AutoCloner

Multiple sequence alignment - TraesCS1B01G218400

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	TraesCS1B01G218400	chr1B	100.000	1840	0	0	1	1840	395942587	395944426	0.000000e+00	3398
1	TraesCS1B01G218400	chr1B	100.000	141	0	0	2202	2342	395944788	395944928	6.420000e-66	261
2	TraesCS1B01G218400	chr1B	91.209	182	15	1	1596	1777	148119921	148119741	1.800000e-61	246
3	TraesCS1B01G218400	chr1B	93.617	141	9	0	2202	2342	401621536	401621676	6.560000e-51	211
4	TraesCS1B01G218400	chr1B	93.617	141	9	0	2202	2342	623198264	623198124	6.560000e-51	211
5	TraesCS1B01G218400	chr1D	95.902	1025	30	6	561	1582	294201318	294202333	0.000000e+00	1650
6	TraesCS1B01G218400	chr1D	90.270	555	46	6	1	552	294200483	294201032	0.000000e+00	719
7	TraesCS1B01G218400	chr1D	93.662	142	8	1	2202	2342	296546598	296546457	6.560000e-51	211
8	TraesCS1B01G218400	chr1A	92.420	1029	59	11	582	1596	366987961	366988984	0.000000e+00	1450
9	TraesCS1B01G218400	chr1A	88.043	184	20	1	1594	1775	22645889	22645706	1.410000e-52	217
10	TraesCS1B01G218400	chr1A	87.568	185	20	2	1588	1770	270613115	270612932	6.560000e-51	211
11	TraesCS1B01G218400	chr5D	86.355	557	64	8	1	552	285021987	285022536	4.310000e-167	597
12	TraesCS1B01G218400	chr5D	86.331	556	62	8	1	552	132930759	132931304	5.570000e-166	593
13	TraesCS1B01G218400	chr5D	85.267	543	68	9	1	539	216052869	216053403	1.220000e-152	549
14	TraesCS1B01G218400	chr5D	87.912	182	21	1	1596	1777	238222522	238222342	1.820000e-51	213
15	TraesCS1B01G218400	chr5D	94.697	132	7	0	2211	2342	238222262	238222131	3.050000e-49	206
16	TraesCS1B01G218400	chr5D	92.908	141	10	0	2202	2342	323869174	323869034	3.050000e-49	206
17	TraesCS1B01G218400	chr2A	85.870	552	64	10	9	552	656830671	656831216	2.020000e-160	575
18	TraesCS1B01G218400	chr2D	85.612	556	68	9	1	552	507862346	507862893	7.260000e-160	573
19	TraesCS1B01G218400	chr2D	84.588	558	74	10	1	553	590277364	590277914	5.690000e-151	544
20	TraesCS1B01G218400	chr2D	88.482	191	21	1	1587	1777	477296086	477295897	1.810000e-56	230
21	TraesCS1B01G218400	chr3A	84.436	559	69	14	1	552	494720756	494721303	3.430000e-148	534
22	TraesCS1B01G218400	chr4D	84.436	559	68	15	1	551	132208404	132207857	1.230000e-147	532
23	TraesCS1B01G218400	chr5A	89.362	188	17	3	1590	1776	412106015	412106200	1.400000e-57	233
24	TraesCS1B01G218400	chr4B	88.172	186	19	3	1591	1775	601096906	601097089	3.920000e-53	219
25	TraesCS1B01G218400	chr4B	87.363	182	22	1	1596	1777	529569803	529569623	8.480000e-50	207
26	TraesCS1B01G218400	chr7A	88.043	184	19	2	1596	1777	24448531	24448349	5.070000e-52	215
27	TraesCS1B01G218400	chr5B	94.853	136	7	0	2207	2342	272432485	272432620	1.820000e-51	213
28	TraesCS1B01G218400	chr7D	93.617	141	9	0	2202	2342	616371495	616371635	6.560000e-51	211
29	TraesCS1B01G218400	chr7D	93.571	140	9	0	2202	2341	53755001	53754862	2.360000e-50	209
30	TraesCS1B01G218400	chr3B	93.617	141	8	1	2202	2342	561043224	561043085	2.360000e-50	209

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	TraesCS1B01G218400	chr1B	395942587	395944928	2341	False	1829.5	3398	100.000	1	2342	2	chr1B.!!$F2	2341
1	TraesCS1B01G218400	chr1D	294200483	294202333	1850	False	1184.5	1650	93.086	1	1582	2	chr1D.!!$F1	1581
2	TraesCS1B01G218400	chr1A	366987961	366988984	1023	False	1450.0	1450	92.420	582	1596	1	chr1A.!!$F1	1014
3	TraesCS1B01G218400	chr5D	285021987	285022536	549	False	597.0	597	86.355	1	552	1	chr5D.!!$F3	551
4	TraesCS1B01G218400	chr5D	132930759	132931304	545	False	593.0	593	86.331	1	552	1	chr5D.!!$F1	551
5	TraesCS1B01G218400	chr5D	216052869	216053403	534	False	549.0	549	85.267	1	539	1	chr5D.!!$F2	538
6	TraesCS1B01G218400	chr2A	656830671	656831216	545	False	575.0	575	85.870	9	552	1	chr2A.!!$F1	543
7	TraesCS1B01G218400	chr2D	507862346	507862893	547	False	573.0	573	85.612	1	552	1	chr2D.!!$F1	551
8	TraesCS1B01G218400	chr2D	590277364	590277914	550	False	544.0	544	84.588	1	553	1	chr2D.!!$F2	552
9	TraesCS1B01G218400	chr3A	494720756	494721303	547	False	534.0	534	84.436	1	552	1	chr3A.!!$F1	551
10	TraesCS1B01G218400	chr4D	132207857	132208404	547	True	532.0	532	84.436	1	551	1	chr4D.!!$R1	550

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
616	903	0.392706	ATGAGACACACAAGCACGGA	59.607	50.0	0.0	0.0	0.0	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2243	2544	0.030101	CGACGAGGAGGATTGAGCTC	59.97	60.0	6.82	6.82	0.0	4.09	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	Self end TH	Hairpin	End Stability
124	126	3.632145	GCCACCATTACAACAAGGGATAG	59.368	47.826	0.00	0.00	0.00	2.08
126	128	4.640201	CCACCATTACAACAAGGGATAGTG	59.360	45.833	0.00	0.00	0.00	2.74
209	212	7.552330	GCAAGGAGAGAAGAGACAGATATTTTT	59.448	37.037	0.00	0.00	0.00	1.94
272	278	2.289631	TGGTGTGCTTCAATCTCGATGT	60.290	45.455	0.00	0.00	0.00	3.06
291	297	2.037511	TGTGGTATCGTTCGAAACCCTT	59.962	45.455	12.96	0.00	0.00	3.95
316	322	2.290367	TGACATGAAGCACTGGAAAACG	59.710	45.455	0.00	0.00	0.00	3.60
320	326	2.360844	TGAAGCACTGGAAAACGTTGA	58.639	42.857	0.00	0.00	0.00	3.18
344	350	4.147321	AGGTGATGACTGCTTGTTTGATT	58.853	39.130	0.00	0.00	0.00	2.57
359	365	9.037737	GCTTGTTTGATTATGCATAACATGATT	57.962	29.630	21.10	4.49	40.06	2.57
404	411	4.287552	ACATCTACGACCTAGGGTTTGAT	58.712	43.478	14.81	7.17	35.25	2.57
405	412	5.452255	ACATCTACGACCTAGGGTTTGATA	58.548	41.667	14.81	0.00	35.25	2.15
406	413	6.075984	ACATCTACGACCTAGGGTTTGATAT	58.924	40.000	14.81	0.00	35.25	1.63
407	414	6.553852	ACATCTACGACCTAGGGTTTGATATT	59.446	38.462	14.81	0.00	35.25	1.28
438	445	4.340381	GGTGAAAATATTGAGCCTGAGCAT	59.660	41.667	0.00	0.00	43.56	3.79
468	478	3.919804	CGGCGACATTTGAACAATTCATT	59.080	39.130	0.00	0.00	39.84	2.57
501	511	6.418141	TCATGAAATGCGTAATTGACATACG	58.582	36.000	0.00	4.58	46.21	3.06
556	566	2.393271	GTGGACTCACATTGGGAGAG	57.607	55.000	22.56	11.43	43.13	3.20
557	567	1.902508	GTGGACTCACATTGGGAGAGA	59.097	52.381	22.56	2.83	43.13	3.10
559	569	2.225369	TGGACTCACATTGGGAGAGAGA	60.225	50.000	22.56	0.74	36.26	3.10
607	894	3.340337	TCGATCATCGATGAGACACAC	57.660	47.619	30.11	16.23	44.82	3.82
616	903	0.392706	ATGAGACACACAAGCACGGA	59.607	50.000	0.00	0.00	0.00	4.69
881	1176	7.103641	TGAGTATAGCCGAAGAACAAAATTCT	58.896	34.615	0.00	0.00	0.00	2.40
883	1178	3.923017	AGCCGAAGAACAAAATTCTGG	57.077	42.857	0.00	0.00	0.00	3.86
901	1196	8.485578	AATTCTGGTTTAAATACTTTGGTCCA	57.514	30.769	0.00	0.00	0.00	4.02
1368	1664	3.762407	TGAGAAGGATCGGTTGTTTCA	57.238	42.857	0.00	0.00	0.00	2.69

Showing 1 to 25 of 290 entries

Previous1 2 3 4 5…12Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	6.149973	CACATTGATACATTGTGAGAACCAGT	59.850	38.462	16.54	0.00	43.83	4.00
124	126	4.142049	GGATAGATACCATCAGCTAGGCAC	60.142	50.000	0.00	0.00	0.00	5.01
126	128	4.099266	CAGGATAGATACCATCAGCTAGGC	59.901	50.000	0.00	0.00	0.00	3.93
168	170	4.346709	TCTCCTTGCGGATTGGATATTGTA	59.653	41.667	0.07	0.00	39.01	2.41
209	212	4.223032	CCTAGCACTTTCTTACTCTTGGGA	59.777	45.833	0.00	0.00	0.00	4.37
272	278	2.299582	TGAAGGGTTTCGAACGATACCA	59.700	45.455	27.46	12.34	44.46	3.25
291	297	3.421919	TCCAGTGCTTCATGTCAATGA	57.578	42.857	11.94	0.00	41.16	2.57
316	322	4.256920	ACAAGCAGTCATCACCTATCAAC	58.743	43.478	0.00	0.00	0.00	3.18
320	326	4.910195	TCAAACAAGCAGTCATCACCTAT	58.090	39.130	0.00	0.00	0.00	2.57
344	350	5.939447	TCCTCCACAATCATGTTATGCATA	58.061	37.500	1.16	1.16	37.82	3.14
359	365	2.265739	GCACGCTCATCCTCCACA	59.734	61.111	0.00	0.00	0.00	4.17
438	445	0.801872	CAAATGTCGCCGGTTCATGA	59.198	50.000	1.90	0.00	0.00	3.07
441	451	0.589223	GTTCAAATGTCGCCGGTTCA	59.411	50.000	1.90	0.00	0.00	3.18
501	511	3.304525	GGTCATCTTGAAGCTGCATATGC	60.305	47.826	21.09	21.09	42.50	3.14
552	562	2.952310	GCTTTCCTCCTCTCTCTCTCTC	59.048	54.545	0.00	0.00	0.00	3.20
554	564	2.689983	CAGCTTTCCTCCTCTCTCTCTC	59.310	54.545	0.00	0.00	0.00	3.20
555	565	2.624029	CCAGCTTTCCTCCTCTCTCTCT	60.624	54.545	0.00	0.00	0.00	3.10
556	566	1.756538	CCAGCTTTCCTCCTCTCTCTC	59.243	57.143	0.00	0.00	0.00	3.20
557	567	1.360852	TCCAGCTTTCCTCCTCTCTCT	59.639	52.381	0.00	0.00	0.00	3.10
559	569	2.187100	CTTCCAGCTTTCCTCCTCTCT	58.813	52.381	0.00	0.00	0.00	3.10
595	882	0.436150	CGTGCTTGTGTGTCTCATCG	59.564	55.000	0.00	0.00	0.00	3.84
607	894	1.275291	TCTAGAAGGGTTCCGTGCTTG	59.725	52.381	0.00	0.00	0.00	4.01
881	1176	6.041069	CCAGTTGGACCAAAGTATTTAAACCA	59.959	38.462	8.94	0.00	34.55	3.67
883	1178	7.013942	AGACCAGTTGGACCAAAGTATTTAAAC	59.986	37.037	8.94	0.00	35.81	2.01
1456	1752	1.093159	CTGGGCAGAAATCTCAGCAC	58.907	55.000	0.00	0.00	37.97	4.40

Showing 1 to 25 of 263 entries

Previous1 2 3 4 5…11Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.