AutoCloner

Multiple sequence alignment - TraesCS6A01G199200

Loading Multiple Alignment...

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	TraesCS6A01G199200	chr6A	100.000	2950	0	0	1	2950	314878779	314881728	0.000000e+00	5448
1	TraesCS6A01G199200	chr6A	92.244	2669	152	19	298	2950	514955038	514957667	0.000000e+00	3731
2	TraesCS6A01G199200	chr6A	92.268	2496	147	17	472	2950	345454388	345456854	0.000000e+00	3498
3	TraesCS6A01G199200	chr3A	92.443	2673	153	19	298	2950	91718052	91715409	0.000000e+00	3771
4	TraesCS6A01G199200	chr3A	92.408	2674	154	20	298	2950	91713427	91710782	0.000000e+00	3768
5	TraesCS6A01G199200	chr2A	92.286	2502	145	18	467	2950	679108818	679106347	0.000000e+00	3507
6	TraesCS6A01G199200	chr2A	84.542	2523	319	50	472	2950	187018680	187021175	0.000000e+00	2433
7	TraesCS6A01G199200	chr2A	78.398	412	76	9	162	565	343022128	343021722	3.770000e-64	255
8	TraesCS6A01G199200	chr7D	87.542	2649	272	32	318	2950	281331117	281328511	0.000000e+00	3011
9	TraesCS6A01G199200	chr3B	86.686	2734	279	58	258	2950	74831251	74828562	0.000000e+00	2953
10	TraesCS6A01G199200	chr3B	83.677	2671	374	43	318	2950	295072636	295069990	0.000000e+00	2460
11	TraesCS6A01G199200	chr3B	84.131	1651	219	23	371	2002	261627126	261628752	0.000000e+00	1557
12	TraesCS6A01G199200	chr1B	86.812	2525	276	28	467	2950	556073153	556070645	0.000000e+00	2765
13	TraesCS6A01G199200	chr1B	86.173	2524	290	36	467	2950	465588382	465585878	0.000000e+00	2673
14	TraesCS6A01G199200	chr1B	85.551	2533	301	36	467	2950	149476566	149474050	0.000000e+00	2590
15	TraesCS6A01G199200	chr1B	77.393	606	98	30	1	590	534458072	534458654	1.020000e-84	324
16	TraesCS6A01G199200	chr1B	78.198	555	83	29	1	539	534471496	534472028	1.320000e-83	320
17	TraesCS6A01G199200	chr7B	86.484	2523	287	34	467	2950	363002345	363004852	0.000000e+00	2721
18	TraesCS6A01G199200	chrUn	84.959	2686	333	45	317	2950	59445077	59442411	0.000000e+00	2656
19	TraesCS6A01G199200	chr1D	84.463	2684	360	42	301	2950	143123644	143120984	0.000000e+00	2593
20	TraesCS6A01G199200	chr5B	84.900	1702	224	26	321	2002	274670986	274672674	0.000000e+00	1688
21	TraesCS6A01G199200	chr5B	89.908	109	10	1	1	109	316552141	316552034	3.960000e-29	139
22	TraesCS6A01G199200	chr2D	85.062	1687	219	25	338	2002	323249224	323247549	0.000000e+00	1688
23	TraesCS6A01G199200	chr4B	83.659	1689	224	30	300	1965	207928347	207926688	0.000000e+00	1543
24	TraesCS6A01G199200	chr4B	84.214	1533	210	16	494	2002	485379641	485381165	0.000000e+00	1461
25	TraesCS6A01G199200	chr3D	86.798	962	95	15	1993	2950	402307764	402306831	0.000000e+00	1044
26	TraesCS6A01G199200	chr3D	95.499	511	23	0	1	511	282541413	282541923	0.000000e+00	817
27	TraesCS6A01G199200	chr3D	83.391	578	74	17	1	565	359453973	359453405	1.570000e-142	516
28	TraesCS6A01G199200	chr3D	85.039	254	32	5	1	251	226746882	226746632	1.360000e-63	254
29	TraesCS6A01G199200	chr3D	84.646	254	33	5	1	251	226751202	226750952	6.310000e-62	248
30	TraesCS6A01G199200	chr4A	96.290	566	21	0	1	566	458964299	458964864	0.000000e+00	929
31	TraesCS6A01G199200	chr4A	85.271	903	107	18	2064	2950	113199403	113200295	0.000000e+00	907
32	TraesCS6A01G199200	chr4A	92.821	390	25	2	178	565	299668236	299668624	1.990000e-156	562
33	TraesCS6A01G199200	chr7A	95.936	566	20	1	1	566	392243175	392242613	0.000000e+00	915
34	TraesCS6A01G199200	chr6D	89.362	235	21	3	163	394	121109734	121109501	2.880000e-75	292

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	TraesCS6A01G199200	chr6A	314878779	314881728	2949	False	5448.0	5448	100.0000	1	2950	1	chr6A.!!$F1	2949
1	TraesCS6A01G199200	chr6A	514955038	514957667	2629	False	3731.0	3731	92.2440	298	2950	1	chr6A.!!$F3	2652
2	TraesCS6A01G199200	chr6A	345454388	345456854	2466	False	3498.0	3498	92.2680	472	2950	1	chr6A.!!$F2	2478
3	TraesCS6A01G199200	chr3A	91710782	91718052	7270	True	3769.5	3771	92.4255	298	2950	2	chr3A.!!$R1	2652
4	TraesCS6A01G199200	chr2A	679106347	679108818	2471	True	3507.0	3507	92.2860	467	2950	1	chr2A.!!$R2	2483
5	TraesCS6A01G199200	chr2A	187018680	187021175	2495	False	2433.0	2433	84.5420	472	2950	1	chr2A.!!$F1	2478
6	TraesCS6A01G199200	chr7D	281328511	281331117	2606	True	3011.0	3011	87.5420	318	2950	1	chr7D.!!$R1	2632
7	TraesCS6A01G199200	chr3B	74828562	74831251	2689	True	2953.0	2953	86.6860	258	2950	1	chr3B.!!$R1	2692
8	TraesCS6A01G199200	chr3B	295069990	295072636	2646	True	2460.0	2460	83.6770	318	2950	1	chr3B.!!$R2	2632
9	TraesCS6A01G199200	chr3B	261627126	261628752	1626	False	1557.0	1557	84.1310	371	2002	1	chr3B.!!$F1	1631
10	TraesCS6A01G199200	chr1B	556070645	556073153	2508	True	2765.0	2765	86.8120	467	2950	1	chr1B.!!$R3	2483
11	TraesCS6A01G199200	chr1B	465585878	465588382	2504	True	2673.0	2673	86.1730	467	2950	1	chr1B.!!$R2	2483
12	TraesCS6A01G199200	chr1B	149474050	149476566	2516	True	2590.0	2590	85.5510	467	2950	1	chr1B.!!$R1	2483
13	TraesCS6A01G199200	chr1B	534458072	534458654	582	False	324.0	324	77.3930	1	590	1	chr1B.!!$F1	589
14	TraesCS6A01G199200	chr1B	534471496	534472028	532	False	320.0	320	78.1980	1	539	1	chr1B.!!$F2	538
15	TraesCS6A01G199200	chr7B	363002345	363004852	2507	False	2721.0	2721	86.4840	467	2950	1	chr7B.!!$F1	2483
16	TraesCS6A01G199200	chrUn	59442411	59445077	2666	True	2656.0	2656	84.9590	317	2950	1	chrUn.!!$R1	2633
17	TraesCS6A01G199200	chr1D	143120984	143123644	2660	True	2593.0	2593	84.4630	301	2950	1	chr1D.!!$R1	2649
18	TraesCS6A01G199200	chr5B	274670986	274672674	1688	False	1688.0	1688	84.9000	321	2002	1	chr5B.!!$F1	1681
19	TraesCS6A01G199200	chr2D	323247549	323249224	1675	True	1688.0	1688	85.0620	338	2002	1	chr2D.!!$R1	1664
20	TraesCS6A01G199200	chr4B	207926688	207928347	1659	True	1543.0	1543	83.6590	300	1965	1	chr4B.!!$R1	1665
21	TraesCS6A01G199200	chr4B	485379641	485381165	1524	False	1461.0	1461	84.2140	494	2002	1	chr4B.!!$F1	1508
22	TraesCS6A01G199200	chr3D	402306831	402307764	933	True	1044.0	1044	86.7980	1993	2950	1	chr3D.!!$R4	957
23	TraesCS6A01G199200	chr3D	282541413	282541923	510	False	817.0	817	95.4990	1	511	1	chr3D.!!$F1	510
24	TraesCS6A01G199200	chr3D	359453405	359453973	568	True	516.0	516	83.3910	1	565	1	chr3D.!!$R3	564
25	TraesCS6A01G199200	chr4A	458964299	458964864	565	False	929.0	929	96.2900	1	566	1	chr4A.!!$F3	565
26	TraesCS6A01G199200	chr4A	113199403	113200295	892	False	907.0	907	85.2710	2064	2950	1	chr4A.!!$F1	886
27	TraesCS6A01G199200	chr7A	392242613	392243175	562	True	915.0	915	95.9360	1	566	1	chr7A.!!$R1	565

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
544	573	1.208535	ACAGTTCGGGCGAAATATCCA	59.791	47.619	0.0	0.0	35.75	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2219	2300	0.392193	CCATGCTCTGAGTCCACCAC	60.392	60.0	6.53	0.0	0.0	4.16	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
423	444	7.166970	CGATTTTCCGAAACGATCTTAGATACA	59.833	37.037	0.00	0.00	0.00	2.29
469	493	9.686683	AATTGTCACTTAAATTGTCTAGGCTAT	57.313	29.630	0.00	0.00	0.00	2.97
506	533	1.415289	TCGCTGATCGTCTAGTCCCTA	59.585	52.381	0.00	0.00	39.67	3.53
544	573	1.208535	ACAGTTCGGGCGAAATATCCA	59.791	47.619	0.00	0.00	35.75	3.41
642	674	8.717821	ACTAGGTTTTTCTTGTTTTCTTTTTGC	58.282	29.630	0.00	0.00	0.00	3.68
648	682	6.959671	TTCTTGTTTTCTTTTTGCGACATT	57.040	29.167	0.00	0.00	0.00	2.71
700	735	8.834749	ACCACTGTTCTAGTTATTTTCTCTTC	57.165	34.615	0.00	0.00	37.60	2.87
713	753	9.249457	GTTATTTTCTCTTCCTTTTCTTGGTTG	57.751	33.333	0.00	0.00	0.00	3.77
730	774	5.941555	TGGTTGTTTTGTAGGTTGGATTT	57.058	34.783	0.00	0.00	0.00	2.17
751	795	8.090214	GGATTTTCTTCTTGGAAATGTCATTCA	58.910	33.333	0.00	0.00	35.51	2.57
753	797	8.876275	TTTTCTTCTTGGAAATGTCATTCAAG	57.124	30.769	15.88	15.88	35.51	3.02
757	801	7.449395	TCTTCTTGGAAATGTCATTCAAGTCAT	59.551	33.333	19.08	0.00	0.00	3.06
758	802	6.916440	TCTTGGAAATGTCATTCAAGTCATG	58.084	36.000	19.08	0.00	0.00	3.07
788	833	5.376947	GCTTATACGAGCAACAGTACAAG	57.623	43.478	0.00	0.00	42.25	3.16
935	989	2.880890	CTCCTACCTGCCATATTTGTGC	59.119	50.000	0.00	0.00	0.00	4.57
940	994	4.556592	ACCTGCCATATTTGTGCATTTT	57.443	36.364	0.00	0.00	33.97	1.82
1054	1112	2.308570	AGCAATTACTCACATGGGTGGA	59.691	45.455	1.53	0.00	45.32	4.02
1088	1146	9.212641	CCAGAATATGTCATATAGGAACAACAG	57.787	37.037	5.76	0.00	0.00	3.16
1105	1163	0.317799	CAGCCCTGAGATCTCATCGG	59.682	60.000	25.30	25.10	39.13	4.18
1177	1248	5.175491	CACAACTATGCACCACAACAATTTC	59.825	40.000	0.00	0.00	0.00	2.17
1214	1285	4.649674	TCATATACCTCAACACCAGGAGAC	59.350	45.833	0.00	0.00	34.75	3.36
1220	1291	0.389391	CAACACCAGGAGACGTGTCT	59.611	55.000	12.92	1.35	42.28	3.41
1280	1360	0.963962	CCAGCACCTGTTGAGCAATT	59.036	50.000	0.00	0.00	0.00	2.32
1329	1409	9.920133	GATGACTTTGATGATATAGACAAGCTA	57.080	33.333	0.00	0.00	0.00	3.32
1372	1452	4.008330	CACTTGGAGTGCTGAAGATGATT	58.992	43.478	0.00	0.00	39.62	2.57
1425	1505	6.708054	TGAAGAAGATCAAGAGTGGAAAAGAC	59.292	38.462	0.00	0.00	0.00	3.01
1467	1547	8.419442	AGGAAAATTGAGAAGAATATCAATGCC	58.581	33.333	1.50	4.57	43.56	4.40
1470	1550	3.743521	TGAGAAGAATATCAATGCCGGG	58.256	45.455	2.18	0.00	0.00	5.73
1471	1551	3.136443	TGAGAAGAATATCAATGCCGGGT	59.864	43.478	2.18	0.00	0.00	5.28
1499	1579	0.399091	TCATCCCTCCTTGAGCCGAT	60.399	55.000	0.00	0.00	0.00	4.18
1530	1610	5.041191	AGATTCCCCTTGATACATGTGAC	57.959	43.478	9.11	2.81	0.00	3.67
1588	1668	6.260663	AGTAAGAGTCCAGAGGAAGAAAGAT	58.739	40.000	0.00	0.00	31.38	2.40
1676	1756	6.594547	AGTGATCAAGTTGAAGACTCATCATG	59.405	38.462	10.14	0.00	38.68	3.07
1835	1915	2.123342	TGTTGTTACTTTGCATTGCGC	58.877	42.857	0.00	0.00	42.89	6.09
2219	2300	0.676782	GGTGACATTCCTTGGGACCG	60.677	60.000	0.00	0.00	0.00	4.79
2290	2372	2.305343	AGAAGAGTGAAGCTGGAGCATT	59.695	45.455	0.65	0.00	45.16	3.56
2681	2785	2.874701	GTGTCAGATGCTGAGTTTGTGT	59.125	45.455	0.00	0.00	41.46	3.72
2700	2804	5.380900	TGTGTCTAATGTGTTCCCATTCAA	58.619	37.500	0.00	0.00	36.48	2.69
2702	2806	6.322456	TGTGTCTAATGTGTTCCCATTCAAAA	59.678	34.615	0.00	0.00	36.48	2.44
2865	7613	1.672881	GTAGCATGTCATGTTCCCTGC	59.327	52.381	14.26	3.09	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
208	214	9.823647	GAGAAAAGAGACATGAATATAGGACAA	57.176	33.333	0.00	0.00	0.00	3.18
261	273	5.305644	ACCAAATGGGCAACAACAATACTAA	59.694	36.000	4.17	0.00	42.05	2.24
275	287	4.606961	CGTACAAATATGACCAAATGGGC	58.393	43.478	4.17	0.37	45.93	5.36
359	376	5.105997	CGAAAAGAAGCAAAGGGAGATTCAT	60.106	40.000	0.00	0.00	0.00	2.57
469	493	1.869754	GCGATGATGCTCGGCTAAAGA	60.870	52.381	0.00	0.00	39.05	2.52
506	533	1.686587	TGTGAGTGTCGTGTTCTCCAT	59.313	47.619	0.00	0.00	0.00	3.41
544	573	7.716998	CCAAAATGATCTATTGTAGGTACAGCT	59.283	37.037	0.00	0.00	37.52	4.24
602	632	9.043548	AGAAAAACCTAGTCTATAGCCTAACAA	57.956	33.333	0.00	0.00	0.00	2.83
663	697	3.978672	AGAACAGTGGTTAGGGGTTAGTT	59.021	43.478	0.00	0.00	37.36	2.24
664	698	3.595021	AGAACAGTGGTTAGGGGTTAGT	58.405	45.455	0.00	0.00	37.36	2.24
700	735	5.972935	ACCTACAAAACAACCAAGAAAAGG	58.027	37.500	0.00	0.00	0.00	3.11
713	753	7.438160	CCAAGAAGAAAATCCAACCTACAAAAC	59.562	37.037	0.00	0.00	0.00	2.43
730	774	7.285172	TGACTTGAATGACATTTCCAAGAAGAA	59.715	33.333	25.21	11.83	0.00	2.52
757	801	4.320608	TGCTCGTATAAGCATGATGACA	57.679	40.909	0.00	0.00	47.00	3.58
772	816	1.502231	CTGCTTGTACTGTTGCTCGT	58.498	50.000	0.00	0.00	0.00	4.18
782	827	1.226746	ACTTTCCGTGCTGCTTGTAC	58.773	50.000	0.00	0.00	0.00	2.90
788	833	2.742053	TCTTGAATACTTTCCGTGCTGC	59.258	45.455	0.00	0.00	0.00	5.25
857	911	3.389656	AGAGCTAGGCCTATCCTCAAAAC	59.610	47.826	28.57	12.60	43.20	2.43
1054	1112	9.784531	CCTATATGACATATTCTGGTTTTCAGT	57.215	33.333	13.09	0.00	43.76	3.41
1088	1146	0.755686	AACCGATGAGATCTCAGGGC	59.244	55.000	31.12	21.75	43.61	5.19
1105	1163	4.199310	TGCATTGGATAACTAGAGGCAAC	58.801	43.478	0.00	0.00	0.00	4.17
1177	1248	6.435591	TGAGGTATATGAGTAGGAGCTGAATG	59.564	42.308	0.00	0.00	0.00	2.67
1214	1285	5.293569	GGACCATTTAACTCCATTAGACACG	59.706	44.000	0.00	0.00	0.00	4.49
1280	1360	0.754587	TGTGGGCACTTGTGCATGAA	60.755	50.000	24.34	7.10	36.33	2.57
1329	1409	4.686554	GTGAACTCGAGACTAAGCAATGTT	59.313	41.667	21.68	0.00	0.00	2.71
1372	1452	4.476297	TCTAGTATCACCGGCCTAATTGA	58.524	43.478	0.00	0.00	0.00	2.57
1425	1505	7.883311	TCAATTTTCCTTACTTCTTCCACTAGG	59.117	37.037	0.00	0.00	0.00	3.02
1467	1547	1.349026	AGGGATGAGATAATGCACCCG	59.651	52.381	0.00	0.00	40.55	5.28
1470	1550	4.070716	CAAGGAGGGATGAGATAATGCAC	58.929	47.826	0.00	0.00	0.00	4.57
1471	1551	3.975982	TCAAGGAGGGATGAGATAATGCA	59.024	43.478	0.00	0.00	0.00	3.96
1475	1555	2.975489	GGCTCAAGGAGGGATGAGATAA	59.025	50.000	6.95	0.00	44.64	1.75
1499	1579	0.404040	AAGGGGAATCTCGGCAACAA	59.596	50.000	0.00	0.00	0.00	2.83
1530	1610	1.931172	GGATGTGACGGTATTGGAACG	59.069	52.381	0.00	0.00	0.00	3.95
1682	1762	7.156876	TCAACTTCTTTTGCTTCTTCAAGAA	57.843	32.000	0.00	0.00	34.74	2.52
2219	2300	0.392193	CCATGCTCTGAGTCCACCAC	60.392	60.000	6.53	0.00	0.00	4.16
2290	2372	4.042062	TCTTCTCCTTTTGCTTCCTCATGA	59.958	41.667	0.00	0.00	0.00	3.07
2700	2804	9.396022	CTAATCCATAGTGGTAAGTGATTGTTT	57.604	33.333	0.00	0.00	39.03	2.83
2702	2806	6.992715	GCTAATCCATAGTGGTAAGTGATTGT	59.007	38.462	0.00	0.00	39.03	2.71
2838	7586	5.419542	GGAACATGACATGCTACTGTTAGA	58.580	41.667	15.49	0.00	30.63	2.10
2865	7613	2.086869	AGATTTCACAAGCCACCGATG	58.913	47.619	0.00	0.00	0.00	3.84

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.