AutoCloner

Multiple sequence alignment - TraesCS4D01G232500

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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	TraesCS4D01G232500	chr4D	100.000	2579	0	0	1	2579	393123743	393121165	0.000000e+00	4763
1	TraesCS4D01G232500	chr4D	96.185	498	11	3	2090	2579	161466857	161466360	0.000000e+00	808
2	TraesCS4D01G232500	chr4D	96.008	501	9	6	2087	2579	297315755	297315258	0.000000e+00	804
3	TraesCS4D01G232500	chr4D	95.565	496	14	4	2091	2579	91060797	91061291	0.000000e+00	787
4	TraesCS4D01G232500	chr4D	93.491	507	17	8	2083	2579	58930444	58930944	0.000000e+00	739
5	TraesCS4D01G232500	chr4A	94.990	2096	90	8	1	2090	74578045	74575959	0.000000e+00	3275
6	TraesCS4D01G232500	chr4B	95.344	988	41	3	929	1915	482779045	482778062	0.000000e+00	1565
7	TraesCS4D01G232500	chr4B	88.798	857	51	19	1	850	482779891	482779073	0.000000e+00	1009
8	TraesCS4D01G232500	chr4B	90.517	116	11	0	1975	2090	482778062	482777947	1.240000e-33	154
9	TraesCS4D01G232500	chr5D	96.393	499	9	3	2089	2579	277072858	277073355	0.000000e+00	813
10	TraesCS4D01G232500	chrUn	95.976	497	12	3	2091	2579	95195418	95194922	0.000000e+00	800
11	TraesCS4D01G232500	chr7D	96.516	488	9	1	2100	2579	121773200	121773687	0.000000e+00	800
12	TraesCS4D01G232500	chr7D	93.988	499	16	6	2090	2579	77509879	77509386	0.000000e+00	743
13	TraesCS4D01G232500	chr2D	95.783	498	12	4	2090	2579	377647252	377646756	0.000000e+00	795
14	TraesCS4D01G232500	chr2D	95.190	499	15	4	2089	2579	435418174	435418671	0.000000e+00	780
15	TraesCS4D01G232500	chr2D	93.775	498	18	6	2091	2579	107559195	107558702	0.000000e+00	736
16	TraesCS4D01G232500	chr6D	93.452	504	18	7	2085	2579	301806857	301807354	0.000000e+00	734
17	TraesCS4D01G232500	chr6D	93.373	498	18	10	2090	2579	473252183	473252673	0.000000e+00	723
18	TraesCS4D01G232500	chr6D	91.379	232	14	6	2088	2317	436883884	436883657	1.930000e-81	313
19	TraesCS4D01G232500	chr1D	93.775	498	14	9	2091	2579	327112128	327112617	0.000000e+00	732
20	TraesCS4D01G232500	chr1D	93.360	497	20	8	2091	2579	486557411	486556920	0.000000e+00	723
21	TraesCS4D01G232500	chr6B	83.475	236	21	16	2091	2317	181165385	181165159	1.210000e-48	204

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	TraesCS4D01G232500	chr4D	393121165	393123743	2578	True	4763.000000	4763	100.000	1	2579	1	chr4D.!!$R3	2578
1	TraesCS4D01G232500	chr4D	58930444	58930944	500	False	739.000000	739	93.491	2083	2579	1	chr4D.!!$F1	496
2	TraesCS4D01G232500	chr4A	74575959	74578045	2086	True	3275.000000	3275	94.990	1	2090	1	chr4A.!!$R1	2089
3	TraesCS4D01G232500	chr4B	482777947	482779891	1944	True	909.333333	1565	91.553	1	2090	3	chr4B.!!$R1	2089

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
934	940	0.169672	CGAAGAACGAACTCCGGCTA	59.83	55.0	0.0	0.0	45.77	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2171	2180	0.251832	GTCAGAGGTGGGAGTGAGGA	60.252	60.0	0.0	0.0	0.0	3.71	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
335	336	1.180029	ACGGCGTCTAAGGCTCTAAA	58.820	50.000	6.77	0.00	34.19	1.85
390	395	6.150318	TCTATCGGCTTAAGCGAGATTTAAG	58.850	40.000	29.41	23.15	43.26	1.85
409	415	1.815421	CATCCAGTTTCTCGCGGGG	60.815	63.158	5.94	0.00	0.00	5.73
433	439	5.570589	GCAGACAAGAAAAATTCTTCCATCG	59.429	40.000	2.47	0.00	46.62	3.84
511	517	1.493311	CAGAAAGCAACTCGGCGAC	59.507	57.895	4.99	0.00	39.27	5.19
599	605	3.741245	TCTGAGCTAAGGTGAGTAGGT	57.259	47.619	0.00	0.00	32.10	3.08
636	642	1.305930	GGCCGGTTTACTGCTTGGAG	61.306	60.000	1.90	0.00	0.00	3.86
676	682	0.744874	TCGGTCGATTCAGATCCACC	59.255	55.000	0.00	0.00	39.40	4.61
728	734	2.166907	ACCACAACACCATTTTCCCA	57.833	45.000	0.00	0.00	0.00	4.37
743	749	6.094603	CCATTTTCCCAAGATGAGAGTACTTG	59.905	42.308	0.00	0.00	40.12	3.16
807	813	0.970640	AGCACATGCAGCCAAATTCA	59.029	45.000	6.64	0.00	45.16	2.57
850	856	6.013554	TCTTTCTCCTTTTCTTCTTTCCCA	57.986	37.500	0.00	0.00	0.00	4.37
896	902	4.722203	GCACATGCATCTGTATCTGTAC	57.278	45.455	0.00	0.00	41.59	2.90
900	906	4.339530	ACATGCATCTGTATCTGTACGACT	59.660	41.667	0.00	0.00	33.36	4.18
934	940	0.169672	CGAAGAACGAACTCCGGCTA	59.830	55.000	0.00	0.00	45.77	3.93
1231	1237	3.352338	CTGTGCTACGACCCCGACC	62.352	68.421	0.00	0.00	39.50	4.79
1234	1240	2.753043	GCTACGACCCCGACCTCA	60.753	66.667	0.00	0.00	39.50	3.86
1308	1314	2.102553	GAGACGTACGCCCAGCTC	59.897	66.667	16.72	10.58	0.00	4.09
1470	1476	2.813908	CTGCCGGTTACAGCGTCC	60.814	66.667	1.90	0.00	37.40	4.79
1633	1639	4.986531	CGTGTCGGCGTGCAAACG	62.987	66.667	6.85	0.23	0.00	3.60
1773	1780	0.608856	TGTGCAAGCCGTTGGATCAT	60.609	50.000	0.00	0.00	36.28	2.45
1811	1819	6.183360	GGATGTATTCTTCTTCCTTGAACTGC	60.183	42.308	0.00	0.00	0.00	4.40
1860	1869	4.434330	CGATTTCTTCTAACACCGTCTTGC	60.434	45.833	0.00	0.00	0.00	4.01
1894	1903	1.146982	GAGCCTCCTATCCTCACCTCT	59.853	57.143	0.00	0.00	0.00	3.69
1897	1906	2.556559	GCCTCCTATCCTCACCTCTAGG	60.557	59.091	0.00	0.00	42.17	3.02
1926	1935	1.374758	CTGAACCCTCACAGGCGAC	60.375	63.158	0.00	0.00	32.73	5.19
1984	1993	4.469945	TCCAAGAGGGAGTCAAAACGATAT	59.530	41.667	0.00	0.00	42.15	1.63
2018	2027	2.878406	CACATGTCAAAACCTCCGACTT	59.122	45.455	0.00	0.00	0.00	3.01
2061	2070	4.083862	GTCACCGGCCCTCACTCC	62.084	72.222	0.00	0.00	0.00	3.85
2067	2076	3.462678	GGCCCTCACTCCGTCCTC	61.463	72.222	0.00	0.00	0.00	3.71
2084	2093	0.745845	CTCGCTTGGCCTTGCACTAT	60.746	55.000	17.94	0.00	0.00	2.12
2086	2095	1.065782	TCGCTTGGCCTTGCACTATTA	60.066	47.619	17.94	0.00	0.00	0.98
2097	2106	7.164803	GGCCTTGCACTATTAGAAATCTCTAT	58.835	38.462	0.00	0.00	34.06	1.98
2118	2127	4.919774	TTCCTAATGGAGCAGTTGGTAA	57.080	40.909	0.00	0.00	44.24	2.85
2123	2132	3.567478	ATGGAGCAGTTGGTAATCTCC	57.433	47.619	0.00	0.00	42.67	3.71
2124	2133	1.207089	TGGAGCAGTTGGTAATCTCCG	59.793	52.381	0.00	0.00	44.67	4.63
2129	2138	2.268298	CAGTTGGTAATCTCCGTTCCG	58.732	52.381	0.00	0.00	0.00	4.30
2147	2156	4.159244	TCCGGATTTATTTTCGTCCCAT	57.841	40.909	0.00	0.00	0.00	4.00
2149	2158	3.880490	CCGGATTTATTTTCGTCCCATCA	59.120	43.478	0.00	0.00	0.00	3.07
2152	2161	6.460953	CCGGATTTATTTTCGTCCCATCATTT	60.461	38.462	0.00	0.00	0.00	2.32
2153	2162	6.978080	CGGATTTATTTTCGTCCCATCATTTT	59.022	34.615	0.00	0.00	0.00	1.82
2154	2163	7.167468	CGGATTTATTTTCGTCCCATCATTTTC	59.833	37.037	0.00	0.00	0.00	2.29
2155	2164	7.167468	GGATTTATTTTCGTCCCATCATTTTCG	59.833	37.037	0.00	0.00	0.00	3.46
2156	2165	6.503589	TTATTTTCGTCCCATCATTTTCGT	57.496	33.333	0.00	0.00	0.00	3.85
2157	2166	4.413495	TTTTCGTCCCATCATTTTCGTC	57.587	40.909	0.00	0.00	0.00	4.20
2158	2167	2.018542	TCGTCCCATCATTTTCGTCC	57.981	50.000	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
308	309	4.752879	TAGACGCCGTTGCCTGCC	62.753	66.667	0.00	0.00	0.00	4.85
335	336	0.250295	CCGAATCATATGGCCGTGGT	60.250	55.000	8.05	0.00	0.00	4.16
390	395	2.464459	CCCGCGAGAAACTGGATGC	61.464	63.158	8.23	0.00	0.00	3.91
433	439	6.480320	ACGGACTCATGATTAATTAGAACTGC	59.520	38.462	0.00	0.00	0.00	4.40
511	517	2.550606	TCCGGAAAAACAAATCACCGAG	59.449	45.455	0.00	0.00	42.40	4.63
599	605	1.391577	CCCGAATTCATGCATGGTCA	58.608	50.000	25.97	11.32	0.00	4.02
676	682	3.730662	CGAAATTGGCTGGAATACAACGG	60.731	47.826	0.00	0.00	0.00	4.44
728	734	4.713814	TGGATCAGCAAGTACTCTCATCTT	59.286	41.667	0.00	0.00	0.00	2.40
743	749	7.169308	CAGATGATTAAAGCATTTTGGATCAGC	59.831	37.037	0.00	0.00	40.09	4.26
807	813	0.178953	AAAAGTGTCCAGCAGCCCAT	60.179	50.000	0.00	0.00	0.00	4.00
850	856	1.882912	TGCTCGACAAATCTTGCTGT	58.117	45.000	0.00	0.00	0.00	4.40
896	902	1.920574	CGCTTTATCTGGACACAGTCG	59.079	52.381	0.00	0.00	45.14	4.18
900	906	3.953712	TCTTCGCTTTATCTGGACACA	57.046	42.857	0.00	0.00	0.00	3.72
934	940	1.485480	CTGCTGGGAGTGATGTGATCT	59.515	52.381	0.00	0.00	0.00	2.75
1017	1023	3.849951	GAGGCGCGGAGGATGGAA	61.850	66.667	8.83	0.00	0.00	3.53
1039	1045	4.521062	GAGCAGCAGGACGGCGAT	62.521	66.667	16.62	0.00	45.09	4.58
1112	1118	2.202570	CCGTGTCGTCGATGGACC	60.203	66.667	14.58	7.27	40.17	4.46
1308	1314	1.421410	GCTTCATGACGTAGCACCCG	61.421	60.000	12.08	0.00	37.91	5.28
1713	1720	2.176045	CAAACGATAGGGGCCCTTTTT	58.824	47.619	33.98	20.91	43.77	1.94
1773	1780	1.193323	TACATCCGGCCGTTCCTTTA	58.807	50.000	26.12	4.33	0.00	1.85
1811	1819	2.987821	GTTCGTCGAGGGAAGAAGAAAG	59.012	50.000	5.12	0.00	40.52	2.62
1871	1880	0.825840	GTGAGGATAGGAGGCTCGCT	60.826	60.000	8.69	9.39	0.00	4.93
1894	1903	2.467880	GGTTCAGATGTGACCTCCCTA	58.532	52.381	0.00	0.00	30.10	3.53
1897	1906	1.208293	GAGGGTTCAGATGTGACCTCC	59.792	57.143	15.20	8.27	38.92	4.30
1926	1935	4.785950	TCGAGAGGCGATTCAACG	57.214	55.556	0.00	0.00	45.59	4.10
2061	2070	3.121030	CAAGGCCAAGCGAGGACG	61.121	66.667	5.01	0.00	43.43	4.79
2067	2076	1.331756	CTAATAGTGCAAGGCCAAGCG	59.668	52.381	5.01	0.00	0.00	4.68
2084	2093	9.159254	TGCTCCATTAGGAATAGAGATTTCTAA	57.841	33.333	0.00	1.79	44.04	2.10
2086	2095	7.292120	ACTGCTCCATTAGGAATAGAGATTTCT	59.708	37.037	0.00	0.00	45.19	2.52
2097	2106	4.919774	TTACCAACTGCTCCATTAGGAA	57.080	40.909	0.00	0.00	45.19	3.36
2124	2133	3.690628	TGGGACGAAAATAAATCCGGAAC	59.309	43.478	9.01	0.00	31.48	3.62
2129	2138	7.167468	CGAAAATGATGGGACGAAAATAAATCC	59.833	37.037	0.00	0.00	0.00	3.01
2131	2140	7.543756	ACGAAAATGATGGGACGAAAATAAAT	58.456	30.769	0.00	0.00	0.00	1.40
2135	2144	4.142469	GGACGAAAATGATGGGACGAAAAT	60.142	41.667	0.00	0.00	0.00	1.82
2140	2149	0.650512	CGGACGAAAATGATGGGACG	59.349	55.000	0.00	0.00	0.00	4.79
2169	2178	1.304547	AGAGGTGGGAGTGAGGACG	60.305	63.158	0.00	0.00	0.00	4.79
2171	2180	0.251832	GTCAGAGGTGGGAGTGAGGA	60.252	60.000	0.00	0.00	0.00	3.71
2172	2181	0.252012	AGTCAGAGGTGGGAGTGAGG	60.252	60.000	0.00	0.00	0.00	3.86
2174	2183	2.992847	TAAGTCAGAGGTGGGAGTGA	57.007	50.000	0.00	0.00	0.00	3.41
2175	2184	2.432510	GGATAAGTCAGAGGTGGGAGTG	59.567	54.545	0.00	0.00	0.00	3.51
2176	2185	2.044492	TGGATAAGTCAGAGGTGGGAGT	59.956	50.000	0.00	0.00	0.00	3.85
2394	2411	5.734720	AGAGATTCGTTGATTTGGCTAAGA	58.265	37.500	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.