AutoCloner

Multiple sequence alignment - TraesCS3A01G231800

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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	TraesCS3A01G231800	chr3A	100.000	2339	0	0	1	2339	433409528	433407190	0.000000e+00	4320
1	TraesCS3A01G231800	chr1B	98.566	976	10	1	1364	2339	42291773	42290802	0.000000e+00	1722
2	TraesCS3A01G231800	chr2A	98.463	976	13	1	1364	2339	54697056	54698029	0.000000e+00	1718
3	TraesCS3A01G231800	chr2B	98.463	976	10	2	1364	2339	9885020	9885990	0.000000e+00	1714
4	TraesCS3A01G231800	chr3B	98.167	982	10	4	1364	2339	651530376	651529397	0.000000e+00	1707
5	TraesCS3A01G231800	chr3B	97.855	979	14	2	1364	2339	1346074	1347048	0.000000e+00	1685
6	TraesCS3A01G231800	chr3B	95.931	639	21	2	5	643	419120667	419120034	0.000000e+00	1031
7	TraesCS3A01G231800	chr3B	88.748	631	37	18	662	1266	419120048	419119426	0.000000e+00	741
8	TraesCS3A01G231800	chr3B	91.398	93	8	0	1265	1357	419119359	419119267	6.780000e-26	128
9	TraesCS3A01G231800	chr6B	98.258	976	13	1	1364	2339	471631505	471632476	0.000000e+00	1705
10	TraesCS3A01G231800	chr6B	97.760	982	10	4	1364	2339	648625209	648626184	0.000000e+00	1681
11	TraesCS3A01G231800	chr7B	98.061	980	15	1	1364	2339	713376524	713375545	0.000000e+00	1701
12	TraesCS3A01G231800	chr7A	98.065	982	11	3	1364	2339	462995146	462996125	0.000000e+00	1701
13	TraesCS3A01G231800	chr3D	94.712	643	27	2	1	643	301849561	301850196	0.000000e+00	992
14	TraesCS3A01G231800	chr3D	88.088	638	35	17	662	1266	301850182	301850811	0.000000e+00	719
15	TraesCS3A01G231800	chr3D	93.939	99	6	0	1265	1363	301850878	301850976	1.450000e-32	150

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	TraesCS3A01G231800	chr3A	433407190	433409528	2338	True	4320.000000	4320	100.000000	1	2339	1	chr3A.!!$R1	2338
1	TraesCS3A01G231800	chr1B	42290802	42291773	971	True	1722.000000	1722	98.566000	1364	2339	1	chr1B.!!$R1	975
2	TraesCS3A01G231800	chr2A	54697056	54698029	973	False	1718.000000	1718	98.463000	1364	2339	1	chr2A.!!$F1	975
3	TraesCS3A01G231800	chr2B	9885020	9885990	970	False	1714.000000	1714	98.463000	1364	2339	1	chr2B.!!$F1	975
4	TraesCS3A01G231800	chr3B	651529397	651530376	979	True	1707.000000	1707	98.167000	1364	2339	1	chr3B.!!$R1	975
5	TraesCS3A01G231800	chr3B	1346074	1347048	974	False	1685.000000	1685	97.855000	1364	2339	1	chr3B.!!$F1	975
6	TraesCS3A01G231800	chr3B	419119267	419120667	1400	True	633.333333	1031	92.025667	5	1357	3	chr3B.!!$R2	1352
7	TraesCS3A01G231800	chr6B	471631505	471632476	971	False	1705.000000	1705	98.258000	1364	2339	1	chr6B.!!$F1	975
8	TraesCS3A01G231800	chr6B	648625209	648626184	975	False	1681.000000	1681	97.760000	1364	2339	1	chr6B.!!$F2	975
9	TraesCS3A01G231800	chr7B	713375545	713376524	979	True	1701.000000	1701	98.061000	1364	2339	1	chr7B.!!$R1	975
10	TraesCS3A01G231800	chr7A	462995146	462996125	979	False	1701.000000	1701	98.065000	1364	2339	1	chr7A.!!$F1	975
11	TraesCS3A01G231800	chr3D	301849561	301850976	1415	False	620.333333	992	92.246333	1	1363	3	chr3D.!!$F1	1362

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
921	954	0.320374	TCAAACGGTCCGCTGATCTT	59.68	50.0	12.28	0.0	0.0	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2046	2186	1.022735	GGAGAGAGCCGTCGACATAA	58.977	55.0	17.16	0.0	0.0	1.9	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
36	37	8.405531	CAAAAACACAGGAATCAGTAGAGAAAA	58.594	33.333	0.00	0.00	0.00	2.29
39	40	7.678947	ACACAGGAATCAGTAGAGAAAATTG	57.321	36.000	0.00	0.00	0.00	2.32
180	181	3.751246	GCGGCAGCCAATCAAGCA	61.751	61.111	13.30	0.00	37.42	3.91
299	300	8.100164	TGTGTTCATGTGGTAGAATAATTCTGA	58.900	33.333	0.00	0.00	40.94	3.27
300	301	9.113838	GTGTTCATGTGGTAGAATAATTCTGAT	57.886	33.333	0.00	0.00	40.94	2.90
384	385	4.619227	CCGTGACCTTGTGCGGGT	62.619	66.667	0.00	0.00	40.45	5.28
466	467	1.474077	GCCATTGTTGTTGCTCCTAGG	59.526	52.381	0.82	0.82	0.00	3.02
531	532	0.962855	GGAAGGCAAGTGCTTCCTCC	60.963	60.000	19.06	8.23	41.17	4.30
557	558	4.576463	GGCTTTCTTGACTCTTCTCAACAA	59.424	41.667	0.00	0.00	0.00	2.83
587	588	1.594293	ACTGGAGGACAAACGCACG	60.594	57.895	0.00	0.00	0.00	5.34
618	619	4.634004	TGACAAATAAGACCCTGCATTACG	59.366	41.667	0.00	0.00	0.00	3.18
643	644	8.177663	CGCTGTATTTCAAACAAGATTAGTGAT	58.822	33.333	0.00	0.00	0.00	3.06
644	645	9.846248	GCTGTATTTCAAACAAGATTAGTGATT	57.154	29.630	0.00	0.00	0.00	2.57
649	650	6.500684	TCAAACAAGATTAGTGATTCAGGC	57.499	37.500	0.00	0.00	0.00	4.85
650	651	6.003326	TCAAACAAGATTAGTGATTCAGGCA	58.997	36.000	0.00	0.00	0.00	4.75
651	652	6.489700	TCAAACAAGATTAGTGATTCAGGCAA	59.510	34.615	0.00	0.00	0.00	4.52
652	653	6.506500	AACAAGATTAGTGATTCAGGCAAG	57.493	37.500	0.00	0.00	0.00	4.01
653	654	5.809001	ACAAGATTAGTGATTCAGGCAAGA	58.191	37.500	0.00	0.00	0.00	3.02
654	655	6.240894	ACAAGATTAGTGATTCAGGCAAGAA	58.759	36.000	0.00	0.00	0.00	2.52
655	656	6.716628	ACAAGATTAGTGATTCAGGCAAGAAA	59.283	34.615	0.00	0.00	0.00	2.52
656	657	7.231317	ACAAGATTAGTGATTCAGGCAAGAAAA	59.769	33.333	0.00	0.00	0.00	2.29
657	658	7.388460	AGATTAGTGATTCAGGCAAGAAAAG	57.612	36.000	0.00	0.00	0.00	2.27
658	659	7.170965	AGATTAGTGATTCAGGCAAGAAAAGA	58.829	34.615	0.00	0.00	0.00	2.52
659	660	7.667219	AGATTAGTGATTCAGGCAAGAAAAGAA	59.333	33.333	0.00	0.00	0.00	2.52
660	661	7.581213	TTAGTGATTCAGGCAAGAAAAGAAA	57.419	32.000	0.00	0.00	0.00	2.52
661	662	6.469782	AGTGATTCAGGCAAGAAAAGAAAA	57.530	33.333	0.00	0.00	0.00	2.29
662	663	6.877236	AGTGATTCAGGCAAGAAAAGAAAAA	58.123	32.000	0.00	0.00	0.00	1.94
728	729	3.672447	CCACGTTGCCATGCTGCA	61.672	61.111	4.13	4.13	40.07	4.41
730	731	2.595463	ACGTTGCCATGCTGCAGT	60.595	55.556	16.64	0.00	43.21	4.40
731	732	2.177531	CGTTGCCATGCTGCAGTC	59.822	61.111	16.64	8.39	43.21	3.51
732	733	2.619165	CGTTGCCATGCTGCAGTCA	61.619	57.895	16.64	14.12	43.21	3.41
821	844	2.514824	GCACAGGCGAGGGATTCC	60.515	66.667	0.00	0.00	0.00	3.01
921	954	0.320374	TCAAACGGTCCGCTGATCTT	59.680	50.000	12.28	0.00	0.00	2.40
923	956	0.391263	AAACGGTCCGCTGATCTTCC	60.391	55.000	12.28	0.00	0.00	3.46
1088	1121	2.190756	GGATCACGTCCTCTTCGGT	58.809	57.895	0.00	0.00	44.16	4.69
1104	1137	4.815108	GTCAATCCCCGCCCACCC	62.815	72.222	0.00	0.00	0.00	4.61
1158	1197	2.358737	AGCCCTTTCGTGAAGCCG	60.359	61.111	0.00	0.00	33.84	5.52
1201	1240	0.796312	GCCGTCGAGCAAAAGATTCA	59.204	50.000	0.00	0.00	0.00	2.57
1211	1250	2.162208	GCAAAAGATTCACGGAGCATGA	59.838	45.455	0.00	0.00	0.00	3.07
1222	1261	1.596477	GAGCATGATCAGGACGGCC	60.596	63.158	12.39	0.00	0.00	6.13
1332	1439	2.998668	CGTTCTTCGGAATTCGGATG	57.001	50.000	15.56	16.78	39.77	3.51
1449	1568	4.217194	TAGGCCACCCCTAGAGGA	57.783	61.111	5.01	0.00	44.08	3.71
2046	2186	1.834263	GGGAGTCACTATCTGCTTGGT	59.166	52.381	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	6.589907	ACTGATTCCTGTGTTTTTGTTTTGAC	59.410	34.615	0.00	0.00	0.00	3.18
36	37	3.151542	AGGGAGGGAACATCCTACAAT	57.848	47.619	0.00	0.00	39.56	2.71
39	40	2.684038	GCAAAGGGAGGGAACATCCTAC	60.684	54.545	0.00	0.00	37.25	3.18
180	181	4.393062	CGATGTGTCTCTTTTGTATGCCTT	59.607	41.667	0.00	0.00	0.00	4.35
299	300	2.762327	AGGAATCATTTTTGCGGCTCAT	59.238	40.909	0.00	0.00	0.00	2.90
300	301	2.170166	AGGAATCATTTTTGCGGCTCA	58.830	42.857	0.00	0.00	0.00	4.26
384	385	1.451927	CCTGCTAGAAATGGGCGCA	60.452	57.895	10.83	5.70	0.00	6.09
388	389	3.745797	GCCTTACTCCTGCTAGAAATGGG	60.746	52.174	0.00	0.00	0.00	4.00
466	467	1.807573	CCAGCTTCTCGGTTCTCGC	60.808	63.158	0.00	0.00	39.05	5.03
489	490	0.682852	GCACTACCACCACCAGTACA	59.317	55.000	0.00	0.00	0.00	2.90
490	491	0.036671	GGCACTACCACCACCAGTAC	60.037	60.000	0.00	0.00	38.86	2.73
531	532	2.734079	GAGAAGAGTCAAGAAAGCCACG	59.266	50.000	0.00	0.00	0.00	4.94
618	619	9.846248	AATCACTAATCTTGTTTGAAATACAGC	57.154	29.630	0.00	0.00	0.00	4.40
662	663	8.883731	CGTATGATTTTCCTCACTAATCTTGTT	58.116	33.333	0.00	0.00	31.25	2.83
663	664	8.041323	ACGTATGATTTTCCTCACTAATCTTGT	58.959	33.333	0.00	0.00	31.25	3.16
664	665	8.425577	ACGTATGATTTTCCTCACTAATCTTG	57.574	34.615	0.00	0.00	31.25	3.02
675	676	9.783256	GCACTTTTATTTACGTATGATTTTCCT	57.217	29.630	0.00	0.00	0.00	3.36
676	677	9.562583	TGCACTTTTATTTACGTATGATTTTCC	57.437	29.630	0.00	0.00	0.00	3.13
678	679	9.057365	CGTGCACTTTTATTTACGTATGATTTT	57.943	29.630	16.19	0.00	0.00	1.82
679	680	8.444715	TCGTGCACTTTTATTTACGTATGATTT	58.555	29.630	16.19	0.00	33.68	2.17
680	681	7.966111	TCGTGCACTTTTATTTACGTATGATT	58.034	30.769	16.19	0.00	33.68	2.57
681	682	7.490079	TCTCGTGCACTTTTATTTACGTATGAT	59.510	33.333	16.19	0.00	33.68	2.45
682	683	6.807720	TCTCGTGCACTTTTATTTACGTATGA	59.192	34.615	16.19	0.00	33.68	2.15
683	684	6.892951	GTCTCGTGCACTTTTATTTACGTATG	59.107	38.462	16.19	0.00	33.68	2.39
684	685	6.237384	CGTCTCGTGCACTTTTATTTACGTAT	60.237	38.462	16.19	0.00	33.68	3.06
685	686	5.059587	CGTCTCGTGCACTTTTATTTACGTA	59.940	40.000	16.19	0.00	33.68	3.57
728	729	1.348036	GGTTTACACTCCAGGCTGACT	59.652	52.381	17.94	0.00	0.00	3.41
730	731	1.071699	GTGGTTTACACTCCAGGCTGA	59.928	52.381	17.94	0.95	46.72	4.26
731	732	1.523758	GTGGTTTACACTCCAGGCTG	58.476	55.000	7.75	7.75	46.72	4.85
778	779	4.421479	CGTTCGGCTGGCTCGTCT	62.421	66.667	0.00	0.00	0.00	4.18
805	806	2.202932	CGGAATCCCTCGCCTGTG	60.203	66.667	0.00	0.00	0.00	3.66
806	807	0.974010	TAACGGAATCCCTCGCCTGT	60.974	55.000	0.00	0.00	0.00	4.00
807	808	0.177141	TTAACGGAATCCCTCGCCTG	59.823	55.000	0.00	0.00	0.00	4.85
808	809	0.464452	CTTAACGGAATCCCTCGCCT	59.536	55.000	0.00	0.00	0.00	5.52
809	810	1.158484	GCTTAACGGAATCCCTCGCC	61.158	60.000	0.00	0.00	0.00	5.54
810	811	0.179081	AGCTTAACGGAATCCCTCGC	60.179	55.000	0.00	0.00	0.00	5.03
811	812	2.311124	AAGCTTAACGGAATCCCTCG	57.689	50.000	0.00	0.00	0.00	4.63
812	813	3.606687	TGAAAGCTTAACGGAATCCCTC	58.393	45.455	0.00	0.00	0.00	4.30
813	814	3.713826	TGAAAGCTTAACGGAATCCCT	57.286	42.857	0.00	0.00	0.00	4.20
821	844	4.611581	GCAGAAGAGGTTGAAAGCTTAACG	60.612	45.833	0.00	0.00	36.78	3.18
882	915	2.366916	GACACCTCGGGATCAGATGAAT	59.633	50.000	0.00	0.00	0.00	2.57
921	954	1.241485	TATGGGAGCTAGGGTCTGGA	58.759	55.000	0.00	0.00	0.00	3.86
923	956	7.202047	GGATATTAATATGGGAGCTAGGGTCTG	60.202	44.444	12.74	0.00	0.00	3.51
1057	1090	0.036388	GTGATCCTCTTGTTCCGGCA	60.036	55.000	0.00	0.00	0.00	5.69
1131	1164	4.394712	AAAGGGCTGAGGGCGTCG	62.395	66.667	2.41	0.00	42.94	5.12
1135	1174	2.747855	CACGAAAGGGCTGAGGGC	60.748	66.667	0.00	0.00	40.90	5.19
1158	1197	0.522180	TGAGCTTCCTCGTCGTCTTC	59.478	55.000	0.00	0.00	41.13	2.87
1201	1240	1.439228	CGTCCTGATCATGCTCCGT	59.561	57.895	0.00	0.00	0.00	4.69
1279	1386	2.265739	GGAGTCTGTGCATGCCGA	59.734	61.111	16.68	6.28	0.00	5.54
1280	1387	3.190849	CGGAGTCTGTGCATGCCG	61.191	66.667	16.68	4.66	0.00	5.69
1332	1439	1.802960	CGTCTCATGCCCTATCAATGC	59.197	52.381	0.00	0.00	0.00	3.56
1357	1464	8.628882	CATGTAAATACAGTCTAACATGTCGA	57.371	34.615	0.00	0.00	39.39	4.20
1548	1688	2.279517	GTCATAGCAGTCGGGCGG	60.280	66.667	0.00	0.00	39.27	6.13
2046	2186	1.022735	GGAGAGAGCCGTCGACATAA	58.977	55.000	17.16	0.00	0.00	1.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.