AutoCloner

Multiple sequence alignment - TraesCS3B01G298300

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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	TraesCS3B01G298300	chr3B	100.000	2286	0	0	1	2286	478550956	478548671	0.000000e+00	4222
1	TraesCS3B01G298300	chr3B	91.242	1610	125	11	1	1603	598917516	598919116	0.000000e+00	2178
2	TraesCS3B01G298300	chr3A	91.917	1732	112	11	1	1710	418765663	418763938	0.000000e+00	2398
3	TraesCS3B01G298300	chr5B	91.691	1685	130	9	1	1679	407222539	407224219	0.000000e+00	2327
4	TraesCS3B01G298300	chr4D	90.972	1728	130	10	1	1708	421048639	421046918	0.000000e+00	2303
5	TraesCS3B01G298300	chr4D	90.799	1739	125	13	1	1715	493971112	493969385	0.000000e+00	2292
6	TraesCS3B01G298300	chr4D	90.611	1736	131	11	1	1715	116524560	116522836	0.000000e+00	2274
7	TraesCS3B01G298300	chr4D	90.226	1729	132	15	1	1707	48683931	48682218	0.000000e+00	2222
8	TraesCS3B01G298300	chr7B	90.757	1731	129	16	1	1710	150842108	150843828	0.000000e+00	2281
9	TraesCS3B01G298300	chr7B	90.126	1742	121	18	1	1713	679357634	679359353	0.000000e+00	2217
10	TraesCS3B01G298300	chr4A	90.578	1730	138	13	1	1710	327748377	327746653	0.000000e+00	2268
11	TraesCS3B01G298300	chr4A	81.471	367	45	10	1934	2286	374702888	374702531	1.730000e-71	279
12	TraesCS3B01G298300	chr5A	90.504	1727	138	12	4	1710	604232060	604230340	0.000000e+00	2257
13	TraesCS3B01G298300	chr2A	91.235	1620	115	12	118	1715	456462405	456460791	0.000000e+00	2180
14	TraesCS3B01G298300	chr2B	91.022	1526	117	7	202	1710	495053922	495055444	0.000000e+00	2041
15	TraesCS3B01G298300	chr2B	88.608	1027	83	11	705	1715	783932662	783931654	0.000000e+00	1218
16	TraesCS3B01G298300	chr1D	88.561	848	63	16	893	1716	318515782	318514945	0.000000e+00	998
17	TraesCS3B01G298300	chr5D	85.223	582	65	7	1719	2286	411782323	411781749	1.520000e-161	579
18	TraesCS3B01G298300	chr5D	82.283	587	76	16	1715	2286	544815507	544814934	1.230000e-132	483
19	TraesCS3B01G298300	chr7D	87.336	229	12	4	1498	1710	182493703	182493930	1.750000e-61	246

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	TraesCS3B01G298300	chr3B	478548671	478550956	2285	True	4222	4222	100.000	1	2286	1	chr3B.!!$R1	2285
1	TraesCS3B01G298300	chr3B	598917516	598919116	1600	False	2178	2178	91.242	1	1603	1	chr3B.!!$F1	1602
2	TraesCS3B01G298300	chr3A	418763938	418765663	1725	True	2398	2398	91.917	1	1710	1	chr3A.!!$R1	1709
3	TraesCS3B01G298300	chr5B	407222539	407224219	1680	False	2327	2327	91.691	1	1679	1	chr5B.!!$F1	1678
4	TraesCS3B01G298300	chr4D	421046918	421048639	1721	True	2303	2303	90.972	1	1708	1	chr4D.!!$R3	1707
5	TraesCS3B01G298300	chr4D	493969385	493971112	1727	True	2292	2292	90.799	1	1715	1	chr4D.!!$R4	1714
6	TraesCS3B01G298300	chr4D	116522836	116524560	1724	True	2274	2274	90.611	1	1715	1	chr4D.!!$R2	1714
7	TraesCS3B01G298300	chr4D	48682218	48683931	1713	True	2222	2222	90.226	1	1707	1	chr4D.!!$R1	1706
8	TraesCS3B01G298300	chr7B	150842108	150843828	1720	False	2281	2281	90.757	1	1710	1	chr7B.!!$F1	1709
9	TraesCS3B01G298300	chr7B	679357634	679359353	1719	False	2217	2217	90.126	1	1713	1	chr7B.!!$F2	1712
10	TraesCS3B01G298300	chr4A	327746653	327748377	1724	True	2268	2268	90.578	1	1710	1	chr4A.!!$R1	1709
11	TraesCS3B01G298300	chr5A	604230340	604232060	1720	True	2257	2257	90.504	4	1710	1	chr5A.!!$R1	1706
12	TraesCS3B01G298300	chr2A	456460791	456462405	1614	True	2180	2180	91.235	118	1715	1	chr2A.!!$R1	1597
13	TraesCS3B01G298300	chr2B	495053922	495055444	1522	False	2041	2041	91.022	202	1710	1	chr2B.!!$F1	1508
14	TraesCS3B01G298300	chr2B	783931654	783932662	1008	True	1218	1218	88.608	705	1715	1	chr2B.!!$R1	1010
15	TraesCS3B01G298300	chr1D	318514945	318515782	837	True	998	998	88.561	893	1716	1	chr1D.!!$R1	823
16	TraesCS3B01G298300	chr5D	411781749	411782323	574	True	579	579	85.223	1719	2286	1	chr5D.!!$R1	567
17	TraesCS3B01G298300	chr5D	544814934	544815507	573	True	483	483	82.283	1715	2286	1	chr5D.!!$R2	571

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
375	381	0.111089	GCGTCTTCAACTCTTGTGCG	60.111	55.0	0.0	0.0	0.0	5.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2079	2161	0.239082	CAGCATGTCGCATGTTGTGT	59.761	50.0	20.27	3.41	46.13	3.72	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
146	150	3.963687	CTCGCTGGCATCTGCACCA	62.964	63.158	4.33	0.00	44.36	4.17
175	179	2.042261	TCCTTAGGCTCCCCACCC	59.958	66.667	0.00	0.00	0.00	4.61
306	310	3.252974	GGAGACGACTTGATTCATGGT	57.747	47.619	4.75	0.00	0.00	3.55
316	320	6.161855	ACTTGATTCATGGTCTAGCGAATA	57.838	37.500	4.75	0.00	0.00	1.75
375	381	0.111089	GCGTCTTCAACTCTTGTGCG	60.111	55.000	0.00	0.00	0.00	5.34
488	495	2.194597	GTCACCAGCCAACCACCA	59.805	61.111	0.00	0.00	0.00	4.17
710	724	6.051717	GCTCTTCAATAAGCCATGAACTCTA	58.948	40.000	0.00	0.00	32.46	2.43
714	728	7.712639	TCTTCAATAAGCCATGAACTCTATGTC	59.287	37.037	0.00	0.00	32.46	3.06
732	746	2.000447	GTCGTGCCTAACTCCATGAAC	59.000	52.381	0.00	0.00	0.00	3.18
741	755	2.346766	ACTCCATGAACTGTGTGCAA	57.653	45.000	0.00	0.00	0.00	4.08
752	766	1.728971	CTGTGTGCAAATCGAGGAGAC	59.271	52.381	0.00	0.00	0.00	3.36
865	879	0.520404	CGAGGAAGAACCGAAGACGA	59.480	55.000	0.00	0.00	44.74	4.20
886	900	2.974489	GAGGTTGGCGACGACGAGA	61.974	63.158	12.29	0.00	46.42	4.04
901	916	3.160047	AGAGCATGGAGGAGCCCG	61.160	66.667	0.00	0.00	34.97	6.13
1091	1119	0.679505	CTGGAAGGTGACGGTGAAGA	59.320	55.000	0.00	0.00	0.00	2.87
1289	1320	3.083997	CCGCCAAGGACTAGGGCT	61.084	66.667	11.58	0.00	45.53	5.19
1322	1353	6.523840	TCCTTCCTAAGTACTATCGAGTCTC	58.476	44.000	0.00	0.00	37.10	3.36
1333	1388	8.216423	AGTACTATCGAGTCTCCTTTATGGTTA	58.784	37.037	0.00	0.00	37.10	2.85
1334	1389	7.513371	ACTATCGAGTCTCCTTTATGGTTAG	57.487	40.000	0.00	0.00	37.07	2.34
1339	1394	4.833390	AGTCTCCTTTATGGTTAGTGCAC	58.167	43.478	9.40	9.40	37.07	4.57
1479	1534	1.800805	CAGTGTGCTGGTAACCTCAG	58.199	55.000	0.00	0.00	39.01	3.35
1487	1542	3.678056	CTGGTAACCTCAGCAACTACA	57.322	47.619	0.00	0.00	0.00	2.74
1497	1552	4.262463	CCTCAGCAACTACACAAAGAGGTA	60.262	45.833	0.00	0.00	37.28	3.08
1744	1820	8.213518	AGAAATTATGCATCAAATACACGTCT	57.786	30.769	0.19	0.00	0.00	4.18
1795	1871	1.065854	CCCATCACTCTTCCACTGACC	60.066	57.143	0.00	0.00	0.00	4.02
1818	1894	4.021719	CACAATTCAACCATTGCTCTTCCT	60.022	41.667	0.00	0.00	37.63	3.36
1842	1918	9.095065	CCTAGTTCACATACCACTTACATAAAC	57.905	37.037	0.00	0.00	0.00	2.01
1879	1955	2.010145	TGTAGAATCAAGTGCCTCGC	57.990	50.000	0.00	0.00	0.00	5.03
1890	1966	2.793946	GCCTCGCGCAATTGTCAT	59.206	55.556	8.75	0.00	37.47	3.06
1897	1973	0.451383	GCGCAATTGTCATGTGCCTA	59.549	50.000	0.30	0.00	45.99	3.93
1919	1995	2.740055	GCACACGCACTCTCCCTG	60.740	66.667	0.00	0.00	38.36	4.45
1939	2015	5.453057	CCCTGTTATCCTCTTCAGAGACATG	60.453	48.000	5.33	0.00	44.74	3.21
1940	2016	5.362143	CCTGTTATCCTCTTCAGAGACATGA	59.638	44.000	5.33	0.00	44.74	3.07
1966	2042	2.517875	GATTCTGCCAGCCCGCAT	60.518	61.111	0.00	0.00	38.30	4.73
1973	2049	4.720902	CCAGCCCGCATGACCACA	62.721	66.667	0.00	0.00	0.00	4.17
1981	2057	1.441738	CGCATGACCACAACTGATGA	58.558	50.000	0.00	0.00	0.00	2.92
2024	2106	2.203126	GAGCCATTCCTGCGAGGG	60.203	66.667	2.86	0.00	35.59	4.30
2025	2107	4.496336	AGCCATTCCTGCGAGGGC	62.496	66.667	0.00	0.00	39.41	5.19
2028	2110	4.161295	CATTCCTGCGAGGGCCGA	62.161	66.667	0.00	0.00	41.76	5.54
2029	2111	3.854669	ATTCCTGCGAGGGCCGAG	61.855	66.667	0.00	0.00	41.76	4.63
2042	2124	4.379243	CCGAGGAGTGCCGCAACT	62.379	66.667	0.00	0.00	39.96	3.16
2043	2125	2.571757	CGAGGAGTGCCGCAACTA	59.428	61.111	0.00	0.00	39.96	2.24
2081	2163	3.867783	CACCACCACACCCCGACA	61.868	66.667	0.00	0.00	0.00	4.35
2103	2186	3.247442	CAACATGCGACATGCTGAAAAT	58.753	40.909	16.43	0.00	46.63	1.82
2113	2196	2.472909	GCTGAAAATCGGAGGGGCG	61.473	63.158	0.00	0.00	0.00	6.13
2150	2233	2.224597	TGCATCTGTCACCACAACATCT	60.225	45.455	0.00	0.00	29.82	2.90
2151	2234	2.161012	GCATCTGTCACCACAACATCTG	59.839	50.000	0.00	0.00	29.82	2.90
2213	2296	1.750399	CCAAAGCACCATCGAGGGG	60.750	63.158	21.86	12.75	46.82	4.79
2218	2301	2.677228	CACCATCGAGGGGGCTTT	59.323	61.111	21.86	0.00	43.89	3.51
2238	2321	2.771089	TGCAACTTCTGATGTCCAGTC	58.229	47.619	0.00	0.00	43.38	3.51
2239	2322	1.728971	GCAACTTCTGATGTCCAGTCG	59.271	52.381	0.00	0.00	43.38	4.18
2240	2323	2.341257	CAACTTCTGATGTCCAGTCGG	58.659	52.381	0.00	0.00	43.38	4.79
2242	2325	0.803768	CTTCTGATGTCCAGTCGGCG	60.804	60.000	0.00	0.00	43.38	6.46
2243	2326	1.248101	TTCTGATGTCCAGTCGGCGA	61.248	55.000	4.99	4.99	43.38	5.54
2244	2327	1.037579	TCTGATGTCCAGTCGGCGAT	61.038	55.000	14.79	0.00	43.38	4.58
2245	2328	0.873312	CTGATGTCCAGTCGGCGATG	60.873	60.000	14.79	12.32	38.10	3.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
103	107	1.823041	GGAGCTAGGCCGTCGTACT	60.823	63.158	0.00	0.00	0.00	2.73
306	310	3.550233	GGCAGTCGACATTATTCGCTAGA	60.550	47.826	19.50	0.00	38.95	2.43
316	320	2.167219	CGCGATGGCAGTCGACATT	61.167	57.895	19.50	0.00	42.68	2.71
375	381	2.439156	GTGCTCATGAGGGCCACC	60.439	66.667	23.89	6.82	0.00	4.61
488	495	0.620121	CTGGAGGGCCTTCTTCCTCT	60.620	60.000	14.33	0.00	46.51	3.69
710	724	1.831106	TCATGGAGTTAGGCACGACAT	59.169	47.619	0.00	0.00	0.00	3.06
714	728	2.002586	CAGTTCATGGAGTTAGGCACG	58.997	52.381	0.00	0.00	0.00	5.34
732	746	1.728971	GTCTCCTCGATTTGCACACAG	59.271	52.381	0.00	0.00	0.00	3.66
741	755	3.070734	CCATCTCATTGGTCTCCTCGATT	59.929	47.826	0.00	0.00	31.74	3.34
752	766	0.816825	CTCCGTGCCCATCTCATTGG	60.817	60.000	0.00	0.00	36.46	3.16
782	796	1.787012	CTTGCCCTTGTTGTCAATGC	58.213	50.000	0.00	0.00	34.21	3.56
865	879	4.353437	GTCGTCGCCAACCTCGGT	62.353	66.667	0.00	0.00	0.00	4.69
976	998	0.035317	ATGCACTCAAGCTTCGGTGA	59.965	50.000	24.11	8.70	34.99	4.02
1091	1119	1.485066	GGTCACCCTACCGTTCATCAT	59.515	52.381	0.00	0.00	0.00	2.45
1226	1257	2.233271	CTTGTTGACCACCTCAATGCT	58.767	47.619	0.00	0.00	41.10	3.79
1289	1320	0.914417	CTTAGGAAGGAGGTGCCCCA	60.914	60.000	0.00	0.00	37.37	4.96
1322	1353	5.003804	AGTTCAGTGCACTAACCATAAAGG	58.996	41.667	21.20	2.86	45.67	3.11
1333	1388	6.311445	CGATAGTTCAAATAGTTCAGTGCACT	59.689	38.462	15.25	15.25	0.00	4.40
1334	1389	6.470160	CGATAGTTCAAATAGTTCAGTGCAC	58.530	40.000	9.40	9.40	0.00	4.57
1385	1440	7.607991	AGCATCAACTACTTAACAGCATAGTTT	59.392	33.333	0.00	0.00	36.06	2.66
1460	1515	1.800805	CTGAGGTTACCAGCACACTG	58.199	55.000	3.51	0.00	44.05	3.66
1479	1534	4.024302	GTGGTTACCTCTTTGTGTAGTTGC	60.024	45.833	2.07	0.00	0.00	4.17
1486	1541	2.616842	GGTGTGTGGTTACCTCTTTGTG	59.383	50.000	2.07	0.00	34.11	3.33
1487	1542	2.240160	TGGTGTGTGGTTACCTCTTTGT	59.760	45.455	2.07	0.00	37.84	2.83
1497	1552	1.806568	CAACGCTTGGTGTGTGGTT	59.193	52.632	0.00	0.00	39.64	3.67
1542	1598	1.470098	GCCTGCATGTTAGTGGACAAG	59.530	52.381	0.00	0.00	32.47	3.16
1646	1722	1.065564	GCCTTCTCAGCTCATTCTGGT	60.066	52.381	0.00	0.00	34.91	4.00
1652	1728	1.767088	TGCATAGCCTTCTCAGCTCAT	59.233	47.619	0.00	0.00	41.83	2.90
1744	1820	7.201835	TGTAAACAGTGACGTATTGTGAACTA	58.798	34.615	0.00	0.00	28.71	2.24
1780	1856	2.620251	TTGTGGTCAGTGGAAGAGTG	57.380	50.000	0.00	0.00	0.00	3.51
1795	1871	4.021719	AGGAAGAGCAATGGTTGAATTGTG	60.022	41.667	0.00	0.00	39.33	3.33
1879	1955	1.739466	ACTAGGCACATGACAATTGCG	59.261	47.619	5.05	0.00	37.11	4.85
1897	1973	3.521529	GAGAGTGCGTGTGCCCACT	62.522	63.158	0.00	0.00	44.43	4.00
1904	1980	1.204941	GATAACAGGGAGAGTGCGTGT	59.795	52.381	0.00	0.00	38.42	4.49
1917	1993	6.272318	GTCATGTCTCTGAAGAGGATAACAG	58.728	44.000	7.47	0.00	42.30	3.16
1919	1995	5.452636	GGGTCATGTCTCTGAAGAGGATAAC	60.453	48.000	7.47	0.00	42.30	1.89
1939	2015	2.109126	GGCAGAATCGCAGTGGGTC	61.109	63.158	7.12	0.00	0.00	4.46
1940	2016	2.045926	GGCAGAATCGCAGTGGGT	60.046	61.111	7.12	0.00	0.00	4.51
1966	2042	2.565046	TGCATCATCAGTTGTGGTCA	57.435	45.000	0.00	0.00	0.00	4.02
2005	2087	2.185350	CTCGCAGGAATGGCTCGT	59.815	61.111	0.00	0.00	0.00	4.18
2025	2107	2.890847	CTAGTTGCGGCACTCCTCGG	62.891	65.000	0.05	0.00	0.00	4.63
2026	2108	1.517257	CTAGTTGCGGCACTCCTCG	60.517	63.158	0.05	0.00	0.00	4.63
2027	2109	1.153549	CCTAGTTGCGGCACTCCTC	60.154	63.158	0.05	0.00	0.00	3.71
2028	2110	1.608717	CTCCTAGTTGCGGCACTCCT	61.609	60.000	0.05	1.42	0.00	3.69
2029	2111	1.153549	CTCCTAGTTGCGGCACTCC	60.154	63.158	0.05	0.00	0.00	3.85
2030	2112	1.153549	CCTCCTAGTTGCGGCACTC	60.154	63.158	0.05	0.00	0.00	3.51
2036	2118	4.530857	CCGCCCCTCCTAGTTGCG	62.531	72.222	0.00	0.00	44.47	4.85
2079	2161	0.239082	CAGCATGTCGCATGTTGTGT	59.761	50.000	20.27	3.41	46.13	3.72
2081	2163	1.237533	TTCAGCATGTCGCATGTTGT	58.762	45.000	24.28	9.51	46.13	3.32
2150	2233	4.575076	GCGATTTGCAACATGGCA	57.425	50.000	17.22	0.00	45.45	4.92
2203	2286	2.830370	GCAAAGCCCCCTCGATGG	60.830	66.667	0.00	0.00	0.00	3.51
2210	2293	0.827507	TCAGAAGTTGCAAAGCCCCC	60.828	55.000	0.00	0.00	0.00	5.40
2213	2296	2.352127	GGACATCAGAAGTTGCAAAGCC	60.352	50.000	0.00	0.00	0.00	4.35
2218	2301	2.771089	GACTGGACATCAGAAGTTGCA	58.229	47.619	0.00	0.00	46.18	4.08
2240	2323	1.098050	AACTGATTTGGAGGCATCGC	58.902	50.000	0.00	0.00	0.00	4.58

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.