AutoCloner

Multiple sequence alignment - TraesCS3A01G485800

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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	TraesCS3A01G485800	chr3A	100.000	2690	0	0	1	2690	714595097	714597786	0.000000e+00	4968.0
1	TraesCS3A01G485800	chr3A	72.468	1264	242	79	581	1800	702421607	702420406	2.600000e-80	309.0
2	TraesCS3A01G485800	chr3A	88.106	227	22	5	510	732	699533357	699533582	5.710000e-67	265.0
3	TraesCS3A01G485800	chr3A	90.625	64	6	0	726	789	700441703	700441640	4.770000e-13	86.1
4	TraesCS3A01G485800	chr3D	91.064	1354	90	4	466	1799	579582863	579581521	0.000000e+00	1801.0
5	TraesCS3A01G485800	chr3D	92.554	1249	76	3	565	1799	579398533	579399778	0.000000e+00	1775.0
6	TraesCS3A01G485800	chr3D	85.112	759	64	19	1935	2682	579581304	579580584	0.000000e+00	730.0
7	TraesCS3A01G485800	chr3D	87.645	518	43	12	1935	2447	579399996	579400497	1.390000e-162	582.0
8	TraesCS3A01G485800	chr3D	92.344	209	14	2	2475	2682	579400493	579400700	2.020000e-76	296.0
9	TraesCS3A01G485800	chr3D	81.299	385	46	16	525	886	565641909	565642290	3.390000e-74	289.0
10	TraesCS3A01G485800	chr3D	74.290	634	133	25	1088	1702	568235447	568236069	9.620000e-60	241.0
11	TraesCS3A01G485800	chr3D	82.593	270	47	0	525	794	565830738	565831007	3.460000e-59	239.0
12	TraesCS3A01G485800	chr3D	74.843	477	78	29	2222	2673	569396125	569395666	7.650000e-41	178.0
13	TraesCS3A01G485800	chr3D	92.857	98	6	1	1783	1880	579399808	579399904	1.000000e-29	141.0
14	TraesCS3A01G485800	chr3D	77.477	222	38	6	1073	1291	567687178	567686966	3.640000e-24	122.0
15	TraesCS3A01G485800	chr3D	85.567	97	14	0	693	789	568136871	568136967	4.740000e-18	102.0
16	TraesCS3A01G485800	chr3D	75.385	195	30	12	136	317	579583233	579583044	7.980000e-11	78.7
17	TraesCS3A01G485800	chr3B	89.978	1357	101	9	466	1799	773746986	773748330	0.000000e+00	1720.0
18	TraesCS3A01G485800	chr3B	86.082	582	49	11	507	1077	773882827	773882267	4.960000e-167	597.0
19	TraesCS3A01G485800	chr3B	91.826	367	29	1	1433	1799	773882268	773881903	6.640000e-141	510.0
20	TraesCS3A01G485800	chr3B	93.438	320	18	2	1933	2249	773881696	773881377	3.130000e-129	472.0
21	TraesCS3A01G485800	chr3B	86.293	321	24	9	2246	2561	773881056	773880751	5.550000e-87	331.0
22	TraesCS3A01G485800	chr3B	72.703	1110	225	57	586	1664	756440294	756439232	1.570000e-77	300.0
23	TraesCS3A01G485800	chr3B	88.584	219	25	0	526	744	752973257	752973039	1.590000e-67	267.0
24	TraesCS3A01G485800	chr3B	83.513	279	38	6	523	800	684514005	684513734	1.240000e-63	254.0
25	TraesCS3A01G485800	chr3B	87.831	189	7	9	139	311	773883146	773882958	9.760000e-50	207.0
26	TraesCS3A01G485800	chr3B	74.833	449	98	11	1224	1663	754331007	754331449	3.540000e-44	189.0
27	TraesCS3A01G485800	chr3B	87.857	140	6	4	66	200	37739787	37739920	1.290000e-33	154.0
28	TraesCS3A01G485800	chr3B	97.368	76	2	0	326	401	773746862	773746937	2.170000e-26	130.0
29	TraesCS3A01G485800	chr3B	97.674	43	0	1	419	460	773746923	773746965	3.710000e-09	73.1
30	TraesCS3A01G485800	chr7A	74.857	525	107	22	1190	1702	41048137	41047626	5.830000e-52	215.0
31	TraesCS3A01G485800	chr7D	74.181	519	107	22	1190	1694	41601215	41600710	9.830000e-45	191.0
32	TraesCS3A01G485800	chr1B	89.209	139	5	5	66	200	670761337	670761205	5.960000e-37	165.0
33	TraesCS3A01G485800	chr4A	72.901	524	116	23	1190	1701	648794677	648794168	9.970000e-35	158.0
34	TraesCS3A01G485800	chr4A	77.778	270	24	19	65	321	714667310	714667064	1.680000e-27	134.0
35	TraesCS3A01G485800	chr4B	87.143	140	7	4	66	200	622342377	622342510	6.000000e-32	148.0
36	TraesCS3A01G485800	chr4B	84.800	125	6	6	65	177	430672208	430672085	2.190000e-21	113.0
37	TraesCS3A01G485800	chr2B	80.583	206	26	7	2382	2585	68197378	68197571	2.160000e-31	147.0
38	TraesCS3A01G485800	chr2B	79.630	162	24	6	1535	1690	773351349	773351507	1.020000e-19	108.0
39	TraesCS3A01G485800	chrUn	77.778	270	24	19	65	321	230759870	230759624	1.680000e-27	134.0
40	TraesCS3A01G485800	chr2D	89.888	89	6	2	2499	2584	43291232	43291320	7.870000e-21	111.0
41	TraesCS3A01G485800	chr1D	88.372	86	9	1	2483	2567	38282296	38282211	4.740000e-18	102.0
42	TraesCS3A01G485800	chr7B	85.567	97	13	1	2468	2563	750344698	750344794	1.700000e-17	100.0

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	TraesCS3A01G485800	chr3A	714595097	714597786	2689	False	4968.000000	4968	100.000000	1	2690	1	chr3A.!!$F2	2689
1	TraesCS3A01G485800	chr3A	702420406	702421607	1201	True	309.000000	309	72.468000	581	1800	1	chr3A.!!$R2	1219
2	TraesCS3A01G485800	chr3D	579580584	579583233	2649	True	869.900000	1801	83.853667	136	2682	3	chr3D.!!$R3	2546
3	TraesCS3A01G485800	chr3D	579398533	579400700	2167	False	698.500000	1775	91.350000	565	2682	4	chr3D.!!$F5	2117
4	TraesCS3A01G485800	chr3D	568235447	568236069	622	False	241.000000	241	74.290000	1088	1702	1	chr3D.!!$F4	614
5	TraesCS3A01G485800	chr3B	773746862	773748330	1468	False	641.033333	1720	95.006667	326	1799	3	chr3B.!!$F3	1473
6	TraesCS3A01G485800	chr3B	773880751	773883146	2395	True	423.400000	597	89.094000	139	2561	5	chr3B.!!$R4	2422
7	TraesCS3A01G485800	chr3B	756439232	756440294	1062	True	300.000000	300	72.703000	586	1664	1	chr3B.!!$R3	1078
8	TraesCS3A01G485800	chr7A	41047626	41048137	511	True	215.000000	215	74.857000	1190	1702	1	chr7A.!!$R1	512

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
296	325	0.457851	CGGTAGGGTTCAGAGCTGAG	59.542	60.0	0.00	0.0	41.13	3.35	F
1053	1193	0.037697	TGTTGATGTTCCGGGACTCG	60.038	55.0	15.59	0.0	38.88	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1155	1295	1.078848	GAATGTCAGCACCTCCGCT	60.079	57.895	0.0	0.0	45.21	5.52	R
2378	3016	1.337703	TGCAACCATGAAACAGTCAGC	59.662	47.619	0.0	0.0	40.43	4.26	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	End Stability
22	23	4.668576	ACAGTACAACATTGAATCAGCG	57.331	40.909	0.00	5.18
23	24	3.120199	ACAGTACAACATTGAATCAGCGC	60.120	43.478	0.00	5.92
24	25	3.073678	AGTACAACATTGAATCAGCGCA	58.926	40.909	11.47	6.09
25	26	3.691118	AGTACAACATTGAATCAGCGCAT	59.309	39.130	11.47	4.73
26	27	4.875536	AGTACAACATTGAATCAGCGCATA	59.124	37.500	11.47	3.14
27	28	4.019919	ACAACATTGAATCAGCGCATAC	57.980	40.909	11.47	2.39
28	29	3.439825	ACAACATTGAATCAGCGCATACA	59.560	39.130	11.47	2.29
29	30	3.680642	ACATTGAATCAGCGCATACAC	57.319	42.857	11.47	2.90
30	31	3.273434	ACATTGAATCAGCGCATACACT	58.727	40.909	11.47	3.55
31	32	3.691118	ACATTGAATCAGCGCATACACTT	59.309	39.130	11.47	3.16
32	33	4.875536	ACATTGAATCAGCGCATACACTTA	59.124	37.500	11.47	2.24
33	34	5.353956	ACATTGAATCAGCGCATACACTTAA	59.646	36.000	11.47	1.85
34	35	4.857871	TGAATCAGCGCATACACTTAAC	57.142	40.909	11.47	2.01
35	36	4.249661	TGAATCAGCGCATACACTTAACA	58.750	39.130	11.47	2.41
36	37	4.875536	TGAATCAGCGCATACACTTAACAT	59.124	37.500	11.47	2.71
37	38	5.006649	TGAATCAGCGCATACACTTAACATC	59.993	40.000	11.47	3.06
38	39	4.123497	TCAGCGCATACACTTAACATCT	57.877	40.909	11.47	2.90
39	40	4.112634	TCAGCGCATACACTTAACATCTC	58.887	43.478	11.47	2.75
40	41	4.115516	CAGCGCATACACTTAACATCTCT	58.884	43.478	11.47	3.10
41	42	4.208047	CAGCGCATACACTTAACATCTCTC	59.792	45.833	11.47	3.20
42	43	3.491267	GCGCATACACTTAACATCTCTCC	59.509	47.826	0.30	3.71
43	44	3.731216	CGCATACACTTAACATCTCTCCG	59.269	47.826	0.00	4.63
44	45	4.497507	CGCATACACTTAACATCTCTCCGA	60.498	45.833	0.00	4.55
45	46	4.740695	GCATACACTTAACATCTCTCCGAC	59.259	45.833	0.00	4.79
46	47	5.678871	GCATACACTTAACATCTCTCCGACA	60.679	44.000	0.00	4.35

Showing 1 to 25 of 131 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	4.613622	GCGCTGATTCAATGTTGTACTGTT	60.614	41.667	0.00	0.00	3.16
1	2	3.120199	GCGCTGATTCAATGTTGTACTGT	60.120	43.478	0.00	0.00	3.55
2	3	3.120234	TGCGCTGATTCAATGTTGTACTG	60.120	43.478	9.73	0.00	2.74
3	4	3.073678	TGCGCTGATTCAATGTTGTACT	58.926	40.909	9.73	0.00	2.73
4	5	3.469899	TGCGCTGATTCAATGTTGTAC	57.530	42.857	9.73	0.00	2.90
5	6	4.633565	TGTATGCGCTGATTCAATGTTGTA	59.366	37.500	9.73	0.00	2.41
6	7	3.439825	TGTATGCGCTGATTCAATGTTGT	59.560	39.130	9.73	0.00	3.32
7	8	3.787634	GTGTATGCGCTGATTCAATGTTG	59.212	43.478	9.73	0.00	3.33
8	9	3.691118	AGTGTATGCGCTGATTCAATGTT	59.309	39.130	9.73	33.62	2.71
9	10	3.273434	AGTGTATGCGCTGATTCAATGT	58.727	40.909	9.73	33.62	2.71
10	11	3.957671	AGTGTATGCGCTGATTCAATG	57.042	42.857	9.73	33.62	2.82
11	12	5.353956	TGTTAAGTGTATGCGCTGATTCAAT	59.646	36.000	9.73	35.34	2.57
12	13	4.693095	TGTTAAGTGTATGCGCTGATTCAA	59.307	37.500	9.73	35.34	2.69
13	14	4.249661	TGTTAAGTGTATGCGCTGATTCA	58.750	39.130	9.73	35.34	2.57
14	15	4.857871	TGTTAAGTGTATGCGCTGATTC	57.142	40.909	9.73	35.34	2.52
15	16	5.118990	AGATGTTAAGTGTATGCGCTGATT	58.881	37.500	9.73	35.34	2.57
16	17	4.697514	AGATGTTAAGTGTATGCGCTGAT	58.302	39.130	9.73	35.34	2.90
17	18	4.112634	GAGATGTTAAGTGTATGCGCTGA	58.887	43.478	9.73	35.34	4.26
18	19	4.115516	AGAGATGTTAAGTGTATGCGCTG	58.884	43.478	9.73	35.34	5.18
19	20	4.363999	GAGAGATGTTAAGTGTATGCGCT	58.636	43.478	9.73	36.97	5.92
20	21	3.491267	GGAGAGATGTTAAGTGTATGCGC	59.509	47.826	0.00	0.00	6.09
21	22	3.731216	CGGAGAGATGTTAAGTGTATGCG	59.269	47.826	0.00	0.00	4.73
22	23	4.740695	GTCGGAGAGATGTTAAGTGTATGC	59.259	45.833	0.00	36.95	3.14
23	24	5.891451	TGTCGGAGAGATGTTAAGTGTATG	58.109	41.667	0.00	36.95	2.39
24	25	6.525578	TTGTCGGAGAGATGTTAAGTGTAT	57.474	37.500	0.00	36.95	2.29

Showing 1 to 25 of 134 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.