AutoCloner

Multiple sequence alignment - TraesCS3D01G202700

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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	TraesCS3D01G202700	chr3D	100.000	2384	0	0	1	2384	249281283	249278900	0.000000e+00	4403
1	TraesCS3D01G202700	chr3D	96.337	1447	50	1	1	1447	249653599	249652156	0.000000e+00	2375
2	TraesCS3D01G202700	chr3D	94.610	1447	75	1	1	1447	249668956	249667513	0.000000e+00	2237
3	TraesCS3D01G202700	chr3D	96.257	935	33	2	1451	2384	249643623	249642690	0.000000e+00	1531
4	TraesCS3D01G202700	chr3D	93.911	542	30	2	906	1447	99848296	99848834	0.000000e+00	815
5	TraesCS3D01G202700	chr3D	88.381	525	58	3	1861	2384	442703546	442703024	1.560000e-176	628
6	TraesCS3D01G202700	chr3D	88.168	524	62	0	1861	2384	256072817	256073340	2.010000e-175	625
7	TraesCS3D01G202700	chr3D	89.383	405	43	0	1456	1860	227984968	227985372	5.880000e-141	510
8	TraesCS3D01G202700	chr3D	89.024	410	45	0	1451	1860	249725499	249725090	2.110000e-140	508
9	TraesCS3D01G202700	chr3D	88.537	410	47	0	1451	1860	249320724	249320315	4.580000e-137	497
10	TraesCS3D01G202700	chr3D	85.116	215	28	2	664	876	249668060	249667848	1.430000e-52	217
11	TraesCS3D01G202700	chr6A	93.538	1300	84	0	148	1447	70186941	70185642	0.000000e+00	1936
12	TraesCS3D01G202700	chr6A	93.609	1064	61	3	148	1211	70152927	70151871	0.000000e+00	1581
13	TraesCS3D01G202700	chr6A	93.358	542	35	1	906	1447	384926892	384926352	0.000000e+00	800
14	TraesCS3D01G202700	chr3A	91.463	574	47	2	874	1447	666048294	666048865	0.000000e+00	787
15	TraesCS3D01G202700	chr4A	91.259	572	47	3	876	1447	258966938	258966370	0.000000e+00	776
16	TraesCS3D01G202700	chr4A	88.060	603	50	14	230	811	658828099	658828700	0.000000e+00	695
17	TraesCS3D01G202700	chr7B	90.925	573	50	2	875	1447	246779750	246779180	0.000000e+00	769
18	TraesCS3D01G202700	chr7B	89.483	561	49	7	230	789	654080800	654081351	0.000000e+00	701
19	TraesCS3D01G202700	chr7B	94.771	153	8	0	1	153	27390059	27390211	3.060000e-59	239
20	TraesCS3D01G202700	chr7B	93.919	148	9	0	6	153	27350313	27350460	8.580000e-55	224
21	TraesCS3D01G202700	chr6D	89.043	575	47	9	230	789	328150271	328150844	0.000000e+00	699
22	TraesCS3D01G202700	chr1D	89.024	574	49	10	230	789	403575684	403576257	0.000000e+00	699
23	TraesCS3D01G202700	chr1D	86.321	212	29	0	665	876	386531798	386532009	5.120000e-57	231
24	TraesCS3D01G202700	chr1D	86.449	214	25	2	665	876	386532147	386532358	5.120000e-57	231
25	TraesCS3D01G202700	chr1D	82.745	255	38	4	665	916	403596849	403597100	3.080000e-54	222
26	TraesCS3D01G202700	chr1D	81.961	255	39	5	665	916	403576420	403576670	2.400000e-50	209
27	TraesCS3D01G202700	chr1B	88.000	575	53	12	230	789	514435734	514436307	0.000000e+00	665
28	TraesCS3D01G202700	chr2D	88.952	525	57	1	1861	2384	457805968	457806492	0.000000e+00	647
29	TraesCS3D01G202700	chr2D	88.046	527	60	1	1861	2384	242144077	242144603	2.600000e-174	621
30	TraesCS3D01G202700	chr2D	87.405	524	66	0	1861	2384	265105372	265105895	9.430000e-169	603
31	TraesCS3D01G202700	chr2D	92.073	164	13	0	1	164	335705958	335706121	5.120000e-57	231
32	TraesCS3D01G202700	chr5A	88.046	527	58	3	1861	2383	265600979	265601504	9.360000e-174	619
33	TraesCS3D01G202700	chr7D	87.739	522	62	1	1862	2383	321178017	321177498	2.030000e-170	608
34	TraesCS3D01G202700	chr7D	87.476	527	62	4	1861	2384	79290404	79289879	2.620000e-169	604
35	TraesCS3D01G202700	chr7D	89.051	411	43	2	1451	1860	359630451	359630860	2.110000e-140	508
36	TraesCS3D01G202700	chr7D	88.293	410	48	0	1451	1860	304484922	304484513	2.130000e-135	492
37	TraesCS3D01G202700	chr5D	88.698	407	44	2	1451	1857	196222674	196223078	1.650000e-136	496
38	TraesCS3D01G202700	chr6B	88.107	412	47	2	1451	1861	325018239	325018649	2.750000e-134	488
39	TraesCS3D01G202700	chr4D	88.049	410	49	0	1451	1860	221048101	221048510	9.910000e-134	486

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	TraesCS3D01G202700	chr3D	249278900	249281283	2383	True	4403	4403	100.0000	1	2384	1	chr3D.!!$R1	2383
1	TraesCS3D01G202700	chr3D	249652156	249653599	1443	True	2375	2375	96.3370	1	1447	1	chr3D.!!$R4	1446
2	TraesCS3D01G202700	chr3D	249642690	249643623	933	True	1531	1531	96.2570	1451	2384	1	chr3D.!!$R3	933
3	TraesCS3D01G202700	chr3D	249667513	249668956	1443	True	1227	2237	89.8630	1	1447	2	chr3D.!!$R7	1446
4	TraesCS3D01G202700	chr3D	99848296	99848834	538	False	815	815	93.9110	906	1447	1	chr3D.!!$F1	541
5	TraesCS3D01G202700	chr3D	442703024	442703546	522	True	628	628	88.3810	1861	2384	1	chr3D.!!$R6	523
6	TraesCS3D01G202700	chr3D	256072817	256073340	523	False	625	625	88.1680	1861	2384	1	chr3D.!!$F3	523
7	TraesCS3D01G202700	chr6A	70185642	70186941	1299	True	1936	1936	93.5380	148	1447	1	chr6A.!!$R2	1299
8	TraesCS3D01G202700	chr6A	70151871	70152927	1056	True	1581	1581	93.6090	148	1211	1	chr6A.!!$R1	1063
9	TraesCS3D01G202700	chr6A	384926352	384926892	540	True	800	800	93.3580	906	1447	1	chr6A.!!$R3	541
10	TraesCS3D01G202700	chr3A	666048294	666048865	571	False	787	787	91.4630	874	1447	1	chr3A.!!$F1	573
11	TraesCS3D01G202700	chr4A	258966370	258966938	568	True	776	776	91.2590	876	1447	1	chr4A.!!$R1	571
12	TraesCS3D01G202700	chr4A	658828099	658828700	601	False	695	695	88.0600	230	811	1	chr4A.!!$F1	581
13	TraesCS3D01G202700	chr7B	246779180	246779750	570	True	769	769	90.9250	875	1447	1	chr7B.!!$R1	572
14	TraesCS3D01G202700	chr7B	654080800	654081351	551	False	701	701	89.4830	230	789	1	chr7B.!!$F3	559
15	TraesCS3D01G202700	chr6D	328150271	328150844	573	False	699	699	89.0430	230	789	1	chr6D.!!$F1	559
16	TraesCS3D01G202700	chr1D	403575684	403576670	986	False	454	699	85.4925	230	916	2	chr1D.!!$F3	686
17	TraesCS3D01G202700	chr1D	386531798	386532358	560	False	231	231	86.3850	665	876	2	chr1D.!!$F2	211
18	TraesCS3D01G202700	chr1B	514435734	514436307	573	False	665	665	88.0000	230	789	1	chr1B.!!$F1	559
19	TraesCS3D01G202700	chr2D	457805968	457806492	524	False	647	647	88.9520	1861	2384	1	chr2D.!!$F4	523
20	TraesCS3D01G202700	chr2D	242144077	242144603	526	False	621	621	88.0460	1861	2384	1	chr2D.!!$F1	523
21	TraesCS3D01G202700	chr2D	265105372	265105895	523	False	603	603	87.4050	1861	2384	1	chr2D.!!$F2	523
22	TraesCS3D01G202700	chr5A	265600979	265601504	525	False	619	619	88.0460	1861	2383	1	chr5A.!!$F1	522
23	TraesCS3D01G202700	chr7D	321177498	321178017	519	True	608	608	87.7390	1862	2383	1	chr7D.!!$R3	521
24	TraesCS3D01G202700	chr7D	79289879	79290404	525	True	604	604	87.4760	1861	2384	1	chr7D.!!$R1	523

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
941	959	0.321564	CATGGAGGACAAAGGCGTGA	60.322	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1742	2143	0.106708	CATGATAGGGGTGACACGGG	59.893	60.0	0.0	0.0	40.46	5.28	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
72	73	2.126882	AGGATGATCGGGTGATTTCCA	58.873	47.619	9.46	0.00	38.61	3.53
221	222	4.122776	CGCTTCACCACATCTAAAGCTAT	58.877	43.478	0.00	0.00	40.06	2.97
226	227	3.940852	CACCACATCTAAAGCTATGCACA	59.059	43.478	0.00	0.00	0.00	4.57
301	302	1.364626	CGCAGCAAGAAGTAGCAGGG	61.365	60.000	0.00	0.00	0.00	4.45
403	407	4.389374	ACATGAACACCAAGTCGATCTTT	58.611	39.130	0.00	0.00	33.63	2.52
606	610	2.283101	GTGTTGATGGGGCTGCCA	60.283	61.111	22.05	0.00	0.00	4.92
662	666	3.950794	TTGGTGATGAGGCCGACGC	62.951	63.158	0.00	0.00	0.00	5.19
683	687	1.291132	GTCTACTTCATCAAGCCGGC	58.709	55.000	21.89	21.89	32.09	6.13
797	815	5.569355	TGTCAACATCATCAACCCTATGTT	58.431	37.500	0.00	0.00	41.87	2.71
811	829	4.654262	ACCCTATGTTGTAAGGATCGTGAT	59.346	41.667	0.00	0.00	34.58	3.06
826	844	0.965439	GTGATGGAGCTCGCTAGGAT	59.035	55.000	7.83	0.00	0.00	3.24
855	873	3.181522	CGACTTCTTCTTCATCAAGCTGC	60.182	47.826	0.00	0.00	0.00	5.25
868	886	1.934459	AAGCTGCTGCCATGGAGGAT	61.934	55.000	18.40	0.00	41.22	3.24
869	887	2.194212	GCTGCTGCCATGGAGGATG	61.194	63.158	18.40	2.88	41.22	3.51
893	911	2.113433	GGAGCTCGCTAGGACGACA	61.113	63.158	7.83	0.00	37.09	4.35
895	913	1.370587	GAGCTCGCTAGGACGACACT	61.371	60.000	0.00	0.00	37.09	3.55
921	939	1.276138	TCTTCTTCATCAAGCCAGCGA	59.724	47.619	0.00	0.00	0.00	4.93
932	950	2.981302	CCAGCGACATGGAGGACA	59.019	61.111	0.00	0.00	43.57	4.02
941	959	0.321564	CATGGAGGACAAAGGCGTGA	60.322	55.000	0.00	0.00	0.00	4.35
943	961	0.534203	TGGAGGACAAAGGCGTGAAC	60.534	55.000	0.00	0.00	0.00	3.18
1447	1848	0.396139	ACCTGGTACCGCGGAGAATA	60.396	55.000	35.90	11.26	0.00	1.75
1448	1849	0.314302	CCTGGTACCGCGGAGAATAG	59.686	60.000	35.90	21.12	0.00	1.73
1449	1850	0.314302	CTGGTACCGCGGAGAATAGG	59.686	60.000	35.90	11.34	0.00	2.57
1493	1894	6.042552	ACTGCAAGAGTTAGGTATGATAGCAT	59.957	38.462	4.33	0.00	37.43	3.79
1500	1901	8.043710	AGAGTTAGGTATGATAGCATTATTGGC	58.956	37.037	0.00	0.00	35.94	4.52
1535	1936	5.435686	AGGTAATGACTGATTTGCCACTA	57.564	39.130	0.00	0.00	0.00	2.74
1572	1973	0.636101	ATAAAAGGAGGGCCATGGCA	59.364	50.000	36.56	14.57	44.11	4.92
1589	1990	8.411524	GCCATGGCAACCTAAAATAGGATTCC	62.412	46.154	32.08	3.26	44.00	3.01
1614	2015	0.179207	CTGTACACTCTTACGCGCGA	60.179	55.000	39.36	17.83	0.00	5.87
1700	2101	3.420893	CAATCCACCAAAGCAGGAGTAA	58.579	45.455	0.00	0.00	34.40	2.24
1807	2209	2.934838	AACATGCCCCTCCCCCTTG	61.935	63.158	0.00	0.00	0.00	3.61
1855	2257	1.878953	AGGTGATCGTGTTGAACCAC	58.121	50.000	0.00	0.00	30.98	4.16
1904	2306	6.915544	TGAGCTAAATAACTTGAGCAGATG	57.084	37.500	0.00	0.00	37.40	2.90
2233	2641	3.809013	GTGGATGGGGTGGCGGAT	61.809	66.667	0.00	0.00	0.00	4.18
2291	2699	5.149976	CCATGGAGTATGAATGGGGAAATT	58.850	41.667	5.56	0.00	39.21	1.82
2294	2702	5.836705	TGGAGTATGAATGGGGAAATTGAA	58.163	37.500	0.00	0.00	0.00	2.69
2343	2752	0.391130	AGGCGCGCTTGTCTCAAATA	60.391	50.000	32.29	0.00	0.00	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	3.458189	CTTTGAGTGGTCTTCTTGTCGT	58.542	45.455	0.00	0.00	0.00	4.34
72	73	0.812811	CATGACCGCTGCTGCTGTAT	60.813	55.000	12.39	4.89	36.78	2.29
301	302	0.958822	GAGGCCGATCTCTCTTCTCC	59.041	60.000	0.00	0.00	0.00	3.71
403	407	9.745880	GATTAGATGATAACTTTACCGTTCAGA	57.254	33.333	0.00	0.00	0.00	3.27
662	666	1.560923	CGGCTTGATGAAGTAGACGG	58.439	55.000	0.00	0.00	0.00	4.79
683	687	2.202932	CCTTCGTCCTCCATGGCG	60.203	66.667	6.96	4.85	36.93	5.69
750	768	1.671742	GTCCTCTTGGCGAACTCCA	59.328	57.895	0.00	0.00	0.00	3.86
751	769	1.446272	CGTCCTCTTGGCGAACTCC	60.446	63.158	0.00	0.00	35.80	3.85
797	815	2.362397	GAGCTCCATCACGATCCTTACA	59.638	50.000	0.87	0.00	0.00	2.41
799	817	1.609072	CGAGCTCCATCACGATCCTTA	59.391	52.381	8.47	0.00	0.00	2.69
811	829	0.964700	CATCATCCTAGCGAGCTCCA	59.035	55.000	8.47	0.00	0.00	3.86
826	844	1.623311	TGAAGAAGAAGTCGGGCATCA	59.377	47.619	0.00	0.00	0.00	3.07
893	911	3.827625	CTTGATGAAGAAGACGACGAGT	58.172	45.455	0.00	0.00	0.00	4.18
895	913	2.596452	GCTTGATGAAGAAGACGACGA	58.404	47.619	0.00	0.00	0.00	4.20
901	919	1.276138	TCGCTGGCTTGATGAAGAAGA	59.724	47.619	0.00	0.00	0.00	2.87
902	920	1.396301	GTCGCTGGCTTGATGAAGAAG	59.604	52.381	0.00	0.00	0.00	2.85
903	921	1.270785	TGTCGCTGGCTTGATGAAGAA	60.271	47.619	0.00	0.00	0.00	2.52
904	922	0.321346	TGTCGCTGGCTTGATGAAGA	59.679	50.000	0.00	0.00	0.00	2.87
921	939	0.606401	CACGCCTTTGTCCTCCATGT	60.606	55.000	0.00	0.00	0.00	3.21
941	959	4.162690	GGCATCCTCCCGAGCGTT	62.163	66.667	0.00	0.00	0.00	4.84
1447	1848	4.102681	AGTTAGGACAAAGTGCACTAACCT	59.897	41.667	22.01	24.44	39.04	3.50
1448	1849	4.213482	CAGTTAGGACAAAGTGCACTAACC	59.787	45.833	22.01	19.31	39.04	2.85
1449	1850	5.344207	CAGTTAGGACAAAGTGCACTAAC	57.656	43.478	22.01	18.02	38.78	2.34
1535	1936	6.103649	CCTTTTATAGGGTAAGGGGTTACCAT	59.896	42.308	14.68	10.82	46.77	3.55
1572	1973	4.141321	GGGGTCGGAATCCTATTTTAGGTT	60.141	45.833	0.00	0.00	46.32	3.50
1589	1990	1.131883	CGTAAGAGTGTACAGGGGTCG	59.868	57.143	0.00	0.00	43.02	4.79
1614	2015	0.836400	TTCCTCGGGGAGAGCAACTT	60.836	55.000	3.09	0.00	45.54	2.66
1652	2053	0.949105	GACCCTGACGAACACGCAAT	60.949	55.000	0.00	0.00	0.00	3.56
1681	2082	2.025887	CCTTACTCCTGCTTTGGTGGAT	60.026	50.000	0.00	0.00	0.00	3.41
1700	2101	2.767505	CCACTGCGAAGAGTAAAACCT	58.232	47.619	0.00	0.00	0.00	3.50
1740	2141	1.261938	TGATAGGGGTGACACGGGTG	61.262	60.000	0.00	0.00	40.46	4.61
1741	2142	0.326238	ATGATAGGGGTGACACGGGT	60.326	55.000	0.00	0.00	40.46	5.28
1742	2143	0.106708	CATGATAGGGGTGACACGGG	59.893	60.000	0.00	0.00	40.46	5.28
1745	2146	1.959042	CAGCATGATAGGGGTGACAC	58.041	55.000	0.00	0.00	39.69	3.67
1746	2147	0.181114	GCAGCATGATAGGGGTGACA	59.819	55.000	0.00	0.00	39.69	3.58
1807	2209	3.625897	GGCCCCTTGTGGTTTGGC	61.626	66.667	0.00	0.00	37.43	4.52
1855	2257	3.865745	AGAAAATAGATCGCCACTTGTCG	59.134	43.478	0.00	0.00	0.00	4.35
1904	2306	4.278419	ACACCAGAGGTTGTATTCTTTTGC	59.722	41.667	0.00	0.00	31.02	3.68
1981	2386	4.393155	TGCTTCCACGCCGCTGAT	62.393	61.111	0.00	0.00	0.00	2.90
2233	2641	1.993301	TCTCCACAGTAGTCTCCTCCA	59.007	52.381	0.00	0.00	0.00	3.86
2291	2699	0.547712	CCCCCAACCTCTCTCCTTCA	60.548	60.000	0.00	0.00	0.00	3.02
2294	2702	0.547954	GTTCCCCCAACCTCTCTCCT	60.548	60.000	0.00	0.00	0.00	3.69
2343	2752	4.215613	GGCTGAGTTTGTAAATTTCCTCGT	59.784	41.667	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.