AutoCloner

Multiple sequence alignment - TraesCS4D01G276000

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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	TraesCS4D01G276000	chr4D	100.000	2448	0	0	1	2448	446917533	446915086	0.000000e+00	4521
1	TraesCS4D01G276000	chr4B	92.291	1829	69	34	653	2448	559288578	559286789	0.000000e+00	2531
2	TraesCS4D01G276000	chr4A	89.839	1801	82	51	658	2411	20259575	20261321	0.000000e+00	2218
3	TraesCS4D01G276000	chr3D	92.481	665	40	6	1	657	16260171	16260833	0.000000e+00	942
4	TraesCS4D01G276000	chr5D	92.249	658	42	6	5	655	14027130	14026475	0.000000e+00	924
5	TraesCS4D01G276000	chr5D	91.554	663	44	6	1	657	212482927	212482271	0.000000e+00	904
6	TraesCS4D01G276000	chr1D	91.982	661	44	4	1	653	49227672	49227013	0.000000e+00	918
7	TraesCS4D01G276000	chr1D	91.679	661	46	6	1	655	409813946	409814603	0.000000e+00	907
8	TraesCS4D01G276000	chr1D	91.390	662	46	5	1	655	375967805	375967148	0.000000e+00	896
9	TraesCS4D01G276000	chr7D	91.717	664	43	7	1	655	501381829	501382489	0.000000e+00	911
10	TraesCS4D01G276000	chr7D	91.239	662	48	8	1	655	131755143	131755801	0.000000e+00	893
11	TraesCS4D01G276000	chr6D	91.454	667	46	6	1	659	45624280	45624943	0.000000e+00	905
12	TraesCS4D01G276000	chr6D	96.154	104	3	1	2039	2142	34401773	34401671	4.190000e-38	169
13	TraesCS4D01G276000	chr2D	94.643	112	2	4	2031	2140	122055654	122055545	1.160000e-38	171
14	TraesCS4D01G276000	chr6B	96.154	104	3	1	2039	2142	71153623	71153521	4.190000e-38	169
15	TraesCS4D01G276000	chr6A	95.192	104	4	1	2039	2142	38556629	38556527	1.950000e-36	163
16	TraesCS4D01G276000	chr5A	95.146	103	3	2	2039	2140	700670659	700670558	7.010000e-36	161
17	TraesCS4D01G276000	chr2B	94.340	106	4	2	2033	2136	175075331	175075226	7.010000e-36	161
18	TraesCS4D01G276000	chr3A	92.727	110	4	3	2033	2142	703900230	703900125	3.260000e-34	156

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	TraesCS4D01G276000	chr4D	446915086	446917533	2447	True	4521	4521	100.000	1	2448	1	chr4D.!!$R1	2447
1	TraesCS4D01G276000	chr4B	559286789	559288578	1789	True	2531	2531	92.291	653	2448	1	chr4B.!!$R1	1795
2	TraesCS4D01G276000	chr4A	20259575	20261321	1746	False	2218	2218	89.839	658	2411	1	chr4A.!!$F1	1753
3	TraesCS4D01G276000	chr3D	16260171	16260833	662	False	942	942	92.481	1	657	1	chr3D.!!$F1	656
4	TraesCS4D01G276000	chr5D	14026475	14027130	655	True	924	924	92.249	5	655	1	chr5D.!!$R1	650
5	TraesCS4D01G276000	chr5D	212482271	212482927	656	True	904	904	91.554	1	657	1	chr5D.!!$R2	656
6	TraesCS4D01G276000	chr1D	49227013	49227672	659	True	918	918	91.982	1	653	1	chr1D.!!$R1	652
7	TraesCS4D01G276000	chr1D	409813946	409814603	657	False	907	907	91.679	1	655	1	chr1D.!!$F1	654
8	TraesCS4D01G276000	chr1D	375967148	375967805	657	True	896	896	91.390	1	655	1	chr1D.!!$R2	654
9	TraesCS4D01G276000	chr7D	501381829	501382489	660	False	911	911	91.717	1	655	1	chr7D.!!$F2	654
10	TraesCS4D01G276000	chr7D	131755143	131755801	658	False	893	893	91.239	1	655	1	chr7D.!!$F1	654
11	TraesCS4D01G276000	chr6D	45624280	45624943	663	False	905	905	91.454	1	659	1	chr6D.!!$F1	658

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
861	880	0.247736	TCGCTCTGCTTTCTTCTCCC	59.752	55.0	0.0	0.0	0.0	4.3	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2031	2096	0.589223	CGGCCAAAGCGTCTTTTGTA	59.411	50.0	2.24	0.0	41.24	2.41	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
139	140	2.203877	TAGGGGTGGTTGTCGGCT	60.204	61.111	0.00	0.00	0.00	5.52
169	170	2.407210	CTCTGGAGCTCTCGTCGC	59.593	66.667	14.64	0.00	0.00	5.19
218	219	2.753043	GCGGTCGTGTCCCCTCTA	60.753	66.667	0.00	0.00	0.00	2.43
253	254	3.069318	GACGGCCGAACCTCCTCT	61.069	66.667	35.90	5.18	35.61	3.69
329	330	1.844289	TGGTTTGGTAGGGACGGCT	60.844	57.895	0.00	0.00	0.00	5.52
368	371	2.031163	GCCGGAGAATAGCGGCAT	59.969	61.111	5.05	0.00	45.77	4.40
370	373	1.668294	CCGGAGAATAGCGGCATCT	59.332	57.895	0.00	2.46	0.00	2.90
410	413	2.185608	GAGAGAGGGTGGAAGCGC	59.814	66.667	0.00	0.00	33.03	5.92
508	518	0.816421	CGTTTCACCCCAAACCGAGT	60.816	55.000	0.00	0.00	33.37	4.18
513	523	1.076632	ACCCCAAACCGAGTGCAAA	60.077	52.632	0.00	0.00	0.00	3.68
529	539	2.366393	AAATTTGGGCCGGGGATGC	61.366	57.895	2.18	0.00	0.00	3.91
593	603	2.513897	GTTGGGCCGCGCTATTCT	60.514	61.111	5.56	0.00	0.00	2.40
605	615	2.674357	GCGCTATTCTTCCGTTTTACCA	59.326	45.455	0.00	0.00	0.00	3.25
655	665	3.056328	GCGGTGGAGTTTGGCCTC	61.056	66.667	3.32	0.00	0.00	4.70
656	666	2.429930	CGGTGGAGTTTGGCCTCA	59.570	61.111	3.32	0.00	32.91	3.86
658	668	1.603739	GGTGGAGTTTGGCCTCACC	60.604	63.158	3.32	8.58	39.84	4.02
659	669	1.456287	GTGGAGTTTGGCCTCACCT	59.544	57.895	3.32	0.00	40.22	4.00
660	670	0.606673	GTGGAGTTTGGCCTCACCTC	60.607	60.000	3.32	3.99	40.22	3.85
661	671	1.002011	GGAGTTTGGCCTCACCTCC	60.002	63.158	3.32	9.84	40.22	4.30
662	672	1.492993	GGAGTTTGGCCTCACCTCCT	61.493	60.000	18.37	1.01	37.86	3.69
809	819	4.742201	CAGTCCCCCTCGTGCACG	62.742	72.222	32.76	32.76	41.45	5.34
854	873	2.164026	CCGCTCTCGCTCTGCTTTC	61.164	63.158	0.00	0.00	0.00	2.62
855	874	1.153862	CGCTCTCGCTCTGCTTTCT	60.154	57.895	0.00	0.00	0.00	2.52
858	877	1.404047	GCTCTCGCTCTGCTTTCTTCT	60.404	52.381	0.00	0.00	0.00	2.85
860	879	1.203523	TCTCGCTCTGCTTTCTTCTCC	59.796	52.381	0.00	0.00	0.00	3.71
861	880	0.247736	TCGCTCTGCTTTCTTCTCCC	59.752	55.000	0.00	0.00	0.00	4.30
863	882	1.738700	CGCTCTGCTTTCTTCTCCCTC	60.739	57.143	0.00	0.00	0.00	4.30
866	885	1.905215	TCTGCTTTCTTCTCCCTCCTG	59.095	52.381	0.00	0.00	0.00	3.86
918	949	3.597728	CCGTCCTCGAGCTAGCCC	61.598	72.222	12.13	0.00	39.71	5.19
1111	1143	3.462483	TGCACTTTCTCCGTGTTTCTA	57.538	42.857	0.00	0.00	34.91	2.10
1151	1183	0.862283	GCTCTAGCTCACACGTACGC	60.862	60.000	16.72	0.00	38.21	4.42
1255	1290	1.215647	GCAGTACTCGTGGGTGGAG	59.784	63.158	0.00	0.00	37.54	3.86
1450	1485	2.031360	GCTCTTCATGCCATGAGCC	58.969	57.895	7.55	0.00	44.16	4.70
1451	1486	1.453762	GCTCTTCATGCCATGAGCCC	61.454	60.000	7.55	0.00	44.16	5.19
1452	1487	0.106868	CTCTTCATGCCATGAGCCCA	60.107	55.000	7.55	0.00	42.71	5.36
1453	1488	0.554305	TCTTCATGCCATGAGCCCAT	59.446	50.000	7.55	0.00	42.71	4.00
1496	1543	4.621510	CGTCTGCACATATATGTATGCCCT	60.622	45.833	17.86	0.00	41.15	5.19
1637	1688	4.042809	CCAGAGGGATCTAGCTAGAGAAGA	59.957	50.000	26.64	7.61	35.50	2.87
1638	1689	5.457487	CCAGAGGGATCTAGCTAGAGAAGAA	60.457	48.000	26.64	4.84	35.50	2.52
1639	1690	5.707298	CAGAGGGATCTAGCTAGAGAAGAAG	59.293	48.000	26.64	11.36	35.50	2.85
1832	1895	3.250744	TGGATCGAGATTGTTCGTTCAC	58.749	45.455	8.25	0.89	39.72	3.18
1833	1896	2.279136	GGATCGAGATTGTTCGTTCACG	59.721	50.000	8.25	0.00	39.72	4.35
1871	1934	2.159490	GGTTCTTCTCCTTCTCGAGTCG	60.159	54.545	13.13	6.09	0.00	4.18
1872	1935	1.088306	TCTTCTCCTTCTCGAGTCGC	58.912	55.000	13.13	0.00	0.00	5.19
1873	1936	0.099791	CTTCTCCTTCTCGAGTCGCC	59.900	60.000	13.13	0.00	0.00	5.54
1874	1937	0.608308	TTCTCCTTCTCGAGTCGCCA	60.608	55.000	13.13	0.00	0.00	5.69
1875	1938	0.608308	TCTCCTTCTCGAGTCGCCAA	60.608	55.000	13.13	1.66	0.00	4.52
1876	1939	0.179150	CTCCTTCTCGAGTCGCCAAG	60.179	60.000	13.13	11.48	0.00	3.61
1915	1978	5.278957	CGGTTTTGAGGAGTGATTTTCCAAT	60.279	40.000	0.00	0.00	37.18	3.16
1956	2020	3.123804	CCGTGATATTTTCTCCTGGACG	58.876	50.000	0.00	0.00	0.00	4.79
1982	2046	4.914983	TCTTCCTCATCATTTTGCTCTGT	58.085	39.130	0.00	0.00	0.00	3.41
2005	2070	1.590238	CGAGCATGCTTCCTTTCGTAG	59.410	52.381	23.61	0.05	0.00	3.51
2011	2076	4.672801	GCATGCTTCCTTTCGTAGAAAAGG	60.673	45.833	11.37	8.76	45.90	3.11
2012	2077	2.812011	TGCTTCCTTTCGTAGAAAAGGC	59.188	45.455	9.96	2.05	45.90	4.35
2030	2095	1.406341	GGCTCAGTATGCCCGTGTAAA	60.406	52.381	0.00	0.00	44.32	2.01
2031	2096	2.561569	GCTCAGTATGCCCGTGTAAAT	58.438	47.619	0.00	0.00	34.76	1.40
2124	2189	0.671251	ATCTCTCAGGCGTCGATTCC	59.329	55.000	0.00	0.00	0.00	3.01
2131	2196	1.661112	CAGGCGTCGATTCCTTTTCTC	59.339	52.381	5.77	0.00	0.00	2.87
2133	2198	1.405661	GGCGTCGATTCCTTTTCTCCT	60.406	52.381	0.00	0.00	0.00	3.69
2286	2363	3.973425	AGAAACAATCTCCCCCATGAAG	58.027	45.455	0.00	0.00	30.46	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	93	0.811616	GTGATCATCGCGGCCTCTTT	60.812	55.000	6.13	0.00	0.00	2.52
122	123	2.203877	AGCCGACAACCACCCCTA	60.204	61.111	0.00	0.00	0.00	3.53
243	244	0.382515	CCGTCGATCAGAGGAGGTTC	59.617	60.000	0.00	0.00	36.91	3.62
253	254	1.717194	GTAGTTTTGGCCGTCGATCA	58.283	50.000	0.00	0.00	0.00	2.92
410	413	2.581354	CAGTCCCTTCGCTCCCAG	59.419	66.667	0.00	0.00	0.00	4.45
508	518	3.317571	CCCCGGCCCAAATTTGCA	61.318	61.111	12.92	0.00	0.00	4.08
649	659	1.000993	GAGAGAGGAGGTGAGGCCA	59.999	63.158	5.01	0.00	40.61	5.36
651	661	0.258774	AGAGAGAGAGGAGGTGAGGC	59.741	60.000	0.00	0.00	0.00	4.70
653	663	1.846439	AGGAGAGAGAGAGGAGGTGAG	59.154	57.143	0.00	0.00	0.00	3.51
655	665	2.826674	AAGGAGAGAGAGAGGAGGTG	57.173	55.000	0.00	0.00	0.00	4.00
656	666	4.803452	CATAAAGGAGAGAGAGAGGAGGT	58.197	47.826	0.00	0.00	0.00	3.85
658	668	3.573967	GGCATAAAGGAGAGAGAGAGGAG	59.426	52.174	0.00	0.00	0.00	3.69
659	669	3.206412	AGGCATAAAGGAGAGAGAGAGGA	59.794	47.826	0.00	0.00	0.00	3.71
660	670	3.573967	GAGGCATAAAGGAGAGAGAGAGG	59.426	52.174	0.00	0.00	0.00	3.69
661	671	3.573967	GGAGGCATAAAGGAGAGAGAGAG	59.426	52.174	0.00	0.00	0.00	3.20
662	672	3.571590	GGAGGCATAAAGGAGAGAGAGA	58.428	50.000	0.00	0.00	0.00	3.10
751	761	1.078072	TGGAGTGGCGTTTGTGTGT	60.078	52.632	0.00	0.00	0.00	3.72
854	873	0.617249	AGCAGGACAGGAGGGAGAAG	60.617	60.000	0.00	0.00	0.00	2.85
855	874	0.616111	GAGCAGGACAGGAGGGAGAA	60.616	60.000	0.00	0.00	0.00	2.87
858	877	2.039624	GGAGCAGGACAGGAGGGA	59.960	66.667	0.00	0.00	0.00	4.20
860	879	3.086600	GGGGAGCAGGACAGGAGG	61.087	72.222	0.00	0.00	0.00	4.30
861	880	3.086600	GGGGGAGCAGGACAGGAG	61.087	72.222	0.00	0.00	0.00	3.69
902	933	3.955101	CGGGCTAGCTCGAGGACG	61.955	72.222	33.26	12.00	43.62	4.79
1044	1076	2.185608	GCGAGGAAGAGGAGGTGC	59.814	66.667	0.00	0.00	0.00	5.01
1111	1143	1.202592	TCGCCATGTATGTAATGCCGT	60.203	47.619	0.00	0.00	28.83	5.68
1120	1152	1.707632	GCTAGAGCTCGCCATGTATG	58.292	55.000	8.37	0.00	38.21	2.39
1165	1200	2.519622	CCCACCTGCAGGAGACACA	61.520	63.158	39.19	0.00	38.94	3.72
1166	1201	2.348998	CCCACCTGCAGGAGACAC	59.651	66.667	39.19	0.00	38.94	3.67
1231	1266	0.108615	CCCACGAGTACTGCTCAAGG	60.109	60.000	0.00	0.00	44.33	3.61
1451	1486	4.386951	TGTGGGCGGACGGTCATG	62.387	66.667	10.76	2.88	0.00	3.07
1452	1487	4.082523	CTGTGGGCGGACGGTCAT	62.083	66.667	10.76	0.00	0.00	3.06
1496	1543	1.219124	GAGTCGGGAGCAGCATCAA	59.781	57.895	0.00	0.00	0.00	2.57
1637	1688	1.896694	CGCTCTGCTCCCTCTTCTT	59.103	57.895	0.00	0.00	0.00	2.52
1638	1689	2.720134	GCGCTCTGCTCCCTCTTCT	61.720	63.158	0.00	0.00	41.73	2.85
1639	1690	2.202864	GCGCTCTGCTCCCTCTTC	60.203	66.667	0.00	0.00	41.73	2.87
1679	1742	2.893489	AGCCTCCATGTTTGGTTTCTTC	59.107	45.455	0.00	0.00	44.06	2.87
1832	1895	1.643292	CAGAGAGAGAGAGAGCGCG	59.357	63.158	0.00	0.00	0.00	6.86
1833	1896	0.748005	ACCAGAGAGAGAGAGAGCGC	60.748	60.000	0.00	0.00	0.00	5.92
1956	2020	5.589452	AGAGCAAAATGATGAGGAAGATGTC	59.411	40.000	0.00	0.00	0.00	3.06
1982	2046	1.464608	CGAAAGGAAGCATGCTCGAAA	59.535	47.619	22.93	0.00	0.00	3.46
2011	2076	2.018542	TTTACACGGGCATACTGAGC	57.981	50.000	0.00	0.00	0.00	4.26
2012	2077	4.689071	TGTATTTACACGGGCATACTGAG	58.311	43.478	4.43	0.00	0.00	3.35
2023	2088	5.338559	CCAAAGCGTCTTTTGTATTTACACG	59.661	40.000	2.65	0.00	36.54	4.49
2024	2089	5.116528	GCCAAAGCGTCTTTTGTATTTACAC	59.883	40.000	2.65	0.00	36.54	2.90
2025	2090	5.216648	GCCAAAGCGTCTTTTGTATTTACA	58.783	37.500	2.65	0.00	36.54	2.41
2026	2091	4.619760	GGCCAAAGCGTCTTTTGTATTTAC	59.380	41.667	0.00	0.00	41.24	2.01
2030	2095	1.199097	CGGCCAAAGCGTCTTTTGTAT	59.801	47.619	2.24	0.00	41.24	2.29
2031	2096	0.589223	CGGCCAAAGCGTCTTTTGTA	59.411	50.000	2.24	0.00	41.24	2.41
2124	2189	8.079809	TCCAGCGTTAAAAATAAAGGAGAAAAG	58.920	33.333	0.00	0.00	0.00	2.27
2131	2196	6.852664	AGACATCCAGCGTTAAAAATAAAGG	58.147	36.000	0.00	0.00	0.00	3.11
2133	2198	6.848451	GGAGACATCCAGCGTTAAAAATAAA	58.152	36.000	0.00	0.00	45.87	1.40
2161	2226	4.007659	ACGCTGGTGGGAATTAGTAAAAG	58.992	43.478	0.00	0.00	0.00	2.27
2165	2230	3.706600	AAACGCTGGTGGGAATTAGTA	57.293	42.857	0.00	0.00	0.00	1.82
2262	2332	4.344104	TCATGGGGGAGATTGTTTCTTTC	58.656	43.478	0.00	0.00	33.74	2.62
2286	2363	9.003658	TGAGGATAAGAAATTGTTCTGAAGTTC	57.996	33.333	0.00	0.00	43.59	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.