AutoCloner

Multiple sequence alignment - TraesCS6D01G307600

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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	TraesCS6D01G307600	chr6D	100.000	2375	0	0	1	2375	418731982	418734356	0.000000e+00	4386.0
1	TraesCS6D01G307600	chr6D	92.949	780	34	10	943	1712	418770023	418769255	0.000000e+00	1116.0
2	TraesCS6D01G307600	chr6D	84.310	580	46	28	202	749	418883778	418883212	2.090000e-145	525.0
3	TraesCS6D01G307600	chr6D	84.854	548	43	13	271	815	418770714	418770204	1.260000e-142	516.0
4	TraesCS6D01G307600	chr6D	88.957	163	17	1	12	174	452911242	452911403	1.440000e-47	200.0
5	TraesCS6D01G307600	chr6D	93.750	48	1	1	1746	1793	418769241	418769196	1.180000e-08	71.3
6	TraesCS6D01G307600	chr6B	92.198	910	32	16	815	1710	631193170	631194054	0.000000e+00	1251.0
7	TraesCS6D01G307600	chr6B	94.643	616	21	4	1750	2364	631194235	631194839	0.000000e+00	944.0
8	TraesCS6D01G307600	chr6B	89.118	680	37	14	943	1604	631246118	631245458	0.000000e+00	811.0
9	TraesCS6D01G307600	chr6B	86.037	709	46	24	830	1526	631741230	631740563	0.000000e+00	712.0
10	TraesCS6D01G307600	chr6B	87.072	642	51	12	175	815	631192520	631193130	0.000000e+00	697.0
11	TraesCS6D01G307600	chr6B	88.156	591	40	16	940	1528	631843969	631843407	0.000000e+00	676.0
12	TraesCS6D01G307600	chr6B	87.479	583	36	14	830	1404	631534986	631534433	2.570000e-179	638.0
13	TraesCS6D01G307600	chr6B	84.274	585	39	29	1602	2167	631245274	631244724	2.710000e-144	521.0
14	TraesCS6D01G307600	chr6B	86.214	486	39	20	280	748	631535623	631535149	3.520000e-138	501.0
15	TraesCS6D01G307600	chr6B	82.444	581	56	21	175	749	631741884	631741344	1.290000e-127	466.0
16	TraesCS6D01G307600	chr6B	91.228	57	1	3	1628	1681	630918911	630918856	9.100000e-10	75.0
17	TraesCS6D01G307600	chr6B	100.000	36	0	0	814	849	631246253	631246218	1.520000e-07	67.6
18	TraesCS6D01G307600	chr6A	89.858	917	46	25	830	1709	562400646	562399740	0.000000e+00	1134.0
19	TraesCS6D01G307600	chr6A	84.701	804	46	35	937	1681	562271928	562272713	0.000000e+00	732.0
20	TraesCS6D01G307600	chr6A	89.127	561	34	14	844	1404	562250747	562251280	0.000000e+00	673.0
21	TraesCS6D01G307600	chr6A	89.847	522	29	7	886	1404	562470580	562470080	0.000000e+00	649.0
22	TraesCS6D01G307600	chr6A	83.651	630	53	31	223	815	562471301	562470685	4.460000e-152	547.0
23	TraesCS6D01G307600	chr6A	87.990	408	32	7	175	574	562249589	562249987	1.290000e-127	466.0
24	TraesCS6D01G307600	chr6A	82.290	559	48	23	271	815	562271221	562271742	1.010000e-118	436.0
25	TraesCS6D01G307600	chr6A	91.045	268	23	1	483	749	562402220	562401953	6.240000e-96	361.0
26	TraesCS6D01G307600	chr6A	85.600	125	7	5	611	735	562250432	562250545	1.150000e-23	121.0
27	TraesCS6D01G307600	chr6A	80.952	126	14	6	1566	1681	291949382	291949257	9.040000e-15	91.6
28	TraesCS6D01G307600	chr6A	100.000	36	0	0	814	849	562271798	562271833	1.520000e-07	67.6
29	TraesCS6D01G307600	chr5D	91.716	169	13	1	1	169	489304186	489304353	1.420000e-57	233.0
30	TraesCS6D01G307600	chr5D	85.030	167	22	3	11	176	406476752	406476916	1.460000e-37	167.0
31	TraesCS6D01G307600	chr7D	87.209	172	21	1	1	172	26811007	26810837	6.700000e-46	195.0
32	TraesCS6D01G307600	chr2D	87.654	162	19	1	12	173	8972227	8972387	1.120000e-43	187.0
33	TraesCS6D01G307600	chr2D	85.549	173	23	2	1	173	191658954	191658784	1.880000e-41	180.0
34	TraesCS6D01G307600	chr2D	86.335	161	19	2	12	172	575685110	575684953	3.140000e-39	172.0
35	TraesCS6D01G307600	chr7B	86.391	169	20	3	5	172	691192451	691192285	5.210000e-42	182.0
36	TraesCS6D01G307600	chr5A	85.714	161	21	2	12	172	28419620	28419778	4.060000e-38	169.0

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	TraesCS6D01G307600	chr6D	418731982	418734356	2374	False	4386.000000	4386	100.000000	1	2375	1	chr6D.!!$F1	2374
1	TraesCS6D01G307600	chr6D	418769196	418770714	1518	True	567.766667	1116	90.517667	271	1793	3	chr6D.!!$R2	1522
2	TraesCS6D01G307600	chr6D	418883212	418883778	566	True	525.000000	525	84.310000	202	749	1	chr6D.!!$R1	547
3	TraesCS6D01G307600	chr6B	631192520	631194839	2319	False	964.000000	1251	91.304333	175	2364	3	chr6B.!!$F1	2189
4	TraesCS6D01G307600	chr6B	631843407	631843969	562	True	676.000000	676	88.156000	940	1528	1	chr6B.!!$R2	588
5	TraesCS6D01G307600	chr6B	631740563	631741884	1321	True	589.000000	712	84.240500	175	1526	2	chr6B.!!$R5	1351
6	TraesCS6D01G307600	chr6B	631534433	631535623	1190	True	569.500000	638	86.846500	280	1404	2	chr6B.!!$R4	1124
7	TraesCS6D01G307600	chr6B	631244724	631246253	1529	True	466.533333	811	91.130667	814	2167	3	chr6B.!!$R3	1353
8	TraesCS6D01G307600	chr6A	562399740	562402220	2480	True	747.500000	1134	90.451500	483	1709	2	chr6A.!!$R2	1226
9	TraesCS6D01G307600	chr6A	562470080	562471301	1221	True	598.000000	649	86.749000	223	1404	2	chr6A.!!$R3	1181
10	TraesCS6D01G307600	chr6A	562249589	562251280	1691	False	420.000000	673	87.572333	175	1404	3	chr6A.!!$F1	1229
11	TraesCS6D01G307600	chr6A	562271221	562272713	1492	False	411.866667	732	88.997000	271	1681	3	chr6A.!!$F2	1410

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
808	2444	0.652592	GCCATACGTACAAGCAGCAG	59.347	55.0	0.0	0.0	0.0	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1958	4148	0.794473	GGAAAGAAACGCGGTACCTG	59.206	55.0	12.47	4.83	0.0	4.0	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
21	22	3.855668	TCAACAAAAATGGGATCCACCT	58.144	40.909	15.23	0.00	35.80	4.00
22	23	3.577848	TCAACAAAAATGGGATCCACCTG	59.422	43.478	15.23	4.17	35.80	4.00
23	24	3.258722	ACAAAAATGGGATCCACCTGT	57.741	42.857	15.23	4.81	35.80	4.00
24	25	3.165071	ACAAAAATGGGATCCACCTGTC	58.835	45.455	15.23	0.00	35.80	3.51
25	26	3.164268	CAAAAATGGGATCCACCTGTCA	58.836	45.455	15.23	0.77	35.80	3.58
26	27	3.763557	AAAATGGGATCCACCTGTCAT	57.236	42.857	15.23	3.47	35.80	3.06
27	28	4.879295	AAAATGGGATCCACCTGTCATA	57.121	40.909	15.23	0.00	35.80	2.15
28	29	4.879295	AAATGGGATCCACCTGTCATAA	57.121	40.909	15.23	0.00	35.80	1.90
29	30	5.408079	AAATGGGATCCACCTGTCATAAT	57.592	39.130	15.23	0.00	35.80	1.28
30	31	4.647564	ATGGGATCCACCTGTCATAATC	57.352	45.455	15.23	0.00	35.80	1.75
31	32	3.392730	TGGGATCCACCTGTCATAATCA	58.607	45.455	15.23	0.00	38.98	2.57
32	33	3.392285	TGGGATCCACCTGTCATAATCAG	59.608	47.826	15.23	0.00	38.98	2.90
42	43	6.573664	CCTGTCATAATCAGGTTCAAAACA	57.426	37.500	4.06	0.00	45.09	2.83
43	44	6.980593	CCTGTCATAATCAGGTTCAAAACAA	58.019	36.000	4.06	0.00	45.09	2.83
44	45	6.863126	CCTGTCATAATCAGGTTCAAAACAAC	59.137	38.462	4.06	0.00	45.09	3.32
45	46	6.744112	TGTCATAATCAGGTTCAAAACAACC	58.256	36.000	0.00	0.00	45.66	3.77
53	54	4.600692	GGTTCAAAACAACCTAAGCCAT	57.399	40.909	0.00	0.00	42.46	4.40
54	55	4.556233	GGTTCAAAACAACCTAAGCCATC	58.444	43.478	0.00	0.00	42.46	3.51
55	56	4.556233	GTTCAAAACAACCTAAGCCATCC	58.444	43.478	0.00	0.00	0.00	3.51
56	57	3.838565	TCAAAACAACCTAAGCCATCCA	58.161	40.909	0.00	0.00	0.00	3.41
57	58	4.219115	TCAAAACAACCTAAGCCATCCAA	58.781	39.130	0.00	0.00	0.00	3.53
58	59	4.837860	TCAAAACAACCTAAGCCATCCAAT	59.162	37.500	0.00	0.00	0.00	3.16
59	60	6.013379	TCAAAACAACCTAAGCCATCCAATA	58.987	36.000	0.00	0.00	0.00	1.90
60	61	6.152661	TCAAAACAACCTAAGCCATCCAATAG	59.847	38.462	0.00	0.00	0.00	1.73
61	62	4.862641	ACAACCTAAGCCATCCAATAGT	57.137	40.909	0.00	0.00	0.00	2.12

Showing 1 to 25 of 155 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	3.577848	CAGGTGGATCCCATTTTTGTTGA	59.422	43.478	9.90	0.00	35.28	3.18
1	2	3.324556	ACAGGTGGATCCCATTTTTGTTG	59.675	43.478	9.90	0.00	35.28	3.33
2	3	3.578282	GACAGGTGGATCCCATTTTTGTT	59.422	43.478	9.90	0.00	35.28	2.83
3	4	3.165071	GACAGGTGGATCCCATTTTTGT	58.835	45.455	9.90	5.28	35.28	2.83
4	5	3.164268	TGACAGGTGGATCCCATTTTTG	58.836	45.455	9.90	1.99	35.28	2.44
5	6	3.541242	TGACAGGTGGATCCCATTTTT	57.459	42.857	9.90	0.00	35.28	1.94
6	7	3.763557	ATGACAGGTGGATCCCATTTT	57.236	42.857	9.90	0.00	35.28	1.82
7	8	4.879295	TTATGACAGGTGGATCCCATTT	57.121	40.909	9.90	0.00	35.28	2.32
8	9	4.416513	TGATTATGACAGGTGGATCCCATT	59.583	41.667	9.90	0.00	35.28	3.16
9	10	3.982730	TGATTATGACAGGTGGATCCCAT	59.017	43.478	9.90	6.72	35.28	4.00
10	11	3.392285	CTGATTATGACAGGTGGATCCCA	59.608	47.826	9.90	0.00	36.75	4.37
11	12	3.244700	CCTGATTATGACAGGTGGATCCC	60.245	52.174	9.90	0.00	46.71	3.85
12	13	4.013267	CCTGATTATGACAGGTGGATCC	57.987	50.000	4.20	4.20	46.71	3.36
20	21	6.863126	GGTTGTTTTGAACCTGATTATGACAG	59.137	38.462	0.00	0.00	42.03	3.51
21	22	6.744112	GGTTGTTTTGAACCTGATTATGACA	58.256	36.000	0.00	0.00	42.03	3.58
32	33	4.556233	GATGGCTTAGGTTGTTTTGAACC	58.444	43.478	0.00	0.00	45.16	3.62
33	34	4.038642	TGGATGGCTTAGGTTGTTTTGAAC	59.961	41.667	0.00	0.00	0.00	3.18
34	35	4.219115	TGGATGGCTTAGGTTGTTTTGAA	58.781	39.130	0.00	0.00	0.00	2.69
35	36	3.838565	TGGATGGCTTAGGTTGTTTTGA	58.161	40.909	0.00	0.00	0.00	2.69
36	37	4.599047	TTGGATGGCTTAGGTTGTTTTG	57.401	40.909	0.00	0.00	0.00	2.44
37	38	6.016555	ACTATTGGATGGCTTAGGTTGTTTT	58.983	36.000	0.00	0.00	0.00	2.43
38	39	5.418840	CACTATTGGATGGCTTAGGTTGTTT	59.581	40.000	0.00	0.00	0.00	2.83
39	40	4.949856	CACTATTGGATGGCTTAGGTTGTT	59.050	41.667	0.00	0.00	0.00	2.83
40	41	4.018415	ACACTATTGGATGGCTTAGGTTGT	60.018	41.667	0.00	0.00	0.00	3.32
41	42	4.526970	ACACTATTGGATGGCTTAGGTTG	58.473	43.478	0.00	0.00	0.00	3.77

Showing 1 to 25 of 178 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.