AutoCloner

Multiple sequence alignment - TraesCS5D01G051200

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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	TraesCS5D01G051200	chr5D	100.000	6388	0	0	1526	7913	49105894	49112281	0.000000e+00	11797.0
1	TraesCS5D01G051200	chr5D	100.000	1585	0	0	8298	9882	49112666	49114250	0.000000e+00	2928.0
2	TraesCS5D01G051200	chr5D	100.000	1122	0	0	1	1122	49104369	49105490	0.000000e+00	2073.0
3	TraesCS5D01G051200	chr5D	92.042	377	30	0	5678	6054	49109953	49110329	1.890000e-146	531.0
4	TraesCS5D01G051200	chr5D	92.042	377	30	0	5585	5961	49110046	49110422	1.890000e-146	531.0
5	TraesCS5D01G051200	chr5D	91.525	118	10	0	4751	4868	49109086	49109203	7.940000e-36	163.0
6	TraesCS5D01G051200	chr5D	91.525	118	10	0	4718	4835	49109119	49109236	7.940000e-36	163.0
7	TraesCS5D01G051200	chr5D	90.588	85	8	0	4784	4868	49109086	49109170	8.110000e-21	113.0
8	TraesCS5D01G051200	chr5D	88.462	52	6	0	4817	4868	49109086	49109137	8.290000e-06	63.9
9	TraesCS5D01G051200	chr5D	88.462	52	6	0	4718	4769	49109185	49109236	8.290000e-06	63.9
10	TraesCS5D01G051200	chr5B	96.813	5523	141	17	1549	7043	51831555	51837070	0.000000e+00	9191.0
11	TraesCS5D01G051200	chr5B	96.839	1582	39	8	8305	9882	51838169	51839743	0.000000e+00	2634.0
12	TraesCS5D01G051200	chr5B	97.516	644	12	3	7035	7674	51837093	51837736	0.000000e+00	1098.0
13	TraesCS5D01G051200	chr5B	79.220	1179	148	47	3	1120	51830339	51831481	0.000000e+00	730.0
14	TraesCS5D01G051200	chr5B	92.308	377	29	0	5678	6054	51835610	51835986	4.060000e-148	536.0
15	TraesCS5D01G051200	chr5B	91.512	377	32	0	5585	5961	51835703	51836079	4.090000e-143	520.0
16	TraesCS5D01G051200	chr5B	92.580	283	21	0	5771	6053	51835610	51835892	3.320000e-109	407.0
17	TraesCS5D01G051200	chr5B	94.495	109	6	0	4751	4859	51834737	51834845	1.710000e-37	169.0
18	TraesCS5D01G051200	chr5A	96.439	5252	160	11	1556	6786	38724767	38730012	0.000000e+00	8637.0
19	TraesCS5D01G051200	chr5A	95.136	1583	66	6	8305	9882	38731354	38732930	0.000000e+00	2486.0
20	TraesCS5D01G051200	chr5A	91.516	884	48	10	1	863	38723287	38724164	0.000000e+00	1192.0
21	TraesCS5D01G051200	chr5A	98.077	572	10	1	7035	7606	38730193	38730763	0.000000e+00	994.0
22	TraesCS5D01G051200	chr5A	92.308	377	29	0	5678	6054	38728810	38729186	4.060000e-148	536.0
23	TraesCS5D01G051200	chr5A	92.308	377	29	0	5585	5961	38728903	38729279	4.060000e-148	536.0
24	TraesCS5D01G051200	chr5A	92.933	283	20	0	5585	5867	38728996	38729278	7.140000e-111	412.0
25	TraesCS5D01G051200	chr5A	96.835	158	3	2	6888	7043	38730013	38730170	7.610000e-66	263.0
26	TraesCS5D01G051200	chr5A	90.116	172	9	6	957	1122	38724528	38724697	6.010000e-52	217.0
27	TraesCS5D01G051200	chr5A	91.525	118	10	0	4751	4868	38727936	38728053	7.940000e-36	163.0
28	TraesCS5D01G051200	chr5A	91.525	118	10	0	4718	4835	38727969	38728086	7.940000e-36	163.0
29	TraesCS5D01G051200	chr5A	92.941	85	6	0	4718	4802	38728002	38728086	3.750000e-24	124.0
30	TraesCS5D01G051200	chr5A	90.385	52	5	0	4718	4769	38728035	38728086	1.780000e-07	69.4
31	TraesCS5D01G051200	chr5A	88.889	45	5	0	4817	4861	38727936	38727980	1.000000e-03	56.5
32	TraesCS5D01G051200	chr4B	93.359	256	16	1	1743	1998	510130092	510130346	2.610000e-100	377.0
33	TraesCS5D01G051200	chr1B	93.359	256	16	1	1743	1998	643923765	643924019	2.610000e-100	377.0
34	TraesCS5D01G051200	chr1B	90.458	262	24	1	1743	2004	8402695	8402435	2.640000e-90	344.0
35	TraesCS5D01G051200	chr3B	91.985	262	20	1	1743	2004	761465824	761465564	5.640000e-97	366.0
36	TraesCS5D01G051200	chr3B	87.850	214	18	7	1549	1756	6593839	6594050	2.760000e-60	244.0
37	TraesCS5D01G051200	chr7B	92.188	256	19	1	1743	1998	100428342	100428596	2.620000e-95	361.0
38	TraesCS5D01G051200	chr7B	100.000	28	0	0	2910	2937	684401764	684401791	1.800000e-02	52.8
39	TraesCS5D01G051200	chr2B	90.840	262	23	1	1743	2004	371337479	371337219	5.680000e-92	350.0
40	TraesCS5D01G051200	chrUn	87.558	217	19	7	1549	1759	287555883	287555669	2.760000e-60	244.0
41	TraesCS5D01G051200	chrUn	87.850	214	18	7	1549	1756	291991694	291991905	2.760000e-60	244.0
42	TraesCS5D01G051200	chr2A	79.937	319	47	12	9536	9849	524846100	524845794	1.670000e-52	219.0
43	TraesCS5D01G051200	chr2A	96.296	108	3	1	6784	6890	746800122	746800229	1.020000e-39	176.0
44	TraesCS5D01G051200	chr2A	93.162	117	7	1	6784	6899	173127265	173127149	4.750000e-38	171.0
45	TraesCS5D01G051200	chr2D	94.872	117	4	2	6781	6896	73968054	73968169	2.190000e-41	182.0
46	TraesCS5D01G051200	chr7D	96.296	108	3	1	6784	6890	185178163	185178056	1.020000e-39	176.0
47	TraesCS5D01G051200	chr6D	94.690	113	5	1	6781	6892	68899898	68900010	3.670000e-39	174.0
48	TraesCS5D01G051200	chr4D	93.966	116	5	2	6783	6896	155576797	155576682	3.670000e-39	174.0
49	TraesCS5D01G051200	chr7A	93.913	115	6	1	6779	6892	538102640	538102526	1.320000e-38	172.0
50	TraesCS5D01G051200	chr7A	89.922	129	9	4	6769	6894	638698951	638699078	7.940000e-36	163.0
51	TraesCS5D01G051200	chr4A	84.314	102	16	0	1858	1959	660522278	660522379	6.320000e-17	100.0

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	TraesCS5D01G051200	chr5D	49104369	49114250	9881	False	1842.680000	11797	93.464600	1	9882	10	chr5D.!!$F1	9881
1	TraesCS5D01G051200	chr5B	51830339	51839743	9404	False	1910.625000	9191	92.660375	3	9882	8	chr5B.!!$F1	9879
2	TraesCS5D01G051200	chr5A	38723287	38732930	9643	False	1132.064286	8637	92.923786	1	9882	14	chr5A.!!$F1	9881

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
654	690	0.245539	TACGAAACCTCTCCGCCTTG	59.754	55.000	0.00	0.0	0.00	3.61	F
912	972	1.128188	AAAGCCAGACCGTTCCTCCT	61.128	55.000	0.00	0.0	0.00	3.69	F
1735	2093	1.525077	GTTGCGTGGAAGGGTCACA	60.525	57.895	0.00	0.0	35.03	3.58	F
2231	2593	1.346395	GGGACATACGGTGCATATCCA	59.654	52.381	0.00	0.0	40.06	3.41	F
3462	3836	1.467734	CACACAGAGCATTCAGAAGCC	59.532	52.381	0.00	0.0	0.00	4.35	F
3895	4269	0.320050	TCAGTCAACTGCGGTGCATA	59.680	50.000	0.00	0.0	43.46	3.14	F
5571	5952	0.771755	GTCCAGGAACCAAGGAAGGT	59.228	55.000	0.00	0.0	45.91	3.50	F
5880	6261	0.401738	CCAAAGGCCTCCAAGAGTCA	59.598	55.000	5.23	0.0	0.00	3.41	F
7690	8110	2.042569	ACTGATTTTAGGTCCAACCCCC	59.957	50.000	0.00	0.0	39.75	5.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1810	2171	0.749091	TGCTGGCGAATCATCCAAGG	60.749	55.000	0.00	0.00	30.98	3.61	R
1943	2304	0.804933	GGTCGTACCGGTCAAGCATC	60.805	60.000	12.40	0.00	0.00	3.91	R
3106	3473	1.616865	TCAACCTCACTGAGTTACCCG	59.383	52.381	5.32	0.00	0.00	5.28	R
3762	4136	0.959372	CCTTCTTGCTGTCAGGCTGG	60.959	60.000	15.73	0.00	0.00	4.85	R
4268	4642	0.242017	GGCTTGCACACTCCAATGTC	59.758	55.000	0.00	0.00	0.00	3.06	R
5767	6148	0.402121	GACTCTTGGAGGCCTTTGGT	59.598	55.000	6.77	0.14	30.04	3.67	R
6587	6968	3.555168	CCAAAGGTAGAGTCAGTGGTCAC	60.555	52.174	0.00	0.00	0.00	3.67	R
7692	8112	0.536460	ATAATTAACAGGGCGCGGGG	60.536	55.000	8.83	0.00	0.00	5.73	R
9522	9949	2.288642	ATCCTCCCATGGCAACGCAT	62.289	55.000	6.09	0.00	42.51	4.73	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
38	39	4.808414	TCCGACTCTGATGAAACTCATT	57.192	40.909	0.00	0.00	37.20	2.57
92	93	8.495260	AGCCTTTACCTTACTATTAGCTTTGAT	58.505	33.333	0.00	0.00	0.00	2.57
137	145	3.028850	TCGAGTTCCCGGTTATGAAGAT	58.971	45.455	0.00	0.00	0.00	2.40
144	152	2.618709	CCCGGTTATGAAGATGAAAGGC	59.381	50.000	0.00	0.00	0.00	4.35
169	177	8.210525	GCGAAGAGATCAAAATTGTTCTTTTTC	58.789	33.333	7.86	11.96	37.36	2.29
178	186	7.338196	TCAAAATTGTTCTTTTTCCCCCTTTTC	59.662	33.333	0.00	0.00	0.00	2.29
193	201	2.029623	CTTTTCTGGGATGGGATGCAG	58.970	52.381	0.00	0.00	0.00	4.41
387	397	0.250513	AGCCTCCTCACCGAATCAAC	59.749	55.000	0.00	0.00	0.00	3.18
390	400	0.613260	CTCCTCACCGAATCAACCCA	59.387	55.000	0.00	0.00	0.00	4.51
434	444	2.436417	CACCTTCATCATCCACGGTTT	58.564	47.619	0.00	0.00	0.00	3.27
448	458	1.296056	CGGTTTCGGCGACCTTCATT	61.296	55.000	10.16	0.00	34.95	2.57
500	521	2.294979	GAATACCTTTGCCCTAACCGG	58.705	52.381	0.00	0.00	0.00	5.28
570	591	3.644265	ACAAACACCCAGAATTAAACCCC	59.356	43.478	0.00	0.00	0.00	4.95
630	666	0.323957	GCGTTCTACCCAAACTCCCT	59.676	55.000	0.00	0.00	0.00	4.20
634	670	3.512724	CGTTCTACCCAAACTCCCTAGAA	59.487	47.826	0.00	0.00	0.00	2.10
636	672	5.361857	CGTTCTACCCAAACTCCCTAGAATA	59.638	44.000	0.00	0.00	0.00	1.75
644	680	5.338137	CCAAACTCCCTAGAATACGAAACCT	60.338	44.000	0.00	0.00	0.00	3.50
652	688	1.136500	GAATACGAAACCTCTCCGCCT	59.864	52.381	0.00	0.00	0.00	5.52
654	690	0.245539	TACGAAACCTCTCCGCCTTG	59.754	55.000	0.00	0.00	0.00	3.61
660	696	2.812619	CCTCTCCGCCTTGATCCCC	61.813	68.421	0.00	0.00	0.00	4.81
726	774	2.287769	GATTCAGAGAAGCAAGGGAGC	58.712	52.381	0.00	0.00	0.00	4.70
793	852	9.396022	GGAAATCAATAATCAGAGGTGAGTAAA	57.604	33.333	0.00	0.00	36.85	2.01
905	965	1.528309	CAACCCAAAGCCAGACCGT	60.528	57.895	0.00	0.00	0.00	4.83
912	972	1.128188	AAAGCCAGACCGTTCCTCCT	61.128	55.000	0.00	0.00	0.00	3.69
1032	1366	1.739049	CTCCGATCTGGTGAGCTCC	59.261	63.158	12.15	2.19	39.52	4.70

Showing 1 to 25 of 247 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	4.808414	AATGAGTTTCATCAGAGTCGGA	57.192	40.909	0.00	0.00	35.76	4.55
38	39	7.145985	GCGATGACAAGTTAGAGGTTATGATA	58.854	38.462	0.00	0.00	0.00	2.15
115	123	2.426024	TCTTCATAACCGGGAACTCGAG	59.574	50.000	11.84	11.84	0.00	4.04
137	145	5.241506	ACAATTTTGATCTCTTCGCCTTTCA	59.758	36.000	0.00	0.00	0.00	2.69
144	152	8.694394	GGAAAAAGAACAATTTTGATCTCTTCG	58.306	33.333	3.89	0.00	39.07	3.79
178	186	2.965671	AATACTGCATCCCATCCCAG	57.034	50.000	0.00	0.00	0.00	4.45
264	273	2.045885	TGAGGAGGAATGGGTCTAGGTT	59.954	50.000	0.00	0.00	0.00	3.50
387	397	0.249398	CGAGTAAGGTGGGAAGTGGG	59.751	60.000	0.00	0.00	0.00	4.61
390	400	0.320697	GTGCGAGTAAGGTGGGAAGT	59.679	55.000	0.00	0.00	0.00	3.01
434	444	1.218047	CAGGAATGAAGGTCGCCGA	59.782	57.895	0.00	0.00	0.00	5.54
448	458	1.381327	GAGTCCCCGTGATCCAGGA	60.381	63.158	5.24	0.00	0.00	3.86
500	521	4.046938	TGGATGAAGATCTACGAGTTGC	57.953	45.455	0.00	0.00	0.00	4.17
570	591	1.201965	GCGGCGAGAAAGATGAAGTTG	60.202	52.381	12.98	0.00	0.00	3.16
600	636	1.226974	TAGAACGCATGAGCCGAGC	60.227	57.895	0.00	0.00	37.52	5.03
606	642	2.673368	GAGTTTGGGTAGAACGCATGAG	59.327	50.000	0.00	0.00	40.81	2.90
630	666	2.360165	GGCGGAGAGGTTTCGTATTCTA	59.640	50.000	0.00	0.00	0.00	2.10
634	670	1.134788	CAAGGCGGAGAGGTTTCGTAT	60.135	52.381	0.00	0.00	0.00	3.06
636	672	1.004918	CAAGGCGGAGAGGTTTCGT	60.005	57.895	0.00	0.00	0.00	3.85
644	680	1.615124	TTGGGGATCAAGGCGGAGA	60.615	57.895	0.00	0.00	0.00	3.71
652	688	0.245539	GACGACGAGTTGGGGATCAA	59.754	55.000	0.00	0.00	0.00	2.57
654	690	0.245539	TTGACGACGAGTTGGGGATC	59.754	55.000	0.00	0.00	0.00	3.36
660	696	1.371267	TCGCCTTGACGACGAGTTG	60.371	57.895	0.00	0.00	37.09	3.16
701	737	0.324614	TTGCTTCTCTGAATCCGGCA	59.675	50.000	0.00	0.00	0.00	5.69
726	774	9.840427	ATGAAGTTTCTATAAATTTGTGTTCCG	57.160	29.630	0.00	0.00	0.00	4.30
755	814	0.968405	TGATTTCCAAACTGGGCAGC	59.032	50.000	0.00	0.00	38.32	5.25

Showing 1 to 25 of 230 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.