AutoCloner

Multiple sequence alignment - TraesCS2B01G346400

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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	TraesCS2B01G346400	chr2B	100.000	2552	0	0	1	2552	493241615	493244166	0.000000e+00	4713
1	TraesCS2B01G346400	chr1A	92.777	2589	138	15	2	2552	548229640	548227063	0.000000e+00	3699
2	TraesCS2B01G346400	chr1A	94.138	1177	63	3	1	1176	452026614	452025443	0.000000e+00	1786
3	TraesCS2B01G346400	chr1A	94.134	716	29	6	1178	1883	452025367	452024655	0.000000e+00	1077
4	TraesCS2B01G346400	chr4A	96.173	1437	33	8	1	1437	725870609	725869195	0.000000e+00	2329
5	TraesCS2B01G346400	chr4A	98.502	1068	15	1	1485	2552	725869206	725868140	0.000000e+00	1882
6	TraesCS2B01G346400	chr4A	93.883	1177	66	3	1	1176	41895267	41896438	0.000000e+00	1770
7	TraesCS2B01G346400	chr4A	94.274	716	29	5	1178	1883	41896514	41897227	0.000000e+00	1085
8	TraesCS2B01G346400	chr5A	92.650	1415	62	13	1178	2552	299773560	299772148	0.000000e+00	1999
9	TraesCS2B01G346400	chr5A	94.771	765	35	2	1	764	299775008	299774248	0.000000e+00	1186
10	TraesCS2B01G346400	chr5A	95.035	423	21	0	754	1176	299774058	299773636	0.000000e+00	665
11	TraesCS2B01G346400	chr1D	92.400	1421	60	18	1178	2552	156777978	156779396	0.000000e+00	1982
12	TraesCS2B01G346400	chr1D	94.138	1177	58	3	1	1176	156776736	156777902	0.000000e+00	1781
13	TraesCS2B01G346400	chr3A	92.313	1418	62	15	1178	2552	662140246	662141659	0.000000e+00	1971
14	TraesCS2B01G346400	chr3A	93.333	630	35	3	1	629	662124529	662125152	0.000000e+00	924
15	TraesCS2B01G346400	chr3A	94.033	553	33	0	624	1176	662139618	662140170	0.000000e+00	839
16	TraesCS2B01G346400	chr6A	91.474	1431	61	18	1178	2552	99977533	99976108	0.000000e+00	1910
17	TraesCS2B01G346400	chr6A	92.739	606	34	5	1	602	100058475	100057876	0.000000e+00	867
18	TraesCS2B01G346400	chr6A	94.539	531	29	0	646	1176	99978139	99977609	0.000000e+00	821
19	TraesCS2B01G346400	chr6A	97.248	109	3	0	1	109	100058688	100058580	4.340000e-43	185
20	TraesCS2B01G346400	chr4B	87.583	1208	105	19	1	1177	570343838	570345031	0.000000e+00	1358
21	TraesCS2B01G346400	chr4B	94.737	152	6	1	1178	1329	570345104	570345253	4.240000e-58	235
22	TraesCS2B01G346400	chr3D	85.075	268	37	2	1354	1620	350130045	350130310	1.160000e-68	270
23	TraesCS2B01G346400	chrUn	86.111	108	13	2	2222	2329	31522499	31522394	5.770000e-22	115

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	TraesCS2B01G346400	chr2B	493241615	493244166	2551	False	4713.000000	4713	100.0000	1	2552	1	chr2B.!!$F1	2551
1	TraesCS2B01G346400	chr1A	548227063	548229640	2577	True	3699.000000	3699	92.7770	2	2552	1	chr1A.!!$R1	2550
2	TraesCS2B01G346400	chr1A	452024655	452026614	1959	True	1431.500000	1786	94.1360	1	1883	2	chr1A.!!$R2	1882
3	TraesCS2B01G346400	chr4A	725868140	725870609	2469	True	2105.500000	2329	97.3375	1	2552	2	chr4A.!!$R1	2551
4	TraesCS2B01G346400	chr4A	41895267	41897227	1960	False	1427.500000	1770	94.0785	1	1883	2	chr4A.!!$F1	1882
5	TraesCS2B01G346400	chr5A	299772148	299775008	2860	True	1283.333333	1999	94.1520	1	2552	3	chr5A.!!$R1	2551
6	TraesCS2B01G346400	chr1D	156776736	156779396	2660	False	1881.500000	1982	93.2690	1	2552	2	chr1D.!!$F1	2551
7	TraesCS2B01G346400	chr3A	662139618	662141659	2041	False	1405.000000	1971	93.1730	624	2552	2	chr3A.!!$F2	1928
8	TraesCS2B01G346400	chr3A	662124529	662125152	623	False	924.000000	924	93.3330	1	629	1	chr3A.!!$F1	628
9	TraesCS2B01G346400	chr6A	99976108	99978139	2031	True	1365.500000	1910	93.0065	646	2552	2	chr6A.!!$R1	1906
10	TraesCS2B01G346400	chr6A	100057876	100058688	812	True	526.000000	867	94.9935	1	602	2	chr6A.!!$R2	601
11	TraesCS2B01G346400	chr4B	570343838	570345253	1415	False	796.500000	1358	91.1600	1	1329	2	chr4B.!!$F1	1328

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
196	411	0.106719	CCATGGACGCCCTAAATGGT	60.107	55.0	5.56	0.0	31.95	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1959	2605	1.882623	AGCCTTGCTTTCACTACAAGC	59.117	47.619	0.0	0.0	45.92	4.01	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
97	311	1.495951	GTTCGATGTGGCGGTTGTC	59.504	57.895	0.00	0.00	0.00	3.18
155	370	4.302455	CGGATGAATTTCTAGTCTCGCAT	58.698	43.478	0.00	0.00	0.00	4.73
167	382	4.329462	AGTCTCGCATCTCCTTATTTCC	57.671	45.455	0.00	0.00	0.00	3.13
186	401	2.690778	GGTCTTGCACCATGGACGC	61.691	63.158	21.47	20.48	45.98	5.19
190	405	2.535485	CTTGCACCATGGACGCCCTA	62.535	60.000	21.47	7.83	0.00	3.53
196	411	0.106719	CCATGGACGCCCTAAATGGT	60.107	55.000	5.56	0.00	31.95	3.55
200	415	0.179468	GGACGCCCTAAATGGTGCTA	59.821	55.000	0.00	0.00	39.60	3.49
213	428	1.566018	GGTGCTAACGCGTGCTTCTT	61.566	55.000	14.98	0.00	39.65	2.52
400	638	9.831737	GAATATGATACATTTACATTGACAGGC	57.168	33.333	0.00	0.00	0.00	4.85
991	1437	7.439381	TCGGATTGTATATGAACTAAGTTCCC	58.561	38.462	0.00	0.00	41.35	3.97
1396	1941	4.413851	TGGTTAACTATGGGATATGCACCA	59.586	41.667	5.42	0.00	41.76	4.17
1437	2042	5.781210	TTTTTCTGTCCATGTATGTTGCA	57.219	34.783	0.00	0.00	0.00	4.08
1438	2043	5.981088	TTTTCTGTCCATGTATGTTGCAT	57.019	34.783	0.00	0.00	0.00	3.96
1439	2044	5.565592	TTTCTGTCCATGTATGTTGCATC	57.434	39.130	0.00	0.00	0.00	3.91
1440	2045	3.544684	TCTGTCCATGTATGTTGCATCC	58.455	45.455	0.00	0.00	0.00	3.51
1441	2046	3.200605	TCTGTCCATGTATGTTGCATCCT	59.799	43.478	0.00	0.00	0.00	3.24
1442	2047	3.949754	CTGTCCATGTATGTTGCATCCTT	59.050	43.478	0.00	0.00	0.00	3.36
1443	2048	4.343231	TGTCCATGTATGTTGCATCCTTT	58.657	39.130	0.00	0.00	0.00	3.11
1444	2049	4.771577	TGTCCATGTATGTTGCATCCTTTT	59.228	37.500	0.00	0.00	0.00	2.27
1445	2050	5.104374	GTCCATGTATGTTGCATCCTTTTG	58.896	41.667	0.00	0.00	0.00	2.44
1446	2051	5.015515	TCCATGTATGTTGCATCCTTTTGA	58.984	37.500	0.00	0.00	0.00	2.69
1447	2052	5.104374	CCATGTATGTTGCATCCTTTTGAC	58.896	41.667	0.00	0.00	0.00	3.18
1448	2053	5.105635	CCATGTATGTTGCATCCTTTTGACT	60.106	40.000	0.00	0.00	0.00	3.41
1449	2054	6.392354	CATGTATGTTGCATCCTTTTGACTT	58.608	36.000	0.00	0.00	0.00	3.01
1450	2055	7.362834	CCATGTATGTTGCATCCTTTTGACTTA	60.363	37.037	0.00	0.00	0.00	2.24
1451	2056	7.701539	TGTATGTTGCATCCTTTTGACTTAT	57.298	32.000	0.00	0.00	0.00	1.73
1452	2057	7.537715	TGTATGTTGCATCCTTTTGACTTATG	58.462	34.615	0.00	0.00	0.00	1.90
1453	2058	6.594788	ATGTTGCATCCTTTTGACTTATGT	57.405	33.333	0.00	0.00	0.00	2.29
1454	2059	7.701539	ATGTTGCATCCTTTTGACTTATGTA	57.298	32.000	0.00	0.00	0.00	2.29
1455	2060	7.701539	TGTTGCATCCTTTTGACTTATGTAT	57.298	32.000	0.00	0.00	0.00	2.29
1456	2061	7.537715	TGTTGCATCCTTTTGACTTATGTATG	58.462	34.615	0.00	0.00	0.00	2.39
1457	2062	7.392953	TGTTGCATCCTTTTGACTTATGTATGA	59.607	33.333	0.00	0.00	0.00	2.15
1458	2063	8.408601	GTTGCATCCTTTTGACTTATGTATGAT	58.591	33.333	0.00	0.00	0.00	2.45
1459	2064	7.933396	TGCATCCTTTTGACTTATGTATGATG	58.067	34.615	0.00	0.00	0.00	3.07
1460	2065	7.557358	TGCATCCTTTTGACTTATGTATGATGT	59.443	33.333	0.00	0.00	0.00	3.06
1461	2066	7.859377	GCATCCTTTTGACTTATGTATGATGTG	59.141	37.037	0.00	0.00	0.00	3.21
1462	2067	8.896744	CATCCTTTTGACTTATGTATGATGTGT	58.103	33.333	0.00	0.00	0.00	3.72
1463	2068	8.862325	TCCTTTTGACTTATGTATGATGTGTT	57.138	30.769	0.00	0.00	0.00	3.32
1464	2069	8.946085	TCCTTTTGACTTATGTATGATGTGTTC	58.054	33.333	0.00	0.00	0.00	3.18
1465	2070	8.729756	CCTTTTGACTTATGTATGATGTGTTCA	58.270	33.333	0.00	0.00	39.12	3.18
1467	2072	9.891828	TTTTGACTTATGTATGATGTGTTCAAC	57.108	29.630	0.00	0.00	38.03	3.18
1468	2073	7.289587	TGACTTATGTATGATGTGTTCAACG	57.710	36.000	0.00	0.00	38.03	4.10
1469	2074	7.093992	TGACTTATGTATGATGTGTTCAACGA	58.906	34.615	0.00	0.00	38.03	3.85
1470	2075	7.763985	TGACTTATGTATGATGTGTTCAACGAT	59.236	33.333	0.00	0.00	38.03	3.73
1471	2076	7.909267	ACTTATGTATGATGTGTTCAACGATG	58.091	34.615	0.00	0.00	38.03	3.84
1472	2077	7.549134	ACTTATGTATGATGTGTTCAACGATGT	59.451	33.333	0.00	0.00	38.03	3.06
1473	2078	5.778161	TGTATGATGTGTTCAACGATGTC	57.222	39.130	0.00	0.00	38.03	3.06
1474	2079	5.233988	TGTATGATGTGTTCAACGATGTCA	58.766	37.500	0.00	0.00	38.03	3.58
1475	2080	5.874261	TGTATGATGTGTTCAACGATGTCAT	59.126	36.000	0.00	0.00	38.03	3.06
1476	2081	5.885230	ATGATGTGTTCAACGATGTCATT	57.115	34.783	0.00	0.00	38.03	2.57
1477	2082	5.033326	TGATGTGTTCAACGATGTCATTG	57.967	39.130	0.00	0.00	0.00	2.82
1478	2083	3.894782	TGTGTTCAACGATGTCATTGG	57.105	42.857	5.04	0.00	0.00	3.16
1479	2084	3.210227	TGTGTTCAACGATGTCATTGGT	58.790	40.909	5.04	0.00	0.00	3.67
1480	2085	3.003171	TGTGTTCAACGATGTCATTGGTG	59.997	43.478	11.45	11.45	32.41	4.17
1481	2086	3.249799	GTGTTCAACGATGTCATTGGTGA	59.750	43.478	15.71	15.71	38.59	4.02
1493	2098	4.356405	TCATTGGTGACTCATGTGAAGT	57.644	40.909	0.94	0.00	0.00	3.01
1494	2099	4.717877	TCATTGGTGACTCATGTGAAGTT	58.282	39.130	0.94	0.00	0.00	2.66
1495	2100	4.516321	TCATTGGTGACTCATGTGAAGTTG	59.484	41.667	0.94	0.00	0.00	3.16
1496	2101	2.221169	TGGTGACTCATGTGAAGTTGC	58.779	47.619	0.94	0.00	0.00	4.17
1891	2533	2.887152	GAGCTCCAACAACCATCAAACT	59.113	45.455	0.87	0.00	0.00	2.66
1959	2605	5.181748	ACCTTAGCAAAGCAATCTGTAGAG	58.818	41.667	0.00	0.00	0.00	2.43
2256	2916	4.668138	TTACTTCCCCATGGTTTTAGCT	57.332	40.909	11.73	0.00	0.00	3.32
2315	2975	4.833390	CCTTAGAATCAGGGAAACGTTCT	58.167	43.478	0.00	0.00	33.96	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
97	311	7.086376	CCATTCTTCACAGTTGGAATAAGTTG	58.914	38.462	0.00	0.00	30.25	3.16
155	370	2.569853	TGCAAGACCGGAAATAAGGAGA	59.430	45.455	9.46	0.00	0.00	3.71
186	401	0.655733	CGCGTTAGCACCATTTAGGG	59.344	55.000	0.00	0.00	45.49	3.53
190	405	1.209127	GCACGCGTTAGCACCATTT	59.791	52.632	10.22	0.00	45.49	2.32
196	411	1.614227	CGAAGAAGCACGCGTTAGCA	61.614	55.000	21.65	0.00	45.49	3.49
200	415	2.022129	CTCCGAAGAAGCACGCGTT	61.022	57.895	10.22	0.00	0.00	4.84
213	428	2.896677	ATCACATGGCCCTCCTCCGA	62.897	60.000	0.00	0.00	0.00	4.55
235	473	1.676678	GGCTATGTCTGCCGGTCTGA	61.677	60.000	1.90	2.12	41.03	3.27
417	655	9.774742	AGCTTAATCAATAAAAAGACTAAAGCG	57.225	29.630	0.00	0.00	0.00	4.68
936	1382	4.080526	GCACTTAAGTTCCCTTCCATCCTA	60.081	45.833	5.07	0.00	31.89	2.94
991	1437	0.729140	GCGGTCACCATTTTTCAGCG	60.729	55.000	0.00	0.00	0.00	5.18
1118	1564	1.909302	TCTGGTTTGAGGGCTTCTAGG	59.091	52.381	0.00	0.00	0.00	3.02
1396	1941	9.321562	CAGAAAAATATGCATAGAAAAATGGCT	57.678	29.630	12.79	0.00	0.00	4.75
1437	2042	9.466497	AACACATCATACATAAGTCAAAAGGAT	57.534	29.630	0.00	0.00	0.00	3.24
1438	2043	8.862325	AACACATCATACATAAGTCAAAAGGA	57.138	30.769	0.00	0.00	0.00	3.36
1439	2044	8.729756	TGAACACATCATACATAAGTCAAAAGG	58.270	33.333	0.00	0.00	31.50	3.11
1441	2046	9.891828	GTTGAACACATCATACATAAGTCAAAA	57.108	29.630	0.00	0.00	38.03	2.44
1442	2047	8.227119	CGTTGAACACATCATACATAAGTCAAA	58.773	33.333	0.00	0.00	38.03	2.69
1443	2048	7.600752	TCGTTGAACACATCATACATAAGTCAA	59.399	33.333	0.00	0.00	38.03	3.18
1444	2049	7.093992	TCGTTGAACACATCATACATAAGTCA	58.906	34.615	0.00	0.00	38.03	3.41
1445	2050	7.520119	TCGTTGAACACATCATACATAAGTC	57.480	36.000	0.00	0.00	38.03	3.01
1446	2051	7.549134	ACATCGTTGAACACATCATACATAAGT	59.451	33.333	0.00	0.00	38.03	2.24
1447	2052	7.909267	ACATCGTTGAACACATCATACATAAG	58.091	34.615	0.00	0.00	38.03	1.73
1448	2053	7.547370	TGACATCGTTGAACACATCATACATAA	59.453	33.333	0.00	0.00	38.03	1.90
1449	2054	7.038659	TGACATCGTTGAACACATCATACATA	58.961	34.615	0.00	0.00	38.03	2.29
1450	2055	5.874261	TGACATCGTTGAACACATCATACAT	59.126	36.000	0.00	0.00	38.03	2.29
1451	2056	5.233988	TGACATCGTTGAACACATCATACA	58.766	37.500	0.00	0.00	38.03	2.29
1452	2057	5.778161	TGACATCGTTGAACACATCATAC	57.222	39.130	0.00	0.00	38.03	2.39
1453	2058	6.183360	CCAATGACATCGTTGAACACATCATA	60.183	38.462	14.18	0.00	43.62	2.15
1454	2059	5.392272	CCAATGACATCGTTGAACACATCAT	60.392	40.000	14.18	0.00	43.62	2.45
1455	2060	4.083377	CCAATGACATCGTTGAACACATCA	60.083	41.667	14.18	0.00	43.62	3.07
1456	2061	4.083324	ACCAATGACATCGTTGAACACATC	60.083	41.667	14.18	0.00	43.62	3.06
1457	2062	3.820467	ACCAATGACATCGTTGAACACAT	59.180	39.130	14.18	0.00	43.62	3.21
1458	2063	3.003171	CACCAATGACATCGTTGAACACA	59.997	43.478	14.18	0.00	43.62	3.72
1459	2064	3.249799	TCACCAATGACATCGTTGAACAC	59.750	43.478	14.18	0.00	43.62	3.32
1460	2065	3.471680	TCACCAATGACATCGTTGAACA	58.528	40.909	14.18	1.06	43.62	3.18
1472	2077	4.356405	ACTTCACATGAGTCACCAATGA	57.644	40.909	0.00	0.00	0.00	2.57
1473	2078	4.790878	CAACTTCACATGAGTCACCAATG	58.209	43.478	0.00	0.00	0.00	2.82
1474	2079	3.254166	GCAACTTCACATGAGTCACCAAT	59.746	43.478	0.00	0.00	0.00	3.16
1475	2080	2.618241	GCAACTTCACATGAGTCACCAA	59.382	45.455	0.00	0.00	0.00	3.67
1476	2081	2.158769	AGCAACTTCACATGAGTCACCA	60.159	45.455	0.00	0.00	0.00	4.17
1477	2082	2.498167	AGCAACTTCACATGAGTCACC	58.502	47.619	0.00	0.00	0.00	4.02
1478	2083	4.201950	ACAAAGCAACTTCACATGAGTCAC	60.202	41.667	0.00	0.00	0.00	3.67
1479	2084	3.947196	ACAAAGCAACTTCACATGAGTCA	59.053	39.130	0.00	0.00	0.00	3.41
1480	2085	4.558538	ACAAAGCAACTTCACATGAGTC	57.441	40.909	0.00	0.00	0.00	3.36
1481	2086	4.989279	AACAAAGCAACTTCACATGAGT	57.011	36.364	0.00	0.00	0.00	3.41
1482	2087	5.342433	TCAAACAAAGCAACTTCACATGAG	58.658	37.500	0.00	0.00	0.00	2.90
1483	2088	5.321959	TCAAACAAAGCAACTTCACATGA	57.678	34.783	0.00	0.00	0.00	3.07
1484	2089	6.256104	TGAATCAAACAAAGCAACTTCACATG	59.744	34.615	0.00	0.00	0.00	3.21
1485	2090	6.339730	TGAATCAAACAAAGCAACTTCACAT	58.660	32.000	0.00	0.00	0.00	3.21
1486	2091	5.718146	TGAATCAAACAAAGCAACTTCACA	58.282	33.333	0.00	0.00	0.00	3.58
1487	2092	6.311200	ACTTGAATCAAACAAAGCAACTTCAC	59.689	34.615	0.00	0.00	0.00	3.18
1488	2093	6.310956	CACTTGAATCAAACAAAGCAACTTCA	59.689	34.615	0.00	0.00	0.00	3.02
1489	2094	6.311200	ACACTTGAATCAAACAAAGCAACTTC	59.689	34.615	0.00	0.00	0.00	3.01
1490	2095	6.165577	ACACTTGAATCAAACAAAGCAACTT	58.834	32.000	0.00	0.00	0.00	2.66
1491	2096	5.723295	ACACTTGAATCAAACAAAGCAACT	58.277	33.333	0.00	0.00	0.00	3.16
1492	2097	7.518731	TTACACTTGAATCAAACAAAGCAAC	57.481	32.000	0.00	0.00	0.00	4.17
1493	2098	8.602328	CAATTACACTTGAATCAAACAAAGCAA	58.398	29.630	0.00	0.00	0.00	3.91
1494	2099	7.224362	CCAATTACACTTGAATCAAACAAAGCA	59.776	33.333	0.00	0.00	0.00	3.91
1495	2100	7.437862	TCCAATTACACTTGAATCAAACAAAGC	59.562	33.333	0.00	0.00	0.00	3.51
1496	2101	8.755018	GTCCAATTACACTTGAATCAAACAAAG	58.245	33.333	0.00	0.00	0.00	2.77
1538	2143	6.063496	ACTCATGGCTTCATGCATATATCT	57.937	37.500	0.00	0.00	45.81	1.98
1959	2605	1.882623	AGCCTTGCTTTCACTACAAGC	59.117	47.619	0.00	0.00	45.92	4.01
2109	2769	6.323996	TGATAAGATCGACCAGACTAAACCAT	59.676	38.462	0.00	0.00	0.00	3.55
2232	2892	4.709886	GCTAAAACCATGGGGAAGTAATGT	59.290	41.667	18.09	0.00	38.05	2.71
2256	2916	5.425196	TGATGATTCTCCATCTGTGACAA	57.575	39.130	0.00	0.00	42.49	3.18
2315	2975	5.798125	TGCATGTTTGGTCTTTAAATGGA	57.202	34.783	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.