AutoCloner

Multiple sequence alignment - TraesCS1D01G170100

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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	TraesCS1D01G170100	chr1D	100.000	2279	0	0	1	2279	244394878	244392600	0.000000e+00	4209.0
1	TraesCS1D01G170100	chr1D	95.828	1558	62	3	723	2279	254483741	254482186	0.000000e+00	2514.0
2	TraesCS1D01G170100	chr3B	95.600	1909	68	6	334	2235	201500690	201498791	0.000000e+00	3046.0
3	TraesCS1D01G170100	chr3B	95.147	989	41	3	1143	2131	544900246	544899265	0.000000e+00	1554.0
4	TraesCS1D01G170100	chr3B	96.875	96	3	0	2183	2278	240800226	240800131	6.520000e-36	161.0
5	TraesCS1D01G170100	chr1A	95.642	1652	57	7	634	2279	554471747	554473389	0.000000e+00	2638.0
6	TraesCS1D01G170100	chr1A	94.912	570	21	3	334	902	554470920	554471482	0.000000e+00	885.0
7	TraesCS1D01G170100	chr2D	96.327	1579	54	3	703	2279	643860126	643858550	0.000000e+00	2591.0
8	TraesCS1D01G170100	chr2D	96.109	1465	49	5	821	2279	628289845	628291307	0.000000e+00	2383.0
9	TraesCS1D01G170100	chr2D	96.117	103	4	0	2	104	406835254	406835356	3.890000e-38	169.0
10	TraesCS1D01G170100	chr5D	96.310	1572	53	2	712	2279	483800997	483802567	0.000000e+00	2577.0
11	TraesCS1D01G170100	chr5D	96.137	1579	55	5	703	2279	6217418	6218992	0.000000e+00	2573.0
12	TraesCS1D01G170100	chr3A	94.365	1473	74	3	334	1798	393237227	393238698	0.000000e+00	2252.0
13	TraesCS1D01G170100	chr3A	94.499	909	35	6	376	1278	435413946	435414845	0.000000e+00	1387.0
14	TraesCS1D01G170100	chr3A	94.581	609	24	4	334	941	593321250	593321850	0.000000e+00	933.0
15	TraesCS1D01G170100	chr3A	94.118	340	10	3	2	333	393236855	393237192	2.020000e-140	508.0
16	TraesCS1D01G170100	chr5B	95.014	361	17	1	334	694	559430066	559429707	1.180000e-157	566.0
17	TraesCS1D01G170100	chr5B	93.750	80	3	1	256	333	548607162	548607083	3.980000e-23	119.0
18	TraesCS1D01G170100	chr4B	95.833	312	13	0	342	653	421404160	421404471	2.610000e-139	505.0
19	TraesCS1D01G170100	chr4B	90.110	91	5	3	3	92	567190469	567190556	5.140000e-22	115.0
20	TraesCS1D01G170100	chr7B	95.987	299	11	1	334	632	300902955	300903252	3.400000e-133	484.0
21	TraesCS1D01G170100	chr7B	96.739	92	3	0	242	333	149445000	149444909	1.090000e-33	154.0
22	TraesCS1D01G170100	chr6A	94.534	311	17	0	380	690	495543047	495543357	4.400000e-132	481.0
23	TraesCS1D01G170100	chr6A	95.455	110	5	0	2	111	192822705	192822596	2.330000e-40	176.0
24	TraesCS1D01G170100	chr6A	97.849	93	2	0	2	94	1715250	1715158	6.520000e-36	161.0
25	TraesCS1D01G170100	chr7D	98.953	191	2	0	2	192	509197413	509197223	2.170000e-90	342.0
26	TraesCS1D01G170100	chr5A	97.600	125	3	0	108	232	570914667	570914791	4.930000e-52	215.0
27	TraesCS1D01G170100	chr5A	85.648	216	16	8	133	333	11091157	11090942	1.770000e-51	213.0
28	TraesCS1D01G170100	chr5A	95.455	132	6	0	2	133	696746532	696746663	6.380000e-51	211.0
29	TraesCS1D01G170100	chr5A	89.189	111	12	0	108	218	644316024	644316134	3.050000e-29	139.0
30	TraesCS1D01G170100	chr6D	91.791	134	7	3	136	265	100526708	100526575	1.390000e-42	183.0
31	TraesCS1D01G170100	chr6D	95.370	108	3	2	137	242	100540908	100540801	1.080000e-38	171.0
32	TraesCS1D01G170100	chr6D	95.699	93	3	1	242	333	354356175	354356083	5.070000e-32	148.0
33	TraesCS1D01G170100	chr6D	90.123	81	4	1	257	333	100540218	100540138	4.010000e-18	102.0
34	TraesCS1D01G170100	chr3D	95.575	113	5	0	2	114	213385234	213385122	5.000000e-42	182.0
35	TraesCS1D01G170100	chr3D	81.169	154	18	7	165	315	597862458	597862313	1.850000e-21	113.0
36	TraesCS1D01G170100	chr6B	85.165	182	14	5	165	333	184718137	184717956	8.370000e-40	174.0
37	TraesCS1D01G170100	chr4A	96.040	101	4	0	2	102	78568321	78568421	5.040000e-37	165.0
38	TraesCS1D01G170100	chr4A	86.517	89	8	2	210	297	75970688	75970603	6.700000e-16	95.3
39	TraesCS1D01G170100	chr7A	88.281	128	5	5	168	285	647448181	647448308	6.560000e-31	145.0
40	TraesCS1D01G170100	chrUn	86.765	136	4	6	194	315	21634271	21634136	3.050000e-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	TraesCS1D01G170100	chr1D	244392600	244394878	2278	True	4209.0	4209	100.0000	1	2279	1	chr1D.!!$R1	2278
1	TraesCS1D01G170100	chr1D	254482186	254483741	1555	True	2514.0	2514	95.8280	723	2279	1	chr1D.!!$R2	1556
2	TraesCS1D01G170100	chr3B	201498791	201500690	1899	True	3046.0	3046	95.6000	334	2235	1	chr3B.!!$R1	1901
3	TraesCS1D01G170100	chr3B	544899265	544900246	981	True	1554.0	1554	95.1470	1143	2131	1	chr3B.!!$R3	988
4	TraesCS1D01G170100	chr1A	554470920	554473389	2469	False	1761.5	2638	95.2770	334	2279	2	chr1A.!!$F1	1945
5	TraesCS1D01G170100	chr2D	643858550	643860126	1576	True	2591.0	2591	96.3270	703	2279	1	chr2D.!!$R1	1576
6	TraesCS1D01G170100	chr2D	628289845	628291307	1462	False	2383.0	2383	96.1090	821	2279	1	chr2D.!!$F2	1458
7	TraesCS1D01G170100	chr5D	483800997	483802567	1570	False	2577.0	2577	96.3100	712	2279	1	chr5D.!!$F2	1567
8	TraesCS1D01G170100	chr5D	6217418	6218992	1574	False	2573.0	2573	96.1370	703	2279	1	chr5D.!!$F1	1576
9	TraesCS1D01G170100	chr3A	435413946	435414845	899	False	1387.0	1387	94.4990	376	1278	1	chr3A.!!$F1	902
10	TraesCS1D01G170100	chr3A	393236855	393238698	1843	False	1380.0	2252	94.2415	2	1798	2	chr3A.!!$F3	1796
11	TraesCS1D01G170100	chr3A	593321250	593321850	600	False	933.0	933	94.5810	334	941	1	chr3A.!!$F2	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
554	597	3.555795	CGATGGCTATTCACAGCTACCAT	60.556	47.826	0.0	0.0	41.5	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1834	2431	1.899814	TGAGTGTCTATGTGGTGGACC	59.1	52.381	0.0	0.0	37.51	4.46	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
55	56	5.047306	GGAGGTTTGGTCCAGAAAAATTAGG	60.047	44.000	0.00	0.00	33.84	2.69
102	103	7.794349	GCATTGAAGTCTATAGCGTTGTATTTC	59.206	37.037	0.00	0.00	0.00	2.17
105	106	7.497595	TGAAGTCTATAGCGTTGTATTTCCAT	58.502	34.615	0.00	0.00	0.00	3.41
217	218	4.437239	TCAAGGATTTCTCGCTCTTGATC	58.563	43.478	0.00	0.00	38.88	2.92
262	271	9.892130	AACTACCTTTTTCTCATGGTTATAGAG	57.108	33.333	0.00	0.00	34.33	2.43
269	278	9.449719	TTTTTCTCATGGTTATAGAGAACTTCC	57.550	33.333	3.80	0.00	45.18	3.46
323	332	7.010023	GCTTCTTTATTTACACACAGTTCGAG	58.990	38.462	0.00	0.00	0.00	4.04
482	525	8.645814	AGGGTAATGATCATACGTCTGTAATA	57.354	34.615	9.04	0.00	33.44	0.98
526	569	6.070136	AGGTCCTATTCTTCTACCTTTTCCAC	60.070	42.308	0.00	0.00	37.25	4.02
554	597	3.555795	CGATGGCTATTCACAGCTACCAT	60.556	47.826	0.00	0.00	41.50	3.55
575	618	6.833933	ACCATCTTAACACCAAAGAAGAGTTT	59.166	34.615	0.00	0.00	36.60	2.66
595	638	7.015584	AGAGTTTGACCCAATGCTTTATTTCTT	59.984	33.333	0.00	0.00	0.00	2.52
614	657	7.996098	TTTCTTTCTTAGTGAATCCCGATTT	57.004	32.000	0.00	0.00	34.24	2.17
846	896	9.166173	CATGATCTATTTTTATCCCGCTCAATA	57.834	33.333	0.00	0.00	0.00	1.90
1053	1650	1.745653	GCCTTCCATACTTCACAAGCC	59.254	52.381	0.00	0.00	0.00	4.35
1055	1652	2.615493	CCTTCCATACTTCACAAGCCGT	60.615	50.000	0.00	0.00	0.00	5.68
1077	1674	4.081087	GTGGCTAGTTCAGGACTCCATTTA	60.081	45.833	0.00	0.00	39.86	1.40
1088	1685	2.680339	GACTCCATTTACAAGCTGCTCC	59.320	50.000	1.00	0.00	0.00	4.70
1148	1745	2.351060	CGTTACGAGCTTGTACACAGGA	60.351	50.000	13.64	0.00	0.00	3.86
1174	1771	1.403814	AGCCACTCGATTAGCTGCTA	58.596	50.000	5.02	5.02	34.53	3.49
1217	1814	3.263425	GGATGTCCTAAAGTTCCTCCACA	59.737	47.826	0.00	0.00	0.00	4.17
1236	1833	8.190784	CCTCCACAAAATTGTAATACAGAATCC	58.809	37.037	0.00	0.00	39.91	3.01
1297	1894	2.504175	TGAATACCACCTGAAGCTACCC	59.496	50.000	0.00	0.00	0.00	3.69
1298	1895	2.263895	ATACCACCTGAAGCTACCCA	57.736	50.000	0.00	0.00	0.00	4.51
1388	1985	6.500775	AAAATCATCGCGCAATAAATCAAG	57.499	33.333	8.75	0.00	0.00	3.02
1409	2006	5.372547	AGAAAACCTAAAGTCATTTCGCC	57.627	39.130	0.00	0.00	35.66	5.54
1459	2056	3.143741	ACCAGAGTGGATATGATCTCCCT	59.856	47.826	0.00	0.00	40.96	4.20
1514	2111	7.068103	ACGGAAATGCATACCATGATTTTTCTA	59.932	33.333	18.61	0.00	33.49	2.10
1572	2169	0.459585	GAAGTAGGCCATTGTCGCGA	60.460	55.000	3.71	3.71	0.00	5.87
1599	2196	8.408601	CAATAATGAGCCAAAGTAGTATTTGCT	58.591	33.333	0.00	0.00	38.57	3.91
1600	2197	9.627123	AATAATGAGCCAAAGTAGTATTTGCTA	57.373	29.630	0.00	0.00	38.57	3.49
1628	2225	3.270877	CCCCAGTTAAGTAGTCATGCAC	58.729	50.000	0.00	0.00	0.00	4.57
1663	2260	6.252995	ACCCCTAATTCTCTTGCAAATACAA	58.747	36.000	0.00	0.00	0.00	2.41
1819	2416	6.127980	TGGTTGTGAGTTTACGTTTTCATCAA	60.128	34.615	0.00	0.00	0.00	2.57
1834	2431	8.479280	CGTTTTCATCAACTTTGGTAAAATCAG	58.521	33.333	0.00	0.00	0.00	2.90
1860	2457	5.425217	TCCACCACATAGACACTCATAACAT	59.575	40.000	0.00	0.00	0.00	2.71
1965	2562	8.152023	ACTTATCTCTTTCAACTTGGATACCT	57.848	34.615	0.00	0.00	0.00	3.08
2054	2651	6.405397	GCACGTAGGGATTTGAAACCAAATAT	60.405	38.462	3.69	0.00	42.47	1.28
2094	2691	7.647907	AGTAAACATGTTAGTAACAGAACCG	57.352	36.000	19.87	9.04	45.95	4.44
2110	2707	4.865365	CAGAACCGTCTTCAAATAGGTCTC	59.135	45.833	0.00	0.00	33.50	3.36
2138	2735	8.097038	TGGATAAGCTACATAACAGATCCATTC	58.903	37.037	0.00	0.00	37.32	2.67
2152	2749	1.633432	TCCATTCGTTGTCTTCCCCAT	59.367	47.619	0.00	0.00	0.00	4.00
2156	2753	3.433306	TTCGTTGTCTTCCCCATCAAT	57.567	42.857	0.00	0.00	0.00	2.57
2165	2762	1.342074	TCCCCATCAATAGGCTCGAG	58.658	55.000	8.45	8.45	0.00	4.04
2173	2770	4.100279	TCAATAGGCTCGAGGTGATAGA	57.900	45.455	15.58	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	2.432874	TCCGACCCAACGATACAATGAT	59.567	45.455	0.00	0.00	35.09	2.45
55	56	3.363128	GCGGTAGAGTAGACGTTTTGTTC	59.637	47.826	0.00	0.00	0.00	3.18
262	271	9.825109	AAATGCTAGAACTAGATAAGGAAGTTC	57.175	33.333	12.33	6.37	46.10	3.01
306	315	4.945246	AGTGACTCGAACTGTGTGTAAAT	58.055	39.130	0.00	0.00	0.00	1.40
482	525	3.463329	ACCTATTCTGGGCCATACAATGT	59.537	43.478	6.72	0.00	0.00	2.71
526	569	3.300857	CTGTGAATAGCCATCGACTACG	58.699	50.000	0.00	0.00	41.26	3.51
554	597	6.317893	GGTCAAACTCTTCTTTGGTGTTAAGA	59.682	38.462	0.00	0.00	32.78	2.10
575	618	6.916360	AGAAAGAAATAAAGCATTGGGTCA	57.084	33.333	0.00	0.00	0.00	4.02
595	638	5.800296	TGTCAAATCGGGATTCACTAAGAA	58.200	37.500	0.00	0.00	41.28	2.52
992	1589	4.710375	AGCCGGTAGATACCATCGATTAAT	59.290	41.667	1.90	0.00	46.80	1.40
999	1596	1.531423	TCGAGCCGGTAGATACCATC	58.469	55.000	1.90	3.49	46.80	3.51
1002	1599	1.266446	GAGTTCGAGCCGGTAGATACC	59.734	57.143	1.90	0.00	42.98	2.73
1053	1650	0.173708	GGAGTCCTGAACTAGCCACG	59.826	60.000	0.41	0.00	38.74	4.94
1055	1652	2.254152	ATGGAGTCCTGAACTAGCCA	57.746	50.000	11.33	0.00	38.74	4.75
1077	1674	3.609853	TGAAATTATCGGAGCAGCTTGT	58.390	40.909	0.00	0.00	0.00	3.16
1088	1685	5.570262	TCGCGAAGGTAATGAAATTATCG	57.430	39.130	6.20	0.00	44.60	2.92
1148	1745	5.053145	CAGCTAATCGAGTGGCTTTAGAAT	58.947	41.667	21.45	0.00	32.30	2.40
1174	1771	1.228862	GGGGAAATGCACCTGGTGT	60.229	57.895	26.48	8.05	36.99	4.16
1217	1814	7.418378	TGGGGAGGATTCTGTATTACAATTTT	58.582	34.615	0.00	0.00	0.00	1.82
1236	1833	2.027192	TCTGACCGAAATCTTTGGGGAG	60.027	50.000	8.34	4.38	39.97	4.30
1297	1894	4.943705	GGTATCCATGCCAGGTGTTATATG	59.056	45.833	0.00	0.00	32.29	1.78
1298	1895	4.018415	GGGTATCCATGCCAGGTGTTATAT	60.018	45.833	0.00	0.00	33.83	0.86
1388	1985	5.372547	AGGCGAAATGACTTTAGGTTTTC	57.627	39.130	0.00	0.00	20.56	2.29
1409	2006	7.068470	CAGTAGTAGGTAAGTTAGAAGGGGAAG	59.932	44.444	0.00	0.00	0.00	3.46
1459	2056	3.309682	GCTAAAGCATTGCGTATGTCTGA	59.690	43.478	2.38	0.00	41.59	3.27
1572	2169	8.190784	GCAAATACTACTTTGGCTCATTATTGT	58.809	33.333	0.00	0.00	36.76	2.71
1599	2196	6.206787	TGACTACTTAACTGGGGGATTCATA	58.793	40.000	0.00	0.00	0.00	2.15
1600	2197	5.036916	TGACTACTTAACTGGGGGATTCAT	58.963	41.667	0.00	0.00	0.00	2.57
1628	2225	7.619512	AGAGAATTAGGGGTTCCTATTGTAG	57.380	40.000	0.00	0.00	44.51	2.74
1819	2416	4.149598	GGTGGACCTGATTTTACCAAAGT	58.850	43.478	0.00	0.00	32.32	2.66
1834	2431	1.899814	TGAGTGTCTATGTGGTGGACC	59.100	52.381	0.00	0.00	37.51	4.46
2054	2651	7.940137	ACATGTTTACTTCCATTGTAGGTAACA	59.060	33.333	0.00	0.00	41.41	2.41
2094	2691	7.172361	GCTTATCCATGAGACCTATTTGAAGAC	59.828	40.741	0.00	0.00	0.00	3.01
2110	2707	7.389232	TGGATCTGTTATGTAGCTTATCCATG	58.611	38.462	0.00	0.00	37.35	3.66
2138	2735	3.206150	CCTATTGATGGGGAAGACAACG	58.794	50.000	0.00	0.00	0.00	4.10
2152	2749	4.100279	TCTATCACCTCGAGCCTATTGA	57.900	45.455	6.99	4.28	0.00	2.57
2156	2753	3.075148	CGATTCTATCACCTCGAGCCTA	58.925	50.000	6.99	0.00	33.07	3.93
2165	2762	5.231568	CGTTACAAAGGACGATTCTATCACC	59.768	44.000	0.00	0.00	41.53	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.