AutoCloner

Multiple sequence alignment - TraesCS2D01G281600

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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	TraesCS2D01G281600	chr2D	100.000	5816	0	0	1	5816	354749070	354743255	0.000000e+00	10741.0
1	TraesCS2D01G281600	chr2D	88.176	296	31	3	3110	3403	459825818	459826111	3.340000e-92	350.0
2	TraesCS2D01G281600	chr2D	80.503	159	31	0	3877	4035	459826173	459826331	7.910000e-24	122.0
3	TraesCS2D01G281600	chr2B	93.815	2603	101	27	934	3505	421712793	421710220	0.000000e+00	3860.0
4	TraesCS2D01G281600	chr2B	96.361	1209	38	6	3504	4710	421710059	421708855	0.000000e+00	1984.0
5	TraesCS2D01G281600	chr2B	93.638	613	29	5	5206	5816	421708332	421707728	0.000000e+00	907.0
6	TraesCS2D01G281600	chr2B	90.612	490	35	6	4729	5208	421708863	421708375	1.770000e-179	640.0
7	TraesCS2D01G281600	chr2B	87.667	300	32	4	3106	3403	541094901	541095197	1.550000e-90	344.0
8	TraesCS2D01G281600	chr2B	83.448	145	18	6	1208	1349	541093581	541093722	4.730000e-26	130.0
9	TraesCS2D01G281600	chr2B	82.000	150	27	0	3886	4035	541095272	541095421	1.700000e-25	128.0
10	TraesCS2D01G281600	chr2A	95.399	1717	43	16	3504	5208	474312262	474310570	0.000000e+00	2700.0
11	TraesCS2D01G281600	chr2A	94.129	1056	47	8	1804	2856	474314643	474313600	0.000000e+00	1592.0
12	TraesCS2D01G281600	chr2A	93.376	785	41	3	1025	1809	474315439	474314666	0.000000e+00	1151.0
13	TraesCS2D01G281600	chr2A	93.689	618	27	2	2841	3446	474313276	474312659	0.000000e+00	915.0
14	TraesCS2D01G281600	chr2A	92.628	624	33	6	5206	5816	474310528	474309905	0.000000e+00	885.0
15	TraesCS2D01G281600	chr2A	83.882	608	75	13	252	841	474324638	474324036	5.090000e-155	558.0
16	TraesCS2D01G281600	chr2A	88.000	300	31	4	3106	3403	602800113	602800409	3.340000e-92	350.0
17	TraesCS2D01G281600	chr2A	95.333	150	5	1	2414	2561	474313597	474313448	2.710000e-58	237.0
18	TraesCS2D01G281600	chr2A	81.132	159	30	0	3877	4035	602800475	602800633	1.700000e-25	128.0
19	TraesCS2D01G281600	chr2A	98.148	54	0	1	969	1021	474315522	474315469	6.210000e-15	93.5
20	TraesCS2D01G281600	chr3B	80.634	852	125	28	137	960	256198552	256197713	1.780000e-174	623.0
21	TraesCS2D01G281600	chr7B	79.180	927	140	29	78	964	12549880	12548967	1.400000e-165	593.0
22	TraesCS2D01G281600	chr7B	79.726	656	86	24	128	754	114397811	114398448	1.160000e-116	431.0
23	TraesCS2D01G281600	chr5D	80.093	859	119	28	137	962	309399927	309400766	5.020000e-165	592.0
24	TraesCS2D01G281600	chr5D	80.247	729	102	26	252	961	424199302	424198597	1.450000e-140	510.0
25	TraesCS2D01G281600	chr5B	79.695	852	137	24	138	962	9581	10423	3.020000e-162	582.0
26	TraesCS2D01G281600	chr5B	87.671	73	8	1	3498	3570	600083688	600083759	3.730000e-12	84.2
27	TraesCS2D01G281600	chr6B	79.415	855	129	27	137	967	49765185	49764354	1.420000e-155	560.0
28	TraesCS2D01G281600	chr6B	89.552	67	6	1	3505	3570	345580074	345580008	3.730000e-12	84.2
29	TraesCS2D01G281600	chr7D	79.201	851	127	31	137	961	628600580	628601406	3.960000e-151	545.0
30	TraesCS2D01G281600	chr6A	89.231	65	6	1	3505	3568	340097850	340097786	4.830000e-11	80.5

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	TraesCS2D01G281600	chr2D	354743255	354749070	5815	True	10741.000000	10741	100.000000	1	5816	1	chr2D.!!$R1	5815
1	TraesCS2D01G281600	chr2D	459825818	459826331	513	False	236.000000	350	84.339500	3110	4035	2	chr2D.!!$F1	925
2	TraesCS2D01G281600	chr2B	421707728	421712793	5065	True	1847.750000	3860	93.606500	934	5816	4	chr2B.!!$R1	4882
3	TraesCS2D01G281600	chr2B	541093581	541095421	1840	False	200.666667	344	84.371667	1208	4035	3	chr2B.!!$F1	2827
4	TraesCS2D01G281600	chr2A	474309905	474315522	5617	True	1081.928571	2700	94.671714	969	5816	7	chr2A.!!$R2	4847
5	TraesCS2D01G281600	chr2A	474324036	474324638	602	True	558.000000	558	83.882000	252	841	1	chr2A.!!$R1	589
6	TraesCS2D01G281600	chr2A	602800113	602800633	520	False	239.000000	350	84.566000	3106	4035	2	chr2A.!!$F1	929
7	TraesCS2D01G281600	chr3B	256197713	256198552	839	True	623.000000	623	80.634000	137	960	1	chr3B.!!$R1	823
8	TraesCS2D01G281600	chr7B	12548967	12549880	913	True	593.000000	593	79.180000	78	964	1	chr7B.!!$R1	886
9	TraesCS2D01G281600	chr7B	114397811	114398448	637	False	431.000000	431	79.726000	128	754	1	chr7B.!!$F1	626
10	TraesCS2D01G281600	chr5D	309399927	309400766	839	False	592.000000	592	80.093000	137	962	1	chr5D.!!$F1	825
11	TraesCS2D01G281600	chr5D	424198597	424199302	705	True	510.000000	510	80.247000	252	961	1	chr5D.!!$R1	709
12	TraesCS2D01G281600	chr5B	9581	10423	842	False	582.000000	582	79.695000	138	962	1	chr5B.!!$F1	824
13	TraesCS2D01G281600	chr6B	49764354	49765185	831	True	560.000000	560	79.415000	137	967	1	chr6B.!!$R1	830
14	TraesCS2D01G281600	chr7D	628600580	628601406	826	False	545.000000	545	79.201000	137	961	1	chr7D.!!$F1	824

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	Hairpin	End Stability	Orientation
192	208	0.030603	GAGGTCCATCTCCCTCCCTT	60.031	60.000	0.00	41.22	3.95	F
412	469	0.034059	CTTCTCTGTGCAGTCCGGTT	59.966	55.000	0.00	0.00	4.44	F
645	717	0.106268	TTGGAGTGGTTGCCATGTGT	60.106	50.000	0.00	35.28	3.72	F
1026	1109	0.248054	CGCCACTTGTTGACACACAC	60.248	55.000	0.00	30.32	3.82	F
1027	1110	0.808125	GCCACTTGTTGACACACACA	59.192	50.000	0.00	30.32	3.72	F
1076	1185	1.452108	CCATTCCGCTTCACTCCCC	60.452	63.158	0.00	0.00	4.81	F
1077	1186	1.604378	CATTCCGCTTCACTCCCCT	59.396	57.895	0.00	0.00	4.79	F
1402	1514	2.430382	TTCCTCCGGCTGTGTTCGTC	62.430	60.000	0.00	0.00	4.20	F
3128	4137	1.007387	GAAGGTGGCACCAAAAGCG	60.007	57.895	36.28	41.95	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1060	1169	0.618968	AGAGGGGAGTGAAGCGGAAT	60.619	55.000	0.00	0.00	0.00	3.01	R
2322	2584	1.002544	GACCTTGACAAGTGGAGGAGG	59.997	57.143	14.03	0.00	33.47	4.30	R
2629	3288	1.423584	TCAGCCAGAAGAACACCTCA	58.576	50.000	0.00	0.00	0.00	3.86	R
2856	3787	1.004394	CTTTCTTACCCTTCCGCCCTT	59.996	52.381	0.00	0.00	0.00	3.95	R
2862	3793	7.231925	TCCAAAACATTACTTTCTTACCCTTCC	59.768	37.037	0.00	0.00	0.00	3.46	R
3032	4041	7.715265	TTACACAAGTCTTCTGTTCATCTTC	57.285	36.000	0.00	0.00	0.00	2.87	R
3105	4114	3.244044	GCTTTTGGTGCCACCTTCAATAA	60.244	43.478	16.23	0.00	39.58	1.40	R
3242	4251	0.962356	CAGCTTGCCGGGAATCTGTT	60.962	55.000	26.01	4.32	0.00	3.16	R
4875	6266	2.156504	GCAAATGGATACTGATCGCTCG	59.843	50.000	0.00	0.00	32.28	5.03	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	2.741092	TCCCTGTGTTCGTCCTGC	59.259	61.111	0.00	0.00	0.00	4.85
18	19	1.837051	TCCCTGTGTTCGTCCTGCT	60.837	57.895	0.00	0.00	0.00	4.24
19	20	1.374758	CCCTGTGTTCGTCCTGCTC	60.375	63.158	0.00	0.00	0.00	4.26
20	21	1.668294	CCTGTGTTCGTCCTGCTCT	59.332	57.895	0.00	0.00	0.00	4.09
21	22	0.888619	CCTGTGTTCGTCCTGCTCTA	59.111	55.000	0.00	0.00	0.00	2.43
22	23	1.135257	CCTGTGTTCGTCCTGCTCTAG	60.135	57.143	0.00	0.00	0.00	2.43
23	24	1.813178	CTGTGTTCGTCCTGCTCTAGA	59.187	52.381	0.00	0.00	0.00	2.43
24	25	2.425312	CTGTGTTCGTCCTGCTCTAGAT	59.575	50.000	0.00	0.00	0.00	1.98
25	26	2.423892	TGTGTTCGTCCTGCTCTAGATC	59.576	50.000	0.00	0.00	0.00	2.75
26	27	2.685897	GTGTTCGTCCTGCTCTAGATCT	59.314	50.000	0.00	0.00	0.00	2.75
27	28	2.685388	TGTTCGTCCTGCTCTAGATCTG	59.315	50.000	5.18	0.00	0.00	2.90
28	29	2.946329	GTTCGTCCTGCTCTAGATCTGA	59.054	50.000	5.18	0.03	0.00	3.27
29	30	3.283259	TCGTCCTGCTCTAGATCTGAA	57.717	47.619	5.18	0.00	0.00	3.02
30	31	3.210227	TCGTCCTGCTCTAGATCTGAAG	58.790	50.000	5.18	3.63	0.00	3.02
31	32	2.293122	CGTCCTGCTCTAGATCTGAAGG	59.707	54.545	5.18	2.05	0.00	3.46
32	33	3.295973	GTCCTGCTCTAGATCTGAAGGT	58.704	50.000	5.18	0.00	0.00	3.50
33	34	3.068024	GTCCTGCTCTAGATCTGAAGGTG	59.932	52.174	5.18	0.00	0.00	4.00
34	35	2.224018	CCTGCTCTAGATCTGAAGGTGC	60.224	54.545	5.18	5.18	0.00	5.01
35	36	1.759445	TGCTCTAGATCTGAAGGTGCC	59.241	52.381	5.18	0.00	0.00	5.01
36	37	2.038659	GCTCTAGATCTGAAGGTGCCT	58.961	52.381	5.18	0.00	0.00	4.75
37	38	2.035832	GCTCTAGATCTGAAGGTGCCTC	59.964	54.545	5.18	0.00	0.00	4.70
38	39	2.627699	CTCTAGATCTGAAGGTGCCTCC	59.372	54.545	5.18	0.00	0.00	4.30
46	47	3.832175	AGGTGCCTCCTTCAGCAT	58.168	55.556	0.00	0.00	45.67	3.79
47	48	1.302285	AGGTGCCTCCTTCAGCATG	59.698	57.895	0.00	0.00	45.67	4.06
48	49	1.001641	GGTGCCTCCTTCAGCATGT	60.002	57.895	0.00	0.00	41.86	3.21

Showing 1 to 25 of 167 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.816863	GAGCAGGACGAACACAGGGA	61.817	60.000	0.00	0.00	0.00	4.20
1	2	1.374758	GAGCAGGACGAACACAGGG	60.375	63.158	0.00	0.00	0.00	4.45
2	3	0.888619	TAGAGCAGGACGAACACAGG	59.111	55.000	0.00	0.00	0.00	4.00
3	4	1.813178	TCTAGAGCAGGACGAACACAG	59.187	52.381	0.00	0.00	0.00	3.66
4	5	1.905637	TCTAGAGCAGGACGAACACA	58.094	50.000	0.00	0.00	0.00	3.72
5	6	2.685897	AGATCTAGAGCAGGACGAACAC	59.314	50.000	11.20	0.00	0.00	3.32
6	7	2.685388	CAGATCTAGAGCAGGACGAACA	59.315	50.000	11.20	0.00	0.00	3.18
7	8	2.946329	TCAGATCTAGAGCAGGACGAAC	59.054	50.000	11.20	0.00	0.00	3.95
8	9	3.283259	TCAGATCTAGAGCAGGACGAA	57.717	47.619	11.20	0.00	0.00	3.85
9	10	3.210227	CTTCAGATCTAGAGCAGGACGA	58.790	50.000	11.20	0.00	0.00	4.20
10	11	2.293122	CCTTCAGATCTAGAGCAGGACG	59.707	54.545	11.20	5.14	0.00	4.79
11	12	3.068024	CACCTTCAGATCTAGAGCAGGAC	59.932	52.174	17.22	0.00	0.00	3.85
12	13	3.295093	CACCTTCAGATCTAGAGCAGGA	58.705	50.000	17.22	8.72	0.00	3.86
13	14	2.224018	GCACCTTCAGATCTAGAGCAGG	60.224	54.545	11.20	10.79	0.00	4.85
14	15	2.224018	GGCACCTTCAGATCTAGAGCAG	60.224	54.545	11.20	1.83	0.00	4.24
15	16	1.759445	GGCACCTTCAGATCTAGAGCA	59.241	52.381	11.20	0.00	0.00	4.26
16	17	2.035832	GAGGCACCTTCAGATCTAGAGC	59.964	54.545	0.00	0.00	0.00	4.09
17	18	2.627699	GGAGGCACCTTCAGATCTAGAG	59.372	54.545	0.00	0.00	35.41	2.43
18	19	2.672098	GGAGGCACCTTCAGATCTAGA	58.328	52.381	0.00	0.00	35.41	2.43
30	31	1.001641	ACATGCTGAAGGAGGCACC	60.002	57.895	0.00	0.00	41.39	5.01
31	32	0.607489	ACACATGCTGAAGGAGGCAC	60.607	55.000	0.00	0.00	41.39	5.01
32	33	0.111061	AACACATGCTGAAGGAGGCA	59.889	50.000	0.00	0.00	42.80	4.75
33	34	2.113860	TAACACATGCTGAAGGAGGC	57.886	50.000	0.00	0.00	0.00	4.70
34	35	3.181493	GCAATAACACATGCTGAAGGAGG	60.181	47.826	0.00	0.00	39.46	4.30
35	36	3.181493	GGCAATAACACATGCTGAAGGAG	60.181	47.826	0.00	0.00	42.20	3.69

Showing 1 to 25 of 175 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.