AutoCloner

Multiple sequence alignment - TraesCS1D01G170000

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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	TraesCS1D01G170000	chr1D	100.000	2507	0	0	1	2507	244392379	244394885	0.000000e+00	4630.0
1	TraesCS1D01G170000	chr1D	96.007	1778	68	3	2	1778	254481966	254483741	0.000000e+00	2887.0
2	TraesCS1D01G170000	chr1D	96.565	524	18	0	2	525	176210578	176211101	0.000000e+00	869.0
3	TraesCS1D01G170000	chr1D	96.389	360	13	0	2	361	446749051	446748692	5.970000e-166	593.0
4	TraesCS1D01G170000	chr3B	95.600	1909	68	6	266	2167	201498791	201500690	0.000000e+00	3046.0
5	TraesCS1D01G170000	chr3B	95.147	989	41	3	370	1358	544899265	544900246	0.000000e+00	1554.0
6	TraesCS1D01G170000	chr1A	95.620	1872	67	7	2	1867	554473609	554471747	0.000000e+00	2988.0
7	TraesCS1D01G170000	chr1A	94.912	570	21	3	1599	2167	554471482	554470920	0.000000e+00	885.0
8	TraesCS1D01G170000	chr2D	96.498	1799	59	3	2	1798	643858330	643860126	0.000000e+00	2970.0
9	TraesCS1D01G170000	chr2D	96.261	1685	55	5	2	1680	628291527	628289845	0.000000e+00	2756.0
10	TraesCS1D01G170000	chr2D	95.495	111	5	0	2397	2507	406835356	406835246	7.130000e-41	178.0
11	TraesCS1D01G170000	chr2D	91.935	62	4	1	2187	2247	221244920	221244859	4.440000e-13	86.1
12	TraesCS1D01G170000	chr5D	96.484	1792	58	2	2	1789	483802787	483800997	0.000000e+00	2955.0
13	TraesCS1D01G170000	chr5D	96.165	1799	63	5	2	1798	6219212	6217418	0.000000e+00	2935.0
14	TraesCS1D01G170000	chr3A	94.365	1473	74	3	703	2167	393238698	393237227	0.000000e+00	2252.0
15	TraesCS1D01G170000	chr3A	94.499	909	35	6	1223	2125	435414845	435413946	0.000000e+00	1387.0
16	TraesCS1D01G170000	chr3A	94.581	609	24	4	1560	2167	593321850	593321250	0.000000e+00	933.0
17	TraesCS1D01G170000	chr3A	93.966	348	11	3	2168	2507	393237192	393236847	3.700000e-143	518.0
18	TraesCS1D01G170000	chr5B	95.014	361	17	1	1807	2167	559429707	559430066	1.300000e-157	566.0
19	TraesCS1D01G170000	chr5B	93.750	80	3	1	2168	2245	548607083	548607162	4.380000e-23	119.0
20	TraesCS1D01G170000	chr4B	95.833	312	13	0	1848	2159	421404471	421404160	2.880000e-139	505.0
21	TraesCS1D01G170000	chr4B	90.110	91	5	3	2409	2498	567190556	567190469	5.670000e-22	115.0
22	TraesCS1D01G170000	chr7B	95.987	299	11	1	1869	2167	300903252	300902955	3.750000e-133	484.0
23	TraesCS1D01G170000	chr7B	96.739	92	3	0	2168	2259	149444909	149445000	1.200000e-33	154.0
24	TraesCS1D01G170000	chr6A	94.534	311	17	0	1811	2121	495543357	495543047	4.850000e-132	481.0
25	TraesCS1D01G170000	chr6A	94.915	118	6	0	2390	2507	192822596	192822713	4.260000e-43	185.0
26	TraesCS1D01G170000	chr6A	97.030	101	3	0	2407	2507	1715158	1715258	1.190000e-38	171.0
27	TraesCS1D01G170000	chr7D	98.492	199	3	0	2309	2507	509197223	509197421	3.970000e-93	351.0
28	TraesCS1D01G170000	chr5A	95.000	140	7	0	2368	2507	696746663	696746524	1.170000e-53	220.0
29	TraesCS1D01G170000	chr5A	97.600	125	3	0	2269	2393	570914791	570914667	5.430000e-52	215.0
30	TraesCS1D01G170000	chr5A	85.648	216	16	8	2168	2368	11090942	11091157	1.950000e-51	213.0
31	TraesCS1D01G170000	chr5A	89.189	111	12	0	2283	2393	644316134	644316024	3.360000e-29	139.0
32	TraesCS1D01G170000	chr3D	95.041	121	6	0	2387	2507	213385122	213385242	9.150000e-45	191.0
33	TraesCS1D01G170000	chr3D	81.169	154	18	7	2186	2336	597862313	597862458	2.040000e-21	113.0
34	TraesCS1D01G170000	chr6D	91.791	134	7	3	2236	2365	100526575	100526708	1.530000e-42	183.0
35	TraesCS1D01G170000	chr6D	95.370	108	3	2	2259	2364	100540801	100540908	1.190000e-38	171.0
36	TraesCS1D01G170000	chr6D	95.699	93	3	1	2168	2259	354356083	354356175	5.590000e-32	148.0
37	TraesCS1D01G170000	chr6D	90.123	81	4	1	2168	2244	100540138	100540218	4.410000e-18	102.0
38	TraesCS1D01G170000	chr6B	85.165	182	14	5	2168	2336	184717956	184718137	9.220000e-40	174.0
39	TraesCS1D01G170000	chr4A	96.040	101	4	0	2399	2499	78568421	78568321	5.550000e-37	165.0
40	TraesCS1D01G170000	chr7A	88.281	128	5	5	2216	2333	647448308	647448181	7.230000e-31	145.0
41	TraesCS1D01G170000	chrUn	86.765	136	4	6	2186	2307	21634136	21634271	3.360000e-29	139.0

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	TraesCS1D01G170000	chr1D	244392379	244394885	2506	False	4630.0	4630	100.0000	1	2507	1	chr1D.!!$F2	2506
1	TraesCS1D01G170000	chr1D	254481966	254483741	1775	False	2887.0	2887	96.0070	2	1778	1	chr1D.!!$F3	1776
2	TraesCS1D01G170000	chr1D	176210578	176211101	523	False	869.0	869	96.5650	2	525	1	chr1D.!!$F1	523
3	TraesCS1D01G170000	chr3B	201498791	201500690	1899	False	3046.0	3046	95.6000	266	2167	1	chr3B.!!$F1	1901
4	TraesCS1D01G170000	chr3B	544899265	544900246	981	False	1554.0	1554	95.1470	370	1358	1	chr3B.!!$F2	988
5	TraesCS1D01G170000	chr1A	554470920	554473609	2689	True	1936.5	2988	95.2660	2	2167	2	chr1A.!!$R1	2165
6	TraesCS1D01G170000	chr2D	643858330	643860126	1796	False	2970.0	2970	96.4980	2	1798	1	chr2D.!!$F1	1796
7	TraesCS1D01G170000	chr2D	628289845	628291527	1682	True	2756.0	2756	96.2610	2	1680	1	chr2D.!!$R3	1678
8	TraesCS1D01G170000	chr5D	483800997	483802787	1790	True	2955.0	2955	96.4840	2	1789	1	chr5D.!!$R2	1787
9	TraesCS1D01G170000	chr5D	6217418	6219212	1794	True	2935.0	2935	96.1650	2	1798	1	chr5D.!!$R1	1796
10	TraesCS1D01G170000	chr3A	435413946	435414845	899	True	1387.0	1387	94.4990	1223	2125	1	chr3A.!!$R1	902
11	TraesCS1D01G170000	chr3A	393236847	393238698	1851	True	1385.0	2252	94.1655	703	2507	2	chr3A.!!$R3	1804
12	TraesCS1D01G170000	chr3A	593321250	593321850	600	True	933.0	933	94.5810	1560	2167	1	chr3A.!!$R2	607

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
217	218	0.117340	AGTAAGTCCTCAGCCTGGGT	59.883	55.000	0.0	0.0	0.00	4.51	F
665	666	1.899814	TGAGTGTCTATGTGGTGGACC	59.100	52.381	0.0	0.0	37.51	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1325	1327	1.403814	AGCCACTCGATTAGCTGCTA	58.596	50.000	5.02	5.02	34.53	3.49	R
1945	2493	3.555795	CGATGGCTATTCACAGCTACCAT	60.556	47.826	0.00	0.00	41.50	3.55	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
80	81	7.417811	AGAGTTATAGGGAGGGACTTATGTA	57.582	40.000	0.00	0.00	41.55	2.29
193	194	3.999663	GGATACTGATATCTTGGCAGCAC	59.000	47.826	3.98	0.00	37.85	4.40
217	218	0.117340	AGTAAGTCCTCAGCCTGGGT	59.883	55.000	0.00	0.00	0.00	4.51
224	225	3.551496	CTCAGCCTGGGTTTCCGCA	62.551	63.158	0.00	0.00	35.24	5.69
334	335	5.231568	CGTTACAAAGGACGATTCTATCACC	59.768	44.000	0.00	0.00	41.53	4.02
343	344	3.075148	CGATTCTATCACCTCGAGCCTA	58.925	50.000	6.99	0.00	33.07	3.93
347	348	4.100279	TCTATCACCTCGAGCCTATTGA	57.900	45.455	6.99	4.28	0.00	2.57
361	362	3.206150	CCTATTGATGGGGAAGACAACG	58.794	50.000	0.00	0.00	0.00	4.10
389	390	7.389232	TGGATCTGTTATGTAGCTTATCCATG	58.611	38.462	0.00	0.00	37.35	3.66
405	406	7.172361	GCTTATCCATGAGACCTATTTGAAGAC	59.828	40.741	0.00	0.00	0.00	3.01
445	446	7.940137	ACATGTTTACTTCCATTGTAGGTAACA	59.060	33.333	0.00	0.00	41.41	2.41
665	666	1.899814	TGAGTGTCTATGTGGTGGACC	59.100	52.381	0.00	0.00	37.51	4.46
680	681	4.149598	GGTGGACCTGATTTTACCAAAGT	58.850	43.478	0.00	0.00	32.32	2.66
871	872	7.619512	AGAGAATTAGGGGTTCCTATTGTAG	57.380	40.000	0.00	0.00	44.51	2.74
899	900	5.036916	TGACTACTTAACTGGGGGATTCAT	58.963	41.667	0.00	0.00	0.00	2.57
900	901	6.206787	TGACTACTTAACTGGGGGATTCATA	58.793	40.000	0.00	0.00	0.00	2.15
927	929	8.190784	GCAAATACTACTTTGGCTCATTATTGT	58.809	33.333	0.00	0.00	36.76	2.71
1040	1042	3.309682	GCTAAAGCATTGCGTATGTCTGA	59.690	43.478	2.38	0.00	41.59	3.27
1090	1092	7.068470	CAGTAGTAGGTAAGTTAGAAGGGGAAG	59.932	44.444	0.00	0.00	0.00	3.46
1111	1113	5.372547	AGGCGAAATGACTTTAGGTTTTC	57.627	39.130	0.00	0.00	20.56	2.29
1201	1203	4.018415	GGGTATCCATGCCAGGTGTTATAT	60.018	45.833	0.00	0.00	33.83	0.86
1202	1204	4.943705	GGTATCCATGCCAGGTGTTATATG	59.056	45.833	0.00	0.00	32.29	1.78
1263	1265	2.027192	TCTGACCGAAATCTTTGGGGAG	60.027	50.000	8.34	4.38	39.97	4.30
1282	1284	7.418378	TGGGGAGGATTCTGTATTACAATTTT	58.582	34.615	0.00	0.00	0.00	1.82
1325	1327	1.228862	GGGGAAATGCACCTGGTGT	60.229	57.895	26.48	8.05	36.99	4.16
1351	1353	5.053145	CAGCTAATCGAGTGGCTTTAGAAT	58.947	41.667	21.45	0.00	32.30	2.40
1411	1413	5.570262	TCGCGAAGGTAATGAAATTATCG	57.430	39.130	6.20	0.00	44.60	2.92
1422	1424	3.609853	TGAAATTATCGGAGCAGCTTGT	58.390	40.909	0.00	0.00	0.00	3.16
1444	1446	2.254152	ATGGAGTCCTGAACTAGCCA	57.746	50.000	11.33	0.00	38.74	4.75
1446	1448	0.173708	GGAGTCCTGAACTAGCCACG	59.826	60.000	0.41	0.00	38.74	4.94
1497	1499	1.266446	GAGTTCGAGCCGGTAGATACC	59.734	57.143	1.90	0.00	42.98	2.73
1500	1502	1.531423	TCGAGCCGGTAGATACCATC	58.469	55.000	1.90	3.49	46.80	3.51
1507	1509	4.710375	AGCCGGTAGATACCATCGATTAAT	59.290	41.667	1.90	0.00	46.80	1.40
1904	2452	5.800296	TGTCAAATCGGGATTCACTAAGAA	58.200	37.500	0.00	0.00	41.28	2.52
1924	2472	6.916360	AGAAAGAAATAAAGCATTGGGTCA	57.084	33.333	0.00	0.00	0.00	4.02
1945	2493	6.317893	GGTCAAACTCTTCTTTGGTGTTAAGA	59.682	38.462	0.00	0.00	32.78	2.10
1973	2521	3.300857	CTGTGAATAGCCATCGACTACG	58.699	50.000	0.00	0.00	41.26	3.51
2017	2565	3.463329	ACCTATTCTGGGCCATACAATGT	59.537	43.478	6.72	0.00	0.00	2.71
2193	2775	4.945246	AGTGACTCGAACTGTGTGTAAAT	58.055	39.130	0.00	0.00	0.00	1.40
2237	2819	9.825109	AAATGCTAGAACTAGATAAGGAAGTTC	57.175	33.333	12.33	6.37	46.10	3.01
2444	3034	3.363128	GCGGTAGAGTAGACGTTTTGTTC	59.637	47.826	0.00	0.00	0.00	3.18
2492	3082	2.432874	TCCGACCCAACGATACAATGAT	59.567	45.455	0.00	0.00	35.09	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	7.201893	GGGTCTACTCGATGTTAATTAGGAGTT	60.202	40.741	7.28	0.00	36.30	3.01
7	8	6.264744	CAGGGTCTACTCGATGTTAATTAGGA	59.735	42.308	0.00	0.00	0.00	2.94
80	81	5.394115	CCTGCTTTAGTTTCTGTTTGTGGTT	60.394	40.000	0.00	0.00	0.00	3.67
193	194	0.741915	GGCTGAGGACTTACTCGGAG	59.258	60.000	2.83	2.83	44.83	4.63
217	218	1.227999	CCTGCTTCTTCGTGCGGAAA	61.228	55.000	0.00	0.00	37.75	3.13
326	327	4.100279	TCAATAGGCTCGAGGTGATAGA	57.900	45.455	15.58	0.00	0.00	1.98
334	335	1.342074	TCCCCATCAATAGGCTCGAG	58.658	55.000	8.45	8.45	0.00	4.04
343	344	3.433306	TTCGTTGTCTTCCCCATCAAT	57.567	42.857	0.00	0.00	0.00	2.57
347	348	1.633432	TCCATTCGTTGTCTTCCCCAT	59.367	47.619	0.00	0.00	0.00	4.00
361	362	8.097038	TGGATAAGCTACATAACAGATCCATTC	58.903	37.037	0.00	0.00	37.32	2.67
389	390	4.865365	CAGAACCGTCTTCAAATAGGTCTC	59.135	45.833	0.00	0.00	33.50	3.36
405	406	7.647907	AGTAAACATGTTAGTAACAGAACCG	57.352	36.000	19.87	9.04	45.95	4.44
445	446	6.405397	GCACGTAGGGATTTGAAACCAAATAT	60.405	38.462	3.69	0.00	42.47	1.28
534	535	8.152023	ACTTATCTCTTTCAACTTGGATACCT	57.848	34.615	0.00	0.00	0.00	3.08
639	640	5.425217	TCCACCACATAGACACTCATAACAT	59.575	40.000	0.00	0.00	0.00	2.71
665	666	8.479280	CGTTTTCATCAACTTTGGTAAAATCAG	58.521	33.333	0.00	0.00	0.00	2.90
680	681	6.127980	TGGTTGTGAGTTTACGTTTTCATCAA	60.128	34.615	0.00	0.00	0.00	2.57
836	837	6.252995	ACCCCTAATTCTCTTGCAAATACAA	58.747	36.000	0.00	0.00	0.00	2.41
871	872	3.270877	CCCCAGTTAAGTAGTCATGCAC	58.729	50.000	0.00	0.00	0.00	4.57
899	900	9.627123	AATAATGAGCCAAAGTAGTATTTGCTA	57.373	29.630	0.00	0.00	38.57	3.49
900	901	8.408601	CAATAATGAGCCAAAGTAGTATTTGCT	58.591	33.333	0.00	0.00	38.57	3.91
927	929	0.459585	GAAGTAGGCCATTGTCGCGA	60.460	55.000	3.71	3.71	0.00	5.87
985	987	7.068103	ACGGAAATGCATACCATGATTTTTCTA	59.932	33.333	18.61	0.00	33.49	2.10
1040	1042	3.143741	ACCAGAGTGGATATGATCTCCCT	59.856	47.826	0.00	0.00	40.96	4.20
1090	1092	5.372547	AGAAAACCTAAAGTCATTTCGCC	57.627	39.130	0.00	0.00	35.66	5.54
1111	1113	6.500775	AAAATCATCGCGCAATAAATCAAG	57.499	33.333	8.75	0.00	0.00	3.02
1201	1203	2.263895	ATACCACCTGAAGCTACCCA	57.736	50.000	0.00	0.00	0.00	4.51
1202	1204	2.504175	TGAATACCACCTGAAGCTACCC	59.496	50.000	0.00	0.00	0.00	3.69
1263	1265	8.190784	CCTCCACAAAATTGTAATACAGAATCC	58.809	37.037	0.00	0.00	39.91	3.01
1282	1284	3.263425	GGATGTCCTAAAGTTCCTCCACA	59.737	47.826	0.00	0.00	0.00	4.17
1325	1327	1.403814	AGCCACTCGATTAGCTGCTA	58.596	50.000	5.02	5.02	34.53	3.49
1351	1353	2.351060	CGTTACGAGCTTGTACACAGGA	60.351	50.000	13.64	0.00	0.00	3.86
1411	1413	2.680339	GACTCCATTTACAAGCTGCTCC	59.320	50.000	1.00	0.00	0.00	4.70
1422	1424	4.081087	GTGGCTAGTTCAGGACTCCATTTA	60.081	45.833	0.00	0.00	39.86	1.40
1444	1446	2.615493	CCTTCCATACTTCACAAGCCGT	60.615	50.000	0.00	0.00	0.00	5.68
1446	1448	1.745653	GCCTTCCATACTTCACAAGCC	59.254	52.381	0.00	0.00	0.00	4.35
1653	1667	9.166173	CATGATCTATTTTTATCCCGCTCAATA	57.834	33.333	0.00	0.00	0.00	1.90
1885	2433	7.996098	TTTCTTTCTTAGTGAATCCCGATTT	57.004	32.000	0.00	0.00	34.24	2.17
1904	2452	7.015584	AGAGTTTGACCCAATGCTTTATTTCTT	59.984	33.333	0.00	0.00	0.00	2.52
1924	2472	6.833933	ACCATCTTAACACCAAAGAAGAGTTT	59.166	34.615	0.00	0.00	36.60	2.66
1945	2493	3.555795	CGATGGCTATTCACAGCTACCAT	60.556	47.826	0.00	0.00	41.50	3.55
1973	2521	6.070136	AGGTCCTATTCTTCTACCTTTTCCAC	60.070	42.308	0.00	0.00	37.25	4.02
2017	2565	8.645814	AGGGTAATGATCATACGTCTGTAATA	57.354	34.615	9.04	0.00	33.44	0.98
2176	2758	7.010023	GCTTCTTTATTTACACACAGTTCGAG	58.990	38.462	0.00	0.00	0.00	4.04
2230	2812	9.449719	TTTTTCTCATGGTTATAGAGAACTTCC	57.550	33.333	3.80	0.00	45.18	3.46
2237	2819	9.892130	AACTACCTTTTTCTCATGGTTATAGAG	57.108	33.333	0.00	0.00	34.33	2.43
2282	2872	4.437239	TCAAGGATTTCTCGCTCTTGATC	58.563	43.478	0.00	0.00	38.88	2.92
2394	2984	7.497595	TGAAGTCTATAGCGTTGTATTTCCAT	58.502	34.615	0.00	0.00	0.00	3.41
2397	2987	7.794349	GCATTGAAGTCTATAGCGTTGTATTTC	59.206	37.037	0.00	0.00	0.00	2.17
2444	3034	5.047306	GGAGGTTTGGTCCAGAAAAATTAGG	60.047	44.000	0.00	0.00	33.84	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.