AutoCloner

Multiple sequence alignment - TraesCS3D01G351500

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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	TraesCS3D01G351500	chr3D	100.000	2583	0	0	1	2583	462791887	462789305	0.000000e+00	4771.0
1	TraesCS3D01G351500	chr3D	78.214	840	114	32	829	1602	462455656	462454820	8.360000e-130	473.0
2	TraesCS3D01G351500	chr3D	77.851	754	103	31	751	1446	462246974	462246227	2.390000e-110	409.0
3	TraesCS3D01G351500	chr3A	94.482	2066	70	14	534	2583	605830680	605828643	0.000000e+00	3144.0
4	TraesCS3D01G351500	chr3A	79.632	761	92	30	743	1446	605241594	605240840	2.990000e-134	488.0
5	TraesCS3D01G351500	chr3A	76.857	821	116	33	847	1595	605180437	605179619	1.860000e-106	396.0
6	TraesCS3D01G351500	chr3B	91.462	1382	66	12	594	1939	614909468	614908103	0.000000e+00	1851.0
7	TraesCS3D01G351500	chr3B	90.510	706	41	5	1896	2583	614899374	614898677	0.000000e+00	909.0
8	TraesCS3D01G351500	chr3B	78.896	815	104	29	849	1602	614252141	614251334	8.310000e-135	490.0
9	TraesCS3D01G351500	chr3B	77.304	868	129	31	771	1574	613812189	613811326	1.410000e-122	449.0
10	TraesCS3D01G351500	chr3B	78.272	787	104	33	736	1462	614266656	614265877	6.560000e-121	444.0
11	TraesCS3D01G351500	chr6D	93.985	532	28	3	3	531	452636312	452636842	0.000000e+00	802.0
12	TraesCS3D01G351500	chr6D	93.985	532	28	3	3	531	452638231	452638761	0.000000e+00	802.0
13	TraesCS3D01G351500	chr6D	93.974	531	29	3	3	531	452637272	452637801	0.000000e+00	800.0
14	TraesCS3D01G351500	chr6D	92.976	541	33	3	3	538	452639191	452639731	0.000000e+00	784.0
15	TraesCS3D01G351500	chr6D	81.918	365	46	11	1101	1446	20813638	20813275	9.040000e-75	291.0
16	TraesCS3D01G351500	chr6D	87.701	187	21	1	353	537	377566476	377566290	1.560000e-52	217.0
17	TraesCS3D01G351500	chr6B	85.067	375	41	7	172	535	135792604	135792974	4.060000e-98	368.0
18	TraesCS3D01G351500	chr6A	82.920	363	43	10	1101	1446	21078622	21078262	2.500000e-80	309.0
19	TraesCS3D01G351500	chr1D	85.149	303	33	5	1173	1463	321710437	321710135	1.500000e-77	300.0
20	TraesCS3D01G351500	chr1A	84.818	303	34	5	1173	1463	400955739	400956041	6.990000e-76	294.0
21	TraesCS3D01G351500	chr2B	87.709	179	21	1	354	532	52624754	52624931	9.370000e-50	207.0
22	TraesCS3D01G351500	chr4B	86.667	165	22	0	371	535	36809685	36809849	1.580000e-42	183.0
23	TraesCS3D01G351500	chr1B	81.383	188	32	3	357	543	3767790	3767605	1.600000e-32	150.0
24	TraesCS3D01G351500	chr2A	84.127	63	10	0	2136	2198	98355618	98355556	7.720000e-06	62.1
25	TraesCS3D01G351500	chr2A	82.540	63	11	0	2136	2198	286599971	286599909	3.590000e-04	56.5

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	TraesCS3D01G351500	chr3D	462789305	462791887	2582	True	4771	4771	100.000	1	2583	1	chr3D.!!$R3	2582
1	TraesCS3D01G351500	chr3D	462454820	462455656	836	True	473	473	78.214	829	1602	1	chr3D.!!$R2	773
2	TraesCS3D01G351500	chr3D	462246227	462246974	747	True	409	409	77.851	751	1446	1	chr3D.!!$R1	695
3	TraesCS3D01G351500	chr3A	605828643	605830680	2037	True	3144	3144	94.482	534	2583	1	chr3A.!!$R3	2049
4	TraesCS3D01G351500	chr3A	605240840	605241594	754	True	488	488	79.632	743	1446	1	chr3A.!!$R2	703
5	TraesCS3D01G351500	chr3A	605179619	605180437	818	True	396	396	76.857	847	1595	1	chr3A.!!$R1	748
6	TraesCS3D01G351500	chr3B	614908103	614909468	1365	True	1851	1851	91.462	594	1939	1	chr3B.!!$R5	1345
7	TraesCS3D01G351500	chr3B	614898677	614899374	697	True	909	909	90.510	1896	2583	1	chr3B.!!$R4	687
8	TraesCS3D01G351500	chr3B	614251334	614252141	807	True	490	490	78.896	849	1602	1	chr3B.!!$R2	753
9	TraesCS3D01G351500	chr3B	613811326	613812189	863	True	449	449	77.304	771	1574	1	chr3B.!!$R1	803
10	TraesCS3D01G351500	chr3B	614265877	614266656	779	True	444	444	78.272	736	1462	1	chr3B.!!$R3	726
11	TraesCS3D01G351500	chr6D	452636312	452639731	3419	False	797	802	93.730	3	538	4	chr6D.!!$F1	535

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
336	1297	0.041535	AATGGAATTGGAGGCCAGCA	59.958	50.0	5.01	0.0	33.44	4.41	F
674	1636	0.330267	ACACCCTTTACCCAATCCCG	59.670	55.0	0.00	0.0	0.00	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1370	3115	1.153066	TGGAAAGACAAGGCGCACA	60.153	52.632	10.83	0.0	0.00	4.57	R
2369	4231	1.040646	TGTTTCAGCGAGTGACCTCT	58.959	50.000	0.00	0.0	33.71	3.69	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
79	80	2.504367	CACGGAGGTGGAAGAAATTGT	58.496	47.619	0.00	0.00	40.58	2.71
93	94	5.957842	AGAAATTGTGACATAAAAGCGGA	57.042	34.783	0.00	0.00	0.00	5.54
238	1199	4.525949	GGGCGGGTCGTAAGGCTC	62.526	72.222	0.00	0.00	45.30	4.70
253	1214	0.872021	GGCTCGTAGCATCCTGAACG	60.872	60.000	8.71	0.00	44.75	3.95
257	1218	3.366476	GCTCGTAGCATCCTGAACGATAT	60.366	47.826	0.00	0.00	42.77	1.63
264	1225	3.620374	GCATCCTGAACGATATATGCCTG	59.380	47.826	0.00	0.00	34.95	4.85
292	1253	1.743394	CGAATGGGCCTTTTAGTGTCC	59.257	52.381	4.53	0.00	0.00	4.02
298	1259	3.161866	GGGCCTTTTAGTGTCCAAATCA	58.838	45.455	0.84	0.00	0.00	2.57
309	1270	2.297701	GTCCAAATCATGTACGCCCAT	58.702	47.619	0.00	0.00	0.00	4.00
336	1297	0.041535	AATGGAATTGGAGGCCAGCA	59.958	50.000	5.01	0.00	33.44	4.41
383	1345	2.416296	CGGTATGTTCACTTAGCGGTGA	60.416	50.000	13.70	6.20	43.41	4.02
442	1404	2.608261	GCTGTAGACCACCGATCTATGC	60.608	54.545	0.00	0.00	31.47	3.14
453	1415	2.397549	CGATCTATGCTGCATCAACGA	58.602	47.619	19.90	11.66	0.00	3.85
457	1419	3.969899	TCTATGCTGCATCAACGACTAG	58.030	45.455	19.90	8.37	0.00	2.57
468	1430	5.106712	GCATCAACGACTAGAACAATTTGGA	60.107	40.000	0.00	0.00	0.00	3.53
511	1473	0.991146	TGCAAATCAGCTAGTGGGGA	59.009	50.000	0.00	0.00	34.99	4.81
532	1494	7.368198	GGGAGCCCCTATTTAGATATAGAAG	57.632	44.000	3.16	0.00	41.34	2.85
579	1541	8.611654	TTAAATGGTTATTATAGGAACCGAGC	57.388	34.615	11.32	0.00	46.87	5.03
674	1636	0.330267	ACACCCTTTACCCAATCCCG	59.670	55.000	0.00	0.00	0.00	5.14
721	1683	1.247567	CAAATCACCACACAGTCCCC	58.752	55.000	0.00	0.00	0.00	4.81
723	1685	2.748058	AATCACCACACAGTCCCCGC	62.748	60.000	0.00	0.00	0.00	6.13
777	1740	2.556559	GCACCCAAAATAGACCTTCCCA	60.557	50.000	0.00	0.00	0.00	4.37
829	1793	3.757493	ACCGTGTAAACTCACCACAAAAA	59.243	39.130	0.00	0.00	35.18	1.94
955	1929	2.074948	AGCCCTCTCCGCCAATCAT	61.075	57.895	0.00	0.00	0.00	2.45
1370	3115	1.760086	CCGGGAGATCCAGACTGCT	60.760	63.158	0.00	0.00	37.91	4.24
1683	3443	6.127253	CCTGTAATTCTGCCTTGGATGATTTT	60.127	38.462	0.00	0.00	0.00	1.82
1716	3476	5.286267	ACCTCCGTGATTAATCCGTTAAT	57.714	39.130	12.90	0.00	41.90	1.40
1928	3688	7.730364	ATCTTTACCTGATAATAAAGCACCG	57.270	36.000	0.00	0.00	37.99	4.94
2020	3781	5.248248	CCCACAATCCCTTTTTAAGTGGATT	59.752	40.000	10.04	12.49	45.92	3.01
2021	3782	6.439058	CCCACAATCCCTTTTTAAGTGGATTA	59.561	38.462	10.04	0.00	45.92	1.75
2056	3819	6.490381	ACTTCTATTTTCACCAAAAGACCCTC	59.510	38.462	0.00	0.00	34.92	4.30
2058	3821	7.324388	TCTATTTTCACCAAAAGACCCTCTA	57.676	36.000	0.00	0.00	34.92	2.43
2131	3895	1.916181	TGGGTCTCCTTCCCTTTGATC	59.084	52.381	2.65	0.00	44.84	2.92
2349	4211	0.249238	GATCCTCGCTCGTGCTGATT	60.249	55.000	7.97	0.00	36.97	2.57
2499	4361	1.066430	GCTTGACTCATTGGTCGGGTA	60.066	52.381	0.00	0.00	38.91	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.876342	CGGCCCTCGTTATCTTCTGC	60.876	60.000	0.00	0.00	0.00	4.26
1	2	3.274393	CGGCCCTCGTTATCTTCTG	57.726	57.895	0.00	0.00	0.00	3.02
23	24	3.043713	CGCCTCGCAGCACTCAAA	61.044	61.111	0.00	0.00	0.00	2.69
79	80	3.057104	TCGTCTTCTCCGCTTTTATGTCA	60.057	43.478	0.00	0.00	0.00	3.58
93	94	3.991367	ACTCCAAATTCGTTCGTCTTCT	58.009	40.909	0.00	0.00	0.00	2.85
222	225	4.867599	CGAGCCTTACGACCCGCC	62.868	72.222	0.00	0.00	0.00	6.13
238	1199	4.500837	GCATATATCGTTCAGGATGCTACG	59.499	45.833	3.37	3.37	42.46	3.51
264	1225	3.140814	GGCCCATTCGAAGCCCAC	61.141	66.667	14.37	0.00	41.00	4.61
292	1253	1.608590	GGGATGGGCGTACATGATTTG	59.391	52.381	0.00	0.00	0.00	2.32
298	1259	0.916086	TTCTTGGGATGGGCGTACAT	59.084	50.000	0.00	0.00	0.00	2.29
309	1270	3.711863	CCTCCAATTCCATTTCTTGGGA	58.288	45.455	0.00	0.00	46.45	4.37
344	1305	1.850441	CCGTTTCGTACTTCGCCATAG	59.150	52.381	0.00	0.00	39.67	2.23
355	1317	4.858692	GCTAAGTGAACATACCGTTTCGTA	59.141	41.667	0.00	0.00	38.19	3.43
383	1345	7.704899	GTGTTTGCCAAATTTACTAAGAGTTGT	59.295	33.333	0.00	0.00	0.00	3.32
442	1404	5.536554	AATTGTTCTAGTCGTTGATGCAG	57.463	39.130	0.00	0.00	0.00	4.41
453	1415	5.126061	GCCACATCATCCAAATTGTTCTAGT	59.874	40.000	0.00	0.00	0.00	2.57
457	1419	4.460948	AGCCACATCATCCAAATTGTTC	57.539	40.909	0.00	0.00	0.00	3.18
468	1430	3.552875	CCTTCTCATGAAGCCACATCAT	58.447	45.455	0.00	0.00	46.13	2.45
492	1454	0.991146	TCCCCACTAGCTGATTTGCA	59.009	50.000	0.00	0.00	34.99	4.08
493	1455	1.673168	CTCCCCACTAGCTGATTTGC	58.327	55.000	0.00	0.00	0.00	3.68
494	1456	1.673168	GCTCCCCACTAGCTGATTTG	58.327	55.000	0.00	0.00	37.01	2.32
531	1493	5.975693	TTTTGCCTTGGTTTCGATAATCT	57.024	34.783	0.00	0.00	0.00	2.40
532	1494	8.696410	TTAATTTTGCCTTGGTTTCGATAATC	57.304	30.769	0.00	0.00	0.00	1.75
539	1501	6.875948	ACCATTTAATTTTGCCTTGGTTTC	57.124	33.333	0.00	0.00	32.23	2.78
567	1529	0.683504	AGACACGGCTCGGTTCCTAT	60.684	55.000	0.00	0.00	0.00	2.57
674	1636	4.466015	TGCTGGGGATTTTTAAGTGGAATC	59.534	41.667	0.00	0.00	0.00	2.52
777	1740	3.433306	TTTGGGATGTGGAATTCGAGT	57.567	42.857	0.00	0.00	0.00	4.18
811	1775	5.707242	TGTGTTTTTGTGGTGAGTTTACA	57.293	34.783	0.00	0.00	0.00	2.41
1109	2116	2.267324	GGCTTCTTCTCTGCGGCT	59.733	61.111	0.00	0.00	0.00	5.52
1370	3115	1.153066	TGGAAAGACAAGGCGCACA	60.153	52.632	10.83	0.00	0.00	4.57
1482	3236	7.593875	TTTGTTGACAAATGAAGAAACCAAG	57.406	32.000	5.25	0.00	40.55	3.61
1683	3443	8.801882	ATTAATCACGGAGGTTTAATTCAAGA	57.198	30.769	0.00	0.00	0.00	3.02
1928	3688	2.110006	GAGCGGGCAGAAGGGATC	59.890	66.667	0.00	0.00	0.00	3.36
1995	3756	3.901222	CCACTTAAAAAGGGATTGTGGGT	59.099	43.478	0.00	0.00	39.58	4.51
2056	3819	2.606272	GCGGGTCGAATAACCAAAGTAG	59.394	50.000	0.00	0.00	41.40	2.57
2058	3821	1.270947	TGCGGGTCGAATAACCAAAGT	60.271	47.619	0.00	0.00	41.40	2.66
2131	3895	1.750572	GCGAATCGAGCAGAGCACAG	61.751	60.000	6.91	0.00	34.19	3.66
2369	4231	1.040646	TGTTTCAGCGAGTGACCTCT	58.959	50.000	0.00	0.00	33.71	3.69
2434	4296	1.157870	GGGTTATGCGTGGTGGATCG	61.158	60.000	0.00	0.00	0.00	3.69
2499	4361	3.801997	CCCGCCAAGGATCCAGCT	61.802	66.667	15.82	0.00	45.00	4.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.