AutoCloner

Multiple sequence alignment - TraesCS3A01G059500

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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	TraesCS3A01G059500	chr3A	100.000	3431	0	0	1	3431	36072330	36068900	0.000000e+00	6336.0
1	TraesCS3A01G059500	chr3A	77.901	2353	453	53	969	3297	658289023	658291332	0.000000e+00	1402.0
2	TraesCS3A01G059500	chr3B	94.440	2572	116	7	872	3431	43527787	43525231	0.000000e+00	3932.0
3	TraesCS3A01G059500	chr3B	77.971	2583	482	50	732	3296	690446667	690449180	0.000000e+00	1537.0
4	TraesCS3A01G059500	chr3B	79.056	2225	419	38	1093	3297	642215463	642213266	0.000000e+00	1483.0
5	TraesCS3A01G059500	chr3B	79.709	2060	374	37	1256	3297	689007196	689005163	0.000000e+00	1448.0
6	TraesCS3A01G059500	chr3B	78.076	2381	439	62	870	3225	690430377	690432699	0.000000e+00	1428.0
7	TraesCS3A01G059500	chr3B	90.272	257	12	2	348	604	43541649	43541406	1.190000e-84	324.0
8	TraesCS3A01G059500	chr3B	100.000	47	0	0	598	644	43535734	43535688	1.700000e-13	87.9
9	TraesCS3A01G059500	chr3D	78.266	2595	462	75	732	3297	523555074	523557595	0.000000e+00	1574.0
10	TraesCS3A01G059500	chr3D	78.487	2459	442	70	870	3297	523407748	523410150	0.000000e+00	1530.0
11	TraesCS3A01G059500	chr3D	79.434	2227	406	39	1093	3297	523334665	523336861	0.000000e+00	1528.0
12	TraesCS3A01G059500	chr3D	77.974	1984	355	51	900	2853	523379353	523381284	0.000000e+00	1168.0
13	TraesCS3A01G059500	chr3D	78.733	1768	311	44	816	2558	523559986	523561713	0.000000e+00	1122.0
14	TraesCS3A01G059500	chr3D	77.304	1476	320	12	1096	2562	523569670	523571139	0.000000e+00	856.0
15	TraesCS3A01G059500	chr3D	84.713	628	86	8	2617	3240	523562709	523563330	1.350000e-173	619.0
16	TraesCS3A01G059500	chrUn	79.032	2375	424	52	917	3268	330561017	330563340	0.000000e+00	1559.0
17	TraesCS3A01G059500	chrUn	78.790	1834	354	27	1481	3297	342677756	342679571	0.000000e+00	1199.0
18	TraesCS3A01G059500	chrUn	79.363	848	156	15	2456	3297	405666919	405667753	2.300000e-161	579.0
19	TraesCS3A01G059500	chrUn	76.799	556	100	17	917	1467	454390269	454389738	5.600000e-73	285.0
20	TraesCS3A01G059500	chr2A	91.232	422	25	4	1	420	753817230	753817641	6.430000e-157	564.0
21	TraesCS3A01G059500	chr2A	85.714	77	10	1	345	420	613480420	613480496	2.840000e-11	80.5
22	TraesCS3A01G059500	chr5D	90.222	225	19	3	198	420	4256061	4256284	1.200000e-74	291.0
23	TraesCS3A01G059500	chr1A	90.710	183	16	1	415	596	9373642	9373824	3.420000e-60	243.0
24	TraesCS3A01G059500	chr7A	89.560	182	18	1	415	595	24409055	24409236	2.660000e-56	230.0
25	TraesCS3A01G059500	chr7A	89.011	182	19	1	415	595	24388433	24388614	1.240000e-54	224.0
26	TraesCS3A01G059500	chr2D	90.435	115	8	3	198	310	562221429	562221316	7.670000e-32	148.0
27	TraesCS3A01G059500	chr2D	85.965	57	6	2	365	420	562221316	562221261	3.700000e-05	60.2

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	TraesCS3A01G059500	chr3A	36068900	36072330	3430	True	6336	6336	100.000000	1	3431	1	chr3A.!!$R1	3430
1	TraesCS3A01G059500	chr3A	658289023	658291332	2309	False	1402	1402	77.901000	969	3297	1	chr3A.!!$F1	2328
2	TraesCS3A01G059500	chr3B	43525231	43527787	2556	True	3932	3932	94.440000	872	3431	1	chr3B.!!$R1	2559
3	TraesCS3A01G059500	chr3B	690446667	690449180	2513	False	1537	1537	77.971000	732	3296	1	chr3B.!!$F2	2564
4	TraesCS3A01G059500	chr3B	642213266	642215463	2197	True	1483	1483	79.056000	1093	3297	1	chr3B.!!$R4	2204
5	TraesCS3A01G059500	chr3B	689005163	689007196	2033	True	1448	1448	79.709000	1256	3297	1	chr3B.!!$R5	2041
6	TraesCS3A01G059500	chr3B	690430377	690432699	2322	False	1428	1428	78.076000	870	3225	1	chr3B.!!$F1	2355
7	TraesCS3A01G059500	chr3D	523407748	523410150	2402	False	1530	1530	78.487000	870	3297	1	chr3D.!!$F3	2427
8	TraesCS3A01G059500	chr3D	523334665	523336861	2196	False	1528	1528	79.434000	1093	3297	1	chr3D.!!$F1	2204
9	TraesCS3A01G059500	chr3D	523379353	523381284	1931	False	1168	1168	77.974000	900	2853	1	chr3D.!!$F2	1953
10	TraesCS3A01G059500	chr3D	523555074	523563330	8256	False	1105	1574	80.570667	732	3297	3	chr3D.!!$F5	2565
11	TraesCS3A01G059500	chr3D	523569670	523571139	1469	False	856	856	77.304000	1096	2562	1	chr3D.!!$F4	1466
12	TraesCS3A01G059500	chrUn	330561017	330563340	2323	False	1559	1559	79.032000	917	3268	1	chrUn.!!$F1	2351
13	TraesCS3A01G059500	chrUn	342677756	342679571	1815	False	1199	1199	78.790000	1481	3297	1	chrUn.!!$F2	1816
14	TraesCS3A01G059500	chrUn	405666919	405667753	834	False	579	579	79.363000	2456	3297	1	chrUn.!!$F3	841
15	TraesCS3A01G059500	chrUn	454389738	454390269	531	True	285	285	76.799000	917	1467	1	chrUn.!!$R1	550

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
530	531	0.025898	GCTCGGAATTTCGCGGTAAC	59.974	55.0	6.13	0.0	0.0	2.50	F
566	567	0.107831	CCCAGTCACCCACGAGAAAA	59.892	55.0	0.00	0.0	0.0	2.29	F
993	1036	0.322997	CCACCCATACCGAAGCCAAA	60.323	55.0	0.00	0.0	0.0	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1964	6863	0.736053	GGTTGCCGTGAAGTCAACAA	59.264	50.000	6.66	0.00	41.17	2.83	R
2266	7171	5.049886	GGTTATTGGCTAGGCGTAAACATAC	60.050	44.000	21.06	9.34	0.00	2.39	R
2601	7507	5.869579	TGAATCTGCCCACTAATTATCTCC	58.130	41.667	0.00	0.00	0.00	3.71	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
72	73	7.416154	TGTATGTTTGTAGAAAAGAAGACCG	57.584	36.000	0.00	0.00	0.00	4.79
73	74	5.941948	ATGTTTGTAGAAAAGAAGACCGG	57.058	39.130	0.00	0.00	0.00	5.28
74	75	5.026038	TGTTTGTAGAAAAGAAGACCGGA	57.974	39.130	9.46	0.00	0.00	5.14
75	76	5.617252	TGTTTGTAGAAAAGAAGACCGGAT	58.383	37.500	9.46	0.00	0.00	4.18
76	77	5.468746	TGTTTGTAGAAAAGAAGACCGGATG	59.531	40.000	9.46	0.00	0.00	3.51
77	78	5.477607	TTGTAGAAAAGAAGACCGGATGA	57.522	39.130	9.46	0.00	0.00	2.92
78	79	5.477607	TGTAGAAAAGAAGACCGGATGAA	57.522	39.130	9.46	0.00	0.00	2.57
79	80	6.049955	TGTAGAAAAGAAGACCGGATGAAT	57.950	37.500	9.46	0.00	0.00	2.57
80	81	6.106673	TGTAGAAAAGAAGACCGGATGAATC	58.893	40.000	9.46	0.00	0.00	2.52
81	82	5.165961	AGAAAAGAAGACCGGATGAATCA	57.834	39.130	9.46	0.00	0.00	2.57
82	83	5.560724	AGAAAAGAAGACCGGATGAATCAA	58.439	37.500	9.46	0.00	0.00	2.57
83	84	6.003950	AGAAAAGAAGACCGGATGAATCAAA	58.996	36.000	9.46	0.00	0.00	2.69
84	85	6.490040	AGAAAAGAAGACCGGATGAATCAAAA	59.510	34.615	9.46	0.00	0.00	2.44
85	86	6.840780	AAAGAAGACCGGATGAATCAAAAT	57.159	33.333	9.46	0.00	0.00	1.82
86	87	6.840780	AAGAAGACCGGATGAATCAAAATT	57.159	33.333	9.46	0.00	0.00	1.82
87	88	6.199937	AGAAGACCGGATGAATCAAAATTG	57.800	37.500	9.46	0.00	0.00	2.32
88	89	4.989279	AGACCGGATGAATCAAAATTGG	57.011	40.909	9.46	0.00	0.00	3.16
89	90	4.344104	AGACCGGATGAATCAAAATTGGT	58.656	39.130	9.46	0.00	0.00	3.67
90	91	4.772100	AGACCGGATGAATCAAAATTGGTT	59.228	37.500	9.46	0.00	33.40	3.67
91	92	5.949354	AGACCGGATGAATCAAAATTGGTTA	59.051	36.000	9.46	0.00	30.22	2.85
92	93	5.961272	ACCGGATGAATCAAAATTGGTTAC	58.039	37.500	9.46	0.00	30.22	2.50
93	94	5.714806	ACCGGATGAATCAAAATTGGTTACT	59.285	36.000	9.46	0.00	30.22	2.24
94	95	6.210584	ACCGGATGAATCAAAATTGGTTACTT	59.789	34.615	9.46	0.00	30.22	2.24
95	96	6.531240	CCGGATGAATCAAAATTGGTTACTTG	59.469	38.462	0.00	0.00	30.22	3.16
96	97	7.090173	CGGATGAATCAAAATTGGTTACTTGT	58.910	34.615	0.00	0.00	30.22	3.16

Showing 1 to 25 of 460 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	9.146984	CGGTCTTCTTTTCTACAAACATACATA	57.853	33.333	0.00	0.00	0.00	2.29
47	48	7.119262	CCGGTCTTCTTTTCTACAAACATACAT	59.881	37.037	0.00	0.00	0.00	2.29
48	49	6.425721	CCGGTCTTCTTTTCTACAAACATACA	59.574	38.462	0.00	0.00	0.00	2.29
49	50	6.647895	TCCGGTCTTCTTTTCTACAAACATAC	59.352	38.462	0.00	0.00	0.00	2.39
50	51	6.761312	TCCGGTCTTCTTTTCTACAAACATA	58.239	36.000	0.00	0.00	0.00	2.29
51	52	5.617252	TCCGGTCTTCTTTTCTACAAACAT	58.383	37.500	0.00	0.00	0.00	2.71
52	53	5.026038	TCCGGTCTTCTTTTCTACAAACA	57.974	39.130	0.00	0.00	0.00	2.83
53	54	5.699458	TCATCCGGTCTTCTTTTCTACAAAC	59.301	40.000	0.00	0.00	0.00	2.93
54	55	5.860611	TCATCCGGTCTTCTTTTCTACAAA	58.139	37.500	0.00	0.00	0.00	2.83
55	56	5.477607	TCATCCGGTCTTCTTTTCTACAA	57.522	39.130	0.00	0.00	0.00	2.41
56	57	5.477607	TTCATCCGGTCTTCTTTTCTACA	57.522	39.130	0.00	0.00	0.00	2.74
57	58	6.106673	TGATTCATCCGGTCTTCTTTTCTAC	58.893	40.000	0.00	0.00	0.00	2.59
58	59	6.294361	TGATTCATCCGGTCTTCTTTTCTA	57.706	37.500	0.00	0.00	0.00	2.10
59	60	5.165961	TGATTCATCCGGTCTTCTTTTCT	57.834	39.130	0.00	0.00	0.00	2.52
60	61	5.880054	TTGATTCATCCGGTCTTCTTTTC	57.120	39.130	0.00	0.00	0.00	2.29
61	62	6.648879	TTTTGATTCATCCGGTCTTCTTTT	57.351	33.333	0.00	0.00	0.00	2.27
62	63	6.840780	ATTTTGATTCATCCGGTCTTCTTT	57.159	33.333	0.00	0.00	0.00	2.52
63	64	6.350445	CCAATTTTGATTCATCCGGTCTTCTT	60.350	38.462	0.00	0.00	0.00	2.52
64	65	5.126061	CCAATTTTGATTCATCCGGTCTTCT	59.874	40.000	0.00	0.00	0.00	2.85
65	66	5.105756	ACCAATTTTGATTCATCCGGTCTTC	60.106	40.000	0.00	0.00	0.00	2.87
66	67	4.772100	ACCAATTTTGATTCATCCGGTCTT	59.228	37.500	0.00	0.00	0.00	3.01
67	68	4.344104	ACCAATTTTGATTCATCCGGTCT	58.656	39.130	0.00	0.00	0.00	3.85
68	69	4.718940	ACCAATTTTGATTCATCCGGTC	57.281	40.909	0.00	0.00	0.00	4.79
69	70	5.714806	AGTAACCAATTTTGATTCATCCGGT	59.285	36.000	0.00	0.00	0.00	5.28
70	71	6.207691	AGTAACCAATTTTGATTCATCCGG	57.792	37.500	0.00	0.00	0.00	5.14

Showing 1 to 25 of 488 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.