AutoCloner

Multiple sequence alignment - TraesCS2D01G498500

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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	TraesCS2D01G498500	chr2D	100.000	2966	0	0	1	2966	593856608	593859573	0.000000e+00	5478
1	TraesCS2D01G498500	chr2D	92.971	1878	70	25	609	2432	593919740	593917871	0.000000e+00	2680
2	TraesCS2D01G498500	chr2D	93.344	1818	60	24	669	2432	593899121	593897311	0.000000e+00	2630
3	TraesCS2D01G498500	chr2D	91.368	1900	93	22	254	2118	593850713	593852576	0.000000e+00	2534
4	TraesCS2D01G498500	chr2D	96.510	831	22	5	2142	2966	593895045	593894216	0.000000e+00	1367
5	TraesCS2D01G498500	chr2D	86.644	292	28	4	384	675	593904903	593904623	2.220000e-81	313
6	TraesCS2D01G498500	chr2D	88.532	218	20	5	1	216	593850431	593850645	2.930000e-65	259
7	TraesCS2D01G498500	chr2A	94.385	2333	112	11	643	2963	728728520	728726195	0.000000e+00	3565
8	TraesCS2D01G498500	chr2A	94.083	2011	89	15	297	2285	728648319	728650321	0.000000e+00	3027
9	TraesCS2D01G498500	chr2A	92.747	1558	75	19	567	2110	728617182	728618715	0.000000e+00	2217
10	TraesCS2D01G498500	chr2A	87.336	1145	88	35	1016	2141	728753334	728752228	0.000000e+00	1258
11	TraesCS2D01G498500	chr2A	95.182	685	28	4	2281	2963	728650703	728651384	0.000000e+00	1077
12	TraesCS2D01G498500	chr2A	97.685	216	5	0	1	216	728648091	728648306	3.610000e-99	372
13	TraesCS2D01G498500	chr2B	90.819	2712	164	33	254	2917	720816647	720819321	0.000000e+00	3550
14	TraesCS2D01G498500	chr2B	90.812	2710	163	33	257	2917	720915078	720912406	0.000000e+00	3546
15	TraesCS2D01G498500	chr2B	88.474	1553	104	40	657	2172	720923954	720922440	0.000000e+00	1807
16	TraesCS2D01G498500	chr2B	91.244	217	15	4	1	216	720813263	720813476	2.890000e-75	292
17	TraesCS2D01G498500	chr2B	82.985	335	39	11	1	333	720918467	720918149	1.350000e-73	287
18	TraesCS2D01G498500	chr2B	89.091	220	17	7	1	216	720816362	720816578	1.750000e-67	267
19	TraesCS2D01G498500	chr2B	89.091	220	17	7	1	216	720915366	720915150	1.750000e-67	267
20	TraesCS2D01G498500	chrUn	93.955	397	20	3	2160	2553	478471682	478472077	5.470000e-167	597

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	TraesCS2D01G498500	chr2D	593856608	593859573	2965	False	5478.000000	5478	100.000000	1	2966	1	chr2D.!!$F1	2965
1	TraesCS2D01G498500	chr2D	593917871	593919740	1869	True	2680.000000	2680	92.971000	609	2432	1	chr2D.!!$R2	1823
2	TraesCS2D01G498500	chr2D	593894216	593899121	4905	True	1998.500000	2630	94.927000	669	2966	2	chr2D.!!$R3	2297
3	TraesCS2D01G498500	chr2D	593850431	593852576	2145	False	1396.500000	2534	89.950000	1	2118	2	chr2D.!!$F2	2117
4	TraesCS2D01G498500	chr2A	728726195	728728520	2325	True	3565.000000	3565	94.385000	643	2963	1	chr2A.!!$R1	2320
5	TraesCS2D01G498500	chr2A	728617182	728618715	1533	False	2217.000000	2217	92.747000	567	2110	1	chr2A.!!$F1	1543
6	TraesCS2D01G498500	chr2A	728648091	728651384	3293	False	1492.000000	3027	95.650000	1	2963	3	chr2A.!!$F2	2962
7	TraesCS2D01G498500	chr2A	728752228	728753334	1106	True	1258.000000	1258	87.336000	1016	2141	1	chr2A.!!$R2	1125
8	TraesCS2D01G498500	chr2B	720912406	720923954	11548	True	1476.750000	3546	87.840500	1	2917	4	chr2B.!!$R1	2916
9	TraesCS2D01G498500	chr2B	720813263	720819321	6058	False	1369.666667	3550	90.384667	1	2917	3	chr2B.!!$F1	2916

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
451	9121	0.24445	AACCGCATGCATGAGTTTGG	59.756	50.0	30.64	21.9	0.0	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	10741	1.080093	GCCACGACCACGATCAGAA	60.08	57.895	0.0	0.0	42.66	3.02	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
56	5544	3.189285	CCAGCCCTGCAATTAAAATTCG	58.811	45.455	0.00	0.00	0.00	3.34
193	8786	8.125978	ACTTCACATCCAACATATGAAACAAT	57.874	30.769	10.38	0.00	0.00	2.71
255	8848	6.906157	AAGATTTATATTCCCCTCGTCGTA	57.094	37.500	0.00	0.00	0.00	3.43
273	8917	4.213906	GTCGTAGTCTACCTATCTTGCCTC	59.786	50.000	4.39	0.00	0.00	4.70
279	8923	5.304101	AGTCTACCTATCTTGCCTCTTCATG	59.696	44.000	0.00	0.00	0.00	3.07
350	8996	4.473520	AGACCAATCGCCGCCTGG	62.474	66.667	3.13	3.13	36.24	4.45
364	9010	2.169769	CCGCCTGGTATCTTCTTTACCA	59.830	50.000	2.83	2.83	45.27	3.25
423	9093	6.335777	TCAACTAGTTATTAGAGCCGGTTTC	58.664	40.000	8.04	0.98	33.39	2.78
450	9120	2.917701	TAACCGCATGCATGAGTTTG	57.082	45.000	30.64	16.16	31.28	2.93
451	9121	0.244450	AACCGCATGCATGAGTTTGG	59.756	50.000	30.64	21.90	0.00	3.28
564	9238	7.190335	TGCCCATTTATGTACTACTAGTGTT	57.810	36.000	5.39	0.00	0.00	3.32
565	9239	8.308851	TGCCCATTTATGTACTACTAGTGTTA	57.691	34.615	5.39	0.00	0.00	2.41
590	9264	1.242076	CTTCTTGGCTCACAGTTGGG	58.758	55.000	0.00	0.00	0.00	4.12
598	9272	1.303236	TCACAGTTGGGGCATTCCG	60.303	57.895	0.00	0.00	36.01	4.30
599	9273	1.603455	CACAGTTGGGGCATTCCGT	60.603	57.895	0.00	0.00	36.01	4.69
600	9274	1.303317	ACAGTTGGGGCATTCCGTC	60.303	57.895	0.00	0.00	36.01	4.79
601	9275	1.303236	CAGTTGGGGCATTCCGTCA	60.303	57.895	0.00	0.00	36.01	4.35
602	9276	0.680921	CAGTTGGGGCATTCCGTCAT	60.681	55.000	0.00	0.00	36.01	3.06
628	9302	1.135721	CTCATCTCATCGACAGGTGCA	59.864	52.381	2.12	0.00	0.00	4.57
787	9464	7.475771	GTGCAACCTGAAGAGAGAATAATAG	57.524	40.000	0.00	0.00	0.00	1.73
840	9518	0.665068	CTACACTACGTGCGCACCAA	60.665	55.000	33.23	20.60	36.98	3.67
955	9641	4.508662	GTCTTCTTGACATACCCTTCCTG	58.491	47.826	0.00	0.00	44.73	3.86
1152	9867	2.592308	GGCCTGACCATGTCCCTC	59.408	66.667	0.00	0.00	38.86	4.30
1215	9930	1.655654	CATCTACGGCAGCGTCTCG	60.656	63.158	0.00	0.00	0.00	4.04
1230	9945	1.205893	GTCTCGACCCTCATCAAGCTT	59.794	52.381	0.00	0.00	0.00	3.74
1333	10072	1.131693	TGTACTGCGATACTGACCGTG	59.868	52.381	0.00	0.00	0.00	4.94
1345	10084	0.106894	TGACCGTGTGTGCACCATTA	59.893	50.000	15.69	0.00	42.39	1.90
1674	10425	2.123251	ATCTGGTCGGCGGAGGAT	60.123	61.111	7.21	3.46	0.00	3.24
1860	10611	4.056125	CTCACCGACCAGCAGCGA	62.056	66.667	0.00	0.00	0.00	4.93
1908	10659	4.193090	CTCACAGGATCTACGACTACTGT	58.807	47.826	0.00	0.00	39.53	3.55
1939	10690	1.600916	GACAACAAGAAGCCCGGCT	60.601	57.895	5.94	5.94	42.56	5.52
2057	10816	2.161808	CCGATCTACTACCACGGCATAG	59.838	54.545	0.00	0.00	37.32	2.23
2359	11547	9.546428	GGCAAATTTACTATGATAATTTTGGCT	57.454	29.630	21.69	0.00	45.61	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	5510	0.174162	GGGCTGGCTGCAAACAATAG	59.826	55.000	18.32	0.00	45.15	1.73
56	5544	8.850454	AATGTGTGTGTGAAAGTGTTATTTAC	57.150	30.769	0.00	0.00	0.00	2.01
193	8786	8.977412	GGGGATAAATCTTTGGATTTTAGAACA	58.023	33.333	8.87	0.00	46.36	3.18
224	8817	8.860088	CGAGGGGAATATAAATCTTTGGATTTT	58.140	33.333	8.87	2.07	46.36	1.82
226	8819	7.526918	ACGAGGGGAATATAAATCTTTGGATT	58.473	34.615	0.00	0.00	43.26	3.01
227	8820	7.091533	ACGAGGGGAATATAAATCTTTGGAT	57.908	36.000	0.00	0.00	0.00	3.41
228	8821	6.509523	ACGAGGGGAATATAAATCTTTGGA	57.490	37.500	0.00	0.00	0.00	3.53
229	8822	5.408604	CGACGAGGGGAATATAAATCTTTGG	59.591	44.000	0.00	0.00	0.00	3.28
230	8823	5.989777	ACGACGAGGGGAATATAAATCTTTG	59.010	40.000	0.00	0.00	0.00	2.77
231	8824	6.170846	ACGACGAGGGGAATATAAATCTTT	57.829	37.500	0.00	0.00	0.00	2.52
232	8825	5.803237	ACGACGAGGGGAATATAAATCTT	57.197	39.130	0.00	0.00	0.00	2.40
233	8826	6.008960	ACTACGACGAGGGGAATATAAATCT	58.991	40.000	0.00	0.00	0.00	2.40
234	8827	6.150809	AGACTACGACGAGGGGAATATAAATC	59.849	42.308	0.00	0.00	0.00	2.17
235	8828	6.008960	AGACTACGACGAGGGGAATATAAAT	58.991	40.000	0.00	0.00	0.00	1.40
236	8829	5.380043	AGACTACGACGAGGGGAATATAAA	58.620	41.667	0.00	0.00	0.00	1.40
237	8830	4.978099	AGACTACGACGAGGGGAATATAA	58.022	43.478	0.00	0.00	0.00	0.98
255	8848	4.873010	TGAAGAGGCAAGATAGGTAGACT	58.127	43.478	0.00	0.00	0.00	3.24
273	8917	2.222376	CGAGCGAAAAGACGACATGAAG	60.222	50.000	0.00	0.00	35.09	3.02
279	8923	2.167591	CTACTCGAGCGAAAAGACGAC	58.832	52.381	13.61	0.00	35.09	4.34
308	8952	8.925161	TGAAAAGACAACATGAAAAGTTAAGG	57.075	30.769	0.00	0.00	0.00	2.69
350	8996	5.163784	GGCGGTTTTCTGGTAAAGAAGATAC	60.164	44.000	0.00	0.00	45.64	2.24
364	9010	2.897969	TCTAGTCAAGAGGCGGTTTTCT	59.102	45.455	0.00	0.00	0.00	2.52
423	9093	0.724549	TGCATGCGGTTAAAGTAGCG	59.275	50.000	14.09	0.00	41.61	4.26
450	9120	1.202698	AGGCAGTTAATCATCCTCGCC	60.203	52.381	0.00	0.00	38.60	5.54
451	9121	2.139118	GAGGCAGTTAATCATCCTCGC	58.861	52.381	0.00	0.00	34.67	5.03
564	9238	3.330701	ACTGTGAGCCAAGAAGGGAAATA	59.669	43.478	0.00	0.00	38.09	1.40
565	9239	2.108952	ACTGTGAGCCAAGAAGGGAAAT	59.891	45.455	0.00	0.00	38.09	2.17
590	9264	2.224137	TGAGATGAGATGACGGAATGCC	60.224	50.000	0.00	0.00	0.00	4.40
598	9272	5.048852	TGTCGATGAGATGAGATGAGATGAC	60.049	44.000	0.00	0.00	0.00	3.06
599	9273	5.068636	TGTCGATGAGATGAGATGAGATGA	58.931	41.667	0.00	0.00	0.00	2.92
600	9274	5.373981	TGTCGATGAGATGAGATGAGATG	57.626	43.478	0.00	0.00	0.00	2.90
601	9275	4.460034	CCTGTCGATGAGATGAGATGAGAT	59.540	45.833	0.00	0.00	0.00	2.75
602	9276	3.819902	CCTGTCGATGAGATGAGATGAGA	59.180	47.826	0.00	0.00	0.00	3.27
628	9302	4.441913	CCTCTTTGTTTCATGCCAAACTGT	60.442	41.667	10.37	0.00	37.20	3.55
840	9518	7.671495	ATTTTCAGTCAAAAGCAAAAGTGTT	57.329	28.000	0.00	0.00	37.40	3.32
948	9634	0.675633	CTTTTGGTGGTGCAGGAAGG	59.324	55.000	0.00	0.00	0.00	3.46
955	9641	0.961753	AGCTTAGCTTTTGGTGGTGC	59.038	50.000	0.00	0.00	33.89	5.01
975	9669	1.154169	CTACGTCGTAGTTGGCGCA	60.154	57.895	21.77	0.00	32.09	6.09
977	9671	0.247974	CTCCTACGTCGTAGTTGGCG	60.248	60.000	26.33	13.66	37.03	5.69
1215	9930	1.680249	GGGACAAGCTTGATGAGGGTC	60.680	57.143	32.50	16.77	0.00	4.46
1230	9945	3.319198	GCAGAGTTCCCCGGGACA	61.319	66.667	26.32	4.64	0.00	4.02
1296	10035	6.196724	CGCAGTACAAGCTCATTAGTAAGTAC	59.803	42.308	8.41	0.00	0.00	2.73
1333	10072	4.808558	ACAATCAATGTAATGGTGCACAC	58.191	39.130	20.43	8.70	41.63	3.82
1345	10084	8.340443	CGATGTCTGATGATTTACAATCAATGT	58.660	33.333	3.36	0.00	46.36	2.71
1860	10611	1.302285	CACCTCCTGCATCTTGGCT	59.698	57.895	0.00	0.00	34.04	4.75
1908	10659	1.694844	TGTTGTCCCTGTAGTCGACA	58.305	50.000	19.50	0.48	34.80	4.35
1990	10741	1.080093	GCCACGACCACGATCAGAA	60.080	57.895	0.00	0.00	42.66	3.02
2057	10816	2.358898	CCAATGGAATCAATGGGTCGTC	59.641	50.000	0.00	0.00	39.65	4.20
2359	11547	2.041686	GTGCCACCGCGGGATTTAA	61.042	57.895	31.76	6.77	37.50	1.52
2519	14268	9.988815	GTACATGTATCTCAAATAGGATCTGTT	57.011	33.333	9.18	0.00	0.00	3.16
2695	14447	4.551388	TGTTTGCCGTATTCCAAATGTTC	58.449	39.130	0.00	0.00	33.96	3.18
2920	14676	3.689649	CCTGTCGTCAAAAATAGAAGGGG	59.310	47.826	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.