AutoCloner

Multiple sequence alignment - TraesCS2A01G533300

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	TraesCS2A01G533300	chr2A	100.000	2456	0	0	1	2456	749102629	749105084	0.000000e+00	4536.0
1	TraesCS2A01G533300	chr2A	82.609	1265	208	10	727	1982	4292548	4293809	0.000000e+00	1107.0
2	TraesCS2A01G533300	chr2D	96.156	2081	64	11	381	2456	618286995	618289064	0.000000e+00	3386.0
3	TraesCS2A01G533300	chr2D	82.560	1250	207	10	727	1969	5748847	5747602	0.000000e+00	1090.0
4	TraesCS2A01G533300	chr2D	92.112	393	17	4	1	379	618286567	618286959	2.150000e-150	542.0
5	TraesCS2A01G533300	chr2D	97.143	35	1	0	345	379	608770145	608770111	2.640000e-05	60.2
6	TraesCS2A01G533300	chr2B	95.264	1499	54	10	653	2139	754927340	754928833	0.000000e+00	2359.0
7	TraesCS2A01G533300	chr2B	81.594	1255	210	17	727	1969	5629618	5628373	0.000000e+00	1018.0
8	TraesCS2A01G533300	chr2B	86.709	158	16	3	2146	2303	754931259	754931411	1.170000e-38	171.0
9	TraesCS2A01G533300	chr2B	93.204	103	6	1	2353	2454	754931424	754931526	1.520000e-32	150.0
10	TraesCS2A01G533300	chr5B	81.361	338	32	14	1	331	18065630	18065943	1.890000e-61	246.0
11	TraesCS2A01G533300	chr5B	87.850	107	11	1	395	499	18070370	18070476	9.220000e-25	124.0
12	TraesCS2A01G533300	chr3A	86.538	156	18	3	185	339	549909424	549909577	4.200000e-38	169.0
13	TraesCS2A01G533300	chr3A	91.453	117	9	1	1	116	549909299	549909415	2.530000e-35	159.0
14	TraesCS2A01G533300	chr6B	78.417	278	24	11	388	651	162550692	162550437	5.470000e-32	148.0
15	TraesCS2A01G533300	chr6B	88.430	121	13	1	1	120	162563086	162562966	7.080000e-31	145.0
16	TraesCS2A01G533300	chr1D	84.932	73	11	0	119	191	104527853	104527925	9.420000e-10	75.0
17	TraesCS2A01G533300	chr3B	100.000	35	0	0	345	379	783006609	783006575	5.670000e-07	65.8
18	TraesCS2A01G533300	chr5A	100.000	33	0	0	346	378	597741367	597741399	7.330000e-06	62.1
19	TraesCS2A01G533300	chr5A	97.222	36	1	0	345	380	650556797	650556762	7.330000e-06	62.1
20	TraesCS2A01G533300	chr4B	97.143	35	1	0	345	379	167362919	167362953	2.640000e-05	60.2
21	TraesCS2A01G533300	chr3D	96.875	32	1	0	179	210	313284757	313284726	1.000000e-03	54.7
22	TraesCS2A01G533300	chr7D	100.000	28	0	0	41	68	496775939	496775912	4.000000e-03	52.8

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	TraesCS2A01G533300	chr2A	749102629	749105084	2455	False	4536.000000	4536	100.000000	1	2456	1	chr2A.!!$F2	2455
1	TraesCS2A01G533300	chr2A	4292548	4293809	1261	False	1107.000000	1107	82.609000	727	1982	1	chr2A.!!$F1	1255
2	TraesCS2A01G533300	chr2D	618286567	618289064	2497	False	1964.000000	3386	94.134000	1	2456	2	chr2D.!!$F1	2455
3	TraesCS2A01G533300	chr2D	5747602	5748847	1245	True	1090.000000	1090	82.560000	727	1969	1	chr2D.!!$R1	1242
4	TraesCS2A01G533300	chr2B	5628373	5629618	1245	True	1018.000000	1018	81.594000	727	1969	1	chr2B.!!$R1	1242
5	TraesCS2A01G533300	chr2B	754927340	754931526	4186	False	893.333333	2359	91.725667	653	2454	3	chr2B.!!$F1	1801

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
339	354	1.321474	CACTGGGCAATGGCGATAAT	58.679	50.0	0.0	0.0	42.47	1.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2142	2215	0.606944	AAATTTGAGGTGCCGCCGTA	60.607	50.0	0.0	0.0	43.7	4.02	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
122	123	7.041098	GCATTATTAGCTAATATTCCCCCATCG	60.041	40.741	23.50	9.31	0.00	3.84
226	227	9.075678	GGAGTAATAGGTACATAGCTTAGACAA	57.924	37.037	0.00	0.00	34.88	3.18
277	292	4.295051	CAACCCGTACACATTTGAAAAGG	58.705	43.478	0.00	0.00	0.00	3.11
301	316	1.695242	TCTTTAACCTTCCAGCGTCCA	59.305	47.619	0.00	0.00	0.00	4.02
316	331	2.804647	CGTCCACACGTATGCATAGAA	58.195	47.619	6.67	0.00	41.42	2.10
334	349	1.526575	AAAGACACTGGGCAATGGCG	61.527	55.000	0.00	0.00	42.47	5.69
335	350	2.359850	GACACTGGGCAATGGCGA	60.360	61.111	0.00	0.00	42.47	5.54
339	354	1.321474	CACTGGGCAATGGCGATAAT	58.679	50.000	0.00	0.00	42.47	1.28
353	368	5.790593	TGGCGATAATGTAATACTCCCTTC	58.209	41.667	0.00	0.00	0.00	3.46
356	371	5.924825	GCGATAATGTAATACTCCCTTCGTT	59.075	40.000	0.00	0.00	0.00	3.85
357	372	6.423001	GCGATAATGTAATACTCCCTTCGTTT	59.577	38.462	0.00	0.00	0.00	3.60
372	387	6.866770	TCCCTTCGTTTCATAATATAAGAGCG	59.133	38.462	0.00	0.00	0.00	5.03
405	454	8.848182	CGGGACAGATAGAGTAATAAAGTAACT	58.152	37.037	0.00	0.00	0.00	2.24
442	491	6.480651	ACTGTGATTACAAACATAACACGTGA	59.519	34.615	25.01	0.00	36.14	4.35
453	502	4.873827	ACATAACACGTGATGAACCATACC	59.126	41.667	25.01	0.00	0.00	2.73
498	547	2.017049	GCGAGCAGATAAACCCAATGT	58.983	47.619	0.00	0.00	0.00	2.71
499	548	2.223340	GCGAGCAGATAAACCCAATGTG	60.223	50.000	0.00	0.00	0.00	3.21
500	549	3.009723	CGAGCAGATAAACCCAATGTGT	58.990	45.455	0.00	0.00	0.00	3.72
581	630	9.528018	CAAATCAACTTAAACAGGCTAAGAAAA	57.472	29.630	1.89	0.00	31.91	2.29
582	631	9.529325	AAATCAACTTAAACAGGCTAAGAAAAC	57.471	29.630	1.89	0.00	31.91	2.43
621	670	2.802719	ACACACTGACCCAAGTTTTGT	58.197	42.857	0.00	0.00	0.00	2.83
687	739	2.162681	CACAATTCCAGGACCCAAGTC	58.837	52.381	0.00	0.00	42.73	3.01
702	754	3.307975	CCCAAGTCACATGAGGAACATCT	60.308	47.826	0.00	0.00	37.07	2.90
821	877	2.596851	GCTGGCAGAGGTCCTTGGA	61.597	63.158	20.86	0.00	0.00	3.53
981	1037	1.582968	CCACTGTGGCACATTGCTC	59.417	57.895	27.00	0.00	44.52	4.26
1437	1493	2.098233	CACGCGCTTCCCGTTGTAT	61.098	57.895	5.73	0.00	36.69	2.29
1743	1799	2.783288	CGGGTAGCTCTCCGGGAAC	61.783	68.421	17.01	0.00	42.32	3.62
2041	2109	1.821136	AGTGAGCTTAATTTGCTGGGC	59.179	47.619	9.85	1.89	41.30	5.36
2071	2139	2.124277	AGCTTGCTGAATGCTGATGA	57.876	45.000	0.00	0.00	43.37	2.92
2072	2140	2.443416	AGCTTGCTGAATGCTGATGAA	58.557	42.857	0.00	0.00	43.37	2.57
2073	2141	2.163815	AGCTTGCTGAATGCTGATGAAC	59.836	45.455	0.00	0.00	43.37	3.18
2074	2142	2.094906	GCTTGCTGAATGCTGATGAACA	60.095	45.455	0.00	0.00	43.37	3.18
2075	2143	3.613193	GCTTGCTGAATGCTGATGAACAA	60.613	43.478	0.00	0.00	43.37	2.83
2076	2144	3.842732	TGCTGAATGCTGATGAACAAG	57.157	42.857	0.00	0.00	43.37	3.16
2078	2146	4.325972	TGCTGAATGCTGATGAACAAGTA	58.674	39.130	0.00	0.00	43.37	2.24
2079	2147	4.154737	TGCTGAATGCTGATGAACAAGTAC	59.845	41.667	0.00	0.00	43.37	2.73
2081	2149	5.582269	GCTGAATGCTGATGAACAAGTACTA	59.418	40.000	0.00	0.00	38.95	1.82
2142	2215	1.471676	GGTGGAGAGATGCGATTCGTT	60.472	52.381	8.03	0.00	0.00	3.85
2170	4662	5.389411	GCGGCACCTCAAATTTAAAATGTTC	60.389	40.000	0.00	0.00	0.00	3.18
2196	4689	7.333921	CCCAAAAGCACAAATCTTAATGCATAA	59.666	33.333	0.00	0.00	40.63	1.90
2317	4810	7.331193	GTGAAGAAAGCTTAAGGATCTAAACGA	59.669	37.037	0.00	0.00	33.61	3.85
2392	4885	5.013568	TGCATGATAATGGCTTTTTCCAG	57.986	39.130	0.00	0.00	39.89	3.86
2403	4896	4.953579	TGGCTTTTTCCAGTTTCTAACAGT	59.046	37.500	0.00	0.00	0.00	3.55
2411	4904	5.492895	TCCAGTTTCTAACAGTGTGTCAAA	58.507	37.500	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	92	7.068593	GGGGAATATTAGCTAATAATGCATGCA	59.931	37.037	25.90	25.04	35.63	3.96
179	180	7.787028	ACTCCCTCAGTCTCAAAATAAGTATC	58.213	38.462	0.00	0.00	0.00	2.24
196	197	6.215515	AGCTATGTACCTATTACTCCCTCA	57.784	41.667	0.00	0.00	0.00	3.86
226	227	6.613153	AGCCTTCTAATACTTGTGAGTTCT	57.387	37.500	0.00	0.00	37.33	3.01
258	259	2.556622	AGCCTTTTCAAATGTGTACGGG	59.443	45.455	0.00	0.00	0.00	5.28
277	292	3.532542	ACGCTGGAAGGTTAAAGATAGC	58.467	45.455	0.00	0.00	0.00	2.97
301	316	4.864806	CAGTGTCTTTCTATGCATACGTGT	59.135	41.667	1.16	0.00	0.00	4.49
316	331	1.973281	CGCCATTGCCCAGTGTCTT	60.973	57.895	0.00	0.00	0.00	3.01
334	349	8.882415	TGAAACGAAGGGAGTATTACATTATC	57.118	34.615	0.00	0.00	0.00	1.75
379	394	8.848182	AGTTACTTTATTACTCTATCTGTCCCG	58.152	37.037	0.00	0.00	0.00	5.14
405	454	3.478857	AATCACAGTCACCGGTGTTTA	57.521	42.857	32.74	12.72	37.90	2.01
442	491	4.280819	CCATCCTGTTTGGTATGGTTCAT	58.719	43.478	0.00	0.00	38.04	2.57
453	502	0.442310	CGTACGTGCCATCCTGTTTG	59.558	55.000	7.22	0.00	0.00	2.93
498	547	1.074775	GGGCCTTGATCCACACACA	59.925	57.895	0.84	0.00	0.00	3.72
499	548	0.962356	CAGGGCCTTGATCCACACAC	60.962	60.000	9.80	0.00	0.00	3.82
500	549	1.379916	CAGGGCCTTGATCCACACA	59.620	57.895	9.80	0.00	0.00	3.72
591	640	3.070446	TGGGTCAGTGTGTAAGTCGATTT	59.930	43.478	0.00	0.00	0.00	2.17
594	643	1.694844	TGGGTCAGTGTGTAAGTCGA	58.305	50.000	0.00	0.00	0.00	4.20
595	644	2.223971	ACTTGGGTCAGTGTGTAAGTCG	60.224	50.000	0.00	0.00	0.00	4.18
621	670	4.219725	GGCTATTGGTAAGTTGGCTGAAAA	59.780	41.667	0.00	0.00	0.00	2.29
687	739	7.466996	GCTTTCAATCTAGATGTTCCTCATGTG	60.467	40.741	5.86	0.00	36.83	3.21
996	1052	0.101399	ATGTCGACGCTGTCATCCTC	59.899	55.000	11.62	0.00	32.09	3.71
1022	1078	3.002583	TGCTCTCCGATGGCACCA	61.003	61.111	0.00	0.00	0.00	4.17
1245	1301	4.020617	TGGCTCCCGCTCTGGTTG	62.021	66.667	0.00	0.00	35.15	3.77
1437	1493	2.992689	TACAAGTCCGGCGAGCCA	60.993	61.111	9.30	0.00	35.37	4.75
1557	1613	1.212935	GGTGCCCAGATGGAGTACATT	59.787	52.381	0.00	0.00	40.72	2.71
2078	2146	9.393786	TCTCCTCCTATATTTAAAAGCCATAGT	57.606	33.333	0.00	0.00	0.00	2.12
2081	2149	8.166726	CCTTCTCCTCCTATATTTAAAAGCCAT	58.833	37.037	0.00	0.00	0.00	4.40
2098	2171	1.206849	CTTCCACTCAGCCTTCTCCTC	59.793	57.143	0.00	0.00	0.00	3.71
2142	2215	0.606944	AAATTTGAGGTGCCGCCGTA	60.607	50.000	0.00	0.00	43.70	4.02
2170	4662	4.996122	TGCATTAAGATTTGTGCTTTTGGG	59.004	37.500	0.00	0.00	38.37	4.12
2196	4689	2.660802	GCAGCTTTGCATGGGCTT	59.339	55.556	5.95	0.00	41.91	4.35
2317	4810	7.287810	ACTCCCTGTGTAAACTTTTGTAAGAT	58.712	34.615	0.00	0.00	35.30	2.40
2335	4828	7.189079	AGTCCTTTTTCTCTAATACTCCCTG	57.811	40.000	0.00	0.00	0.00	4.45
2336	4829	7.565768	CCTAGTCCTTTTTCTCTAATACTCCCT	59.434	40.741	0.00	0.00	0.00	4.20
2392	4885	5.220796	GGAGGTTTGACACACTGTTAGAAAC	60.221	44.000	0.00	0.00	0.00	2.78
2403	4896	1.388547	GCACAAGGAGGTTTGACACA	58.611	50.000	0.00	0.00	0.00	3.72

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.