AutoCloner

Multiple sequence alignment - TraesCS5D01G185000

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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	TraesCS5D01G185000	chr5D	100.000	2588	0	0	1	2588	287406018	287403431	0.000000e+00	4780.0
1	TraesCS5D01G185000	chr5D	89.189	74	8	0	1688	1761	488244903	488244830	2.740000e-15	93.5
2	TraesCS5D01G185000	chr2B	97.010	903	22	4	1688	2588	772707801	772708700	0.000000e+00	1513.0
3	TraesCS5D01G185000	chr2B	81.818	121	15	5	1688	1805	449115704	449115588	7.620000e-16	95.3
4	TraesCS5D01G185000	chr7B	95.600	909	29	4	1688	2588	63584311	63583406	0.000000e+00	1447.0
5	TraesCS5D01G185000	chr7B	73.774	469	75	34	1	438	705250424	705250875	9.660000e-30	141.0
6	TraesCS5D01G185000	chr5A	93.548	899	53	5	789	1687	379228567	379227674	0.000000e+00	1334.0
7	TraesCS5D01G185000	chr5A	84.615	273	32	9	2315	2582	566657098	566656831	1.970000e-66	263.0
8	TraesCS5D01G185000	chr5A	92.473	93	5	2	1	92	379228713	379228622	5.810000e-27	132.0
9	TraesCS5D01G185000	chr5A	89.610	77	5	2	1688	1763	403932931	403933005	7.620000e-16	95.3
10	TraesCS5D01G185000	chr5B	85.246	976	87	34	1	954	326163323	326162383	0.000000e+00	952.0
11	TraesCS5D01G185000	chr5B	87.883	652	65	7	1049	1687	326090677	326090027	0.000000e+00	754.0
12	TraesCS5D01G185000	chr5B	92.105	76	6	0	978	1053	326162231	326162156	9.790000e-20	108.0
13	TraesCS5D01G185000	chr7D	74.304	467	77	30	1	439	613865152	613865603	9.590000e-35	158.0
14	TraesCS5D01G185000	chr7D	73.913	460	88	20	1	440	613804672	613805119	3.450000e-34	156.0
15	TraesCS5D01G185000	chr7D	73.469	490	90	29	1	462	13471981	13471504	5.770000e-32	148.0
16	TraesCS5D01G185000	chr7A	76.151	239	42	11	1	233	654992746	654992975	7.570000e-21	111.0
17	TraesCS5D01G185000	chr3B	83.193	119	13	6	1684	1799	177021119	177021233	4.560000e-18	102.0
18	TraesCS5D01G185000	chr3B	83.636	110	12	5	1686	1790	523284430	523284322	5.890000e-17	99.0
19	TraesCS5D01G185000	chr1A	89.189	74	7	1	1688	1761	481768171	481768243	9.860000e-15	91.6
20	TraesCS5D01G185000	chr4A	88.312	77	6	2	1688	1763	465888855	465888781	3.550000e-14	89.8

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	TraesCS5D01G185000	chr5D	287403431	287406018	2587	True	4780	4780	100.0000	1	2588	1	chr5D.!!$R1	2587
1	TraesCS5D01G185000	chr2B	772707801	772708700	899	False	1513	1513	97.0100	1688	2588	1	chr2B.!!$F1	900
2	TraesCS5D01G185000	chr7B	63583406	63584311	905	True	1447	1447	95.6000	1688	2588	1	chr7B.!!$R1	900
3	TraesCS5D01G185000	chr5A	379227674	379228713	1039	True	733	1334	93.0105	1	1687	2	chr5A.!!$R2	1686
4	TraesCS5D01G185000	chr5B	326090027	326090677	650	True	754	754	87.8830	1049	1687	1	chr5B.!!$R1	638
5	TraesCS5D01G185000	chr5B	326162156	326163323	1167	True	530	952	88.6755	1	1053	2	chr5B.!!$R2	1052

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
606	612	0.314935	AAAGTAAACCGGTCGAGCGA	59.685	50.0	36.08	15.28	0.0	4.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2330	2501	0.75085	GATTGGCAAGGCAGATGCAT	59.249	50.0	5.96	0.0	45.6	3.96	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
166	171	4.955925	ATAAATGATCACGCGTTTCCAA	57.044	36.364	10.22	0.00	0.00	3.53
214	219	4.455917	AATGTTTGTGCAATGCGAAAAG	57.544	36.364	0.00	0.00	0.00	2.27
215	220	3.156511	TGTTTGTGCAATGCGAAAAGA	57.843	38.095	0.00	0.00	0.00	2.52
284	289	9.058424	GTAAAACGAGTATTTGGAAAATGCTAC	57.942	33.333	3.72	0.00	0.00	3.58
285	290	6.811253	AACGAGTATTTGGAAAATGCTACA	57.189	33.333	3.72	0.00	0.00	2.74
288	293	7.101054	ACGAGTATTTGGAAAATGCTACAGTA	58.899	34.615	3.72	0.00	0.00	2.74
383	388	6.606234	TTCACGTGTGCTCTAAAAATGTTA	57.394	33.333	16.51	0.00	0.00	2.41
461	467	8.716646	ACCAAAAATGAAAGTAAACCAGAAAG	57.283	30.769	0.00	0.00	0.00	2.62
463	469	9.377312	CCAAAAATGAAAGTAAACCAGAAAGAA	57.623	29.630	0.00	0.00	0.00	2.52
508	514	7.850501	AGCGAAGGAAAAATTACAAAACAATG	58.149	30.769	0.00	0.00	0.00	2.82
526	532	6.293004	ACAATGAGAAAACAAAGGAAACCA	57.707	33.333	0.00	0.00	0.00	3.67
568	574	5.890424	AAAACTCGGTGAAAAACTGAAGA	57.110	34.783	0.00	0.00	43.75	2.87
602	608	4.961435	AAAAACAAAGTAAACCGGTCGA	57.039	36.364	8.04	0.00	0.00	4.20
603	609	4.541085	AAAACAAAGTAAACCGGTCGAG	57.459	40.909	8.04	0.00	0.00	4.04
604	610	1.505425	ACAAAGTAAACCGGTCGAGC	58.495	50.000	8.04	4.06	0.00	5.03
605	611	0.437295	CAAAGTAAACCGGTCGAGCG	59.563	55.000	28.88	28.88	0.00	5.03
606	612	0.314935	AAAGTAAACCGGTCGAGCGA	59.685	50.000	36.08	15.28	0.00	4.93
607	613	0.314935	AAGTAAACCGGTCGAGCGAA	59.685	50.000	36.08	16.51	0.00	4.70
608	614	0.387750	AGTAAACCGGTCGAGCGAAC	60.388	55.000	36.08	25.32	0.00	3.95
609	615	0.387750	GTAAACCGGTCGAGCGAACT	60.388	55.000	36.08	21.21	0.00	3.01
651	657	1.211709	GCAACCAACCGCGCTAAAT	59.788	52.632	5.56	0.00	0.00	1.40
668	674	2.604046	AATCAGCTAGCCCGTTAGTG	57.396	50.000	12.13	0.79	0.00	2.74
676	682	4.462280	CCCGTTAGTGGTCGCCCC	62.462	72.222	0.00	0.00	0.00	5.80
700	720	2.526304	CGATTATGTCGGGGACACAT	57.474	50.000	0.00	0.00	45.65	3.21
717	737	1.993370	ACATCTGTCGCGAAGTTTAGC	59.007	47.619	12.06	0.00	0.00	3.09
718	738	1.324736	CATCTGTCGCGAAGTTTAGCC	59.675	52.381	12.06	0.00	0.00	3.93
739	759	0.314935	TCCCGCGTAAGAAGAAACGT	59.685	50.000	4.92	0.00	41.10	3.99
746	766	5.013861	GCGTAAGAAGAAACGTGAAATGA	57.986	39.130	0.00	0.00	41.10	2.57
753	773	4.452890	AGAAACGTGAAATGACACTTCG	57.547	40.909	0.00	0.00	38.47	3.79
778	798	2.401766	CCATCAGCTCACCAACGGC	61.402	63.158	0.00	0.00	0.00	5.68
785	805	3.220999	CTCACCAACGGCTCGGACA	62.221	63.158	0.00	0.00	0.00	4.02
791	811	2.642254	AACGGCTCGGACATCGGAA	61.642	57.895	0.00	0.00	39.77	4.30
792	812	2.582498	CGGCTCGGACATCGGAAC	60.582	66.667	0.00	0.00	39.77	3.62
864	884	4.857251	GCATAGGGCGCTAGTTGT	57.143	55.556	16.27	0.00	0.00	3.32
899	919	2.351447	CCAAGCAAACTACTCGTCTCGA	60.351	50.000	0.00	0.00	0.00	4.04
933	953	5.091261	ACTAAACAACAGCAGATAGGAGG	57.909	43.478	0.00	0.00	0.00	4.30
934	954	4.777896	ACTAAACAACAGCAGATAGGAGGA	59.222	41.667	0.00	0.00	0.00	3.71
936	956	2.114616	ACAACAGCAGATAGGAGGAGG	58.885	52.381	0.00	0.00	0.00	4.30
938	958	2.364970	CAACAGCAGATAGGAGGAGGAG	59.635	54.545	0.00	0.00	0.00	3.69
939	959	1.856259	ACAGCAGATAGGAGGAGGAGA	59.144	52.381	0.00	0.00	0.00	3.71
940	960	2.158475	ACAGCAGATAGGAGGAGGAGAG	60.158	54.545	0.00	0.00	0.00	3.20
941	961	2.108075	CAGCAGATAGGAGGAGGAGAGA	59.892	54.545	0.00	0.00	0.00	3.10
980	1000	7.144661	AGAGAGACGCATCATATCAAACTTAG	58.855	38.462	0.00	0.00	0.00	2.18
981	1001	7.013750	AGAGAGACGCATCATATCAAACTTAGA	59.986	37.037	0.00	0.00	0.00	2.10
1141	1297	1.221840	GTGCACCTCATGATCCGGT	59.778	57.895	5.22	0.00	0.00	5.28
1601	1770	1.824230	GGCTTGAACATGCATTGGGTA	59.176	47.619	0.00	0.00	33.64	3.69
1603	1772	2.731968	GCTTGAACATGCATTGGGTACG	60.732	50.000	0.00	0.00	0.00	3.67
1623	1792	6.316390	GGTACGGTCATTGAGATTTGAGAATT	59.684	38.462	0.00	0.00	0.00	2.17
1655	1824	2.644418	GGCAATGTTCGTGCAGCA	59.356	55.556	0.00	0.00	44.07	4.41
1656	1825	1.007502	GGCAATGTTCGTGCAGCAA	60.008	52.632	0.00	0.00	44.07	3.91
1663	1832	0.111266	GTTCGTGCAGCAACGTGTAG	60.111	55.000	14.39	0.00	43.96	2.74
1683	1852	7.148705	CGTGTAGTTGGATGTTCGAATTCTAAA	60.149	37.037	0.00	0.00	0.00	1.85
1684	1853	8.169268	GTGTAGTTGGATGTTCGAATTCTAAAG	58.831	37.037	0.00	0.00	0.00	1.85
1685	1854	8.092068	TGTAGTTGGATGTTCGAATTCTAAAGA	58.908	33.333	0.00	0.00	0.00	2.52
1686	1855	7.602517	AGTTGGATGTTCGAATTCTAAAGAG	57.397	36.000	0.00	0.00	0.00	2.85
1730	1899	2.281831	TGCGCCCGTCCATTTTGA	60.282	55.556	4.18	0.00	0.00	2.69
1774	1943	5.527214	TGCCTAAATATGTCGATCCACAAAG	59.473	40.000	0.00	0.00	0.00	2.77
2254	2424	8.409358	AAGCAAAACCAAGAGTTATTAGTCAT	57.591	30.769	0.00	0.00	37.88	3.06
2255	2425	9.515226	AAGCAAAACCAAGAGTTATTAGTCATA	57.485	29.630	0.00	0.00	37.88	2.15
2330	2501	1.131638	ATGCCGAATAGCTCAAGGGA	58.868	50.000	0.00	0.00	0.00	4.20
2333	2504	1.517242	CCGAATAGCTCAAGGGATGC	58.483	55.000	0.00	0.00	0.00	3.91
2368	2539	4.966965	ATCTCCTACAGTACAGTTGACG	57.033	45.455	0.00	0.00	0.00	4.35
2440	2618	9.680315	CTAGTAGTGCCAAAATACTGTAGATAC	57.320	37.037	0.00	0.00	32.25	2.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	34	6.756074	GTCACAAACATTTTCTGGAAACATGA	59.244	34.615	0.00	0.00	41.51	3.07
34	36	6.638610	TGTCACAAACATTTTCTGGAAACAT	58.361	32.000	0.00	0.00	33.77	2.71
146	151	4.750952	TTTGGAAACGCGTGATCATTTA	57.249	36.364	14.98	0.00	0.00	1.40
259	264	8.784994	TGTAGCATTTTCCAAATACTCGTTTTA	58.215	29.630	0.00	0.00	0.00	1.52
264	269	6.422776	ACTGTAGCATTTTCCAAATACTCG	57.577	37.500	0.00	0.00	0.00	4.18
383	388	9.620259	ATCTCTTCTTTTTCTCAGTACAAAACT	57.380	29.630	0.00	0.00	39.81	2.66
403	408	7.630242	TGTTTCTTTTCTCAACACATCTCTT	57.370	32.000	0.00	0.00	0.00	2.85
467	473	9.974980	TTTCCTTCGCTATAATTTTGTTTTCTT	57.025	25.926	0.00	0.00	0.00	2.52
496	502	9.712305	TTCCTTTGTTTTCTCATTGTTTTGTAA	57.288	25.926	0.00	0.00	0.00	2.41
508	514	8.766000	TTTACTTTGGTTTCCTTTGTTTTCTC	57.234	30.769	0.00	0.00	0.00	2.87
584	590	1.869132	GCTCGACCGGTTTACTTTGTT	59.131	47.619	9.42	0.00	0.00	2.83
585	591	1.505425	GCTCGACCGGTTTACTTTGT	58.495	50.000	9.42	0.00	0.00	2.83
586	592	0.437295	CGCTCGACCGGTTTACTTTG	59.563	55.000	9.42	0.00	0.00	2.77
587	593	0.314935	TCGCTCGACCGGTTTACTTT	59.685	50.000	9.42	0.00	0.00	2.66
591	597	0.314935	AAGTTCGCTCGACCGGTTTA	59.685	50.000	9.42	0.00	0.00	2.01
592	598	1.068585	AAGTTCGCTCGACCGGTTT	59.931	52.632	9.42	0.00	0.00	3.27
593	599	1.663702	CAAGTTCGCTCGACCGGTT	60.664	57.895	9.42	0.00	0.00	4.44
594	600	2.049433	CAAGTTCGCTCGACCGGT	60.049	61.111	6.92	6.92	0.00	5.28
595	601	3.479269	GCAAGTTCGCTCGACCGG	61.479	66.667	0.00	0.00	0.00	5.28
596	602	2.720758	CTGCAAGTTCGCTCGACCG	61.721	63.158	0.00	0.00	0.00	4.79
597	603	3.016474	GCTGCAAGTTCGCTCGACC	62.016	63.158	0.00	0.00	35.30	4.79
598	604	2.472049	GCTGCAAGTTCGCTCGAC	59.528	61.111	0.00	0.00	35.30	4.20
599	605	3.105782	CGCTGCAAGTTCGCTCGA	61.106	61.111	0.00	0.00	35.30	4.04
600	606	3.105782	TCGCTGCAAGTTCGCTCG	61.106	61.111	0.00	0.00	35.30	5.03
601	607	2.472049	GTCGCTGCAAGTTCGCTC	59.528	61.111	0.00	0.00	35.30	5.03
602	608	3.044305	GGTCGCTGCAAGTTCGCT	61.044	61.111	0.00	0.00	35.30	4.93
603	609	4.430423	CGGTCGCTGCAAGTTCGC	62.430	66.667	0.00	0.00	35.30	4.70
604	610	4.430423	GCGGTCGCTGCAAGTTCG	62.430	66.667	8.20	0.00	35.55	3.95
637	643	1.062525	GCTGATTTAGCGCGGTTGG	59.937	57.895	19.09	1.87	43.63	3.77
638	644	4.670606	GCTGATTTAGCGCGGTTG	57.329	55.556	19.09	1.47	43.63	3.77
651	657	0.613853	ACCACTAACGGGCTAGCTGA	60.614	55.000	15.72	0.00	0.00	4.26
656	662	2.713967	GGCGACCACTAACGGGCTA	61.714	63.158	0.00	0.00	0.00	3.93
681	687	6.526910	ACAGATGTGTCCCCGACATAATCG	62.527	50.000	0.00	4.95	44.63	3.34
686	692	0.537188	GACAGATGTGTCCCCGACAT	59.463	55.000	11.88	0.00	46.58	3.06
687	693	1.972198	GACAGATGTGTCCCCGACA	59.028	57.895	11.88	0.00	46.58	4.35
688	694	4.913126	GACAGATGTGTCCCCGAC	57.087	61.111	11.88	0.00	46.58	4.79
700	720	0.389426	GGGCTAAACTTCGCGACAGA	60.389	55.000	9.15	0.00	0.00	3.41
718	738	1.356938	GTTTCTTCTTACGCGGGAGG	58.643	55.000	12.47	6.42	0.00	4.30
753	773	0.179124	GGTGAGCTGATGGACTCGAC	60.179	60.000	0.00	0.00	35.61	4.20
778	798	2.582498	GCCGTTCCGATGTCCGAG	60.582	66.667	0.00	0.00	41.76	4.63
785	805	1.671054	CCACAACTGCCGTTCCGAT	60.671	57.895	0.00	0.00	0.00	4.18
791	811	3.049674	CATCGCCACAACTGCCGT	61.050	61.111	0.00	0.00	0.00	5.68
792	812	2.741985	TCATCGCCACAACTGCCG	60.742	61.111	0.00	0.00	0.00	5.69
864	884	0.884704	GCTTGGTTCTTGCGTCAGGA	60.885	55.000	0.00	0.00	0.00	3.86
899	919	6.142817	GCTGTTGTTTAGTTTGACGATCAAT	58.857	36.000	0.00	0.00	36.11	2.57
914	934	3.054802	CCTCCTCCTATCTGCTGTTGTTT	60.055	47.826	0.00	0.00	0.00	2.83
917	937	2.364970	CTCCTCCTCCTATCTGCTGTTG	59.635	54.545	0.00	0.00	0.00	3.33
933	953	4.219115	TCTCTCTCTCTCTCTCTCTCCTC	58.781	52.174	0.00	0.00	0.00	3.71
934	954	4.078922	TCTCTCTCTCTCTCTCTCTCTCCT	60.079	50.000	0.00	0.00	0.00	3.69
936	956	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
938	958	5.009610	GTCTCTCTCTCTCTCTCTCTCTCTC	59.990	52.000	0.00	0.00	0.00	3.20
939	959	4.892934	GTCTCTCTCTCTCTCTCTCTCTCT	59.107	50.000	0.00	0.00	0.00	3.10
940	960	4.261405	CGTCTCTCTCTCTCTCTCTCTCTC	60.261	54.167	0.00	0.00	0.00	3.20
941	961	3.634448	CGTCTCTCTCTCTCTCTCTCTCT	59.366	52.174	0.00	0.00	0.00	3.10
980	1000	4.277258	CATGCACACGAAGCTATCAATTC	58.723	43.478	0.00	0.00	0.00	2.17
981	1001	3.065786	CCATGCACACGAAGCTATCAATT	59.934	43.478	0.00	0.00	0.00	2.32
988	1144	1.086067	CGATCCATGCACACGAAGCT	61.086	55.000	0.00	0.00	0.00	3.74
991	1147	2.106074	GCCGATCCATGCACACGAA	61.106	57.895	0.00	0.00	0.00	3.85
992	1148	2.511373	GCCGATCCATGCACACGA	60.511	61.111	0.00	0.00	0.00	4.35
994	1150	1.709147	GACTGCCGATCCATGCACAC	61.709	60.000	0.00	0.00	33.17	3.82
1222	1378	2.993853	CCTGAGGAGGAACAGGGC	59.006	66.667	0.00	0.00	46.76	5.19
1583	1741	2.159393	CCGTACCCAATGCATGTTCAAG	60.159	50.000	0.00	0.00	0.00	3.02
1601	1770	7.227512	GGATAATTCTCAAATCTCAATGACCGT	59.772	37.037	0.00	0.00	0.00	4.83
1603	1772	8.455903	TGGATAATTCTCAAATCTCAATGACC	57.544	34.615	0.00	0.00	0.00	4.02
1655	1824	3.374220	TCGAACATCCAACTACACGTT	57.626	42.857	0.00	0.00	35.88	3.99
1656	1825	3.374220	TTCGAACATCCAACTACACGT	57.626	42.857	0.00	0.00	0.00	4.49
1663	1832	7.332182	AGTCTCTTTAGAATTCGAACATCCAAC	59.668	37.037	0.00	0.00	32.16	3.77
1666	1835	8.407064	TCTAGTCTCTTTAGAATTCGAACATCC	58.593	37.037	0.00	0.00	32.16	3.51
1683	1852	3.305950	GCGCCATCAATGATCTAGTCTCT	60.306	47.826	0.00	0.00	0.00	3.10
1684	1853	2.992543	GCGCCATCAATGATCTAGTCTC	59.007	50.000	0.00	0.00	0.00	3.36
1685	1854	2.608998	CGCGCCATCAATGATCTAGTCT	60.609	50.000	0.00	0.00	0.00	3.24
1686	1855	1.723542	CGCGCCATCAATGATCTAGTC	59.276	52.381	0.00	0.00	0.00	2.59
1887	2056	8.637986	GCATCTCTTACTCCCCTAATATGATAG	58.362	40.741	0.00	0.00	0.00	2.08
2330	2501	0.750850	GATTGGCAAGGCAGATGCAT	59.249	50.000	5.96	0.00	45.60	3.96
2333	2504	1.030457	GGAGATTGGCAAGGCAGATG	58.970	55.000	5.96	0.00	0.00	2.90
2397	2568	8.462811	GCACTACTAGCTATTCATTGCTCTATA	58.537	37.037	0.00	0.00	39.48	1.31

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.