AutoCloner

Multiple sequence alignment - TraesCS7A01G545500

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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	TraesCS7A01G545500	chr7A	100.000	2348	0	0	1	2348	721643451	721641104	0.000000e+00	4337.0
1	TraesCS7A01G545500	chr7A	88.756	1672	171	11	27	1685	717769086	717767419	0.000000e+00	2030.0
2	TraesCS7A01G545500	chr7A	96.177	654	24	1	1696	2348	721577058	721576405	0.000000e+00	1068.0
3	TraesCS7A01G545500	chr6D	94.451	1676	90	3	27	1700	367879766	367878092	0.000000e+00	2577.0
4	TraesCS7A01G545500	chr5D	94.269	1675	89	7	27	1696	564670391	564672063	0.000000e+00	2555.0
5	TraesCS7A01G545500	chr5D	83.621	116	19	0	1964	2079	129237436	129237321	2.470000e-20	110.0
6	TraesCS7A01G545500	chr5D	82.203	118	15	4	1952	2065	177236101	177236216	1.920000e-16	97.1
7	TraesCS7A01G545500	chr5D	100.000	33	0	0	1	33	564670349	564670381	7.010000e-06	62.1
8	TraesCS7A01G545500	chr6A	93.437	1676	100	6	27	1700	183314285	183312618	0.000000e+00	2477.0
9	TraesCS7A01G545500	chr6A	93.075	1675	114	2	27	1700	183929709	183931382	0.000000e+00	2449.0
10	TraesCS7A01G545500	chr5A	88.994	1690	173	11	27	1709	31278732	31280415	0.000000e+00	2078.0
11	TraesCS7A01G545500	chr1B	88.843	1685	171	13	27	1699	145446312	145444633	0.000000e+00	2054.0
12	TraesCS7A01G545500	chr2B	82.171	1621	257	26	90	1696	748211381	748212983	0.000000e+00	1363.0
13	TraesCS7A01G545500	chr2B	79.529	552	89	19	1154	1696	748363425	748363961	2.850000e-99	372.0
14	TraesCS7A01G545500	chr6B	81.641	1694	264	30	32	1700	715763231	715761560	0.000000e+00	1362.0
15	TraesCS7A01G545500	chr6B	74.897	243	45	13	1955	2188	655328297	655328062	1.920000e-16	97.1
16	TraesCS7A01G545500	chr3A	87.625	299	30	6	1405	1696	621497548	621497846	8.040000e-90	340.0
17	TraesCS7A01G545500	chr7D	74.603	252	55	8	1952	2198	60578110	60578357	4.130000e-18	102.0
18	TraesCS7A01G545500	chr7D	81.356	118	18	4	1952	2069	440218483	440218370	2.480000e-15	93.5
19	TraesCS7A01G545500	chr3D	75.000	232	48	9	1952	2179	569836154	569836379	5.340000e-17	99.0
20	TraesCS7A01G545500	chr1D	84.112	107	10	4	1955	2056	252542838	252542734	1.920000e-16	97.1
21	TraesCS7A01G545500	chrUn	74.089	247	52	11	1959	2198	194638114	194638355	8.940000e-15	91.6

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	TraesCS7A01G545500	chr7A	721641104	721643451	2347	True	4337.00	4337	100.0000	1	2348	1	chr7A.!!$R3	2347
1	TraesCS7A01G545500	chr7A	717767419	717769086	1667	True	2030.00	2030	88.7560	27	1685	1	chr7A.!!$R1	1658
2	TraesCS7A01G545500	chr7A	721576405	721577058	653	True	1068.00	1068	96.1770	1696	2348	1	chr7A.!!$R2	652
3	TraesCS7A01G545500	chr6D	367878092	367879766	1674	True	2577.00	2577	94.4510	27	1700	1	chr6D.!!$R1	1673
4	TraesCS7A01G545500	chr5D	564670349	564672063	1714	False	1308.55	2555	97.1345	1	1696	2	chr5D.!!$F2	1695
5	TraesCS7A01G545500	chr6A	183312618	183314285	1667	True	2477.00	2477	93.4370	27	1700	1	chr6A.!!$R1	1673
6	TraesCS7A01G545500	chr6A	183929709	183931382	1673	False	2449.00	2449	93.0750	27	1700	1	chr6A.!!$F1	1673
7	TraesCS7A01G545500	chr5A	31278732	31280415	1683	False	2078.00	2078	88.9940	27	1709	1	chr5A.!!$F1	1682
8	TraesCS7A01G545500	chr1B	145444633	145446312	1679	True	2054.00	2054	88.8430	27	1699	1	chr1B.!!$R1	1672
9	TraesCS7A01G545500	chr2B	748211381	748212983	1602	False	1363.00	1363	82.1710	90	1696	1	chr2B.!!$F1	1606
10	TraesCS7A01G545500	chr2B	748363425	748363961	536	False	372.00	372	79.5290	1154	1696	1	chr2B.!!$F2	542
11	TraesCS7A01G545500	chr6B	715761560	715763231	1671	True	1362.00	1362	81.6410	32	1700	1	chr6B.!!$R2	1668

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
556	586	0.106918	AACTCCCTTGCGTGTCCAAA	60.107	50.0	0.0	0.0	0.0	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1378	1421	0.319555	CTCAGGAGGAAACGCGTTGA	60.32	55.0	27.34	16.08	0.0	3.18	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
84	109	3.420397	CTCTTCGGGAGGTCGTTTC	57.580	57.895	0.00	0.00	38.35	2.78
108	133	8.806429	TCATTCTCCTTAATGCATCTTTAACA	57.194	30.769	0.00	0.00	36.89	2.41
183	208	4.638865	GGGAAACTTGATAAGCACCGTAAT	59.361	41.667	0.00	0.00	0.00	1.89
184	209	5.124936	GGGAAACTTGATAAGCACCGTAATT	59.875	40.000	0.00	0.00	0.00	1.40
189	217	7.391148	ACTTGATAAGCACCGTAATTGATTT	57.609	32.000	0.00	0.00	0.00	2.17
208	236	1.171308	TTTCTGGCAAGAGCATGAGC	58.829	50.000	0.00	0.00	44.61	4.26
273	301	3.318313	CTCCAAGGATAAAGGAGGCCTA	58.682	50.000	4.42	0.00	44.10	3.93
471	501	4.623932	AGTCAAAGAACACTATCTGGCA	57.376	40.909	0.00	0.00	0.00	4.92
556	586	0.106918	AACTCCCTTGCGTGTCCAAA	60.107	50.000	0.00	0.00	0.00	3.28
660	690	2.201490	CGCCTCCATCCCCCTCTA	59.799	66.667	0.00	0.00	0.00	2.43
741	771	4.080919	CCTGATCAGATTGTGTGGTCCTTA	60.081	45.833	24.62	0.00	0.00	2.69
800	833	1.719529	TACCTGGAACGGAACTTGGA	58.280	50.000	0.00	0.00	36.31	3.53
872	906	6.707440	TCAAATCTTCTTGTGGCAACTTTA	57.293	33.333	0.00	0.00	37.61	1.85
924	958	1.072505	GAGGCGAAACTGGTTGGGA	59.927	57.895	0.00	0.00	0.00	4.37
985	1022	3.504906	CCAACATCTGTTCTTCACATGCT	59.495	43.478	0.00	0.00	35.83	3.79
1123	1161	8.103935	AGAAGTTCTATACTTTTGGCTTAGCTT	58.896	33.333	2.75	0.00	47.00	3.74
1141	1179	0.684153	TTCCCTTTGCTGGGCTATGC	60.684	55.000	5.33	0.00	46.67	3.14
1150	1188	1.392589	CTGGGCTATGCGGAATTGTT	58.607	50.000	0.00	0.00	0.00	2.83
1155	1193	2.481795	GGCTATGCGGAATTGTTGCAAT	60.482	45.455	0.59	0.00	42.65	3.56
1211	1249	9.778741	ATCTCCATTTAACGTGATATATGTTGT	57.221	29.630	0.00	0.00	38.88	3.32
1315	1353	2.989909	TCAATGCCTCGAACATGATGT	58.010	42.857	0.00	0.00	0.00	3.06
1410	1453	2.092753	CCTCCTGAGCCATGCTTTTCTA	60.093	50.000	0.00	0.00	39.88	2.10
1463	1511	1.137872	GGTGGTGTGTTTGGCATTCAA	59.862	47.619	0.00	0.00	0.00	2.69
1469	1517	3.568007	GTGTGTTTGGCATTCAACTCCTA	59.432	43.478	2.57	0.00	34.67	2.94
1564	1616	2.480555	CGACGAACTGCCCAATGC	59.519	61.111	0.00	0.00	41.77	3.56
1601	1654	2.460669	GTTTCCCAGGGATGCTTGAAT	58.539	47.619	9.80	0.00	0.00	2.57
1615	1668	1.130561	CTTGAATTCGCGTTCCCCTTC	59.869	52.381	5.77	2.38	0.00	3.46
1625	1678	2.036387	CGTTCCCCTTCCTTTGGTTTT	58.964	47.619	0.00	0.00	0.00	2.43
1627	1680	3.035363	GTTCCCCTTCCTTTGGTTTTCA	58.965	45.455	0.00	0.00	0.00	2.69
1632	1685	3.038280	CCTTCCTTTGGTTTTCAGGGTT	58.962	45.455	0.00	0.00	0.00	4.11
1681	1735	9.197306	GTTATGAAAGTAATGGAAAGGGGTTAT	57.803	33.333	0.00	0.00	0.00	1.89
1734	1788	1.078759	CAAGCGTACAAGAGCTCCCG	61.079	60.000	10.93	4.04	43.78	5.14
1786	1840	9.347240	CAATAATATTTCTCCCTTGATCAGTGT	57.653	33.333	0.00	0.00	0.00	3.55
1818	1873	1.471119	TACTCTGCCGAAGTGTAGGG	58.529	55.000	0.00	0.00	34.51	3.53
1871	1926	5.591099	GCCAACAAAATCATATTGGTCGAT	58.409	37.500	3.96	0.00	43.02	3.59
1883	1938	3.417069	TTGGTCGATGTTGGAAGACAT	57.583	42.857	0.00	0.00	42.68	3.06
1888	1943	5.116180	GGTCGATGTTGGAAGACATGAATA	58.884	41.667	0.00	0.00	40.21	1.75
1947	2002	5.627499	TTTAAAGCAGCAGACTTGTATGG	57.373	39.130	0.00	0.00	0.00	2.74
1948	2003	1.457346	AAGCAGCAGACTTGTATGGC	58.543	50.000	0.00	0.00	0.00	4.40
1992	2047	0.324738	TGGAAGCAGAGGACGAGGAT	60.325	55.000	0.00	0.00	0.00	3.24
2002	2057	1.009829	GGACGAGGATGCACATGAAC	58.990	55.000	0.00	0.00	0.00	3.18
2006	2061	1.386533	GAGGATGCACATGAACCAGG	58.613	55.000	0.00	0.00	0.00	4.45
2054	2109	0.969894	ATCTTATCGCCCTTCTCCCG	59.030	55.000	0.00	0.00	0.00	5.14
2055	2110	1.113517	TCTTATCGCCCTTCTCCCGG	61.114	60.000	0.00	0.00	0.00	5.73
2082	2137	0.037590	TCACAAGGGATGGGGTTTCG	59.962	55.000	0.00	0.00	31.35	3.46
2091	2146	3.118000	GGGATGGGGTTTCGAAAGTCTAT	60.118	47.826	11.66	9.61	0.00	1.98
2180	2235	0.886490	GGATGATGGCTAGGGTTGCG	60.886	60.000	0.00	0.00	0.00	4.85
2193	2248	1.302192	GTTGCGCAAGGAGTGGGTA	60.302	57.895	25.78	0.00	42.13	3.69
2303	2358	0.759060	GGGAAGGCAAACAACCCACT	60.759	55.000	0.00	0.00	40.20	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	74	0.393537	CTCCCGAAGAGGCAGCATTT	60.394	55.000	0.00	0.00	39.13	2.32
84	109	9.512435	CTTGTTAAAGATGCATTAAGGAGAATG	57.488	33.333	0.00	0.00	36.46	2.67
183	208	4.281435	TCATGCTCTTGCCAGAAAAATCAA	59.719	37.500	0.00	0.00	38.71	2.57
184	209	3.827876	TCATGCTCTTGCCAGAAAAATCA	59.172	39.130	0.00	0.00	38.71	2.57
189	217	1.171308	GCTCATGCTCTTGCCAGAAA	58.829	50.000	0.00	0.00	38.71	2.52
273	301	0.550914	TGTGCAAGTCTTTCACCCCT	59.449	50.000	12.06	0.00	0.00	4.79
351	379	2.092968	AGCTCGAATAATGTCCTGCCAA	60.093	45.455	0.00	0.00	0.00	4.52
392	422	2.305858	AGTCTTAACCGAGACCACCT	57.694	50.000	1.68	0.00	45.69	4.00
471	501	9.945904	CCAGATTTAAGAACTACTTTTCTACCT	57.054	33.333	0.00	0.00	39.72	3.08
505	535	5.010112	CGATACAATCATCCCACACTCTAGT	59.990	44.000	0.00	0.00	0.00	2.57
556	586	2.776536	AGATGCTGTAAAGCTCAGGGAT	59.223	45.455	6.43	0.00	35.49	3.85
599	629	9.206870	CATCTACACCATTTTTAAACTTTGCAT	57.793	29.630	0.00	0.00	0.00	3.96
660	690	2.180946	TATCCATCCACTGCTCCAGT	57.819	50.000	0.00	0.00	46.51	4.00
741	771	5.012251	GGTAGAGAACTTGTTCTTTCTCCCT	59.988	44.000	15.94	10.26	46.11	4.20
800	833	6.154363	CCAAATCCACTTGTAATTACACCCAT	59.846	38.462	17.85	3.81	35.64	4.00
872	906	5.074115	CCCTAGTCCGAATAGAGTCTTGAT	58.926	45.833	4.42	0.00	0.00	2.57
924	958	2.110721	ACAAAAGGAGCAGGAGGGATTT	59.889	45.455	0.00	0.00	0.00	2.17
985	1022	1.271871	CCACATGACCCTAGCAACCAA	60.272	52.381	0.00	0.00	0.00	3.67
1044	1081	9.603921	CAGGAGAAATATTGCCAAATGTTATTT	57.396	29.630	0.00	0.00	0.00	1.40
1141	1179	4.165779	GTGGTTCTATTGCAACAATTCCG	58.834	43.478	0.00	0.00	0.00	4.30
1150	1188	4.469657	AGTTCAAAGGTGGTTCTATTGCA	58.530	39.130	0.00	0.00	0.00	4.08
1155	1193	5.623956	TCTTGAGTTCAAAGGTGGTTCTA	57.376	39.130	0.00	0.00	35.15	2.10
1211	1249	8.768501	TGCCCAATATGTAATATAACCACAAA	57.231	30.769	0.00	0.00	38.94	2.83
1331	1369	1.628846	GCCCTCAGTTGTTTCCTCCTA	59.371	52.381	0.00	0.00	0.00	2.94
1378	1421	0.319555	CTCAGGAGGAAACGCGTTGA	60.320	55.000	27.34	16.08	0.00	3.18
1383	1426	1.078143	ATGGCTCAGGAGGAAACGC	60.078	57.895	0.00	0.00	0.00	4.84
1410	1453	3.245122	ACACCAAAAGGTAATCCGGACAT	60.245	43.478	6.12	0.34	39.05	3.06
1463	1511	3.378742	CAGAGTTATGCTCACGTAGGAGT	59.621	47.826	4.97	0.00	46.47	3.85
1469	1517	1.893137	TGACCAGAGTTATGCTCACGT	59.107	47.619	0.00	0.00	46.47	4.49
1560	1612	1.091537	CACGATAAACACCCGGCATT	58.908	50.000	0.00	0.00	0.00	3.56
1564	1616	0.321830	AACCCACGATAAACACCCGG	60.322	55.000	0.00	0.00	0.00	5.73
1615	1668	2.223711	CGACAACCCTGAAAACCAAAGG	60.224	50.000	0.00	0.00	0.00	3.11
1625	1678	1.208535	ACAGTTCAACGACAACCCTGA	59.791	47.619	0.00	0.00	0.00	3.86
1627	1680	2.014128	CAACAGTTCAACGACAACCCT	58.986	47.619	0.00	0.00	0.00	4.34
1632	1685	4.025563	CGGAAATACAACAGTTCAACGACA	60.026	41.667	0.00	0.00	32.80	4.35
1773	1827	1.209019	AGCAGCTACACTGATCAAGGG	59.791	52.381	0.00	0.00	42.85	3.95
1786	1840	3.057245	CGGCAGAGTATGATAAGCAGCTA	60.057	47.826	0.00	0.00	0.00	3.32
1818	1873	0.947244	CATGGGAAATCCTACGCTGC	59.053	55.000	0.00	0.00	36.20	5.25
1871	1926	7.174413	TCTGGAATTATTCATGTCTTCCAACA	58.826	34.615	7.29	0.00	43.41	3.33
1883	1938	4.631377	CACAAGCGACTCTGGAATTATTCA	59.369	41.667	7.29	0.00	0.00	2.57
1888	1943	1.160137	GCACAAGCGACTCTGGAATT	58.840	50.000	0.00	0.00	0.00	2.17
1947	2002	3.869272	CCTGCATTGACTCCGCGC	61.869	66.667	0.00	0.00	0.00	6.86
1948	2003	3.197790	CCCTGCATTGACTCCGCG	61.198	66.667	0.00	0.00	0.00	6.46
1992	2047	3.364441	GCGCCTGGTTCATGTGCA	61.364	61.111	0.00	0.00	36.00	4.57
2027	2082	5.377478	AGAAGGGCGATAAGATTTTTAGGG	58.623	41.667	0.00	0.00	0.00	3.53
2054	2109	1.747355	CATCCCTTGTGATCTTGCACC	59.253	52.381	0.00	0.00	37.99	5.01
2055	2110	1.747355	CCATCCCTTGTGATCTTGCAC	59.253	52.381	0.00	0.00	39.22	4.57
2082	2137	3.739810	GCCGTTCGGGATAATAGACTTTC	59.260	47.826	13.16	0.00	38.47	2.62
2091	2146	1.153588	GAACGGCCGTTCGGGATAA	60.154	57.895	44.72	0.00	43.82	1.75
2112	2167	0.460311	GATTCCATCCAGTCGACCGT	59.540	55.000	13.01	0.00	0.00	4.83
2132	2187	2.560542	CTCTTGCTATGCTATCTCCCGT	59.439	50.000	0.00	0.00	0.00	5.28
2134	2189	4.881019	TTCTCTTGCTATGCTATCTCCC	57.119	45.455	0.00	0.00	0.00	4.30
2180	2235	1.202770	ACACACTTACCCACTCCTTGC	60.203	52.381	0.00	0.00	0.00	4.01
2193	2248	2.278404	TGGCCAGCCAACACACTT	59.722	55.556	9.42	0.00	44.12	3.16
2303	2358	3.118629	GCCACTATCTGAGATGTTGGACA	60.119	47.826	21.73	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.