AutoCloner

Multiple sequence alignment - TraesCS1D01G453800

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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	TraesCS1D01G453800	chr1D	100.000	5412	0	0	1	5412	494545947	494551358	0.000000e+00	9995.0
1	TraesCS1D01G453800	chr1D	87.682	2947	311	35	1880	4790	448119	451049	0.000000e+00	3384.0
2	TraesCS1D01G453800	chr1D	87.461	2855	324	17	1941	4771	697003	694159	0.000000e+00	3258.0
3	TraesCS1D01G453800	chr1D	86.833	2681	323	19	1843	4500	460073	462746	0.000000e+00	2968.0
4	TraesCS1D01G453800	chr1D	89.326	2239	226	7	2183	4416	619901	617671	0.000000e+00	2798.0
5	TraesCS1D01G453800	chr1D	85.236	1375	187	10	822	2190	621330	619966	0.000000e+00	1400.0
6	TraesCS1D01G453800	chr1D	85.370	1203	174	2	993	2194	647396	648597	0.000000e+00	1245.0
7	TraesCS1D01G453800	chr1D	82.258	186	31	2	667	851	33989178	33989362	5.610000e-35	159.0
8	TraesCS1D01G453800	chr1B	97.164	4266	116	5	541	4804	687785027	687789289	0.000000e+00	7203.0
9	TraesCS1D01G453800	chr1B	86.866	2642	281	35	2180	4798	3943618	3946216	0.000000e+00	2896.0
10	TraesCS1D01G453800	chr1B	88.404	2337	253	8	2180	4500	4096814	4099148	0.000000e+00	2798.0
11	TraesCS1D01G453800	chr1B	89.058	2239	220	14	2180	4410	4115772	4117993	0.000000e+00	2754.0
12	TraesCS1D01G453800	chr1B	86.182	1375	170	14	824	2190	4856573	4855211	0.000000e+00	1469.0
13	TraesCS1D01G453800	chr1B	86.111	1332	171	10	856	2184	4150621	4151941	0.000000e+00	1423.0
14	TraesCS1D01G453800	chr1B	84.370	1318	189	15	881	2190	4591761	4590453	0.000000e+00	1277.0
15	TraesCS1D01G453800	chr1B	86.435	1150	150	5	1044	2190	4483642	4482496	0.000000e+00	1254.0
16	TraesCS1D01G453800	chr1B	86.177	1143	154	4	1044	2184	3951180	3952320	0.000000e+00	1232.0
17	TraesCS1D01G453800	chr1B	84.644	534	22	22	54	543	687784481	687784998	1.360000e-130	477.0
18	TraesCS1D01G453800	chr1B	93.502	277	13	2	4804	5080	687789321	687789592	1.810000e-109	407.0
19	TraesCS1D01G453800	chr1B	84.752	282	39	4	4509	4789	4759006	4758728	4.130000e-71	279.0
20	TraesCS1D01G453800	chr1B	81.953	338	51	7	554	884	4911560	4911226	1.480000e-70	278.0
21	TraesCS1D01G453800	chr1B	84.328	268	22	8	54	301	4859258	4858991	1.510000e-60	244.0
22	TraesCS1D01G453800	chr1B	85.849	212	24	5	551	758	4538414	4538205	2.540000e-53	220.0
23	TraesCS1D01G453800	chr1B	82.870	216	35	2	638	852	4511232	4511018	5.530000e-45	193.0
24	TraesCS1D01G453800	chr1B	78.481	316	46	11	543	852	46695630	46695929	2.570000e-43	187.0
25	TraesCS1D01G453800	chr1B	82.063	223	30	7	543	758	4951072	4950853	1.200000e-41	182.0
26	TraesCS1D01G453800	chr1B	88.333	60	5	2	5312	5369	4189284	4189343	2.700000e-08	71.3
27	TraesCS1D01G453800	chr1A	87.322	2595	283	23	2183	4746	3655977	3653398	0.000000e+00	2928.0
28	TraesCS1D01G453800	chr1A	85.973	1383	167	21	822	2190	3657555	3656186	0.000000e+00	1454.0
29	TraesCS1D01G453800	chr1A	84.615	286	40	4	4509	4793	3488365	3488083	1.150000e-71	281.0
30	TraesCS1D01G453800	chr1A	86.142	267	18	8	54	301	3695688	3695422	2.480000e-68	270.0
31	TraesCS1D01G453800	chr1A	85.149	202	24	4	545	742	3016700	3016899	9.190000e-48	202.0
32	TraesCS1D01G453800	chr1A	78.201	289	50	11	545	831	3726208	3725931	7.210000e-39	172.0
33	TraesCS1D01G453800	chr1A	85.593	118	16	1	4896	5013	3450544	3450428	7.360000e-24	122.0
34	TraesCS1D01G453800	chr1A	80.272	147	27	2	667	813	32549080	32549224	5.730000e-20	110.0
35	TraesCS1D01G453800	chr3D	89.408	2313	223	10	2183	4480	560056873	560054568	0.000000e+00	2894.0
36	TraesCS1D01G453800	chr3D	93.750	64	2	1	4804	4865	457400802	457400865	1.600000e-15	95.3
37	TraesCS1D01G453800	chr3B	91.781	73	5	1	4804	4876	669331004	669331075	3.450000e-17	100.0
38	TraesCS1D01G453800	chr3B	91.304	69	5	1	4804	4871	5175513	5175445	5.770000e-15	93.5
39	TraesCS1D01G453800	chr3B	92.424	66	2	2	4804	4866	257512425	257512490	2.080000e-14	91.6
40	TraesCS1D01G453800	chr2B	92.754	69	5	0	4804	4872	614917156	614917224	3.450000e-17	100.0
41	TraesCS1D01G453800	chr2A	93.750	64	2	2	4804	4865	549890403	549890466	1.600000e-15	95.3
42	TraesCS1D01G453800	chr7A	91.304	69	4	2	4804	4872	32013152	32013218	5.770000e-15	93.5
43	TraesCS1D01G453800	chr5B	87.654	81	2	4	4804	4877	669713697	669713618	2.690000e-13	87.9

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	TraesCS1D01G453800	chr1D	494545947	494551358	5411	False	9995.000000	9995	100.0000	1	5412	1	chr1D.!!$F5	5411
1	TraesCS1D01G453800	chr1D	448119	451049	2930	False	3384.000000	3384	87.6820	1880	4790	1	chr1D.!!$F1	2910
2	TraesCS1D01G453800	chr1D	694159	697003	2844	True	3258.000000	3258	87.4610	1941	4771	1	chr1D.!!$R1	2830
3	TraesCS1D01G453800	chr1D	460073	462746	2673	False	2968.000000	2968	86.8330	1843	4500	1	chr1D.!!$F2	2657
4	TraesCS1D01G453800	chr1D	617671	621330	3659	True	2099.000000	2798	87.2810	822	4416	2	chr1D.!!$R2	3594
5	TraesCS1D01G453800	chr1D	647396	648597	1201	False	1245.000000	1245	85.3700	993	2194	1	chr1D.!!$F3	1201
6	TraesCS1D01G453800	chr1B	3943618	3946216	2598	False	2896.000000	2896	86.8660	2180	4798	1	chr1B.!!$F1	2618
7	TraesCS1D01G453800	chr1B	4096814	4099148	2334	False	2798.000000	2798	88.4040	2180	4500	1	chr1B.!!$F3	2320
8	TraesCS1D01G453800	chr1B	4115772	4117993	2221	False	2754.000000	2754	89.0580	2180	4410	1	chr1B.!!$F4	2230
9	TraesCS1D01G453800	chr1B	687784481	687789592	5111	False	2695.666667	7203	91.7700	54	5080	3	chr1B.!!$F8	5026
10	TraesCS1D01G453800	chr1B	4150621	4151941	1320	False	1423.000000	1423	86.1110	856	2184	1	chr1B.!!$F5	1328
11	TraesCS1D01G453800	chr1B	4590453	4591761	1308	True	1277.000000	1277	84.3700	881	2190	1	chr1B.!!$R4	1309
12	TraesCS1D01G453800	chr1B	4482496	4483642	1146	True	1254.000000	1254	86.4350	1044	2190	1	chr1B.!!$R1	1146
13	TraesCS1D01G453800	chr1B	3951180	3952320	1140	False	1232.000000	1232	86.1770	1044	2184	1	chr1B.!!$F2	1140
14	TraesCS1D01G453800	chr1B	4855211	4859258	4047	True	856.500000	1469	85.2550	54	2190	2	chr1B.!!$R8	2136
15	TraesCS1D01G453800	chr1A	3653398	3657555	4157	True	2191.000000	2928	86.6475	822	4746	2	chr1A.!!$R5	3924
16	TraesCS1D01G453800	chr3D	560054568	560056873	2305	True	2894.000000	2894	89.4080	2183	4480	1	chr3D.!!$R1	2297

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
445	2333	0.178068	AGTTGCTGAGGTCAACACGT	59.822	50.000	8.33	0.00	44.50	4.49	F
446	2334	1.014352	GTTGCTGAGGTCAACACGTT	58.986	50.000	0.00	0.00	42.35	3.99	F
449	2337	1.411246	TGCTGAGGTCAACACGTTACT	59.589	47.619	0.00	0.00	0.00	2.24	F
917	2943	1.444553	GCGTTCACTGAGGACCTCG	60.445	63.158	16.81	13.32	32.35	4.63	F
1677	3720	2.040544	CAACAGCACCTTAGGCGGG	61.041	63.158	0.00	0.00	36.08	6.13	F
2613	4876	2.358898	AGCACAAAATATGATCACGGGC	59.641	45.455	0.00	0.00	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1672	3715	1.067425	GGTTTTTGGTATCAACCCGCC	60.067	52.381	0.00	46.16	6.13	R
1704	3747	3.690628	GGCGCAAAGTATTTAGTTGGGTA	59.309	43.478	10.83	35.03	3.69	R
1823	3866	7.840716	TGAGATTGGTTATGGAGATTGGAATTT	59.159	33.333	0.00	0.00	1.82	R
2613	4876	6.500589	TTAGAAAGGATTGGAGGTATGGAG	57.499	41.667	0.00	0.00	3.86	R
3672	5944	4.672587	TCCCTGCTGAATGTAGTCATAC	57.327	45.455	0.00	33.49	2.39	R
4581	6888	0.030638	CAGGAAAAACCACAGGCACG	59.969	55.000	0.00	42.04	5.34	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	Hairpin	End Stability
22	23	5.063180	TCATGATGATGCTTTGGTTGTTC	57.937	39.130	0.00	3.18
23	24	4.523558	TCATGATGATGCTTTGGTTGTTCA	59.476	37.500	0.00	3.18
24	25	4.508461	TGATGATGCTTTGGTTGTTCAG	57.492	40.909	0.00	3.02
25	26	3.256383	TGATGATGCTTTGGTTGTTCAGG	59.744	43.478	0.00	3.86
26	27	1.340889	TGATGCTTTGGTTGTTCAGGC	59.659	47.619	0.00	4.85
27	28	1.615392	GATGCTTTGGTTGTTCAGGCT	59.385	47.619	0.00	4.58
28	29	1.484038	TGCTTTGGTTGTTCAGGCTT	58.516	45.000	0.00	4.35
29	30	1.830477	TGCTTTGGTTGTTCAGGCTTT	59.170	42.857	0.00	3.51
30	31	2.159114	TGCTTTGGTTGTTCAGGCTTTC	60.159	45.455	0.00	2.62
31	32	2.159114	GCTTTGGTTGTTCAGGCTTTCA	60.159	45.455	0.00	2.69
32	33	3.678529	GCTTTGGTTGTTCAGGCTTTCAA	60.679	43.478	0.00	2.69
33	34	4.696455	CTTTGGTTGTTCAGGCTTTCAAT	58.304	39.130	0.00	2.57
34	35	4.751767	TTGGTTGTTCAGGCTTTCAATT	57.248	36.364	0.00	2.32
35	36	4.320608	TGGTTGTTCAGGCTTTCAATTC	57.679	40.909	0.00	2.17
36	37	3.069443	TGGTTGTTCAGGCTTTCAATTCC	59.931	43.478	0.00	3.01
37	38	3.069443	GGTTGTTCAGGCTTTCAATTCCA	59.931	43.478	0.00	3.53
38	39	4.051237	GTTGTTCAGGCTTTCAATTCCAC	58.949	43.478	0.00	4.02
39	40	3.565307	TGTTCAGGCTTTCAATTCCACT	58.435	40.909	0.00	4.00
40	41	3.318839	TGTTCAGGCTTTCAATTCCACTG	59.681	43.478	0.00	3.66
41	42	1.888512	TCAGGCTTTCAATTCCACTGC	59.111	47.619	0.00	4.40
42	43	1.067354	CAGGCTTTCAATTCCACTGCC	60.067	52.381	39.19	4.85
43	44	1.203100	AGGCTTTCAATTCCACTGCCT	60.203	47.619	43.61	4.75
44	45	1.203287	GGCTTTCAATTCCACTGCCTC	59.797	52.381	36.32	4.70
45	46	1.888512	GCTTTCAATTCCACTGCCTCA	59.111	47.619	0.00	3.86
46	47	2.494870	GCTTTCAATTCCACTGCCTCAT	59.505	45.455	0.00	2.90

Showing 1 to 25 of 366 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
0	1	4.523558	TGAACAACCAAAGCATCATCATGA	59.476	37.500	30.57	3.07
1	2	4.811908	TGAACAACCAAAGCATCATCATG	58.188	39.130	0.00	3.07
2	3	4.081862	CCTGAACAACCAAAGCATCATCAT	60.082	41.667	0.00	2.45
3	4	3.256383	CCTGAACAACCAAAGCATCATCA	59.744	43.478	0.00	3.07
4	5	3.841643	CCTGAACAACCAAAGCATCATC	58.158	45.455	0.00	2.92
5	6	2.028748	GCCTGAACAACCAAAGCATCAT	60.029	45.455	0.00	2.45
6	7	1.340889	GCCTGAACAACCAAAGCATCA	59.659	47.619	0.00	3.07
7	8	1.615392	AGCCTGAACAACCAAAGCATC	59.385	47.619	0.00	3.91
8	9	1.708341	AGCCTGAACAACCAAAGCAT	58.292	45.000	0.00	3.79
9	10	1.484038	AAGCCTGAACAACCAAAGCA	58.516	45.000	0.00	3.91
10	11	2.159114	TGAAAGCCTGAACAACCAAAGC	60.159	45.455	0.00	3.51
11	12	3.799281	TGAAAGCCTGAACAACCAAAG	57.201	42.857	0.00	2.77
12	13	4.751767	ATTGAAAGCCTGAACAACCAAA	57.248	36.364	0.00	3.28
13	14	4.442753	GGAATTGAAAGCCTGAACAACCAA	60.443	41.667	0.00	3.67
14	15	3.069443	GGAATTGAAAGCCTGAACAACCA	59.931	43.478	0.00	3.67
15	16	3.069443	TGGAATTGAAAGCCTGAACAACC	59.931	43.478	0.00	3.77
16	17	4.051237	GTGGAATTGAAAGCCTGAACAAC	58.949	43.478	0.00	3.32
17	18	3.960102	AGTGGAATTGAAAGCCTGAACAA	59.040	39.130	0.00	2.83
18	19	3.318839	CAGTGGAATTGAAAGCCTGAACA	59.681	43.478	0.00	3.18
19	20	3.858503	GCAGTGGAATTGAAAGCCTGAAC	60.859	47.826	0.00	3.18
20	21	2.297033	GCAGTGGAATTGAAAGCCTGAA	59.703	45.455	0.00	3.02
21	22	1.888512	GCAGTGGAATTGAAAGCCTGA	59.111	47.619	0.00	3.86
22	23	1.067354	GGCAGTGGAATTGAAAGCCTG	60.067	52.381	37.67	4.85
23	24	1.203100	AGGCAGTGGAATTGAAAGCCT	60.203	47.619	45.49	4.58
24	25	1.203287	GAGGCAGTGGAATTGAAAGCC	59.797	52.381	40.85	4.35

Showing 1 to 25 of 363 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.