AutoCloner

Multiple sequence alignment - TraesCS2D01G329800

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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	TraesCS2D01G329800	chr2D	100.000	3058	0	0	1	3058	422827990	422824933	0.000000e+00	5648.0
1	TraesCS2D01G329800	chr2D	84.244	622	87	9	2111	2724	563759100	563759718	2.030000e-166	595.0
2	TraesCS2D01G329800	chr2D	83.625	629	93	10	2116	2739	619938241	619938864	1.580000e-162	582.0
3	TraesCS2D01G329800	chr2D	95.000	40	2	0	2822	2861	615121839	615121800	2.550000e-06	63.9
4	TraesCS2D01G329800	chr2B	89.420	1947	133	30	87	1986	495494755	495492835	0.000000e+00	2386.0
5	TraesCS2D01G329800	chr2B	95.385	130	5	1	1980	2108	495492429	495492300	4.000000e-49	206.0
6	TraesCS2D01G329800	chr2B	92.135	89	7	0	2970	3058	752861416	752861504	3.200000e-25	126.0
7	TraesCS2D01G329800	chr2A	91.006	1779	121	19	1006	2760	566083368	566085131	0.000000e+00	2362.0
8	TraesCS2D01G329800	chr2A	90.968	919	46	16	87	1003	566082451	566083334	0.000000e+00	1203.0
9	TraesCS2D01G329800	chr2A	93.066	274	16	2	2787	3058	566085130	566085402	6.140000e-107	398.0
10	TraesCS2D01G329800	chr2A	93.258	89	6	0	2970	3058	747253925	747254013	6.880000e-27	132.0
11	TraesCS2D01G329800	chr2A	92.500	40	3	0	2822	2861	517925304	517925265	1.180000e-04	58.4
12	TraesCS2D01G329800	chr7A	84.689	627	88	4	2128	2750	700634058	700634680	1.200000e-173	619.0
13	TraesCS2D01G329800	chr7A	84.211	627	91	4	2128	2750	700610819	700611441	1.210000e-168	603.0
14	TraesCS2D01G329800	chr5B	84.395	628	91	7	2116	2738	311547259	311547884	7.250000e-171	610.0
15	TraesCS2D01G329800	chr5B	94.318	88	4	1	2972	3058	666833665	666833752	1.910000e-27	134.0
16	TraesCS2D01G329800	chr5B	93.258	89	4	2	2972	3058	666808563	666808651	2.470000e-26	130.0
17	TraesCS2D01G329800	chr5B	90.566	53	4	1	2822	2873	658585926	658585978	5.470000e-08	69.4
18	TraesCS2D01G329800	chr5B	89.796	49	4	1	2834	2881	411784360	411784408	9.160000e-06	62.1
19	TraesCS2D01G329800	chr6D	83.906	640	97	5	2116	2749	29378918	29379557	9.380000e-170	606.0
20	TraesCS2D01G329800	chr6D	84.244	622	92	6	2111	2727	106077892	106077272	4.360000e-168	601.0
21	TraesCS2D01G329800	chr6D	93.407	91	4	1	2970	3058	411993583	411993673	1.910000e-27	134.0
22	TraesCS2D01G329800	chr7D	83.780	635	96	5	2118	2746	628134506	628135139	2.030000e-166	595.0
23	TraesCS2D01G329800	chr7D	83.754	634	93	9	2111	2739	182613638	182613010	2.630000e-165	592.0
24	TraesCS2D01G329800	chr7B	94.186	86	5	0	2973	3058	219625867	219625952	6.880000e-27	132.0
25	TraesCS2D01G329800	chr5D	93.103	87	6	0	2972	3058	529174442	529174528	8.900000e-26	128.0
26	TraesCS2D01G329800	chr1D	93.103	87	6	0	2972	3058	329618174	329618260	8.900000e-26	128.0
27	TraesCS2D01G329800	chr1D	95.122	41	2	0	2823	2863	364731823	364731783	7.080000e-07	65.8
28	TraesCS2D01G329800	chr3D	95.238	42	2	0	2822	2863	491957262	491957221	1.970000e-07	67.6
29	TraesCS2D01G329800	chr4B	91.489	47	2	2	2822	2866	636785759	636785713	2.550000e-06	63.9
30	TraesCS2D01G329800	chr1B	94.737	38	2	0	2826	2863	122360582	122360545	3.290000e-05	60.2

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	TraesCS2D01G329800	chr2D	422824933	422827990	3057	True	5648	5648	100.0000	1	3058	1	chr2D.!!$R1	3057
1	TraesCS2D01G329800	chr2D	563759100	563759718	618	False	595	595	84.2440	2111	2724	1	chr2D.!!$F1	613
2	TraesCS2D01G329800	chr2D	619938241	619938864	623	False	582	582	83.6250	2116	2739	1	chr2D.!!$F2	623
3	TraesCS2D01G329800	chr2B	495492300	495494755	2455	True	1296	2386	92.4025	87	2108	2	chr2B.!!$R1	2021
4	TraesCS2D01G329800	chr2A	566082451	566085402	2951	False	1321	2362	91.6800	87	3058	3	chr2A.!!$F2	2971
5	TraesCS2D01G329800	chr7A	700634058	700634680	622	False	619	619	84.6890	2128	2750	1	chr7A.!!$F2	622
6	TraesCS2D01G329800	chr7A	700610819	700611441	622	False	603	603	84.2110	2128	2750	1	chr7A.!!$F1	622
7	TraesCS2D01G329800	chr5B	311547259	311547884	625	False	610	610	84.3950	2116	2738	1	chr5B.!!$F1	622
8	TraesCS2D01G329800	chr6D	29378918	29379557	639	False	606	606	83.9060	2116	2749	1	chr6D.!!$F1	633
9	TraesCS2D01G329800	chr6D	106077272	106077892	620	True	601	601	84.2440	2111	2727	1	chr6D.!!$R1	616
10	TraesCS2D01G329800	chr7D	628134506	628135139	633	False	595	595	83.7800	2118	2746	1	chr7D.!!$F1	628
11	TraesCS2D01G329800	chr7D	182613010	182613638	628	True	592	592	83.7540	2111	2739	1	chr7D.!!$R1	628

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
55	56	0.109781	CGTTTTGATCTTGCACCGGG	60.110	55.0	6.32	0.0	0.0	5.73	F
1004	1069	0.036388	CCACCACACGTCCTAGCAAT	60.036	55.0	0.00	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1140	1205	0.815095	TACACAGACGGACGCATCAT	59.185	50.000	0.0	0.0	0.00	2.45	R
2766	3281	1.132453	GCCCAATAGGAACACGAAAGC	59.868	52.381	0.0	0.0	38.24	3.51	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	End Stability
30	31	9.696917	AAGCAAGAAAAATATGTAAAGTTGAGG	57.303	29.630	0.00	0.00	3.86
31	32	8.306761	AGCAAGAAAAATATGTAAAGTTGAGGG	58.693	33.333	0.00	0.00	4.30
32	33	7.063426	GCAAGAAAAATATGTAAAGTTGAGGGC	59.937	37.037	0.00	0.00	5.19
33	34	7.170393	AGAAAAATATGTAAAGTTGAGGGCC	57.830	36.000	0.00	0.00	5.80
34	35	5.932619	AAAATATGTAAAGTTGAGGGCCC	57.067	39.130	16.46	16.46	5.80
35	36	4.601406	AATATGTAAAGTTGAGGGCCCA	57.399	40.909	27.56	0.00	5.36
36	37	2.215942	ATGTAAAGTTGAGGGCCCAC	57.784	50.000	27.56	20.25	4.61
37	38	0.250553	TGTAAAGTTGAGGGCCCACG	60.251	55.000	27.56	0.00	4.94
38	39	0.250597	GTAAAGTTGAGGGCCCACGT	60.251	55.000	27.56	9.22	4.49
39	40	0.475044	TAAAGTTGAGGGCCCACGTT	59.525	50.000	27.56	19.81	3.99
40	41	0.396556	AAAGTTGAGGGCCCACGTTT	60.397	50.000	27.56	15.67	3.60
41	42	0.396556	AAGTTGAGGGCCCACGTTTT	60.397	50.000	27.56	9.91	2.43
42	43	1.106944	AGTTGAGGGCCCACGTTTTG	61.107	55.000	27.56	0.00	2.44
43	44	1.104577	GTTGAGGGCCCACGTTTTGA	61.105	55.000	27.56	0.00	2.69
44	45	0.178975	TTGAGGGCCCACGTTTTGAT	60.179	50.000	27.56	0.00	2.57
45	46	0.608035	TGAGGGCCCACGTTTTGATC	60.608	55.000	27.56	9.98	2.92
46	47	0.322546	GAGGGCCCACGTTTTGATCT	60.323	55.000	27.56	0.00	2.75
47	48	0.112412	AGGGCCCACGTTTTGATCTT	59.888	50.000	27.56	0.00	2.40
48	49	0.243636	GGGCCCACGTTTTGATCTTG	59.756	55.000	19.95	0.00	3.02
49	50	0.388520	GGCCCACGTTTTGATCTTGC	60.389	55.000	0.00	0.00	4.01
50	51	0.313672	GCCCACGTTTTGATCTTGCA	59.686	50.000	0.00	0.00	4.08
51	52	1.930371	GCCCACGTTTTGATCTTGCAC	60.930	52.381	0.00	0.00	4.57
52	53	1.335872	CCCACGTTTTGATCTTGCACC	60.336	52.381	0.00	0.00	5.01
53	54	1.662876	CCACGTTTTGATCTTGCACCG	60.663	52.381	0.00	0.00	4.94
54	55	0.591170	ACGTTTTGATCTTGCACCGG	59.409	50.000	0.00	0.00	5.28

Showing 1 to 25 of 153 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability
7	8	7.545615	GGCCCTCAACTTTACATATTTTTCTTG	59.454	37.037	0.00	0.00	3.02
9	10	6.154534	GGGCCCTCAACTTTACATATTTTTCT	59.845	38.462	17.04	0.00	2.52
10	11	6.071051	TGGGCCCTCAACTTTACATATTTTTC	60.071	38.462	25.70	0.00	2.29
11	12	5.782845	TGGGCCCTCAACTTTACATATTTTT	59.217	36.000	25.70	0.00	1.94
12	13	5.186992	GTGGGCCCTCAACTTTACATATTTT	59.813	40.000	25.70	0.00	1.82
13	14	4.709886	GTGGGCCCTCAACTTTACATATTT	59.290	41.667	25.70	0.00	1.40
14	15	4.278310	GTGGGCCCTCAACTTTACATATT	58.722	43.478	25.70	0.00	1.28
15	16	3.684413	CGTGGGCCCTCAACTTTACATAT	60.684	47.826	25.70	0.00	1.78
16	17	2.355310	CGTGGGCCCTCAACTTTACATA	60.355	50.000	25.70	0.00	2.29
17	18	1.613255	CGTGGGCCCTCAACTTTACAT	60.613	52.381	25.70	0.00	2.29
18	19	0.250553	CGTGGGCCCTCAACTTTACA	60.251	55.000	25.70	0.00	2.41
19	20	0.250597	ACGTGGGCCCTCAACTTTAC	60.251	55.000	25.70	9.12	2.01
20	21	0.475044	AACGTGGGCCCTCAACTTTA	59.525	50.000	25.70	0.00	1.85
21	22	0.396556	AAACGTGGGCCCTCAACTTT	60.397	50.000	25.70	10.12	2.66
22	23	0.396556	AAAACGTGGGCCCTCAACTT	60.397	50.000	25.70	9.69	2.66
23	24	1.106944	CAAAACGTGGGCCCTCAACT	61.107	55.000	25.70	3.19	3.16
24	25	1.104577	TCAAAACGTGGGCCCTCAAC	61.105	55.000	25.70	12.48	3.18
25	26	0.178975	ATCAAAACGTGGGCCCTCAA	60.179	50.000	25.70	0.00	3.02
26	27	0.608035	GATCAAAACGTGGGCCCTCA	60.608	55.000	25.70	0.00	3.86
27	28	0.322546	AGATCAAAACGTGGGCCCTC	60.323	55.000	25.70	19.74	4.30
28	29	0.112412	AAGATCAAAACGTGGGCCCT	59.888	50.000	25.70	0.00	5.19
29	30	0.243636	CAAGATCAAAACGTGGGCCC	59.756	55.000	17.59	17.59	5.80
30	31	0.388520	GCAAGATCAAAACGTGGGCC	60.389	55.000	0.00	0.00	5.80
31	32	0.313672	TGCAAGATCAAAACGTGGGC	59.686	50.000	0.00	0.00	5.36
32	33	1.335872	GGTGCAAGATCAAAACGTGGG	60.336	52.381	0.00	0.00	4.61

Showing 1 to 25 of 180 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.