AutoCloner

Multiple sequence alignment - TraesCS2D01G461300

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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	TraesCS2D01G461300	chr2D	100.000	2240	0	0	1	2240	567641046	567643285	0.000000e+00	4137.0
1	TraesCS2D01G461300	chr2D	81.125	800	64	35	743	1490	567594592	567595356	5.400000e-156	560.0
2	TraesCS2D01G461300	chr2D	79.032	558	68	26	894	1430	567677811	567678340	9.910000e-89	337.0
3	TraesCS2D01G461300	chr2D	91.045	134	12	0	993	1126	567806020	567806153	4.910000e-42	182.0
4	TraesCS2D01G461300	chr2A	96.429	784	26	1	1457	2240	707176780	707177561	0.000000e+00	1291.0
5	TraesCS2D01G461300	chr2A	90.997	622	25	8	866	1463	707168574	707169188	0.000000e+00	809.0
6	TraesCS2D01G461300	chr2A	81.234	762	70	27	743	1449	707077211	707077954	4.210000e-152	547.0
7	TraesCS2D01G461300	chr2A	91.255	263	21	2	467	728	742051742	742051481	7.610000e-95	357.0
8	TraesCS2D01G461300	chr2A	91.255	263	21	2	467	728	742083610	742083349	7.610000e-95	357.0
9	TraesCS2D01G461300	chr2A	79.107	560	74	19	894	1430	707235726	707236265	1.650000e-91	346.0
10	TraesCS2D01G461300	chr2A	90.114	263	24	2	467	728	742115888	742115627	7.660000e-90	340.0
11	TraesCS2D01G461300	chr2A	78.383	532	68	20	894	1395	707222022	707222536	3.620000e-78	302.0
12	TraesCS2D01G461300	chr2A	75.073	686	97	44	788	1453	707064116	707064747	3.690000e-63	252.0
13	TraesCS2D01G461300	chr2A	76.050	238	54	3	1882	2118	595386938	595386703	1.090000e-23	121.0
14	TraesCS2D01G461300	chr2A	81.481	135	10	6	960	1079	706922491	706922625	1.830000e-16	97.1
15	TraesCS2D01G461300	chr2A	89.583	48	5	0	1543	1590	374072100	374072147	6.680000e-06	62.1
16	TraesCS2D01G461300	chr2A	85.000	60	7	2	1997	2056	719734570	719734513	2.400000e-05	60.2
17	TraesCS2D01G461300	chr2B	90.143	842	37	7	727	1546	680408716	680409533	0.000000e+00	1053.0
18	TraesCS2D01G461300	chr2B	93.956	364	21	1	1878	2240	680409628	680409991	1.170000e-152	549.0
19	TraesCS2D01G461300	chr2B	80.267	750	66	35	797	1490	680322333	680323056	7.190000e-135	490.0
20	TraesCS2D01G461300	chr2B	78.585	537	61	28	864	1373	680221227	680221736	2.790000e-79	305.0
21	TraesCS2D01G461300	chr2B	79.412	476	49	19	993	1430	680446078	680446542	7.830000e-75	291.0
22	TraesCS2D01G461300	chr2B	74.474	760	118	42	788	1521	680237369	680238078	2.210000e-65	259.0
23	TraesCS2D01G461300	chr2B	79.429	350	46	16	993	1336	680308726	680309055	8.050000e-55	224.0
24	TraesCS2D01G461300	chr2B	94.828	58	3	0	274	331	141541561	141541504	8.520000e-15	91.6
25	TraesCS2D01G461300	chr2B	96.296	54	2	0	269	322	111667195	111667248	3.060000e-14	89.8
26	TraesCS2D01G461300	chr2B	93.333	45	3	0	1546	1590	477002101	477002145	1.440000e-07	67.6
27	TraesCS2D01G461300	chr7D	97.289	332	6	2	1	332	62282509	62282181	5.400000e-156	560.0
28	TraesCS2D01G461300	chr1D	94.152	342	9	6	1	331	318477181	318476840	5.520000e-141	510.0
29	TraesCS2D01G461300	chr5D	96.444	225	8	0	462	686	538716880	538716656	2.720000e-99	372.0
30	TraesCS2D01G461300	chr5D	96.364	220	8	0	467	686	413283043	413282824	1.640000e-96	363.0
31	TraesCS2D01G461300	chr5D	95.909	220	9	0	467	686	340514238	340514019	7.610000e-95	357.0
32	TraesCS2D01G461300	chr5D	85.981	214	18	7	467	679	296966029	296966231	3.750000e-53	219.0
33	TraesCS2D01G461300	chr5D	83.505	194	30	2	142	334	210775241	210775049	1.770000e-41	180.0
34	TraesCS2D01G461300	chr5D	94.000	50	3	0	1544	1593	285859483	285859434	2.390000e-10	76.8
35	TraesCS2D01G461300	chr3D	90.840	262	20	2	467	728	485206655	485206398	4.580000e-92	348.0
36	TraesCS2D01G461300	chr3D	89.888	267	20	4	463	728	61600621	61600881	9.910000e-89	337.0
37	TraesCS2D01G461300	chr3D	87.019	208	15	3	467	673	388809882	388809686	8.050000e-55	224.0
38	TraesCS2D01G461300	chr3D	83.417	199	31	2	136	333	553331464	553331661	1.370000e-42	183.0
39	TraesCS2D01G461300	chr3D	79.325	237	43	5	1885	2119	427084545	427084313	6.400000e-36	161.0
40	TraesCS2D01G461300	chr4D	89.179	268	23	6	462	728	480816457	480816195	1.660000e-86	329.0
41	TraesCS2D01G461300	chr4D	87.500	48	6	0	1543	1590	292176079	292176126	3.110000e-04	56.5
42	TraesCS2D01G461300	chr5A	92.544	228	16	1	456	682	616634248	616634475	2.150000e-85	326.0
43	TraesCS2D01G461300	chr6D	83.505	194	30	2	136	328	460806927	460807119	1.770000e-41	180.0
44	TraesCS2D01G461300	chr1B	79.545	220	39	5	1887	2104	185077600	185077815	3.850000e-33	152.0
45	TraesCS2D01G461300	chr1B	76.471	187	31	12	1938	2118	594003290	594003111	3.060000e-14	89.8
46	TraesCS2D01G461300	chr7B	78.218	202	39	5	1907	2106	52921600	52921798	8.400000e-25	124.0
47	TraesCS2D01G461300	chr7B	77.835	194	37	5	1929	2119	731855758	731855948	5.060000e-22	115.0
48	TraesCS2D01G461300	chr5B	77.000	200	34	7	143	341	461708567	461708379	1.090000e-18	104.0
49	TraesCS2D01G461300	chr3A	86.486	74	10	0	269	342	21335295	21335222	5.130000e-12	82.4
50	TraesCS2D01G461300	chr3A	91.304	46	4	0	1545	1590	681753517	681753562	1.860000e-06	63.9
51	TraesCS2D01G461300	chr3B	92.157	51	4	0	1543	1593	55365475	55365425	3.090000e-09	73.1
52	TraesCS2D01G461300	chr4B	91.667	48	4	0	1546	1593	371286826	371286779	1.440000e-07	67.6
53	TraesCS2D01G461300	chr6A	90.000	50	5	0	1544	1593	98181482	98181433	5.160000e-07	65.8

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	TraesCS2D01G461300	chr2D	567641046	567643285	2239	False	4137	4137	100.0000	1	2240	1	chr2D.!!$F2	2239
1	TraesCS2D01G461300	chr2D	567594592	567595356	764	False	560	560	81.1250	743	1490	1	chr2D.!!$F1	747
2	TraesCS2D01G461300	chr2D	567677811	567678340	529	False	337	337	79.0320	894	1430	1	chr2D.!!$F3	536
3	TraesCS2D01G461300	chr2A	707176780	707177561	781	False	1291	1291	96.4290	1457	2240	1	chr2A.!!$F6	783
4	TraesCS2D01G461300	chr2A	707168574	707169188	614	False	809	809	90.9970	866	1463	1	chr2A.!!$F5	597
5	TraesCS2D01G461300	chr2A	707077211	707077954	743	False	547	547	81.2340	743	1449	1	chr2A.!!$F4	706
6	TraesCS2D01G461300	chr2A	707235726	707236265	539	False	346	346	79.1070	894	1430	1	chr2A.!!$F8	536
7	TraesCS2D01G461300	chr2A	707222022	707222536	514	False	302	302	78.3830	894	1395	1	chr2A.!!$F7	501
8	TraesCS2D01G461300	chr2A	707064116	707064747	631	False	252	252	75.0730	788	1453	1	chr2A.!!$F3	665
9	TraesCS2D01G461300	chr2B	680408716	680409991	1275	False	801	1053	92.0495	727	2240	2	chr2B.!!$F8	1513
10	TraesCS2D01G461300	chr2B	680322333	680323056	723	False	490	490	80.2670	797	1490	1	chr2B.!!$F6	693
11	TraesCS2D01G461300	chr2B	680221227	680221736	509	False	305	305	78.5850	864	1373	1	chr2B.!!$F3	509
12	TraesCS2D01G461300	chr2B	680237369	680238078	709	False	259	259	74.4740	788	1521	1	chr2B.!!$F4	733

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
46	47	0.031994	GACATGCGGGCTGTTTTGTT	59.968	50.0	0.0	0.0	0.00	2.83	F
163	164	0.034767	CATGGAGGCAGAGGCAGAAA	60.035	55.0	0.0	0.0	43.71	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1174	1319	0.985760	ATGGTGCTGGTACCGGTAAA	59.014	50.0	21.95	9.97	43.87	2.01	R
1342	1529	1.035139	CCATTAAGGAGCATGGGCAC	58.965	55.0	0.00	0.00	44.61	5.01	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
18	19	2.654939	GAGCAACGAACTAGCGAGG	58.345	57.895	0.00	0.00	34.83	4.63
19	20	0.802607	GAGCAACGAACTAGCGAGGG	60.803	60.000	0.00	0.00	34.83	4.30
20	21	1.214589	GCAACGAACTAGCGAGGGA	59.785	57.895	0.00	0.00	34.83	4.20
21	22	0.179108	GCAACGAACTAGCGAGGGAT	60.179	55.000	0.00	0.00	34.83	3.85
22	23	1.560923	CAACGAACTAGCGAGGGATG	58.439	55.000	0.00	0.00	34.83	3.51
23	24	1.135083	CAACGAACTAGCGAGGGATGT	60.135	52.381	0.00	0.00	34.83	3.06
24	25	1.183549	ACGAACTAGCGAGGGATGTT	58.816	50.000	0.00	0.00	34.83	2.71
25	26	1.135083	ACGAACTAGCGAGGGATGTTG	60.135	52.381	0.00	0.00	34.83	3.33
26	27	1.291132	GAACTAGCGAGGGATGTTGC	58.709	55.000	0.00	0.00	0.00	4.17
27	28	0.460284	AACTAGCGAGGGATGTTGCG	60.460	55.000	0.00	0.00	31.41	4.85
28	29	1.320344	ACTAGCGAGGGATGTTGCGA	61.320	55.000	0.00	0.00	31.41	5.10
29	30	0.872021	CTAGCGAGGGATGTTGCGAC	60.872	60.000	0.00	0.00	31.41	5.19
30	31	1.600511	TAGCGAGGGATGTTGCGACA	61.601	55.000	9.77	9.77	40.71	4.35
32	33	2.009108	CGAGGGATGTTGCGACATG	58.991	57.895	24.47	5.65	46.27	3.21
42	43	3.737172	GCGACATGCGGGCTGTTT	61.737	61.111	10.70	0.00	41.29	2.83
43	44	2.953821	CGACATGCGGGCTGTTTT	59.046	55.556	0.00	0.00	36.03	2.43
44	45	1.442520	CGACATGCGGGCTGTTTTG	60.443	57.895	0.00	0.00	36.03	2.44
45	46	1.659794	GACATGCGGGCTGTTTTGT	59.340	52.632	0.00	0.00	0.00	2.83
46	47	0.031994	GACATGCGGGCTGTTTTGTT	59.968	50.000	0.00	0.00	0.00	2.83
47	48	0.249405	ACATGCGGGCTGTTTTGTTG	60.249	50.000	0.00	0.00	0.00	3.33
48	49	0.945265	CATGCGGGCTGTTTTGTTGG	60.945	55.000	0.00	0.00	0.00	3.77
49	50	1.112315	ATGCGGGCTGTTTTGTTGGA	61.112	50.000	0.00	0.00	0.00	3.53
50	51	1.323271	TGCGGGCTGTTTTGTTGGAA	61.323	50.000	0.00	0.00	0.00	3.53
51	52	0.874175	GCGGGCTGTTTTGTTGGAAC	60.874	55.000	0.00	0.00	0.00	3.62
52	53	0.249280	CGGGCTGTTTTGTTGGAACC	60.249	55.000	0.00	0.00	0.00	3.62

Showing 1 to 25 of 411 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	0.802607	CCCTCGCTAGTTCGTTGCTC	60.803	60.000	0.00	4.26
1	2	1.215647	CCCTCGCTAGTTCGTTGCT	59.784	57.895	0.00	3.91
4	5	1.183549	ACATCCCTCGCTAGTTCGTT	58.816	50.000	0.00	3.85
5	6	1.135083	CAACATCCCTCGCTAGTTCGT	60.135	52.381	0.00	3.85
6	7	1.560923	CAACATCCCTCGCTAGTTCG	58.439	55.000	0.00	3.95
7	8	1.291132	GCAACATCCCTCGCTAGTTC	58.709	55.000	0.00	3.01
8	9	0.460284	CGCAACATCCCTCGCTAGTT	60.460	55.000	0.00	2.24
9	10	1.141881	CGCAACATCCCTCGCTAGT	59.858	57.895	0.00	2.57
10	11	0.872021	GTCGCAACATCCCTCGCTAG	60.872	60.000	0.00	3.42
11	12	1.141019	GTCGCAACATCCCTCGCTA	59.859	57.895	0.00	4.26
12	13	2.125512	GTCGCAACATCCCTCGCT	60.126	61.111	0.00	4.93
13	14	1.815421	ATGTCGCAACATCCCTCGC	60.815	57.895	42.59	5.03
14	15	2.009108	CATGTCGCAACATCCCTCG	58.991	57.895	44.41	4.63
15	16	1.723870	GCATGTCGCAACATCCCTC	59.276	57.895	44.41	4.30
16	17	2.108514	CGCATGTCGCAACATCCCT	61.109	57.895	44.41	4.20
17	18	2.404789	CGCATGTCGCAACATCCC	59.595	61.111	44.41	3.85
18	19	2.404789	CCGCATGTCGCAACATCC	59.595	61.111	44.41	3.51
19	20	2.404789	CCCGCATGTCGCAACATC	59.595	61.111	44.41	3.06
22	23	4.465512	CAGCCCGCATGTCGCAAC	62.466	66.667	42.60	4.17
25	26	3.267597	AAAACAGCCCGCATGTCGC	62.268	57.895	36.73	5.19
26	27	1.442520	CAAAACAGCCCGCATGTCG	60.443	57.895	38.08	4.35
27	28	0.031994	AACAAAACAGCCCGCATGTC	59.968	50.000	0.00	3.06
28	29	0.249405	CAACAAAACAGCCCGCATGT	60.249	50.000	0.00	3.21
29	30	0.945265	CCAACAAAACAGCCCGCATG	60.945	55.000	0.00	4.06
30	31	1.112315	TCCAACAAAACAGCCCGCAT	61.112	50.000	0.00	4.73

Showing 1 to 25 of 425 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.