AutoCloner

Multiple sequence alignment - TraesCS1D01G234100

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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	TraesCS1D01G234100	chr1D	100.000	3012	0	0	1	3012	322284449	322287460	0.000000e+00	5563.0
1	TraesCS1D01G234100	chr1D	95.486	1573	43	10	1	1555	227131597	227130035	0.000000e+00	2486.0
2	TraesCS1D01G234100	chr1D	96.066	1144	36	4	1628	2768	227129637	227128500	0.000000e+00	1855.0
3	TraesCS1D01G234100	chr1D	95.169	207	9	1	2806	3012	227128505	227128300	2.900000e-85	326.0
4	TraesCS1D01G234100	chr1D	84.112	107	9	5	516	622	112443562	112443464	2.470000e-16	97.1
5	TraesCS1D01G234100	chr1D	96.078	51	1	1	1573	1623	227130041	227129992	6.920000e-12	82.4
6	TraesCS1D01G234100	chr1D	94.595	37	0	2	2757	2791	15304273	15304309	4.190000e-04	56.5
7	TraesCS1D01G234100	chr1B	94.484	2792	114	18	1	2768	327025306	327022531	0.000000e+00	4266.0
8	TraesCS1D01G234100	chr1B	95.221	1632	46	10	1	1614	435193414	435195031	0.000000e+00	2553.0
9	TraesCS1D01G234100	chr1B	96.621	1095	34	3	1650	2742	435195411	435196504	0.000000e+00	1814.0
10	TraesCS1D01G234100	chr1B	91.336	277	16	5	2739	3012	435309439	435309710	3.670000e-99	372.0
11	TraesCS1D01G234100	chr1B	95.652	207	8	1	2806	3012	327022536	327022331	6.220000e-87	331.0
12	TraesCS1D01G234100	chr1A	95.534	2508	63	9	126	2587	406188904	406191408	0.000000e+00	3965.0
13	TraesCS1D01G234100	chr1A	100.000	207	0	0	2806	3012	406203213	406203419	1.690000e-102	383.0
14	TraesCS1D01G234100	chr1A	96.094	128	4	1	2578	2704	406203055	406203182	1.090000e-49	207.0
15	TraesCS1D01G234100	chr1A	95.276	127	5	1	1	126	406187723	406187849	1.830000e-47	200.0
16	TraesCS1D01G234100	chr1A	100.000	30	0	0	2762	2791	63336185	63336156	4.190000e-04	56.5
17	TraesCS1D01G234100	chr3A	86.991	884	91	13	692	1569	739735331	739734466	0.000000e+00	974.0
18	TraesCS1D01G234100	chr3A	84.659	880	90	15	668	1536	739322282	739323127	0.000000e+00	835.0
19	TraesCS1D01G234100	chr3A	85.258	407	41	17	1613	2004	739323281	739323683	4.680000e-108	401.0
20	TraesCS1D01G234100	chr3A	84.328	134	12	4	504	637	739770403	739770279	4.080000e-24	122.0
21	TraesCS1D01G234100	chr3B	84.995	973	113	18	656	1621	816692410	816691464	0.000000e+00	957.0
22	TraesCS1D01G234100	chr3B	81.757	444	50	13	1607	2032	816691438	816691008	2.880000e-90	342.0
23	TraesCS1D01G234100	chr3B	81.733	427	47	18	1607	2015	816265220	816265633	8.050000e-86	327.0
24	TraesCS1D01G234100	chr3B	100.000	31	0	0	2761	2791	68873002	68872972	1.170000e-04	58.4
25	TraesCS1D01G234100	chr3D	86.565	856	93	13	720	1569	607310709	607309870	0.000000e+00	924.0
26	TraesCS1D01G234100	chr3D	84.906	901	96	19	655	1547	606929722	606930590	0.000000e+00	874.0
27	TraesCS1D01G234100	chr3D	82.688	439	48	13	1614	2035	606930677	606931104	6.140000e-97	364.0
28	TraesCS1D01G234100	chr3D	81.777	439	50	14	1614	2034	607309805	607309379	1.030000e-89	340.0
29	TraesCS1D01G234100	chr3D	81.020	353	55	12	271	614	606929372	606929721	1.380000e-68	270.0
30	TraesCS1D01G234100	chrUn	84.112	107	9	6	516	622	101646648	101646550	2.470000e-16	97.1
31	TraesCS1D01G234100	chr7B	94.737	38	1	1	2754	2791	63936142	63936178	1.170000e-04	58.4
32	TraesCS1D01G234100	chr7D	100.000	30	0	0	2762	2791	555660548	555660577	4.190000e-04	56.5
33	TraesCS1D01G234100	chr4B	100.000	30	0	0	2762	2791	476358116	476358145	4.190000e-04	56.5
34	TraesCS1D01G234100	chr4A	100.000	30	0	0	2762	2791	11590661	11590690	4.190000e-04	56.5
35	TraesCS1D01G234100	chr4A	100.000	30	0	0	2761	2790	93683443	93683414	4.190000e-04	56.5
36	TraesCS1D01G234100	chr6B	91.892	37	3	0	2755	2791	135505587	135505623	5.000000e-03	52.8

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	TraesCS1D01G234100	chr1D	322284449	322287460	3011	False	5563.000000	5563	100.000000	1	3012	1	chr1D.!!$F2	3011
1	TraesCS1D01G234100	chr1D	227128300	227131597	3297	True	1187.350000	2486	95.699750	1	3012	4	chr1D.!!$R2	3011
2	TraesCS1D01G234100	chr1B	327022331	327025306	2975	True	2298.500000	4266	95.068000	1	3012	2	chr1B.!!$R1	3011
3	TraesCS1D01G234100	chr1B	435193414	435196504	3090	False	2183.500000	2553	95.921000	1	2742	2	chr1B.!!$F2	2741
4	TraesCS1D01G234100	chr1A	406187723	406191408	3685	False	2082.500000	3965	95.405000	1	2587	2	chr1A.!!$F1	2586
5	TraesCS1D01G234100	chr3A	739734466	739735331	865	True	974.000000	974	86.991000	692	1569	1	chr3A.!!$R1	877
6	TraesCS1D01G234100	chr3A	739322282	739323683	1401	False	618.000000	835	84.958500	668	2004	2	chr3A.!!$F1	1336
7	TraesCS1D01G234100	chr3B	816691008	816692410	1402	True	649.500000	957	83.376000	656	2032	2	chr3B.!!$R2	1376
8	TraesCS1D01G234100	chr3D	607309379	607310709	1330	True	632.000000	924	84.171000	720	2034	2	chr3D.!!$R1	1314
9	TraesCS1D01G234100	chr3D	606929372	606931104	1732	False	502.666667	874	82.871333	271	2035	3	chr3D.!!$F1	1764

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
70	71	1.067060	TGGGAATCGTACTCATGCTCG	59.933	52.381	0.0	0.0	0.00	5.03	F
774	1865	1.588404	CGACTGTGTGTGTCAGTTGTC	59.412	52.381	0.0	0.0	44.68	3.18	F
1727	3280	0.823356	TGCAGGCAGTGGAAAAGGAC	60.823	55.000	0.0	0.0	0.00	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1054	2161	0.039764	AGTCGAGGAGGACCATCACA	59.960	55.0	0.00	0.0	37.66	3.58	R
1864	3426	1.392589	CATGGCCGCTGAAACCTAAT	58.607	50.0	0.00	0.0	0.00	1.73	R
2797	4386	2.040012	AGTTGACGAGTACTCCCTCTGA	59.960	50.0	17.23	3.3	0.00	3.27	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	4.839668	TTGTTTTTGTACCTGGGAATCG	57.160	40.909	0.00	0.00	0.00	3.34
70	71	1.067060	TGGGAATCGTACTCATGCTCG	59.933	52.381	0.00	0.00	0.00	5.03
315	1386	6.772716	AGGACACAACTGAAATTCTGTTATGT	59.227	34.615	23.12	23.12	44.66	2.29
514	1599	3.199946	CCTACTGGAGCTTATTTCCACCA	59.800	47.826	0.00	0.00	39.74	4.17
572	1657	6.865205	GCTCAAAAGAAGTAATCAATGCTGTT	59.135	34.615	0.00	0.00	0.00	3.16
595	1681	2.497138	TCTGAGGTTGTGTGCAATGAG	58.503	47.619	0.00	0.00	36.92	2.90
618	1704	9.589461	TGAGGGTTATGTTTCCTTAAATGTTTA	57.411	29.630	0.00	0.00	0.00	2.01
723	1809	5.305585	ACTACCAAGTTGACAACGATTCAT	58.694	37.500	12.54	1.20	36.23	2.57
774	1865	1.588404	CGACTGTGTGTGTCAGTTGTC	59.412	52.381	0.00	0.00	44.68	3.18
863	1967	9.284968	ACAAATATAGGACAAATACATAGTGGC	57.715	33.333	0.00	0.00	0.00	5.01
885	1989	3.658988	CACACGTCATGTTTCAACAATCG	59.341	43.478	0.00	5.05	40.64	3.34
1054	2161	3.721087	ATGAGGAACCACGAGGATTTT	57.279	42.857	5.68	0.00	38.69	1.82
1107	2220	1.816835	TCTATCTCACCACGTCGCTTT	59.183	47.619	0.00	0.00	0.00	3.51
1345	2458	4.200092	CTCTTTAGAACCCCATAGGCAAC	58.800	47.826	0.00	0.00	40.58	4.17
1480	2593	1.347707	GCATACCTGCCATGGTAGCTA	59.652	52.381	23.41	15.14	44.69	3.32
1563	2680	3.543680	TCTGGTTTAGTAGATGCAGCC	57.456	47.619	0.00	0.00	0.00	4.85
1727	3280	0.823356	TGCAGGCAGTGGAAAAGGAC	60.823	55.000	0.00	0.00	0.00	3.85
1787	3346	3.448934	TGAGATTGAGAAGAGAAGGCCT	58.551	45.455	0.00	0.00	0.00	5.19
1791	3350	1.566211	TGAGAAGAGAAGGCCTCCTG	58.434	55.000	5.23	0.00	42.97	3.86
1858	3420	9.477484	CTGTTGTGGTTAACCTATATCATACTC	57.523	37.037	24.78	10.04	36.82	2.59
1978	3558	2.358247	AAACGCTACGGTGCTGGG	60.358	61.111	0.00	0.00	0.00	4.45
2180	3760	1.331447	CAGCGCTGCTTATATTGCACA	59.669	47.619	26.68	0.00	36.40	4.57
2304	3884	3.008813	TCTGAAGGCAGATTGCTCTTTCT	59.991	43.478	0.67	0.00	45.88	2.52
2550	4139	3.068590	CCAGCCATCCCAATTTACATGTC	59.931	47.826	0.00	0.00	0.00	3.06
2551	4140	3.700539	CAGCCATCCCAATTTACATGTCA	59.299	43.478	0.00	0.00	0.00	3.58
2552	4141	4.342951	CAGCCATCCCAATTTACATGTCAT	59.657	41.667	0.00	0.00	0.00	3.06
2553	4142	4.964262	AGCCATCCCAATTTACATGTCATT	59.036	37.500	0.00	0.00	0.00	2.57
2554	4143	5.426185	AGCCATCCCAATTTACATGTCATTT	59.574	36.000	0.00	0.00	0.00	2.32
2771	4360	8.919777	AACATAAAAGCAGTTAAGTACTTCCT	57.080	30.769	12.39	6.65	33.85	3.36
2772	4361	8.549338	ACATAAAAGCAGTTAAGTACTTCCTC	57.451	34.615	12.39	4.09	33.85	3.71
2773	4362	7.606839	ACATAAAAGCAGTTAAGTACTTCCTCC	59.393	37.037	12.39	0.00	33.85	4.30
2774	4363	3.870633	AGCAGTTAAGTACTTCCTCCG	57.129	47.619	12.39	0.00	33.85	4.63
2775	4364	3.163467	AGCAGTTAAGTACTTCCTCCGT	58.837	45.455	12.39	0.00	33.85	4.69
2776	4365	4.338879	AGCAGTTAAGTACTTCCTCCGTA	58.661	43.478	12.39	0.00	33.85	4.02
2777	4366	4.768968	AGCAGTTAAGTACTTCCTCCGTAA	59.231	41.667	12.39	0.00	33.85	3.18
2778	4367	5.244626	AGCAGTTAAGTACTTCCTCCGTAAA	59.755	40.000	12.39	0.00	33.85	2.01
2779	4368	5.575995	GCAGTTAAGTACTTCCTCCGTAAAG	59.424	44.000	12.39	0.00	33.85	1.85
2780	4369	6.571150	GCAGTTAAGTACTTCCTCCGTAAAGA	60.571	42.308	12.39	0.00	33.85	2.52
2781	4370	7.373493	CAGTTAAGTACTTCCTCCGTAAAGAA	58.627	38.462	12.39	0.00	33.85	2.52
2782	4371	7.869429	CAGTTAAGTACTTCCTCCGTAAAGAAA	59.131	37.037	12.39	0.00	33.85	2.52
2783	4372	8.591940	AGTTAAGTACTTCCTCCGTAAAGAAAT	58.408	33.333	12.39	0.00	31.29	2.17
2784	4373	9.860898	GTTAAGTACTTCCTCCGTAAAGAAATA	57.139	33.333	12.39	0.00	0.00	1.40
2791	4380	9.198475	ACTTCCTCCGTAAAGAAATATAAGAGA	57.802	33.333	0.00	0.00	0.00	3.10
2794	4383	9.198475	TCCTCCGTAAAGAAATATAAGAGAAGT	57.802	33.333	0.00	0.00	0.00	3.01
2795	4384	9.250624	CCTCCGTAAAGAAATATAAGAGAAGTG	57.749	37.037	0.00	0.00	0.00	3.16
2804	4393	8.869109	AGAAATATAAGAGAAGTGATCAGAGGG	58.131	37.037	0.00	0.00	0.00	4.30
2832	4421	0.038251	TCAACTAGTCAGCCTGTGCG	60.038	55.000	0.00	0.00	44.33	5.34
2843	4432	0.099436	GCCTGTGCGGATCAACATTC	59.901	55.000	0.00	0.00	33.16	2.67
2855	4444	6.257849	GCGGATCAACATTCTGTTCTAACATA	59.742	38.462	0.00	0.00	38.77	2.29
2938	4527	4.597507	TGTGTTCCCTAAAAGAGTGGAGAT	59.402	41.667	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
281	1352	7.581213	ATTTCAGTTGTGTCCTATTTTGACA	57.419	32.000	0.00	0.00	40.28	3.58
326	1399	7.954788	ATTTAACCGCAGAAGCAAAATAAAA	57.045	28.000	0.00	0.00	42.27	1.52
327	1400	9.646427	ATTATTTAACCGCAGAAGCAAAATAAA	57.354	25.926	0.00	0.00	42.27	1.40
328	1401	9.081997	CATTATTTAACCGCAGAAGCAAAATAA	57.918	29.630	0.00	0.00	42.27	1.40
329	1402	7.704472	CCATTATTTAACCGCAGAAGCAAAATA	59.296	33.333	0.00	0.00	42.27	1.40
330	1403	6.534793	CCATTATTTAACCGCAGAAGCAAAAT	59.465	34.615	0.00	0.00	42.27	1.82
380	1460	6.126863	TGTCCCTGAACTTTAATCACATCT	57.873	37.500	0.00	0.00	0.00	2.90
514	1599	4.019174	CCAGAAACAGGCTTATGGATTGT	58.981	43.478	0.00	0.00	39.58	2.71
572	1657	2.708216	TTGCACACAACCTCAGAAGA	57.292	45.000	0.00	0.00	0.00	2.87
618	1704	6.301486	TGCCTATGAAGAATGCATCATTAGT	58.699	36.000	0.00	0.00	34.81	2.24
723	1809	3.188460	GCGCCTGTCTCAGTTTCAAATTA	59.812	43.478	0.00	0.00	0.00	1.40
774	1865	3.173599	CAAGTGCGTTGCCATAAATGAG	58.826	45.455	0.00	0.00	0.00	2.90
863	1967	3.658988	CGATTGTTGAAACATGACGTGTG	59.341	43.478	0.00	0.00	41.14	3.82
885	1989	4.035091	GGTTTCCTCATTGTTTTGTTTGGC	59.965	41.667	0.00	0.00	0.00	4.52
1054	2161	0.039764	AGTCGAGGAGGACCATCACA	59.960	55.000	0.00	0.00	37.66	3.58
1107	2220	3.199290	GCTAGACAGCTCTCCCTCA	57.801	57.895	0.00	0.00	44.93	3.86
1345	2458	0.585357	GATCGTAGCTGCAAGGCATG	59.415	55.000	1.02	0.00	38.13	4.06
1539	2656	4.938226	GCTGCATCTACTAAACCAGAAACT	59.062	41.667	0.00	0.00	0.00	2.66
1727	3280	3.452627	ACTCCTGAGCCATAGTTACAAGG	59.547	47.826	0.00	0.00	0.00	3.61
1787	3346	3.460340	TGAGGAAACAAAACCTACCAGGA	59.540	43.478	0.00	0.00	37.67	3.86
1791	3350	4.499188	GCAAGTGAGGAAACAAAACCTACC	60.499	45.833	0.00	0.00	36.57	3.18
1858	3420	4.759693	TGGCCGCTGAAACCTAATATTATG	59.240	41.667	0.00	0.00	0.00	1.90
1864	3426	1.392589	CATGGCCGCTGAAACCTAAT	58.607	50.000	0.00	0.00	0.00	1.73
2180	3760	8.576442	ACAACGGTTATGATTTTCTGAAGAATT	58.424	29.630	0.00	0.00	33.54	2.17
2304	3884	3.661911	CCGCATCAAACCGGTCAA	58.338	55.556	8.04	0.00	39.67	3.18
2518	4102	2.516702	TGGGATGGCTGGAGTACTACTA	59.483	50.000	6.66	0.00	0.00	1.82
2522	4106	1.898863	ATTGGGATGGCTGGAGTACT	58.101	50.000	0.00	0.00	0.00	2.73
2554	4143	9.332301	GGTCAATTAAAAATCACGAAATACGAA	57.668	29.630	0.00	0.00	45.77	3.85
2765	4354	9.198475	TCTCTTATATTTCTTTACGGAGGAAGT	57.802	33.333	0.00	0.00	0.00	3.01
2768	4357	9.198475	ACTTCTCTTATATTTCTTTACGGAGGA	57.802	33.333	0.00	0.00	0.00	3.71
2769	4358	9.250624	CACTTCTCTTATATTTCTTTACGGAGG	57.749	37.037	0.00	0.00	0.00	4.30
2778	4367	8.869109	CCCTCTGATCACTTCTCTTATATTTCT	58.131	37.037	0.00	0.00	0.00	2.52
2779	4368	8.865090	TCCCTCTGATCACTTCTCTTATATTTC	58.135	37.037	0.00	0.00	0.00	2.17
2780	4369	8.789767	TCCCTCTGATCACTTCTCTTATATTT	57.210	34.615	0.00	0.00	0.00	1.40
2781	4370	8.010105	ACTCCCTCTGATCACTTCTCTTATATT	58.990	37.037	0.00	0.00	0.00	1.28
2782	4371	7.534852	ACTCCCTCTGATCACTTCTCTTATAT	58.465	38.462	0.00	0.00	0.00	0.86
2783	4372	6.916909	ACTCCCTCTGATCACTTCTCTTATA	58.083	40.000	0.00	0.00	0.00	0.98
2784	4373	5.776358	ACTCCCTCTGATCACTTCTCTTAT	58.224	41.667	0.00	0.00	0.00	1.73
2785	4374	5.199982	ACTCCCTCTGATCACTTCTCTTA	57.800	43.478	0.00	0.00	0.00	2.10
2786	4375	4.059773	ACTCCCTCTGATCACTTCTCTT	57.940	45.455	0.00	0.00	0.00	2.85
2787	4376	3.756082	ACTCCCTCTGATCACTTCTCT	57.244	47.619	0.00	0.00	0.00	3.10
2788	4377	4.532834	AGTACTCCCTCTGATCACTTCTC	58.467	47.826	0.00	0.00	0.00	2.87
2789	4378	4.532834	GAGTACTCCCTCTGATCACTTCT	58.467	47.826	12.13	0.00	0.00	2.85
2790	4379	3.314080	CGAGTACTCCCTCTGATCACTTC	59.686	52.174	17.23	0.00	0.00	3.01
2791	4380	3.283751	CGAGTACTCCCTCTGATCACTT	58.716	50.000	17.23	0.00	0.00	3.16
2792	4381	2.240160	ACGAGTACTCCCTCTGATCACT	59.760	50.000	17.23	0.00	0.00	3.41
2793	4382	2.614983	GACGAGTACTCCCTCTGATCAC	59.385	54.545	17.23	0.00	0.00	3.06
2794	4383	2.238898	TGACGAGTACTCCCTCTGATCA	59.761	50.000	17.23	6.93	0.00	2.92
2795	4384	2.920524	TGACGAGTACTCCCTCTGATC	58.079	52.381	17.23	4.64	0.00	2.92
2796	4385	3.018149	GTTGACGAGTACTCCCTCTGAT	58.982	50.000	17.23	0.00	0.00	2.90
2797	4386	2.040012	AGTTGACGAGTACTCCCTCTGA	59.960	50.000	17.23	3.30	0.00	3.27
2798	4387	2.438411	AGTTGACGAGTACTCCCTCTG	58.562	52.381	17.23	5.29	0.00	3.35
2799	4388	2.883122	AGTTGACGAGTACTCCCTCT	57.117	50.000	17.23	6.17	0.00	3.69
2800	4389	3.608796	ACTAGTTGACGAGTACTCCCTC	58.391	50.000	17.23	11.96	29.97	4.30
2801	4390	3.008813	TGACTAGTTGACGAGTACTCCCT	59.991	47.826	17.23	2.26	31.94	4.20
2802	4391	3.341823	TGACTAGTTGACGAGTACTCCC	58.658	50.000	17.23	9.78	31.94	4.30
2803	4392	3.181508	GCTGACTAGTTGACGAGTACTCC	60.182	52.174	17.23	4.79	31.94	3.85
2804	4393	3.181508	GGCTGACTAGTTGACGAGTACTC	60.182	52.174	13.18	13.18	31.94	2.59
2905	4494	4.268720	GGAACACACCCAGGCAAA	57.731	55.556	0.00	0.00	0.00	3.68
2920	4509	3.115390	CCCATCTCCACTCTTTTAGGGA	58.885	50.000	0.00	0.00	35.81	4.20
2923	4512	5.604650	AGTATCCCCATCTCCACTCTTTTAG	59.395	44.000	0.00	0.00	0.00	1.85
2928	4517	2.248686	ACAGTATCCCCATCTCCACTCT	59.751	50.000	0.00	0.00	0.00	3.24
2938	4527	2.790433	GTCAAAAGCACAGTATCCCCA	58.210	47.619	0.00	0.00	0.00	4.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.