AutoCloner

Multiple sequence alignment - TraesCS5D01G176800

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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	TraesCS5D01G176800	chr5D	100.000	3280	0	0	533	3812	276917025	276920304	0.000000e+00	6058.0
1	TraesCS5D01G176800	chr5D	94.144	2015	82	19	902	2902	276924748	276926740	0.000000e+00	3035.0
2	TraesCS5D01G176800	chr5D	100.000	112	0	0	1	112	276916493	276916604	1.390000e-49	207.0
3	TraesCS5D01G176800	chr5D	95.745	47	2	0	601	647	276924620	276924666	4.080000e-10	76.8
4	TraesCS5D01G176800	chr5D	100.000	34	0	0	1855	1888	276918380	276918347	3.180000e-06	63.9
5	TraesCS5D01G176800	chr5D	100.000	34	0	0	1855	1888	276925717	276925684	3.180000e-06	63.9
6	TraesCS5D01G176800	chr5A	90.799	2402	130	38	533	2906	365253108	365255446	0.000000e+00	3127.0
7	TraesCS5D01G176800	chr5A	92.580	1981	81	37	902	2868	365599388	365601316	0.000000e+00	2784.0
8	TraesCS5D01G176800	chr5A	78.889	360	47	18	3247	3584	41454728	41454376	2.310000e-52	217.0
9	TraesCS5D01G176800	chr5B	92.562	1963	86	25	925	2868	314276583	314278504	0.000000e+00	2761.0
10	TraesCS5D01G176800	chr5B	94.435	1707	68	12	2119	3812	314192811	314191119	0.000000e+00	2601.0
11	TraesCS5D01G176800	chr5B	92.018	1591	76	30	544	2123	314194444	314192894	0.000000e+00	2187.0
12	TraesCS5D01G176800	chr5B	76.454	361	39	27	3279	3606	485878388	485878041	1.830000e-33	154.0
13	TraesCS5D01G176800	chr5B	90.991	111	5	2	1	111	314194545	314194440	1.100000e-30	145.0
14	TraesCS5D01G176800	chr5B	95.745	47	2	0	601	647	314276471	314276517	4.080000e-10	76.8
15	TraesCS5D01G176800	chr7D	83.784	333	44	9	2469	2796	400170111	400169784	1.330000e-79	307.0
16	TraesCS5D01G176800	chr7D	77.931	290	37	15	3278	3545	173919731	173920015	5.100000e-34	156.0
17	TraesCS5D01G176800	chr7D	84.028	144	18	4	1324	1463	159736614	159736756	2.390000e-27	134.0
18	TraesCS5D01G176800	chr7A	83.030	330	52	4	2469	2796	457866162	457865835	2.880000e-76	296.0
19	TraesCS5D01G176800	chr7A	78.523	298	31	20	3290	3569	149594025	149594307	8.470000e-37	165.0
20	TraesCS5D01G176800	chr7A	84.028	144	18	4	1324	1463	158395273	158395415	2.390000e-27	134.0
21	TraesCS5D01G176800	chr4D	78.649	370	48	20	3247	3593	133626658	133626297	2.310000e-52	217.0
22	TraesCS5D01G176800	chr1D	77.551	392	67	19	1318	1698	56530535	56530154	2.310000e-52	217.0
23	TraesCS5D01G176800	chr1D	84.874	119	11	5	3283	3394	470935924	470936042	3.110000e-21	113.0
24	TraesCS5D01G176800	chr3D	79.706	340	31	20	3265	3571	89258055	89257721	1.070000e-50	211.0
25	TraesCS5D01G176800	chr3D	82.533	229	19	17	3239	3452	11430838	11430616	8.410000e-42	182.0
26	TraesCS5D01G176800	chr4A	77.364	349	44	22	3247	3567	427505659	427506000	1.410000e-39	174.0
27	TraesCS5D01G176800	chr7B	84.028	144	18	4	1324	1463	120586995	120587137	2.390000e-27	134.0
28	TraesCS5D01G176800	chr6D	96.970	33	1	0	1799	1831	426336790	426336822	5.320000e-04	56.5

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	TraesCS5D01G176800	chr5D	276916493	276920304	3811	False	3132.500000	6058	100.000000	1	3812	2	chr5D.!!$F1	3811
1	TraesCS5D01G176800	chr5D	276924620	276926740	2120	False	1555.900000	3035	94.944500	601	2902	2	chr5D.!!$F2	2301
2	TraesCS5D01G176800	chr5A	365253108	365255446	2338	False	3127.000000	3127	90.799000	533	2906	1	chr5A.!!$F1	2373
3	TraesCS5D01G176800	chr5A	365599388	365601316	1928	False	2784.000000	2784	92.580000	902	2868	1	chr5A.!!$F2	1966
4	TraesCS5D01G176800	chr5B	314191119	314194545	3426	True	1644.333333	2601	92.481333	1	3812	3	chr5B.!!$R2	3811
5	TraesCS5D01G176800	chr5B	314276471	314278504	2033	False	1418.900000	2761	94.153500	601	2868	2	chr5B.!!$F1	2267

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
988	1027	1.011968	TAGCTAAGCACCAACGCACG	61.012	55.0	0.00	0.0	0.00	5.34	F
1218	1259	0.174162	ACGCCTCCAATGTACGTACC	59.826	55.0	22.43	5.8	34.79	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2143	2334	0.810031	CCTTATACGTGCGCAGGCTT	60.810	55.0	28.53	18.42	40.82	4.35	R
3122	3346	0.815734	GCAATGGCAACTCAGATGCT	59.184	50.0	6.89	0.00	43.34	3.79	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
67	68	4.903355	GCGCGCGCCATTTATGCA	62.903	61.111	42.83	0.00	34.56	3.96
68	69	2.277820	CGCGCGCCATTTATGCAA	60.278	55.556	27.72	0.00	0.00	4.08
69	70	1.658102	CGCGCGCCATTTATGCAAT	60.658	52.632	27.72	0.00	0.00	3.56
90	91	1.304381	ATGCACCGGTGAGCCATTT	60.304	52.632	38.30	9.75	34.09	2.32
102	103	4.432712	GTGAGCCATTTTCTCTCTCTCTC	58.567	47.826	0.00	0.00	0.00	3.20
111	112	6.627087	TTTTCTCTCTCTCTCTCTCTCTCT	57.373	41.667	0.00	0.00	0.00	3.10
591	592	7.920160	AAAAGCAACCAAAAAGAATGAGAAA	57.080	28.000	0.00	0.00	0.00	2.52
592	593	7.543947	AAAGCAACCAAAAAGAATGAGAAAG	57.456	32.000	0.00	0.00	0.00	2.62
597	598	7.483307	CAACCAAAAAGAATGAGAAAGAGTCA	58.517	34.615	0.00	0.00	0.00	3.41
705	734	5.804639	TGAATCCCATCCCGTTCTATAATG	58.195	41.667	0.00	0.00	0.00	1.90
706	735	5.309543	TGAATCCCATCCCGTTCTATAATGT	59.690	40.000	0.00	0.00	0.00	2.71
853	882	1.726791	CCAATCTCGGACGAACAACTG	59.273	52.381	0.00	0.00	0.00	3.16
856	885	2.355363	TCGGACGAACAACTGCCG	60.355	61.111	0.00	0.00	43.11	5.69
889	918	1.556911	CACCTTCCATCAGTACTGCCT	59.443	52.381	18.45	5.00	0.00	4.75
897	926	2.113860	TCAGTACTGCCTTTCCATGC	57.886	50.000	18.45	0.00	0.00	4.06
988	1027	1.011968	TAGCTAAGCACCAACGCACG	61.012	55.000	0.00	0.00	0.00	5.34
1215	1256	1.296056	GCAACGCCTCCAATGTACGT	61.296	55.000	0.00	0.00	38.88	3.57
1216	1257	1.999048	CAACGCCTCCAATGTACGTA	58.001	50.000	0.00	0.00	35.64	3.57
1217	1258	1.657094	CAACGCCTCCAATGTACGTAC	59.343	52.381	18.90	18.90	35.64	3.67
1218	1259	0.174162	ACGCCTCCAATGTACGTACC	59.826	55.000	22.43	5.80	34.79	3.34
1260	1305	1.324005	TGGACACATGCCATGCCATG	61.324	55.000	14.80	14.80	46.19	3.66
1261	1306	1.227147	GACACATGCCATGCCATGC	60.227	57.895	16.19	0.42	44.98	4.06
1262	1307	2.108157	CACATGCCATGCCATGCC	59.892	61.111	16.19	0.00	44.98	4.40
1263	1308	2.364448	ACATGCCATGCCATGCCA	60.364	55.556	16.19	0.00	44.98	4.92
1266	1311	1.764454	ATGCCATGCCATGCCATGT	60.764	52.632	14.98	0.00	40.72	3.21
1691	1738	2.928396	CCTCCCTGGTGTTCCGGT	60.928	66.667	0.00	0.00	38.38	5.28
2143	2334	2.429930	CTGCAGAACCGGGTGGAA	59.570	61.111	8.42	0.00	39.21	3.53
2158	2349	2.106683	GGAAAGCCTGCGCACGTAT	61.107	57.895	5.66	0.00	37.52	3.06
2438	2636	6.371825	GCCCCTAGACGAAATATTAAGATTGG	59.628	42.308	0.00	0.00	0.00	3.16
2529	2731	0.249322	CGGGGATGTCGTACATGGTC	60.249	60.000	0.00	0.00	39.27	4.02
2868	3092	6.824196	TGGTTGAACTTGAACTGTGTATGTAA	59.176	34.615	0.00	0.00	0.00	2.41
2927	3151	2.951642	GCATAGCCATTAGACCTTTGCA	59.048	45.455	0.00	0.00	34.88	4.08
2986	3210	3.306156	CCATGCATCATTTTGTCACACCA	60.306	43.478	0.00	0.00	0.00	4.17
3049	3273	4.380843	TGGACACAACATTTACCCTCAT	57.619	40.909	0.00	0.00	0.00	2.90
3050	3274	4.735369	TGGACACAACATTTACCCTCATT	58.265	39.130	0.00	0.00	0.00	2.57
3062	3286	1.179152	CCCTCATTGATTGCAGCACA	58.821	50.000	0.00	0.00	0.00	4.57
3086	3310	2.408704	GTCTCACTCGTTGGAACATTCG	59.591	50.000	0.00	0.00	39.30	3.34
3122	3346	4.390603	GCATCATTAGTCACAACGGTTGTA	59.609	41.667	24.68	10.71	43.23	2.41
3130	3354	2.036604	TCACAACGGTTGTAGCATCTGA	59.963	45.455	24.68	13.79	43.23	3.27
3131	3355	2.413112	CACAACGGTTGTAGCATCTGAG	59.587	50.000	24.68	6.96	43.23	3.35
3136	3360	1.740025	GGTTGTAGCATCTGAGTTGCC	59.260	52.381	11.59	0.00	41.06	4.52
3137	3361	2.426522	GTTGTAGCATCTGAGTTGCCA	58.573	47.619	11.59	1.61	41.06	4.92
3194	3418	0.810031	AGTTGTGCCACTCGTCACAC	60.810	55.000	0.00	0.00	42.21	3.82
3397	3623	8.499162	CAAAACTCATGTACAGTTAGAGAAAGG	58.501	37.037	18.48	6.83	32.71	3.11
3413	3639	7.587037	AGAGAAAGGACAAATTTGAATGTGA	57.413	32.000	24.64	0.00	0.00	3.58
3421	3647	6.867816	GGACAAATTTGAATGTGAATAGTGCA	59.132	34.615	24.64	0.00	0.00	4.57
3441	3667	5.588648	GTGCAAGCTTTGGGTGAATAGTATA	59.411	40.000	0.00	0.00	0.00	1.47
3468	3694	5.989168	TGACACTACACATTCAATTTCGTCT	59.011	36.000	0.00	0.00	0.00	4.18
3469	3695	6.481976	TGACACTACACATTCAATTTCGTCTT	59.518	34.615	0.00	0.00	0.00	3.01
3506	3732	9.330063	CAGTTAATGTAGATTGAATTAGGAGCA	57.670	33.333	0.00	0.00	0.00	4.26
3635	3861	7.400339	ACAGTAGTCTTCCCTCATTAAATCTCA	59.600	37.037	0.00	0.00	0.00	3.27
3666	3892	6.846283	GTGAATTCTACACACACTCTTTTTCG	59.154	38.462	7.05	0.00	38.05	3.46
3669	3895	8.827177	AATTCTACACACACTCTTTTTCGATA	57.173	30.769	0.00	0.00	0.00	2.92
3680	3914	5.124457	ACTCTTTTTCGATAAGTGCATGCAT	59.876	36.000	25.64	11.73	0.00	3.96
3719	3953	9.883142	AGGAAGAATTACTCAGAAACTGATTAG	57.117	33.333	1.92	0.00	28.40	1.73
3782	4018	9.408069	CCCAAAAAGTATCTATATACGTGTCTC	57.592	37.037	0.00	0.00	42.45	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	1.138036	CTCACCGGTGCATGCATTG	59.862	57.895	30.25	18.58	0.00	2.82
67	68	2.703798	GCTCACCGGTGCATGCATT	61.704	57.895	30.25	5.93	33.80	3.56
68	69	3.136123	GCTCACCGGTGCATGCAT	61.136	61.111	30.25	4.32	33.80	3.96
78	79	2.093764	AGAGAGAGAAAATGGCTCACCG	60.094	50.000	0.00	0.00	39.70	4.94
80	81	4.160252	AGAGAGAGAGAGAAAATGGCTCAC	59.840	45.833	0.00	0.00	34.85	3.51
532	533	0.701147	TGGCCAGAGTCTCAGAGAGA	59.299	55.000	0.00	0.00	36.22	3.10
533	534	1.682854	GATGGCCAGAGTCTCAGAGAG	59.317	57.143	13.05	0.00	0.00	3.20
534	535	1.774110	GATGGCCAGAGTCTCAGAGA	58.226	55.000	13.05	0.00	0.00	3.10
535	536	0.385029	CGATGGCCAGAGTCTCAGAG	59.615	60.000	13.05	0.00	0.00	3.35
536	537	1.039785	CCGATGGCCAGAGTCTCAGA	61.040	60.000	13.05	0.00	0.00	3.27
537	538	1.440893	CCGATGGCCAGAGTCTCAG	59.559	63.158	13.05	0.05	0.00	3.35
538	539	2.060383	CCCGATGGCCAGAGTCTCA	61.060	63.158	13.05	0.00	0.00	3.27
539	540	1.617947	AACCCGATGGCCAGAGTCTC	61.618	60.000	13.05	1.67	33.59	3.36
540	541	1.201429	AAACCCGATGGCCAGAGTCT	61.201	55.000	13.05	0.00	33.59	3.24
541	542	0.744771	GAAACCCGATGGCCAGAGTC	60.745	60.000	13.05	2.56	33.59	3.36
542	543	1.299976	GAAACCCGATGGCCAGAGT	59.700	57.895	13.05	2.34	33.59	3.24
543	544	1.026718	GTGAAACCCGATGGCCAGAG	61.027	60.000	13.05	7.50	33.59	3.35
544	545	1.002624	GTGAAACCCGATGGCCAGA	60.003	57.895	13.05	0.00	33.59	3.86
545	546	0.893270	TTGTGAAACCCGATGGCCAG	60.893	55.000	13.05	0.00	34.36	4.85
546	547	0.251564	ATTGTGAAACCCGATGGCCA	60.252	50.000	8.56	8.56	34.36	5.36
547	548	1.757682	TATTGTGAAACCCGATGGCC	58.242	50.000	0.00	0.00	34.36	5.36
717	746	4.760715	CGATAGCTTCTACTGTAGCCCTTA	59.239	45.833	9.98	1.65	37.31	2.69
807	836	3.660111	GGGAAGTGTGGCGTGTGC	61.660	66.667	0.00	0.00	41.71	4.57
827	856	1.878522	CGTCCGAGATTGGAAGCGG	60.879	63.158	0.00	0.00	44.83	5.52
853	882	1.204941	AGGTGATCTGACAGTTACGGC	59.795	52.381	1.59	0.00	0.00	5.68
856	885	4.537135	TGGAAGGTGATCTGACAGTTAC	57.463	45.455	1.59	0.66	0.00	2.50
889	918	1.357420	AGGTGGTGGTATGCATGGAAA	59.643	47.619	10.16	0.00	0.00	3.13
897	926	3.282021	CTCCATGAAAGGTGGTGGTATG	58.718	50.000	0.00	0.00	37.96	2.39
988	1027	2.569404	GGGATCCCATGTCTATCAGGAC	59.431	54.545	26.95	0.00	35.09	3.85
1080	1121	1.808390	GGCGTCCGCGTAGTTGAAT	60.808	57.895	4.92	0.00	43.06	2.57
1113	1154	2.125912	TGCGCCTCGAAGAAGAGC	60.126	61.111	4.18	0.00	43.98	4.09
1215	1256	5.555017	ACTTGTCGTCTGAGTAAGTAGGTA	58.445	41.667	0.00	0.00	33.39	3.08
1216	1257	4.396522	ACTTGTCGTCTGAGTAAGTAGGT	58.603	43.478	0.00	0.00	33.39	3.08
1217	1258	4.142643	GGACTTGTCGTCTGAGTAAGTAGG	60.143	50.000	0.00	0.00	42.44	3.18
1218	1259	4.696402	AGGACTTGTCGTCTGAGTAAGTAG	59.304	45.833	0.00	0.00	42.44	2.57
1263	1308	3.258228	TCGTTAACGACATGCATGACAT	58.742	40.909	32.75	19.21	44.22	3.06
1266	1311	3.179048	CTCTCGTTAACGACATGCATGA	58.821	45.455	32.75	17.82	44.22	3.07
1577	1624	2.509336	CGTGTCCATGTCCTCCGC	60.509	66.667	0.00	0.00	0.00	5.54
2026	2130	1.301087	CGTGTGCCCGTTGGAGTTA	60.301	57.895	0.00	0.00	0.00	2.24
2143	2334	0.810031	CCTTATACGTGCGCAGGCTT	60.810	55.000	28.53	18.42	40.82	4.35
2455	2653	1.226660	GCGCCAAAATGACCGATGG	60.227	57.895	0.00	0.00	36.00	3.51
2709	2911	4.287781	TTGTCGCGGCTGTCGGAA	62.288	61.111	13.81	0.00	39.69	4.30
2927	3151	4.746089	GCTCAGTCCAGCATAAATCTCCAT	60.746	45.833	0.00	0.00	39.43	3.41
2986	3210	5.536161	ACCAGTAGAAAGAAATGTTGCACAT	59.464	36.000	0.00	0.00	41.31	3.21
2997	3221	3.207265	TGCTGCAACCAGTAGAAAGAA	57.793	42.857	0.00	0.00	41.26	2.52
3049	3273	1.733912	GAGACGATGTGCTGCAATCAA	59.266	47.619	2.77	0.00	0.00	2.57
3050	3274	1.338011	TGAGACGATGTGCTGCAATCA	60.338	47.619	2.77	0.00	0.00	2.57
3062	3286	1.611977	TGTTCCAACGAGTGAGACGAT	59.388	47.619	0.00	0.00	34.70	3.73
3122	3346	0.815734	GCAATGGCAACTCAGATGCT	59.184	50.000	6.89	0.00	43.34	3.79
3194	3418	3.585862	AGTTACATCTGCGTAGTTGTGG	58.414	45.455	22.58	3.52	37.41	4.17
3397	3623	7.872163	TGCACTATTCACATTCAAATTTGTC	57.128	32.000	17.47	0.00	0.00	3.18
3413	3639	2.875296	TCACCCAAAGCTTGCACTATT	58.125	42.857	0.00	0.00	0.00	1.73
3421	3647	8.903820	GTCAAATATACTATTCACCCAAAGCTT	58.096	33.333	0.00	0.00	0.00	3.74
3441	3667	7.648142	ACGAAATTGAATGTGTAGTGTCAAAT	58.352	30.769	0.00	0.00	33.93	2.32
3481	3707	9.553064	CTGCTCCTAATTCAATCTACATTAACT	57.447	33.333	0.00	0.00	0.00	2.24
3482	3708	9.547753	TCTGCTCCTAATTCAATCTACATTAAC	57.452	33.333	0.00	0.00	0.00	2.01
3635	3861	4.278669	AGTGTGTGTAGAATTCACTCGACT	59.721	41.667	8.44	7.97	34.87	4.18
3666	3892	5.936372	TGAAGATCCTATGCATGCACTTATC	59.064	40.000	25.37	21.30	0.00	1.75
3669	3895	4.160642	TGAAGATCCTATGCATGCACTT	57.839	40.909	25.37	19.95	0.00	3.16
3706	3940	8.954950	AGGACATCATTACTAATCAGTTTCTG	57.045	34.615	0.00	0.00	36.14	3.02
3772	4008	6.923508	CACAATATACACCATGAGACACGTAT	59.076	38.462	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.