37.77	3.07
4	5	1.771255	GATGGAGGCAACCTACCTGAT	59.229	52.381	0.00	0.00	37.77	2.90
6	7	0.911769	TGATGGAGGCAACCTACCTG	59.088	55.000	0.00	0.00	37.77	4.00
7	8	1.207791	CTGATGGAGGCAACCTACCT	58.792	55.000	0.00	0.00	41.41	3.08
8	9	0.181350	CCTGATGGAGGCAACCTACC	59.819	60.000	0.00	0.00	32.29	3.18
9	10	3.788672	CCTGATGGAGGCAACCTAC	57.211	57.895	2.74	0.00	34.01	3.18
18	19	1.418334	CCCACCTAGACCTGATGGAG	58.582	60.000	0.00	0.00	37.04	3.86
19	20	0.031111	CCCCACCTAGACCTGATGGA	60.031	60.000	0.00	0.00	37.04	3.41
20	21	1.056700	CCCCCACCTAGACCTGATGG	61.057	65.000	0.00	0.00	39.83	3.51
21	22	1.700042	GCCCCCACCTAGACCTGATG	61.700	65.000	0.00	0.00	0.00	3.07
22	23	1.384643	GCCCCCACCTAGACCTGAT	60.385	63.158	0.00	0.00	0.00	2.90
23	24	2.040606	GCCCCCACCTAGACCTGA	59.959	66.667	0.00	0.00	0.00	3.86
24	25	2.041265	AGCCCCCACCTAGACCTG	59.959	66.667	0.00	0.00	0.00	4.00
25	26	2.041265	CAGCCCCCACCTAGACCT	59.959	66.667	0.00	0.00	0.00	3.85
26	27	1.615424	TTCAGCCCCCACCTAGACC	60.615	63.158	0.00	0.00	0.00	3.85
27	28	1.908483	CTTCAGCCCCCACCTAGAC	59.092	63.158	0.00	0.00	0.00	2.59
28	29	1.995626	GCTTCAGCCCCCACCTAGA	60.996	63.158	0.00	0.00	34.31	2.43
29	30	1.566298	AAGCTTCAGCCCCCACCTAG	61.566	60.000	0.00	0.00	43.38	3.02
30	31	1.541368	AAGCTTCAGCCCCCACCTA	60.541	57.895	0.00	0.00	43.38	3.08
46	47	3.740128	ATGGCGGTCGGCTAGCAAG	62.740	63.158	18.24	10.13	42.94	4.01
57	59	1.106351	TGCAAGTCAACAATGGCGGT	61.106	50.000	0.00	0.00	35.88	5.68
59	61	0.387622	CCTGCAAGTCAACAATGGCG	60.388	55.000	0.00	0.00	35.88	5.69
60	62	0.961019	TCCTGCAAGTCAACAATGGC	59.039	50.000	0.00	0.00	0.00	4.40
72	74	1.273048	GTTGTGAATGCCATCCTGCAA	59.727	47.619	0.00	0.00	45.84	4.08

Showing 1 to 25 of 889 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.