AutoCloner

Multiple sequence alignment - TraesCS4A01G166800

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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	TraesCS4A01G166800	chr4A	100.000	2833	0	0	1	2833	407612328	407609496	0.000000e+00	5232.0
1	TraesCS4A01G166800	chr4A	95.736	1454	59	3	3	1455	712218408	712219859	0.000000e+00	2338.0
2	TraesCS4A01G166800	chr2A	95.597	2385	92	2	3	2386	114324756	114322384	0.000000e+00	3810.0
3	TraesCS4A01G166800	chr2A	92.945	1630	92	6	757	2386	203540849	203539243	0.000000e+00	2351.0
4	TraesCS4A01G166800	chr2A	97.083	480	14	0	2354	2833	114322346	114321867	0.000000e+00	809.0
5	TraesCS4A01G166800	chr2A	94.008	484	21	4	2357	2833	203539198	203538716	0.000000e+00	726.0
6	TraesCS4A01G166800	chr2A	91.383	499	37	3	264	756	203541603	203541105	0.000000e+00	678.0
7	TraesCS4A01G166800	chr2A	93.284	268	16	2	3	269	203566295	203566029	7.360000e-106	394.0
8	TraesCS4A01G166800	chr2A	93.233	266	16	2	5	269	203543431	203543167	9.520000e-105	390.0
9	TraesCS4A01G166800	chr2A	84.478	335	37	8	1490	1817	1602227	1602553	1.640000e-82	316.0
10	TraesCS4A01G166800	chr2A	95.000	60	3	0	2504	2563	1603236	1603295	8.360000e-16	95.3
11	TraesCS4A01G166800	chr7B	96.011	1454	56	2	3	1455	682905156	682906608	0.000000e+00	2362.0
12	TraesCS4A01G166800	chr6A	84.995	993	133	10	523	1503	531462564	531461576	0.000000e+00	994.0
13	TraesCS4A01G166800	chr6A	84.074	923	114	19	1321	2230	531461572	531460670	0.000000e+00	859.0
14	TraesCS4A01G166800	chr6A	84.667	750	80	13	1491	2228	557927421	557926695	0.000000e+00	715.0
15	TraesCS4A01G166800	chr6A	91.489	517	40	4	4	519	22162552	22162039	0.000000e+00	708.0
16	TraesCS4A01G166800	chr6A	85.366	492	68	3	1019	1506	557928906	557928415	9.060000e-140	507.0
17	TraesCS4A01G166800	chr6A	84.962	399	43	10	2399	2786	531460605	531460213	3.420000e-104	388.0
18	TraesCS4A01G166800	chr6A	92.391	184	8	2	2656	2833	442023274	442023091	1.010000e-64	257.0
19	TraesCS4A01G166800	chr6A	86.070	201	21	6	2400	2596	557926627	557926430	2.860000e-50	209.0
20	TraesCS4A01G166800	chr6B	84.515	1001	123	22	529	1503	114458320	114457326	0.000000e+00	961.0
21	TraesCS4A01G166800	chr6B	83.710	620	77	11	1493	2102	80785819	80785214	5.300000e-157	564.0
22	TraesCS4A01G166800	chr6B	84.925	398	44	10	2400	2786	114456332	114455940	3.420000e-104	388.0
23	TraesCS4A01G166800	chr6B	95.000	60	3	0	2504	2563	80784586	80784527	8.360000e-16	95.3
24	TraesCS4A01G166800	chr3B	91.120	518	41	5	4	519	387428278	387428792	0.000000e+00	697.0
25	TraesCS4A01G166800	chr3B	82.626	495	76	8	608	1097	536277539	536277050	2.020000e-116	429.0
26	TraesCS4A01G166800	chr3B	81.466	491	80	6	2351	2832	799988687	799989175	2.650000e-105	392.0
27	TraesCS4A01G166800	chr1A	90.909	517	43	4	4	519	8010190	8009677	0.000000e+00	691.0
28	TraesCS4A01G166800	chr7A	90.366	519	48	2	1	519	675042112	675042628	0.000000e+00	680.0
29	TraesCS4A01G166800	chr4B	82.979	470	68	10	2351	2809	662532336	662532804	5.650000e-112	414.0
30	TraesCS4A01G166800	chr3D	92.771	166	5	5	2654	2812	22075472	22075637	1.700000e-57	233.0
31	TraesCS4A01G166800	chr3D	81.275	251	39	3	2539	2783	24867379	24867627	2.230000e-46	196.0
32	TraesCS4A01G166800	chr7D	92.169	166	6	5	2654	2812	138341536	138341371	7.900000e-56	228.0
33	TraesCS4A01G166800	chr1D	92.169	166	6	2	2654	2812	332606932	332607097	7.900000e-56	228.0
34	TraesCS4A01G166800	chr2D	91.566	166	7	2	2654	2812	33882858	33882693	3.670000e-54	222.0
35	TraesCS4A01G166800	chr1B	86.772	189	23	2	1295	1481	400774742	400774554	2.860000e-50	209.0

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	TraesCS4A01G166800	chr4A	407609496	407612328	2832	True	5232.00	5232	100.000000	1	2833	1	chr4A.!!$R1	2832
1	TraesCS4A01G166800	chr4A	712218408	712219859	1451	False	2338.00	2338	95.736000	3	1455	1	chr4A.!!$F1	1452
2	TraesCS4A01G166800	chr2A	114321867	114324756	2889	True	2309.50	3810	96.340000	3	2833	2	chr2A.!!$R2	2830
3	TraesCS4A01G166800	chr2A	203538716	203543431	4715	True	1036.25	2351	92.892250	5	2833	4	chr2A.!!$R3	2828
4	TraesCS4A01G166800	chr2A	1602227	1603295	1068	False	205.65	316	89.739000	1490	2563	2	chr2A.!!$F1	1073
5	TraesCS4A01G166800	chr7B	682905156	682906608	1452	False	2362.00	2362	96.011000	3	1455	1	chr7B.!!$F1	1452
6	TraesCS4A01G166800	chr6A	531460213	531462564	2351	True	747.00	994	84.677000	523	2786	3	chr6A.!!$R3	2263
7	TraesCS4A01G166800	chr6A	22162039	22162552	513	True	708.00	708	91.489000	4	519	1	chr6A.!!$R1	515
8	TraesCS4A01G166800	chr6A	557926430	557928906	2476	True	477.00	715	85.367667	1019	2596	3	chr6A.!!$R4	1577
9	TraesCS4A01G166800	chr6B	114455940	114458320	2380	True	674.50	961	84.720000	529	2786	2	chr6B.!!$R2	2257
10	TraesCS4A01G166800	chr6B	80784527	80785819	1292	True	329.65	564	89.355000	1493	2563	2	chr6B.!!$R1	1070
11	TraesCS4A01G166800	chr3B	387428278	387428792	514	False	697.00	697	91.120000	4	519	1	chr3B.!!$F1	515
12	TraesCS4A01G166800	chr1A	8009677	8010190	513	True	691.00	691	90.909000	4	519	1	chr1A.!!$R1	515
13	TraesCS4A01G166800	chr7A	675042112	675042628	516	False	680.00	680	90.366000	1	519	1	chr7A.!!$F1	518

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
937	2779	1.415659	CCAGTTTTGGCAATGTTGGGA	59.584	47.619	0.0	0.0	37.73	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1837	4738	0.034059	AGCCGACACCTCTTTGTCAG	59.966	55.0	4.28	0.0	45.38	3.51	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
107	108	3.771216	AGTGAAGGAGGTGAATGCATTT	58.229	40.909	14.33	0.00	0.00	2.32
122	123	4.274602	TGCATTTTTCACCATGAAGCAT	57.725	36.364	0.00	0.00	37.70	3.79
219	222	5.235186	CGGCCAGTCTGAACTTATTTATGAG	59.765	44.000	2.24	0.00	31.71	2.90
379	1951	2.566833	TGTCAGGTTGTTGATGGAGG	57.433	50.000	0.00	0.00	0.00	4.30
463	2035	5.187772	AGAGGTACTGATGTTATGCAGACAA	59.812	40.000	9.43	0.00	41.55	3.18
500	2072	3.589735	TGATACCTTAGGTTTGAAGGCCA	59.410	43.478	10.01	0.00	46.41	5.36
601	2173	4.414337	AAGCATTGCAGGTTTGGTAAAA	57.586	36.364	11.91	0.00	0.00	1.52
602	2174	4.414337	AGCATTGCAGGTTTGGTAAAAA	57.586	36.364	11.91	0.00	0.00	1.94
692	2270	4.949856	GGTGGTCACATTCATTAGATGGTT	59.050	41.667	3.40	0.00	0.00	3.67
693	2271	5.066505	GGTGGTCACATTCATTAGATGGTTC	59.933	44.000	3.40	0.00	0.00	3.62
717	2300	7.130099	TCCTTTCTATAGTTCATGGTGTCCTA	58.870	38.462	0.00	0.00	0.00	2.94
802	2640	3.441572	CCATCACCCTTCAGCTTTGTTAG	59.558	47.826	0.00	0.00	0.00	2.34
937	2779	1.415659	CCAGTTTTGGCAATGTTGGGA	59.584	47.619	0.00	0.00	37.73	4.37
1021	2863	2.422597	TGGAGTGCAACAAGTATTCCG	58.577	47.619	0.00	0.00	40.83	4.30
1049	2893	5.336213	GCAACATTTATATGCAGCATAGCCT	60.336	40.000	19.83	6.73	39.81	4.58
1101	2945	7.645002	ACCACATAAAGGGCCTAAATAGTAAA	58.355	34.615	6.41	0.00	0.00	2.01
1102	2946	8.286620	ACCACATAAAGGGCCTAAATAGTAAAT	58.713	33.333	6.41	0.00	0.00	1.40
1138	2990	3.350912	CCAAACAAGCATACGTAATCGC	58.649	45.455	0.00	2.95	41.18	4.58
1157	3009	3.382227	TCGCGTTCCATAGGAGTATTTCA	59.618	43.478	5.77	0.00	31.21	2.69
1182	3035	2.226437	AGCAACAGTTCCGTGCAATTAG	59.774	45.455	0.00	0.00	0.00	1.73
1190	3043	6.377146	ACAGTTCCGTGCAATTAGGAAAATAT	59.623	34.615	13.50	1.88	44.56	1.28
1194	3047	6.353323	TCCGTGCAATTAGGAAAATATCAGA	58.647	36.000	0.00	0.00	0.00	3.27
1289	3156	1.806542	GTTGCGCAATCGGGATATGAT	59.193	47.619	27.79	0.00	35.95	2.45
1290	3157	1.725641	TGCGCAATCGGGATATGATC	58.274	50.000	8.16	0.00	35.95	2.92
1291	3158	1.001860	TGCGCAATCGGGATATGATCA	59.998	47.619	8.16	0.00	35.95	2.92
1292	3159	2.283298	GCGCAATCGGGATATGATCAT	58.717	47.619	13.81	13.81	35.95	2.45
1293	3160	2.031314	GCGCAATCGGGATATGATCATG	59.969	50.000	18.72	0.89	35.95	3.07
1294	3161	3.264947	CGCAATCGGGATATGATCATGT	58.735	45.455	18.72	11.93	0.00	3.21
1295	3162	3.308053	CGCAATCGGGATATGATCATGTC	59.692	47.826	20.86	20.86	0.00	3.06
1296	3163	4.256110	GCAATCGGGATATGATCATGTCA	58.744	43.478	27.43	12.57	42.06	3.58
1297	3164	4.696877	GCAATCGGGATATGATCATGTCAA	59.303	41.667	27.43	15.89	40.97	3.18
1298	3165	5.181811	GCAATCGGGATATGATCATGTCAAA	59.818	40.000	27.43	15.60	40.97	2.69
1299	3166	6.294120	GCAATCGGGATATGATCATGTCAAAA	60.294	38.462	27.43	15.31	40.97	2.44
1300	3167	7.650890	CAATCGGGATATGATCATGTCAAAAA	58.349	34.615	27.43	13.88	40.97	1.94
1653	4546	8.978874	AAAAAGGAAGGTTAGATTTTGCAATT	57.021	26.923	0.00	0.00	0.00	2.32
1659	4554	5.640732	AGGTTAGATTTTGCAATTGTAGCG	58.359	37.500	7.40	0.00	33.85	4.26
1781	4676	3.539604	GCAGTGGACTAAAGATGAGCAT	58.460	45.455	0.00	0.00	0.00	3.79
1820	4721	3.119101	TGCTTAGAAAGGATGTCTCGGAC	60.119	47.826	0.00	0.00	32.53	4.79
1837	4738	2.416547	CGGACAGTGTTGAATGATGGAC	59.583	50.000	0.00	0.00	0.00	4.02
1931	4833	0.238289	GTGGTGGCGTTCAAGACATG	59.762	55.000	0.00	0.00	0.00	3.21
2060	4971	6.348213	CCGTCGAAAACCAAAGTATGATCTTT	60.348	38.462	0.00	0.00	38.04	2.52
2104	5016	6.989169	ACTACTATCTCATGACCTTGATTTGC	59.011	38.462	0.00	0.00	0.00	3.68
2114	5026	6.176975	TGACCTTGATTTGCGTTATAACAG	57.823	37.500	15.67	9.24	0.00	3.16
2118	5039	4.253352	TGATTTGCGTTATAACAGCGTC	57.747	40.909	15.67	15.91	32.76	5.19
2197	5118	6.097981	TGCATATCATCTTTAAATTGCCACCA	59.902	34.615	0.00	0.00	0.00	4.17
2213	5134	7.716799	TTGCCACCATTATTGTCTTTATCTT	57.283	32.000	0.00	0.00	0.00	2.40
2260	5182	5.785243	AGAAAGTGAGCTAAGTACTTCCAC	58.215	41.667	12.39	14.92	33.82	4.02
2301	5223	9.709495	CTTTAACCATTTCCATTCATGAGAAAA	57.291	29.630	11.35	5.01	37.29	2.29
2387	5384	6.884295	TCCAACTTGGAATTTAGTACCATGAG	59.116	38.462	8.15	0.00	45.00	2.90
2441	5462	0.389757	GAGTTGGAGGTAGATCCGGC	59.610	60.000	0.00	0.00	42.77	6.13
2815	6070	8.212312	TGGAGTTGGTTTGTTTAGTTATGACTA	58.788	33.333	0.00	0.00	37.33	2.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	5.357878	GGACTGATTATGCTTCATGGTGAAA	59.642	40.000	0.00	0.00	35.73	2.69
219	222	2.736192	GCTCAGAGTTCAGAAACTGCTC	59.264	50.000	11.60	3.02	45.80	4.26
274	1846	4.411013	CCTGGGAGATTCAAAAGGAGTTT	58.589	43.478	0.00	0.00	0.00	2.66
379	1951	9.965824	AATAACATCGATTACCAATTTGAATCC	57.034	29.630	0.00	0.00	0.00	3.01
435	2007	6.040955	TCTGCATAACATCAGTACCTCTTAGG	59.959	42.308	0.00	0.00	42.49	2.69
463	2035	3.117512	AGGTATCAAATGGGCGGAATCTT	60.118	43.478	0.00	0.00	0.00	2.40
601	2173	8.526147	CAGAAACATCATCAAGGTAGGAAATTT	58.474	33.333	0.00	0.00	0.00	1.82
602	2174	7.671398	ACAGAAACATCATCAAGGTAGGAAATT	59.329	33.333	0.00	0.00	0.00	1.82
603	2175	7.177878	ACAGAAACATCATCAAGGTAGGAAAT	58.822	34.615	0.00	0.00	0.00	2.17
692	2270	5.964477	AGGACACCATGAACTATAGAAAGGA	59.036	40.000	6.78	0.00	0.00	3.36
693	2271	6.240549	AGGACACCATGAACTATAGAAAGG	57.759	41.667	6.78	3.64	0.00	3.11
717	2300	7.090173	CCCGAAAAATATGAACTCACAAACAT	58.910	34.615	0.00	0.00	0.00	2.71
802	2640	7.543520	AGTTACGTACATGCTAAACTCCTTAAC	59.456	37.037	0.00	0.00	0.00	2.01
919	2761	3.454082	TCTTTCCCAACATTGCCAAAACT	59.546	39.130	0.00	0.00	0.00	2.66
937	2779	2.246719	AGACTGCTTGCGAACTCTTT	57.753	45.000	0.00	0.00	0.00	2.52
1021	2863	4.935702	TGCTGCATATAAATGTTGCCTTC	58.064	39.130	0.00	0.00	35.51	3.46
1049	2893	1.212688	CAATGCTACCCCAGACATCCA	59.787	52.381	0.00	0.00	0.00	3.41
1138	2990	7.441157	TGCTAATTGAAATACTCCTATGGAACG	59.559	37.037	0.00	0.00	0.00	3.95
1157	3009	2.226330	TGCACGGAACTGTTGCTAATT	58.774	42.857	10.33	0.00	0.00	1.40
1225	3080	7.338957	TGACATGATTACCTCAATTGCACATAA	59.661	33.333	0.00	0.00	37.44	1.90
1227	3082	5.653330	TGACATGATTACCTCAATTGCACAT	59.347	36.000	0.00	0.00	37.44	3.21
1418	3473	7.373617	TCCTATTCATTCCATGTTACTGCTA	57.626	36.000	0.00	0.00	0.00	3.49
1653	4546	4.083057	TGAAAAATATGCTTGCACGCTACA	60.083	37.500	16.80	1.73	0.00	2.74
1781	4676	5.900699	TCTAAGCATGGTGTATACAACCCTA	59.099	40.000	18.18	0.00	31.06	3.53
1820	4721	4.067192	TGTCAGTCCATCATTCAACACTG	58.933	43.478	0.00	0.00	33.90	3.66
1837	4738	0.034059	AGCCGACACCTCTTTGTCAG	59.966	55.000	4.28	0.00	45.38	3.51
1931	4833	7.543520	CCATAAATCTTTGGTTTCTTGCTCTTC	59.456	37.037	0.00	0.00	0.00	2.87
2104	5016	8.048436	CACTTACAAATAGACGCTGTTATAACG	58.952	37.037	10.92	7.03	0.00	3.18
2213	5134	2.568062	TCTTTACCAACAGGCCATCGTA	59.432	45.455	5.01	0.00	0.00	3.43
2387	5384	4.931002	TCAATATAAGCCGGCCGTTAATAC	59.069	41.667	26.15	5.90	0.00	1.89
2569	5818	2.363680	TCATGTGTTGCCACGGAAAAAT	59.636	40.909	0.00	0.00	44.92	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.