AutoCloner

Multiple sequence alignment - TraesCS7A01G104000

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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	TraesCS7A01G104000	chr7A	100.000	2735	0	0	1	2735	63441442	63444176	0.000000e+00	5051.0
1	TraesCS7A01G104000	chr7A	79.159	547	70	38	93	612	156870867	156871396	3.370000e-89	339.0
2	TraesCS7A01G104000	chr7A	80.208	192	23	11	5	185	8416987	8416800	2.210000e-26	130.0
3	TraesCS7A01G104000	chr4A	90.913	2091	119	34	706	2735	675965827	675967907	0.000000e+00	2743.0
4	TraesCS7A01G104000	chr4A	79.726	656	80	37	1	640	155595656	155595038	2.520000e-115	425.0
5	TraesCS7A01G104000	chr7D	91.055	1554	75	29	708	2203	58867364	58868911	0.000000e+00	2041.0
6	TraesCS7A01G104000	chr7D	92.687	670	39	7	1	661	58866025	58866693	0.000000e+00	957.0
7	TraesCS7A01G104000	chr7D	96.455	536	18	1	2201	2735	58868944	58869479	0.000000e+00	883.0
8	TraesCS7A01G104000	chr7D	94.231	52	2	1	657	707	58867291	58867342	8.120000e-11	78.7
9	TraesCS7A01G104000	chr3A	80.984	610	86	25	46	638	12342881	12342285	8.930000e-125	457.0
10	TraesCS7A01G104000	chr3A	80.153	524	76	26	1	504	594346574	594347089	1.550000e-97	366.0
11	TraesCS7A01G104000	chr3A	78.437	371	50	18	260	624	600891358	600891704	5.930000e-52	215.0
12	TraesCS7A01G104000	chr3D	80.905	597	90	20	66	645	537044156	537043567	1.490000e-122	449.0
13	TraesCS7A01G104000	chr2A	81.589	516	70	18	141	645	590978621	590978120	1.180000e-108	403.0
14	TraesCS7A01G104000	chr1B	79.143	537	82	23	1	522	487483579	487483058	7.250000e-91	344.0
15	TraesCS7A01G104000	chr5B	78.309	544	76	32	88	611	676057258	676057779	2.040000e-81	313.0

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	TraesCS7A01G104000	chr7A	63441442	63444176	2734	False	5051.000	5051	100.000	1	2735	1	chr7A.!!$F1	2734
1	TraesCS7A01G104000	chr7A	156870867	156871396	529	False	339.000	339	79.159	93	612	1	chr7A.!!$F2	519
2	TraesCS7A01G104000	chr4A	675965827	675967907	2080	False	2743.000	2743	90.913	706	2735	1	chr4A.!!$F1	2029
3	TraesCS7A01G104000	chr4A	155595038	155595656	618	True	425.000	425	79.726	1	640	1	chr4A.!!$R1	639
4	TraesCS7A01G104000	chr7D	58866025	58869479	3454	False	989.925	2041	93.607	1	2735	4	chr7D.!!$F1	2734
5	TraesCS7A01G104000	chr3A	12342285	12342881	596	True	457.000	457	80.984	46	638	1	chr3A.!!$R1	592
6	TraesCS7A01G104000	chr3A	594346574	594347089	515	False	366.000	366	80.153	1	504	1	chr3A.!!$F1	503
7	TraesCS7A01G104000	chr3D	537043567	537044156	589	True	449.000	449	80.905	66	645	1	chr3D.!!$R1	579
8	TraesCS7A01G104000	chr2A	590978120	590978621	501	True	403.000	403	81.589	141	645	1	chr2A.!!$R1	504
9	TraesCS7A01G104000	chr1B	487483058	487483579	521	True	344.000	344	79.143	1	522	1	chr1B.!!$R1	521
10	TraesCS7A01G104000	chr5B	676057258	676057779	521	False	313.000	313	78.309	88	611	1	chr5B.!!$F1	523

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
691	1488	2.480845	ACTTAGCGACCACAAACTCAC	58.519	47.619	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2452	3380	0.737219	GCATGCAGGATGACCTTGAC	59.263	55.0	14.21	0.0	45.36	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
316	401	5.280945	AGAAAAATGTTGACCATGTGTTCG	58.719	37.500	0.00	0.00	32.82	3.95
322	407	4.416620	TGTTGACCATGTGTTCGAAAAAC	58.583	39.130	0.00	2.00	0.00	2.43
323	408	4.082733	TGTTGACCATGTGTTCGAAAAACA	60.083	37.500	15.10	15.10	0.00	2.83
328	414	6.693545	TGACCATGTGTTCGAAAAACATTAAC	59.306	34.615	19.80	14.88	32.27	2.01
374	554	7.122550	TCAAGCATTTGAAAAATTGTTAACGC	58.877	30.769	0.26	0.00	40.26	4.84
549	743	7.397970	TCAAGCATTTGAAAAATGTTCGAAAC	58.602	30.769	0.00	0.00	40.26	2.78
590	784	8.977505	AGTTGACAATGTATTACAAAAATGTGC	58.022	29.630	0.00	1.36	0.00	4.57
691	1488	2.480845	ACTTAGCGACCACAAACTCAC	58.519	47.619	0.00	0.00	0.00	3.51
701	1498	5.929992	CGACCACAAACTCACCTTCTATTTA	59.070	40.000	0.00	0.00	0.00	1.40
702	1499	6.128634	CGACCACAAACTCACCTTCTATTTAC	60.129	42.308	0.00	0.00	0.00	2.01
703	1500	5.699458	ACCACAAACTCACCTTCTATTTACG	59.301	40.000	0.00	0.00	0.00	3.18
704	1501	5.699458	CCACAAACTCACCTTCTATTTACGT	59.301	40.000	0.00	0.00	0.00	3.57
705	1502	6.128634	CCACAAACTCACCTTCTATTTACGTC	60.129	42.308	0.00	0.00	0.00	4.34
707	1504	5.997384	AACTCACCTTCTATTTACGTCCT	57.003	39.130	0.00	0.00	0.00	3.85
708	1505	5.997384	ACTCACCTTCTATTTACGTCCTT	57.003	39.130	0.00	0.00	0.00	3.36
709	1506	5.963594	ACTCACCTTCTATTTACGTCCTTC	58.036	41.667	0.00	0.00	0.00	3.46
711	1508	4.773674	TCACCTTCTATTTACGTCCTTCCA	59.226	41.667	0.00	0.00	0.00	3.53
712	1509	5.424252	TCACCTTCTATTTACGTCCTTCCAT	59.576	40.000	0.00	0.00	0.00	3.41
713	1510	5.753921	CACCTTCTATTTACGTCCTTCCATC	59.246	44.000	0.00	0.00	0.00	3.51
837	1656	4.157120	CCCACCCATCCCGACGAC	62.157	72.222	0.00	0.00	0.00	4.34
978	1812	4.452733	GCCCCCGTTCGTGGAGAG	62.453	72.222	0.00	0.00	0.00	3.20
1495	2350	6.857964	CACTTCTTTGTTCTTTCGCATTACAT	59.142	34.615	0.00	0.00	0.00	2.29
1510	2365	3.989705	TTACATCATGCACGTTCTTCG	57.010	42.857	0.00	0.00	46.00	3.79
1562	2441	1.002430	GTGCAGTCTGATGGAGGACAA	59.998	52.381	3.32	0.00	35.18	3.18
1730	2621	1.823041	GGATGCCCTGCTGCTCTTC	60.823	63.158	0.00	0.00	0.00	2.87
1737	2628	1.667724	CCCTGCTGCTCTTCATAAACG	59.332	52.381	0.00	0.00	0.00	3.60
1745	2636	3.427528	TGCTCTTCATAAACGACGTCAAC	59.572	43.478	17.16	0.00	0.00	3.18
1781	2672	2.758852	AAACCGGCTAGGAGGGGTGA	62.759	60.000	0.00	0.00	45.00	4.02
1798	2689	1.207089	GTGATCATCTTGTCGGGACCA	59.793	52.381	0.00	0.00	0.00	4.02
1821	2712	1.299541	CCGGCAACATTAGCTCGAAT	58.700	50.000	0.00	0.00	0.00	3.34
1822	2713	1.003545	CCGGCAACATTAGCTCGAATG	60.004	52.381	7.53	7.53	41.69	2.67
1859	2750	4.323868	GCCAGAGACAGGAAAAGGAAGTAT	60.324	45.833	0.00	0.00	0.00	2.12
1915	2806	8.504812	ACACAATCAAAACCAGCTTTTAAATT	57.495	26.923	0.00	0.00	30.39	1.82
1978	2869	2.794350	CCTTTTTGGTCACAAATGTCGC	59.206	45.455	0.00	0.00	45.31	5.19
2002	2894	6.624861	GCCCACAACGATGAATTTGAGATTTA	60.625	38.462	0.00	0.00	0.00	1.40
2009	2901	9.559958	AACGATGAATTTGAGATTTATGTGAAC	57.440	29.630	0.00	0.00	0.00	3.18
2084	2976	8.426569	ACAGGTTAAACTCATGTAAGGTACTA	57.573	34.615	0.00	0.00	38.49	1.82
2107	2999	4.630644	ATCTACCTAACCAGATGCATGG	57.369	45.455	2.46	3.82	46.47	3.66
2132	3024	7.572523	CATTTCTCTATGCAAAAGATACCCA	57.427	36.000	0.00	0.00	0.00	4.51
2151	3043	2.095768	CCACTGCACAATACAGAAACCG	60.096	50.000	0.00	0.00	38.55	4.44
2183	3075	3.318275	TGCTAGTATCAGATTCGTCACCC	59.682	47.826	0.00	0.00	0.00	4.61
2196	3088	3.033764	CACCCGTTCACGACACCG	61.034	66.667	0.00	0.00	43.02	4.94
2197	3089	3.218470	ACCCGTTCACGACACCGA	61.218	61.111	0.00	0.00	43.02	4.69
2223	3150	7.831193	AGAAAATACAAGGTAGATTGCAGTGAT	59.169	33.333	0.00	0.00	33.28	3.06
2231	3158	5.704515	AGGTAGATTGCAGTGATTGATATGC	59.295	40.000	0.00	0.00	39.14	3.14
2298	3225	3.728845	TCTCCACAGCAGTAAAAGTGTC	58.271	45.455	0.00	0.00	0.00	3.67
2367	3295	2.233922	ACCATTGAACTAGGGTGACTCG	59.766	50.000	0.00	0.00	31.04	4.18
2449	3377	5.923733	TTTTCTTAACAACTTGCTTGGGA	57.076	34.783	0.00	0.00	33.66	4.37
2452	3380	5.452078	TCTTAACAACTTGCTTGGGAATG	57.548	39.130	0.00	0.00	33.66	2.67
2595	3523	1.675310	CAAGGGCATCAACCAGCGA	60.675	57.895	0.00	0.00	0.00	4.93
2671	3599	5.491982	ACTATGTCCATGGTGAAGTTCTTC	58.508	41.667	12.58	5.70	31.01	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
374	554	9.859427	AATACATGGTCAACATTTTTCTATGTG	57.141	29.630	0.00	0.00	38.69	3.21
519	712	8.486383	CGAACATTTTTCAAATGCTTGATTACA	58.514	29.630	8.77	0.00	41.22	2.41
520	713	8.698854	TCGAACATTTTTCAAATGCTTGATTAC	58.301	29.630	8.77	0.00	41.22	1.89
656	851	2.094700	GCTAAGTTTGGGTAGGCTTTGC	60.095	50.000	0.00	0.00	34.08	3.68
691	1488	5.298347	GGATGGAAGGACGTAAATAGAAGG	58.702	45.833	0.00	0.00	0.00	3.46
701	1498	1.345715	GGGATGGGATGGAAGGACGT	61.346	60.000	0.00	0.00	0.00	4.34
702	1499	1.344953	TGGGATGGGATGGAAGGACG	61.345	60.000	0.00	0.00	0.00	4.79
703	1500	0.183731	GTGGGATGGGATGGAAGGAC	59.816	60.000	0.00	0.00	0.00	3.85
704	1501	0.253583	TGTGGGATGGGATGGAAGGA	60.254	55.000	0.00	0.00	0.00	3.36
705	1502	0.630673	TTGTGGGATGGGATGGAAGG	59.369	55.000	0.00	0.00	0.00	3.46
707	1504	2.534990	GTTTTGTGGGATGGGATGGAA	58.465	47.619	0.00	0.00	0.00	3.53
708	1505	1.272985	GGTTTTGTGGGATGGGATGGA	60.273	52.381	0.00	0.00	0.00	3.41
709	1506	1.194218	GGTTTTGTGGGATGGGATGG	58.806	55.000	0.00	0.00	0.00	3.51
711	1508	0.042581	GGGGTTTTGTGGGATGGGAT	59.957	55.000	0.00	0.00	0.00	3.85
712	1509	1.467432	GGGGTTTTGTGGGATGGGA	59.533	57.895	0.00	0.00	0.00	4.37
713	1510	1.612146	GGGGGTTTTGTGGGATGGG	60.612	63.158	0.00	0.00	0.00	4.00
817	1635	4.109675	GTCGGGATGGGTGGGTGG	62.110	72.222	0.00	0.00	0.00	4.61
818	1636	4.467084	CGTCGGGATGGGTGGGTG	62.467	72.222	0.00	0.00	0.00	4.61
819	1637	4.707768	TCGTCGGGATGGGTGGGT	62.708	66.667	0.00	0.00	0.00	4.51
820	1638	4.157120	GTCGTCGGGATGGGTGGG	62.157	72.222	0.00	0.00	0.00	4.61
821	1639	4.157120	GGTCGTCGGGATGGGTGG	62.157	72.222	0.00	0.00	0.00	4.61
957	1791	3.666253	CCACGAACGGGGGCAAAC	61.666	66.667	7.68	0.00	34.36	2.93
964	1798	2.005960	CTAGCCTCTCCACGAACGGG	62.006	65.000	0.00	0.00	0.00	5.28
971	1805	1.657556	CGCTAGCTAGCCTCTCCAC	59.342	63.158	34.27	9.97	46.34	4.02
1389	2244	3.047877	GGGACGGCGTTGAACTGG	61.048	66.667	16.19	0.00	0.00	4.00
1562	2441	2.733956	CTCTCTTGGAGCTGTACCTCT	58.266	52.381	0.00	0.00	35.08	3.69
1692	2583	2.753966	CGAGAACATGCCGCCCTTG	61.754	63.158	0.00	0.00	0.00	3.61
1730	2621	2.036004	CGATCCGTTGACGTCGTTTATG	60.036	50.000	11.62	1.89	34.56	1.90
1760	2651	1.077716	CCCCTCCTAGCCGGTTTTG	60.078	63.158	1.90	0.00	0.00	2.44
1781	2672	2.118679	TGATGGTCCCGACAAGATGAT	58.881	47.619	0.00	0.00	0.00	2.45
1798	2689	1.668419	GAGCTAATGTTGCCGGTGAT	58.332	50.000	1.90	0.00	0.00	3.06
1821	2712	3.059386	GGCCGCCATTTTCGACCA	61.059	61.111	3.91	0.00	29.63	4.02
1822	2713	3.051392	CTGGCCGCCATTTTCGACC	62.051	63.158	13.86	0.00	30.82	4.79
1859	2750	6.423905	GTCCTTCGAATCGATCCATAATTTCA	59.576	38.462	6.06	0.00	35.23	2.69
1915	2806	2.038659	CCACTCTGGGGCAAAGAAAAA	58.961	47.619	0.00	0.00	32.67	1.94
1978	2869	4.970662	ATCTCAAATTCATCGTTGTGGG	57.029	40.909	0.00	0.00	0.00	4.61
2084	2976	5.338708	GCCATGCATCTGGTTAGGTAGATAT	60.339	44.000	8.13	0.00	38.63	1.63
2127	3019	4.069304	GTTTCTGTATTGTGCAGTGGGTA	58.931	43.478	0.00	0.00	35.60	3.69
2132	3024	2.151202	CCGGTTTCTGTATTGTGCAGT	58.849	47.619	0.00	0.00	35.60	4.40
2183	3075	1.202203	TTTTCTCGGTGTCGTGAACG	58.798	50.000	0.00	0.00	44.84	3.95
2196	3088	7.334421	TCACTGCAATCTACCTTGTATTTTCTC	59.666	37.037	0.00	0.00	0.00	2.87
2197	3089	7.168219	TCACTGCAATCTACCTTGTATTTTCT	58.832	34.615	0.00	0.00	0.00	2.52
2223	3150	5.360429	TGCTCCTTTATTTGCAGCATATCAA	59.640	36.000	1.05	0.00	35.17	2.57
2231	3158	9.585099	TTGTATAAATTGCTCCTTTATTTGCAG	57.415	29.630	0.00	0.00	36.75	4.41
2298	3225	1.838112	TGTAAAGGGCCAAGCAGATG	58.162	50.000	6.18	0.00	0.00	2.90
2367	3295	1.153469	GTCTCCAGCAGCCAGTAGC	60.153	63.158	0.00	0.00	44.25	3.58
2449	3377	2.885135	TGCAGGATGACCTTGACATT	57.115	45.000	0.00	0.00	45.36	2.71
2452	3380	0.737219	GCATGCAGGATGACCTTGAC	59.263	55.000	14.21	0.00	45.36	3.18
2595	3523	1.877443	GCCCACAAAACGTGTATGACT	59.123	47.619	0.00	0.00	44.78	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.