AutoCloner

Multiple sequence alignment - TraesCS3D01G343200

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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	TraesCS3D01G343200	chr3D	100.000	2569	0	0	1	2569	455722221	455719653	0.000000e+00	4745.0
1	TraesCS3D01G343200	chr3D	79.801	604	72	36	44	608	455752375	455752967	6.660000e-106	394.0
2	TraesCS3D01G343200	chr3D	77.470	253	36	16	151	392	564915935	564916177	5.770000e-27	132.0
3	TraesCS3D01G343200	chr3D	75.234	214	37	12	1	201	598992667	598992457	1.270000e-13	87.9
4	TraesCS3D01G343200	chr3A	95.280	2140	90	7	433	2569	597932308	597930177	0.000000e+00	3382.0
5	TraesCS3D01G343200	chr3A	85.827	381	34	16	16	388	597932699	597932331	1.110000e-103	387.0
6	TraesCS3D01G343200	chr3A	81.105	344	46	12	49	378	597966937	597967275	9.120000e-65	257.0
7	TraesCS3D01G343200	chr3B	87.923	2128	173	35	89	2156	598996885	598994782	0.000000e+00	2429.0
8	TraesCS3D01G343200	chr3B	80.845	355	50	14	44	386	599098677	599099025	1.960000e-66	263.0
9	TraesCS3D01G343200	chr7D	80.442	588	74	27	39	609	568766040	568765477	6.620000e-111	411.0
10	TraesCS3D01G343200	chr7D	88.636	44	4	1	2234	2276	156105475	156105432	5.000000e-03	52.8
11	TraesCS3D01G343200	chr5A	76.991	339	51	16	151	467	109934786	109935119	4.400000e-38	169.0
12	TraesCS3D01G343200	chr5A	100.000	28	0	0	1745	1772	8743543	8743516	5.000000e-03	52.8
13	TraesCS3D01G343200	chr2B	75.526	380	69	19	1755	2124	494370317	494369952	5.690000e-37	165.0
14	TraesCS3D01G343200	chr2D	75.510	343	66	15	61	392	17018108	17017773	4.430000e-33	152.0
15	TraesCS3D01G343200	chr2D	79.630	108	18	4	1986	2090	495787395	495787289	9.860000e-10	75.0
16	TraesCS3D01G343200	chr2A	79.570	186	33	5	2331	2515	134617370	134617551	7.460000e-26	128.0
17	TraesCS3D01G343200	chr6A	77.075	253	30	18	151	386	77606823	77606582	1.250000e-23	121.0
18	TraesCS3D01G343200	chr6A	76.923	169	28	9	34	197	600895236	600895398	4.550000e-13	86.1
19	TraesCS3D01G343200	chr1B	76.442	208	40	7	1748	1950	268840929	268841132	1.260000e-18	104.0
20	TraesCS3D01G343200	chr1D	74.895	239	53	6	1742	1976	194181181	194181416	4.520000e-18	102.0
21	TraesCS3D01G343200	chrUn	84.706	85	12	1	2315	2399	88050965	88051048	1.640000e-12	84.2
22	TraesCS3D01G343200	chrUn	87.755	49	6	0	2521	2569	272055339	272055387	9.930000e-05	58.4
23	TraesCS3D01G343200	chr4A	87.755	49	6	0	2521	2569	677432078	677432126	9.930000e-05	58.4

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	TraesCS3D01G343200	chr3D	455719653	455722221	2568	True	4745.0	4745	100.0000	1	2569	1	chr3D.!!$R1	2568
1	TraesCS3D01G343200	chr3D	455752375	455752967	592	False	394.0	394	79.8010	44	608	1	chr3D.!!$F1	564
2	TraesCS3D01G343200	chr3A	597930177	597932699	2522	True	1884.5	3382	90.5535	16	2569	2	chr3A.!!$R1	2553
3	TraesCS3D01G343200	chr3B	598994782	598996885	2103	True	2429.0	2429	87.9230	89	2156	1	chr3B.!!$R1	2067
4	TraesCS3D01G343200	chr7D	568765477	568766040	563	True	411.0	411	80.4420	39	609	1	chr7D.!!$R2	570

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
404	556	0.252927	AAAGGGAGGGAGAGAGTGGG	60.253	60.0	0.0	0.0	0.0	4.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2290	2478	0.620556	AAATCAGATGGCGGTGACCT	59.379	50.0	0.0	0.0	0.0	3.85	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
64	65	5.982890	AGAATGAATTAGTGGGTTTGGTG	57.017	39.130	0.00	0.00	0.00	4.17
79	80	6.659745	GGTTTGGTGTTACCCTTTAAGAAT	57.340	37.500	0.00	0.00	37.50	2.40
136	143	2.352715	GGGGTTTTCTTGCGAAGAATGG	60.353	50.000	10.72	0.00	46.15	3.16
148	155	4.022935	TGCGAAGAATGGATTAATGGCATC	60.023	41.667	0.00	0.00	0.00	3.91
158	165	5.013704	TGGATTAATGGCATCGGTATTACCT	59.986	40.000	11.05	0.00	35.66	3.08
213	306	6.935741	TGTACAGACAACTTTGCACTAAAT	57.064	33.333	0.00	0.00	30.68	1.40
215	308	7.414436	TGTACAGACAACTTTGCACTAAATTC	58.586	34.615	0.00	0.00	30.68	2.17
280	373	8.412456	TGTAATTTTCCCACATATTGCATAGTG	58.588	33.333	0.00	0.00	0.00	2.74
292	385	8.183536	ACATATTGCATAGTGTTTGTGTGTATG	58.816	33.333	0.00	0.00	0.00	2.39
319	413	2.292828	ACTGACCCAACATCCCAAAG	57.707	50.000	0.00	0.00	0.00	2.77
404	556	0.252927	AAAGGGAGGGAGAGAGTGGG	60.253	60.000	0.00	0.00	0.00	4.61
428	584	1.079612	GGGCTGCACAGAAAATGGC	60.080	57.895	0.50	0.00	0.00	4.40
462	619	4.261578	AGCAAATCAACTGACCCAAATG	57.738	40.909	0.00	0.00	0.00	2.32
481	638	5.596836	AATGTGTGGTCAGTCAAAAACAT	57.403	34.783	0.00	0.00	0.00	2.71
701	866	5.275067	AGCAAAGCTTGTGGTTTTCATTA	57.725	34.783	0.00	0.00	41.31	1.90
718	883	8.404000	GTTTTCATTATGATCAGAACAGAGCAT	58.596	33.333	4.61	3.79	45.62	3.79
729	894	5.526479	TCAGAACAGAGCATGCAATCTAATC	59.474	40.000	21.98	14.79	0.00	1.75
738	903	5.926542	AGCATGCAATCTAATCATCAAATGC	59.073	36.000	21.98	0.00	37.53	3.56
758	923	7.470289	AATGCTAATCGCTTCTTTGTAGTAG	57.530	36.000	0.00	0.00	40.11	2.57
760	925	7.092137	TGCTAATCGCTTCTTTGTAGTAGTA	57.908	36.000	0.00	0.00	40.11	1.82
761	926	7.541162	TGCTAATCGCTTCTTTGTAGTAGTAA	58.459	34.615	0.00	0.00	40.11	2.24
762	927	8.195436	TGCTAATCGCTTCTTTGTAGTAGTAAT	58.805	33.333	0.00	0.00	40.11	1.89
763	928	9.032420	GCTAATCGCTTCTTTGTAGTAGTAATT	57.968	33.333	0.00	0.00	35.14	1.40
765	930	8.997621	AATCGCTTCTTTGTAGTAGTAATTCA	57.002	30.769	0.00	0.00	0.00	2.57
766	931	9.601217	AATCGCTTCTTTGTAGTAGTAATTCAT	57.399	29.630	0.00	0.00	0.00	2.57
808	973	6.561519	TCTTAAAATAGCTAGCTTGGGAGT	57.438	37.500	24.88	0.00	0.00	3.85
809	974	6.349300	TCTTAAAATAGCTAGCTTGGGAGTG	58.651	40.000	24.88	9.30	0.00	3.51
811	976	4.844349	AAATAGCTAGCTTGGGAGTGAA	57.156	40.909	24.88	0.74	0.00	3.18
812	977	4.414337	AATAGCTAGCTTGGGAGTGAAG	57.586	45.455	24.88	0.00	0.00	3.02
834	999	3.507622	GGCACAAATATGGCCTCCTATTC	59.492	47.826	3.32	0.00	38.86	1.75
863	1028	3.838565	TGTTTGCACCAAATCTAGGGAA	58.161	40.909	0.00	0.00	35.74	3.97
866	1031	2.274542	TGCACCAAATCTAGGGAAGGA	58.725	47.619	0.00	0.00	0.00	3.36
1054	1219	1.973812	GAGGCCCAAACAGGACAGC	60.974	63.158	0.00	0.00	37.41	4.40
1217	1382	1.447938	CGCACGCATGTTTCTTTCAAC	59.552	47.619	0.00	0.00	0.00	3.18
1219	1384	2.468777	GCACGCATGTTTCTTTCAACTG	59.531	45.455	0.00	0.00	0.00	3.16
1221	1386	4.104776	CACGCATGTTTCTTTCAACTGTT	58.895	39.130	0.00	0.00	0.00	3.16
1223	1388	5.396362	CACGCATGTTTCTTTCAACTGTTAG	59.604	40.000	0.00	0.00	0.00	2.34
1440	1605	0.603975	GCCACTAGGATCGGATTGGC	60.604	60.000	13.25	13.25	42.57	4.52
1460	1625	0.537188	GTTGCTACTAGGCAGGCAGA	59.463	55.000	0.00	0.00	43.39	4.26
1481	1646	2.039405	CCTCGTCTCCTCGTCCGTT	61.039	63.158	0.00	0.00	0.00	4.44
1487	1652	3.048941	CTCCTCGTCCGTTCGTCCC	62.049	68.421	0.00	0.00	0.00	4.46
1505	1670	0.034059	CCTCGTCAGTTGAGCACCTT	59.966	55.000	0.00	0.00	31.98	3.50
1507	1672	0.318699	TCGTCAGTTGAGCACCTTCG	60.319	55.000	0.00	0.00	0.00	3.79
1536	1701	2.729862	GCAGACTGCGACGTCGTT	60.730	61.111	35.48	21.92	42.22	3.85
1912	2096	7.548196	GCTACAACACATAGCTAAATTACCA	57.452	36.000	0.00	0.00	41.59	3.25
1973	2157	1.828595	TCTCGAAAATCCATCACCGGA	59.171	47.619	9.46	0.00	40.07	5.14
2092	2280	1.128188	AAGAGGGGCACGGAGAAAGT	61.128	55.000	0.00	0.00	0.00	2.66
2093	2281	1.079057	GAGGGGCACGGAGAAAGTC	60.079	63.158	0.00	0.00	0.00	3.01
2167	2355	2.579684	GAAGAACCTCGCCGCCATCT	62.580	60.000	0.00	0.00	0.00	2.90
2242	2430	3.222354	AGGTCGTGACAACGCCTCC	62.222	63.158	2.00	4.45	46.47	4.30
2267	2455	2.158959	GGGAACGACGCTGACATCG	61.159	63.158	0.00	0.00	43.97	3.84
2279	2467	3.208884	GACATCGCCGCCGTCCTAT	62.209	63.158	0.00	0.00	35.54	2.57
2290	2478	1.108776	CCGTCCTATCCGAAGAACCA	58.891	55.000	0.00	0.00	0.00	3.67
2366	2554	4.499019	CGAAGAGGAGCATAGAGAAAGGTC	60.499	50.000	0.00	0.00	0.00	3.85
2430	2618	2.137523	CTTTGCCAGCATCAACAAACC	58.862	47.619	0.00	0.00	0.00	3.27
2502	2690	1.343478	ACAGGATCTGAAGACCGGGAT	60.343	52.381	6.32	0.00	35.18	3.85
2517	2705	1.784525	GGGATACATGTCGCTAGCAC	58.215	55.000	16.45	12.39	39.74	4.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	9.807921	AAACCCACTAATTCATTCTTTCTTAGA	57.192	29.630	0.00	0.00	0.00	2.10
38	39	6.782494	ACCAAACCCACTAATTCATTCTTTCT	59.218	34.615	0.00	0.00	0.00	2.52
123	129	4.202040	TGCCATTAATCCATTCTTCGCAAG	60.202	41.667	0.00	0.00	0.00	4.01
136	143	7.448748	AAAGGTAATACCGATGCCATTAATC	57.551	36.000	3.47	0.00	44.90	1.75
192	283	6.655062	CGAATTTAGTGCAAAGTTGTCTGTA	58.345	36.000	0.00	0.00	0.00	2.74
196	289	4.146443	GTGCGAATTTAGTGCAAAGTTGTC	59.854	41.667	0.00	0.00	40.83	3.18
280	373	6.359617	GTCAGTACAAATGCATACACACAAAC	59.640	38.462	0.00	0.00	0.00	2.93
292	385	3.119495	GGATGTTGGGTCAGTACAAATGC	60.119	47.826	0.00	0.00	0.00	3.56
428	584	3.025978	TGATTTGCTAATGGGCTGAAGG	58.974	45.455	0.00	0.00	0.00	3.46
439	595	5.304101	ACATTTGGGTCAGTTGATTTGCTAA	59.696	36.000	0.00	0.00	0.00	3.09
462	619	4.630894	TGATGTTTTTGACTGACCACAC	57.369	40.909	0.00	0.00	0.00	3.82
481	638	5.011125	TGTTCTTTGAGTTGTTTTGGGTTGA	59.989	36.000	0.00	0.00	0.00	3.18
532	691	2.742053	TGCCGTAGATTTCTGCTTTGAC	59.258	45.455	0.00	0.00	0.00	3.18
617	782	8.851416	GCATCAAAGTACATATCGACATAGTAC	58.149	37.037	9.84	9.84	36.26	2.73
694	859	7.468220	GCATGCTCTGTTCTGATCATAATGAAA	60.468	37.037	11.37	0.00	0.00	2.69
701	866	3.277142	TGCATGCTCTGTTCTGATCAT	57.723	42.857	20.33	0.00	0.00	2.45
718	883	8.019094	CGATTAGCATTTGATGATTAGATTGCA	58.981	33.333	0.00	0.00	0.00	4.08
812	977	2.656947	TAGGAGGCCATATTTGTGCC	57.343	50.000	5.01	7.32	45.70	5.01
834	999	1.039068	TTGGTGCAAACATGTCCCTG	58.961	50.000	0.00	0.00	0.00	4.45
863	1028	7.224297	AGTATAGTCAACACAAACATGTTCCT	58.776	34.615	12.39	0.00	40.89	3.36
866	1031	8.445275	TCAAGTATAGTCAACACAAACATGTT	57.555	30.769	4.92	4.92	43.67	2.71
962	1127	5.278561	GGAGCTACGGTCTGCATATATATCC	60.279	48.000	8.39	0.00	0.00	2.59
1054	1219	4.452455	GGAACAGGAGAATGTACACAACAG	59.548	45.833	0.00	0.00	42.70	3.16
1201	1366	5.396362	CACTAACAGTTGAAAGAAACATGCG	59.604	40.000	0.00	0.00	32.21	4.73
1217	1382	4.314961	TCACACAGCCATAACACTAACAG	58.685	43.478	0.00	0.00	0.00	3.16
1219	1384	5.631026	CAATCACACAGCCATAACACTAAC	58.369	41.667	0.00	0.00	0.00	2.34
1221	1386	3.689161	GCAATCACACAGCCATAACACTA	59.311	43.478	0.00	0.00	0.00	2.74
1223	1388	2.489329	AGCAATCACACAGCCATAACAC	59.511	45.455	0.00	0.00	0.00	3.32
1440	1605	0.807667	CTGCCTGCCTAGTAGCAACG	60.808	60.000	0.00	0.00	43.52	4.10
1460	1625	3.126225	GACGAGGAGACGAGGCGT	61.126	66.667	0.00	0.00	45.10	5.68
1481	1646	1.863662	GCTCAACTGACGAGGGACGA	61.864	60.000	0.00	0.00	45.77	4.20
1487	1652	1.423395	GAAGGTGCTCAACTGACGAG	58.577	55.000	0.00	0.00	0.00	4.18
1523	1688	2.583868	TTGCAACGACGTCGCAGT	60.584	55.556	35.92	19.76	44.43	4.40
1533	1698	1.463528	GCTAAGCCGTAACTTGCAACG	60.464	52.381	0.00	0.00	38.80	4.10
1536	1701	3.194861	CATAGCTAAGCCGTAACTTGCA	58.805	45.455	0.00	0.00	0.00	4.08
1907	2091	4.072131	GTTGCTTCTCTTGGTCATGGTAA	58.928	43.478	0.00	0.00	0.00	2.85
1912	2096	2.373169	TCAGGTTGCTTCTCTTGGTCAT	59.627	45.455	0.00	0.00	0.00	3.06
2137	2325	2.885266	CGAGGTTCTTCGGATAGGATGA	59.115	50.000	0.00	0.00	36.95	2.92
2200	2388	1.592669	CGTGCCCCTATTCGAGCAG	60.593	63.158	0.00	0.00	35.56	4.24
2242	2430	1.079127	AGCGTCGTTCCCCTTCATG	60.079	57.895	0.00	0.00	0.00	3.07
2267	2455	3.843117	CTTCGGATAGGACGGCGGC	62.843	68.421	13.24	8.60	0.00	6.53
2279	2467	1.812686	CGGTGACCTGGTTCTTCGGA	61.813	60.000	0.00	0.00	0.00	4.55
2290	2478	0.620556	AAATCAGATGGCGGTGACCT	59.379	50.000	0.00	0.00	0.00	3.85
2355	2543	1.689813	TGTTGCCACGACCTTTCTCTA	59.310	47.619	0.00	0.00	0.00	2.43
2366	2554	0.817634	TTCTTGGAGGTGTTGCCACG	60.818	55.000	0.00	0.00	42.80	4.94
2430	2618	2.897350	GGGCGAAATCCCTGCTCG	60.897	66.667	0.00	0.00	43.13	5.03
2502	2690	0.525455	CTGCGTGCTAGCGACATGTA	60.525	55.000	10.77	0.00	40.67	2.29
2517	2705	1.812571	AGATTTGTTTGGCTACCTGCG	59.187	47.619	0.00	0.00	44.05	5.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.