AutoCloner

Multiple sequence alignment - TraesCS2B01G551200

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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	TraesCS2B01G551200	chr2B	100.000	3377	0	0	1	3377	747182881	747179505	0.000000e+00	6237.0
1	TraesCS2B01G551200	chr2B	92.857	42	2	1	354	394	797881546	797881587	3.640000e-05	60.2
2	TraesCS2B01G551200	chr2A	94.282	3410	147	22	1	3377	744451077	744447683	0.000000e+00	5173.0
3	TraesCS2B01G551200	chr2A	84.158	303	34	10	7	298	127727862	127727563	7.130000e-72	281.0
4	TraesCS2B01G551200	chr2D	94.868	3098	126	20	307	3375	612345823	612342730	0.000000e+00	4809.0
5	TraesCS2B01G551200	chr5B	89.783	460	46	1	1667	2125	382333070	382332611	3.750000e-164	588.0
6	TraesCS2B01G551200	chr7D	82.933	375	38	9	2250	2620	618084818	618084466	7.030000e-82	315.0
7	TraesCS2B01G551200	chr7D	89.412	85	5	2	2527	2611	618084093	618084013	1.660000e-18	104.0
8	TraesCS2B01G551200	chr6D	84.718	301	33	10	8	298	452576425	452576722	4.260000e-74	289.0
9	TraesCS2B01G551200	chr7A	84.211	304	33	12	7	299	207923178	207923477	7.130000e-72	281.0
10	TraesCS2B01G551200	chr7A	83.946	299	39	7	8	298	426642056	426641759	9.230000e-71	278.0
11	TraesCS2B01G551200	chr7A	84.175	297	33	10	7	292	491512328	491512621	3.320000e-70	276.0
12	TraesCS2B01G551200	chr7A	83.882	304	34	12	7	298	567641638	567641938	3.320000e-70	276.0
13	TraesCS2B01G551200	chr7A	80.769	312	26	18	2320	2627	711814462	711814181	2.640000e-51	213.0
14	TraesCS2B01G551200	chr7A	89.655	87	5	2	2525	2611	711813879	711813797	1.280000e-19	108.0
15	TraesCS2B01G551200	chr4A	84.211	304	32	13	7	298	43384924	43385223	7.130000e-72	281.0
16	TraesCS2B01G551200	chr4A	83.882	304	35	11	7	299	333911572	333911272	9.230000e-71	278.0
17	TraesCS2B01G551200	chr3A	75.101	494	79	29	1906	2371	587878227	587878704	1.240000e-44	191.0
18	TraesCS2B01G551200	chr3A	90.909	55	4	1	355	408	601346528	601346474	4.670000e-09	73.1
19	TraesCS2B01G551200	chr3D	86.452	155	15	5	1902	2052	446064953	446065105	7.500000e-37	165.0
20	TraesCS2B01G551200	chr6A	90.909	55	4	1	355	408	90753588	90753534	4.670000e-09	73.1
21	TraesCS2B01G551200	chr5A	90.909	55	4	1	355	408	169999764	169999818	4.670000e-09	73.1
22	TraesCS2B01G551200	chr1A	90.909	55	4	1	355	408	450226699	450226753	4.670000e-09	73.1
23	TraesCS2B01G551200	chr6B	87.273	55	6	1	355	408	36222126	36222072	1.010000e-05	62.1

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	TraesCS2B01G551200	chr2B	747179505	747182881	3376	True	6237.0	6237	100.0000	1	3377	1	chr2B.!!$R1	3376
1	TraesCS2B01G551200	chr2A	744447683	744451077	3394	True	5173.0	5173	94.2820	1	3377	1	chr2A.!!$R2	3376
2	TraesCS2B01G551200	chr2D	612342730	612345823	3093	True	4809.0	4809	94.8680	307	3375	1	chr2D.!!$R1	3068
3	TraesCS2B01G551200	chr7D	618084013	618084818	805	True	209.5	315	86.1725	2250	2620	2	chr7D.!!$R1	370

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
701	715	0.321564	TCAACATCTGGCCAGTTCCG	60.322	55.0	31.58	19.68	0.00	4.30	F
1204	1222	2.209064	GAGCAAGTACGCGACCCTGA	62.209	60.0	15.93	0.00	36.85	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2310	1.783031	CGTCGGGGTCGTCCTCATAG	61.783	65.0	0.0	0.0	37.69	2.23	R
3069	3157	1.043816	CGGGAGCTATGATGGTGTCT	58.956	55.0	0.0	0.0	0.00	3.41	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
30	31	3.639561	GGCCTCCTTTGGTTTGTAGAAAA	59.360	43.478	0.00	0.00	0.00	2.29
170	175	3.906720	AAATTAGCCTAGCCTCAACGA	57.093	42.857	0.00	0.00	0.00	3.85
188	193	9.612620	CCTCAACGAAAATAATTTATCCTATGC	57.387	33.333	0.00	0.00	0.00	3.14
209	214	3.814283	GCATCAAATGACATCTCTCTCCC	59.186	47.826	0.00	0.00	0.00	4.30
211	216	2.432146	TCAAATGACATCTCTCTCCCCG	59.568	50.000	0.00	0.00	0.00	5.73
248	253	7.436673	GGTACATGTCATCTCACTTTCTATGAC	59.563	40.741	0.00	7.23	45.40	3.06
300	305	7.860872	CCTATTAACCAAACGAAGCCATAATTC	59.139	37.037	0.00	0.00	0.00	2.17
305	310	4.396166	CCAAACGAAGCCATAATTCTGAGT	59.604	41.667	0.00	0.00	0.00	3.41
324	329	9.793259	TTCTGAGTCTAACCTTGACATAAAAAT	57.207	29.630	0.00	0.00	36.94	1.82
445	458	4.699522	GGCGGCTCGGTTTGTCCT	62.700	66.667	0.00	0.00	0.00	3.85
446	459	2.668550	GCGGCTCGGTTTGTCCTT	60.669	61.111	0.00	0.00	0.00	3.36
483	496	9.361315	CAATCATTTCAAATTTGCTCATCACTA	57.639	29.630	13.54	0.00	0.00	2.74
510	523	7.095816	GCCTAAAATTAACACCACATTTGTGTC	60.096	37.037	9.66	0.00	45.78	3.67
543	556	2.599645	CTAGCCCGCTCCAGTTGCAT	62.600	60.000	0.00	0.00	0.00	3.96
558	571	4.813161	CAGTTGCATCCCTAACTCATACAG	59.187	45.833	0.00	0.00	35.08	2.74
563	576	4.572389	GCATCCCTAACTCATACAGTGTTG	59.428	45.833	0.00	0.00	34.56	3.33
609	623	4.127171	TCGAAAGGACCAAGACTGAAAAG	58.873	43.478	0.00	0.00	0.00	2.27
701	715	0.321564	TCAACATCTGGCCAGTTCCG	60.322	55.000	31.58	19.68	0.00	4.30
843	857	3.146847	AGGAAACTGTTGGATCCGTTTC	58.853	45.455	24.04	24.04	42.57	2.78
1204	1222	2.209064	GAGCAAGTACGCGACCCTGA	62.209	60.000	15.93	0.00	36.85	3.86
1622	1640	2.644992	GCAACAGGCAAAGGTCGG	59.355	61.111	0.00	0.00	43.97	4.79
2286	2310	0.723981	GCTGCAAGATCTTCGTCCAC	59.276	55.000	4.57	0.00	34.07	4.02
2289	2313	3.739519	GCTGCAAGATCTTCGTCCACTAT	60.740	47.826	4.57	0.00	34.07	2.12
2300	2324	0.745468	GTCCACTATGAGGACGACCC	59.255	60.000	0.00	0.00	45.35	4.46
2385	2409	1.983196	GCTGCTGCTGATGCTCTGTG	61.983	60.000	10.92	0.00	40.48	3.66
2397	2422	3.955771	TGCTCTGTGTTTTTCGTTACC	57.044	42.857	0.00	0.00	0.00	2.85
2449	2478	7.486802	TGTTTAGTTGCTTCTACTTTGTACC	57.513	36.000	0.00	0.00	0.00	3.34
2494	2523	7.726033	AGAATTCTACTATATCCGGCAAGAT	57.274	36.000	6.06	0.00	0.00	2.40
2511	2540	4.475944	CAAGATGTTTTGCTTAGGTTCCG	58.524	43.478	0.00	0.00	0.00	4.30
2522	2558	8.795842	TTTGCTTAGGTTCCGAATAATTTCTA	57.204	30.769	0.00	0.00	0.00	2.10
2550	2587	7.713750	TCCCTAATAAGTTCTGTTGTAGATCG	58.286	38.462	0.00	0.00	34.80	3.69
2586	2627	7.581213	TTTTGTTGGTGAAGAGTGAATACAT	57.419	32.000	0.00	0.00	0.00	2.29
2587	2628	8.684386	TTTTGTTGGTGAAGAGTGAATACATA	57.316	30.769	0.00	0.00	0.00	2.29
2588	2629	7.667043	TTGTTGGTGAAGAGTGAATACATAC	57.333	36.000	0.00	0.00	0.00	2.39
2589	2630	6.764379	TGTTGGTGAAGAGTGAATACATACA	58.236	36.000	0.00	0.00	0.00	2.29
2590	2631	7.394016	TGTTGGTGAAGAGTGAATACATACAT	58.606	34.615	0.00	0.00	0.00	2.29
2735	2823	5.455525	GCGTCAACACTAAAATGGATAATGC	59.544	40.000	0.00	0.00	0.00	3.56
2807	2895	2.880890	ACCTTGACTGAATTCTGCACAC	59.119	45.455	11.86	3.22	0.00	3.82
2872	2960	6.737254	TTTTTCTAGCTACCACAATACTGC	57.263	37.500	0.00	0.00	0.00	4.40
3003	3091	2.067766	TCGAACGGGGTGTTTATTTCG	58.932	47.619	0.00	0.00	42.09	3.46
3132	3220	3.374058	CGATGGTGTTCATAACCTTGACC	59.626	47.826	0.00	0.00	38.60	4.02
3150	3238	2.281484	GCTGTTCTTCCGGTGGCA	60.281	61.111	0.00	0.00	0.00	4.92
3210	3298	1.550072	TCGTCCACTGATCTGATTGCA	59.450	47.619	6.60	0.00	0.00	4.08
3345	3433	3.118775	ACAATGCGTCCTTGCTCAGTATA	60.119	43.478	0.00	0.00	35.36	1.47

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	2.378547	ACAAACCAAAGGAGGCCTATGA	59.621	45.455	4.42	0.00	31.13	2.15
59	60	5.532032	CCAAAGGCACCAAATGATTTTTCTT	59.468	36.000	0.00	0.00	0.00	2.52
60	61	5.065235	CCAAAGGCACCAAATGATTTTTCT	58.935	37.500	0.00	0.00	0.00	2.52
61	62	4.821260	ACCAAAGGCACCAAATGATTTTTC	59.179	37.500	0.00	0.00	0.00	2.29
151	156	3.906720	TTCGTTGAGGCTAGGCTAATT	57.093	42.857	20.27	0.00	0.00	1.40
156	161	5.500645	AATTATTTTCGTTGAGGCTAGGC	57.499	39.130	8.55	8.55	0.00	3.93
188	193	4.387598	GGGGAGAGAGATGTCATTTGATG	58.612	47.826	0.00	0.00	0.00	3.07
209	214	4.142026	TGACATGTACCTTTGATCCTACGG	60.142	45.833	0.00	0.00	0.00	4.02
211	216	6.821388	AGATGACATGTACCTTTGATCCTAC	58.179	40.000	0.00	0.00	0.00	3.18
217	222	5.745312	AGTGAGATGACATGTACCTTTGA	57.255	39.130	0.00	0.00	0.00	2.69
270	275	6.053005	TGGCTTCGTTTGGTTAATAGGATAG	58.947	40.000	0.00	0.00	0.00	2.08
287	292	5.463724	GGTTAGACTCAGAATTATGGCTTCG	59.536	44.000	0.00	0.00	0.00	3.79
300	305	9.831737	CAATTTTTATGTCAAGGTTAGACTCAG	57.168	33.333	0.00	0.00	36.94	3.35
324	329	9.337396	AGATCCAACGCATAATTTATTAGTCAA	57.663	29.630	0.00	0.00	0.00	3.18
341	346	8.299262	ACGATATATTTTTCTGAGATCCAACG	57.701	34.615	0.00	0.00	0.00	4.10
431	444	0.536460	TTGGAAGGACAAACCGAGCC	60.536	55.000	0.00	0.00	44.74	4.70
483	496	6.928492	CACAAATGTGGTGTTAATTTTAGGCT	59.072	34.615	5.63	0.00	42.10	4.58
509	522	2.484770	GGGCTAGCGGACAATAACATGA	60.485	50.000	9.00	0.00	0.00	3.07
510	523	1.873591	GGGCTAGCGGACAATAACATG	59.126	52.381	9.00	0.00	0.00	3.21
536	549	4.471386	ACTGTATGAGTTAGGGATGCAACT	59.529	41.667	0.00	0.00	37.69	3.16
537	550	4.572389	CACTGTATGAGTTAGGGATGCAAC	59.428	45.833	0.00	0.00	29.75	4.17
543	556	5.818678	AACAACACTGTATGAGTTAGGGA	57.181	39.130	0.41	0.00	33.45	4.20
661	675	8.902806	TGTTGATTGACAAATTTAAGAGACTGT	58.097	29.630	0.00	0.00	40.36	3.55
715	729	2.417239	TGGCCGCGTTTGACTTTAATAG	59.583	45.455	4.92	0.00	0.00	1.73
716	730	2.424557	TGGCCGCGTTTGACTTTAATA	58.575	42.857	4.92	0.00	0.00	0.98
717	731	1.240256	TGGCCGCGTTTGACTTTAAT	58.760	45.000	4.92	0.00	0.00	1.40
719	733	1.198178	GAATGGCCGCGTTTGACTTTA	59.802	47.619	4.92	0.00	0.00	1.85
843	857	1.823899	GATGCGGCTTTGTAGGGGG	60.824	63.158	0.00	0.00	0.00	5.40
1176	1194	2.150837	GTACTTGCTCGACGACGCC	61.151	63.158	14.03	0.00	39.58	5.68
1204	1222	0.395862	ACCATGATCTCCTCGACCGT	60.396	55.000	0.00	0.00	0.00	4.83
1371	1389	3.882326	CCGGCCATGAGCTCCCAT	61.882	66.667	12.15	0.00	43.05	4.00
1709	1727	2.368875	TCCTTCTTTTCCTTCTGCGACT	59.631	45.455	0.00	0.00	0.00	4.18
1722	1740	3.998672	TCGGCGCCGTCCTTCTTT	61.999	61.111	44.16	0.00	40.74	2.52
1821	1839	4.216257	CGCTCTTGGATCTTTTCTTGGAAA	59.784	41.667	0.00	0.00	0.00	3.13
2229	2253	4.353437	GGCACGAACCGGACGTCT	62.353	66.667	22.97	0.00	42.07	4.18
2286	2310	1.783031	CGTCGGGGTCGTCCTCATAG	61.783	65.000	0.00	0.00	37.69	2.23
2289	2313	4.334118	TCGTCGGGGTCGTCCTCA	62.334	66.667	0.00	0.00	37.69	3.86
2449	2478	4.686091	TCTTCTGTAAATGCTCTTCACACG	59.314	41.667	0.00	0.00	0.00	4.49
2494	2523	6.827586	ATTATTCGGAACCTAAGCAAAACA	57.172	33.333	0.00	0.00	0.00	2.83
2507	2536	7.679732	TTAGGGAGGTAGAAATTATTCGGAA	57.320	36.000	0.00	0.00	40.63	4.30
2522	2558	6.958192	TCTACAACAGAACTTATTAGGGAGGT	59.042	38.462	0.00	0.00	0.00	3.85
2550	2587	5.841810	TCACCAACAAAATTTGACCTCATC	58.158	37.500	13.19	0.00	0.00	2.92
2587	2628	9.726438	GGCTGAGTACTAAATTTATATGGATGT	57.274	33.333	0.00	0.00	0.00	3.06
2588	2629	9.950496	AGGCTGAGTACTAAATTTATATGGATG	57.050	33.333	0.00	0.00	0.00	3.51
2589	2630	9.950496	CAGGCTGAGTACTAAATTTATATGGAT	57.050	33.333	9.42	0.00	0.00	3.41
2590	2631	8.934697	ACAGGCTGAGTACTAAATTTATATGGA	58.065	33.333	23.66	0.00	0.00	3.41
2735	2823	8.689251	TTCTGATACTCTTGTTTATTCGAGTG	57.311	34.615	0.00	0.00	37.32	3.51
2766	2854	1.545582	TGATCGTGCAGTCATGTCTCA	59.454	47.619	0.00	0.00	0.00	3.27
2917	3005	4.165372	ACCAGGGTTGAACTTAAAGAGTCA	59.835	41.667	0.00	0.00	37.72	3.41
3003	3091	1.398390	CACGGCAGGCAGAATTAAGTC	59.602	52.381	0.00	0.00	0.00	3.01
3069	3157	1.043816	CGGGAGCTATGATGGTGTCT	58.956	55.000	0.00	0.00	0.00	3.41
3132	3220	3.423154	GCCACCGGAAGAACAGCG	61.423	66.667	9.46	0.00	0.00	5.18
3150	3238	3.222354	GACCAAGACCGTCGCCACT	62.222	63.158	0.00	0.00	0.00	4.00
3210	3298	0.179045	GAGTCAGTGCTGGTGTTGGT	60.179	55.000	0.00	0.00	0.00	3.67
3345	3433	3.959495	ACAATGCTGTCAAGGGGATAT	57.041	42.857	0.00	0.00	0.00	1.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.