AutoCloner

Multiple sequence alignment - TraesCS3A01G512600

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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	TraesCS3A01G512600	chr3A	100.000	4467	0	0	1	4467	732242137	732237671	0.000000e+00	8250.0
1	TraesCS3A01G512600	chr3A	98.958	192	2	0	2640	2831	732239460	732239269	1.190000e-90	344.0
2	TraesCS3A01G512600	chr3A	98.958	192	2	0	2678	2869	732239498	732239307	1.190000e-90	344.0
3	TraesCS3A01G512600	chr3A	98.701	154	2	0	2640	2793	732239422	732239269	1.580000e-69	274.0
4	TraesCS3A01G512600	chr3A	98.701	154	2	0	2716	2869	732239498	732239345	1.580000e-69	274.0
5	TraesCS3A01G512600	chr3A	98.276	116	2	0	2640	2755	732239384	732239269	2.110000e-48	204.0
6	TraesCS3A01G512600	chr3A	98.276	116	2	0	2754	2869	732239498	732239383	2.110000e-48	204.0
7	TraesCS3A01G512600	chr3A	97.436	78	2	0	2640	2717	732239346	732239269	2.800000e-27	134.0
8	TraesCS3A01G512600	chr3A	97.436	78	2	0	2792	2869	732239498	732239421	2.800000e-27	134.0
9	TraesCS3A01G512600	chr3A	87.179	117	14	1	1	117	627785118	627785233	1.010000e-26	132.0
10	TraesCS3A01G512600	chr3B	91.211	1718	98	17	2792	4467	809814933	809813227	0.000000e+00	2287.0
11	TraesCS3A01G512600	chr3B	87.273	385	41	6	2336	2719	809815231	809814854	2.470000e-117	433.0
12	TraesCS3A01G512600	chr3B	83.770	191	18	4	290	479	745291046	745291224	7.680000e-38	169.0
13	TraesCS3A01G512600	chr3B	97.500	80	2	0	2754	2833	809814933	809814854	2.170000e-28	137.0
14	TraesCS3A01G512600	chr3B	97.500	80	2	0	2716	2795	809814933	809814854	2.170000e-28	137.0
15	TraesCS3A01G512600	chr3B	97.500	80	2	0	2678	2757	809814933	809814854	2.170000e-28	137.0
16	TraesCS3A01G512600	chr6D	87.055	309	24	3	273	577	80295547	80295843	7.160000e-88	335.0
17	TraesCS3A01G512600	chr6D	87.121	264	23	1	292	555	44819377	44819629	5.650000e-74	289.0
18	TraesCS3A01G512600	chr6D	90.155	193	15	3	388	577	44504401	44504592	9.600000e-62	248.0
19	TraesCS3A01G512600	chr6D	81.277	235	37	6	2	234	24479604	24479833	2.740000e-42	183.0
20	TraesCS3A01G512600	chr6D	83.019	106	17	1	2	107	30154861	30154965	1.320000e-15	95.3
21	TraesCS3A01G512600	chr6B	85.577	208	19	3	272	479	653583450	653583254	1.630000e-49	207.0
22	TraesCS3A01G512600	chr6B	77.778	234	37	9	2	234	142808348	142808567	3.630000e-26	130.0
23	TraesCS3A01G512600	chr4B	85.577	208	19	7	272	479	76050146	76050342	1.630000e-49	207.0
24	TraesCS3A01G512600	chr4B	84.804	204	16	7	279	479	591996053	591995862	1.640000e-44	191.0
25	TraesCS3A01G512600	chr4B	84.158	202	19	10	279	478	592119824	592119634	2.740000e-42	183.0
26	TraesCS3A01G512600	chr4B	83.621	116	18	1	2	117	575625633	575625519	1.700000e-19	108.0
27	TraesCS3A01G512600	chr1D	85.047	214	16	6	271	479	76981711	76981509	2.110000e-48	204.0
28	TraesCS3A01G512600	chr6A	82.051	234	35	7	4	234	376484464	376484235	4.560000e-45	193.0
29	TraesCS3A01G512600	chr1A	85.263	190	17	3	290	479	56614291	56614113	7.630000e-43	185.0
30	TraesCS3A01G512600	chr2D	85.185	189	17	5	291	479	156035430	156035607	2.740000e-42	183.0
31	TraesCS3A01G512600	chr2D	83.246	191	18	7	285	474	614868165	614868342	3.580000e-36	163.0
32	TraesCS3A01G512600	chr7A	83.099	213	20	10	272	479	516497455	516497254	3.550000e-41	180.0
33	TraesCS3A01G512600	chr2A	80.833	240	28	12	306	541	404907337	404907112	5.940000e-39	172.0
34	TraesCS3A01G512600	chr2A	82.162	185	20	4	296	479	654602965	654603137	3.600000e-31	147.0
35	TraesCS3A01G512600	chr2B	79.130	230	43	5	2	228	252101798	252102025	2.150000e-33	154.0
36	TraesCS3A01G512600	chr5B	87.912	91	10	1	296	385	232781430	232781340	6.110000e-19	106.0
37	TraesCS3A01G512600	chr7B	81.720	93	16	1	5	97	570400958	570400867	4.790000e-10	76.8

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	TraesCS3A01G512600	chr3A	732237671	732242137	4466	True	1129.111111	8250	98.526889	1	4467	9	chr3A.!!$R1	4466
1	TraesCS3A01G512600	chr3B	809813227	809815231	2004	True	626.200000	2287	94.196800	2336	4467	5	chr3B.!!$R1	2131

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
745	746	0.028770	TTGCGAGTGTTGCGGAAAAG	59.971	50.0	0.00	36.18	2.27	F
1062	1063	0.034756	AGTCCAGCAACGTATGTGCA	59.965	50.0	12.86	0.00	4.57	F
1385	1386	0.035439	TTTGGAGATGCCTTCCGGTC	60.035	55.0	0.00	37.63	4.79	F
1568	1569	0.036010	CCGAGTTCATGTGGAGCCTT	60.036	55.0	0.00	0.00	4.35	F
1653	1654	0.035439	GTTCCATCTCCGGCCTTTGA	60.035	55.0	0.00	0.00	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1634	1635	0.035439	TCAAAGGCCGGAGATGGAAC	60.035	55.000	5.05	0.00	0.00	3.62	R
2468	2469	0.038166	GTCTTCCACCTGGCATTCCA	59.962	55.000	0.00	0.00	40.85	3.53	R
3199	3200	0.179100	ACTCTTCCACATCGGATGCG	60.179	55.000	17.61	8.44	45.80	4.73	R
3418	3419	0.108615	CTTGTTCCTCGGCATCTCGT	60.109	55.000	0.00	0.00	0.00	4.18	R
3626	3627	2.200081	ACATCTTCCTAGCCACCATGT	58.800	47.619	0.00	0.00	0.00	3.21	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	4.096558	TGCCGCGCGAAAATGTCC	62.097	61.111	34.63	8.88	0.00	4.02
18	19	4.829518	GCCGCGCGAAAATGTCCC	62.830	66.667	34.63	3.56	0.00	4.46
19	20	3.124921	CCGCGCGAAAATGTCCCT	61.125	61.111	34.63	0.00	0.00	4.20
20	21	2.399611	CGCGCGAAAATGTCCCTC	59.600	61.111	28.94	0.00	0.00	4.30
21	22	2.791927	GCGCGAAAATGTCCCTCC	59.208	61.111	12.10	0.00	0.00	4.30
22	23	2.761195	GCGCGAAAATGTCCCTCCC	61.761	63.158	12.10	0.00	0.00	4.30
23	24	2.461110	CGCGAAAATGTCCCTCCCG	61.461	63.158	0.00	0.00	0.00	5.14
24	25	2.761195	GCGAAAATGTCCCTCCCGC	61.761	63.158	0.00	0.00	0.00	6.13
25	26	1.078426	CGAAAATGTCCCTCCCGCT	60.078	57.895	0.00	0.00	0.00	5.52
26	27	0.676782	CGAAAATGTCCCTCCCGCTT	60.677	55.000	0.00	0.00	0.00	4.68
27	28	0.811281	GAAAATGTCCCTCCCGCTTG	59.189	55.000	0.00	0.00	0.00	4.01
28	29	0.404040	AAAATGTCCCTCCCGCTTGA	59.596	50.000	0.00	0.00	0.00	3.02
29	30	0.625849	AAATGTCCCTCCCGCTTGAT	59.374	50.000	0.00	0.00	0.00	2.57
30	31	0.181350	AATGTCCCTCCCGCTTGATC	59.819	55.000	0.00	0.00	0.00	2.92
31	32	0.692419	ATGTCCCTCCCGCTTGATCT	60.692	55.000	0.00	0.00	0.00	2.75
32	33	1.330655	TGTCCCTCCCGCTTGATCTC	61.331	60.000	0.00	0.00	0.00	2.75
33	34	2.127869	TCCCTCCCGCTTGATCTCG	61.128	63.158	0.00	0.00	0.00	4.04
34	35	2.279784	CCTCCCGCTTGATCTCGC	60.280	66.667	0.00	0.00	0.00	5.03
35	36	2.496341	CTCCCGCTTGATCTCGCA	59.504	61.111	7.41	0.00	0.00	5.10
36	37	1.591059	CTCCCGCTTGATCTCGCAG	60.591	63.158	7.41	0.00	0.00	5.18
37	38	3.267860	CCCGCTTGATCTCGCAGC	61.268	66.667	7.41	3.05	0.00	5.25
38	39	3.267860	CCGCTTGATCTCGCAGCC	61.268	66.667	7.41	0.00	0.00	4.85
39	40	3.624300	CGCTTGATCTCGCAGCCG	61.624	66.667	7.41	0.00	0.00	5.52
40	41	2.202797	GCTTGATCTCGCAGCCGA	60.203	61.111	0.00	0.00	42.01	5.54
41	42	1.593750	GCTTGATCTCGCAGCCGAT	60.594	57.895	0.00	0.00	43.47	4.18

Showing 1 to 25 of 1,705 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	4.096558	GGACATTTTCGCGCGGCA	62.097	61.111	31.69	14.80	0.00	5.69
1	2	4.829518	GGGACATTTTCGCGCGGC	62.830	66.667	31.69	1.52	0.00	6.53
2	3	3.095898	GAGGGACATTTTCGCGCGG	62.096	63.158	31.69	16.11	42.11	6.46
3	4	2.399611	GAGGGACATTTTCGCGCG	59.600	61.111	26.76	26.76	42.11	6.86
4	5	2.761195	GGGAGGGACATTTTCGCGC	61.761	63.158	0.00	0.00	42.11	6.86
5	6	2.461110	CGGGAGGGACATTTTCGCG	61.461	63.158	0.00	0.00	42.11	5.87
6	7	2.761195	GCGGGAGGGACATTTTCGC	61.761	63.158	0.00	0.00	37.44	4.70
7	8	0.676782	AAGCGGGAGGGACATTTTCG	60.677	55.000	0.00	0.00	0.00	3.46
8	9	0.811281	CAAGCGGGAGGGACATTTTC	59.189	55.000	0.00	0.00	0.00	2.29
9	10	0.404040	TCAAGCGGGAGGGACATTTT	59.596	50.000	0.00	0.00	0.00	1.82
10	11	0.625849	ATCAAGCGGGAGGGACATTT	59.374	50.000	0.00	0.00	0.00	2.32
11	12	0.181350	GATCAAGCGGGAGGGACATT	59.819	55.000	0.00	0.00	0.00	2.71
12	13	0.692419	AGATCAAGCGGGAGGGACAT	60.692	55.000	0.00	0.00	0.00	3.06
13	14	1.306141	AGATCAAGCGGGAGGGACA	60.306	57.895	0.00	0.00	0.00	4.02
14	15	1.443828	GAGATCAAGCGGGAGGGAC	59.556	63.158	0.00	0.00	0.00	4.46
15	16	2.127869	CGAGATCAAGCGGGAGGGA	61.128	63.158	0.00	0.00	0.00	4.20
16	17	2.419198	CGAGATCAAGCGGGAGGG	59.581	66.667	0.00	0.00	0.00	4.30
17	18	2.279784	GCGAGATCAAGCGGGAGG	60.280	66.667	0.00	0.00	0.00	4.30
18	19	1.591059	CTGCGAGATCAAGCGGGAG	60.591	63.158	11.94	0.16	36.18	4.30
19	20	2.496341	CTGCGAGATCAAGCGGGA	59.504	61.111	11.94	0.00	36.18	5.14
20	21	3.267860	GCTGCGAGATCAAGCGGG	61.268	66.667	18.72	10.49	39.94	6.13
21	22	3.267860	GGCTGCGAGATCAAGCGG	61.268	66.667	14.58	14.58	42.31	5.52
22	23	3.624300	CGGCTGCGAGATCAAGCG	61.624	66.667	7.72	3.60	35.87	4.68
23	24	0.319040	TATCGGCTGCGAGATCAAGC	60.319	55.000	11.54	5.60	0.00	4.01
24	25	1.668337	CCTATCGGCTGCGAGATCAAG	60.668	57.143	11.54	6.17	0.00	3.02

Showing 1 to 25 of 1,709 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.