AutoCloner

Multiple sequence alignment - TraesCS2D01G481000

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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	TraesCS2D01G481000	chr2D	100.000	4030	0	0	1	4030	584259237	584255208	0.000000e+00	7443.0
1	TraesCS2D01G481000	chr2D	92.929	99	5	2	451	549	603512114	603512018	4.200000e-30	143.0
2	TraesCS2D01G481000	chr2D	90.385	104	9	1	455	558	143253619	143253517	7.030000e-28	135.0
3	TraesCS2D01G481000	chr2A	91.823	2727	89	45	601	3230	718385646	718382957	0.000000e+00	3677.0
4	TraesCS2D01G481000	chr2A	93.128	553	22	7	2515	3066	1608659	1609196	0.000000e+00	797.0
5	TraesCS2D01G481000	chr2B	91.988	2596	93	57	624	3144	703625080	703622525	0.000000e+00	3535.0
6	TraesCS2D01G481000	chr2B	81.500	400	24	12	3658	4030	703622286	703621910	2.370000e-72	283.0
7	TraesCS2D01G481000	chr3A	89.258	1173	124	2	1860	3031	16631612	16632783	0.000000e+00	1467.0
8	TraesCS2D01G481000	chr3A	76.364	605	89	41	1008	1579	16629885	16630468	3.970000e-70	276.0
9	TraesCS2D01G481000	chr3B	89.031	1176	127	2	1860	3034	26752898	26751724	0.000000e+00	1456.0
10	TraesCS2D01G481000	chr3B	88.520	1176	133	2	1860	3034	14525616	14524442	0.000000e+00	1423.0
11	TraesCS2D01G481000	chr3B	75.743	606	95	38	1008	1579	14526516	14525929	1.440000e-64	257.0
12	TraesCS2D01G481000	chr3B	85.321	218	14	12	1008	1207	26753822	26753605	4.080000e-50	209.0
13	TraesCS2D01G481000	chr3B	91.509	106	7	2	458	563	43422847	43422744	1.170000e-30	145.0
14	TraesCS2D01G481000	chr3B	79.275	193	36	3	1388	1579	26753440	26753251	9.090000e-27	132.0
15	TraesCS2D01G481000	chr3B	92.000	50	1	3	1663	1710	14525830	14525782	2.600000e-07	67.6
16	TraesCS2D01G481000	chr3D	88.832	1173	129	2	1860	3031	10454963	10456134	0.000000e+00	1439.0
17	TraesCS2D01G481000	chr3D	75.331	604	101	33	1008	1579	10453849	10454436	3.110000e-61	246.0
18	TraesCS2D01G481000	chr3D	89.256	121	6	7	451	569	358168749	358168634	1.170000e-30	145.0
19	TraesCS2D01G481000	chr7A	80.390	1178	215	14	1860	3029	207901380	207900211	0.000000e+00	881.0
20	TraesCS2D01G481000	chr7B	80.253	1185	216	16	1855	3030	162779676	162780851	0.000000e+00	876.0
21	TraesCS2D01G481000	chr7D	80.000	1180	214	20	1858	3026	198622870	198621702	0.000000e+00	852.0
22	TraesCS2D01G481000	chrUn	94.033	553	25	5	2515	3066	337092337	337092882	0.000000e+00	832.0
23	TraesCS2D01G481000	chr5A	90.667	450	31	4	2622	3063	219244659	219245105	4.490000e-164	588.0
24	TraesCS2D01G481000	chr5A	89.189	111	9	3	451	560	35659997	35659889	7.030000e-28	135.0
25	TraesCS2D01G481000	chr6B	93.878	98	5	1	451	548	706113363	706113267	3.250000e-31	147.0
26	TraesCS2D01G481000	chr1D	90.000	110	10	1	451	560	320585046	320585154	1.510000e-29	141.0
27	TraesCS2D01G481000	chr5B	92.000	100	6	2	451	550	308557009	308557106	5.430000e-29	139.0
28	TraesCS2D01G481000	chr4D	91.176	102	7	2	457	557	35722393	35722493	1.950000e-28	137.0

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	TraesCS2D01G481000	chr2D	584255208	584259237	4029	True	7443.000000	7443	100.000000	1	4030	1	chr2D.!!$R2	4029
1	TraesCS2D01G481000	chr2A	718382957	718385646	2689	True	3677.000000	3677	91.823000	601	3230	1	chr2A.!!$R1	2629
2	TraesCS2D01G481000	chr2A	1608659	1609196	537	False	797.000000	797	93.128000	2515	3066	1	chr2A.!!$F1	551
3	TraesCS2D01G481000	chr2B	703621910	703625080	3170	True	1909.000000	3535	86.744000	624	4030	2	chr2B.!!$R1	3406
4	TraesCS2D01G481000	chr3A	16629885	16632783	2898	False	871.500000	1467	82.811000	1008	3031	2	chr3A.!!$F1	2023
5	TraesCS2D01G481000	chr3B	26751724	26753822	2098	True	599.000000	1456	84.542333	1008	3034	3	chr3B.!!$R3	2026
6	TraesCS2D01G481000	chr3B	14524442	14526516	2074	True	582.533333	1423	85.421000	1008	3034	3	chr3B.!!$R2	2026
7	TraesCS2D01G481000	chr3D	10453849	10456134	2285	False	842.500000	1439	82.081500	1008	3031	2	chr3D.!!$F1	2023
8	TraesCS2D01G481000	chr7A	207900211	207901380	1169	True	881.000000	881	80.390000	1860	3029	1	chr7A.!!$R1	1169
9	TraesCS2D01G481000	chr7B	162779676	162780851	1175	False	876.000000	876	80.253000	1855	3030	1	chr7B.!!$F1	1175
10	TraesCS2D01G481000	chr7D	198621702	198622870	1168	True	852.000000	852	80.000000	1858	3026	1	chr7D.!!$R1	1168
11	TraesCS2D01G481000	chrUn	337092337	337092882	545	False	832.000000	832	94.033000	2515	3066	1	chrUn.!!$F1	551

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
171	172	0.036671	GCGCTAGGGTACACCAAGTT	60.037	55.0	8.77	0.0	43.89	2.66	F
182	183	0.099791	CACCAAGTTTTGCGACGGTT	59.900	50.0	0.00	0.0	0.00	4.44	F
255	256	0.109723	ACGCAGGGGTACAAACACAT	59.890	50.0	0.00	0.0	0.00	3.21	F
404	405	0.253894	TCCTGCATGTCCCACTGATG	59.746	55.0	0.00	0.0	0.00	3.07	F
691	704	0.376852	CTCTCTCCAGCTCGTCTTCG	59.623	60.0	0.00	0.0	38.55	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1385	1512	0.396435	TGAATGTGGTGTCTTCGGCT	59.604	50.000	0.0	0.0	0.00	5.52	R
1593	1721	0.606673	AGGTGCGAGGAAAAAGGAGC	60.607	55.000	0.0	0.0	0.00	4.70	R
1844	3035	1.002033	CTCATCTTTGCTAATGCCGCC	60.002	52.381	0.0	0.0	38.71	6.13	R
1991	3182	2.506438	CCGTTCTCGTCGAAGCCC	60.506	66.667	0.0	0.0	35.01	5.19	R
3069	4284	3.641906	AGTAGTATACCTGCCATCACCAC	59.358	47.826	0.0	0.0	44.47	4.16	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
26	27	3.595709	TTTGTTAACACTGCAGTACGC	57.404	42.857	21.20	8.89	42.89	4.42
27	28	1.133407	TGTTAACACTGCAGTACGCG	58.867	50.000	21.20	9.88	46.97	6.01
33	34	2.125912	CTGCAGTACGCGGCTCTT	60.126	61.111	12.47	0.00	46.97	2.85
34	35	2.432456	TGCAGTACGCGGCTCTTG	60.432	61.111	12.47	2.35	46.97	3.02
35	36	3.188786	GCAGTACGCGGCTCTTGG	61.189	66.667	12.47	0.00	33.03	3.61
36	37	2.571757	CAGTACGCGGCTCTTGGA	59.428	61.111	12.47	0.00	0.00	3.53
37	38	1.805945	CAGTACGCGGCTCTTGGAC	60.806	63.158	12.47	0.00	0.00	4.02
44	45	4.821589	GGCTCTTGGACGGAGGCG	62.822	72.222	0.00	0.00	44.17	5.52
45	46	4.821589	GCTCTTGGACGGAGGCGG	62.822	72.222	0.00	0.00	0.00	6.13
46	47	4.148825	CTCTTGGACGGAGGCGGG	62.149	72.222	0.00	0.00	0.00	6.13
48	49	4.016706	CTTGGACGGAGGCGGGTT	62.017	66.667	0.00	0.00	0.00	4.11
49	50	3.546714	CTTGGACGGAGGCGGGTTT	62.547	63.158	0.00	0.00	0.00	3.27
50	51	3.122727	TTGGACGGAGGCGGGTTTT	62.123	57.895	0.00	0.00	0.00	2.43
51	52	2.745100	GGACGGAGGCGGGTTTTC	60.745	66.667	0.00	0.00	0.00	2.29
52	53	2.031465	GACGGAGGCGGGTTTTCA	59.969	61.111	0.00	0.00	0.00	2.69
53	54	1.598685	GACGGAGGCGGGTTTTCAA	60.599	57.895	0.00	0.00	0.00	2.69
54	55	0.958876	GACGGAGGCGGGTTTTCAAT	60.959	55.000	0.00	0.00	0.00	2.57
55	56	0.958876	ACGGAGGCGGGTTTTCAATC	60.959	55.000	0.00	0.00	0.00	2.67
56	57	0.676782	CGGAGGCGGGTTTTCAATCT	60.677	55.000	0.00	0.00	0.00	2.40
57	58	1.406341	CGGAGGCGGGTTTTCAATCTA	60.406	52.381	0.00	0.00	0.00	1.98
58	59	2.014857	GGAGGCGGGTTTTCAATCTAC	58.985	52.381	0.00	0.00	0.00	2.59
59	60	2.355818	GGAGGCGGGTTTTCAATCTACT	60.356	50.000	0.00	0.00	0.00	2.57
60	61	3.344515	GAGGCGGGTTTTCAATCTACTT	58.655	45.455	0.00	0.00	0.00	2.24
61	62	3.756963	GAGGCGGGTTTTCAATCTACTTT	59.243	43.478	0.00	0.00	0.00	2.66
62	63	3.506067	AGGCGGGTTTTCAATCTACTTTG	59.494	43.478	0.00	0.00	0.00	2.77

Showing 1 to 25 of 609 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	4.344448	GCGTACTGCAGTGTTAACAAAAA	58.656	39.130	29.57	1.60	45.45	1.94
5	6	3.544440	CGCGTACTGCAGTGTTAACAAAA	60.544	43.478	29.57	2.44	46.97	2.44
6	7	2.033577	CGCGTACTGCAGTGTTAACAAA	60.034	45.455	29.57	3.27	46.97	2.83
7	8	1.523515	CGCGTACTGCAGTGTTAACAA	59.476	47.619	29.57	4.12	46.97	2.83
8	9	1.133407	CGCGTACTGCAGTGTTAACA	58.867	50.000	29.57	3.59	46.97	2.41
9	10	0.437295	CCGCGTACTGCAGTGTTAAC	59.563	55.000	29.57	17.77	46.97	2.01
10	11	1.286354	GCCGCGTACTGCAGTGTTAA	61.286	55.000	29.57	6.24	46.97	2.01
11	12	1.735198	GCCGCGTACTGCAGTGTTA	60.735	57.895	29.57	6.67	46.97	2.41
12	13	3.041940	GCCGCGTACTGCAGTGTT	61.042	61.111	29.57	4.92	46.97	3.32
13	14	3.916392	GAGCCGCGTACTGCAGTGT	62.916	63.158	29.57	6.74	46.97	3.55
14	15	3.181967	GAGCCGCGTACTGCAGTG	61.182	66.667	29.57	14.69	46.97	3.66
15	16	2.932234	AAGAGCCGCGTACTGCAGT	61.932	57.895	25.12	25.12	46.97	4.40
16	17	2.125912	AAGAGCCGCGTACTGCAG	60.126	61.111	13.48	13.48	46.97	4.41
17	18	2.432456	CAAGAGCCGCGTACTGCA	60.432	61.111	4.92	0.00	46.97	4.41
18	19	3.188786	CCAAGAGCCGCGTACTGC	61.189	66.667	4.92	0.00	41.47	4.40
19	20	1.805945	GTCCAAGAGCCGCGTACTG	60.806	63.158	4.92	0.00	0.00	2.74
20	21	2.572284	GTCCAAGAGCCGCGTACT	59.428	61.111	4.92	0.90	0.00	2.73
21	22	2.879462	CGTCCAAGAGCCGCGTAC	60.879	66.667	4.92	0.00	0.00	3.67
22	23	4.124351	CCGTCCAAGAGCCGCGTA	62.124	66.667	4.92	0.00	0.00	4.42
25	26	4.821589	CCTCCGTCCAAGAGCCGC	62.822	72.222	0.00	0.00	0.00	6.53
26	27	4.821589	GCCTCCGTCCAAGAGCCG	62.822	72.222	0.00	0.00	0.00	5.52
27	28	4.821589	CGCCTCCGTCCAAGAGCC	62.822	72.222	0.00	0.00	0.00	4.70
28	29	4.821589	CCGCCTCCGTCCAAGAGC	62.822	72.222	0.00	0.00	0.00	4.09
29	30	4.148825	CCCGCCTCCGTCCAAGAG	62.149	72.222	0.00	0.00	0.00	2.85
31	32	3.546714	AAACCCGCCTCCGTCCAAG	62.547	63.158	0.00	0.00	0.00	3.61

Showing 1 to 25 of 658 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.