AutoCloner

Multiple sequence alignment - TraesCS5A01G054600

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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	TraesCS5A01G054600	chr5A	100.000	2663	0	0	1	2663	51427188	51429850	0.000000e+00	4918.0
1	TraesCS5A01G054600	chr5A	87.719	171	21	0	2493	2663	76724560	76724390	1.620000e-47	200.0
2	TraesCS5A01G054600	chr5D	94.122	2671	148	6	1	2663	61345692	61348361	0.000000e+00	4054.0
3	TraesCS5A01G054600	chr5D	87.594	1588	169	16	329	1890	80317684	80316099	0.000000e+00	1816.0
4	TraesCS5A01G054600	chr5B	91.148	2395	187	11	291	2663	69308471	69306080	0.000000e+00	3225.0
5	TraesCS5A01G054600	chr5B	86.885	2196	235	30	329	2489	88979092	88976915	0.000000e+00	2410.0
6	TraesCS5A01G054600	chr5B	86.207	87	11	1	542	627	70277681	70277767	2.820000e-15	93.5
7	TraesCS5A01G054600	chr4D	86.041	2228	254	21	297	2493	48467925	48465724	0.000000e+00	2338.0
8	TraesCS5A01G054600	chr4D	94.690	113	6	0	2494	2606	48465790	48465678	2.720000e-40	176.0
9	TraesCS5A01G054600	chr4B	86.116	2204	265	22	313	2494	71147230	71145046	0.000000e+00	2337.0
10	TraesCS5A01G054600	chr4A	86.612	1957	223	23	556	2494	549392191	549394126	0.000000e+00	2126.0
11	TraesCS5A01G054600	chr3A	82.582	1975	298	30	542	2494	750537738	750539688	0.000000e+00	1700.0
12	TraesCS5A01G054600	chr3A	79.067	2164	380	46	388	2494	750696829	750698976	0.000000e+00	1419.0
13	TraesCS5A01G054600	chr3A	78.679	2134	379	45	408	2485	750670309	750672422	0.000000e+00	1351.0
14	TraesCS5A01G054600	chr3A	84.795	171	14	7	2488	2657	750550876	750551035	7.630000e-36	161.0
15	TraesCS5A01G054600	chr3D	79.621	2164	364	46	388	2494	614336466	614338609	0.000000e+00	1482.0
16	TraesCS5A01G054600	chr2A	91.319	288	24	1	1	287	513222213	513222500	2.490000e-105	392.0
17	TraesCS5A01G054600	chr2A	87.676	284	31	3	2	283	513161324	513161605	7.110000e-86	327.0
18	TraesCS5A01G054600	chr2A	86.364	88	9	3	542	627	578388244	578388330	2.820000e-15	93.5
19	TraesCS5A01G054600	chr6D	89.789	284	27	2	3	285	77418108	77417826	1.950000e-96	363.0
20	TraesCS5A01G054600	chrUn	88.889	288	31	1	1	287	43399046	43399333	1.170000e-93	353.0
21	TraesCS5A01G054600	chr1D	88.421	285	29	4	5	287	274668389	274668107	9.130000e-90	340.0
22	TraesCS5A01G054600	chr6A	88.112	286	33	1	3	288	178863215	178862931	3.280000e-89	339.0
23	TraesCS5A01G054600	chr2D	87.108	287	36	1	1	287	67144304	67144589	9.190000e-85	324.0
24	TraesCS5A01G054600	chr6B	86.806	288	36	2	1	287	150032067	150031781	1.190000e-83	320.0
25	TraesCS5A01G054600	chr6B	82.178	101	15	3	542	640	605184869	605184770	1.700000e-12	84.2
26	TraesCS5A01G054600	chr3B	78.154	325	59	11	389	704	823713103	823713424	2.090000e-46	196.0
27	TraesCS5A01G054600	chr3B	81.395	129	18	6	410	534	823694363	823694489	1.690000e-17	100.0
28	TraesCS5A01G054600	chr3B	81.395	129	17	7	410	534	823657707	823657832	6.070000e-17	99.0

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	TraesCS5A01G054600	chr5A	51427188	51429850	2662	False	4918	4918	100.0000	1	2663	1	chr5A.!!$F1	2662
1	TraesCS5A01G054600	chr5D	61345692	61348361	2669	False	4054	4054	94.1220	1	2663	1	chr5D.!!$F1	2662
2	TraesCS5A01G054600	chr5D	80316099	80317684	1585	True	1816	1816	87.5940	329	1890	1	chr5D.!!$R1	1561
3	TraesCS5A01G054600	chr5B	69306080	69308471	2391	True	3225	3225	91.1480	291	2663	1	chr5B.!!$R1	2372
4	TraesCS5A01G054600	chr5B	88976915	88979092	2177	True	2410	2410	86.8850	329	2489	1	chr5B.!!$R2	2160
5	TraesCS5A01G054600	chr4D	48465678	48467925	2247	True	1257	2338	90.3655	297	2606	2	chr4D.!!$R1	2309
6	TraesCS5A01G054600	chr4B	71145046	71147230	2184	True	2337	2337	86.1160	313	2494	1	chr4B.!!$R1	2181
7	TraesCS5A01G054600	chr4A	549392191	549394126	1935	False	2126	2126	86.6120	556	2494	1	chr4A.!!$F1	1938
8	TraesCS5A01G054600	chr3A	750537738	750539688	1950	False	1700	1700	82.5820	542	2494	1	chr3A.!!$F1	1952
9	TraesCS5A01G054600	chr3A	750696829	750698976	2147	False	1419	1419	79.0670	388	2494	1	chr3A.!!$F4	2106
10	TraesCS5A01G054600	chr3A	750670309	750672422	2113	False	1351	1351	78.6790	408	2485	1	chr3A.!!$F3	2077
11	TraesCS5A01G054600	chr3D	614336466	614338609	2143	False	1482	1482	79.6210	388	2494	1	chr3D.!!$F1	2106

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
370	371	0.108186	TAGCCCACATGACTCGCAAG	60.108	55.0	0.0	0.0	0.0	4.01	F
1524	1605	0.469494	TGGCCGCTGTGATATGTGAT	59.531	50.0	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1660	1743	0.900182	AGGAGCACATGGACGTCTCA	60.900	55.0	16.46	12.14	0.00	3.27	R
2369	2468	2.433604	CAGTCCTCATCACTATGTGGCT	59.566	50.0	2.34	1.38	43.53	4.75	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
113	114	6.625532	AGAAAAATATTCCCAAGGCAATGT	57.374	33.333	0.00	0.00	0.00	2.71
117	118	8.476064	AAAAATATTCCCAAGGCAATGTTTTT	57.524	26.923	13.80	13.80	37.94	1.94
131	132	8.489489	AGGCAATGTTTTTAGATATCAGAGAGA	58.511	33.333	5.32	0.00	0.00	3.10
184	185	7.319142	CACTTGGGTGAAAATCAAAACAATT	57.681	32.000	0.00	0.00	45.61	2.32
261	262	6.808008	TTGCAATAAACTCCAGAGAAAGAG	57.192	37.500	0.00	0.00	36.16	2.85
281	282	2.104622	AGAAATGGCAAAAACCAGGGTG	59.895	45.455	0.00	0.00	44.71	4.61
287	288	1.412343	GCAAAAACCAGGGTGTCACAT	59.588	47.619	5.12	0.00	0.00	3.21
289	290	1.703411	AAAACCAGGGTGTCACATGG	58.297	50.000	19.74	19.74	38.83	3.66
327	328	2.158295	GGGAGATAGAGTTGGGGAGCTA	60.158	54.545	0.00	0.00	0.00	3.32
345	346	2.416027	GCTAGGGCAAAGCTTTTGCTAC	60.416	50.000	23.53	18.67	46.59	3.58
370	371	0.108186	TAGCCCACATGACTCGCAAG	60.108	55.000	0.00	0.00	0.00	4.01
643	672	6.850263	TTTGGGATTTGGGGAGTATATGTA	57.150	37.500	0.00	0.00	0.00	2.29
795	831	4.702131	GGTGGAAGCAAATCATGACTTACT	59.298	41.667	0.00	0.00	31.29	2.24
965	1044	4.736126	AGCCCCATGTTATTTGTTTAGC	57.264	40.909	0.00	0.00	0.00	3.09
992	1072	1.202651	CCAACCTCGCCGAAATCCTAT	60.203	52.381	0.00	0.00	0.00	2.57
996	1076	0.969894	CTCGCCGAAATCCTATCCCT	59.030	55.000	0.00	0.00	0.00	4.20
1005	1085	2.741159	ATCCTATCCCTACCATGCCA	57.259	50.000	0.00	0.00	0.00	4.92
1006	1086	2.505672	TCCTATCCCTACCATGCCAA	57.494	50.000	0.00	0.00	0.00	4.52
1008	1088	1.270839	CCTATCCCTACCATGCCAACG	60.271	57.143	0.00	0.00	0.00	4.10
1272	1353	2.040884	ATCCCTTCGGGCCAGCTA	60.041	61.111	4.39	0.00	43.94	3.32
1524	1605	0.469494	TGGCCGCTGTGATATGTGAT	59.531	50.000	0.00	0.00	0.00	3.06
1660	1743	3.006217	GGTGTACTACCTCACTCGGTTTT	59.994	47.826	7.10	0.00	46.51	2.43
1680	1763	0.459237	GAGACGTCCATGTGCTCCTG	60.459	60.000	13.01	0.00	0.00	3.86
1690	1773	1.121407	TGTGCTCCTGCTACCACAGT	61.121	55.000	0.00	0.00	40.48	3.55
1738	1822	2.375174	GAGGGCCCCACATCAACATATA	59.625	50.000	21.43	0.00	0.00	0.86
1886	1973	2.955660	CCCCGCCATACAACACAATATT	59.044	45.455	0.00	0.00	0.00	1.28
1977	2064	2.546368	CTGCACGGTTACTTTGCAACTA	59.454	45.455	0.00	0.00	45.31	2.24
2114	2202	3.593442	TGGGAGGAACAATTCAGTGTT	57.407	42.857	0.00	0.00	44.38	3.32
2142	2230	3.766691	GAAGGCGTGCCGGGACTA	61.767	66.667	24.50	0.00	41.95	2.59
2247	2335	1.149174	CATTCCCCTCGTGGATGGG	59.851	63.158	4.76	0.00	42.98	4.00
2254	2342	0.328258	CCTCGTGGATGGGGTTCTTT	59.672	55.000	0.00	0.00	34.57	2.52
2303	2391	7.464830	GCTTGTACTTTCTAAGCGATGAATA	57.535	36.000	0.00	0.00	37.64	1.75
2369	2468	1.163420	ACAAAAGTGATGCGTCGCCA	61.163	50.000	15.88	3.07	35.43	5.69
2436	2535	6.482898	TGCTATACAATCGGTAAAGGGTTA	57.517	37.500	0.00	0.00	35.14	2.85
2509	2608	2.874086	CGTCGGTAAAGGGTTTTGTTCT	59.126	45.455	0.00	0.00	0.00	3.01
2517	2617	7.412129	CGGTAAAGGGTTTTGTTCTTGTTTTTC	60.412	37.037	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.751479	ACACCCATTTTTCTTGCTTCC	57.249	42.857	0.00	0.00	0.00	3.46
9	10	3.248363	GCAACACCCATTTTTCTTGCTTC	59.752	43.478	0.00	0.00	32.92	3.86
131	132	7.993183	TCCTCTCACTCTCAAAAACAACTATTT	59.007	33.333	0.00	0.00	0.00	1.40
137	138	5.104941	TGACTCCTCTCACTCTCAAAAACAA	60.105	40.000	0.00	0.00	0.00	2.83
174	175	7.176589	ACTTAACACTTGGGAATTGTTTTGA	57.823	32.000	0.00	0.00	36.03	2.69
180	181	5.782893	TTGGACTTAACACTTGGGAATTG	57.217	39.130	0.00	0.00	0.00	2.32
184	185	5.055265	TCATTTGGACTTAACACTTGGGA	57.945	39.130	0.00	0.00	0.00	4.37
261	262	2.158827	ACACCCTGGTTTTTGCCATTTC	60.159	45.455	0.00	0.00	37.96	2.17
281	282	0.464036	TCCCTGATACGCCATGTGAC	59.536	55.000	0.00	0.00	0.00	3.67
287	288	1.105167	CGTAGGTCCCTGATACGCCA	61.105	60.000	0.00	0.00	36.28	5.69
327	328	1.615392	CAGTAGCAAAAGCTTTGCCCT	59.385	47.619	21.98	17.22	45.98	5.19
341	342	3.561725	GTCATGTGGGCTATTTCAGTAGC	59.438	47.826	0.00	0.00	44.96	3.58
345	346	2.868583	CGAGTCATGTGGGCTATTTCAG	59.131	50.000	0.00	0.00	0.00	3.02
370	371	1.577328	CGTCACTGTGTGGGCCATTC	61.577	60.000	10.70	6.74	33.87	2.67
371	372	1.600636	CGTCACTGTGTGGGCCATT	60.601	57.895	10.70	0.00	33.87	3.16
643	672	6.597672	TGGTAAGTCGTGATTGCTTGAAATAT	59.402	34.615	0.00	0.00	0.00	1.28
803	839	9.555727	AATTGCGGTAACAACTATATTATCTGT	57.444	29.630	0.00	0.00	31.03	3.41
813	856	5.064558	TCCAGAAAATTGCGGTAACAACTA	58.935	37.500	0.00	0.00	31.03	2.24
965	1044	2.406616	CGGCGAGGTTGGGGAATTG	61.407	63.158	0.00	0.00	0.00	2.32
992	1072	2.675242	CCCGTTGGCATGGTAGGGA	61.675	63.158	7.26	0.00	41.26	4.20
1641	1724	4.217118	TCTCAAAACCGAGTGAGGTAGTAC	59.783	45.833	1.14	0.00	45.21	2.73
1660	1743	0.900182	AGGAGCACATGGACGTCTCA	60.900	55.000	16.46	12.14	0.00	3.27
1680	1763	2.966309	GCGGCAACACTGTGGTAGC	61.966	63.158	13.09	11.57	0.00	3.58
1690	1773	1.847798	ATAGGTTCCCAGCGGCAACA	61.848	55.000	1.45	0.00	0.00	3.33
1738	1822	2.715749	TGCCTATTATGCACTGCAGT	57.284	45.000	15.25	15.25	43.65	4.40
1886	1973	5.128827	AGGTTCTTGACACTAGTGAAAGTCA	59.871	40.000	29.30	18.42	39.06	3.41
1977	2064	1.049289	GGCATCGACCCCCTTCTAGT	61.049	60.000	0.00	0.00	0.00	2.57
2114	2202	1.939381	GCACGCCTTCCGCATATATCA	60.939	52.381	0.00	0.00	41.76	2.15
2142	2230	3.137544	TCCAGTACACACAATCACCCTTT	59.862	43.478	0.00	0.00	0.00	3.11
2282	2370	9.647797	TCTTTTATTCATCGCTTAGAAAGTACA	57.352	29.630	0.00	0.00	0.00	2.90
2303	2391	4.102054	TCGGGTCTGGTAAACTCTTCTTTT	59.898	41.667	0.00	0.00	0.00	2.27
2369	2468	2.433604	CAGTCCTCATCACTATGTGGCT	59.566	50.000	2.34	1.38	43.53	4.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.