AutoCloner

Multiple sequence alignment - TraesCS5B01G232800

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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	TraesCS5B01G232800	chr5B	100.000	2287	0	0	1	2287	410846052	410848338	0.000000e+00	4224
1	TraesCS5B01G232800	chr3A	92.762	1727	122	3	2	1726	418765665	418763940	0.000000e+00	2494
2	TraesCS5B01G232800	chr4D	92.219	1735	126	6	1	1733	116524563	116522836	0.000000e+00	2447
3	TraesCS5B01G232800	chr4D	91.696	1734	127	10	1	1730	48683934	48682214	0.000000e+00	2388
4	TraesCS5B01G232800	chr4D	91.322	1740	135	11	1	1733	493971115	493969385	0.000000e+00	2362
5	TraesCS5B01G232800	chr4D	91.219	1731	149	3	2	1731	421048641	421046913	0.000000e+00	2351
6	TraesCS5B01G232800	chr5A	91.667	1728	139	5	1	1726	604232066	604230342	0.000000e+00	2388
7	TraesCS5B01G232800	chr5A	93.676	506	21	3	1784	2287	450551387	450551883	0.000000e+00	747
8	TraesCS5B01G232800	chr7D	91.412	1735	143	6	1	1733	432740549	432738819	0.000000e+00	2374
9	TraesCS5B01G232800	chr1A	91.450	1731	136	7	1	1726	327011924	327010201	0.000000e+00	2366
10	TraesCS5B01G232800	chr4A	91.204	1728	148	4	1	1726	327748380	327746655	0.000000e+00	2346
11	TraesCS5B01G232800	chr5D	95.303	511	19	3	1782	2287	350224944	350225454	0.000000e+00	806
12	TraesCS5B01G232800	chr2A	84.058	207	21	2	1517	1723	186680829	186681023	3.000000e-44	189

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	TraesCS5B01G232800	chr5B	410846052	410848338	2286	False	4224	4224	100.000	1	2287	1	chr5B.!!$F1	2286
1	TraesCS5B01G232800	chr3A	418763940	418765665	1725	True	2494	2494	92.762	2	1726	1	chr3A.!!$R1	1724
2	TraesCS5B01G232800	chr4D	116522836	116524563	1727	True	2447	2447	92.219	1	1733	1	chr4D.!!$R2	1732
3	TraesCS5B01G232800	chr4D	48682214	48683934	1720	True	2388	2388	91.696	1	1730	1	chr4D.!!$R1	1729
4	TraesCS5B01G232800	chr4D	493969385	493971115	1730	True	2362	2362	91.322	1	1733	1	chr4D.!!$R4	1732
5	TraesCS5B01G232800	chr4D	421046913	421048641	1728	True	2351	2351	91.219	2	1731	1	chr4D.!!$R3	1729
6	TraesCS5B01G232800	chr5A	604230342	604232066	1724	True	2388	2388	91.667	1	1726	1	chr5A.!!$R1	1725
7	TraesCS5B01G232800	chr7D	432738819	432740549	1730	True	2374	2374	91.412	1	1733	1	chr7D.!!$R1	1732
8	TraesCS5B01G232800	chr1A	327010201	327011924	1723	True	2366	2366	91.450	1	1726	1	chr1A.!!$R1	1725
9	TraesCS5B01G232800	chr4A	327746655	327748380	1725	True	2346	2346	91.204	1	1726	1	chr4A.!!$R1	1725
10	TraesCS5B01G232800	chr5D	350224944	350225454	510	False	806	806	95.303	1782	2287	1	chr5D.!!$F1	505

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
54	55	0.032815	TTCTTGTCCATCGTCGTGCA	59.967	50.0	0.0	0.0	0.0	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1844	1856	0.10104	CGTCGGTATGGTTTCGCCTA	59.899	55.0	0.0	0.0	38.35	3.93	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
54	55	0.032815	TTCTTGTCCATCGTCGTGCA	59.967	50.000	0.00	0.00	0.00	4.57
57	58	1.811645	TTGTCCATCGTCGTGCAGGA	61.812	55.000	4.68	4.68	0.00	3.86
159	160	0.473117	TGGACCGGTTCTTCCTCCTT	60.473	55.000	15.59	0.00	33.27	3.36
174	175	0.118346	TCCTTCTTAGGCTCCCCACA	59.882	55.000	0.00	0.00	41.69	4.17
186	187	3.770040	CCCACAGATGACCGCCGA	61.770	66.667	0.00	0.00	0.00	5.54
189	190	4.796231	ACAGATGACCGCCGACGC	62.796	66.667	0.00	0.00	38.22	5.19
213	214	2.478031	CGATTGTCGTCTCCCAGTACAG	60.478	54.545	0.00	0.00	34.72	2.74
226	227	1.008194	GTACAGTGTGGCACGACGA	60.008	57.895	13.77	0.00	39.64	4.20
241	242	1.603172	CGACGATCATTAGGAGCCCAC	60.603	57.143	0.00	0.00	0.00	4.61
451	453	3.788227	AAGTTTGAGCACACCTCCATA	57.212	42.857	0.00	0.00	39.98	2.74
506	508	1.078143	CCAAGGAAGAAGGCCCTCG	60.078	63.158	0.00	0.00	31.17	4.63
533	535	3.600919	CCCAAGGGAAGGGGTTGA	58.399	61.111	0.00	0.00	42.90	3.18
622	626	2.369532	GTGGGTAAGTAGTGGTGGTCAA	59.630	50.000	0.00	0.00	0.00	3.18
624	628	2.636403	GGGTAAGTAGTGGTGGTCAAGT	59.364	50.000	0.00	0.00	0.00	3.16
661	668	2.750135	GCGATGGAGAGGAGGAAGAGTA	60.750	54.545	0.00	0.00	0.00	2.59
665	672	3.432378	TGGAGAGGAGGAAGAGTAACAC	58.568	50.000	0.00	0.00	0.00	3.32
768	775	0.622136	AGAGCAATGAGATGGGCACA	59.378	50.000	0.00	0.00	0.00	4.57
857	864	1.533469	CCCACCGTCGAGGAAGAACT	61.533	60.000	6.70	0.00	45.00	3.01
864	871	2.031069	CGTCGAGGAAGAACTGAAGACA	60.031	50.000	0.00	0.00	0.00	3.41
883	890	1.963855	CCAACGGTTGGCGATGACA	60.964	57.895	25.60	0.00	45.17	3.58
991	998	1.208614	CTTGCACCGAAGCTTGAGC	59.791	57.895	2.10	0.86	42.49	4.26
1016	1024	1.616921	CCATGCCCCTGGACTTCAT	59.383	57.895	0.00	0.00	38.69	2.57
1056	1064	4.683432	ACGGAGTTCAAGCTGAGC	57.317	55.556	0.00	0.00	37.78	4.26
1095	1103	1.255667	GGAGGGTGACGGTGAAGCTA	61.256	60.000	0.00	0.00	0.00	3.32
1110	1118	3.512329	TGAAGCTAATGAACGACAGGGTA	59.488	43.478	0.00	0.00	0.00	3.69
1254	1263	2.203280	TGGTCAACAAGTGCGGGG	60.203	61.111	0.00	0.00	0.00	5.73
1294	1303	4.798682	CAGGGACTAGGGCCGGGT	62.799	72.222	2.18	0.00	36.02	5.28
1305	1314	3.003763	GCCGGGTCACCTCCTTCT	61.004	66.667	2.18	0.00	33.28	2.85
1315	1324	5.126869	GGGTCACCTCCTTCTTAAGTACTAC	59.873	48.000	1.63	0.00	0.00	2.73
1322	1331	5.189180	TCCTTCTTAAGTACTACCGAGTCC	58.811	45.833	1.63	0.00	37.10	3.85
1328	1337	2.165998	AGTACTACCGAGTCCGCTTTT	58.834	47.619	0.00	0.00	37.10	2.27
1443	1452	3.385755	TGCTCTGCTCTGCTTATGATGTA	59.614	43.478	0.00	0.00	0.00	2.29
1577	1587	0.757512	TGCATGCAACCAAACACCAT	59.242	45.000	20.30	0.00	0.00	3.55
1617	1628	2.044650	GGCAAGAGGGCATGCAGA	60.045	61.111	21.36	0.00	44.32	4.26
1627	1638	0.387239	GGCATGCAGACAACGAAACC	60.387	55.000	21.36	0.00	0.00	3.27
1635	1646	2.033299	CAGACAACGAAACCACTTGCAT	59.967	45.455	0.00	0.00	0.00	3.96
1638	1649	4.154195	AGACAACGAAACCACTTGCATATC	59.846	41.667	0.00	0.00	0.00	1.63
1693	1704	6.045318	GCTGAGTTGAGAAGACTATGCAATA	58.955	40.000	0.00	0.00	0.00	1.90
1694	1705	6.536582	GCTGAGTTGAGAAGACTATGCAATAA	59.463	38.462	0.00	0.00	0.00	1.40
1728	1740	0.741574	ACGACAACCAAACACGCTCA	60.742	50.000	0.00	0.00	0.00	4.26
1733	1745	3.211045	ACAACCAAACACGCTCATAGTT	58.789	40.909	0.00	0.00	0.00	2.24
1734	1746	3.250040	ACAACCAAACACGCTCATAGTTC	59.750	43.478	0.00	0.00	0.00	3.01
1735	1747	3.402628	ACCAAACACGCTCATAGTTCT	57.597	42.857	0.00	0.00	0.00	3.01
1736	1748	3.740115	ACCAAACACGCTCATAGTTCTT	58.260	40.909	0.00	0.00	0.00	2.52
1737	1749	4.890088	ACCAAACACGCTCATAGTTCTTA	58.110	39.130	0.00	0.00	0.00	2.10
1738	1750	5.302360	ACCAAACACGCTCATAGTTCTTAA	58.698	37.500	0.00	0.00	0.00	1.85
1739	1751	5.761234	ACCAAACACGCTCATAGTTCTTAAA	59.239	36.000	0.00	0.00	0.00	1.52
1740	1752	6.261381	ACCAAACACGCTCATAGTTCTTAAAA	59.739	34.615	0.00	0.00	0.00	1.52
1741	1753	7.136119	CCAAACACGCTCATAGTTCTTAAAAA	58.864	34.615	0.00	0.00	0.00	1.94
1762	1774	1.895051	AAAAGTTGTCGCGCATATGC	58.105	45.000	18.08	18.08	37.78	3.14
1802	1814	1.095228	AACAACTGTGCACCCAGTCG	61.095	55.000	15.69	3.98	44.74	4.18
1804	1816	1.095228	CAACTGTGCACCCAGTCGTT	61.095	55.000	15.69	5.28	44.74	3.85
1821	1833	1.149401	TTCAACCATGCCACGGTCA	59.851	52.632	0.00	0.00	34.99	4.02
1844	1856	2.357034	AATCACGTCGCGCCAAGT	60.357	55.556	0.00	0.00	0.00	3.16
1989	2004	0.244994	ATCGATCGCCACCATCTAGC	59.755	55.000	11.09	0.00	0.00	3.42
2021	2036	0.243907	TTCCAGAAGCTTCTCGACGG	59.756	55.000	26.18	22.49	34.74	4.79
2164	2180	3.729489	TCTCGCCTCTCCCCGTCT	61.729	66.667	0.00	0.00	0.00	4.18
2204	2221	2.317371	TTTGAGCTCCTCTCTGACCT	57.683	50.000	12.15	0.00	42.38	3.85
2209	2226	1.724582	GCTCCTCTCTGACCTCGAGC	61.725	65.000	6.99	0.00	36.33	5.03
2281	2298	3.479269	GTGGAGTTCTTCGCGCCG	61.479	66.667	0.00	0.00	0.00	6.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	3.681034	CGATGGACAAGAAGATGAAGGCT	60.681	47.826	0.00	0.00	0.00	4.58
142	143	1.268066	AGAAGGAGGAAGAACCGGTC	58.732	55.000	8.04	0.95	44.74	4.79
159	160	1.008327	TCATCTGTGGGGAGCCTAAGA	59.992	52.381	0.00	0.00	0.00	2.10
213	214	1.588404	CTAATGATCGTCGTGCCACAC	59.412	52.381	0.00	0.00	0.00	3.82
226	227	4.561752	AGAACTAGTGGGCTCCTAATGAT	58.438	43.478	0.00	0.00	0.00	2.45
241	242	6.608002	AGAGGTGGTCCAAGTATAAGAACTAG	59.392	42.308	0.00	0.00	35.89	2.57
342	344	4.019681	TGAAGACGTTGATTCCTAACCCAT	60.020	41.667	0.00	0.00	0.00	4.00
451	453	1.583054	GCACCAAGTTCGAGAACACT	58.417	50.000	17.00	2.35	43.47	3.55
490	492	1.904990	GCTCGAGGGCCTTCTTCCTT	61.905	60.000	15.58	0.00	32.74	3.36
506	508	0.629058	TTCCCTTGGGGTATTGGCTC	59.371	55.000	5.78	0.00	44.74	4.70
558	560	1.753368	CTTCCTCCTCTCCATCGCCC	61.753	65.000	0.00	0.00	0.00	6.13
622	626	4.579454	TCGCGCCTATATTTACTCAACT	57.421	40.909	0.00	0.00	0.00	3.16
624	628	4.021807	TCCATCGCGCCTATATTTACTCAA	60.022	41.667	0.00	0.00	0.00	3.02
677	684	5.945784	TGGCTTATTGAAGAGCATGTAGTTT	59.054	36.000	5.83	0.00	40.63	2.66
857	864	3.088259	CCAACCGTTGGTGTCTTCA	57.912	52.632	20.55	0.00	45.93	3.02
883	890	4.496336	GGGCTCCTCCATGCGCTT	62.496	66.667	9.73	0.00	38.77	4.68
1276	1285	4.475444	CCCGGCCCTAGTCCCTGA	62.475	72.222	0.00	0.00	0.00	3.86
1294	1303	4.946157	CGGTAGTACTTAAGAAGGAGGTGA	59.054	45.833	10.09	0.00	0.00	4.02
1305	1314	2.991250	AGCGGACTCGGTAGTACTTAA	58.009	47.619	0.00	0.00	45.89	1.85
1315	1324	1.734163	AACCATAAAAGCGGACTCGG	58.266	50.000	0.00	0.00	36.79	4.63
1328	1337	5.950758	AACAGTTCAACGCATAAACCATA	57.049	34.783	0.00	0.00	0.00	2.74
1414	1423	2.354259	AGCAGAGCAGAGCATAAACAC	58.646	47.619	0.00	0.00	0.00	3.32
1443	1452	0.326595	TCGGCACAACCATGTACCAT	59.673	50.000	0.00	0.00	42.31	3.55
1547	1556	4.015764	TGGTTGCATGCATGTTAGTGTAT	58.984	39.130	26.79	0.00	0.00	2.29
1549	1558	2.237643	TGGTTGCATGCATGTTAGTGT	58.762	42.857	26.79	0.00	0.00	3.55
1577	1587	1.343789	CATGGGTTGAACCACATTGCA	59.656	47.619	17.27	3.89	44.72	4.08
1617	1628	3.120338	CGATATGCAAGTGGTTTCGTTGT	60.120	43.478	0.00	0.00	0.00	3.32
1635	1646	2.971307	TGCAGTCTCAAATGCACGATA	58.029	42.857	0.00	0.00	46.97	2.92
1693	1704	5.335504	GGTTGTCGTAGTCTACAGTAGCTTT	60.336	44.000	10.59	0.00	0.00	3.51
1694	1705	4.155644	GGTTGTCGTAGTCTACAGTAGCTT	59.844	45.833	10.59	0.00	0.00	3.74
1742	1754	2.250188	GCATATGCGCGACAACTTTTT	58.750	42.857	12.10	0.00	0.00	1.94
1743	1755	1.895051	GCATATGCGCGACAACTTTT	58.105	45.000	12.10	0.00	0.00	2.27
1744	1756	3.604130	GCATATGCGCGACAACTTT	57.396	47.368	12.10	0.00	0.00	2.66
1766	1778	3.768185	TTCGTCGCTATCGGCAGGC	62.768	63.158	0.00	0.00	41.03	4.85
1767	1779	1.944676	GTTCGTCGCTATCGGCAGG	60.945	63.158	0.00	0.00	41.03	4.85
1768	1780	0.800683	TTGTTCGTCGCTATCGGCAG	60.801	55.000	0.00	0.00	41.03	4.85
1769	1781	1.074319	GTTGTTCGTCGCTATCGGCA	61.074	55.000	0.00	0.00	41.03	5.69
1770	1782	0.801067	AGTTGTTCGTCGCTATCGGC	60.801	55.000	0.00	0.00	36.88	5.54
1771	1783	0.914551	CAGTTGTTCGTCGCTATCGG	59.085	55.000	0.00	0.00	36.13	4.18
1772	1784	1.317611	CACAGTTGTTCGTCGCTATCG	59.682	52.381	0.00	0.00	0.00	2.92
1773	1785	1.059264	GCACAGTTGTTCGTCGCTATC	59.941	52.381	0.00	0.00	0.00	2.08
1774	1786	1.068474	GCACAGTTGTTCGTCGCTAT	58.932	50.000	0.00	0.00	0.00	2.97
1775	1787	0.249114	TGCACAGTTGTTCGTCGCTA	60.249	50.000	0.00	0.00	0.00	4.26
1776	1788	1.520564	TGCACAGTTGTTCGTCGCT	60.521	52.632	0.00	0.00	0.00	4.93
1777	1789	1.367665	GTGCACAGTTGTTCGTCGC	60.368	57.895	13.17	0.00	0.00	5.19
1778	1790	1.275657	GGTGCACAGTTGTTCGTCG	59.724	57.895	20.43	0.00	0.00	5.12
1779	1791	1.092921	TGGGTGCACAGTTGTTCGTC	61.093	55.000	20.43	0.00	0.00	4.20
1780	1792	1.078072	TGGGTGCACAGTTGTTCGT	60.078	52.632	20.43	0.00	0.00	3.85
1802	1814	1.169661	TGACCGTGGCATGGTTGAAC	61.170	55.000	30.86	18.82	37.69	3.18
1804	1816	1.599518	GTGACCGTGGCATGGTTGA	60.600	57.895	30.86	18.44	37.69	3.18
1844	1856	0.101040	CGTCGGTATGGTTTCGCCTA	59.899	55.000	0.00	0.00	38.35	3.93
1888	1900	3.047280	TGTGCGGACCAATCGTGC	61.047	61.111	4.04	0.00	0.00	5.34
1889	1901	2.860293	GTGTGCGGACCAATCGTG	59.140	61.111	4.04	0.00	0.00	4.35
2050	2065	2.485795	CGGCGAGAAGGAGGAGGAG	61.486	68.421	0.00	0.00	0.00	3.69
2091	2106	2.829458	GAGCCGGCGGAGTAGAGT	60.829	66.667	33.44	0.00	0.00	3.24
2164	2180	1.152652	GGAGGAGAGCCGATCTGGA	60.153	63.158	7.64	0.00	42.00	3.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.