AutoCloner

Multiple sequence alignment - TraesCS1B01G357500

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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	TraesCS1B01G357500	chr1B	100.000	2459	0	0	1	2459	587490258	587487800	0.000000e+00	4542.0
1	TraesCS1B01G357500	chr5B	98.513	1547	22	1	1	1547	528557622	528559167	0.000000e+00	2728.0
2	TraesCS1B01G357500	chr3B	98.320	1548	24	2	1	1547	445989444	445987898	0.000000e+00	2713.0
3	TraesCS1B01G357500	chr3B	97.738	1547	28	2	1	1547	761604294	761602755	0.000000e+00	2656.0
4	TraesCS1B01G357500	chr3B	97.590	1079	24	2	471	1547	771121328	771122406	0.000000e+00	1847.0
5	TraesCS1B01G357500	chr3B	94.346	283	16	0	1	283	802892261	802892543	3.760000e-118	435.0
6	TraesCS1B01G357500	chr6B	97.053	1493	41	2	1	1493	674922651	674924140	0.000000e+00	2510.0
7	TraesCS1B01G357500	chrUn	96.804	1502	45	2	1	1502	315538280	315536782	0.000000e+00	2505.0
8	TraesCS1B01G357500	chrUn	94.737	57	2	1	1491	1547	79243447	79243502	1.210000e-13	87.9
9	TraesCS1B01G357500	chrUn	94.737	57	2	1	1491	1547	315536698	315536643	1.210000e-13	87.9
10	TraesCS1B01G357500	chr7A	96.804	1502	44	2	1	1502	18100602	18099105	0.000000e+00	2505.0
11	TraesCS1B01G357500	chr7A	76.640	869	174	16	1549	2401	202039759	202038904	1.040000e-123	453.0
12	TraesCS1B01G357500	chr7A	84.279	229	35	1	2217	2444	250318625	250318853	3.180000e-54	222.0
13	TraesCS1B01G357500	chr7A	92.982	57	3	1	1491	1547	18099021	18098966	5.640000e-12	82.4
14	TraesCS1B01G357500	chr6A	95.184	1495	67	3	1	1493	23196304	23194813	0.000000e+00	2357.0
15	TraesCS1B01G357500	chr7B	89.505	1496	137	11	1	1489	133703935	133705417	0.000000e+00	1875.0
16	TraesCS1B01G357500	chr5A	90.451	576	52	2	1	575	335710345	335710918	0.000000e+00	756.0
17	TraesCS1B01G357500	chr5A	82.969	229	38	1	2217	2444	52887579	52887351	3.210000e-49	206.0
18	TraesCS1B01G357500	chr1D	77.229	931	188	13	1547	2459	314114962	314114038	7.790000e-145	523.0
19	TraesCS1B01G357500	chr4A	89.333	75	8	0	1546	1620	608386951	608387025	7.240000e-16	95.3

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	TraesCS1B01G357500	chr1B	587487800	587490258	2458	True	4542.00	4542	100.0000	1	2459	1	chr1B.!!$R1	2458
1	TraesCS1B01G357500	chr5B	528557622	528559167	1545	False	2728.00	2728	98.5130	1	1547	1	chr5B.!!$F1	1546
2	TraesCS1B01G357500	chr3B	445987898	445989444	1546	True	2713.00	2713	98.3200	1	1547	1	chr3B.!!$R1	1546
3	TraesCS1B01G357500	chr3B	761602755	761604294	1539	True	2656.00	2656	97.7380	1	1547	1	chr3B.!!$R2	1546
4	TraesCS1B01G357500	chr3B	771121328	771122406	1078	False	1847.00	1847	97.5900	471	1547	1	chr3B.!!$F1	1076
5	TraesCS1B01G357500	chr6B	674922651	674924140	1489	False	2510.00	2510	97.0530	1	1493	1	chr6B.!!$F1	1492
6	TraesCS1B01G357500	chrUn	315536643	315538280	1637	True	1296.45	2505	95.7705	1	1547	2	chrUn.!!$R1	1546
7	TraesCS1B01G357500	chr7A	18098966	18100602	1636	True	1293.70	2505	94.8930	1	1547	2	chr7A.!!$R2	1546
8	TraesCS1B01G357500	chr7A	202038904	202039759	855	True	453.00	453	76.6400	1549	2401	1	chr7A.!!$R1	852
9	TraesCS1B01G357500	chr6A	23194813	23196304	1491	True	2357.00	2357	95.1840	1	1493	1	chr6A.!!$R1	1492
10	TraesCS1B01G357500	chr7B	133703935	133705417	1482	False	1875.00	1875	89.5050	1	1489	1	chr7B.!!$F1	1488
11	TraesCS1B01G357500	chr5A	335710345	335710918	573	False	756.00	756	90.4510	1	575	1	chr5A.!!$F1	574
12	TraesCS1B01G357500	chr1D	314114038	314114962	924	True	523.00	523	77.2290	1547	2459	1	chr1D.!!$R1	912

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
549	552	3.198853	GGGACCAGATTAGCAGAAGAAGT	59.801	47.826	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1628	1733	0.037326	GAGCACCACCAGACGATGAA	60.037	55.0	0.0	0.0	0.0	2.57	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
549	552	3.198853	GGGACCAGATTAGCAGAAGAAGT	59.801	47.826	0.00	0.00	0.00	3.01
955	958	5.724328	TGAAGATACGTGCTGAAGAAGATT	58.276	37.500	0.00	0.00	0.00	2.40
1058	1069	1.307097	GAGTGGCTGAATGAGGATGC	58.693	55.000	0.00	0.00	0.00	3.91
1452	1463	3.054802	CCAAGGAAGTGAACAGCCTCTAT	60.055	47.826	0.00	0.00	0.00	1.98
1555	1660	2.185004	ATTGCTACTTGCGGTGAAGT	57.815	45.000	0.00	0.00	46.63	3.01
1556	1661	1.508632	TTGCTACTTGCGGTGAAGTC	58.491	50.000	0.00	0.00	46.63	3.01
1582	1687	3.379445	GACCGGACTCGCCTCCAA	61.379	66.667	9.46	0.00	34.56	3.53
1673	1778	2.815647	GCTCTTGGCGTCTTCCCG	60.816	66.667	0.00	0.00	0.00	5.14
1683	1788	1.371558	GTCTTCCCGCTTGTCCTGT	59.628	57.895	0.00	0.00	0.00	4.00
1693	1798	0.874175	CTTGTCCTGTCGACGCAACA	60.874	55.000	11.62	11.43	45.23	3.33
1723	1828	3.319198	AGGGAACATGGCGACGGT	61.319	61.111	0.00	0.00	0.00	4.83
1724	1829	3.124921	GGGAACATGGCGACGGTG	61.125	66.667	0.00	0.00	0.00	4.94
1738	1843	2.106074	CGGTGCCGCATCAAGCTTA	61.106	57.895	4.14	0.00	42.61	3.09
1745	1850	3.882288	TGCCGCATCAAGCTTATTATCAA	59.118	39.130	0.00	0.00	42.61	2.57
1769	1874	1.505353	GGTGCAGCAACATCAGCTC	59.495	57.895	11.86	0.00	41.14	4.09
1775	1880	2.544686	GCAGCAACATCAGCTCTATCAG	59.455	50.000	0.00	0.00	41.14	2.90
1780	1885	4.633175	CAACATCAGCTCTATCAGATGCT	58.367	43.478	8.87	0.00	41.08	3.79
1784	1889	5.774184	ACATCAGCTCTATCAGATGCTTCTA	59.226	40.000	8.87	0.00	41.08	2.10
1786	1891	5.384336	TCAGCTCTATCAGATGCTTCTACT	58.616	41.667	1.16	0.00	38.52	2.57
1816	1921	0.884704	ACAGCCAGTTACCAGCAACG	60.885	55.000	0.00	0.00	33.50	4.10
1834	1939	1.414919	ACGGCTGTACTTTCAACCTCA	59.585	47.619	0.00	0.00	0.00	3.86
1840	1945	1.807142	GTACTTTCAACCTCAGGCAGC	59.193	52.381	0.00	0.00	0.00	5.25
1862	1967	1.182667	ATGTGCAGCAACATCAGCAT	58.817	45.000	0.00	0.00	35.92	3.79
1877	1982	1.375908	GCATCCCGCAGTGTTCTCA	60.376	57.895	0.00	0.00	41.79	3.27
1887	1992	2.030946	GCAGTGTTCTCATATCAACCGC	59.969	50.000	0.00	0.00	0.00	5.68
1890	1995	2.866762	GTGTTCTCATATCAACCGCCTC	59.133	50.000	0.00	0.00	0.00	4.70
1901	2006	0.458669	AACCGCCTCGTACACCTATG	59.541	55.000	0.00	0.00	0.00	2.23
1902	2007	1.299926	CCGCCTCGTACACCTATGC	60.300	63.158	0.00	0.00	0.00	3.14
1903	2008	1.435925	CGCCTCGTACACCTATGCA	59.564	57.895	0.00	0.00	0.00	3.96
1953	2061	2.293122	CAGCCGGTTTCTTTCAATGTCA	59.707	45.455	1.90	0.00	0.00	3.58
1956	2064	2.228822	CCGGTTTCTTTCAATGTCAGGG	59.771	50.000	0.00	0.00	0.00	4.45
1957	2065	2.884639	CGGTTTCTTTCAATGTCAGGGT	59.115	45.455	0.00	0.00	0.00	4.34
1959	2067	3.888930	GGTTTCTTTCAATGTCAGGGTGA	59.111	43.478	0.00	0.00	0.00	4.02
1971	2079	0.389296	CAGGGTGACGTACAATGCGA	60.389	55.000	0.00	0.00	0.00	5.10
1973	2081	0.389426	GGGTGACGTACAATGCGACT	60.389	55.000	0.00	0.00	0.00	4.18
1980	2088	1.745115	TACAATGCGACTGCTGGGC	60.745	57.895	0.00	0.00	43.34	5.36
1992	2100	2.911143	CTGGGCCCGTCAGCTAAT	59.089	61.111	19.37	0.00	0.00	1.73
2008	2116	2.238847	TAATGCTCGCCCTCGCAAGT	62.239	55.000	0.00	0.00	39.89	3.16
2046	2154	0.751643	GACGCCCCAAATACCAGCAT	60.752	55.000	0.00	0.00	0.00	3.79
2125	2248	1.228429	GGGGTGCCTGCAACAACTA	60.228	57.895	9.70	0.00	34.85	2.24
2127	2262	1.340600	GGGGTGCCTGCAACAACTATA	60.341	52.381	9.70	0.00	34.85	1.31
2131	2266	3.254657	GGTGCCTGCAACAACTATAACAA	59.745	43.478	1.51	0.00	33.07	2.83
2135	2270	4.023193	GCCTGCAACAACTATAACAACAGT	60.023	41.667	0.00	0.00	0.00	3.55
2148	2283	4.908601	AACAACAGTCCATGGTCAGATA	57.091	40.909	12.58	0.00	0.00	1.98
2156	2291	3.004524	GTCCATGGTCAGATAGTACCGAC	59.995	52.174	12.58	0.00	38.70	4.79
2162	2297	3.560896	GGTCAGATAGTACCGACTCAGAC	59.439	52.174	0.00	0.00	37.10	3.51
2172	2307	0.170116	CGACTCAGACTCAGCCTCAC	59.830	60.000	0.00	0.00	0.00	3.51
2175	2310	1.265236	CTCAGACTCAGCCTCACCTT	58.735	55.000	0.00	0.00	0.00	3.50
2178	2313	0.178921	AGACTCAGCCTCACCTTCCA	60.179	55.000	0.00	0.00	0.00	3.53
2187	2322	2.290577	GCCTCACCTTCCAGTTCAATCT	60.291	50.000	0.00	0.00	0.00	2.40
2207	2342	2.448542	AGGGTCTGCTGGTGTGGT	60.449	61.111	0.00	0.00	0.00	4.16
2215	2350	0.476338	TGCTGGTGTGGTTATGGTGT	59.524	50.000	0.00	0.00	0.00	4.16
2247	2382	1.579429	GTGCACCAAATGTCCGTCC	59.421	57.895	5.22	0.00	0.00	4.79
2271	2406	1.745653	GGACACCTGGCTAAAGAATGC	59.254	52.381	0.00	0.00	0.00	3.56
2280	2415	2.742053	GGCTAAAGAATGCGAGACACAA	59.258	45.455	0.00	0.00	0.00	3.33
2282	2417	2.949714	AAAGAATGCGAGACACAACG	57.050	45.000	0.00	0.00	0.00	4.10
2288	2423	4.870426	AGAATGCGAGACACAACGATATTT	59.130	37.500	0.00	0.00	0.00	1.40
2327	2462	0.327924	AACCATCCGATGACCTTGCA	59.672	50.000	10.12	0.00	0.00	4.08
2360	2496	2.754946	TTAAGATGTCGAAGCCGGTT	57.245	45.000	1.90	0.00	36.24	4.44
2413	2549	0.455005	GCCTTCTTTCAGATGCCTGC	59.545	55.000	0.00	0.00	40.20	4.85
2417	2553	2.519771	TCTTTCAGATGCCTGCCAAT	57.480	45.000	0.00	0.00	40.20	3.16
2420	2556	1.466856	TTCAGATGCCTGCCAATGTC	58.533	50.000	0.00	0.00	40.20	3.06
2433	2569	1.770658	CCAATGTCTGCAGGGAGGATA	59.229	52.381	15.13	0.00	0.00	2.59
2436	2572	3.784511	ATGTCTGCAGGGAGGATATTG	57.215	47.619	15.13	0.00	0.00	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
228	229	1.792757	ATCCTCTTGCCCACCTTGCA	61.793	55.000	0.00	0.00	36.84	4.08
493	496	4.594062	TGGCACTCCCTAAACTTACTTACA	59.406	41.667	0.00	0.00	0.00	2.41
549	552	2.819595	GCTCCATTCTCGCCGCAA	60.820	61.111	0.00	0.00	0.00	4.85
868	871	6.306987	AGGACAATACAAGGTTGACAAAGAT	58.693	36.000	0.00	0.00	0.00	2.40
982	993	2.559668	CCATCAACAGTGCACTTGGATT	59.440	45.455	24.34	11.58	0.00	3.01
1097	1108	6.801575	AGACGCCTTATTTTCTCAAAAACAA	58.198	32.000	0.00	0.00	37.20	2.83
1571	1676	2.224159	ATGGTGGTTGGAGGCGAGT	61.224	57.895	0.00	0.00	0.00	4.18
1575	1680	3.070576	GCCATGGTGGTTGGAGGC	61.071	66.667	14.67	0.00	40.46	4.70
1576	1681	2.362889	GGCCATGGTGGTTGGAGG	60.363	66.667	14.67	0.00	40.46	4.30
1628	1733	0.037326	GAGCACCACCAGACGATGAA	60.037	55.000	0.00	0.00	0.00	2.57
1664	1769	1.738099	CAGGACAAGCGGGAAGACG	60.738	63.158	0.00	0.00	0.00	4.18
1667	1772	1.738099	CGACAGGACAAGCGGGAAG	60.738	63.158	0.00	0.00	0.00	3.46
1673	1778	1.954146	TTGCGTCGACAGGACAAGC	60.954	57.895	17.16	9.32	46.42	4.01
1675	1780	1.142097	TGTTGCGTCGACAGGACAA	59.858	52.632	17.16	10.88	46.42	3.18
1676	1781	1.590525	GTGTTGCGTCGACAGGACA	60.591	57.895	17.16	12.93	46.42	4.02
1757	1862	3.186817	GCATCTGATAGAGCTGATGTTGC	59.813	47.826	13.81	1.19	42.63	4.17
1763	1868	5.241285	CAGTAGAAGCATCTGATAGAGCTGA	59.759	44.000	0.71	0.00	37.41	4.26
1769	1874	3.989167	GCTGCAGTAGAAGCATCTGATAG	59.011	47.826	16.64	0.00	46.44	2.08
1780	1885	2.759191	CTGTGAACTGCTGCAGTAGAA	58.241	47.619	34.60	19.44	44.62	2.10
1786	1891	1.895231	CTGGCTGTGAACTGCTGCA	60.895	57.895	0.88	0.88	40.16	4.41
1816	1921	2.427506	CCTGAGGTTGAAAGTACAGCC	58.572	52.381	0.00	0.00	40.59	4.85
1819	1924	2.810400	GCTGCCTGAGGTTGAAAGTACA	60.810	50.000	0.00	0.00	0.00	2.90
1822	1927	0.183492	TGCTGCCTGAGGTTGAAAGT	59.817	50.000	0.00	0.00	0.00	2.66
1840	1945	2.098443	TGCTGATGTTGCTGCACATATG	59.902	45.455	0.00	0.00	37.52	1.78
1856	1961	1.375908	GAACACTGCGGGATGCTGA	60.376	57.895	0.00	0.00	46.63	4.26
1862	1967	2.107366	TGATATGAGAACACTGCGGGA	58.893	47.619	0.00	0.00	0.00	5.14
1877	1982	1.068127	GGTGTACGAGGCGGTTGATAT	59.932	52.381	0.00	0.00	0.00	1.63
1887	1992	0.459899	TGCTGCATAGGTGTACGAGG	59.540	55.000	0.00	0.00	0.00	4.63
1890	1995	0.460109	TGCTGCTGCATAGGTGTACG	60.460	55.000	14.93	0.00	45.31	3.67
1901	2006	3.745803	GACCCTTGCTGCTGCTGC	61.746	66.667	22.51	22.51	40.48	5.25
1902	2007	2.033757	AGACCCTTGCTGCTGCTG	59.966	61.111	17.00	9.29	40.48	4.41
1903	2008	2.350514	GAGACCCTTGCTGCTGCT	59.649	61.111	17.00	0.00	40.48	4.24
1917	2025	4.100084	CTGCATGCCGGTGGGAGA	62.100	66.667	16.68	0.00	34.06	3.71
1953	2061	0.389426	GTCGCATTGTACGTCACCCT	60.389	55.000	0.00	0.00	0.00	4.34
1956	2064	0.093026	GCAGTCGCATTGTACGTCAC	59.907	55.000	0.00	0.00	38.36	3.67
1957	2065	0.038618	AGCAGTCGCATTGTACGTCA	60.039	50.000	0.00	0.00	42.27	4.35
1959	2067	1.014044	CCAGCAGTCGCATTGTACGT	61.014	55.000	0.00	0.00	42.27	3.57
2008	2116	1.544825	CCTCCCTTGCCACTCTTCGA	61.545	60.000	0.00	0.00	0.00	3.71
2014	2122	4.021925	GCGTCCTCCCTTGCCACT	62.022	66.667	0.00	0.00	0.00	4.00
2054	2162	1.000955	CAACAACGACAGTAGGAGGCT	59.999	52.381	0.00	0.00	0.00	4.58
2093	2201	3.338250	CCCCCTGCTACCCTTGCA	61.338	66.667	0.00	0.00	38.81	4.08
2119	2242	5.876357	ACCATGGACTGTTGTTATAGTTGT	58.124	37.500	21.47	0.00	0.00	3.32
2125	2248	4.908601	TCTGACCATGGACTGTTGTTAT	57.091	40.909	21.47	0.00	0.00	1.89
2127	2262	3.795688	ATCTGACCATGGACTGTTGTT	57.204	42.857	21.47	0.00	0.00	2.83
2131	2266	3.961408	GGTACTATCTGACCATGGACTGT	59.039	47.826	21.47	9.61	35.65	3.55
2135	2270	3.117625	AGTCGGTACTATCTGACCATGGA	60.118	47.826	21.47	0.00	42.68	3.41
2148	2283	1.455248	GCTGAGTCTGAGTCGGTACT	58.545	55.000	19.66	1.55	39.21	2.73
2156	2291	1.204467	GAAGGTGAGGCTGAGTCTGAG	59.796	57.143	0.00	0.00	0.00	3.35
2162	2297	0.689623	AACTGGAAGGTGAGGCTGAG	59.310	55.000	0.00	0.00	39.30	3.35
2172	2307	2.089980	CCTGCAGATTGAACTGGAAGG	58.910	52.381	17.39	0.00	39.30	3.46
2175	2310	1.003580	GACCCTGCAGATTGAACTGGA	59.996	52.381	17.39	0.00	38.22	3.86
2178	2313	2.486472	CAGACCCTGCAGATTGAACT	57.514	50.000	17.39	2.77	0.00	3.01
2198	2333	2.859165	AGACACCATAACCACACCAG	57.141	50.000	0.00	0.00	0.00	4.00
2207	2342	6.460399	GCACCACAACTTTTTAGACACCATAA	60.460	38.462	0.00	0.00	0.00	1.90
2215	2350	3.357203	TGGTGCACCACAACTTTTTAGA	58.643	40.909	34.74	7.07	42.01	2.10
2259	2394	2.346803	TGTGTCTCGCATTCTTTAGCC	58.653	47.619	0.00	0.00	0.00	3.93
2268	2403	5.545658	AAAAATATCGTTGTGTCTCGCAT	57.454	34.783	0.00	0.00	0.00	4.73
2297	2432	5.749109	GTCATCGGATGGTTCTACTTGTTAG	59.251	44.000	17.42	0.00	0.00	2.34
2306	2441	1.407437	GCAAGGTCATCGGATGGTTCT	60.407	52.381	17.42	9.76	0.00	3.01
2327	2462	5.584067	ACATCTTAATGCAGGGCACCGAT	62.584	47.826	0.00	0.00	45.97	4.18
2360	2496	1.472082	CCATAGCCACAAAACATCGCA	59.528	47.619	0.00	0.00	0.00	5.10
2367	2503	4.901197	TCTCAGTACCATAGCCACAAAA	57.099	40.909	0.00	0.00	0.00	2.44
2413	2549	0.549950	ATCCTCCCTGCAGACATTGG	59.450	55.000	17.39	7.53	0.00	3.16
2417	2553	1.141657	GCAATATCCTCCCTGCAGACA	59.858	52.381	17.39	0.00	34.87	3.41
2420	2556	1.271271	GGAGCAATATCCTCCCTGCAG	60.271	57.143	6.78	6.78	42.46	4.41
2433	2569	3.726557	TGGAGAAATCTGTGGAGCAAT	57.273	42.857	0.00	0.00	0.00	3.56
2436	2572	1.734465	CGTTGGAGAAATCTGTGGAGC	59.266	52.381	0.00	0.00	0.00	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.