AutoCloner

Multiple sequence alignment - TraesCS1D01G366100

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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	TraesCS1D01G366100	chr1D	100.000	2264	0	0	1	2264	446419304	446421567	0.000000e+00	4181.0
1	TraesCS1D01G366100	chr3D	94.067	2073	106	6	1	2060	310406090	310408158	0.000000e+00	3131.0
2	TraesCS1D01G366100	chr3D	94.501	1982	90	12	1	1969	446922420	446924395	0.000000e+00	3038.0
3	TraesCS1D01G366100	chr3D	89.655	145	13	2	2072	2215	310408404	310408547	1.380000e-42	183.0
4	TraesCS1D01G366100	chrUn	93.661	2098	115	11	1	2082	10399169	10401264	0.000000e+00	3121.0
5	TraesCS1D01G366100	chr4D	93.539	2105	110	20	1	2083	470196642	470194542	0.000000e+00	3110.0
6	TraesCS1D01G366100	chr4D	83.784	185	24	2	2036	2215	495818543	495818726	1.080000e-38	171.0
7	TraesCS1D01G366100	chr7D	93.470	2098	120	10	1	2082	131689390	131691486	0.000000e+00	3099.0
8	TraesCS1D01G366100	chr7D	93.190	2100	124	10	1	2082	528561183	528563281	0.000000e+00	3068.0
9	TraesCS1D01G366100	chr7D	83.117	231	23	12	2030	2251	131691515	131691738	1.770000e-46	196.0
10	TraesCS1D01G366100	chr7D	89.474	95	5	4	2162	2251	72156942	72157036	5.110000e-22	115.0
11	TraesCS1D01G366100	chr2D	93.245	2102	118	16	1	2082	619853627	619855724	0.000000e+00	3073.0
12	TraesCS1D01G366100	chr6D	95.038	1955	80	9	1	1939	377212201	377214154	0.000000e+00	3057.0
13	TraesCS1D01G366100	chr6D	81.435	237	30	12	2035	2264	377214289	377214518	4.970000e-42	182.0
14	TraesCS1D01G366100	chr4B	91.567	2099	153	19	1	2082	551060033	551062124	0.000000e+00	2874.0
15	TraesCS1D01G366100	chr5B	85.294	170	19	5	2035	2202	98047896	98047731	1.080000e-38	171.0
16	TraesCS1D01G366100	chr5B	84.028	144	23	0	2055	2198	89728991	89728848	3.030000e-29	139.0
17	TraesCS1D01G366100	chr6B	86.508	126	13	4	2130	2251	710885809	710885934	3.920000e-28	135.0
18	TraesCS1D01G366100	chr1A	79.121	182	26	9	2055	2230	311770496	311770321	5.110000e-22	115.0
19	TraesCS1D01G366100	chr2B	87.952	83	5	5	2169	2246	682782425	682782343	2.390000e-15	93.5

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	TraesCS1D01G366100	chr1D	446419304	446421567	2263	False	4181.0	4181	100.0000	1	2264	1	chr1D.!!$F1	2263
1	TraesCS1D01G366100	chr3D	446922420	446924395	1975	False	3038.0	3038	94.5010	1	1969	1	chr3D.!!$F1	1968
2	TraesCS1D01G366100	chr3D	310406090	310408547	2457	False	1657.0	3131	91.8610	1	2215	2	chr3D.!!$F2	2214
3	TraesCS1D01G366100	chrUn	10399169	10401264	2095	False	3121.0	3121	93.6610	1	2082	1	chrUn.!!$F1	2081
4	TraesCS1D01G366100	chr4D	470194542	470196642	2100	True	3110.0	3110	93.5390	1	2083	1	chr4D.!!$R1	2082
5	TraesCS1D01G366100	chr7D	528561183	528563281	2098	False	3068.0	3068	93.1900	1	2082	1	chr7D.!!$F2	2081
6	TraesCS1D01G366100	chr7D	131689390	131691738	2348	False	1647.5	3099	88.2935	1	2251	2	chr7D.!!$F3	2250
7	TraesCS1D01G366100	chr2D	619853627	619855724	2097	False	3073.0	3073	93.2450	1	2082	1	chr2D.!!$F1	2081
8	TraesCS1D01G366100	chr6D	377212201	377214518	2317	False	1619.5	3057	88.2365	1	2264	2	chr6D.!!$F1	2263
9	TraesCS1D01G366100	chr4B	551060033	551062124	2091	False	2874.0	2874	91.5670	1	2082	1	chr4B.!!$F1	2081

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
339	341	1.221466	CGCGTATCCGATGGCACAAT	61.221	55.0	0.0	0.0	36.66	2.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1518	1528	0.321122	CCTCCTCACGAGCAAGCTTT	60.321	55.0	0.0	0.0	37.27	3.51	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
96	97	5.581874	CCATTAAAGGTTCATGATTGGTTGC	59.418	40.000	0.00	0.00	0.00	4.17
339	341	1.221466	CGCGTATCCGATGGCACAAT	61.221	55.000	0.00	0.00	36.66	2.71
463	465	2.514592	ATTGTGCCAGATCCCGCG	60.515	61.111	0.00	0.00	0.00	6.46
528	530	4.588106	CCAGAGTGACATGGATGATCTAGT	59.412	45.833	0.00	0.00	39.02	2.57
567	569	5.048083	TGAAGCAATTTGGTAGTGGTCATTC	60.048	40.000	0.82	0.00	30.22	2.67
690	692	1.681327	GTGGACGGAGGACTAGCCA	60.681	63.158	6.07	0.00	40.02	4.75
772	775	1.307084	GACTAGCCTTGGAGGGGGT	60.307	63.158	0.00	0.00	35.37	4.95
888	891	1.737838	GTGTTGCTCAATCCGGATGA	58.262	50.000	19.95	16.00	0.00	2.92
968	975	7.025365	CCTCTTTACATGTCAATGTGTTCATG	58.975	38.462	0.00	0.00	46.66	3.07
1039	1049	4.063967	CGAGGCCACCGTGTGCTA	62.064	66.667	5.01	0.00	31.34	3.49
1054	1064	4.065088	GTGTGCTAACCAAGAAGACATGA	58.935	43.478	0.00	0.00	26.84	3.07
1056	1066	3.437049	GTGCTAACCAAGAAGACATGACC	59.563	47.826	0.00	0.00	0.00	4.02
1083	1093	1.073125	TGGAAGGACGCATCTTTGGAA	59.927	47.619	0.00	0.00	0.00	3.53
1155	1165	1.425066	TGCAAGGTGAAGGAGTCCATT	59.575	47.619	12.86	2.61	0.00	3.16
1206	1216	4.222810	AGGAGATATTTTGTTTGCCCCAAC	59.777	41.667	0.00	0.00	0.00	3.77
1226	1236	1.266124	TATGCTTACGATCGTGCGCG	61.266	55.000	30.23	14.79	39.92	6.86
1253	1263	1.276622	AACGCCTATGACCTTCCACT	58.723	50.000	0.00	0.00	0.00	4.00
1350	1360	4.160439	CCTCCTCTATGCAAGTACTTCACA	59.840	45.833	4.77	7.72	0.00	3.58
1469	1479	0.179184	GAGGAAGAGCGTCGTCAGAC	60.179	60.000	0.00	0.00	43.72	3.51
1518	1528	2.044650	GAGAGGGCATGCCAAGCA	60.045	61.111	36.56	0.00	44.86	3.91
1578	1588	2.645838	AAGCTCTCAAGGCACAAGAA	57.354	45.000	0.00	0.00	0.00	2.52
1588	1598	2.264455	AGGCACAAGAAGAGGATGAGT	58.736	47.619	0.00	0.00	0.00	3.41
1734	1745	2.209273	CCATGTGTCGTGAACTTGTCA	58.791	47.619	0.00	0.00	0.00	3.58
1767	1778	7.432350	TTTGCCATTTGTATTGAATTTGGTC	57.568	32.000	0.00	0.00	0.00	4.02
1791	1802	3.304659	GGAGATGTTTGCAATGTGTCGTT	60.305	43.478	0.00	0.00	0.00	3.85
1833	1846	7.803659	CAGCATATTCTGTGATTTGTCATGATC	59.196	37.037	0.00	0.00	0.00	2.92
1863	1877	5.643379	AAAAACTGTTGTGCTGAGAAGAA	57.357	34.783	0.00	0.00	0.00	2.52
1915	1936	1.814394	GTTTTTAACCCTACCGCCAGG	59.186	52.381	0.00	0.00	45.13	4.45
1936	1957	2.351276	CCTGGCGGTAGGTTGCTT	59.649	61.111	0.00	0.00	32.99	3.91
1939	1960	0.392998	CTGGCGGTAGGTTGCTTGAT	60.393	55.000	0.00	0.00	0.00	2.57
1952	1973	0.178068	GCTTGATCCTACCGCCAGAA	59.822	55.000	0.00	0.00	0.00	3.02
1956	1977	0.179081	GATCCTACCGCCAGAACACC	60.179	60.000	0.00	0.00	0.00	4.16
1982	2011	2.410322	TAGGGGTGCACTTGCTGTGG	62.410	60.000	17.98	0.00	46.27	4.17
1989	2018	1.580845	GCACTTGCTGTGGCGAAGAT	61.581	55.000	11.26	0.00	46.27	2.40
1995	2024	3.819564	TGCTGTGGCGAAGATAGTAAT	57.180	42.857	0.00	0.00	42.25	1.89
2032	2061	2.824880	AAACCCTACCGCCACAGCA	61.825	57.895	0.00	0.00	39.83	4.41
2048	2077	1.003580	CAGCATCTGGTGGTAGGTTGT	59.996	52.381	1.45	0.00	39.67	3.32
2074	2103	3.935456	TACCGCCAGGGACCATGGT	62.935	63.158	25.46	19.89	43.47	3.55
2111	2374	1.173043	CGCCAGGGTGCTCATTTTTA	58.827	50.000	0.00	0.00	0.00	1.52
2121	2384	2.225491	TGCTCATTTTTACCGTCACAGC	59.775	45.455	0.00	0.00	0.00	4.40
2159	2423	4.815973	ATGGGCCCTGGCGGTAGA	62.816	66.667	25.70	0.00	43.06	2.59
2163	2427	4.208686	GCCCTGGCGGTAGAGTCG	62.209	72.222	0.00	0.00	0.00	4.18
2215	2480	2.261729	GGTTTGAACCCTCTCCTCTCT	58.738	52.381	1.32	0.00	43.43	3.10
2217	2482	3.073209	GGTTTGAACCCTCTCCTCTCTTT	59.927	47.826	1.32	0.00	43.43	2.52
2220	2485	2.039084	TGAACCCTCTCCTCTCTTTTGC	59.961	50.000	0.00	0.00	0.00	3.68
2246	2516	7.041780	CCCCTTCTGTCGAATGTTAGAATAATG	60.042	40.741	0.00	0.00	0.00	1.90
2251	2521	8.471609	TCTGTCGAATGTTAGAATAATGTACCA	58.528	33.333	0.00	0.00	0.00	3.25
2252	2522	8.415192	TGTCGAATGTTAGAATAATGTACCAC	57.585	34.615	0.00	0.00	0.00	4.16
2253	2523	7.493320	TGTCGAATGTTAGAATAATGTACCACC	59.507	37.037	0.00	0.00	0.00	4.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	2.576053	CTTGCGCGCTTGATGCAG	60.576	61.111	33.29	12.08	43.06	4.41
426	428	1.702401	TGTCTGGCCCAACATACTCAA	59.298	47.619	0.00	0.00	0.00	3.02
463	465	0.250640	CCCTCATAGGCACCATGAGC	60.251	60.000	17.02	0.00	45.33	4.26
528	530	2.026729	TGCTTCATTCCGGTGTATCCAA	60.027	45.455	0.00	0.00	35.57	3.53
567	569	2.669133	TTCTCCGGTGCCTCCATGG	61.669	63.158	4.97	4.97	39.35	3.66
772	775	3.691342	CTTCCTCCACGGCCACGA	61.691	66.667	2.24	0.00	44.60	4.35
942	949	6.295249	TGAACACATTGACATGTAAAGAGGA	58.705	36.000	0.00	0.00	42.14	3.71
1039	1049	2.174639	TGTGGGTCATGTCTTCTTGGTT	59.825	45.455	0.00	0.00	0.00	3.67
1054	1064	1.450211	CGTCCTTCCACTTGTGGGT	59.550	57.895	18.45	0.00	0.00	4.51
1056	1066	0.606401	ATGCGTCCTTCCACTTGTGG	60.606	55.000	13.24	13.24	0.00	4.17
1083	1093	5.310409	TCACATCTTTCTCCTTCACCTTT	57.690	39.130	0.00	0.00	0.00	3.11
1155	1165	2.609491	CGTCCATGACTTCTTTCGGTCA	60.609	50.000	0.00	0.00	44.84	4.02
1206	1216	0.431233	GCGCACGATCGTAAGCATAG	59.569	55.000	29.91	15.94	32.57	2.23
1226	1236	2.167900	AGGTCATAGGCGTTAGTTGGAC	59.832	50.000	0.00	0.00	0.00	4.02
1253	1263	6.791867	ACATGTTACTTCTCTAGCATACCA	57.208	37.500	0.00	0.00	0.00	3.25
1350	1360	4.987963	TGGCACTTCATGATCTATCCAT	57.012	40.909	0.00	0.00	0.00	3.41
1469	1479	0.388659	CTTCCGCTCCATCCTCTCTG	59.611	60.000	0.00	0.00	0.00	3.35
1518	1528	0.321122	CCTCCTCACGAGCAAGCTTT	60.321	55.000	0.00	0.00	37.27	3.51
1565	1575	2.639347	TCATCCTCTTCTTGTGCCTTGA	59.361	45.455	0.00	0.00	0.00	3.02
1578	1588	1.911057	TGTCACGTGACTCATCCTCT	58.089	50.000	39.62	0.00	44.99	3.69
1588	1598	1.124780	TTCCCCTTCTTGTCACGTGA	58.875	50.000	15.76	15.76	0.00	4.35
1734	1745	9.451002	TTCAATACAAATGGCAAATTCATTCAT	57.549	25.926	0.00	0.00	34.15	2.57
1767	1778	3.668757	CGACACATTGCAAACATCTCCAG	60.669	47.826	1.71	0.00	0.00	3.86
1791	1802	8.097038	AGAATATGCTGACAAACTGAAGTTCTA	58.903	33.333	4.17	0.00	37.25	2.10
1833	1846	8.134895	TCTCAGCACAACAGTTTTTAAATAAGG	58.865	33.333	0.00	0.00	0.00	2.69
1863	1877	4.953940	GAGCAATCCTCTGTTCTATCCT	57.046	45.455	0.00	0.00	37.60	3.24
1936	1957	0.535335	GTGTTCTGGCGGTAGGATCA	59.465	55.000	0.00	0.00	0.00	2.92
1939	1960	1.229082	AGGTGTTCTGGCGGTAGGA	60.229	57.895	0.00	0.00	0.00	2.94
1956	1977	4.778143	GTGCACCCCTACCGCCAG	62.778	72.222	5.22	0.00	0.00	4.85
1982	2011	3.600388	CCATGGGGATTACTATCTTCGC	58.400	50.000	2.85	0.00	35.59	4.70
1989	2018	2.253610	CTACCGCCATGGGGATTACTA	58.746	52.381	29.29	9.48	44.64	1.82
1995	2024	1.841556	GATCCTACCGCCATGGGGA	60.842	63.158	29.29	18.80	44.64	4.81
2032	2061	3.105283	GTCCTACAACCTACCACCAGAT	58.895	50.000	0.00	0.00	0.00	2.90
2048	2077	2.281091	CCTGGCGGTAGGGTCCTA	59.719	66.667	0.00	0.00	34.06	2.94
2105	2368	4.911514	AACTTGCTGTGACGGTAAAAAT	57.088	36.364	0.00	0.00	0.00	1.82
2111	2374	1.589803	GGTAAACTTGCTGTGACGGT	58.410	50.000	0.00	0.00	0.00	4.83
2159	2423	2.048503	GCGGTAGGTTGCACGACT	60.049	61.111	0.00	0.00	0.00	4.18
2163	2427	1.078426	ATCTGGCGGTAGGTTGCAC	60.078	57.895	0.00	0.00	0.00	4.57
2215	2480	1.885887	CATTCGACAGAAGGGGCAAAA	59.114	47.619	0.00	0.00	40.09	2.44
2217	2482	0.400213	ACATTCGACAGAAGGGGCAA	59.600	50.000	0.00	0.00	41.95	4.52
2220	2485	3.887621	TCTAACATTCGACAGAAGGGG	57.112	47.619	0.00	0.00	41.95	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.