AutoCloner

Multiple sequence alignment - TraesCS1D01G007400

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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	TraesCS1D01G007400	chr1D	100.000	3021	0	0	1	3021	3711563	3708543	0.000000e+00	5579.0
1	TraesCS1D01G007400	chr1D	88.107	3111	251	62	1	3021	5355703	5358784	0.000000e+00	3585.0
2	TraesCS1D01G007400	chr1D	92.303	1702	76	9	976	2652	3826365	3824694	0.000000e+00	2366.0
3	TraesCS1D01G007400	chr1D	84.811	1929	183	56	1179	3021	5139386	5141290	0.000000e+00	1838.0
4	TraesCS1D01G007400	chr1D	95.040	988	43	6	1	983	3842308	3841322	0.000000e+00	1548.0
5	TraesCS1D01G007400	chr1D	83.103	1373	160	34	1178	2486	7156316	7154952	0.000000e+00	1184.0
6	TraesCS1D01G007400	chr1D	81.845	1377	169	44	1179	2486	4342079	4343443	0.000000e+00	1083.0
7	TraesCS1D01G007400	chr1D	85.684	950	95	21	459	1372	84072	85016	0.000000e+00	963.0
8	TraesCS1D01G007400	chr1D	84.169	1017	110	31	405	1372	98694	99708	0.000000e+00	939.0
9	TraesCS1D01G007400	chr1D	85.464	571	59	15	1173	1721	99668	100236	9.390000e-160	573.0
10	TraesCS1D01G007400	chr1D	79.191	346	35	12	2705	3021	4347177	4347514	3.950000e-49	206.0
11	TraesCS1D01G007400	chr1A	88.857	3114	237	49	1	3021	6516358	6519454	0.000000e+00	3727.0
12	TraesCS1D01G007400	chr1A	88.985	1743	138	27	465	2175	6561199	6562919	0.000000e+00	2106.0
13	TraesCS1D01G007400	chr1A	86.546	721	64	20	415	1105	4204244	4203527	0.000000e+00	763.0
14	TraesCS1D01G007400	chr1A	81.105	778	115	17	1731	2484	4095936	4095167	7.210000e-166	593.0
15	TraesCS1D01G007400	chr1A	89.172	471	47	4	1	467	6560648	6561118	4.340000e-163	584.0
16	TraesCS1D01G007400	chr1B	82.900	1386	152	49	1173	2486	6437219	6435847	0.000000e+00	1168.0
17	TraesCS1D01G007400	chr1B	82.580	1372	168	33	1176	2486	22186012	22187373	0.000000e+00	1144.0
18	TraesCS1D01G007400	chr1B	83.532	1008	123	26	405	1372	5688353	5687349	0.000000e+00	902.0
19	TraesCS1D01G007400	chr1B	85.997	707	72	18	650	1331	5585870	5585166	0.000000e+00	732.0
20	TraesCS1D01G007400	chr1B	85.195	743	72	23	650	1372	5521150	5520426	0.000000e+00	728.0
21	TraesCS1D01G007400	chr1B	84.071	339	24	14	2705	3021	7314103	7313773	1.760000e-77	300.0
22	TraesCS1D01G007400	chr1B	79.769	346	32	12	2705	3021	22191150	22191486	1.820000e-52	217.0
23	TraesCS1D01G007400	chr1B	94.340	53	3	0	2969	3021	6192508	6192456	6.940000e-12	82.4
24	TraesCS1D01G007400	chrUn	88.947	380	41	1	1	379	349408942	349409321	4.560000e-128	468.0
25	TraesCS1D01G007400	chrUn	88.684	380	42	1	1	379	374223878	374224257	2.120000e-126	462.0

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	TraesCS1D01G007400	chr1D	3708543	3711563	3020	True	5579.0	5579	100.0000	1	3021	1	chr1D.!!$R1	3020
1	TraesCS1D01G007400	chr1D	5355703	5358784	3081	False	3585.0	3585	88.1070	1	3021	1	chr1D.!!$F3	3020
2	TraesCS1D01G007400	chr1D	3824694	3826365	1671	True	2366.0	2366	92.3030	976	2652	1	chr1D.!!$R2	1676
3	TraesCS1D01G007400	chr1D	5139386	5141290	1904	False	1838.0	1838	84.8110	1179	3021	1	chr1D.!!$F2	1842
4	TraesCS1D01G007400	chr1D	3841322	3842308	986	True	1548.0	1548	95.0400	1	983	1	chr1D.!!$R3	982
5	TraesCS1D01G007400	chr1D	7154952	7156316	1364	True	1184.0	1184	83.1030	1178	2486	1	chr1D.!!$R4	1308
6	TraesCS1D01G007400	chr1D	84072	85016	944	False	963.0	963	85.6840	459	1372	1	chr1D.!!$F1	913
7	TraesCS1D01G007400	chr1D	98694	100236	1542	False	756.0	939	84.8165	405	1721	2	chr1D.!!$F4	1316
8	TraesCS1D01G007400	chr1D	4342079	4347514	5435	False	644.5	1083	80.5180	1179	3021	2	chr1D.!!$F5	1842
9	TraesCS1D01G007400	chr1A	6516358	6519454	3096	False	3727.0	3727	88.8570	1	3021	1	chr1A.!!$F1	3020
10	TraesCS1D01G007400	chr1A	6560648	6562919	2271	False	1345.0	2106	89.0785	1	2175	2	chr1A.!!$F2	2174
11	TraesCS1D01G007400	chr1A	4203527	4204244	717	True	763.0	763	86.5460	415	1105	1	chr1A.!!$R2	690
12	TraesCS1D01G007400	chr1A	4095167	4095936	769	True	593.0	593	81.1050	1731	2484	1	chr1A.!!$R1	753
13	TraesCS1D01G007400	chr1B	6435847	6437219	1372	True	1168.0	1168	82.9000	1173	2486	1	chr1B.!!$R5	1313
14	TraesCS1D01G007400	chr1B	5687349	5688353	1004	True	902.0	902	83.5320	405	1372	1	chr1B.!!$R3	967
15	TraesCS1D01G007400	chr1B	5585166	5585870	704	True	732.0	732	85.9970	650	1331	1	chr1B.!!$R2	681
16	TraesCS1D01G007400	chr1B	5520426	5521150	724	True	728.0	728	85.1950	650	1372	1	chr1B.!!$R1	722
17	TraesCS1D01G007400	chr1B	22186012	22191486	5474	False	680.5	1144	81.1745	1176	3021	2	chr1B.!!$F1	1845

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
608	713	0.883833	GACAAACCCTCCACATGCAG	59.116	55.0	0.00	0.0	0.00	4.41	F
1432	1995	0.313672	TTTTGCAGCAGCTAAACCCG	59.686	50.0	6.61	0.0	39.82	5.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1555	2118	0.107361	GGGATTGTTCGGGGATTCGT	60.107	55.000	0.00	0.0	0.00	3.85	R
2744	7207	1.200020	GTTTGGCACTGTGTATGGCTC	59.800	52.381	9.86	0.0	42.86	4.70	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
62	64	3.064545	GTGCTTGTTGTCCATGATCTAGC	59.935	47.826	0.00	0.00	0.00	3.42
143	146	6.112058	CACTTTTCCTTTTGGGTTGATGAAA	58.888	36.000	0.00	0.00	40.87	2.69
154	157	5.607477	TGGGTTGATGAAATACCTCGATAC	58.393	41.667	0.00	0.00	32.46	2.24
168	171	9.719355	AATACCTCGATACATGTAAATGCATTA	57.281	29.630	13.39	0.00	0.00	1.90
215	218	8.952278	CATAGTAAACCAAACTATGTTTGCCTA	58.048	33.333	15.29	10.33	46.14	3.93
379	382	7.039313	ACAAACTTAGTCCACCAAAAGAATC	57.961	36.000	0.00	0.00	0.00	2.52
388	391	7.637511	AGTCCACCAAAAGAATCATCTTATCT	58.362	34.615	0.00	0.00	45.19	1.98
501	599	7.013655	CCATCCTTACATGTAAAGGGAATTCTG	59.986	40.741	23.21	17.89	0.00	3.02
505	603	7.393234	CCTTACATGTAAAGGGAATTCTGTGAA	59.607	37.037	18.55	0.00	0.00	3.18
525	627	6.868339	TGTGAATTATGTCATGCTCTATACGG	59.132	38.462	0.00	0.00	0.00	4.02
608	713	0.883833	GACAAACCCTCCACATGCAG	59.116	55.000	0.00	0.00	0.00	4.41
655	774	2.289444	ACATCCCACAAGGTTCTACACG	60.289	50.000	0.00	0.00	36.75	4.49
713	832	2.689983	CAAGGTTCCAAACTCAGTTGCT	59.310	45.455	0.00	0.00	0.00	3.91
730	849	9.593134	CTCAGTTGCTAAAGTGATACTATTCTT	57.407	33.333	0.00	0.00	43.26	2.52
854	977	7.830739	ACTTTGATGATCAATCCAAAAGTACC	58.169	34.615	8.90	0.00	38.65	3.34
855	978	6.435430	TTGATGATCAATCCAAAAGTACCG	57.565	37.500	3.29	0.00	34.00	4.02
875	1001	2.921754	CGTTGTAGCTAGTGCAACCTAC	59.078	50.000	16.02	7.83	46.10	3.18
1161	1292	2.223923	GGCAGCAACAACCATTACAACA	60.224	45.455	0.00	0.00	0.00	3.33
1163	1294	3.868077	GCAGCAACAACCATTACAACAAA	59.132	39.130	0.00	0.00	0.00	2.83
1166	1297	6.476896	CAGCAACAACCATTACAACAAAAAG	58.523	36.000	0.00	0.00	0.00	2.27
1175	1306	8.871686	ACCATTACAACAAAAAGAGACATTTC	57.128	30.769	0.00	0.00	0.00	2.17
1191	1373	3.069443	ACATTTCCACAACAACCACCATC	59.931	43.478	0.00	0.00	0.00	3.51
1246	1599	2.093021	ACCATTTTTGCAGCAACAACCT	60.093	40.909	7.54	0.00	0.00	3.50
1263	1619	1.000274	ACCTTCATTTTCGCAGCAACC	60.000	47.619	0.00	0.00	0.00	3.77
1276	1635	3.568538	GCAGCAACCACTATTTTCACAG	58.431	45.455	0.00	0.00	0.00	3.66
1277	1636	3.253188	GCAGCAACCACTATTTTCACAGA	59.747	43.478	0.00	0.00	0.00	3.41
1281	1643	5.359576	AGCAACCACTATTTTCACAGAAACA	59.640	36.000	0.00	0.00	0.00	2.83
1432	1995	0.313672	TTTTGCAGCAGCTAAACCCG	59.686	50.000	6.61	0.00	39.82	5.28
1520	2083	2.981909	GGCAGCAGAGCAGTTGCA	60.982	61.111	6.90	0.00	46.00	4.08
1555	2118	2.219458	CAATGTTGCCAACAATTGCCA	58.781	42.857	15.17	0.00	45.86	4.92
1781	2380	4.337145	ACCTCAACAACAACAGGTACAAA	58.663	39.130	0.00	0.00	37.50	2.83
1909	2508	1.760029	TCCATCACTAGTGCGCCATTA	59.240	47.619	18.45	0.00	0.00	1.90
2161	2767	4.178545	ACCATGCTTGCAAGTTCATAAC	57.821	40.909	26.55	9.43	0.00	1.89
2175	2781	3.953712	TCATAACTTCGTCTTGCCTGA	57.046	42.857	0.00	0.00	0.00	3.86
2273	2894	2.887152	GGTTGAACTGAAGCAAGGACAT	59.113	45.455	0.00	0.00	0.00	3.06
2301	2922	8.616076	CATACAACTCTTTAATGGTTGGAGATC	58.384	37.037	18.27	0.00	42.93	2.75
2303	2924	7.234355	ACAACTCTTTAATGGTTGGAGATCTT	58.766	34.615	18.27	0.00	42.93	2.40
2304	2925	7.175641	ACAACTCTTTAATGGTTGGAGATCTTG	59.824	37.037	18.27	7.07	42.93	3.02
2305	2926	6.784031	ACTCTTTAATGGTTGGAGATCTTGT	58.216	36.000	0.00	0.00	0.00	3.16
2306	2927	7.234355	ACTCTTTAATGGTTGGAGATCTTGTT	58.766	34.615	0.00	0.00	0.00	2.83
2371	3028	6.204688	CACAACTGGTTTCATAGTTTGCTAGA	59.795	38.462	0.00	0.00	35.08	2.43
2559	3310	1.204467	GGGGGTTGTTGCATGTGTATG	59.796	52.381	0.00	0.00	37.36	2.39
2672	3625	8.974060	TGTAGAAACCATAAAACTTGAGACTT	57.026	30.769	0.00	0.00	0.00	3.01
2744	7207	4.823157	CAATAGCCCTCATGAGATCAGAG	58.177	47.826	24.62	5.87	0.00	3.35
2764	7227	1.200020	GAGCCATACACAGTGCCAAAC	59.800	52.381	0.00	0.00	0.00	2.93
2856	7344	7.321153	CAGACATATGAGACATCATGAGCATA	58.679	38.462	10.38	4.79	45.89	3.14
2934	7427	6.596888	TGCAGTTTTTCAAAATGATGTTCCAA	59.403	30.769	1.03	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
62	64	3.890147	AGAACCTATTCGTAGCTACCCTG	59.110	47.826	18.16	4.65	40.04	4.45
121	124	7.387673	GGTATTTCATCAACCCAAAAGGAAAAG	59.612	37.037	0.00	0.00	39.89	2.27
143	146	9.890629	ATAATGCATTTACATGTATCGAGGTAT	57.109	29.630	18.75	0.80	34.85	2.73
163	166	6.808212	GGGCATGTTCATGTGTATAATAATGC	59.192	38.462	13.24	0.00	0.00	3.56
168	171	4.802307	TGGGGCATGTTCATGTGTATAAT	58.198	39.130	13.24	0.00	0.00	1.28
177	180	4.215109	GGTTTACTATGGGGCATGTTCAT	58.785	43.478	0.00	0.00	0.00	2.57
413	419	7.283354	TCACTCTAGATACGTCATCATCAGTTT	59.717	37.037	0.00	0.00	35.96	2.66
501	599	6.183360	GCCGTATAGAGCATGACATAATTCAC	60.183	42.308	0.00	0.00	0.00	3.18
505	603	5.047021	ACTGCCGTATAGAGCATGACATAAT	60.047	40.000	0.00	0.00	38.56	1.28
525	627	8.977505	GTTCTCTAAGATGATAAGATGAACTGC	58.022	37.037	0.00	0.00	31.72	4.40
655	774	6.280643	ACCATAAACAAGAAAGGCAAAACTC	58.719	36.000	0.00	0.00	0.00	3.01
739	858	5.935206	TCGCCTTATTCACTTTACATGTCAA	59.065	36.000	0.00	0.00	0.00	3.18
854	977	2.080286	AGGTTGCACTAGCTACAACG	57.920	50.000	15.57	0.00	46.27	4.10
855	978	3.259902	GGTAGGTTGCACTAGCTACAAC	58.740	50.000	22.62	14.34	46.07	3.32
908	1036	8.924691	TGCATCAACTTTAATAATTCTGTTTGC	58.075	29.630	0.00	0.00	0.00	3.68
1161	1292	6.106003	GGTTGTTGTGGAAATGTCTCTTTTT	58.894	36.000	0.00	0.00	0.00	1.94
1163	1294	4.709397	TGGTTGTTGTGGAAATGTCTCTTT	59.291	37.500	0.00	0.00	0.00	2.52
1166	1297	3.243401	GGTGGTTGTTGTGGAAATGTCTC	60.243	47.826	0.00	0.00	0.00	3.36
1175	1306	2.034558	GTGAAGATGGTGGTTGTTGTGG	59.965	50.000	0.00	0.00	0.00	4.17
1191	1373	5.063312	GGAAATGGTTGTTGTTGTTGTGAAG	59.937	40.000	0.00	0.00	0.00	3.02
1246	1599	1.680735	AGTGGTTGCTGCGAAAATGAA	59.319	42.857	0.00	0.00	0.00	2.57
1263	1619	7.032580	TGGTTGTTGTTTCTGTGAAAATAGTG	58.967	34.615	0.00	0.00	0.00	2.74
1276	1635	4.396790	TGTGGTAGAACTGGTTGTTGTTTC	59.603	41.667	0.00	0.00	39.30	2.78
1277	1636	4.337145	TGTGGTAGAACTGGTTGTTGTTT	58.663	39.130	0.00	0.00	39.30	2.83
1281	1643	3.958018	TGTTGTGGTAGAACTGGTTGTT	58.042	40.909	0.00	0.00	42.38	2.83
1520	2083	3.671008	ACATTGTTGCTGCATCACATT	57.329	38.095	12.62	4.72	0.00	2.71
1555	2118	0.107361	GGGATTGTTCGGGGATTCGT	60.107	55.000	0.00	0.00	0.00	3.85
2045	2648	7.664318	CCAGAATTTAACTACTAGTTTGGGTGT	59.336	37.037	0.00	0.00	39.51	4.16
2161	2767	2.084610	TGTGATCAGGCAAGACGAAG	57.915	50.000	0.00	0.00	0.00	3.79
2175	2781	1.494721	ACACCAGGTTGAGGTTGTGAT	59.505	47.619	0.00	0.00	37.23	3.06
2273	2894	8.598916	TCTCCAACCATTAAAGAGTTGTATGTA	58.401	33.333	12.08	0.00	39.36	2.29
2601	3553	7.039434	TCCATCAAGTAAAAATGTGGTATTGCA	60.039	33.333	0.00	0.00	0.00	4.08
2602	3554	7.319646	TCCATCAAGTAAAAATGTGGTATTGC	58.680	34.615	0.00	0.00	0.00	3.56
2640	3592	6.977213	AGTTTTATGGTTTCTACATGCGTTT	58.023	32.000	0.00	0.00	0.00	3.60
2672	3625	2.948979	GGATGTGAAGTTGACAACACCA	59.051	45.455	20.08	13.53	33.08	4.17
2744	7207	1.200020	GTTTGGCACTGTGTATGGCTC	59.800	52.381	9.86	0.00	42.86	4.70
2764	7227	7.359262	TCGTTAATGTCATCACCTTGTTTAG	57.641	36.000	0.00	0.00	0.00	1.85
2819	7282	1.206878	TATGTCTGCTGGTGCCTCAT	58.793	50.000	0.00	0.00	38.71	2.90
2829	7293	5.785243	CTCATGATGTCTCATATGTCTGCT	58.215	41.667	1.90	0.00	40.20	4.24
2856	7344	8.159447	TGCTCTACTTGCAATATTCTGGATTAT	58.841	33.333	0.00	0.00	37.51	1.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.