AutoCloner

Multiple sequence alignment - TraesCS5A01G340000

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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	TraesCS5A01G340000	chr5A	100.000	2571	0	0	1	2571	546883783	546886353	0.000000e+00	4748.0
1	TraesCS5A01G340000	chr5A	90.770	1571	123	15	230	1790	546723806	546722248	0.000000e+00	2078.0
2	TraesCS5A01G340000	chr5A	92.076	631	40	9	1823	2444	546718685	546718056	0.000000e+00	880.0
3	TraesCS5A01G340000	chr5A	93.724	239	11	3	1	236	546724097	546723860	3.150000e-94	355.0
4	TraesCS5A01G340000	chr5A	93.798	129	7	1	2444	2571	546715123	546714995	2.610000e-45	193.0
5	TraesCS5A01G340000	chr5B	90.142	1623	98	22	964	2571	522498960	522500535	0.000000e+00	2054.0
6	TraesCS5A01G340000	chr5B	90.293	649	51	4	1147	1794	521241486	521240849	0.000000e+00	839.0
7	TraesCS5A01G340000	chr5B	90.805	522	47	1	410	930	521254849	521254328	0.000000e+00	697.0
8	TraesCS5A01G340000	chr5B	96.137	233	9	0	2339	2571	521240772	521240540	5.190000e-102	381.0
9	TraesCS5A01G340000	chr5B	96.296	54	2	0	1817	1870	521240859	521240806	3.520000e-14	89.8
10	TraesCS5A01G340000	chr5D	90.957	763	38	10	1817	2571	431626849	431626110	0.000000e+00	998.0
11	TraesCS5A01G340000	chr5D	90.437	732	55	6	1071	1794	431627563	431626839	0.000000e+00	950.0
12	TraesCS5A01G340000	chr5D	83.372	872	114	22	234	1091	527144951	527145805	0.000000e+00	778.0
13	TraesCS5A01G340000	chr5D	90.996	522	46	1	410	930	431640165	431639644	0.000000e+00	702.0
14	TraesCS5A01G340000	chr5D	81.109	884	126	29	234	1091	421490683	421491551	0.000000e+00	669.0
15	TraesCS5A01G340000	chr5D	94.118	238	10	2	1	236	431640603	431640368	2.430000e-95	359.0
16	TraesCS5A01G340000	chr1A	82.492	891	116	15	234	1091	572220730	572219847	0.000000e+00	745.0
17	TraesCS5A01G340000	chr1A	89.177	231	24	1	1938	2168	259970193	259969964	1.160000e-73	287.0
18	TraesCS5A01G340000	chr7B	82.353	867	124	22	248	1091	534537303	534536443	0.000000e+00	726.0
19	TraesCS5A01G340000	chr7B	84.519	239	22	9	1938	2174	451096922	451097147	3.330000e-54	222.0
20	TraesCS5A01G340000	chr4D	82.057	875	133	18	234	1091	13250495	13251362	0.000000e+00	725.0
21	TraesCS5A01G340000	chr7D	81.797	857	118	29	232	1058	589242499	589241651	0.000000e+00	684.0
22	TraesCS5A01G340000	chr3A	81.257	875	138	21	234	1091	613497776	613498641	0.000000e+00	684.0
23	TraesCS5A01G340000	chr3B	80.326	859	144	19	235	1074	66475634	66474782	6.040000e-176	627.0
24	TraesCS5A01G340000	chr2A	77.423	877	142	30	234	1091	579443388	579442549	2.990000e-129	472.0
25	TraesCS5A01G340000	chr1D	79.930	568	82	20	536	1091	252304188	252304735	3.100000e-104	388.0
26	TraesCS5A01G340000	chr1D	81.233	373	62	4	727	1091	448221581	448221209	6.960000e-76	294.0
27	TraesCS5A01G340000	chr1D	91.304	184	15	1	1938	2121	204224161	204223979	1.530000e-62	250.0
28	TraesCS5A01G340000	chr1B	78.552	373	68	9	727	1090	613525536	613525167	4.280000e-58	235.0

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	TraesCS5A01G340000	chr5A	546883783	546886353	2570	False	4748.0	4748	100.000	1	2571	1	chr5A.!!$F1	2570
1	TraesCS5A01G340000	chr5A	546714995	546724097	9102	True	876.5	2078	92.592	1	2571	4	chr5A.!!$R1	2570
2	TraesCS5A01G340000	chr5B	522498960	522500535	1575	False	2054.0	2054	90.142	964	2571	1	chr5B.!!$F1	1607
3	TraesCS5A01G340000	chr5B	521254328	521254849	521	True	697.0	697	90.805	410	930	1	chr5B.!!$R1	520
4	TraesCS5A01G340000	chr5B	521240540	521241486	946	True	436.6	839	94.242	1147	2571	3	chr5B.!!$R2	1424
5	TraesCS5A01G340000	chr5D	431626110	431627563	1453	True	974.0	998	90.697	1071	2571	2	chr5D.!!$R1	1500
6	TraesCS5A01G340000	chr5D	527144951	527145805	854	False	778.0	778	83.372	234	1091	1	chr5D.!!$F2	857
7	TraesCS5A01G340000	chr5D	421490683	421491551	868	False	669.0	669	81.109	234	1091	1	chr5D.!!$F1	857
8	TraesCS5A01G340000	chr5D	431639644	431640603	959	True	530.5	702	92.557	1	930	2	chr5D.!!$R2	929
9	TraesCS5A01G340000	chr1A	572219847	572220730	883	True	745.0	745	82.492	234	1091	1	chr1A.!!$R2	857
10	TraesCS5A01G340000	chr7B	534536443	534537303	860	True	726.0	726	82.353	248	1091	1	chr7B.!!$R1	843
11	TraesCS5A01G340000	chr4D	13250495	13251362	867	False	725.0	725	82.057	234	1091	1	chr4D.!!$F1	857
12	TraesCS5A01G340000	chr7D	589241651	589242499	848	True	684.0	684	81.797	232	1058	1	chr7D.!!$R1	826
13	TraesCS5A01G340000	chr3A	613497776	613498641	865	False	684.0	684	81.257	234	1091	1	chr3A.!!$F1	857
14	TraesCS5A01G340000	chr3B	66474782	66475634	852	True	627.0	627	80.326	235	1074	1	chr3B.!!$R1	839
15	TraesCS5A01G340000	chr2A	579442549	579443388	839	True	472.0	472	77.423	234	1091	1	chr2A.!!$R1	857
16	TraesCS5A01G340000	chr1D	252304188	252304735	547	False	388.0	388	79.930	536	1091	1	chr1D.!!$F1	555

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
724	853	0.593128	GGTGCGTGGGATTGATATGC	59.407	55.0	0.0	0.0	0.0	3.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1620	1813	1.933853	GCGATCAAGCGGAAACATACT	59.066	47.619	0.0	0.0	0.0	2.12	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
64	65	9.525826	AGAAAAGGAATAAAGTTCAGATGATGT	57.474	29.630	0.00	0.00	0.00	3.06
186	190	2.927553	AGCTGGATTTTTAAGCGCTG	57.072	45.000	12.58	0.00	41.88	5.18
256	354	8.730680	TGCTTTCTTAAAATGATTACTCACTCC	58.269	33.333	0.00	0.00	33.22	3.85
451	566	7.706179	TGAACTTGGTCAAAGCTAAAGAAATTG	59.294	33.333	0.00	0.00	39.76	2.32
641	764	3.331150	AGATATTTTCGCGTTGGTGACA	58.669	40.909	5.77	0.00	39.83	3.58
724	853	0.593128	GGTGCGTGGGATTGATATGC	59.407	55.000	0.00	0.00	0.00	3.14
729	858	3.181488	TGCGTGGGATTGATATGCTTTTG	60.181	43.478	0.00	0.00	0.00	2.44
754	883	2.523015	CCGTTTGCTGCTGATTGATTC	58.477	47.619	0.00	0.00	0.00	2.52
756	885	3.567530	CGTTTGCTGCTGATTGATTCAA	58.432	40.909	0.75	0.75	32.78	2.69
778	909	0.610785	AATCGTTGGCCCGGTCAAAT	60.611	50.000	5.89	0.00	0.00	2.32
887	1042	0.897621	GCCCTTGAGAAATTGTGGGG	59.102	55.000	0.00	0.00	35.41	4.96
906	1062	1.211709	CCGGTCAAAATCGGGTTGC	59.788	57.895	0.00	0.00	42.32	4.17
1012	1185	4.837093	TGAGAAATTATTGACCCGGTCT	57.163	40.909	18.54	1.82	33.15	3.85
1078	1251	5.932883	GTGGACTCTTTAAAACTAGGGAGTG	59.067	44.000	9.51	0.00	35.52	3.51
1120	1293	5.622180	TGACACGCTCTCTTCTACCTATAT	58.378	41.667	0.00	0.00	0.00	0.86
1130	1307	8.226819	TCTCTTCTACCTATATTGTGTGTCTG	57.773	38.462	0.00	0.00	0.00	3.51
1175	1352	4.932200	GTGTTCCAGATTCAATTCGACTCT	59.068	41.667	0.00	0.00	34.11	3.24
1184	1361	2.420372	TCAATTCGACTCTGTCCTCTCG	59.580	50.000	0.00	0.00	0.00	4.04
1281	1460	1.376037	GCTCTTGCAGCGGGTACTT	60.376	57.895	0.00	0.00	38.76	2.24
1304	1483	1.606601	GCCCCGCCCTTCTCTTTTT	60.607	57.895	0.00	0.00	0.00	1.94
1366	1550	7.472381	GCATCCATCCATCCATGTATTTCTTTT	60.472	37.037	0.00	0.00	0.00	2.27
1381	1565	0.946221	CTTTTCGCGCAGAGAGGTGT	60.946	55.000	8.75	0.00	37.80	4.16
1396	1580	2.563179	GAGGTGTGAGGAAGAGCACTTA	59.437	50.000	0.00	0.00	36.39	2.24
1423	1607	2.303890	CCTGATATGCATGGACTGGCTA	59.696	50.000	10.16	0.00	0.00	3.93
1467	1651	3.647367	CCCGGACATGAGGGTCAT	58.353	61.111	0.73	0.00	42.67	3.06
1521	1705	3.016736	GCTATTGCCACTGTACCATGTT	58.983	45.455	0.00	0.00	0.00	2.71
1581	1774	7.824289	AGTAGCTGCTAATAAATTGACAGTTCA	59.176	33.333	11.57	0.00	0.00	3.18
1611	1804	4.021192	TCATCTGTATCGCTCATGGCAATA	60.021	41.667	0.00	0.00	41.91	1.90
1620	1813	5.606505	TCGCTCATGGCAATAATGTTACTA	58.393	37.500	0.00	0.00	41.91	1.82
1683	1877	5.635280	CCATGTTGTTGTGTTGTGTTTTACA	59.365	36.000	0.00	0.00	37.56	2.41
1733	1927	2.350522	CTGAATTCTTCACCGGTCCTG	58.649	52.381	2.59	0.00	35.46	3.86
1742	1936	2.060980	ACCGGTCCTGGCATCTCTC	61.061	63.158	0.00	0.00	0.00	3.20
1748	1942	1.956477	GTCCTGGCATCTCTCTCTCTC	59.044	57.143	0.00	0.00	0.00	3.20
1750	1944	2.158623	TCCTGGCATCTCTCTCTCTCTC	60.159	54.545	0.00	0.00	0.00	3.20
1753	1947	2.779430	TGGCATCTCTCTCTCTCTCTCT	59.221	50.000	0.00	0.00	0.00	3.10
1754	1948	3.181451	TGGCATCTCTCTCTCTCTCTCTC	60.181	52.174	0.00	0.00	0.00	3.20
1760	1954	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1761	1955	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1762	1956	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1763	1957	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1764	1958	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1765	1959	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1766	1960	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1767	1961	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1768	1962	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1769	1963	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1770	1964	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1771	1965	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1772	1966	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
1773	1967	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
1774	1968	6.101881	TCTCTCTCTCTCTCTCTCTCTCTCTA	59.898	46.154	0.00	0.00	0.00	2.43
1775	1969	6.857848	TCTCTCTCTCTCTCTCTCTCTCTAT	58.142	44.000	0.00	0.00	0.00	1.98
1776	1970	7.990055	TCTCTCTCTCTCTCTCTCTCTCTATA	58.010	42.308	0.00	0.00	0.00	1.31
1777	1971	8.619281	TCTCTCTCTCTCTCTCTCTCTCTATAT	58.381	40.741	0.00	0.00	0.00	0.86
1778	1972	9.913310	CTCTCTCTCTCTCTCTCTCTCTATATA	57.087	40.741	0.00	0.00	0.00	0.86
1972	5708	0.514691	GACTGCTTTCACTTGGCTCG	59.485	55.000	0.00	0.00	0.00	5.03
2036	5772	1.188863	ATGGGCTGGCACATTTCTTC	58.811	50.000	4.30	0.00	36.54	2.87
2110	5846	5.914033	TCCTGAATTCTTATTACCTCGTGG	58.086	41.667	7.05	0.99	39.83	4.94
2148	5885	7.391148	AACTCTGCCACGACATAAATAAAAT	57.609	32.000	0.00	0.00	0.00	1.82
2153	5890	5.105554	TGCCACGACATAAATAAAATTGCCT	60.106	36.000	0.00	0.00	0.00	4.75
2244	5986	5.272283	TCCAATGACTATAGTCCCGAAAC	57.728	43.478	26.37	4.68	44.15	2.78
2253	5995	9.277783	TGACTATAGTCCCGAAACTATAACTAC	57.722	37.037	26.37	0.26	41.72	2.73
2258	6000	6.996509	AGTCCCGAAACTATAACTACACAAA	58.003	36.000	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	9.614792	GGAACCTGAACTTTATTACTACATCAT	57.385	33.333	0.00	0.00	0.00	2.45
64	65	6.290294	AGCGGAACCTGAACTTTATTACTA	57.710	37.500	0.00	0.00	0.00	1.82
129	133	7.778853	AGGATCAATCATAGCTGTTGAAAATCT	59.221	33.333	0.00	0.00	35.70	2.40
186	190	8.511604	TGGGAGAAAGAGAAATGATTAATCAC	57.488	34.615	20.19	8.24	40.03	3.06
270	368	8.528044	AAGGTTTGACTTAGAAAAATACACCA	57.472	30.769	0.00	0.00	0.00	4.17
493	612	6.011981	TCCCCACCAGTCAAACTAAATATTCT	60.012	38.462	0.00	0.00	0.00	2.40
641	764	7.792032	ACTATAGCACCAATACAGTACATGTT	58.208	34.615	2.30	0.00	39.96	2.71
651	777	7.331934	CACCATGTGATACTATAGCACCAATAC	59.668	40.741	0.00	0.00	44.02	1.89
724	853	1.930371	GCAGCAAACGGCCTACAAAAG	60.930	52.381	0.00	0.00	46.50	2.27
729	858	1.026718	ATCAGCAGCAAACGGCCTAC	61.027	55.000	0.00	0.00	46.50	3.18
756	885	0.824182	TGACCGGGCCAACGATTTTT	60.824	50.000	3.83	0.00	35.47	1.94
820	951	4.933400	TCTATGTTACCGTTTTGAAGCTCC	59.067	41.667	0.00	0.00	0.00	4.70
887	1042	1.211709	CAACCCGATTTTGACCGGC	59.788	57.895	0.00	0.00	44.07	6.13
931	1103	9.301897	ACATGCTTCCTAATTTTTAAAGTCTCT	57.698	29.630	0.00	0.00	0.00	3.10
1012	1185	3.772572	TGGAGATTGAGTCACCCGATTTA	59.227	43.478	0.00	0.00	36.82	1.40
1097	1270	2.201921	AGGTAGAAGAGAGCGTGTCA	57.798	50.000	0.00	0.00	0.00	3.58
1100	1273	6.146216	CACAATATAGGTAGAAGAGAGCGTG	58.854	44.000	0.00	0.00	0.00	5.34
1120	1293	0.815213	GCACTCTGCCAGACACACAA	60.815	55.000	0.00	0.00	37.42	3.33
1130	1307	4.337555	ACAAGATTGATATTGCACTCTGCC	59.662	41.667	0.00	0.00	44.23	4.85
1175	1352	2.933906	GTGTGTTTGTTTCGAGAGGACA	59.066	45.455	0.00	0.00	0.00	4.02
1184	1361	3.296628	CATAGGTGCGTGTGTTTGTTTC	58.703	45.455	0.00	0.00	0.00	2.78
1274	1453	2.119029	GCGGGGCAATCAAGTACCC	61.119	63.158	0.00	0.00	42.01	3.69
1281	1460	3.338250	AGAAGGGCGGGGCAATCA	61.338	61.111	0.00	0.00	0.00	2.57
1304	1483	6.386342	AGATCTTTTCCATGGAAGAGAGATGA	59.614	38.462	36.84	24.88	44.68	2.92
1366	1550	2.982744	CTCACACCTCTCTGCGCGA	61.983	63.158	12.10	1.90	0.00	5.87
1381	1565	3.452627	GGGAGAATAAGTGCTCTTCCTCA	59.547	47.826	18.59	1.19	34.80	3.86
1471	1655	3.612247	CTTGGCGGTGCAGTAGGCT	62.612	63.158	10.15	0.00	45.15	4.58
1538	1722	5.590663	CAGCTACTACTCTCTAACCACATCA	59.409	44.000	0.00	0.00	0.00	3.07
1581	1774	5.268118	TGAGCGATACAGATGAACATCTT	57.732	39.130	13.69	8.85	45.31	2.40
1611	1804	7.101054	TCAAGCGGAAACATACTAGTAACATT	58.899	34.615	6.70	2.12	0.00	2.71
1620	1813	1.933853	GCGATCAAGCGGAAACATACT	59.066	47.619	0.00	0.00	0.00	2.12
1683	1877	3.010584	ACAACCAAGGCATGAGAGGTAAT	59.989	43.478	0.00	0.00	31.10	1.89
1733	1927	3.072184	AGAGAGAGAGAGAGAGAGATGCC	59.928	52.174	0.00	0.00	0.00	4.40
1742	1936	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1748	1942	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1750	1944	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1972	5708	6.312918	ACTGAACGATATTGATGTAACACCAC	59.687	38.462	0.00	0.00	0.00	4.16
2036	5772	8.328864	GTTTTAGAATCATAACAAGTCCTAGCG	58.671	37.037	0.00	0.00	0.00	4.26
2075	5811	6.380079	AAGAATTCAGGAGTAACATCCACT	57.620	37.500	8.44	0.00	42.26	4.00
2110	5846	4.937620	TGGCAGAGTTACATCATGAAAGTC	59.062	41.667	0.00	2.30	0.00	3.01
2253	5995	9.906660	TCAAACAAATTAGCCTAACTATTTGTG	57.093	29.630	12.86	5.09	39.64	3.33
2258	6000	8.823220	ACCATCAAACAAATTAGCCTAACTAT	57.177	30.769	0.00	0.00	0.00	2.12
2366	6113	4.327087	CGGGATGCTAAAATTTGACAAAGC	59.673	41.667	6.77	4.43	0.00	3.51
2466	9148	3.610040	ACAAGATGCGTTGGATGTCTA	57.390	42.857	0.00	0.00	0.00	2.59

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.