AutoCloner

Multiple sequence alignment - TraesCS7D01G324700

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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	TraesCS7D01G324700	chr7D	100.000	2666	0	0	1	2666	414491027	414488362	0.000000e+00	4924
1	TraesCS7D01G324700	chr7B	93.657	2160	87	18	546	2666	428922126	428919978	0.000000e+00	3184
2	TraesCS7D01G324700	chr7B	89.286	224	13	9	337	551	428922712	428922491	1.220000e-68	270
3	TraesCS7D01G324700	chr7B	89.308	159	6	6	3	160	428926069	428925921	3.500000e-44	189
4	TraesCS7D01G324700	chr7A	93.139	2157	80	25	562	2666	476937001	476934861	0.000000e+00	3101
5	TraesCS7D01G324700	chr7A	94.081	321	8	5	1	311	476937744	476937425	6.680000e-131	477
6	TraesCS7D01G324700	chr7A	86.420	162	19	2	399	558	476937338	476937178	9.810000e-40	174
7	TraesCS7D01G324700	chr2B	84.694	196	28	2	1449	1643	568635412	568635606	7.530000e-46	195
8	TraesCS7D01G324700	chr2B	87.582	153	19	0	1169	1321	568634964	568635116	7.580000e-41	178
9	TraesCS7D01G324700	chr2B	80.203	197	30	7	367	558	597000073	596999881	3.580000e-29	139
10	TraesCS7D01G324700	chr2B	78.818	203	35	6	326	521	465132922	465133123	2.150000e-26	130
11	TraesCS7D01G324700	chr2A	84.694	196	28	2	1449	1643	627610950	627611144	7.530000e-46	195
12	TraesCS7D01G324700	chr2A	86.928	153	20	0	1169	1321	627610493	627610645	3.530000e-39	172
13	TraesCS7D01G324700	chr2D	88.889	153	17	0	1169	1321	483785481	483785633	3.500000e-44	189
14	TraesCS7D01G324700	chr2D	84.184	196	29	2	1449	1643	483785932	483786126	3.500000e-44	189
15	TraesCS7D01G324700	chr2D	80.000	185	31	5	342	521	566268422	566268239	5.990000e-27	132
16	TraesCS7D01G324700	chr6B	83.158	190	25	5	352	537	694255289	694255475	1.640000e-37	167
17	TraesCS7D01G324700	chr6B	80.100	201	34	5	326	521	81010772	81010573	7.690000e-31	145
18	TraesCS7D01G324700	chr4B	80.000	235	33	9	326	553	101712692	101712919	7.640000e-36	161
19	TraesCS7D01G324700	chr1B	80.105	191	20	8	341	527	667386760	667386584	2.790000e-25	126

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	TraesCS7D01G324700	chr7D	414488362	414491027	2665	True	4924.000000	4924	100.000000	1	2666	1	chr7D.!!$R1	2665
1	TraesCS7D01G324700	chr7B	428919978	428926069	6091	True	1214.333333	3184	90.750333	3	2666	3	chr7B.!!$R1	2663
2	TraesCS7D01G324700	chr7A	476934861	476937744	2883	True	1250.666667	3101	91.213333	1	2666	3	chr7A.!!$R1	2665

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
772	4316	0.032615	ACCACTCCTGCAAACCCAAA	60.033	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
1763	5329	0.171903	ATGGCGCAGAAAGCACAATC	59.828	50.0	10.83	0.0	46.13	2.67	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
232	1630	6.453791	GGCTTCGAACTTGTTTTTCTTTTGAC	60.454	38.462	0.00	0.00	0.00	3.18
307	2192	6.652481	TGTGCAATATTATGGTTGGGTTTTTG	59.348	34.615	0.00	0.00	0.00	2.44
335	2247	3.025262	CTCAGTTGTAGTACTCCCTCCC	58.975	54.545	0.00	0.00	0.00	4.30
352	3389	4.266714	CCTCCCTTTATTTTTACTCCGCA	58.733	43.478	0.00	0.00	0.00	5.69
386	3423	9.646427	TGTTTGAAGTTAAACTATGCAAACTTT	57.354	25.926	19.67	3.02	41.08	2.66
573	4098	2.111384	GCTGAAGGAGGGAGTACATCA	58.889	52.381	0.00	0.00	0.00	3.07
613	4138	6.071051	ACCTTGTTTGAACTTTTGCCTCTTTA	60.071	34.615	0.00	0.00	0.00	1.85
680	4219	1.070786	GTTGAACTGCTCCCGGTCA	59.929	57.895	0.00	0.00	0.00	4.02
743	4287	4.618489	CAGTTAGAAAAGCAAATTCCAGCG	59.382	41.667	0.00	0.00	35.48	5.18
772	4316	0.032615	ACCACTCCTGCAAACCCAAA	60.033	50.000	0.00	0.00	0.00	3.28
870	4415	0.746923	TGCACCTGATCTGCATGCTC	60.747	55.000	20.33	8.93	39.76	4.26
872	4417	0.107361	CACCTGATCTGCATGCTCCA	60.107	55.000	20.33	10.05	0.00	3.86
930	4481	2.159421	CGCAGCAAGCAATCTTCATCTT	60.159	45.455	0.00	0.00	46.13	2.40
931	4482	3.436496	GCAGCAAGCAATCTTCATCTTC	58.564	45.455	0.00	0.00	44.79	2.87
932	4483	3.128938	GCAGCAAGCAATCTTCATCTTCT	59.871	43.478	0.00	0.00	44.79	2.85
933	4484	4.380655	GCAGCAAGCAATCTTCATCTTCTT	60.381	41.667	0.00	0.00	44.79	2.52
934	4485	5.333513	CAGCAAGCAATCTTCATCTTCTTC	58.666	41.667	0.00	0.00	0.00	2.87
935	4486	5.124138	CAGCAAGCAATCTTCATCTTCTTCT	59.876	40.000	0.00	0.00	0.00	2.85
1449	5009	2.502080	CTCGTCTGCGACACGGTC	60.502	66.667	8.91	0.00	42.81	4.79
1621	5181	1.586564	GCCGTCCTCGTCTTCATCG	60.587	63.158	0.00	0.00	35.01	3.84
1683	5249	1.299926	GGCTACCTACGTGCCATCG	60.300	63.158	8.85	0.00	45.46	3.84
1708	5274	1.021390	CGAGGTCGCTCCATGCTTTT	61.021	55.000	0.00	0.00	40.11	2.27
1739	5305	4.464008	TCTGGTCTTGATTGTGCTTTCTT	58.536	39.130	0.00	0.00	0.00	2.52
1749	5315	9.173939	CTTGATTGTGCTTTCTTTACTTTACTG	57.826	33.333	0.00	0.00	0.00	2.74
1750	5316	7.138736	TGATTGTGCTTTCTTTACTTTACTGC	58.861	34.615	0.00	0.00	0.00	4.40
1762	5328	8.604035	TCTTTACTTTACTGCGATTTGATCATC	58.396	33.333	0.00	0.00	0.00	2.92
1774	5340	6.729104	GATTTGATCATCGATTGTGCTTTC	57.271	37.500	0.00	0.00	0.00	2.62
1776	5342	4.870221	TGATCATCGATTGTGCTTTCTG	57.130	40.909	0.00	0.00	0.00	3.02
1777	5343	3.064408	TGATCATCGATTGTGCTTTCTGC	59.936	43.478	0.00	0.00	43.25	4.26
1778	5344	1.394572	TCATCGATTGTGCTTTCTGCG	59.605	47.619	0.00	0.00	46.63	5.18
1784	5350	3.583383	GTGCTTTCTGCGCCATCT	58.417	55.556	4.18	0.00	45.73	2.90
1908	5489	1.182673	CATTTTCGATTTCCAGCGCG	58.817	50.000	0.00	0.00	0.00	6.86
1909	5490	1.083489	ATTTTCGATTTCCAGCGCGA	58.917	45.000	12.10	0.00	0.00	5.87
1910	5491	0.869068	TTTTCGATTTCCAGCGCGAA	59.131	45.000	12.10	0.00	40.49	4.70
1911	5492	0.442310	TTTCGATTTCCAGCGCGAAG	59.558	50.000	12.10	0.00	42.66	3.79
2064	5649	3.123050	GCTGGCAGAACAAACGAAAAAT	58.877	40.909	20.86	0.00	0.00	1.82
2168	5776	1.071471	GCGGTAGTATGCCATGCCT	59.929	57.895	0.00	0.00	43.25	4.75
2663	6271	1.758514	CCTCCTCGGGCTGAGCTTA	60.759	63.158	18.14	4.60	43.82	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	2.489329	ACTGCTTCCAAAACATCCATCG	59.511	45.455	0.00	0.00	0.00	3.84
212	1610	7.326063	AGTTCAGTCAAAAGAAAAACAAGTTCG	59.674	33.333	0.00	0.00	0.00	3.95
232	1630	1.208614	GCCTTGCGCTTCAGTTCAG	59.791	57.895	9.73	0.00	0.00	3.02
307	2192	6.433716	AGGGAGTACTACAACTGAGTAAACTC	59.566	42.308	7.57	3.08	43.15	3.01
539	3588	9.166222	TCCCTCCTTCAGCATATAAAACTTATA	57.834	33.333	0.00	0.00	0.00	0.98
544	3593	5.685728	ACTCCCTCCTTCAGCATATAAAAC	58.314	41.667	0.00	0.00	0.00	2.43
558	3607	1.771255	GGCAATGATGTACTCCCTCCT	59.229	52.381	0.00	0.00	0.00	3.69
573	4098	3.078836	GGTGGCTGGCATGGCAAT	61.079	61.111	23.47	0.00	44.02	3.56
625	4159	5.405571	GCGTACAGATACCCTCACATATTTG	59.594	44.000	0.00	0.00	0.00	2.32
660	4199	0.250338	GACCGGGAGCAGTTCAACTT	60.250	55.000	6.32	0.00	0.00	2.66
680	4219	3.231818	CCGGAATAGGAGTACAGGACAT	58.768	50.000	0.00	0.00	0.00	3.06
743	4287	1.807142	GCAGGAGTGGTTGCTTAGTTC	59.193	52.381	0.00	0.00	37.35	3.01
772	4316	4.673968	TGAGAGGGATGTAGTTAGTGTGT	58.326	43.478	0.00	0.00	0.00	3.72
892	4437	1.153647	CGTAGAGACCATGCCGCAA	60.154	57.895	0.00	0.00	0.00	4.85
930	4481	3.055530	GCTTGTCTGGGAGATTGAGAAGA	60.056	47.826	0.00	0.00	34.37	2.87
931	4482	3.269178	GCTTGTCTGGGAGATTGAGAAG	58.731	50.000	0.00	0.00	35.20	2.85
932	4483	2.639347	TGCTTGTCTGGGAGATTGAGAA	59.361	45.455	0.00	0.00	0.00	2.87
933	4484	2.235650	CTGCTTGTCTGGGAGATTGAGA	59.764	50.000	0.00	0.00	0.00	3.27
934	4485	2.630158	CTGCTTGTCTGGGAGATTGAG	58.370	52.381	0.00	0.00	0.00	3.02
935	4486	1.280133	CCTGCTTGTCTGGGAGATTGA	59.720	52.381	0.00	0.00	0.00	2.57
983	4534	1.380785	ATGTTGGCTGGGATGGCTG	60.381	57.895	0.00	0.00	0.00	4.85
1371	4931	1.443828	GACGATGGAGAAGGGGAGC	59.556	63.158	0.00	0.00	0.00	4.70
1404	4964	3.197790	CTGATGCCGGTCGCCTTG	61.198	66.667	1.90	0.00	36.24	3.61
1417	4977	2.124653	GAGCAGCAGCAGCCTGAT	60.125	61.111	6.10	0.00	45.49	2.90
1449	5009	2.327343	CGTCACCAGCACCACCATG	61.327	63.158	0.00	0.00	0.00	3.66
1621	5181	1.820481	CGGAGAGGAGGACGAGGAC	60.820	68.421	0.00	0.00	0.00	3.85
1739	5305	6.933130	CGATGATCAAATCGCAGTAAAGTAA	58.067	36.000	0.00	0.00	42.57	2.24
1762	5328	1.512734	GGCGCAGAAAGCACAATCG	60.513	57.895	10.83	0.00	46.13	3.34
1763	5329	0.171903	ATGGCGCAGAAAGCACAATC	59.828	50.000	10.83	0.00	46.13	2.67
1764	5330	0.171903	GATGGCGCAGAAAGCACAAT	59.828	50.000	10.83	0.00	46.13	2.71
1765	5331	0.890542	AGATGGCGCAGAAAGCACAA	60.891	50.000	10.83	0.00	46.13	3.33
1766	5332	1.300971	GAGATGGCGCAGAAAGCACA	61.301	55.000	10.83	0.00	46.13	4.57
1767	5333	1.300971	TGAGATGGCGCAGAAAGCAC	61.301	55.000	10.83	0.00	46.13	4.40
1768	5334	0.393402	ATGAGATGGCGCAGAAAGCA	60.393	50.000	10.83	0.00	46.13	3.91
1769	5335	0.307146	GATGAGATGGCGCAGAAAGC	59.693	55.000	10.83	0.00	40.87	3.51
1770	5336	1.865970	GAGATGAGATGGCGCAGAAAG	59.134	52.381	10.83	0.00	0.00	2.62
1772	5338	0.826062	TGAGATGAGATGGCGCAGAA	59.174	50.000	10.83	0.00	0.00	3.02
1773	5339	1.046204	ATGAGATGAGATGGCGCAGA	58.954	50.000	10.83	0.00	0.00	4.26
1774	5340	2.738013	TATGAGATGAGATGGCGCAG	57.262	50.000	10.83	0.00	0.00	5.18
1776	5342	4.358851	GAGTATATGAGATGAGATGGCGC	58.641	47.826	0.00	0.00	0.00	6.53
1777	5343	4.644234	AGGAGTATATGAGATGAGATGGCG	59.356	45.833	0.00	0.00	0.00	5.69
1778	5344	5.681954	GCAGGAGTATATGAGATGAGATGGC	60.682	48.000	0.00	0.00	0.00	4.40
1779	5345	5.657745	AGCAGGAGTATATGAGATGAGATGG	59.342	44.000	0.00	0.00	0.00	3.51
1781	5347	6.734532	AGAGCAGGAGTATATGAGATGAGAT	58.265	40.000	0.00	0.00	0.00	2.75
1782	5348	6.012596	AGAGAGCAGGAGTATATGAGATGAGA	60.013	42.308	0.00	0.00	0.00	3.27
1783	5349	6.094464	CAGAGAGCAGGAGTATATGAGATGAG	59.906	46.154	0.00	0.00	0.00	2.90
1784	5350	5.945191	CAGAGAGCAGGAGTATATGAGATGA	59.055	44.000	0.00	0.00	0.00	2.92
1908	5489	4.558538	TTCTCTCTTGTTTGCTTGCTTC	57.441	40.909	0.00	0.00	0.00	3.86
1909	5490	4.989279	TTTCTCTCTTGTTTGCTTGCTT	57.011	36.364	0.00	0.00	0.00	3.91
1910	5491	5.068198	TGAATTTCTCTCTTGTTTGCTTGCT	59.932	36.000	0.00	0.00	0.00	3.91
1911	5492	5.284079	TGAATTTCTCTCTTGTTTGCTTGC	58.716	37.500	0.00	0.00	0.00	4.01
2064	5649	8.196771	TCTGCTTTGCATTTCTTTCTTTCTTTA	58.803	29.630	0.00	0.00	38.13	1.85
2423	6031	4.687215	GAGCACAGCGAGGTGGCA	62.687	66.667	14.56	0.00	39.19	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.