AutoCloner

Multiple sequence alignment - TraesCS3D01G322300

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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	TraesCS3D01G322300	chr3D	100.000	2283	0	0	894	3176	435295477	435297759	0.000000e+00	4217.0
1	TraesCS3D01G322300	chr3D	100.000	370	0	0	1	370	435294584	435294953	0.000000e+00	684.0
2	TraesCS3D01G322300	chr3B	94.616	2303	98	6	894	3176	571300142	571302438	0.000000e+00	3542.0
3	TraesCS3D01G322300	chr3B	97.297	333	7	2	1	331	571299740	571300072	5.950000e-157	564.0
4	TraesCS3D01G322300	chr3B	100.000	29	0	0	329	357	571300088	571300116	2.000000e-03	54.7
5	TraesCS3D01G322300	chr3A	94.971	2207	86	11	894	3088	574013284	574015477	0.000000e+00	3437.0
6	TraesCS3D01G322300	chr3A	94.324	370	8	8	1	357	574012888	574013257	3.580000e-154	555.0
7	TraesCS3D01G322300	chr3A	95.556	90	4	0	3087	3176	574015829	574015918	9.180000e-31	145.0
8	TraesCS3D01G322300	chr3A	95.082	61	3	0	2293	2353	66036782	66036722	2.610000e-16	97.1
9	TraesCS3D01G322300	chrUn	95.082	61	3	0	2293	2353	45094289	45094349	2.610000e-16	97.1
10	TraesCS3D01G322300	chrUn	95.082	61	3	0	2293	2353	171044576	171044636	2.610000e-16	97.1
11	TraesCS3D01G322300	chrUn	95.082	61	3	0	2293	2353	336782471	336782531	2.610000e-16	97.1
12	TraesCS3D01G322300	chrUn	95.082	61	3	0	2293	2353	405916073	405916133	2.610000e-16	97.1
13	TraesCS3D01G322300	chr6D	95.082	61	3	0	2293	2353	425972912	425972972	2.610000e-16	97.1
14	TraesCS3D01G322300	chr1A	95.082	61	3	0	2293	2353	94759164	94759224	2.610000e-16	97.1
15	TraesCS3D01G322300	chr2A	100.000	32	0	0	2357	2388	764734321	764734352	3.420000e-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	TraesCS3D01G322300	chr3D	435294584	435297759	3175	False	2450.5	4217	100.000000	1	3176	2	chr3D.!!$F1	3175
1	TraesCS3D01G322300	chr3B	571299740	571302438	2698	False	1386.9	3542	97.304333	1	3176	3	chr3B.!!$F1	3175
2	TraesCS3D01G322300	chr3A	574012888	574015918	3030	False	1379.0	3437	94.950333	1	3176	3	chr3A.!!$F1	3175

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
360	382	0.735632	GTCTTGGTCTCTGCGCTCTG	60.736	60.0	9.73	0.0	0.0	3.35	F
1138	1160	0.550914	AGCCACTTCTTCCACCAACA	59.449	50.0	0.00	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1414	1436	0.314935	TGTTGGTCGAACCCGTAGAC	59.685	55.0	0.00	0.0	37.5	2.59	R
2627	2654	0.250252	TGTGAGCGCATTGTCAGGAA	60.250	50.0	11.47	0.0	0.0	3.36	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
70	71	4.254709	AGGAACACCTGCAGCGCA	62.255	61.111	11.47	3.35	36.92	6.09
357	379	1.291588	CTGTCTTGGTCTCTGCGCT	59.708	57.895	9.73	0.00	0.00	5.92
359	381	1.181741	TGTCTTGGTCTCTGCGCTCT	61.182	55.000	9.73	0.00	0.00	4.09
360	382	0.735632	GTCTTGGTCTCTGCGCTCTG	60.736	60.000	9.73	0.00	0.00	3.35
1047	1069	5.642491	GGTTAGAAAGTTCGTTGATAGCCTT	59.358	40.000	0.00	0.00	0.00	4.35
1124	1146	1.973812	GGTTGGAGAAGGCAGCCAC	60.974	63.158	15.80	7.42	0.00	5.01
1138	1160	0.550914	AGCCACTTCTTCCACCAACA	59.449	50.000	0.00	0.00	0.00	3.33
1339	1361	3.379865	GACCCCAACGGCGATGCTA	62.380	63.158	16.62	0.00	33.26	3.49
1414	1436	2.045536	GGGTTGAGCAGAGCAGGG	60.046	66.667	0.00	0.00	0.00	4.45
1488	1510	3.073101	AGCCCCGGACGACTTACC	61.073	66.667	0.73	0.00	0.00	2.85
1558	1580	1.594293	CTCGTGTTCAACAGCCCGT	60.594	57.895	0.00	0.00	0.00	5.28
1767	1789	4.333690	AGCGGTACCTCATAGTATTCGAT	58.666	43.478	10.90	0.00	0.00	3.59
1780	1802	5.598416	AGTATTCGATGATGTCTGGAACA	57.402	39.130	0.00	0.00	43.51	3.18
1798	1820	2.042259	ATCGACGACTGGTACGCCA	61.042	57.895	0.00	0.00	43.73	5.69
1801	1823	2.049802	ACGACTGGTACGCCAACG	60.050	61.111	0.00	9.85	45.51	4.10
1848	1870	4.146640	GGCGAACAATTGCCGAAC	57.853	55.556	20.51	10.91	46.11	3.95
1957	1979	0.668401	GGGTAGTGTGTACCGTGTGC	60.668	60.000	0.00	0.00	38.46	4.57
1962	1984	2.280524	GTGTACCGTGTGCAGCCA	60.281	61.111	0.00	0.00	0.00	4.75
2004	2026	1.142667	TGGGCGATCTTTATGGATGCA	59.857	47.619	0.00	0.00	0.00	3.96
2010	2032	4.214971	GCGATCTTTATGGATGCACTGAAT	59.785	41.667	0.00	0.00	0.00	2.57
2025	2047	4.326826	CACTGAATAAGGAAAGACAGCCA	58.673	43.478	0.00	0.00	0.00	4.75
2047	2069	2.917363	TCGATCTCGCAGCTATTAACG	58.083	47.619	0.00	0.00	39.60	3.18
2187	2209	8.547967	TTAAGCTTGAGTAGTGGAAATGTAAG	57.452	34.615	9.86	0.00	0.00	2.34
2189	2211	4.095036	GCTTGAGTAGTGGAAATGTAAGGC	59.905	45.833	0.00	0.00	0.00	4.35
2229	2256	7.174253	GTCATGGACCAAAAAGACACTACATAA	59.826	37.037	0.00	0.00	0.00	1.90
2313	2340	4.081972	TGGCTGTGAGAAGAAGATCTACAC	60.082	45.833	0.00	1.44	32.69	2.90
2319	2346	3.452474	AGAAGAAGATCTACACGCATGC	58.548	45.455	7.91	7.91	0.00	4.06
2320	2347	3.131933	AGAAGAAGATCTACACGCATGCT	59.868	43.478	17.13	0.00	0.00	3.79
2321	2348	3.090952	AGAAGATCTACACGCATGCTC	57.909	47.619	17.13	4.33	0.00	4.26
2617	2644	9.241919	TCTGATCAAACTTGCTTTCCATTAATA	57.758	29.630	0.00	0.00	0.00	0.98
2618	2645	9.294030	CTGATCAAACTTGCTTTCCATTAATAC	57.706	33.333	0.00	0.00	0.00	1.89
2627	2654	8.579850	TTGCTTTCCATTAATACATCACTCTT	57.420	30.769	0.00	0.00	0.00	2.85
2672	2699	7.729116	TGAAAAAGCCTGAAAAGAAGAATGAT	58.271	30.769	0.00	0.00	0.00	2.45
2894	2933	4.478206	TTTTGTTTCAACATTGAGGGCA	57.522	36.364	0.00	0.00	38.95	5.36
2949	2992	4.620982	ACTCACTTTATTTGGTGCTTTGC	58.379	39.130	0.00	0.00	33.91	3.68
2972	3015	2.715763	ACTCTCTGGTTTCCTGGGTA	57.284	50.000	0.00	0.00	0.00	3.69
3140	3536	3.708403	ATCTCAATGTTCCACTGCTCA	57.292	42.857	0.00	0.00	0.00	4.26
3148	3544	0.671472	TTCCACTGCTCAGACATGCG	60.671	55.000	3.60	0.00	0.00	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	71	1.900498	GCTTGTGCTCACCAGCCTT	60.900	57.895	13.27	0.00	46.26	4.35
299	301	2.034939	TGTTTCTTCTTCCAGACGCGTA	59.965	45.455	13.97	0.00	0.00	4.42
300	302	1.202486	TGTTTCTTCTTCCAGACGCGT	60.202	47.619	13.85	13.85	0.00	6.01
301	303	1.497991	TGTTTCTTCTTCCAGACGCG	58.502	50.000	3.53	3.53	0.00	6.01
302	304	3.131396	TCTTGTTTCTTCTTCCAGACGC	58.869	45.455	0.00	0.00	0.00	5.19
303	305	3.185391	GCTCTTGTTTCTTCTTCCAGACG	59.815	47.826	0.00	0.00	0.00	4.18
304	306	3.500299	GGCTCTTGTTTCTTCTTCCAGAC	59.500	47.826	0.00	0.00	0.00	3.51
305	307	3.136443	TGGCTCTTGTTTCTTCTTCCAGA	59.864	43.478	0.00	0.00	0.00	3.86
306	308	3.480470	TGGCTCTTGTTTCTTCTTCCAG	58.520	45.455	0.00	0.00	0.00	3.86
905	927	9.288576	GTTGATTGATGGATTCACAGGATAATA	57.711	33.333	0.00	0.00	32.84	0.98
1061	1083	3.302347	CTGAAAGGGAGCTCCGCGT	62.302	63.158	26.36	14.43	41.52	6.01
1124	1146	1.806542	CATCGGTGTTGGTGGAAGAAG	59.193	52.381	0.00	0.00	0.00	2.85
1138	1160	1.077357	ACTCTCGGAGCTCATCGGT	60.077	57.895	17.19	4.49	32.04	4.69
1229	1251	1.990614	GCTTCGGAGGGGGAGAAGT	60.991	63.158	0.00	0.00	42.28	3.01
1346	1368	4.161295	TGGCATTCTCCTCCGGCG	62.161	66.667	0.00	0.00	0.00	6.46
1414	1436	0.314935	TGTTGGTCGAACCCGTAGAC	59.685	55.000	0.00	0.00	37.50	2.59
1647	1669	1.072331	CCGAGGGCCATAAGTATGCTT	59.928	52.381	6.18	0.56	38.66	3.91
1780	1802	2.042259	TGGCGTACCAGTCGTCGAT	61.042	57.895	0.00	0.00	42.67	3.59
1814	1836	1.937546	GCCCCTCGACAAGGCATTTG	61.938	60.000	10.06	0.00	46.34	2.32
1844	1866	3.777925	CGAGCACAAGGCCGTTCG	61.778	66.667	0.00	0.00	46.50	3.95
1845	1867	3.423154	CCGAGCACAAGGCCGTTC	61.423	66.667	0.00	0.00	46.50	3.95
1962	1984	2.347322	GCTCTCTCTGTCGGCCAGT	61.347	63.158	2.24	0.00	42.19	4.00
2004	2026	4.640771	TGGCTGTCTTTCCTTATTCAGT	57.359	40.909	0.00	0.00	0.00	3.41
2010	2032	3.973206	TCGATTGGCTGTCTTTCCTTA	57.027	42.857	0.00	0.00	0.00	2.69
2025	2047	3.914966	CGTTAATAGCTGCGAGATCGATT	59.085	43.478	6.39	0.00	43.02	3.34
2047	2069	6.148645	GTCTGAAGAATTTCCTCTTTCAGGTC	59.851	42.308	18.53	12.15	43.95	3.85
2256	2283	9.754382	GAATTTATGCCATAACTTTCATGTGAT	57.246	29.630	11.63	0.00	0.00	3.06
2313	2340	1.450531	GGGAGAAATGGGAGCATGCG	61.451	60.000	13.01	0.00	0.00	4.73
2319	2346	2.220653	TTTGCAGGGAGAAATGGGAG	57.779	50.000	0.00	0.00	0.00	4.30
2320	2347	2.692709	TTTTGCAGGGAGAAATGGGA	57.307	45.000	0.00	0.00	0.00	4.37
2321	2348	4.467438	ACTTATTTTGCAGGGAGAAATGGG	59.533	41.667	4.00	0.52	0.00	4.00
2440	2467	9.814899	TGTATGTTTGTCTTGAATTTTTGTCAT	57.185	25.926	0.00	0.00	0.00	3.06
2617	2644	3.755378	GCATTGTCAGGAAAGAGTGATGT	59.245	43.478	0.00	0.00	0.00	3.06
2618	2645	3.181513	CGCATTGTCAGGAAAGAGTGATG	60.182	47.826	0.00	0.00	0.00	3.07
2627	2654	0.250252	TGTGAGCGCATTGTCAGGAA	60.250	50.000	11.47	0.00	0.00	3.36
2672	2699	4.402829	TCCATTTTCACTGATTTCCCGAA	58.597	39.130	0.00	0.00	0.00	4.30
2935	2978	5.046304	AGAGAGTAGAGCAAAGCACCAAATA	60.046	40.000	0.00	0.00	0.00	1.40
2949	2992	2.763448	CCCAGGAAACCAGAGAGTAGAG	59.237	54.545	0.00	0.00	0.00	2.43
2972	3015	3.096852	TGGAGTGTGGATGAACTACGAT	58.903	45.455	0.00	0.00	32.52	3.73
3140	3536	0.610174	TTGGAGAGAAGCGCATGTCT	59.390	50.000	12.45	12.45	0.00	3.41
3148	3544	0.110010	GCGCACTTTTGGAGAGAAGC	60.110	55.000	0.30	0.00	0.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.