AutoCloner

Multiple sequence alignment - TraesCS3B01G225200

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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	TraesCS3B01G225200	chr3B	100.000	2744	0	0	1	2744	309408514	309411257	0.000000e+00	5068.0
1	TraesCS3B01G225200	chr3B	94.444	36	1	1	2505	2540	123121327	123121361	1.000000e-03	54.7
2	TraesCS3B01G225200	chr3A	89.962	2112	68	64	723	2744	336612653	336610596	0.000000e+00	2593.0
3	TraesCS3B01G225200	chr3A	88.965	734	47	9	1	728	336613732	336613027	0.000000e+00	876.0
4	TraesCS3B01G225200	chr3A	95.238	42	1	1	2499	2540	496990041	496990081	6.340000e-07	65.8
5	TraesCS3B01G225200	chr3A	80.460	87	12	4	2458	2540	527938618	527938703	8.200000e-06	62.1
6	TraesCS3B01G225200	chr2A	87.301	2071	96	59	768	2744	712064651	712066648	0.000000e+00	2213.0
7	TraesCS3B01G225200	chr2A	83.001	753	35	26	1	745	712063992	712064659	1.820000e-166	595.0
8	TraesCS3B01G225200	chr2D	87.854	1869	64	59	768	2520	572804641	572806462	0.000000e+00	2043.0
9	TraesCS3B01G225200	chr2D	83.777	752	30	23	1	745	572803983	572804649	1.790000e-176	628.0
10	TraesCS3B01G225200	chr2D	96.907	97	3	0	2648	2744	572806653	572806749	2.190000e-36	163.0
11	TraesCS3B01G225200	chr2D	92.857	84	6	0	2530	2613	572806568	572806651	3.710000e-24	122.0
12	TraesCS3B01G225200	chr3D	91.483	1362	64	23	1	1355	253565129	253563813	0.000000e+00	1825.0
13	TraesCS3B01G225200	chr3D	94.040	453	14	7	1431	1874	253556952	253556504	0.000000e+00	675.0
14	TraesCS3B01G225200	chr3D	89.928	417	14	4	2167	2556	253554342	253553927	1.880000e-141	512.0
15	TraesCS3B01G225200	chr3D	95.806	310	6	4	1866	2174	253556414	253556111	6.830000e-136	494.0
16	TraesCS3B01G225200	chr3D	97.744	133	3	0	2612	2744	253553806	253553674	2.130000e-56	230.0
17	TraesCS3B01G225200	chr3D	100.000	38	0	0	1371	1408	253556988	253556951	1.360000e-08	71.3
18	TraesCS3B01G225200	chr3D	95.238	42	1	1	2499	2540	374358800	374358840	6.340000e-07	65.8
19	TraesCS3B01G225200	chr1A	83.451	284	22	10	768	1027	457344230	457344512	9.820000e-60	241.0
20	TraesCS3B01G225200	chr1A	82.517	286	8	12	464	745	457343991	457344238	2.140000e-51	213.0
21	TraesCS3B01G225200	chr1A	81.250	128	6	7	383	509	457344639	457344529	1.350000e-13	87.9
22	TraesCS3B01G225200	chr4A	92.857	42	2	1	2499	2540	684505053	684505013	2.950000e-05	60.2
23	TraesCS3B01G225200	chr5B	92.308	39	2	1	2506	2544	50646857	50646894	1.000000e-03	54.7
24	TraesCS3B01G225200	chr5D	100.000	28	0	0	634	661	342702682	342702709	5.000000e-03	52.8

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	TraesCS3B01G225200	chr3B	309408514	309411257	2743	False	5068.00	5068	100.00000	1	2744	1	chr3B.!!$F2	2743
1	TraesCS3B01G225200	chr3A	336610596	336613732	3136	True	1734.50	2593	89.46350	1	2744	2	chr3A.!!$R1	2743
2	TraesCS3B01G225200	chr2A	712063992	712066648	2656	False	1404.00	2213	85.15100	1	2744	2	chr2A.!!$F1	2743
3	TraesCS3B01G225200	chr2D	572803983	572806749	2766	False	739.00	2043	90.34875	1	2744	4	chr2D.!!$F1	2743
4	TraesCS3B01G225200	chr3D	253563813	253565129	1316	True	1825.00	1825	91.48300	1	1355	1	chr3D.!!$R1	1354
5	TraesCS3B01G225200	chr3D	253553674	253556988	3314	True	396.46	675	95.50360	1371	2744	5	chr3D.!!$R2	1373
6	TraesCS3B01G225200	chr1A	457343991	457344512	521	False	227.00	241	82.98400	464	1027	2	chr1A.!!$F1	563

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
577	614	0.311165	GCATGATGCATGAGCCAGAC	59.689	55.0	13.36	0.0	43.81	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1956	2661	0.035458	CGGATATTGGTCCTCAGCCC	59.965	60.0	0.0	0.0	36.07	5.19	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
67	68	2.034305	CCGTTCTATAGGACTTGTCCGG	59.966	54.545	13.41	34.28	5.14
102	103	1.006832	GGCGTCGATTTGCTACACAT	58.993	50.000	0.00	0.00	3.21
157	158	0.667792	AACTTCTCGGACGCTGCTTC	60.668	55.000	0.00	0.00	3.86
163	164	2.250939	CGGACGCTGCTTCCACAAA	61.251	57.895	22.88	31.94	2.83
175	176	3.118775	GCTTCCACAAACTCTTGGGTTTT	60.119	43.478	0.00	37.32	2.43
230	235	1.098869	TTGCCACGAGTTTTGCTCAA	58.901	45.000	0.00	44.33	3.02
390	419	6.377146	AGGAAAACTGAGTAGCACAAAAGAAA	59.623	34.615	0.00	0.00	2.52
456	485	3.391382	CGGAGGAGGCGGGAACTT	61.391	66.667	0.00	0.00	2.66
491	520	3.794717	CACAGTGATCTCTAGCTTGCAT	58.205	45.455	0.00	0.00	3.96
577	614	0.311165	GCATGATGCATGAGCCAGAC	59.689	55.000	13.36	43.81	3.51
582	619	0.461516	ATGCATGAGCCAGACAGACG	60.462	55.000	0.00	41.13	4.18
602	645	2.724977	GCTACTGAGCTACACACACA	57.275	50.000	0.00	45.98	3.72
603	646	2.329379	GCTACTGAGCTACACACACAC	58.671	52.381	0.00	45.98	3.82
604	647	2.029828	GCTACTGAGCTACACACACACT	60.030	50.000	0.00	45.98	3.55
605	648	2.802787	ACTGAGCTACACACACACTC	57.197	50.000	0.00	0.00	3.51
606	649	2.031870	ACTGAGCTACACACACACTCA	58.968	47.619	0.00	36.08	3.41
607	650	2.223829	ACTGAGCTACACACACACTCAC	60.224	50.000	0.00	33.95	3.51
608	651	2.031870	TGAGCTACACACACACTCACT	58.968	47.619	0.00	32.65	3.41
745	1167	2.814023	GCTAGCCAGCTCTACTCCA	58.186	57.895	2.29	44.93	3.86
754	1176	0.757561	GCTCTACTCCACTCCTCCCC	60.758	65.000	0.00	0.00	4.81
755	1177	0.466555	CTCTACTCCACTCCTCCCCG	60.467	65.000	0.00	0.00	5.73
756	1178	1.455959	CTACTCCACTCCTCCCCGG	60.456	68.421	0.00	0.00	5.73
757	1179	3.674050	TACTCCACTCCTCCCCGGC	62.674	68.421	0.00	0.00	6.13
761	1183	4.787280	CACTCCTCCCCGGCCTCT	62.787	72.222	0.00	0.00	3.69
762	1184	4.467107	ACTCCTCCCCGGCCTCTC	62.467	72.222	0.00	0.00	3.20

Showing 1 to 25 of 62 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
67	68	1.081175	GCCCTGAAGAAGCAAACGC	60.081	57.895	0.00	0.00	4.84
157	158	6.876789	ACTTTTTAAAACCCAAGAGTTTGTGG	59.123	34.615	0.00	39.83	4.17
163	164	7.604927	GGAACAAACTTTTTAAAACCCAAGAGT	59.395	33.333	0.00	0.00	3.24
175	176	5.561993	CGTCTCAACGGAACAAACTTTTTA	58.438	37.500	0.00	45.21	1.52
230	235	2.156098	ATCCACCCACAGTGCACCT	61.156	57.895	14.63	45.83	4.00
347	375	3.218453	TCCTTCATTTGCGAAAAGGACA	58.782	40.909	13.75	41.74	4.02
390	419	7.498443	TCTCGTCTTCTCTTTCCTTAGTTTTT	58.502	34.615	0.00	0.00	1.94
491	520	0.400381	TGATGGGCCTCTCCATGCTA	60.400	55.000	4.53	46.67	3.49
597	640	2.099756	TGAGTGAGTGAGTGAGTGTGTG	59.900	50.000	0.00	0.00	3.82
598	641	2.360483	CTGAGTGAGTGAGTGAGTGTGT	59.640	50.000	0.00	0.00	3.72
599	642	2.861750	GCTGAGTGAGTGAGTGAGTGTG	60.862	54.545	0.00	0.00	3.82
600	643	1.339610	GCTGAGTGAGTGAGTGAGTGT	59.660	52.381	0.00	0.00	3.55
601	644	1.336702	GGCTGAGTGAGTGAGTGAGTG	60.337	57.143	0.00	0.00	3.51
602	645	0.965439	GGCTGAGTGAGTGAGTGAGT	59.035	55.000	0.00	0.00	3.41
603	646	1.067706	CAGGCTGAGTGAGTGAGTGAG	60.068	57.143	9.42	0.00	3.51
604	647	0.964700	CAGGCTGAGTGAGTGAGTGA	59.035	55.000	9.42	0.00	3.41
605	648	0.669932	GCAGGCTGAGTGAGTGAGTG	60.670	60.000	20.86	0.00	3.51
606	649	1.670590	GCAGGCTGAGTGAGTGAGT	59.329	57.895	20.86	0.00	3.41
607	650	1.079266	GGCAGGCTGAGTGAGTGAG	60.079	63.158	20.86	0.00	3.51
608	651	2.587247	GGGCAGGCTGAGTGAGTGA	61.587	63.158	20.86	0.00	3.41
745	1167	4.467107	GAGAGGCCGGGGAGGAGT	62.467	72.222	2.18	45.00	3.85
757	1179	2.520741	GAGGAGAGGCCGGAGAGG	60.521	72.222	5.05	43.43	3.69
758	1180	2.520741	GGAGGAGAGGCCGGAGAG	60.521	72.222	5.05	43.43	3.20
759	1181	3.024356	AGGAGGAGAGGCCGGAGA	61.024	66.667	5.05	43.43	3.71
760	1182	2.837291	CAGGAGGAGAGGCCGGAG	60.837	72.222	5.05	43.43	4.63

Showing 1 to 25 of 67 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.