AutoCloner

Multiple sequence alignment - TraesCS1A01G305800

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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	TraesCS1A01G305800	chr1A	100.000	5873	0	0	1	5873	498162906	498168778	0.000000e+00	10846.0
1	TraesCS1A01G305800	chr1A	91.463	82	5	1	4384	4463	311077264	311077345	1.730000e-20	111.0
2	TraesCS1A01G305800	chr1B	94.687	4028	133	29	1	3977	540999537	541003534	0.000000e+00	6178.0
3	TraesCS1A01G305800	chr1B	93.790	1417	76	8	4458	5867	541003829	541005240	0.000000e+00	2119.0
4	TraesCS1A01G305800	chr1B	91.722	302	21	3	4080	4381	541003531	541003828	3.270000e-112	416.0
5	TraesCS1A01G305800	chr1B	90.361	83	4	3	4384	4464	392878983	392878903	8.050000e-19	106.0
6	TraesCS1A01G305800	chr1D	95.560	1847	51	9	2158	3977	403050401	403052243	0.000000e+00	2928.0
7	TraesCS1A01G305800	chr1D	90.087	2189	96	40	1	2149	403048244	403050351	0.000000e+00	2728.0
8	TraesCS1A01G305800	chr1D	93.404	1410	62	12	4458	5864	403052541	403053922	0.000000e+00	2060.0
9	TraesCS1A01G305800	chr1D	95.349	301	13	1	4080	4380	403052240	403052539	1.480000e-130	477.0
10	TraesCS1A01G305800	chr1D	95.370	108	5	0	3976	4083	465596804	465596911	7.820000e-39	172.0
11	TraesCS1A01G305800	chr1D	96.491	57	2	0	2208	2264	403050347	403050403	1.740000e-15	95.3
12	TraesCS1A01G305800	chr3D	80.101	397	70	6	3236	3624	443710792	443710397	2.680000e-73	287.0
13	TraesCS1A01G305800	chr3D	73.498	649	139	22	2334	2961	443711482	443710846	1.280000e-51	215.0
14	TraesCS1A01G305800	chr3D	92.982	114	8	0	3970	4083	388791373	388791486	3.640000e-37	167.0
15	TraesCS1A01G305800	chr3D	93.590	78	3	1	4384	4459	105151047	105151124	1.340000e-21	115.0
16	TraesCS1A01G305800	chr3D	92.308	78	4	1	4384	4459	105182932	105183009	6.220000e-20	110.0
17	TraesCS1A01G305800	chr3D	91.667	84	0	2	4384	4460	563133639	563133556	6.220000e-20	110.0
18	TraesCS1A01G305800	chr3B	79.899	398	69	7	3236	3624	581705672	581705277	1.250000e-71	281.0
19	TraesCS1A01G305800	chr3B	90.984	122	9	2	3971	4090	753999902	753999781	4.710000e-36	163.0
20	TraesCS1A01G305800	chr3B	93.750	80	2	2	4384	4460	828548736	828548657	3.720000e-22	117.0
21	TraesCS1A01G305800	chr3B	91.463	82	4	2	4384	4462	169261818	169261737	6.220000e-20	110.0
22	TraesCS1A01G305800	chr3A	84.729	203	31	0	3236	3438	584934343	584934141	2.770000e-48	204.0
23	TraesCS1A01G305800	chr3A	73.118	651	138	24	2334	2961	584935033	584934397	1.290000e-46	198.0
24	TraesCS1A01G305800	chr6B	95.690	116	5	0	3968	4083	506127975	506128090	2.790000e-43	187.0
25	TraesCS1A01G305800	chr6B	93.694	111	7	0	3973	4083	204159134	204159244	3.640000e-37	167.0
26	TraesCS1A01G305800	chr2A	96.296	108	4	0	3976	4083	449280138	449280031	1.680000e-40	178.0
27	TraesCS1A01G305800	chr6D	93.966	116	7	0	3968	4083	318149932	318149817	6.050000e-40	176.0
28	TraesCS1A01G305800	chr7D	95.413	109	4	1	3975	4083	60693372	60693479	7.820000e-39	172.0
29	TraesCS1A01G305800	chrUn	93.750	112	7	0	3976	4087	94181871	94181982	1.010000e-37	169.0
30	TraesCS1A01G305800	chr4D	91.667	84	2	2	4384	4462	134142504	134142421	1.730000e-20	111.0
31	TraesCS1A01G305800	chr5D	84.762	105	8	3	4367	4463	509559194	509559298	1.350000e-16	99.0
32	TraesCS1A01G305800	chr5A	89.831	59	6	0	5813	5871	660403916	660403974	6.310000e-10	76.8

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	TraesCS1A01G305800	chr1A	498162906	498168778	5872	False	10846.000000	10846	100.000000	1	5873	1	chr1A.!!$F2	5872
1	TraesCS1A01G305800	chr1B	540999537	541005240	5703	False	2904.333333	6178	93.399667	1	5867	3	chr1B.!!$F1	5866
2	TraesCS1A01G305800	chr1D	403048244	403053922	5678	False	1657.660000	2928	94.178200	1	5864	5	chr1D.!!$F2	5863
3	TraesCS1A01G305800	chr3D	443710397	443711482	1085	True	251.000000	287	76.799500	2334	3624	2	chr3D.!!$R2	1290
4	TraesCS1A01G305800	chr3A	584934141	584935033	892	True	201.000000	204	78.923500	2334	3438	2	chr3A.!!$R1	1104

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
553	562	0.615331	TGTCTCCTGTTCATCCCTGC	59.385	55.000	0.00	0.00	0.00	4.85	F
827	854	0.961019	TTTCTGGGACAAGTGCATGC	59.039	50.000	11.82	11.82	38.70	4.06	F
1198	1230	1.077625	AGACCGTCCAAGCTCCTCT	59.922	57.895	0.00	0.00	0.00	3.69	F
1628	1681	0.316204	GCACTTTGCTGCACTGGATT	59.684	50.000	0.00	0.00	40.96	3.01	F
2073	2126	1.098712	AGACTTGCGGTGCCGAAAAA	61.099	50.000	15.45	4.46	42.83	1.94	F
2802	2911	1.821753	TCTGCTTCTGCCTCTAGTGAC	59.178	52.381	0.00	0.00	38.71	3.67	F
3696	3841	3.412237	TTTCCCCAACGAGGAACTAAG	57.588	47.619	0.00	0.00	43.08	2.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1538	1591	1.203441	TGGAGGAGCTTGGTGCAGAT	61.203	55.000	0.00	0.0	45.94	2.90	R
1628	1681	1.630369	ACCAGCAGCATCCAAAGAGTA	59.370	47.619	0.00	0.0	0.00	2.59	R
2577	2686	4.061596	GCATGTAAGGCTTCCTGATAGAC	58.938	47.826	1.30	0.0	42.67	2.59	R
3225	3362	6.064060	TGATATACATCCCTGAAGCCAAAAG	58.936	40.000	0.00	0.0	0.00	2.27	R
4019	4164	0.176680	ATGAGCTACTTCGCACCCTG	59.823	55.000	0.00	0.0	0.00	4.45	R
4020	4165	0.905357	AATGAGCTACTTCGCACCCT	59.095	50.000	0.00	0.0	0.00	4.34	R
4909	5054	0.108585	AGCCGCAGAAAGTTTCCTCA	59.891	50.000	12.05	0.0	0.00	3.86	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
70	72	1.180029	TTTTCTCGGGTAGGAGGACG	58.820	55.000	0.00	0.00	34.74	4.79
72	74	3.217743	CTCGGGTAGGAGGACGGC	61.218	72.222	0.00	0.00	0.00	5.68
198	207	4.436998	GTGCCCTCCTCGACCGTG	62.437	72.222	0.00	0.00	0.00	4.94
248	257	1.935327	CTTCCAGGGGTCGTCGTCTC	61.935	65.000	0.00	0.00	0.00	3.36
249	258	3.450115	CCAGGGGTCGTCGTCTCC	61.450	72.222	0.00	0.00	0.00	3.71
250	259	3.812019	CAGGGGTCGTCGTCTCCG	61.812	72.222	2.62	0.00	0.00	4.63
277	286	3.775654	CGCCGCTCCTCTTCCCTT	61.776	66.667	0.00	0.00	0.00	3.95
279	288	2.904131	CCGCTCCTCTTCCCTTCC	59.096	66.667	0.00	0.00	0.00	3.46
280	289	2.736826	CCGCTCCTCTTCCCTTCCC	61.737	68.421	0.00	0.00	0.00	3.97
281	290	2.736826	CGCTCCTCTTCCCTTCCCC	61.737	68.421	0.00	0.00	0.00	4.81
325	334	2.045634	GGCCTTCCCGGTGGTTAC	60.046	66.667	0.00	0.00	34.25	2.50
342	351	4.452733	CGGGGAGGAGTCGTTGGC	62.453	72.222	0.00	0.00	0.00	4.52
404	413	2.448736	GGTGGGGGAGGAGGGATC	60.449	72.222	0.00	0.00	0.00	3.36
405	414	2.844839	GTGGGGGAGGAGGGATCG	60.845	72.222	0.00	0.00	0.00	3.69
454	463	4.133796	GGCCGGATTTGCTGGTGC	62.134	66.667	5.05	0.00	45.49	5.01
535	544	3.951306	TGTTTCATTTCGTGCTGTTCTG	58.049	40.909	0.00	0.00	0.00	3.02
553	562	0.615331	TGTCTCCTGTTCATCCCTGC	59.385	55.000	0.00	0.00	0.00	4.85
616	627	3.551046	CCGTGTGTCAGATACAGATAGGC	60.551	52.174	0.00	0.00	39.29	3.93
619	630	3.638627	TGTGTCAGATACAGATAGGCAGG	59.361	47.826	0.00	0.00	39.29	4.85
628	639	3.878778	ACAGATAGGCAGGCTACTTTTG	58.121	45.455	5.70	5.28	0.00	2.44
635	646	2.514803	GCAGGCTACTTTTGGGAAAGA	58.485	47.619	5.95	0.00	44.03	2.52
638	649	2.108250	AGGCTACTTTTGGGAAAGAGCA	59.892	45.455	17.02	0.00	44.03	4.26
640	651	3.129462	GGCTACTTTTGGGAAAGAGCATC	59.871	47.826	17.02	5.55	44.03	3.91
717	728	3.209410	GGGCCATACATCAGTTCTTCAG	58.791	50.000	4.39	0.00	0.00	3.02
718	729	3.209410	GGCCATACATCAGTTCTTCAGG	58.791	50.000	0.00	0.00	0.00	3.86

Showing 1 to 25 of 252 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
281	290	2.717139	GAAAGGCGAGGCGGATAGGG	62.717	65.000	0.00	0.00	0.00	3.53
325	334	4.452733	GCCAACGACTCCTCCCCG	62.453	72.222	0.00	0.00	0.00	5.73
348	357	4.166144	TCCTCCTAAATTAGCCAAGAAGGG	59.834	45.833	0.00	0.00	38.09	3.95
358	367	2.373502	CAGGGCCCTCCTCCTAAATTAG	59.626	54.545	25.77	0.95	46.12	1.73
404	413	3.827898	GGGAGAGCCGTGGACTCG	61.828	72.222	0.00	0.00	39.23	4.18
405	414	3.827898	CGGGAGAGCCGTGGACTC	61.828	72.222	0.00	0.00	33.83	3.36
459	468	1.425428	CCGAATCGGCAGCAGTTTC	59.575	57.895	9.39	6.34	41.17	2.78
535	544	0.107459	GGCAGGGATGAACAGGAGAC	60.107	60.000	0.00	0.00	0.00	3.36
553	562	1.662629	CATTACAGCTCGCAACAGAGG	59.337	52.381	0.00	0.00	38.63	3.69
616	627	2.489722	GCTCTTTCCCAAAAGTAGCCTG	59.510	50.000	9.34	0.00	42.17	4.85
619	630	3.129462	GGATGCTCTTTCCCAAAAGTAGC	59.871	47.826	11.80	11.80	42.17	3.58
628	639	1.407989	CCACAGAGGATGCTCTTTCCC	60.408	57.143	14.94	0.00	41.22	3.97
640	651	3.001514	CCCCCACATCCACAGAGG	58.998	66.667	0.00	0.00	39.47	3.69
666	677	8.792633	CCAGAATAAACAGAAACCTTTCACATA	58.207	33.333	0.78	0.00	39.61	2.29
677	688	3.258123	GCCCAAGCCAGAATAAACAGAAA	59.742	43.478	0.00	0.00	0.00	2.52
704	715	5.184864	ACACTCTAGACCTGAAGAACTGATG	59.815	44.000	0.00	0.00	0.00	3.07
708	719	3.829601	CCACACTCTAGACCTGAAGAACT	59.170	47.826	0.00	0.00	0.00	3.01
717	728	2.838202	TCAAATCCCCACACTCTAGACC	59.162	50.000	0.00	0.00	0.00	3.85
718	729	4.553330	TTCAAATCCCCACACTCTAGAC	57.447	45.455	0.00	0.00	0.00	2.59
724	735	4.653341	TGTTCAAATTCAAATCCCCACACT	59.347	37.500	0.00	0.00	0.00	3.55
725	736	4.954875	TGTTCAAATTCAAATCCCCACAC	58.045	39.130	0.00	0.00	0.00	3.82
726	737	5.104776	TGTTGTTCAAATTCAAATCCCCACA	60.105	36.000	0.00	0.00	0.00	4.17
728	739	5.620738	TGTTGTTCAAATTCAAATCCCCA	57.379	34.783	0.00	0.00	0.00	4.96
798	819	6.223120	CACTTGTCCCAGAAAATAAAAAGGG	58.777	40.000	0.00	0.00	37.65	3.95
806	829	2.028748	GCATGCACTTGTCCCAGAAAAT	60.029	45.455	14.21	0.00	0.00	1.82

Showing 1 to 25 of 231 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.