AutoCloner

Multiple sequence alignment - TraesCS1B01G199500

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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	TraesCS1B01G199500	chr1B	100.000	2510	0	0	1	2510	357469190	357471699	0.000000e+00	4636
1	TraesCS1B01G199500	chr1B	95.188	478	22	1	2034	2510	532660623	532660146	0.000000e+00	754
2	TraesCS1B01G199500	chr1B	94.526	475	22	2	2038	2510	370035758	370036230	0.000000e+00	730
3	TraesCS1B01G199500	chr1A	93.916	1545	53	18	470	2004	327272395	327270882	0.000000e+00	2294
4	TraesCS1B01G199500	chr1D	93.371	1433	51	14	584	2004	255427843	255426443	0.000000e+00	2080
5	TraesCS1B01G199500	chr1D	90.517	116	9	2	471	585	255436266	255436152	4.320000e-33	152
6	TraesCS1B01G199500	chr7B	96.406	473	17	0	1	473	626045684	626045212	0.000000e+00	780
7	TraesCS1B01G199500	chr7B	94.926	473	21	3	2038	2510	712768171	712768640	0.000000e+00	737
8	TraesCS1B01G199500	chr7B	94.292	473	25	1	2038	2510	685999869	686000339	0.000000e+00	723
9	TraesCS1B01G199500	chr2A	95.137	473	23	0	1	473	585191637	585191165	0.000000e+00	747
10	TraesCS1B01G199500	chr2A	93.658	473	30	0	1	473	595236869	595236397	0.000000e+00	708
11	TraesCS1B01G199500	chr5B	94.781	479	20	3	2034	2510	694236788	694236313	0.000000e+00	741
12	TraesCS1B01G199500	chr5B	94.480	471	25	1	2040	2510	326508932	326509401	0.000000e+00	725
13	TraesCS1B01G199500	chr2D	94.926	473	24	0	1	473	100427034	100426562	0.000000e+00	741
14	TraesCS1B01G199500	chr6B	95.117	471	20	2	2040	2510	182449992	182450459	0.000000e+00	739
15	TraesCS1B01G199500	chr6B	94.715	473	22	2	2038	2510	659251370	659251839	0.000000e+00	732
16	TraesCS1B01G199500	chr2B	94.503	473	22	2	2040	2510	585193424	585192954	0.000000e+00	726
17	TraesCS1B01G199500	chr5A	92.812	473	34	0	1	473	698753397	698752925	0.000000e+00	686
18	TraesCS1B01G199500	chr7A	86.596	470	63	0	4	473	271639725	271639256	1.030000e-143	520
19	TraesCS1B01G199500	chr7D	86.170	470	65	0	1	470	140815260	140815729	2.230000e-140	508
20	TraesCS1B01G199500	chr3D	86.170	470	65	0	4	473	432509480	432509011	2.230000e-140	508
21	TraesCS1B01G199500	chr4D	85.957	470	66	0	1	470	494282601	494283070	1.040000e-138	503

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	TraesCS1B01G199500	chr1B	357469190	357471699	2509	False	4636	4636	100.000	1	2510	1	chr1B.!!$F1	2509
1	TraesCS1B01G199500	chr1A	327270882	327272395	1513	True	2294	2294	93.916	470	2004	1	chr1A.!!$R1	1534
2	TraesCS1B01G199500	chr1D	255426443	255427843	1400	True	2080	2080	93.371	584	2004	1	chr1D.!!$R1	1420

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
203	204	0.03213	GTGTGTCGGAGAAGTGCTCA	59.968	55.0	0.0	0.0	45.81	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2076	2096	0.042621	CGCGCGGCAAACAAATTTTT	60.043	45.0	24.84	0.0	0.0	1.94	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	Hairpin	End Stability
20	21	3.017265	CTTGCATGGGCGAAAATATCC	57.983	47.619	45.35	2.59
21	22	1.327303	TGCATGGGCGAAAATATCCC	58.673	50.000	45.35	3.85
22	23	1.133513	TGCATGGGCGAAAATATCCCT	60.134	47.619	45.35	4.20
23	24	1.541588	GCATGGGCGAAAATATCCCTC	59.458	52.381	40.69	4.30
24	25	2.162681	CATGGGCGAAAATATCCCTCC	58.837	52.381	40.69	4.30
25	26	1.217916	TGGGCGAAAATATCCCTCCA	58.782	50.000	40.69	3.86
26	27	1.566703	TGGGCGAAAATATCCCTCCAA	59.433	47.619	40.69	3.53
27	28	2.230660	GGGCGAAAATATCCCTCCAAG	58.769	52.381	37.08	3.61
28	29	1.609072	GGCGAAAATATCCCTCCAAGC	59.391	52.381	0.00	4.01
29	30	2.297701	GCGAAAATATCCCTCCAAGCA	58.702	47.619	0.00	3.91
30	31	2.887152	GCGAAAATATCCCTCCAAGCAT	59.113	45.455	0.00	3.79
31	32	3.319122	GCGAAAATATCCCTCCAAGCATT	59.681	43.478	0.00	3.56
33	34	4.339247	CGAAAATATCCCTCCAAGCATTGT	59.661	41.667	46.99	2.71
34	35	5.163519	CGAAAATATCCCTCCAAGCATTGTT	60.164	40.000	46.99	2.83
35	36	6.039270	CGAAAATATCCCTCCAAGCATTGTTA	59.961	38.462	46.99	2.41
36	37	6.966534	AAATATCCCTCCAAGCATTGTTAG	57.033	37.500	46.99	2.34
37	38	2.128771	TCCCTCCAAGCATTGTTAGC	57.871	50.000	46.99	3.09
38	39	1.106285	CCCTCCAAGCATTGTTAGCC	58.894	55.000	46.99	3.93
39	40	1.616725	CCCTCCAAGCATTGTTAGCCA	60.617	52.381	46.99	4.75
40	41	1.474077	CCTCCAAGCATTGTTAGCCAC	59.526	52.381	46.99	5.01
41	42	2.161855	CTCCAAGCATTGTTAGCCACA	58.838	47.619	46.99	4.17
42	43	2.161855	TCCAAGCATTGTTAGCCACAG	58.838	47.619	46.99	3.66
43	44	1.403249	CCAAGCATTGTTAGCCACAGC	60.403	52.381	46.99	4.40
44	45	1.270274	CAAGCATTGTTAGCCACAGCA	59.730	47.619	42.34	4.41
45	46	0.883833	AGCATTGTTAGCCACAGCAC	59.116	50.000	43.56	4.40

Showing 1 to 25 of 595 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	1.780309	TGGAGGGATATTTTCGCCCAT	59.220	47.619	0.00	0.00	44.55	4.00
6	7	1.217916	TGGAGGGATATTTTCGCCCA	58.782	50.000	0.00	0.00	44.55	5.36
7	8	2.230660	CTTGGAGGGATATTTTCGCCC	58.769	52.381	0.00	0.00	42.37	6.13
8	9	1.609072	GCTTGGAGGGATATTTTCGCC	59.391	52.381	0.00	0.00	38.02	5.54
9	10	2.297701	TGCTTGGAGGGATATTTTCGC	58.702	47.619	0.00	0.00	37.56	4.70
10	11	4.339247	ACAATGCTTGGAGGGATATTTTCG	59.661	41.667	1.84	0.00	34.12	3.46
11	12	5.859205	ACAATGCTTGGAGGGATATTTTC	57.141	39.130	1.84	0.00	34.12	2.29
12	13	6.183360	GCTAACAATGCTTGGAGGGATATTTT	60.183	38.462	1.84	0.00	34.12	1.82
13	14	5.302823	GCTAACAATGCTTGGAGGGATATTT	59.697	40.000	1.84	0.00	34.12	1.40
14	15	4.829492	GCTAACAATGCTTGGAGGGATATT	59.171	41.667	1.84	0.00	34.12	1.28
15	16	4.401925	GCTAACAATGCTTGGAGGGATAT	58.598	43.478	1.84	0.00	34.12	1.63
16	17	3.435026	GGCTAACAATGCTTGGAGGGATA	60.435	47.826	1.84	0.00	34.12	2.59
17	18	2.659428	GCTAACAATGCTTGGAGGGAT	58.341	47.619	1.84	0.00	34.12	3.85
18	19	1.340991	GGCTAACAATGCTTGGAGGGA	60.341	52.381	1.84	0.00	34.12	4.20
19	20	1.106285	GGCTAACAATGCTTGGAGGG	58.894	55.000	1.84	0.00	34.12	4.30
20	21	1.474077	GTGGCTAACAATGCTTGGAGG	59.526	52.381	1.84	0.00	34.12	4.30
21	22	2.161855	TGTGGCTAACAATGCTTGGAG	58.838	47.619	1.84	0.48	35.24	3.86
22	23	2.161855	CTGTGGCTAACAATGCTTGGA	58.838	47.619	1.84	0.00	38.67	3.53
23	24	1.403249	GCTGTGGCTAACAATGCTTGG	60.403	52.381	1.84	0.00	38.67	3.61
24	25	1.270274	TGCTGTGGCTAACAATGCTTG	59.730	47.619	6.10	0.00	38.67	4.01
25	26	1.270550	GTGCTGTGGCTAACAATGCTT	59.729	47.619	6.10	0.00	38.67	3.91
26	27	0.883833	GTGCTGTGGCTAACAATGCT	59.116	50.000	6.10	0.00	38.67	3.79
27	28	0.454957	CGTGCTGTGGCTAACAATGC	60.455	55.000	0.00	0.00	38.67	3.56
28	29	0.168788	CCGTGCTGTGGCTAACAATG	59.831	55.000	0.00	0.00	38.67	2.82
29	30	0.250727	ACCGTGCTGTGGCTAACAAT	60.251	50.000	0.00	0.00	38.67	2.71

Showing 1 to 25 of 598 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.