AutoCloner

Multiple sequence alignment - TraesCS2A01G428100

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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	TraesCS2A01G428100	chr2A	100.000	6263	0	0	1	6263	680514381	680520643	0.000000e+00	11566.0
1	TraesCS2A01G428100	chr2A	84.528	1060	109	32	3433	4469	680543601	680544628	0.000000e+00	998.0
2	TraesCS2A01G428100	chr2A	87.818	747	80	7	2535	3277	680542470	680543209	0.000000e+00	865.0
3	TraesCS2A01G428100	chr2A	88.310	710	76	4	4588	5292	680544639	680545346	0.000000e+00	845.0
4	TraesCS2A01G428100	chr2A	85.008	647	91	2	1815	2461	680541831	680542471	0.000000e+00	652.0
5	TraesCS2A01G428100	chr2A	86.192	478	42	14	950	1426	680541046	680541500	4.360000e-136	496.0
6	TraesCS2A01G428100	chr2A	82.437	279	47	1	5985	6263	719552163	719551887	6.270000e-60	243.0
7	TraesCS2A01G428100	chr2A	100.000	32	0	0	5496	5527	680545691	680545722	6.780000e-05	60.2
8	TraesCS2A01G428100	chr2A	94.595	37	1	1	3400	3436	680543467	680543502	8.770000e-04	56.5
9	TraesCS2A01G428100	chr2B	95.782	4694	161	15	821	5492	641169899	641174577	0.000000e+00	7537.0
10	TraesCS2A01G428100	chr2B	85.978	920	90	20	4206	5113	641190220	641191112	0.000000e+00	948.0
11	TraesCS2A01G428100	chr2B	84.690	934	103	19	2535	3436	641188458	641189383	0.000000e+00	896.0
12	TraesCS2A01G428100	chr2B	87.240	721	76	12	3433	4144	641189482	641190195	0.000000e+00	808.0
13	TraesCS2A01G428100	chr2B	92.585	499	23	5	5495	5991	641174729	641175215	0.000000e+00	704.0
14	TraesCS2A01G428100	chr2B	87.755	441	43	3	987	1426	641187076	641187506	7.250000e-139	505.0
15	TraesCS2A01G428100	chr2B	100.000	32	0	0	5496	5527	641191673	641191704	6.780000e-05	60.2
16	TraesCS2A01G428100	chr2D	95.662	4680	142	19	847	5492	538308409	538313061	0.000000e+00	7461.0
17	TraesCS2A01G428100	chr2D	87.533	1885	165	40	3433	5294	538319518	538321355	0.000000e+00	2115.0
18	TraesCS2A01G428100	chr2D	84.906	1060	107	31	3433	4469	538592129	538593158	0.000000e+00	1022.0
19	TraesCS2A01G428100	chr2D	84.764	932	106	14	2535	3436	538591105	538592030	0.000000e+00	902.0
20	TraesCS2A01G428100	chr2D	88.169	710	77	4	4588	5292	538593169	538593876	0.000000e+00	839.0
21	TraesCS2A01G428100	chr2D	85.369	827	83	16	2644	3436	538318597	538319419	0.000000e+00	822.0
22	TraesCS2A01G428100	chr2D	91.968	498	26	5	5495	5991	538313213	538313697	0.000000e+00	686.0
23	TraesCS2A01G428100	chr2D	85.516	649	88	2	1815	2463	538317783	538318425	0.000000e+00	673.0
24	TraesCS2A01G428100	chr2D	87.029	478	41	13	950	1426	538589740	538590197	2.590000e-143	520.0
25	TraesCS2A01G428100	chr2D	87.727	440	46	4	987	1425	538317087	538317519	2.010000e-139	507.0
26	TraesCS2A01G428100	chr2D	91.545	343	26	3	484	823	591268619	591268961	2.640000e-128	470.0
27	TraesCS2A01G428100	chr2D	87.407	405	32	7	5592	5991	538585820	538586210	1.240000e-121	448.0
28	TraesCS2A01G428100	chr2D	88.136	118	13	1	1	117	538283183	538283300	8.470000e-29	139.0
29	TraesCS2A01G428100	chr2D	93.590	78	5	0	5495	5572	538585695	538585772	3.970000e-22	117.0
30	TraesCS2A01G428100	chr2D	100.000	33	0	0	436	468	538283300	538283332	1.890000e-05	62.1
31	TraesCS2A01G428100	chr5A	95.724	304	13	0	119	422	139481495	139481192	2.030000e-134	490.0
32	TraesCS2A01G428100	chr5A	82.918	281	47	1	5984	6263	18914267	18914547	1.040000e-62	252.0
33	TraesCS2A01G428100	chr5A	83.214	280	42	4	5985	6263	647478290	647478565	1.040000e-62	252.0
34	TraesCS2A01G428100	chr4D	95.724	304	13	0	119	422	459568961	459568658	2.030000e-134	490.0
35	TraesCS2A01G428100	chr4D	92.857	42	3	0	1278	1319	276138084	276138043	1.890000e-05	62.1
36	TraesCS2A01G428100	chr3B	95.724	304	13	0	119	422	536901300	536900997	2.030000e-134	490.0
37	TraesCS2A01G428100	chr3B	94.551	312	17	0	119	430	4554887	4554576	3.400000e-132	483.0
38	TraesCS2A01G428100	chr3B	85.185	81	12	0	2828	2908	66599654	66599574	4.020000e-12	84.2
39	TraesCS2A01G428100	chr7A	95.410	305	14	0	119	423	8660471	8660167	2.620000e-133	486.0
40	TraesCS2A01G428100	chr7A	86.833	281	32	5	5985	6263	681717935	681717658	6.100000e-80	309.0
41	TraesCS2A01G428100	chr4B	95.395	304	14	0	119	422	40215532	40215229	9.440000e-133	484.0
42	TraesCS2A01G428100	chr4B	89.394	66	7	0	5984	6049	11675041	11675106	4.020000e-12	84.2
43	TraesCS2A01G428100	chr1A	95.395	304	14	0	119	422	42226162	42225859	9.440000e-133	484.0
44	TraesCS2A01G428100	chr1A	91.496	341	27	2	84	422	557511852	557511512	9.510000e-128	468.0
45	TraesCS2A01G428100	chr1A	85.053	281	41	1	5984	6263	564346030	564346310	1.030000e-72	285.0
46	TraesCS2A01G428100	chr1A	82.079	279	40	2	5985	6263	5769884	5769616	4.880000e-56	230.0
47	TraesCS2A01G428100	chrUn	94.304	316	17	1	107	422	200950198	200950512	3.400000e-132	483.0
48	TraesCS2A01G428100	chrUn	90.671	343	29	3	484	823	51420409	51420751	2.660000e-123	453.0
49	TraesCS2A01G428100	chr1D	91.813	342	26	2	484	823	446756337	446755996	5.680000e-130	475.0
50	TraesCS2A01G428100	chr1D	87.018	285	31	2	5984	6263	236322315	236322032	3.640000e-82	316.0
51	TraesCS2A01G428100	chr1D	83.929	280	43	2	5985	6263	81732942	81733220	3.720000e-67	267.0
52	TraesCS2A01G428100	chr1D	81.928	166	28	1	5985	6150	415320212	415320375	8.470000e-29	139.0
53	TraesCS2A01G428100	chr1D	84.112	107	15	2	5979	6084	492361839	492361944	1.110000e-17	102.0
54	TraesCS2A01G428100	chr6B	91.420	338	24	4	488	823	663015768	663016102	5.720000e-125	459.0
55	TraesCS2A01G428100	chr6B	90.909	341	30	1	484	823	24970193	24969853	2.060000e-124	457.0
56	TraesCS2A01G428100	chr5D	91.150	339	26	4	488	823	535901861	535902198	2.060000e-124	457.0
57	TraesCS2A01G428100	chr5B	90.909	341	30	1	484	823	700196533	700196873	2.060000e-124	457.0
58	TraesCS2A01G428100	chr6D	90.671	343	28	4	484	823	303445924	303445583	2.660000e-123	453.0
59	TraesCS2A01G428100	chr6D	88.742	151	17	0	5984	6134	3084020	3083870	1.070000e-42	185.0
60	TraesCS2A01G428100	chr6D	82.258	186	26	7	5985	6169	15713955	15713776	3.020000e-33	154.0
61	TraesCS2A01G428100	chr3D	90.671	343	29	3	484	823	147839111	147838769	2.660000e-123	453.0
62	TraesCS2A01G428100	chr3D	84.211	152	20	4	5985	6134	133104135	133104284	1.820000e-30	145.0
63	TraesCS2A01G428100	chr1B	85.915	284	32	3	5985	6263	480369986	480370266	4.750000e-76	296.0
64	TraesCS2A01G428100	chr4A	86.555	238	32	0	5984	6221	49202826	49203063	4.810000e-66	263.0
65	TraesCS2A01G428100	chr4A	86.555	238	31	1	5985	6222	621820691	621820455	1.730000e-65	261.0
66	TraesCS2A01G428100	chr6A	84.242	165	22	2	6099	6263	13406154	13405994	2.340000e-34	158.0
67	TraesCS2A01G428100	chr7B	84.000	100	10	4	4083	4178	387157693	387157790	2.400000e-14	91.6

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	TraesCS2A01G428100	chr2A	680514381	680520643	6262	False	11566.000000	11566	100.000000	1	6263	1	chr2A.!!$F1	6262
1	TraesCS2A01G428100	chr2A	680541046	680545722	4676	False	567.528571	998	89.493000	950	5527	7	chr2A.!!$F2	4577
2	TraesCS2A01G428100	chr2B	641169899	641175215	5316	False	4120.500000	7537	94.183500	821	5991	2	chr2B.!!$F1	5170
3	TraesCS2A01G428100	chr2B	641187076	641191704	4628	False	643.440000	948	89.132600	987	5527	5	chr2B.!!$F2	4540
4	TraesCS2A01G428100	chr2D	538308409	538321355	12946	False	2044.000000	7461	88.962500	847	5991	6	chr2D.!!$F3	5144
5	TraesCS2A01G428100	chr2D	538585695	538593876	8181	False	641.333333	1022	87.644167	950	5991	6	chr2D.!!$F4	5041

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	Hairpin	End Stability	Orientation
527	528	0.027979	TGTTCGTCGTTCGTCTTCGT	59.972	50.0	0.00	40.80	3.85	F
613	614	0.034477	CGTTGGTTCTATGGGGCCTT	60.034	55.0	0.84	0.00	4.35	F
715	716	0.109272	CGGCTCGCTTCAGTCTTGTA	60.109	55.0	0.00	0.00	2.41	F
895	896	0.466555	AGGTAAGCACGCAAAACCCA	60.467	50.0	4.44	0.00	4.51	F
2357	13948	0.908198	GGAGAAGAGGCATCCACTGT	59.092	55.0	0.00	33.08	3.55	F
3060	14723	0.179097	CTCTAGAAAGCGACCCTGGC	60.179	60.0	0.00	0.00	4.85	F
3901	15802	0.109132	CCAAAGGAACAATGGCGAGC	60.109	55.0	0.00	30.07	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2529	14120	0.461870	CACGAATTGCCTGATCCGGA	60.462	55.000	6.61	6.61	0.00	5.14	R
2532	14123	0.659957	GCTCACGAATTGCCTGATCC	59.340	55.000	0.00	0.00	0.00	3.36	R
2682	14339	6.128282	CCTGTTGTATATTGTGGTTCAGTGAC	60.128	42.308	0.00	0.00	0.00	3.67	R
2813	14470	4.360951	TTCGGAGGTGTAAAATGTTCCT	57.639	40.909	0.00	0.00	0.00	3.36	R
3887	15788	0.393808	TAAGGGCTCGCCATTGTTCC	60.394	55.000	17.19	0.00	40.57	3.62	R
4662	16584	1.080569	CTTTTCGCACCCATGGCAC	60.081	57.895	6.09	0.00	0.00	5.01	R
5599	17749	0.462047	AGCCCGATAAGTCAAAGGCG	60.462	55.000	0.00	0.00	45.16	5.52	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
21	22	2.997986	CCTCAAAGAACCATGCATTTGC	59.002	45.455	42.50	3.68
22	23	2.664568	CTCAAAGAACCATGCATTTGCG	59.335	45.455	45.83	4.85
23	24	2.035704	TCAAAGAACCATGCATTTGCGT	59.964	40.909	45.83	5.24
24	25	2.801679	CAAAGAACCATGCATTTGCGTT	59.198	40.909	45.83	4.84
26	27	4.454728	AAGAACCATGCATTTGCGTTAT	57.545	36.364	45.83	1.89
28	29	5.574891	AGAACCATGCATTTGCGTTATAA	57.425	34.783	45.83	0.98
29	30	5.960113	AGAACCATGCATTTGCGTTATAAA	58.040	33.333	45.83	1.40
31	32	6.870965	AGAACCATGCATTTGCGTTATAAAAA	59.129	30.769	45.83	1.94
32	33	6.401955	ACCATGCATTTGCGTTATAAAAAC	57.598	33.333	45.83	2.43
33	34	5.350091	ACCATGCATTTGCGTTATAAAAACC	59.650	36.000	45.83	3.27
34	35	5.220567	CCATGCATTTGCGTTATAAAAACCC	60.221	40.000	45.83	4.11
35	36	4.246458	TGCATTTGCGTTATAAAAACCCC	58.754	39.130	45.83	4.95
36	37	4.246458	GCATTTGCGTTATAAAAACCCCA	58.754	39.130	0.00	4.96
37	38	4.328712	GCATTTGCGTTATAAAAACCCCAG	59.671	41.667	0.00	4.45
38	39	5.715070	CATTTGCGTTATAAAAACCCCAGA	58.285	37.500	0.00	3.86
39	40	5.786264	TTTGCGTTATAAAAACCCCAGAA	57.214	34.783	0.00	3.02
40	41	5.786264	TTGCGTTATAAAAACCCCAGAAA	57.214	34.783	0.00	2.52
41	42	5.379732	TGCGTTATAAAAACCCCAGAAAG	57.620	39.130	0.00	2.62
45	46	6.515365	GCGTTATAAAAACCCCAGAAAGACAA	60.515	38.462	0.00	3.18
47	48	7.040961	CGTTATAAAAACCCCAGAAAGACAAGA	60.041	37.037	0.00	3.02
48	49	6.901081	ATAAAAACCCCAGAAAGACAAGAG	57.099	37.500	0.00	2.85
49	50	4.519906	AAAACCCCAGAAAGACAAGAGA	57.480	40.909	0.00	3.10
50	51	4.731313	AAACCCCAGAAAGACAAGAGAT	57.269	40.909	0.00	2.75
51	52	5.843019	AAACCCCAGAAAGACAAGAGATA	57.157	39.130	0.00	1.98
52	53	5.843019	AACCCCAGAAAGACAAGAGATAA	57.157	39.130	0.00	1.75

Showing 1 to 25 of 573 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.997986	GCAAATGCATGGTTCTTTGAGG	59.002	45.455	11.41	0.00	41.59	3.86
1	2	2.664568	CGCAAATGCATGGTTCTTTGAG	59.335	45.455	11.41	5.23	42.21	3.02
3	4	2.406130	ACGCAAATGCATGGTTCTTTG	58.594	42.857	0.00	1.44	42.21	2.77
4	5	2.818130	ACGCAAATGCATGGTTCTTT	57.182	40.000	0.00	0.00	42.21	2.52
5	6	2.818130	AACGCAAATGCATGGTTCTT	57.182	40.000	0.00	0.00	42.21	2.52
7	8	6.639671	TTTTATAACGCAAATGCATGGTTC	57.360	33.333	0.00	0.00	42.21	3.62
8	9	6.128418	GGTTTTTATAACGCAAATGCATGGTT	60.128	34.615	0.00	5.49	42.21	3.67
10	11	5.220567	GGGTTTTTATAACGCAAATGCATGG	60.221	40.000	0.00	0.00	42.21	3.66
11	12	5.220567	GGGGTTTTTATAACGCAAATGCATG	60.221	40.000	0.00	0.00	42.21	4.06
12	13	4.873259	GGGGTTTTTATAACGCAAATGCAT	59.127	37.500	6.18	0.00	42.21	3.96
14	15	4.246458	TGGGGTTTTTATAACGCAAATGC	58.754	39.130	5.21	0.00	35.14	3.56
15	16	5.715070	TCTGGGGTTTTTATAACGCAAATG	58.285	37.500	5.21	0.00	35.14	2.32
16	17	5.986501	TCTGGGGTTTTTATAACGCAAAT	57.013	34.783	5.21	0.00	35.14	2.32
17	18	5.786264	TTCTGGGGTTTTTATAACGCAAA	57.214	34.783	5.21	0.00	35.14	3.68
18	19	5.535406	TCTTTCTGGGGTTTTTATAACGCAA	59.465	36.000	5.21	0.00	35.14	4.85
19	20	5.048573	GTCTTTCTGGGGTTTTTATAACGCA	60.049	40.000	5.21	0.00	35.14	5.24
20	21	5.048573	TGTCTTTCTGGGGTTTTTATAACGC	60.049	40.000	0.00	0.00	0.00	4.84
21	22	6.563222	TGTCTTTCTGGGGTTTTTATAACG	57.437	37.500	0.00	0.00	0.00	3.18
22	23	8.173542	TCTTGTCTTTCTGGGGTTTTTATAAC	57.826	34.615	0.00	0.00	0.00	1.89
23	24	8.221944	TCTCTTGTCTTTCTGGGGTTTTTATAA	58.778	33.333	0.00	0.00	0.00	0.98
24	25	7.751646	TCTCTTGTCTTTCTGGGGTTTTTATA	58.248	34.615	0.00	0.00	0.00	0.98
26	27	6.008696	TCTCTTGTCTTTCTGGGGTTTTTA	57.991	37.500	0.00	0.00	0.00	1.52
28	29	4.519906	TCTCTTGTCTTTCTGGGGTTTT	57.480	40.909	0.00	0.00	0.00	2.43
29	30	4.731313	ATCTCTTGTCTTTCTGGGGTTT	57.269	40.909	0.00	0.00	0.00	3.27
31	32	5.843019	TTTATCTCTTGTCTTTCTGGGGT	57.157	39.130	0.00	0.00	0.00	4.95

Showing 1 to 25 of 573 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.