AutoCloner

Multiple sequence alignment - TraesCS4A01G154500

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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	TraesCS4A01G154500	chr4A	100.000	2255	0	0	1	2255	310738447	310736193	0.000000e+00	4165
1	TraesCS4A01G154500	chr4A	94.221	2267	97	15	1	2255	309514981	309512737	0.000000e+00	3430
2	TraesCS4A01G154500	chr1D	96.021	2262	59	17	1	2255	254398259	254400496	0.000000e+00	3650
3	TraesCS4A01G154500	chr3D	95.887	2261	61	17	1	2255	589279692	589281926	0.000000e+00	3631
4	TraesCS4A01G154500	chr3D	94.855	1205	36	13	1	1201	571592150	571593332	0.000000e+00	1858
5	TraesCS4A01G154500	chr5D	95.843	2261	64	15	1	2255	6188790	6186554	0.000000e+00	3627
6	TraesCS4A01G154500	chr5D	95.796	2260	66	15	1	2255	503278376	503280611	0.000000e+00	3620
7	TraesCS4A01G154500	chr5D	95.213	2256	74	19	1	2249	432403647	432405875	0.000000e+00	3537
8	TraesCS4A01G154500	chr5D	95.458	1321	34	12	1	1317	503218068	503216770	0.000000e+00	2084
9	TraesCS4A01G154500	chr1A	95.518	2231	61	17	1	2224	554512098	554509900	0.000000e+00	3530
10	TraesCS4A01G154500	chr5A	94.737	2261	89	16	1	2255	607274250	607272014	0.000000e+00	3489
11	TraesCS4A01G154500	chr4B	93.681	2263	97	18	1	2255	308696320	308694096	0.000000e+00	3345
12	TraesCS4A01G154500	chr6D	95.428	1859	70	11	406	2255	45519037	45517185	0.000000e+00	2948
13	TraesCS4A01G154500	chr6D	95.461	1322	33	12	1	1317	168251914	168253213	0.000000e+00	2084
14	TraesCS4A01G154500	chrUn	95.461	1322	32	14	1	1317	93409781	93411079	0.000000e+00	2084
15	TraesCS4A01G154500	chr4D	94.327	1322	49	14	1	1316	19928425	19927124	0.000000e+00	2002
16	TraesCS4A01G154500	chr7D	97.647	85	2	0	1	85	231574685	231574601	1.800000e-31	147

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	TraesCS4A01G154500	chr4A	310736193	310738447	2254	True	4165	4165	100.000	1	2255	1	chr4A.!!$R2	2254
1	TraesCS4A01G154500	chr4A	309512737	309514981	2244	True	3430	3430	94.221	1	2255	1	chr4A.!!$R1	2254
2	TraesCS4A01G154500	chr1D	254398259	254400496	2237	False	3650	3650	96.021	1	2255	1	chr1D.!!$F1	2254
3	TraesCS4A01G154500	chr3D	589279692	589281926	2234	False	3631	3631	95.887	1	2255	1	chr3D.!!$F2	2254
4	TraesCS4A01G154500	chr3D	571592150	571593332	1182	False	1858	1858	94.855	1	1201	1	chr3D.!!$F1	1200
5	TraesCS4A01G154500	chr5D	6186554	6188790	2236	True	3627	3627	95.843	1	2255	1	chr5D.!!$R1	2254
6	TraesCS4A01G154500	chr5D	503278376	503280611	2235	False	3620	3620	95.796	1	2255	1	chr5D.!!$F2	2254
7	TraesCS4A01G154500	chr5D	432403647	432405875	2228	False	3537	3537	95.213	1	2249	1	chr5D.!!$F1	2248
8	TraesCS4A01G154500	chr5D	503216770	503218068	1298	True	2084	2084	95.458	1	1317	1	chr5D.!!$R2	1316
9	TraesCS4A01G154500	chr1A	554509900	554512098	2198	True	3530	3530	95.518	1	2224	1	chr1A.!!$R1	2223
10	TraesCS4A01G154500	chr5A	607272014	607274250	2236	True	3489	3489	94.737	1	2255	1	chr5A.!!$R1	2254
11	TraesCS4A01G154500	chr4B	308694096	308696320	2224	True	3345	3345	93.681	1	2255	1	chr4B.!!$R1	2254
12	TraesCS4A01G154500	chr6D	45517185	45519037	1852	True	2948	2948	95.428	406	2255	1	chr6D.!!$R1	1849
13	TraesCS4A01G154500	chr6D	168251914	168253213	1299	False	2084	2084	95.461	1	1317	1	chr6D.!!$F1	1316
14	TraesCS4A01G154500	chrUn	93409781	93411079	1298	False	2084	2084	95.461	1	1317	1	chrUn.!!$F1	1316
15	TraesCS4A01G154500	chr4D	19927124	19928425	1301	True	2002	2002	94.327	1	1316	1	chr4D.!!$R1	1315

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
122	123	0.806102	CGGAACATGAGCGATTCGGT	60.806	55.0	11.02	11.02	41.33	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2048	2078	0.10852	GTTTCCGTCTGGGTATGCGA	60.109	55.0	0.0	0.0	37.0	5.1	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
82	83	4.951094	ACACAGAGACCTAGGATGTAGAAC	59.049	45.833	17.98	0.00	0.00	3.01
85	86	6.773200	CACAGAGACCTAGGATGTAGAACATA	59.227	42.308	17.98	0.00	39.27	2.29
86	87	7.285629	CACAGAGACCTAGGATGTAGAACATAA	59.714	40.741	17.98	0.00	39.27	1.90
87	88	7.504238	ACAGAGACCTAGGATGTAGAACATAAG	59.496	40.741	17.98	0.00	39.27	1.73
88	89	6.492087	AGAGACCTAGGATGTAGAACATAAGC	59.508	42.308	17.98	0.00	39.27	3.09
89	90	5.540719	AGACCTAGGATGTAGAACATAAGCC	59.459	44.000	17.98	0.00	39.27	4.35
90	91	5.216622	ACCTAGGATGTAGAACATAAGCCA	58.783	41.667	17.98	0.00	39.27	4.75
91	92	5.846714	ACCTAGGATGTAGAACATAAGCCAT	59.153	40.000	17.98	0.00	39.27	4.40
92	93	7.016914	ACCTAGGATGTAGAACATAAGCCATA	58.983	38.462	17.98	0.00	39.27	2.74
93	94	7.512746	ACCTAGGATGTAGAACATAAGCCATAA	59.487	37.037	17.98	0.00	39.27	1.90
94	95	8.037758	CCTAGGATGTAGAACATAAGCCATAAG	58.962	40.741	1.05	0.00	39.27	1.73
95	96	6.234177	AGGATGTAGAACATAAGCCATAAGC	58.766	40.000	0.00	0.00	39.27	3.09
96	97	5.412904	GGATGTAGAACATAAGCCATAAGCC	59.587	44.000	0.00	0.00	40.03	4.35
97	98	5.366482	TGTAGAACATAAGCCATAAGCCA	57.634	39.130	0.00	0.00	45.47	4.75
98	99	5.750524	TGTAGAACATAAGCCATAAGCCAA	58.249	37.500	0.00	0.00	45.47	4.52
99	100	6.184068	TGTAGAACATAAGCCATAAGCCAAA	58.816	36.000	0.00	0.00	45.47	3.28
100	101	6.833416	TGTAGAACATAAGCCATAAGCCAAAT	59.167	34.615	0.00	0.00	45.47	2.32
101	102	6.152932	AGAACATAAGCCATAAGCCAAATG	57.847	37.500	0.00	0.00	45.47	2.32
102	103	5.893255	AGAACATAAGCCATAAGCCAAATGA	59.107	36.000	0.00	0.00	45.47	2.57
105	106	1.392589	AGCCATAAGCCAAATGACGG	58.607	50.000	0.00	0.00	45.47	4.79
122	123	0.806102	CGGAACATGAGCGATTCGGT	60.806	55.000	11.02	11.02	41.33	4.69
538	540	1.679032	GCCGGATCTAAGTGTTGGCTT	60.679	52.381	5.05	0.00	38.00	4.35
545	547	5.652452	GGATCTAAGTGTTGGCTTGGTAAAT	59.348	40.000	0.00	0.00	0.00	1.40
556	558	2.014128	CTTGGTAAATGCCCCGTAGTG	58.986	52.381	0.00	0.00	0.00	2.74
792	801	2.584970	GCGATGGGCGAACGATGA	60.585	61.111	2.92	0.00	44.57	2.92
853	863	2.195727	TGATCCACTTGGCTACATCCA	58.804	47.619	0.00	0.00	34.44	3.41
1194	1213	4.948341	TCCTATGGTAGCTCGCAAATTA	57.052	40.909	0.00	0.00	0.00	1.40
1206	1225	3.349022	TCGCAAATTAGGGGAATTCGTT	58.651	40.909	0.00	0.00	36.71	3.85
1224	1243	2.695359	GTTCCTACTCGGCATTTCACA	58.305	47.619	0.00	0.00	0.00	3.58
1232	1251	4.323417	ACTCGGCATTTCACAAGTTATGA	58.677	39.130	0.00	0.00	0.00	2.15
1361	1382	9.474313	TTGCTAGAACAAGATATTGGGTATTTT	57.526	29.630	4.88	0.00	0.00	1.82
1438	1460	7.994425	TTAATAGATGGAACTTCAACAGCAA	57.006	32.000	0.00	0.00	0.00	3.91
1465	1487	2.828520	TCTAGAGGGAAGTTGTGAGCAG	59.171	50.000	0.00	0.00	0.00	4.24
1501	1523	4.862641	ACTTCCATACCAAGGTTAGCAT	57.137	40.909	0.00	0.00	0.00	3.79
1604	1633	6.698766	GGTTGAACACCATAGTACTAATACCG	59.301	42.308	6.70	0.00	46.42	4.02
1797	1827	7.609532	AGATTCATTTTCAGTAGTTTCCCTGAG	59.390	37.037	0.00	0.00	38.81	3.35
1846	1876	5.914201	TGCATAGCACTGAATAGGGAACCA	61.914	45.833	0.00	0.00	43.44	3.67
1900	1930	3.966979	TGGATGCATAAGGATGTTGTGT	58.033	40.909	0.00	0.00	35.30	3.72
2048	2078	5.887598	TGAATATGCAACAGCAATCTAAGGT	59.112	36.000	0.00	0.00	42.37	3.50
2119	2149	5.780984	AGCTACACCAAGTAAGAAGTGTAC	58.219	41.667	0.00	0.00	43.02	2.90
2153	2183	6.770785	GCTCATAAGGACCACCATTGTATAAA	59.229	38.462	0.00	0.00	38.94	1.40
2204	2235	3.426615	TGGGTAAAAGTGCAATCCGATT	58.573	40.909	0.00	0.00	0.00	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	83	4.539870	CGTCATTTGGCTTATGGCTTATG	58.460	43.478	3.78	7.10	41.46	1.90
85	86	1.750778	CCGTCATTTGGCTTATGGCTT	59.249	47.619	3.78	0.00	41.46	4.35
86	87	1.064758	TCCGTCATTTGGCTTATGGCT	60.065	47.619	3.78	0.00	41.46	4.75
87	88	1.388547	TCCGTCATTTGGCTTATGGC	58.611	50.000	0.00	0.00	40.90	4.40
88	89	2.752354	TGTTCCGTCATTTGGCTTATGG	59.248	45.455	0.00	0.00	0.00	2.74
89	90	4.096231	TCATGTTCCGTCATTTGGCTTATG	59.904	41.667	0.00	0.00	0.00	1.90
90	91	4.269183	TCATGTTCCGTCATTTGGCTTAT	58.731	39.130	0.00	0.00	0.00	1.73
91	92	3.680490	TCATGTTCCGTCATTTGGCTTA	58.320	40.909	0.00	0.00	0.00	3.09
92	93	2.489329	CTCATGTTCCGTCATTTGGCTT	59.511	45.455	0.00	0.00	0.00	4.35
93	94	2.086869	CTCATGTTCCGTCATTTGGCT	58.913	47.619	0.00	0.00	0.00	4.75
94	95	1.468054	GCTCATGTTCCGTCATTTGGC	60.468	52.381	0.00	0.00	0.00	4.52
95	96	1.202065	CGCTCATGTTCCGTCATTTGG	60.202	52.381	0.00	0.00	0.00	3.28
96	97	1.731709	TCGCTCATGTTCCGTCATTTG	59.268	47.619	0.00	0.00	0.00	2.32
97	98	2.093306	TCGCTCATGTTCCGTCATTT	57.907	45.000	0.00	0.00	0.00	2.32
98	99	2.315925	ATCGCTCATGTTCCGTCATT	57.684	45.000	0.00	0.00	0.00	2.57
99	100	2.205074	GAATCGCTCATGTTCCGTCAT	58.795	47.619	0.00	0.00	0.00	3.06
100	101	1.640428	GAATCGCTCATGTTCCGTCA	58.360	50.000	0.00	0.00	0.00	4.35
101	102	0.572590	CGAATCGCTCATGTTCCGTC	59.427	55.000	0.00	0.00	0.00	4.79
102	103	0.806102	CCGAATCGCTCATGTTCCGT	60.806	55.000	0.00	0.00	0.00	4.69
105	106	3.079960	TCTACCGAATCGCTCATGTTC	57.920	47.619	0.00	0.00	0.00	3.18
386	388	5.163519	CCGATTTACCCTCTTTTGCAATGAT	60.164	40.000	0.00	0.00	0.00	2.45
516	518	1.656652	CCAACACTTAGATCCGGCTG	58.343	55.000	0.00	0.00	0.00	4.85
538	540	1.208535	CTCACTACGGGGCATTTACCA	59.791	52.381	0.00	0.00	0.00	3.25
545	547	2.363795	CCCTCTCACTACGGGGCA	60.364	66.667	0.00	0.00	34.22	5.36
556	558	4.470304	ACAAGGTTCATAACTACCCCTCTC	59.530	45.833	0.00	0.00	34.90	3.20
695	704	5.961395	GGCGACGAAGAATAAAACTATCA	57.039	39.130	0.00	0.00	0.00	2.15
757	766	6.201425	CCCATCGCATTATTGAAAATTCCAAG	59.799	38.462	0.00	0.00	0.00	3.61
767	776	1.601903	GTTCGCCCATCGCATTATTGA	59.398	47.619	0.00	0.00	37.30	2.57
790	799	0.676466	ATGCGCGGGTTCAATTCTCA	60.676	50.000	8.83	0.00	0.00	3.27
792	801	1.656818	CCATGCGCGGGTTCAATTCT	61.657	55.000	8.83	0.00	0.00	2.40
853	863	3.145559	TCCTTTAGCTGGATAAGGGGT	57.854	47.619	14.75	0.00	39.12	4.95
932	944	8.267620	AGTGGAATTCTATGTCCAATATCTCA	57.732	34.615	5.23	0.00	45.42	3.27
952	964	9.470399	ACTACTTTTTCCTTTTTAAAGAGTGGA	57.530	29.630	5.15	1.77	38.28	4.02
974	987	4.092771	TCGTGTCACAGCTGATTACTAC	57.907	45.455	23.35	13.29	0.00	2.73
975	988	4.776795	TTCGTGTCACAGCTGATTACTA	57.223	40.909	23.35	3.20	0.00	1.82
1184	1203	2.943033	ACGAATTCCCCTAATTTGCGAG	59.057	45.455	0.00	0.00	41.13	5.03
1206	1225	2.301870	ACTTGTGAAATGCCGAGTAGGA	59.698	45.455	0.00	0.00	45.00	2.94
1424	1446	5.993106	AGACTTAGTTGCTGTTGAAGTTC	57.007	39.130	0.00	0.00	30.66	3.01
1438	1460	5.642165	TCACAACTTCCCTCTAGACTTAGT	58.358	41.667	0.00	0.00	0.00	2.24
1465	1487	2.988493	TGGAAGTAATGCACGAACGTAC	59.012	45.455	0.00	0.00	0.00	3.67
1501	1523	3.202818	ACTTGGGCTGATATCATCAACCA	59.797	43.478	5.72	9.40	45.25	3.67
1533	1555	5.008331	TCTGTAGTTGATAGTCAAGGTCGT	58.992	41.667	0.00	0.00	37.00	4.34
1586	1615	6.509656	TGCTTTCGGTATTAGTACTATGGTG	58.490	40.000	2.79	0.00	0.00	4.17
1587	1616	6.323225	ACTGCTTTCGGTATTAGTACTATGGT	59.677	38.462	2.79	0.00	0.00	3.55
1604	1633	3.416156	AGGAATCTGGTTCACTGCTTTC	58.584	45.455	2.68	0.00	38.64	2.62
1797	1827	4.281898	TCCTTGGTAACCTCTAGTTTGC	57.718	45.455	0.00	0.00	40.05	3.68
1846	1876	1.206371	GGTGTAGCTGGTGTATTCGGT	59.794	52.381	0.00	0.00	0.00	4.69
1900	1930	7.118723	ACTTTATGATTGTATTCCAGGCAGAA	58.881	34.615	0.00	0.00	0.00	3.02
1998	2028	3.393800	CTGTTGCAGTTGCTACTACTGT	58.606	45.455	17.06	0.00	44.85	3.55
2010	2040	3.276857	CATATTCAGCTCCTGTTGCAGT	58.723	45.455	0.00	0.00	32.61	4.40
2048	2078	0.108520	GTTTCCGTCTGGGTATGCGA	60.109	55.000	0.00	0.00	37.00	5.10
2119	2149	5.066505	GGTGGTCCTTATGAGCTAATTGTTG	59.933	44.000	0.00	0.00	42.12	3.33
2204	2235	2.067365	TATCCCTACTTCTGCGAGCA	57.933	50.000	0.00	0.00	0.00	4.26
2207	2238	4.022242	GTGCTATTATCCCTACTTCTGCGA	60.022	45.833	0.00	0.00	0.00	5.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.