AutoCloner

Multiple sequence alignment - TraesCS3D01G266200

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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	TraesCS3D01G266200	chr3D	100.000	6059	0	0	1	6059	369402672	369408730	0.000000e+00	11189.0
1	TraesCS3D01G266200	chr3D	99.296	142	1	0	2425	2566	369404926	369405067	2.170000e-64	257.0
2	TraesCS3D01G266200	chr3D	99.296	142	1	0	2255	2396	369405096	369405237	2.170000e-64	257.0
3	TraesCS3D01G266200	chr3D	93.684	95	6	0	2162	2256	458883365	458883459	6.330000e-30	143.0
4	TraesCS3D01G266200	chr3D	81.159	138	12	5	2145	2268	134505021	134505158	1.390000e-16	99.0
5	TraesCS3D01G266200	chr3D	87.179	78	7	2	2177	2251	496120321	496120398	1.080000e-12	86.1
6	TraesCS3D01G266200	chr3A	97.452	5062	103	9	1	5044	490612232	490617285	0.000000e+00	8610.0
7	TraesCS3D01G266200	chr3A	99.296	142	1	0	2255	2396	490614654	490614795	2.170000e-64	257.0
8	TraesCS3D01G266200	chr3A	94.366	142	8	0	2425	2566	490614484	490614625	1.020000e-52	219.0
9	TraesCS3D01G266200	chr3A	93.684	95	6	0	2162	2256	601131332	601131426	6.330000e-30	143.0
10	TraesCS3D01G266200	chr3A	88.506	87	7	2	2168	2251	635387505	635387591	1.070000e-17	102.0
11	TraesCS3D01G266200	chr3B	97.197	2640	60	4	2425	5059	480340905	480343535	0.000000e+00	4453.0
12	TraesCS3D01G266200	chr3B	93.793	1740	68	19	671	2396	480339333	480341046	0.000000e+00	2579.0
13	TraesCS3D01G266200	chr3B	90.323	62	4	2	542	601	480332230	480332291	5.030000e-11	80.5
14	TraesCS3D01G266200	chr5A	99.800	1001	2	0	5059	6059	82311245	82310245	0.000000e+00	1838.0
15	TraesCS3D01G266200	chr5A	99.700	1001	3	0	5059	6059	24342070	24343070	0.000000e+00	1832.0
16	TraesCS3D01G266200	chr5A	99.600	1001	4	0	5059	6059	257360851	257359851	0.000000e+00	1827.0
17	TraesCS3D01G266200	chr7A	99.700	1001	3	0	5059	6059	85880682	85879682	0.000000e+00	1832.0
18	TraesCS3D01G266200	chr2B	99.700	1001	3	0	5059	6059	674788729	674789729	0.000000e+00	1832.0
19	TraesCS3D01G266200	chr2B	99.700	1000	3	0	5059	6058	423433812	423434811	0.000000e+00	1831.0
20	TraesCS3D01G266200	chr5B	99.600	1001	4	0	5059	6059	5047509	5046509	0.000000e+00	1827.0
21	TraesCS3D01G266200	chr1B	99.600	1001	4	0	5059	6059	151844246	151843246	0.000000e+00	1827.0
22	TraesCS3D01G266200	chr1B	84.259	108	4	5	2162	2256	451736453	451736560	6.470000e-15	93.5
23	TraesCS3D01G266200	chr1A	99.600	1001	4	0	5059	6059	127928031	127927031	0.000000e+00	1827.0
24	TraesCS3D01G266200	chr1A	82.301	113	6	5	2160	2259	542140197	542140308	1.080000e-12	86.1
25	TraesCS3D01G266200	chr1D	85.185	108	3	5	2162	2256	335588794	335588901	1.390000e-16	99.0
26	TraesCS3D01G266200	chr1D	84.071	113	5	5	2160	2259	446428281	446428393	5.000000e-16	97.1

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	TraesCS3D01G266200	chr3D	369402672	369408730	6058	False	3901.000000	11189	99.530667	1	6059	3	chr3D.!!$F4	6058
1	TraesCS3D01G266200	chr3A	490612232	490617285	5053	False	3028.666667	8610	97.038000	1	5044	3	chr3A.!!$F3	5043
2	TraesCS3D01G266200	chr3B	480339333	480343535	4202	False	3516.000000	4453	95.495000	671	5059	2	chr3B.!!$F2	4388
3	TraesCS3D01G266200	chr5A	82310245	82311245	1000	True	1838.000000	1838	99.800000	5059	6059	1	chr5A.!!$R1	1000
4	TraesCS3D01G266200	chr5A	24342070	24343070	1000	False	1832.000000	1832	99.700000	5059	6059	1	chr5A.!!$F1	1000
5	TraesCS3D01G266200	chr5A	257359851	257360851	1000	True	1827.000000	1827	99.600000	5059	6059	1	chr5A.!!$R2	1000
6	TraesCS3D01G266200	chr7A	85879682	85880682	1000	True	1832.000000	1832	99.700000	5059	6059	1	chr7A.!!$R1	1000
7	TraesCS3D01G266200	chr2B	674788729	674789729	1000	False	1832.000000	1832	99.700000	5059	6059	1	chr2B.!!$F2	1000
8	TraesCS3D01G266200	chr2B	423433812	423434811	999	False	1831.000000	1831	99.700000	5059	6058	1	chr2B.!!$F1	999
9	TraesCS3D01G266200	chr5B	5046509	5047509	1000	True	1827.000000	1827	99.600000	5059	6059	1	chr5B.!!$R1	1000
10	TraesCS3D01G266200	chr1B	151843246	151844246	1000	True	1827.000000	1827	99.600000	5059	6059	1	chr1B.!!$R1	1000
11	TraesCS3D01G266200	chr1A	127927031	127928031	1000	True	1827.000000	1827	99.600000	5059	6059	1	chr1A.!!$R1	1000

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
367	369	0.321210	CCACATAGGCACGGTCAACA	60.321	55.000	0.00	0.00	3.33	F
661	665	0.842635	ACTGGGCCTGAGGAATCATC	59.157	55.000	18.12	0.00	2.92	F
1544	1560	2.173519	AGTGAAGGCAAACCATCCATG	58.826	47.619	0.00	39.06	3.66	F
2352	2369	3.508793	ACAAATGAAAGATCTGGGTGCAG	59.491	43.478	0.00	0.00	4.41	F
2365	2382	1.476110	GGGTGCAGAAGTGTGTTACCA	60.476	52.381	0.00	31.93	3.25	F
4127	4149	1.635817	AACCGAGGGTGGATCATGGG	61.636	60.000	0.00	35.34	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1486	1502	1.067776	GGAAGCCACTCCGGTATATCG	60.068	57.143	0.00	0.00	36.97	2.92	R
1850	1866	1.376543	ACAAGGATGCAGATTCAGCG	58.623	50.000	0.00	0.00	33.85	5.18	R
2365	2382	2.398588	TGCTATGAGGGAGGAATTCGT	58.601	47.619	0.00	0.00	0.00	3.85	R
4127	4149	1.542915	TCTTGCAGCTTGAAGCCATTC	59.457	47.619	14.45	1.23	43.77	2.67	R
4204	4226	5.249622	TGGTGTACCATCAGGAATTTGACTA	59.750	40.000	0.00	0.00	42.01	2.59	R
5268	5299	0.323725	GGCCCACCACATGACATTCT	60.324	55.000	0.00	0.00	35.26	2.40	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
69	70	2.908073	GCCAAAGCACACCACTCGG	61.908	63.158	0.00	0.00	39.53	4.63
125	126	4.043310	AGACCCTTCAAATGACAAGGATCA	59.957	41.667	3.23	0.00	41.74	2.92
126	127	4.739793	ACCCTTCAAATGACAAGGATCAA	58.260	39.130	3.23	0.00	41.74	2.57
136	137	3.258123	TGACAAGGATCAAGACGATGACA	59.742	43.478	0.00	0.00	33.17	3.58
224	226	3.188254	TCGAATGCAAAAGAAATCTGCGA	59.812	39.130	0.00	0.00	38.97	5.10
286	288	4.140354	CCTTTGGGGGTCTACCGA	57.860	61.111	0.00	0.00	41.60	4.69
319	321	1.126488	GGTAGGGTTAGTGGCCTACC	58.874	60.000	3.32	2.45	44.92	3.18
320	322	0.749049	GTAGGGTTAGTGGCCTACCG	59.251	60.000	3.32	0.00	39.70	4.02
339	341	1.902556	CCGGGGTTAGTGGTGGTAG	59.097	63.158	0.00	0.00	0.00	3.18
340	342	1.219935	CGGGGTTAGTGGTGGTAGC	59.780	63.158	0.00	0.00	0.00	3.58
341	343	1.605992	GGGGTTAGTGGTGGTAGCC	59.394	63.158	0.00	0.00	0.00	3.93
367	369	0.321210	CCACATAGGCACGGTCAACA	60.321	55.000	0.00	0.00	0.00	3.33
377	379	0.879765	ACGGTCAACAGGTCTAGACG	59.120	55.000	16.56	6.52	31.93	4.18
391	393	4.549516	GACGAGCGTCTACCGGGC	62.550	72.222	15.13	0.00	41.57	6.13
413	415	3.431766	CGGTAGCCTGTTAGCTTTACCAT	60.432	47.826	0.00	0.00	41.41	3.55
415	417	4.383770	GGTAGCCTGTTAGCTTTACCATCA	60.384	45.833	0.00	0.00	41.41	3.07
503	507	9.450807	CTAAACTCAATGTTACAAGGTCAAAAG	57.549	33.333	0.00	0.00	38.03	2.27
509	513	4.367450	TGTTACAAGGTCAAAAGCAATGC	58.633	39.130	0.00	0.00	0.00	3.56
661	665	0.842635	ACTGGGCCTGAGGAATCATC	59.157	55.000	18.12	0.00	0.00	2.92
674	678	8.040132	CCTGAGGAATCATCTATAGTCCAAATC	58.960	40.741	0.00	0.20	0.00	2.17
1393	1409	4.275810	AGAACGCTCTTATACCTGGTACA	58.724	43.478	9.09	0.00	0.00	2.90
1438	1454	8.656806	TGGTTATTTAGATCCCCTGTACAATAG	58.343	37.037	0.00	0.00	0.00	1.73
1473	1489	4.053295	GCGATCGGTACCTTAGCAAAATA	58.947	43.478	18.30	0.00	0.00	1.40
1474	1490	4.150098	GCGATCGGTACCTTAGCAAAATAG	59.850	45.833	18.30	0.00	0.00	1.73
1479	1495	4.135306	GGTACCTTAGCAAAATAGAGGGC	58.865	47.826	4.06	0.00	0.00	5.19
1486	1502	4.143986	AGCAAAATAGAGGGCTGAGTAC	57.856	45.455	0.00	0.00	34.83	2.73
1544	1560	2.173519	AGTGAAGGCAAACCATCCATG	58.826	47.619	0.00	0.00	39.06	3.66
1580	1596	9.063615	TCAAGTATTCATCTTATCGTGCTAGTA	57.936	33.333	0.00	0.00	0.00	1.82
1927	1943	6.796785	ATATTTCAAGCCTGCCATTAAAGT	57.203	33.333	0.00	0.00	0.00	2.66
2070	2086	9.241919	ACACACAGAATCAATTTTGTCCATATA	57.758	29.630	0.00	0.00	33.44	0.86
2172	2189	5.259832	AGAGTAAATAGTACAACCTCCGC	57.740	43.478	0.00	0.00	0.00	5.54
2204	2221	3.928992	ACTGTCGCTGAAATGAGTGTATG	59.071	43.478	0.00	0.00	0.00	2.39
2322	2339	3.645212	TCACAGGGAAATGCCAAAATTCA	59.355	39.130	0.00	0.00	38.95	2.57
2352	2369	3.508793	ACAAATGAAAGATCTGGGTGCAG	59.491	43.478	0.00	0.00	0.00	4.41
2365	2382	1.476110	GGGTGCAGAAGTGTGTTACCA	60.476	52.381	0.00	0.00	31.93	3.25
2403	2420	2.749076	AGCAAGCATTTTCAGCGACATA	59.251	40.909	0.00	0.00	37.01	2.29
2741	2758	5.121454	CAGAGAGTTCAGGCAAATGAAGTAC	59.879	44.000	6.03	0.00	41.76	2.73
2800	2817	3.561213	CGAGCTGCATGGCTGTCG	61.561	66.667	5.01	0.40	43.20	4.35
3414	3431	4.176752	GGAGTGCCCACCGGATCC	62.177	72.222	9.46	0.00	34.14	3.36
3784	3801	9.449550	GGTTTATTTTCATTTTTCAGCAAAAGG	57.550	29.630	0.00	0.00	37.79	3.11
4127	4149	1.635817	AACCGAGGGTGGATCATGGG	61.636	60.000	0.00	0.00	35.34	4.00
4204	4226	7.452880	TGTTTCACTACTACCGTACTACATT	57.547	36.000	0.00	0.00	0.00	2.71
4216	4238	7.179076	ACCGTACTACATTAGTCAAATTCCT	57.821	36.000	0.00	0.00	40.14	3.36
4270	4292	0.821301	TGGTGCTCGCCATTTTGACA	60.821	50.000	0.00	0.00	32.81	3.58
4519	4541	6.430925	TGTGTGCTTCAAATATACTTCTTGCT	59.569	34.615	0.00	0.00	0.00	3.91
4767	4789	6.694447	AGATTGTTTGATCTGGGAATGTTTG	58.306	36.000	0.00	0.00	35.13	2.93
4884	4907	1.299468	GGATCTACAGGCGACAGCG	60.299	63.158	0.00	0.00	46.35	5.18
5046	5077	2.035704	CAGTGGGCTGTGCAAATACAAA	59.964	45.455	0.00	0.00	37.92	2.83
5268	5299	3.441101	AGGCCTATGATAAGATACCGCA	58.559	45.455	1.29	0.00	0.00	5.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
95	96	4.141505	TGTCATTTGAAGGGTCTTCTGTCA	60.142	41.667	8.80	1.79	0.00	3.58
125	126	0.324943	CCCCCTGTTGTCATCGTCTT	59.675	55.000	0.00	0.00	0.00	3.01
126	127	0.544357	TCCCCCTGTTGTCATCGTCT	60.544	55.000	0.00	0.00	0.00	4.18
136	137	2.907179	CGGGCTTCTTCCCCCTGTT	61.907	63.158	0.00	0.00	43.56	3.16
255	257	2.092323	CCAAAGGGGTAACTAGCTTGC	58.908	52.381	0.00	0.00	0.00	4.01
286	288	1.043816	CCTACCATCTGATCCTGCGT	58.956	55.000	0.00	0.00	0.00	5.24
319	321	4.770874	CCACCACTAACCCCGGCG	62.771	72.222	0.00	0.00	0.00	6.46
320	322	2.248086	CTACCACCACTAACCCCGGC	62.248	65.000	0.00	0.00	0.00	6.13
324	326	1.605992	GGGCTACCACCACTAACCC	59.394	63.158	0.00	0.00	36.50	4.11
339	341	3.939564	CCTATGTGGCAAAGGGGC	58.060	61.111	0.00	0.00	43.73	5.80
360	362	1.135344	GCTCGTCTAGACCTGTTGACC	60.135	57.143	17.23	0.00	0.00	4.02
391	393	2.093869	TGGTAAAGCTAACAGGCTACCG	60.094	50.000	0.00	0.00	41.39	4.02
413	415	3.774734	AGTCTACCACCATACACAGTGA	58.225	45.455	7.81	0.00	36.01	3.41
415	417	5.187186	CCTTTAGTCTACCACCATACACAGT	59.813	44.000	0.00	0.00	0.00	3.55
531	535	9.801714	CTGTTTTGATTTTGTGATTTTAGCATC	57.198	29.630	0.00	0.00	0.00	3.91
550	554	5.448904	CCAAAAGCCCAAAATCACTGTTTTG	60.449	40.000	5.39	5.39	44.63	2.44
603	607	3.367646	TCGGGCCCAAATGTTATAACA	57.632	42.857	24.92	20.14	44.06	2.41
604	608	4.583073	AGAATCGGGCCCAAATGTTATAAC	59.417	41.667	24.92	8.75	0.00	1.89
605	609	4.798882	AGAATCGGGCCCAAATGTTATAA	58.201	39.130	24.92	0.00	0.00	0.98
606	610	4.104102	AGAGAATCGGGCCCAAATGTTATA	59.896	41.667	24.92	0.00	42.67	0.98
674	678	2.843113	AGGACCTTGGAATCTCTTGGAG	59.157	50.000	0.00	0.00	0.00	3.86
1024	1040	2.064723	ATCTCCCATCGACTGACGCG	62.065	60.000	3.53	3.53	42.26	6.01
1132	1148	1.362717	GGCTTCGGCTGCGTATCTA	59.637	57.895	0.00	0.00	41.44	1.98
1393	1409	3.951680	ACCACGGTGAAAAAGAAGATTGT	59.048	39.130	10.28	0.00	0.00	2.71
1438	1454	2.128035	CCGATCGCTCCACTACAAATC	58.872	52.381	10.32	0.00	0.00	2.17
1473	1489	3.688235	GGTATATCGTACTCAGCCCTCT	58.312	50.000	0.00	0.00	0.00	3.69
1474	1490	2.419324	CGGTATATCGTACTCAGCCCTC	59.581	54.545	0.00	0.00	0.00	4.30
1479	1495	3.436015	CCACTCCGGTATATCGTACTCAG	59.564	52.174	4.41	0.00	0.00	3.35
1486	1502	1.067776	GGAAGCCACTCCGGTATATCG	60.068	57.143	0.00	0.00	36.97	2.92
1580	1596	9.961265	CATGAACATATGAACTGATAAATTGCT	57.039	29.630	10.38	0.00	0.00	3.91
1610	1626	2.732658	GGCCATATGCTGCTTGCC	59.267	61.111	0.00	0.00	42.00	4.52
1850	1866	1.376543	ACAAGGATGCAGATTCAGCG	58.623	50.000	0.00	0.00	33.85	5.18
1898	1914	3.119531	TGGCAGGCTTGAAATATTGAACG	60.120	43.478	0.00	0.00	0.00	3.95
1927	1943	4.523558	TCACAGATTTCATCATGGCAAACA	59.476	37.500	0.00	0.00	0.00	2.83
2070	2086	8.495949	CATGTCTTCAACGTCAGTTTAACTAAT	58.504	33.333	0.00	0.00	38.79	1.73
2084	2100	3.899734	TGAAATTGGCATGTCTTCAACG	58.100	40.909	0.00	0.00	0.00	4.10
2088	2104	4.159135	ACCATCTGAAATTGGCATGTCTTC	59.841	41.667	0.00	0.00	36.41	2.87
2172	2189	2.972625	TCAGCGACAGTTAATTCTGGG	58.027	47.619	0.00	0.00	39.48	4.45
2204	2221	3.427528	TGAAATGAGTGAAACGCGTCTAC	59.572	43.478	14.44	12.35	45.86	2.59
2302	2319	4.914177	ATGAATTTTGGCATTTCCCTGT	57.086	36.364	0.00	0.00	0.00	4.00
2304	2321	5.627503	GCACTATGAATTTTGGCATTTCCCT	60.628	40.000	0.00	0.00	0.00	4.20
2322	2339	6.127535	CCCAGATCTTTCATTTGTTGCACTAT	60.128	38.462	0.00	0.00	0.00	2.12
2365	2382	2.398588	TGCTATGAGGGAGGAATTCGT	58.601	47.619	0.00	0.00	0.00	3.85
2403	2420	6.476378	ACTATGAATTAAAGCAGACACAGGT	58.524	36.000	0.00	0.00	0.00	4.00
2741	2758	3.589988	AGAAACCAAGTGCGAGTGATAG	58.410	45.455	0.00	0.00	0.00	2.08
2800	2817	5.822519	TGCAGATAACCACACAATATCCTTC	59.177	40.000	0.00	0.00	0.00	3.46
3683	3700	9.770097	CAAGTCTTAAGATCCATAGCTAATTGA	57.230	33.333	8.75	0.00	0.00	2.57
3784	3801	6.144080	CGCTGTATAAAATGTAGAGTAGGCAC	59.856	42.308	0.00	0.00	0.00	5.01
4127	4149	1.542915	TCTTGCAGCTTGAAGCCATTC	59.457	47.619	14.45	1.23	43.77	2.67
4204	4226	5.249622	TGGTGTACCATCAGGAATTTGACTA	59.750	40.000	0.00	0.00	42.01	2.59
4216	4238	6.299922	TGAACTTTGTATTGGTGTACCATCA	58.700	36.000	4.31	0.00	46.97	3.07
4270	4292	5.426689	ACATGGCATATAGGACGATCAAT	57.573	39.130	0.00	0.00	0.00	2.57
4469	4491	0.034896	GTCCGTGGAAGGAAGCTCAA	59.965	55.000	0.00	0.00	42.77	3.02
4767	4789	8.247562	ACATCTGTTACACTGTTCTAGATCTTC	58.752	37.037	0.00	0.00	0.00	2.87
4884	4907	5.495640	AGACAGATCAATTTTCTCCCACTC	58.504	41.667	0.00	0.00	0.00	3.51
4944	4967	3.845781	ATCCAGCATCCTTACGAACAT	57.154	42.857	0.00	0.00	0.00	2.71
5268	5299	0.323725	GGCCCACCACATGACATTCT	60.324	55.000	0.00	0.00	35.26	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.