AutoCloner

Multiple sequence alignment - TraesCS2D01G383400

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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	TraesCS2D01G383400	chr2D	100.000	4632	0	0	1	4632	487935890	487931259	0.000000e+00	8554.0
1	TraesCS2D01G383400	chr2D	84.172	2723	228	83	991	3652	487725380	487722800	0.000000e+00	2453.0
2	TraesCS2D01G383400	chr2D	85.501	2076	181	51	1689	3718	486390982	486392983	0.000000e+00	2056.0
3	TraesCS2D01G383400	chr2D	83.402	1946	194	65	988	2907	487594597	487592755	0.000000e+00	1685.0
4	TraesCS2D01G383400	chr2D	85.372	834	51	34	794	1602	486390121	486390908	0.000000e+00	798.0
5	TraesCS2D01G383400	chr2D	94.382	178	10	0	1	178	201456385	201456562	1.640000e-69	274.0
6	TraesCS2D01G383400	chr2D	94.857	175	9	0	4	178	442966911	442966737	1.640000e-69	274.0
7	TraesCS2D01G383400	chr2D	79.830	352	33	13	987	1320	488059614	488059283	6.030000e-54	222.0
8	TraesCS2D01G383400	chr2D	88.701	177	20	0	1426	1602	488058838	488058662	2.810000e-52	217.0
9	TraesCS2D01G383400	chr2D	76.267	375	40	21	218	586	486389770	486390101	2.230000e-33	154.0
10	TraesCS2D01G383400	chr2D	83.582	67	8	3	149	213	186318031	186318096	5.010000e-05	60.2
11	TraesCS2D01G383400	chr2D	94.737	38	1	1	3938	3975	81313522	81313558	1.800000e-04	58.4
12	TraesCS2D01G383400	chr2B	90.272	2827	169	45	1166	3936	572314291	572311515	0.000000e+00	3600.0
13	TraesCS2D01G383400	chr2B	84.288	2985	289	97	988	3922	572180170	572177316	0.000000e+00	2748.0
14	TraesCS2D01G383400	chr2B	85.444	1690	139	58	794	2453	571345302	571346914	0.000000e+00	1659.0
15	TraesCS2D01G383400	chr2B	86.556	662	31	26	3978	4611	572311341	572310710	0.000000e+00	676.0
16	TraesCS2D01G383400	chr2B	82.313	441	59	10	1908	2347	572324577	572324155	9.470000e-97	364.0
17	TraesCS2D01G383400	chr2B	80.876	502	49	27	269	744	572315137	572314657	7.370000e-93	351.0
18	TraesCS2D01G383400	chr2B	87.719	285	21	8	794	1073	572314564	572314289	2.080000e-83	320.0
19	TraesCS2D01G383400	chr2B	84.228	298	35	6	3485	3771	82961420	82961124	3.530000e-71	279.0
20	TraesCS2D01G383400	chr2B	78.252	492	60	22	3072	3559	572322504	572322056	5.910000e-69	272.0
21	TraesCS2D01G383400	chr2B	84.884	258	27	8	1384	1633	572325289	572325036	2.770000e-62	250.0
22	TraesCS2D01G383400	chr2B	86.452	155	21	0	1687	1841	572324909	572324755	2.220000e-38	171.0
23	TraesCS2D01G383400	chr2B	89.130	138	10	2	4482	4614	572177194	572177057	2.870000e-37	167.0
24	TraesCS2D01G383400	chr2B	97.500	40	1	0	187	226	599206733	599206694	8.320000e-08	69.4
25	TraesCS2D01G383400	chr2A	84.404	3097	288	101	794	3752	631854841	631857880	0.000000e+00	2863.0
26	TraesCS2D01G383400	chr2A	88.458	1906	94	51	543	2384	632590038	632588195	0.000000e+00	2185.0
27	TraesCS2D01G383400	chr2A	91.441	1554	86	20	2388	3918	632588115	632586586	0.000000e+00	2089.0
28	TraesCS2D01G383400	chr2A	85.648	648	73	9	2424	3065	46336674	46337307	0.000000e+00	664.0
29	TraesCS2D01G383400	chr2A	80.000	480	51	25	3073	3535	46337343	46337794	3.480000e-81	313.0
30	TraesCS2D01G383400	chr2A	95.025	201	6	2	3984	4183	632585760	632585563	3.480000e-81	313.0
31	TraesCS2D01G383400	chr2A	92.308	169	4	5	218	377	632590283	632590115	1.000000e-56	231.0
32	TraesCS2D01G383400	chr2A	78.393	361	37	15	987	1320	632596477	632596131	3.660000e-46	196.0
33	TraesCS2D01G383400	chr2A	87.742	155	19	0	1687	1841	632595149	632594995	1.020000e-41	182.0
34	TraesCS2D01G383400	chr2A	76.533	375	42	20	218	586	631854487	631854821	3.710000e-36	163.0
35	TraesCS2D01G383400	chr2A	77.606	259	31	18	4222	4460	632585310	632585059	1.050000e-26	132.0
36	TraesCS2D01G383400	chr2A	94.340	53	3	0	4312	4364	632585239	632585187	1.070000e-11	82.4
37	TraesCS2D01G383400	chr7D	86.883	648	65	8	2424	3065	446551195	446550562	0.000000e+00	708.0
38	TraesCS2D01G383400	chr7D	82.151	437	43	20	1936	2364	446551626	446551217	4.440000e-90	342.0
39	TraesCS2D01G383400	chr7D	78.452	478	72	23	3073	3539	446550526	446550069	2.730000e-72	283.0
40	TraesCS2D01G383400	chr7D	94.318	176	9	1	4	178	402316513	402316338	7.640000e-68	268.0
41	TraesCS2D01G383400	chr7D	90.196	51	3	2	187	237	71621323	71621371	1.080000e-06	65.8
42	TraesCS2D01G383400	chr7A	85.031	648	73	9	2424	3065	321636676	321636047	5.050000e-179	638.0
43	TraesCS2D01G383400	chr7A	94.767	172	9	0	7	178	711960407	711960578	7.640000e-68	268.0
44	TraesCS2D01G383400	chr7A	84.000	150	15	7	3073	3216	321636011	321635865	8.080000e-28	135.0
45	TraesCS2D01G383400	chr3D	86.978	407	38	6	2664	3065	16449279	16449675	1.180000e-120	444.0
46	TraesCS2D01G383400	chr3D	79.079	478	69	22	3073	3539	16449711	16450168	2.710000e-77	300.0
47	TraesCS2D01G383400	chr3D	86.667	60	7	1	162	220	291768074	291768015	1.080000e-06	65.8
48	TraesCS2D01G383400	chr6B	82.517	429	53	14	1936	2362	247035824	247035416	1.580000e-94	357.0
49	TraesCS2D01G383400	chr4B	82.517	429	53	14	1936	2362	16786690	16787098	1.580000e-94	357.0
50	TraesCS2D01G383400	chr4A	82.517	429	53	14	1936	2362	729645110	729644702	1.580000e-94	357.0
51	TraesCS2D01G383400	chr3B	82.284	429	54	14	1936	2362	555551109	555550701	7.370000e-93	351.0
52	TraesCS2D01G383400	chr6A	81.944	432	47	19	3360	3771	226334895	226334475	2.060000e-88	337.0
53	TraesCS2D01G383400	chr6A	87.727	220	22	5	3972	4187	226334308	226334090	7.690000e-63	252.0
54	TraesCS2D01G383400	chr1D	91.892	222	16	2	1	220	366248530	366248751	4.500000e-80	309.0
55	TraesCS2D01G383400	chr1D	76.077	209	30	10	30	223	164858967	164859170	1.770000e-14	91.6
56	TraesCS2D01G383400	chr1D	100.000	30	0	0	3938	3967	68407115	68407086	6.470000e-04	56.5
57	TraesCS2D01G383400	chr5D	89.686	223	22	1	1	222	525765464	525765686	2.730000e-72	283.0
58	TraesCS2D01G383400	chr5D	88.696	230	14	5	4	221	410392676	410392447	2.120000e-68	270.0
59	TraesCS2D01G383400	chr5D	100.000	31	0	0	3938	3968	357533757	357533727	1.800000e-04	58.4
60	TraesCS2D01G383400	chr5D	100.000	30	0	0	3938	3967	37884743	37884772	6.470000e-04	56.5
61	TraesCS2D01G383400	chr5A	95.402	174	8	0	4	177	559696380	559696207	1.270000e-70	278.0
62	TraesCS2D01G383400	chr5A	93.820	178	11	0	1	178	32738690	32738867	7.640000e-68	268.0
63	TraesCS2D01G383400	chr5A	100.000	33	0	0	188	220	445551411	445551443	1.390000e-05	62.1
64	TraesCS2D01G383400	chr1B	76.923	234	38	7	5	226	575841963	575841734	8.140000e-23	119.0
65	TraesCS2D01G383400	chr4D	100.000	38	0	0	187	224	499680150	499680113	2.310000e-08	71.3
66	TraesCS2D01G383400	chr4D	100.000	30	0	0	3938	3967	433111226	433111255	6.470000e-04	56.5
67	TraesCS2D01G383400	chrUn	100.000	30	0	0	3938	3967	355919783	355919812	6.470000e-04	56.5
68	TraesCS2D01G383400	chrUn	100.000	30	0	0	3938	3967	362350230	362350259	6.470000e-04	56.5
69	TraesCS2D01G383400	chrUn	100.000	30	0	0	3938	3967	454067043	454067072	6.470000e-04	56.5
70	TraesCS2D01G383400	chr6D	100.000	30	0	0	3938	3967	467421785	467421814	6.470000e-04	56.5

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	TraesCS2D01G383400	chr2D	487931259	487935890	4631	True	8554.000000	8554	100.000000	1	4632	1	chr2D.!!$R4	4631
1	TraesCS2D01G383400	chr2D	487722800	487725380	2580	True	2453.000000	2453	84.172000	991	3652	1	chr2D.!!$R3	2661
2	TraesCS2D01G383400	chr2D	487592755	487594597	1842	True	1685.000000	1685	83.402000	988	2907	1	chr2D.!!$R2	1919
3	TraesCS2D01G383400	chr2D	486389770	486392983	3213	False	1002.666667	2056	82.380000	218	3718	3	chr2D.!!$F4	3500
4	TraesCS2D01G383400	chr2D	488058662	488059614	952	True	219.500000	222	84.265500	987	1602	2	chr2D.!!$R5	615
5	TraesCS2D01G383400	chr2B	571345302	571346914	1612	False	1659.000000	1659	85.444000	794	2453	1	chr2B.!!$F1	1659
6	TraesCS2D01G383400	chr2B	572177057	572180170	3113	True	1457.500000	2748	86.709000	988	4614	2	chr2B.!!$R3	3626
7	TraesCS2D01G383400	chr2B	572310710	572315137	4427	True	1236.750000	3600	86.355750	269	4611	4	chr2B.!!$R4	4342
8	TraesCS2D01G383400	chr2B	572322056	572325289	3233	True	264.250000	364	82.975250	1384	3559	4	chr2B.!!$R5	2175
9	TraesCS2D01G383400	chr2A	631854487	631857880	3393	False	1513.000000	2863	80.468500	218	3752	2	chr2A.!!$F2	3534
10	TraesCS2D01G383400	chr2A	632585059	632590283	5224	True	838.733333	2185	89.863000	218	4460	6	chr2A.!!$R1	4242
11	TraesCS2D01G383400	chr2A	46336674	46337794	1120	False	488.500000	664	82.824000	2424	3535	2	chr2A.!!$F1	1111
12	TraesCS2D01G383400	chr7D	446550069	446551626	1557	True	444.333333	708	82.495333	1936	3539	3	chr7D.!!$R2	1603
13	TraesCS2D01G383400	chr7A	321635865	321636676	811	True	386.500000	638	84.515500	2424	3216	2	chr7A.!!$R1	792
14	TraesCS2D01G383400	chr3D	16449279	16450168	889	False	372.000000	444	83.028500	2664	3539	2	chr3D.!!$F1	875
15	TraesCS2D01G383400	chr6A	226334090	226334895	805	True	294.500000	337	84.835500	3360	4187	2	chr6A.!!$R1	827

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
187	188	0.099791	CCAAACAGACGGCGTTTTGT	59.900	50.000	25.21	23.04	34.40	2.83	F
199	200	0.316360	CGTTTTGTCCGTTTGGGTCG	60.316	55.000	0.00	0.00	37.00	4.79	F
284	288	0.324943	AAGTGCATACGCTGTCCCTT	59.675	50.000	0.00	0.00	39.64	3.95	F
737	834	0.388649	AGAAACAGTAGCGTGCGAGG	60.389	55.000	0.00	0.00	0.00	4.63	F
977	1107	0.391661	CGATCACACTTCACCCCCTG	60.392	60.000	0.00	0.00	0.00	4.45	F
1414	1991	1.474478	ACGATTGTTTGTGGTGTTGCA	59.526	42.857	0.00	0.00	0.00	4.08	F
2961	4760	0.250727	TCGGGAAGCTTGTCTTTGGG	60.251	55.000	2.10	0.00	34.56	4.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1416	1993	0.179119	GGCCTATACGTCGTGCAAGT	60.179	55.0	8.47	0.00	0.00	3.16	R
1726	2435	0.619255	TCCCCAGGAGAACCGCATAA	60.619	55.0	0.00	0.00	41.83	1.90	R
2269	3133	1.899437	GAGGAGGTGGCGTTCCATCA	61.899	60.0	4.83	0.00	46.18	3.07	R
2627	4048	1.442769	TTCTGATGCTTGACTTCGCC	58.557	50.0	0.00	0.00	0.00	5.54	R
2961	4760	1.524008	CCAAAGGCCCCTTGTCGAAC	61.524	60.0	12.85	0.00	36.26	3.95	R
3329	5200	2.101415	CTGCTGCTGCCATGTAGTAGTA	59.899	50.0	13.47	7.98	38.71	1.82	R
4369	7517	0.169009	GTTTCTTCAGCATGTCGGGC	59.831	55.0	0.00	0.00	37.40	6.13	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	2.658593	CTATCGCCGGCCTTCGTG	60.659	66.667	23.46	5.48	37.11	4.35
18	19	3.133767	CTATCGCCGGCCTTCGTGA	62.134	63.158	23.46	11.83	37.11	4.35
19	20	3.420214	TATCGCCGGCCTTCGTGAC	62.420	63.158	23.46	0.00	37.11	3.67
25	26	4.699522	GGCCTTCGTGACCGGCTT	62.700	66.667	0.00	0.00	43.29	4.35
26	27	2.668550	GCCTTCGTGACCGGCTTT	60.669	61.111	0.00	0.00	40.62	3.51
27	28	2.258726	GCCTTCGTGACCGGCTTTT	61.259	57.895	0.00	0.00	40.62	2.27
28	29	0.952010	GCCTTCGTGACCGGCTTTTA	60.952	55.000	0.00	0.00	40.62	1.52
29	30	1.734163	CCTTCGTGACCGGCTTTTAT	58.266	50.000	0.00	0.00	33.95	1.40
30	31	1.396996	CCTTCGTGACCGGCTTTTATG	59.603	52.381	0.00	0.00	33.95	1.90
31	32	2.073816	CTTCGTGACCGGCTTTTATGT	58.926	47.619	0.00	0.00	33.95	2.29
32	33	2.172851	TCGTGACCGGCTTTTATGTT	57.827	45.000	0.00	0.00	33.95	2.71
33	34	2.496111	TCGTGACCGGCTTTTATGTTT	58.504	42.857	0.00	0.00	33.95	2.83
34	35	3.661944	TCGTGACCGGCTTTTATGTTTA	58.338	40.909	0.00	0.00	33.95	2.01
35	36	4.063689	TCGTGACCGGCTTTTATGTTTAA	58.936	39.130	0.00	0.00	33.95	1.52
36	37	4.696402	TCGTGACCGGCTTTTATGTTTAAT	59.304	37.500	0.00	0.00	33.95	1.40
37	38	5.181622	TCGTGACCGGCTTTTATGTTTAATT	59.818	36.000	0.00	0.00	33.95	1.40
38	39	6.370994	TCGTGACCGGCTTTTATGTTTAATTA	59.629	34.615	0.00	0.00	33.95	1.40
39	40	7.022384	CGTGACCGGCTTTTATGTTTAATTAA	58.978	34.615	0.00	0.00	0.00	1.40
40	41	7.537991	CGTGACCGGCTTTTATGTTTAATTAAA	59.462	33.333	0.00	6.54	0.00	1.52
41	42	9.361315	GTGACCGGCTTTTATGTTTAATTAAAT	57.639	29.630	13.54	1.99	0.00	1.40
42	43	9.360093	TGACCGGCTTTTATGTTTAATTAAATG	57.640	29.630	13.54	0.00	0.00	2.32
43	44	8.192068	ACCGGCTTTTATGTTTAATTAAATGC	57.808	30.769	13.54	6.26	37.56	3.56
44	45	7.819900	ACCGGCTTTTATGTTTAATTAAATGCA	59.180	29.630	13.54	8.51	38.87	3.96
45	46	8.825745	CCGGCTTTTATGTTTAATTAAATGCAT	58.174	29.630	13.54	14.28	38.87	3.96
46	47	9.635632	CGGCTTTTATGTTTAATTAAATGCATG	57.364	29.630	13.54	3.94	38.87	4.06

Showing 1 to 25 of 234 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.658593	CACGAAGGCCGGCGATAG	60.659	66.667	22.54	14.31	43.93	2.08
2	3	4.814294	GTCACGAAGGCCGGCGAT	62.814	66.667	22.54	12.00	43.93	4.58
10	11	1.396996	CATAAAAGCCGGTCACGAAGG	59.603	52.381	1.90	0.00	44.60	3.46
11	12	2.073816	ACATAAAAGCCGGTCACGAAG	58.926	47.619	1.90	0.00	44.60	3.79
12	13	2.172851	ACATAAAAGCCGGTCACGAA	57.827	45.000	1.90	0.00	44.60	3.85
13	14	2.172851	AACATAAAAGCCGGTCACGA	57.827	45.000	1.90	0.00	44.60	4.35
14	15	2.981400	AAACATAAAAGCCGGTCACG	57.019	45.000	1.90	0.00	40.55	4.35
15	16	8.745464	TTTAATTAAACATAAAAGCCGGTCAC	57.255	30.769	6.54	0.00	0.00	3.67
16	17	9.360093	CATTTAATTAAACATAAAAGCCGGTCA	57.640	29.630	12.74	0.00	0.00	4.02
17	18	8.325282	GCATTTAATTAAACATAAAAGCCGGTC	58.675	33.333	12.74	0.00	32.48	4.79
18	19	7.819900	TGCATTTAATTAAACATAAAAGCCGGT	59.180	29.630	12.74	0.00	35.80	5.28
19	20	8.190888	TGCATTTAATTAAACATAAAAGCCGG	57.809	30.769	12.74	0.00	35.80	6.13
20	21	9.635632	CATGCATTTAATTAAACATAAAAGCCG	57.364	29.630	12.74	0.00	35.80	5.52
76	77	2.033328	TTTCGTCGGCGCGTCAAAAA	62.033	50.000	12.89	11.86	38.14	1.94
77	78	1.833434	ATTTCGTCGGCGCGTCAAAA	61.833	50.000	12.89	14.32	38.14	2.44
78	79	2.311701	ATTTCGTCGGCGCGTCAAA	61.312	52.632	12.89	3.58	38.14	2.69
79	80	2.735478	ATTTCGTCGGCGCGTCAA	60.735	55.556	12.89	14.84	38.14	3.18
80	81	3.474904	CATTTCGTCGGCGCGTCA	61.475	61.111	12.89	10.46	38.14	4.35
81	82	4.204891	CCATTTCGTCGGCGCGTC	62.205	66.667	19.58	3.30	38.14	5.19
84	85	3.861263	GACCCATTTCGTCGGCGC	61.861	66.667	3.52	0.00	38.14	6.53
89	90	2.822701	GGCCCGACCCATTTCGTC	60.823	66.667	0.00	0.00	37.29	4.20
90	91	3.622060	CTGGCCCGACCCATTTCGT	62.622	63.158	0.00	0.00	37.29	3.85
91	92	2.824041	CTGGCCCGACCCATTTCG	60.824	66.667	0.00	0.00	37.83	3.46
92	93	3.140814	GCTGGCCCGACCCATTTC	61.141	66.667	0.00	0.00	37.83	2.17
118	119	1.154225	GTGTTTGGATCGGCGCAAG	60.154	57.895	10.83	1.95	43.44	4.01

Showing 1 to 25 of 210 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.