AutoCloner

Multiple sequence alignment - TraesCS3A01G206900

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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	TraesCS3A01G206900	chr3A	100.000	2315	0	0	1	2315	364138859	364141173	0.000000e+00	4276.0
1	TraesCS3A01G206900	chr1B	99.591	734	3	0	1	734	60346938	60346205	0.000000e+00	1339.0
2	TraesCS3A01G206900	chr1B	99.456	735	4	0	1	735	39872044	39872778	0.000000e+00	1336.0
3	TraesCS3A01G206900	chr1B	99.054	740	6	1	1	740	419947711	419948449	0.000000e+00	1327.0
4	TraesCS3A01G206900	chr6B	99.455	734	4	0	1	734	46325136	46324403	0.000000e+00	1334.0
5	TraesCS3A01G206900	chr6B	78.648	843	148	17	1489	2302	4273925	4274764	4.380000e-147	531.0
6	TraesCS3A01G206900	chr6A	99.455	734	4	0	1	734	569701073	569701806	0.000000e+00	1334.0
7	TraesCS3A01G206900	chr6A	90.545	275	22	1	2041	2311	595825278	595825004	6.080000e-96	361.0
8	TraesCS3A01G206900	chr5B	99.321	736	5	0	1	736	595157977	595158712	0.000000e+00	1332.0
9	TraesCS3A01G206900	chr4A	99.188	739	5	1	1	739	441956773	441957510	0.000000e+00	1330.0
10	TraesCS3A01G206900	chr1A	99.057	742	6	1	1	742	559618168	559618908	0.000000e+00	1330.0
11	TraesCS3A01G206900	chr1A	99.320	735	5	0	1	735	590335706	590334972	0.000000e+00	1330.0
12	TraesCS3A01G206900	chr1A	77.174	736	135	21	1490	2196	577445381	577444650	4.630000e-107	398.0
13	TraesCS3A01G206900	chr3B	93.305	717	38	5	775	1486	375173556	375174267	0.000000e+00	1050.0
14	TraesCS3A01G206900	chr3D	93.572	669	30	6	735	1390	276091858	276091190	0.000000e+00	985.0
15	TraesCS3A01G206900	chr3D	93.542	511	21	5	735	1233	276112993	276112483	0.000000e+00	750.0
16	TraesCS3A01G206900	chr2A	85.346	853	93	16	1490	2313	594579026	594578177	0.000000e+00	854.0
17	TraesCS3A01G206900	chr2A	82.857	70	10	2	1487	1555	699169342	699169274	6.910000e-06	62.1
18	TraesCS3A01G206900	chr7D	78.292	843	150	22	1489	2302	633361891	633361053	1.590000e-141	512.0
19	TraesCS3A01G206900	chr2D	81.987	594	98	5	1726	2311	577711410	577710818	1.600000e-136	496.0
20	TraesCS3A01G206900	chr7B	77.804	838	151	19	1489	2298	689859166	689858336	3.460000e-133	484.0
21	TraesCS3A01G206900	chr2B	79.056	678	123	17	1640	2302	769982582	769983255	4.540000e-122	448.0
22	TraesCS3A01G206900	chr6D	80.907	529	69	18	1489	2008	450486448	450485943	2.790000e-104	388.0
23	TraesCS3A01G206900	chr6D	90.614	277	22	1	2041	2313	450485944	450485668	4.700000e-97	364.0

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	TraesCS3A01G206900	chr3A	364138859	364141173	2314	False	4276	4276	100.0000	1	2315	1	chr3A.!!$F1	2314
1	TraesCS3A01G206900	chr1B	60346205	60346938	733	True	1339	1339	99.5910	1	734	1	chr1B.!!$R1	733
2	TraesCS3A01G206900	chr1B	39872044	39872778	734	False	1336	1336	99.4560	1	735	1	chr1B.!!$F1	734
3	TraesCS3A01G206900	chr1B	419947711	419948449	738	False	1327	1327	99.0540	1	740	1	chr1B.!!$F2	739
4	TraesCS3A01G206900	chr6B	46324403	46325136	733	True	1334	1334	99.4550	1	734	1	chr6B.!!$R1	733
5	TraesCS3A01G206900	chr6B	4273925	4274764	839	False	531	531	78.6480	1489	2302	1	chr6B.!!$F1	813
6	TraesCS3A01G206900	chr6A	569701073	569701806	733	False	1334	1334	99.4550	1	734	1	chr6A.!!$F1	733
7	TraesCS3A01G206900	chr5B	595157977	595158712	735	False	1332	1332	99.3210	1	736	1	chr5B.!!$F1	735
8	TraesCS3A01G206900	chr4A	441956773	441957510	737	False	1330	1330	99.1880	1	739	1	chr4A.!!$F1	738
9	TraesCS3A01G206900	chr1A	559618168	559618908	740	False	1330	1330	99.0570	1	742	1	chr1A.!!$F1	741
10	TraesCS3A01G206900	chr1A	590334972	590335706	734	True	1330	1330	99.3200	1	735	1	chr1A.!!$R2	734
11	TraesCS3A01G206900	chr1A	577444650	577445381	731	True	398	398	77.1740	1490	2196	1	chr1A.!!$R1	706
12	TraesCS3A01G206900	chr3B	375173556	375174267	711	False	1050	1050	93.3050	775	1486	1	chr3B.!!$F1	711
13	TraesCS3A01G206900	chr3D	276091190	276091858	668	True	985	985	93.5720	735	1390	1	chr3D.!!$R1	655
14	TraesCS3A01G206900	chr3D	276112483	276112993	510	True	750	750	93.5420	735	1233	1	chr3D.!!$R2	498
15	TraesCS3A01G206900	chr2A	594578177	594579026	849	True	854	854	85.3460	1490	2313	1	chr2A.!!$R1	823
16	TraesCS3A01G206900	chr7D	633361053	633361891	838	True	512	512	78.2920	1489	2302	1	chr7D.!!$R1	813
17	TraesCS3A01G206900	chr2D	577710818	577711410	592	True	496	496	81.9870	1726	2311	1	chr2D.!!$R1	585
18	TraesCS3A01G206900	chr7B	689858336	689859166	830	True	484	484	77.8040	1489	2298	1	chr7B.!!$R1	809
19	TraesCS3A01G206900	chr2B	769982582	769983255	673	False	448	448	79.0560	1640	2302	1	chr2B.!!$F1	662
20	TraesCS3A01G206900	chr6D	450485668	450486448	780	True	376	388	85.7605	1489	2313	2	chr6D.!!$R1	824

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
766	770	1.891919	GGAACCAGCGAGTGCAACA	60.892	57.895	0.0	0.0	46.23	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1637	1652	0.035739	AACGTGCCCAATAACGAGGT	59.964	50.0	1.8	0.0	42.32	3.85	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
601	602	7.440856	CCTTCTAGATTCATTAGAAAGTGGCTC	59.559	40.741	0.00	0.00	36.87	4.70
746	747	3.876589	CTTACACCACCGCTGCCGT	62.877	63.158	0.00	0.00	0.00	5.68
766	770	1.891919	GGAACCAGCGAGTGCAACA	60.892	57.895	0.00	0.00	46.23	3.33
1047	1051	2.032634	GCACATCCGGTTCGCTGAA	61.033	57.895	0.00	0.00	0.00	3.02
1065	1069	0.395311	AACGGCTGGAGAGGATACGA	60.395	55.000	0.00	0.00	46.39	3.43
1096	1100	1.212229	GGAGGAGACAACGACGACC	59.788	63.158	0.00	0.00	0.00	4.79
1277	1290	4.351938	CGGCGTCCTCGACAACCA	62.352	66.667	0.00	0.00	46.73	3.67
1326	1340	2.028883	GCGCTTGTAGTTAAACGCCTAG	59.971	50.000	0.00	0.00	40.43	3.02
1353	1367	6.863645	TGATGTTTTCAGTGTTTCGTTTTTCA	59.136	30.769	0.00	0.00	0.00	2.69
1354	1368	6.683090	TGTTTTCAGTGTTTCGTTTTTCAG	57.317	33.333	0.00	0.00	0.00	3.02
1355	1369	6.210078	TGTTTTCAGTGTTTCGTTTTTCAGT	58.790	32.000	0.00	0.00	0.00	3.41
1391	1406	4.662278	TCTTCCTTATTGGGTCTGTTTGG	58.338	43.478	0.00	0.00	36.20	3.28
1417	1432	3.810941	TCGTCTCACACCAAACCAAATAC	59.189	43.478	0.00	0.00	0.00	1.89
1428	1443	2.288961	ACCAAATACTAGTGACGCCG	57.711	50.000	5.39	0.00	0.00	6.46
1437	1452	2.953466	TAGTGACGCCGCTAGAAAAT	57.047	45.000	0.00	0.00	34.50	1.82
1438	1453	2.094762	AGTGACGCCGCTAGAAAATT	57.905	45.000	0.00	0.00	0.00	1.82
1459	1474	7.728847	AATTTATCCTTGTTTGCTTTTCCAC	57.271	32.000	0.00	0.00	0.00	4.02
1479	1494	2.810650	CGATAGTTCTGTAGCACCCAC	58.189	52.381	0.00	0.00	0.00	4.61
1480	1495	2.481449	CGATAGTTCTGTAGCACCCACC	60.481	54.545	0.00	0.00	0.00	4.61
1481	1496	2.018355	TAGTTCTGTAGCACCCACCA	57.982	50.000	0.00	0.00	0.00	4.17
1482	1497	1.136828	AGTTCTGTAGCACCCACCAA	58.863	50.000	0.00	0.00	0.00	3.67
1483	1498	1.493022	AGTTCTGTAGCACCCACCAAA	59.507	47.619	0.00	0.00	0.00	3.28
1484	1499	2.108250	AGTTCTGTAGCACCCACCAAAT	59.892	45.455	0.00	0.00	0.00	2.32
1485	1500	2.890945	GTTCTGTAGCACCCACCAAATT	59.109	45.455	0.00	0.00	0.00	1.82
1486	1501	2.790433	TCTGTAGCACCCACCAAATTC	58.210	47.619	0.00	0.00	0.00	2.17
1487	1502	2.107378	TCTGTAGCACCCACCAAATTCA	59.893	45.455	0.00	0.00	0.00	2.57
1516	1531	9.898152	AAAAATCCAAAATAAACCTTGAACTCA	57.102	25.926	0.00	0.00	0.00	3.41
1517	1532	8.887036	AAATCCAAAATAAACCTTGAACTCAC	57.113	30.769	0.00	0.00	0.00	3.51
1519	1534	7.595819	TCCAAAATAAACCTTGAACTCACAT	57.404	32.000	0.00	0.00	0.00	3.21
1547	1562	5.248380	AGCTAAATCAAACCCTGAACTCT	57.752	39.130	0.00	0.00	37.67	3.24
1552	1567	8.523658	GCTAAATCAAACCCTGAACTCTAAATT	58.476	33.333	0.00	0.00	37.67	1.82
1556	1571	4.903045	AACCCTGAACTCTAAATTCCGA	57.097	40.909	0.00	0.00	0.00	4.55
1561	1576	6.116126	CCCTGAACTCTAAATTCCGAGAATT	58.884	40.000	10.03	6.17	0.00	2.17
1570	1585	8.842358	TCTAAATTCCGAGAATTAACACACTT	57.158	30.769	10.87	0.00	0.00	3.16
1600	1615	3.833559	ATCCTGGTCCAAATTGAACCT	57.166	42.857	2.47	0.00	34.05	3.50
1605	1620	4.284234	CCTGGTCCAAATTGAACCTTGATT	59.716	41.667	2.47	0.00	34.05	2.57
1634	1649	1.453155	AACAGGGATTGATGACGTGC	58.547	50.000	0.00	0.00	0.00	5.34
1635	1650	0.324614	ACAGGGATTGATGACGTGCA	59.675	50.000	0.00	0.00	0.00	4.57
1636	1651	1.012086	CAGGGATTGATGACGTGCAG	58.988	55.000	0.00	0.00	0.00	4.41
1637	1652	0.904649	AGGGATTGATGACGTGCAGA	59.095	50.000	0.00	0.00	0.00	4.26
1638	1653	1.009829	GGGATTGATGACGTGCAGAC	58.990	55.000	0.00	0.00	0.00	3.51
1645	1675	0.885879	ATGACGTGCAGACCTCGTTA	59.114	50.000	0.00	0.00	42.97	3.18
1756	1791	1.097547	CAATCCATCCCCACTCGTGC	61.098	60.000	0.00	0.00	0.00	5.34
1758	1793	3.716195	CCATCCCCACTCGTGCCA	61.716	66.667	0.00	0.00	0.00	4.92
1761	1796	3.094062	ATCCCCACTCGTGCCATCG	62.094	63.158	0.00	0.00	0.00	3.84
1795	1831	2.046796	TTAGCGACGGCAATGGCA	60.047	55.556	7.75	0.00	43.71	4.92
1804	1840	4.049640	GCAATGGCAACGGGCGAA	62.050	61.111	0.00	0.00	46.16	4.70
1831	1867	0.957395	CTCCAGTGGCAGCAATCGTT	60.957	55.000	3.51	0.00	0.00	3.85
1836	1872	1.004320	TGGCAGCAATCGTTACGGT	60.004	52.632	4.53	0.00	0.00	4.83
1848	1884	2.606961	TTACGGTGCGACGACGAGT	61.607	57.895	12.29	7.34	42.66	4.18
1873	1909	3.613193	CGTCAAAGGTATTGTCTCCGACA	60.613	47.826	0.00	0.00	41.09	4.35
1905	1941	2.687935	CTGGTGGCCGTAATTTATGCTT	59.312	45.455	0.00	0.00	0.00	3.91
1936	1972	6.148315	GCGTTGTTAGTGTTAGGGTTTTAGAT	59.852	38.462	0.00	0.00	0.00	1.98
1971	2007	8.246180	TGAGGCTTTTCTTCAATTATAAAGCTG	58.754	33.333	14.97	0.00	46.02	4.24
1973	2009	7.179160	AGGCTTTTCTTCAATTATAAAGCTGGT	59.821	33.333	14.97	1.69	46.02	4.00
2017	2060	5.179742	GCATTTTTGTCATTCCAATTGCTCA	59.820	36.000	0.00	0.00	0.00	4.26
2031	2076	5.525378	CCAATTGCTCAGATTAGGACAGTAC	59.475	44.000	0.00	0.00	0.00	2.73
2130	2179	3.304911	TCCACAATGGTCCTGTTTTGA	57.695	42.857	0.00	0.00	39.03	2.69
2216	2266	2.627699	TCAAGGGCATTTGAAAGACCAC	59.372	45.455	1.73	0.00	34.32	4.16
2219	2269	2.378547	AGGGCATTTGAAAGACCACCTA	59.621	45.455	2.84	0.00	0.00	3.08
2268	2318	7.840716	TGTATTTTCATCATCCTGGGAAAGAAT	59.159	33.333	0.00	0.00	31.62	2.40
2271	2321	8.663209	TTTTCATCATCCTGGGAAAGAATTAA	57.337	30.769	0.00	0.00	31.62	1.40
2275	2325	5.509498	TCATCCTGGGAAAGAATTAACTGG	58.491	41.667	0.00	0.00	0.00	4.00
2298	2348	5.180492	GGTGGTTTGATGTTCTTGTTCGATA	59.820	40.000	0.00	0.00	0.00	2.92
2313	2363	6.474819	TGTTCGATAACAATACTTGTGTGG	57.525	37.500	0.00	0.00	44.59	4.17
2314	2364	5.410132	TGTTCGATAACAATACTTGTGTGGG	59.590	40.000	0.00	0.00	44.59	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
314	315	4.917906	ACTTAACTCCTGAAGCAAGGAT	57.082	40.909	3.55	0.00	45.41	3.24
601	602	3.107601	TCTAACACCCTCCCTCAATCTG	58.892	50.000	0.00	0.00	0.00	2.90
746	747	3.158537	TTGCACTCGCTGGTTCCGA	62.159	57.895	0.00	0.00	39.64	4.55
748	749	1.845809	CTGTTGCACTCGCTGGTTCC	61.846	60.000	0.00	0.00	39.64	3.62
750	751	2.546494	GCTGTTGCACTCGCTGGTT	61.546	57.895	0.00	0.00	39.64	3.67
835	839	3.730761	GCAGCTCTTGGCCGTGTG	61.731	66.667	0.00	0.00	43.05	3.82
856	860	2.470821	GTGCAGATCGCCTACGTTAAT	58.529	47.619	0.00	0.00	41.33	1.40
1047	1051	0.178987	ATCGTATCCTCTCCAGCCGT	60.179	55.000	0.00	0.00	0.00	5.68
1277	1290	3.142838	GCCTGCATGAACCGCCAT	61.143	61.111	0.00	0.00	0.00	4.40
1391	1406	1.499049	GTTTGGTGTGAGACGAGGTC	58.501	55.000	0.00	0.00	0.00	3.85
1417	1432	2.273370	TTTTCTAGCGGCGTCACTAG	57.727	50.000	9.37	11.09	37.76	2.57
1428	1443	8.763049	AAGCAAACAAGGATAAATTTTCTAGC	57.237	30.769	0.00	0.00	0.00	3.42
1435	1450	6.423604	CGTGGAAAAGCAAACAAGGATAAATT	59.576	34.615	0.00	0.00	0.00	1.82
1436	1451	5.925969	CGTGGAAAAGCAAACAAGGATAAAT	59.074	36.000	0.00	0.00	0.00	1.40
1437	1452	5.067936	TCGTGGAAAAGCAAACAAGGATAAA	59.932	36.000	0.00	0.00	0.00	1.40
1438	1453	4.580995	TCGTGGAAAAGCAAACAAGGATAA	59.419	37.500	0.00	0.00	0.00	1.75
1455	1470	2.426024	GGTGCTACAGAACTATCGTGGA	59.574	50.000	0.00	0.00	0.00	4.02
1459	1474	2.481449	GGTGGGTGCTACAGAACTATCG	60.481	54.545	0.00	0.00	0.00	2.92
1467	1482	2.489329	CTGAATTTGGTGGGTGCTACAG	59.511	50.000	0.00	0.00	0.00	2.74
1472	1487	3.467374	TTTTCTGAATTTGGTGGGTGC	57.533	42.857	0.00	0.00	0.00	5.01
1516	1531	4.142469	GGGTTTGATTTAGCTAACGCATGT	60.142	41.667	5.45	0.00	36.80	3.21
1517	1532	4.096382	AGGGTTTGATTTAGCTAACGCATG	59.904	41.667	5.45	0.00	38.31	4.06
1519	1534	3.438781	CAGGGTTTGATTTAGCTAACGCA	59.561	43.478	5.45	4.52	38.31	5.24
1561	1576	7.942341	ACCAGGATTTGAGAATTAAGTGTGTTA	59.058	33.333	0.00	0.00	0.00	2.41
1570	1585	7.673504	TCAATTTGGACCAGGATTTGAGAATTA	59.326	33.333	0.00	0.00	0.00	1.40
1573	1588	5.392995	TCAATTTGGACCAGGATTTGAGAA	58.607	37.500	0.00	0.00	0.00	2.87
1578	1593	4.492646	AGGTTCAATTTGGACCAGGATTT	58.507	39.130	25.48	4.17	35.89	2.17
1584	1599	4.502950	GCAATCAAGGTTCAATTTGGACCA	60.503	41.667	25.48	8.49	35.89	4.02
1600	1615	1.962807	CCTGTTTGGGAGTGCAATCAA	59.037	47.619	16.99	0.00	0.00	2.57
1634	1649	1.369625	GTGCCCAATAACGAGGTCTG	58.630	55.000	0.00	0.00	0.00	3.51
1635	1650	0.108329	CGTGCCCAATAACGAGGTCT	60.108	55.000	0.00	0.00	42.32	3.85
1636	1651	0.390735	ACGTGCCCAATAACGAGGTC	60.391	55.000	1.80	0.00	42.32	3.85
1637	1652	0.035739	AACGTGCCCAATAACGAGGT	59.964	50.000	1.80	0.00	42.32	3.85
1638	1653	0.446222	CAACGTGCCCAATAACGAGG	59.554	55.000	1.80	0.00	42.32	4.63
1739	1771	2.746375	GGCACGAGTGGGGATGGAT	61.746	63.158	5.32	0.00	0.00	3.41
1758	1793	1.533711	CAGGGGAATTCCAGGCGAT	59.466	57.895	25.67	1.97	37.91	4.58
1761	1796	0.258774	TAAGCAGGGGAATTCCAGGC	59.741	55.000	25.67	22.69	37.91	4.85
1795	1831	2.895372	GCCGATCATTCGCCCGTT	60.895	61.111	0.00	0.00	44.12	4.44
1804	1840	2.321263	CTGCCACTGGAGCCGATCAT	62.321	60.000	0.00	0.00	0.00	2.45
1818	1854	1.004320	ACCGTAACGATTGCTGCCA	60.004	52.632	0.00	0.00	0.00	4.92
1825	1861	1.067199	GTCGTCGCACCGTAACGATT	61.067	55.000	0.00	0.00	45.88	3.34
1831	1867	3.043713	ACTCGTCGTCGCACCGTA	61.044	61.111	0.00	0.00	36.96	4.02
1848	1884	3.613193	CGGAGACAATACCTTTGACGTCA	60.613	47.826	15.76	15.76	0.00	4.35
1873	1909	0.399233	GGCCACCAGAGGAGGAGTAT	60.399	60.000	0.00	0.00	35.40	2.12
1905	1941	1.654317	AACACTAACAACGCGGTCAA	58.346	45.000	12.47	0.00	0.00	3.18
1990	2026	5.375717	CAATTGGAATGACAAAAATGCACG	58.624	37.500	0.00	0.00	33.48	5.34
1991	2027	5.049267	AGCAATTGGAATGACAAAAATGCAC	60.049	36.000	7.72	0.00	39.17	4.57
2017	2060	9.821240	ATGAGAATATCAGTACTGTCCTAATCT	57.179	33.333	21.99	17.43	42.53	2.40
2130	2179	5.429762	TCTCTTCATCTCCACCCACATAATT	59.570	40.000	0.00	0.00	0.00	1.40
2216	2266	7.108847	ACTTCATTGATTCCTTGAACTCTAGG	58.891	38.462	1.19	1.19	39.70	3.02
2219	2269	6.774656	ACAACTTCATTGATTCCTTGAACTCT	59.225	34.615	0.00	0.00	41.23	3.24
2268	2318	5.654650	ACAAGAACATCAAACCACCAGTTAA	59.345	36.000	0.00	0.00	37.88	2.01
2271	2321	3.631250	ACAAGAACATCAAACCACCAGT	58.369	40.909	0.00	0.00	0.00	4.00
2275	2325	4.545823	TCGAACAAGAACATCAAACCAC	57.454	40.909	0.00	0.00	0.00	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.