AutoCloner

Multiple sequence alignment - TraesCS5B01G055100

Loading Multiple Alignment...

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	TraesCS5B01G055100	chr5B	100.000	3458	0	0	1	3458	60826660	60823203	0.000000e+00	6386.0
1	TraesCS5B01G055100	chr5D	97.695	2863	50	8	28	2887	57818899	57821748	0.000000e+00	4907.0
2	TraesCS5B01G055100	chr5D	96.290	566	16	1	2898	3458	57821810	57822375	0.000000e+00	924.0
3	TraesCS5B01G055100	chr5D	84.466	103	7	1	3051	3144	497870076	497870178	3.670000e-15	93.5
4	TraesCS5B01G055100	chr5D	81.250	80	14	1	3340	3419	514464057	514464135	2.880000e-06	63.9
5	TraesCS5B01G055100	chr1B	89.486	2511	197	39	580	3057	4954565	4952089	0.000000e+00	3112.0
6	TraesCS5B01G055100	chr1B	89.162	2519	212	34	688	3177	4597570	4595084	0.000000e+00	3083.0
7	TraesCS5B01G055100	chr1B	88.925	2456	201	37	560	2987	4110073	4112485	0.000000e+00	2963.0
8	TraesCS5B01G055100	chr1B	88.991	2398	195	34	560	2939	4519104	4516758	0.000000e+00	2902.0
9	TraesCS5B01G055100	chr1B	92.548	2013	111	14	668	2653	70232782	70234782	0.000000e+00	2850.0
10	TraesCS5B01G055100	chr1B	88.814	1189	110	10	1806	2987	4798955	4797783	0.000000e+00	1437.0
11	TraesCS5B01G055100	chr1B	83.254	209	26	8	302	507	538505598	538505800	2.120000e-42	183.0
12	TraesCS5B01G055100	chr1B	85.057	174	18	5	362	533	4519267	4519100	1.650000e-38	171.0
13	TraesCS5B01G055100	chr1B	77.714	350	27	28	169	500	46691134	46691450	2.130000e-37	167.0
14	TraesCS5B01G055100	chr1B	92.174	115	9	0	3165	3279	4951889	4951775	2.760000e-36	163.0
15	TraesCS5B01G055100	chr1B	84.615	156	13	5	304	458	70232545	70232690	1.000000e-30	145.0
16	TraesCS5B01G055100	chr1B	88.235	119	10	3	3165	3279	4147204	4147322	4.650000e-29	139.0
17	TraesCS5B01G055100	chr1B	85.321	109	8	7	250	355	4542967	4542864	4.720000e-19	106.0
18	TraesCS5B01G055100	chr1B	90.196	51	2	2	3127	3177	4951962	4951915	2.880000e-06	63.9
19	TraesCS5B01G055100	chr1B	100.000	29	0	0	3281	3309	4147337	4147365	2.000000e-03	54.7
20	TraesCS5B01G055100	chr6A	88.423	2626	226	45	580	3177	613493534	613496109	0.000000e+00	3094.0
21	TraesCS5B01G055100	chr6A	85.627	1475	140	42	1660	3109	64065216	64063789	0.000000e+00	1483.0
22	TraesCS5B01G055100	chr3D	88.255	2648	223	42	560	3177	560024990	560022401	0.000000e+00	3086.0
23	TraesCS5B01G055100	chr7D	87.628	2336	186	53	301	2615	548230735	548232988	0.000000e+00	2617.0
24	TraesCS5B01G055100	chr6D	89.506	2106	160	30	565	2653	51342828	51344889	0.000000e+00	2608.0
25	TraesCS5B01G055100	chr6D	88.884	2105	179	19	560	2653	53176117	53174057	0.000000e+00	2540.0
26	TraesCS5B01G055100	chr6D	87.143	140	11	4	369	507	51067935	51068068	5.980000e-33	152.0
27	TraesCS5B01G055100	chr6D	79.386	228	20	13	306	532	51342625	51342826	6.020000e-28	135.0
28	TraesCS5B01G055100	chr6B	89.380	2081	167	22	565	2629	120595525	120593483	0.000000e+00	2569.0
29	TraesCS5B01G055100	chr6B	89.000	2109	171	23	560	2653	120355193	120353131	0.000000e+00	2553.0
30	TraesCS5B01G055100	chr1D	85.385	650	67	17	2505	3145	387236	387866	0.000000e+00	649.0
31	TraesCS5B01G055100	chr1D	96.825	63	2	0	3047	3109	33988075	33988137	4.720000e-19	106.0
32	TraesCS5B01G055100	chr1A	86.639	479	44	13	2708	3177	3015094	3015561	2.380000e-141	512.0
33	TraesCS5B01G055100	chr1A	86.885	244	24	5	2873	3109	3520957	3520715	2.050000e-67	267.0
34	TraesCS5B01G055100	chr1A	79.693	261	24	18	288	533	2942920	2943166	9.930000e-36	161.0
35	TraesCS5B01G055100	chr1A	88.496	113	13	0	3167	3279	3015589	3015701	1.670000e-28	137.0
36	TraesCS5B01G055100	chr1A	82.979	94	9	4	237	327	3542170	3542081	1.030000e-10	78.7
37	TraesCS5B01G055100	chrUn	93.913	115	7	0	3165	3279	318171401	318171515	1.280000e-39	174.0
38	TraesCS5B01G055100	chrUn	79.693	261	24	18	288	533	361631325	361631571	9.930000e-36	161.0
39	TraesCS5B01G055100	chrUn	83.740	123	10	3	415	533	325465862	325465978	1.310000e-19	108.0
40	TraesCS5B01G055100	chrUn	81.250	80	14	1	3340	3419	305539649	305539571	2.880000e-06	63.9
41	TraesCS5B01G055100	chr3A	83.750	80	5	2	3340	3419	7442360	7442431	6.190000e-08	69.4

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	TraesCS5B01G055100	chr5B	60823203	60826660	3457	True	6386.000000	6386	100.000000	1	3458	1	chr5B.!!$R1	3457
1	TraesCS5B01G055100	chr5D	57818899	57822375	3476	False	2915.500000	4907	96.992500	28	3458	2	chr5D.!!$F3	3430
2	TraesCS5B01G055100	chr1B	4595084	4597570	2486	True	3083.000000	3083	89.162000	688	3177	1	chr1B.!!$R2	2489
3	TraesCS5B01G055100	chr1B	4110073	4112485	2412	False	2963.000000	2963	88.925000	560	2987	1	chr1B.!!$F1	2427
4	TraesCS5B01G055100	chr1B	4516758	4519267	2509	True	1536.500000	2902	87.024000	362	2939	2	chr1B.!!$R4	2577
5	TraesCS5B01G055100	chr1B	70232545	70234782	2237	False	1497.500000	2850	88.581500	304	2653	2	chr1B.!!$F5	2349
6	TraesCS5B01G055100	chr1B	4797783	4798955	1172	True	1437.000000	1437	88.814000	1806	2987	1	chr1B.!!$R3	1181
7	TraesCS5B01G055100	chr1B	4951775	4954565	2790	True	1112.966667	3112	90.618667	580	3279	3	chr1B.!!$R5	2699
8	TraesCS5B01G055100	chr6A	613493534	613496109	2575	False	3094.000000	3094	88.423000	580	3177	1	chr6A.!!$F1	2597
9	TraesCS5B01G055100	chr6A	64063789	64065216	1427	True	1483.000000	1483	85.627000	1660	3109	1	chr6A.!!$R1	1449
10	TraesCS5B01G055100	chr3D	560022401	560024990	2589	True	3086.000000	3086	88.255000	560	3177	1	chr3D.!!$R1	2617
11	TraesCS5B01G055100	chr7D	548230735	548232988	2253	False	2617.000000	2617	87.628000	301	2615	1	chr7D.!!$F1	2314
12	TraesCS5B01G055100	chr6D	53174057	53176117	2060	True	2540.000000	2540	88.884000	560	2653	1	chr6D.!!$R1	2093
13	TraesCS5B01G055100	chr6D	51342625	51344889	2264	False	1371.500000	2608	84.446000	306	2653	2	chr6D.!!$F2	2347
14	TraesCS5B01G055100	chr6B	120593483	120595525	2042	True	2569.000000	2569	89.380000	565	2629	1	chr6B.!!$R2	2064
15	TraesCS5B01G055100	chr6B	120353131	120355193	2062	True	2553.000000	2553	89.000000	560	2653	1	chr6B.!!$R1	2093
16	TraesCS5B01G055100	chr1D	387236	387866	630	False	649.000000	649	85.385000	2505	3145	1	chr1D.!!$F1	640
17	TraesCS5B01G055100	chr1A	3015094	3015701	607	False	324.500000	512	87.567500	2708	3279	2	chr1A.!!$F2	571

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
91	92	0.412640	ACCCTCCTCTCCTACGGTTT	59.587	55.000	0.00	0.00	0.00	3.27	F
92	93	0.824759	CCCTCCTCTCCTACGGTTTG	59.175	60.000	0.00	0.00	0.00	2.93	F
166	167	2.251040	CTGGTTCGACATGTAGACGTG	58.749	52.381	8.29	0.22	36.76	4.49	F
2090	2188	1.200020	GGGTTTTCTGGTGCTCATTCG	59.800	52.381	0.00	0.00	0.00	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1072	1158	2.360801	GCTGCTTTGACACAAGGGTAAA	59.639	45.455	0.00	0.00	0.00	2.01	R
1586	1673	2.781757	TGGAGCTTCATCCATCCAGAAT	59.218	45.455	0.00	0.00	44.56	2.40	R
2106	2204	0.111704	CGTTGTTGAGCACGAGAACG	60.112	55.000	16.95	16.95	45.59	3.95	R
3068	3285	6.550854	TCAACTTCAGGTCATTTTGGAATCTT	59.449	34.615	0.00	0.00	0.00	2.40	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
17	18	3.353836	TCAAAGAAGCGGCGGCAC	61.354	61.111	19.21	11.65	43.41	5.01
18	19	3.357079	CAAAGAAGCGGCGGCACT	61.357	61.111	19.21	13.69	43.41	4.40
19	20	3.050275	AAAGAAGCGGCGGCACTC	61.050	61.111	19.21	13.75	43.41	3.51
20	21	3.537206	AAAGAAGCGGCGGCACTCT	62.537	57.895	19.21	15.72	43.41	3.24
21	22	3.941657	AAGAAGCGGCGGCACTCTC	62.942	63.158	19.21	8.95	43.41	3.20
26	27	4.200283	CGGCGGCACTCTCCTCTC	62.200	72.222	10.53	0.00	0.00	3.20
91	92	0.412640	ACCCTCCTCTCCTACGGTTT	59.587	55.000	0.00	0.00	0.00	3.27
92	93	0.824759	CCCTCCTCTCCTACGGTTTG	59.175	60.000	0.00	0.00	0.00	2.93
166	167	2.251040	CTGGTTCGACATGTAGACGTG	58.749	52.381	8.29	0.22	36.76	4.49
194	196	7.707774	TTTTAATTCGCTTTCCTTTTCTTGG	57.292	32.000	0.00	0.00	0.00	3.61
274	276	6.442564	TGTAAAGCCATTCTCTTCCTAGGTAA	59.557	38.462	9.08	1.10	0.00	2.85
352	355	8.997621	TGTGGTATTTCTAGTTGAACAGATAC	57.002	34.615	0.00	0.38	33.88	2.24
353	356	8.812972	TGTGGTATTTCTAGTTGAACAGATACT	58.187	33.333	0.00	0.00	33.88	2.12
509	522	9.657121	GCTCTGCTTTTCATGTTACTATTAATC	57.343	33.333	0.00	0.00	0.00	1.75
684	714	9.277783	CTTGCTACTTAATTATGATGGTAGCTT	57.722	33.333	20.30	0.00	46.75	3.74
720	750	2.378634	GGCCCACCTGTAGCCTCAT	61.379	63.158	0.00	0.00	43.62	2.90
1072	1158	4.262808	CCAGGACAAGTGATCTCAAGTCTT	60.263	45.833	14.90	8.25	0.00	3.01
1586	1673	8.733458	CAATCATCATGACTTCCTAAAGTTTGA	58.267	33.333	0.00	0.00	45.80	2.69
1663	1760	3.327464	TGATTGTCTTCCAGGTGATGTGA	59.673	43.478	0.00	0.00	0.00	3.58
1692	1789	1.893137	TCCTTGTACGATGCTCACAGT	59.107	47.619	0.00	0.00	0.00	3.55
2010	2108	3.055819	ACTGTCGTATGCTTCAGATGGTT	60.056	43.478	8.49	0.00	0.00	3.67
2090	2188	1.200020	GGGTTTTCTGGTGCTCATTCG	59.800	52.381	0.00	0.00	0.00	3.34
2184	2282	0.174389	CCTCACCACATCTGGAGACG	59.826	60.000	0.00	0.00	40.55	4.18
2228	2326	0.463654	GTAACTGATGCCGGGATGCA	60.464	55.000	15.46	10.45	46.94	3.96
2660	2780	2.100252	GCATCTGGTGAATGGTGAATGG	59.900	50.000	0.00	0.00	0.00	3.16
2679	2804	9.918630	GTGAATGGAACTTTAGTACTGTAGTAA	57.081	33.333	5.39	10.33	31.52	2.24
2783	2915	0.897621	GCCCCAAGATTCCCAGTTTG	59.102	55.000	0.00	0.00	0.00	2.93
2886	3031	6.992123	TGCGGAAGTGATTTGAAGACATATAT	59.008	34.615	0.00	0.00	0.00	0.86
2997	3202	4.268644	CGACATGCTTGTTGATATCGACTT	59.731	41.667	21.26	2.12	39.29	3.01
3006	3211	7.011482	GCTTGTTGATATCGACTTAATTGGAGT	59.989	37.037	21.26	0.00	0.00	3.85
3010	3215	9.477484	GTTGATATCGACTTAATTGGAGTATGT	57.523	33.333	14.90	0.00	0.00	2.29
3011	3216	9.692749	TTGATATCGACTTAATTGGAGTATGTC	57.307	33.333	0.00	0.00	0.00	3.06
3012	3217	9.078990	TGATATCGACTTAATTGGAGTATGTCT	57.921	33.333	0.00	0.00	0.00	3.41
3013	3218	9.915629	GATATCGACTTAATTGGAGTATGTCTT	57.084	33.333	0.00	0.00	0.00	3.01
3015	3220	7.827819	TCGACTTAATTGGAGTATGTCTTTG	57.172	36.000	0.00	0.00	0.00	2.77
3016	3221	7.608153	TCGACTTAATTGGAGTATGTCTTTGA	58.392	34.615	0.00	0.00	0.00	2.69
3017	3222	8.258007	TCGACTTAATTGGAGTATGTCTTTGAT	58.742	33.333	0.00	0.00	0.00	2.57
3018	3223	8.883731	CGACTTAATTGGAGTATGTCTTTGATT	58.116	33.333	0.00	0.00	0.00	2.57
3019	3224	9.994432	GACTTAATTGGAGTATGTCTTTGATTG	57.006	33.333	0.00	0.00	0.00	2.67
3020	3225	9.739276	ACTTAATTGGAGTATGTCTTTGATTGA	57.261	29.630	0.00	0.00	0.00	2.57
3175	3504	3.490419	GGCATTCATCATGTTCTTGCCTC	60.490	47.826	16.60	0.00	43.68	4.70
3181	3510	5.258841	TCATCATGTTCTTGCCTCTTTGAT	58.741	37.500	0.00	0.00	0.00	2.57
3281	3610	3.580731	TCGAGATTCATGTGTTTGCGTA	58.419	40.909	0.00	0.00	0.00	4.42
3317	3646	7.021196	CCTGAAATTGTAAATCTAACACACCG	58.979	38.462	0.00	0.00	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.314388	GAGTGCCGCCGCTTCTTTG	62.314	63.158	0.00	0.00	35.36	2.77
2	3	3.050275	GAGTGCCGCCGCTTCTTT	61.050	61.111	0.00	0.00	35.36	2.52
3	4	3.941657	GAGAGTGCCGCCGCTTCTT	62.942	63.158	0.00	0.00	32.21	2.52
4	5	4.443266	GAGAGTGCCGCCGCTTCT	62.443	66.667	0.00	1.81	33.94	2.85
9	10	4.200283	GAGAGGAGAGTGCCGCCG	62.200	72.222	0.00	0.00	39.97	6.46
10	11	3.844090	GGAGAGGAGAGTGCCGCC	61.844	72.222	0.00	0.00	34.63	6.13
11	12	2.757917	AGGAGAGGAGAGTGCCGC	60.758	66.667	0.00	0.00	0.00	6.53
12	13	1.077068	AGAGGAGAGGAGAGTGCCG	60.077	63.158	0.00	0.00	0.00	5.69
13	14	0.755327	GGAGAGGAGAGGAGAGTGCC	60.755	65.000	0.00	0.00	0.00	5.01
14	15	0.258774	AGGAGAGGAGAGGAGAGTGC	59.741	60.000	0.00	0.00	0.00	4.40
15	16	1.846439	AGAGGAGAGGAGAGGAGAGTG	59.154	57.143	0.00	0.00	0.00	3.51
16	17	2.127708	GAGAGGAGAGGAGAGGAGAGT	58.872	57.143	0.00	0.00	0.00	3.24
17	18	1.421646	GGAGAGGAGAGGAGAGGAGAG	59.578	61.905	0.00	0.00	0.00	3.20
18	19	1.010793	AGGAGAGGAGAGGAGAGGAGA	59.989	57.143	0.00	0.00	0.00	3.71
19	20	1.421646	GAGGAGAGGAGAGGAGAGGAG	59.578	61.905	0.00	0.00	0.00	3.69
20	21	1.010793	AGAGGAGAGGAGAGGAGAGGA	59.989	57.143	0.00	0.00	0.00	3.71
21	22	1.421646	GAGAGGAGAGGAGAGGAGAGG	59.578	61.905	0.00	0.00	0.00	3.69
22	23	1.421646	GGAGAGGAGAGGAGAGGAGAG	59.578	61.905	0.00	0.00	0.00	3.20
23	24	1.010793	AGGAGAGGAGAGGAGAGGAGA	59.989	57.143	0.00	0.00	0.00	3.71
24	25	1.421646	GAGGAGAGGAGAGGAGAGGAG	59.578	61.905	0.00	0.00	0.00	3.69
25	26	1.518367	GAGGAGAGGAGAGGAGAGGA	58.482	60.000	0.00	0.00	0.00	3.71
26	27	0.478507	GGAGGAGAGGAGAGGAGAGG	59.521	65.000	0.00	0.00	0.00	3.69
194	196	2.951269	CCGGTTTGGTTTCCCCTAC	58.049	57.895	0.00	0.00	0.00	3.18
509	522	2.627515	TATTTGGAGGCAGCTAGCTG	57.372	50.000	35.54	35.54	46.15	4.24
554	568	5.958955	GCTGAATCTGAACCAGCTTTTATT	58.041	37.500	20.32	0.00	46.96	1.40
555	569	5.573337	GCTGAATCTGAACCAGCTTTTAT	57.427	39.130	20.32	0.00	46.96	1.40
562	576	1.462283	CACGTGCTGAATCTGAACCAG	59.538	52.381	0.82	5.60	0.00	4.00
684	714	6.183360	GGTGGGCCATATCATCAAATTAAACA	60.183	38.462	10.70	0.00	34.09	2.83
1072	1158	2.360801	GCTGCTTTGACACAAGGGTAAA	59.639	45.455	0.00	0.00	0.00	2.01
1586	1673	2.781757	TGGAGCTTCATCCATCCAGAAT	59.218	45.455	0.00	0.00	44.56	2.40
1663	1760	4.830046	AGCATCGTACAAGGAGTCATAGAT	59.170	41.667	0.00	0.00	0.00	1.98
1692	1789	6.150474	CACAGCAGAAATCATATGCATCCATA	59.850	38.462	0.19	0.00	42.45	2.74
1777	1874	4.783227	TGCTTTACACTTCCCTAGGAGAAT	59.217	41.667	11.48	0.54	31.21	2.40
2010	2108	2.906389	ACATCCTGTAAAGCTGAGGTCA	59.094	45.455	0.00	0.00	0.00	4.02
2106	2204	0.111704	CGTTGTTGAGCACGAGAACG	60.112	55.000	16.95	16.95	45.59	3.95
2184	2282	4.376819	GCATGACACAATATAAGCTCGAGC	60.377	45.833	30.01	30.01	42.49	5.03
2228	2326	2.268076	GGGGTGTGCGCAATGAAGT	61.268	57.895	14.00	0.00	0.00	3.01
2381	2480	4.625324	AGTAGTGAACTGACTTGGCAACAA	60.625	41.667	0.00	0.00	46.66	2.83
2497	2600	4.977963	CACACTGAACAACTTAATGGCTTG	59.022	41.667	0.00	0.00	0.00	4.01
2660	2780	7.328005	GTGGTGCTTACTACAGTACTAAAGTTC	59.672	40.741	12.96	5.86	30.58	3.01
2886	3031	1.083806	CGCGAACATAGCAGGCAGAA	61.084	55.000	0.00	0.00	34.19	3.02
3019	3224	6.836577	ACTAGCGCTATTCTTTTGAGAATC	57.163	37.500	19.19	0.00	39.10	2.52
3020	3225	7.982354	AGTAACTAGCGCTATTCTTTTGAGAAT	59.018	33.333	19.19	6.84	41.02	2.40
3021	3226	7.321153	AGTAACTAGCGCTATTCTTTTGAGAA	58.679	34.615	19.19	0.00	0.00	2.87
3036	3253	8.648097	CCACAATTATGCTAATAGTAACTAGCG	58.352	37.037	9.07	0.00	42.89	4.26
3068	3285	6.550854	TCAACTTCAGGTCATTTTGGAATCTT	59.449	34.615	0.00	0.00	0.00	2.40
3175	3504	9.799106	ACTATTGATAGATAAACCCCATCAAAG	57.201	33.333	5.08	0.00	38.65	2.77
3317	3646	9.481340	AAATAAAAGAATTCAGAACCTTTGAGC	57.519	29.630	8.44	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.