AutoCloner

Multiple sequence alignment - TraesCS7D01G250200

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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	TraesCS7D01G250200	chr7D	100.000	3425	0	0	1	3425	222146211	222149635	0.000000e+00	6325.0
1	TraesCS7D01G250200	chr7D	97.308	260	7	0	8	267	477113580	477113839	3.140000e-120	442.0
2	TraesCS7D01G250200	chr7D	95.939	197	6	2	260	455	477113681	477113486	5.520000e-83	318.0
3	TraesCS7D01G250200	chr7B	95.943	2736	87	17	704	3425	174568006	174565281	0.000000e+00	4416.0
4	TraesCS7D01G250200	chr7A	93.438	3002	104	28	452	3425	236621394	236624330	0.000000e+00	4366.0
5	TraesCS7D01G250200	chr4A	97.308	260	7	0	8	267	636070587	636070846	3.140000e-120	442.0
6	TraesCS7D01G250200	chr4A	96.923	260	8	0	8	267	332644299	332644558	1.460000e-118	436.0
7	TraesCS7D01G250200	chr4A	96.923	260	8	0	8	267	604810787	604810528	1.460000e-118	436.0
8	TraesCS7D01G250200	chr4A	97.423	194	4	1	262	455	604810689	604810881	2.550000e-86	329.0
9	TraesCS7D01G250200	chr4A	97.423	194	4	1	260	452	604812364	604812557	2.550000e-86	329.0
10	TraesCS7D01G250200	chr4A	95.431	197	7	2	260	455	496071191	496070996	2.570000e-81	313.0
11	TraesCS7D01G250200	chr3D	97.308	260	7	0	8	267	278443943	278444202	3.140000e-120	442.0
12	TraesCS7D01G250200	chr3D	97.308	260	7	0	8	267	278445370	278445629	3.140000e-120	442.0
13	TraesCS7D01G250200	chr2A	97.308	260	7	0	8	267	526341888	526341629	3.140000e-120	442.0
14	TraesCS7D01G250200	chr2A	95.545	202	6	3	255	455	187957441	187957640	1.530000e-83	320.0
15	TraesCS7D01G250200	chr2D	96.923	260	8	0	8	267	156555454	156555195	1.460000e-118	436.0
16	TraesCS7D01G250200	chr2D	96.923	260	8	0	8	267	318549148	318548889	1.460000e-118	436.0
17	TraesCS7D01G250200	chr5B	95.939	197	6	2	260	455	289253636	289253831	5.520000e-83	318.0
18	TraesCS7D01G250200	chr3A	95.939	197	6	2	260	455	306867847	306867652	5.520000e-83	318.0
19	TraesCS7D01G250200	chr1D	95.431	197	7	2	260	455	226419766	226419571	2.570000e-81	313.0
20	TraesCS7D01G250200	chr1B	95.431	197	7	2	260	455	648676347	648676152	2.570000e-81	313.0
21	TraesCS7D01G250200	chr6A	93.333	45	2	1	660	704	486004226	486004183	7.930000e-07	65.8

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	TraesCS7D01G250200	chr7D	222146211	222149635	3424	False	6325	6325	100.000	1	3425	1	chr7D.!!$F1	3424
1	TraesCS7D01G250200	chr7B	174565281	174568006	2725	True	4416	4416	95.943	704	3425	1	chr7B.!!$R1	2721
2	TraesCS7D01G250200	chr7A	236621394	236624330	2936	False	4366	4366	93.438	452	3425	1	chr7A.!!$F1	2973
3	TraesCS7D01G250200	chr4A	604810689	604812557	1868	False	329	329	97.423	260	455	2	chr4A.!!$F3	195
4	TraesCS7D01G250200	chr3D	278443943	278445629	1686	False	442	442	97.308	8	267	2	chr3D.!!$F1	259

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
910	936	0.040958	GATTCCCGCGATGCATTGAC	60.041	55.000	18.58	8.06	0.0	3.18	F
1482	2110	1.446966	GCTGCTCTCCTTCCACGAC	60.447	63.158	0.00	0.00	0.0	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1852	3289	0.329596	GGAAGAGCTCCACCACCAAT	59.670	55.0	10.93	0.0	44.67	3.16	R
2450	3887	1.265236	AGTCTGGAACAGCCTCTCTG	58.735	55.0	0.00	0.0	43.12	3.35	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
216	217	2.829458	CGTCCTCGTCCTCCTCCC	60.829	72.222	0.00	0.00	0.00	4.30
234	235	3.783082	CTCCCTCTTTCCCCTACAATCTT	59.217	47.826	0.00	0.00	0.00	2.40
320	321	9.269453	CTTGCTTGATTAGATTGATACATCTCA	57.731	33.333	0.00	0.00	0.00	3.27
396	397	4.502016	GGCTAAGCCCCTAATAACGATAC	58.498	47.826	0.00	0.00	44.06	2.24
476	477	2.761208	ACCTCTTGGACCATCTAGAACG	59.239	50.000	0.00	0.00	37.04	3.95
477	478	3.024547	CCTCTTGGACCATCTAGAACGA	58.975	50.000	0.00	0.00	34.57	3.85
511	512	2.933906	TGTCTTCCGTCACAAAAGTGTC	59.066	45.455	0.00	0.00	35.07	3.67
516	517	0.661020	CGTCACAAAAGTGTCCCACC	59.339	55.000	0.00	0.00	35.07	4.61
519	520	1.133915	TCACAAAAGTGTCCCACCCTC	60.134	52.381	0.00	0.00	35.07	4.30
597	598	2.816087	AGAAGTTGCGTTTGATCATGCT	59.184	40.909	13.96	0.00	0.00	3.79
658	659	6.926630	ACTCTGTAACTCTTTGATCCTCTT	57.073	37.500	0.00	0.00	0.00	2.85
663	664	9.490379	TCTGTAACTCTTTGATCCTCTTTTAAC	57.510	33.333	0.00	0.00	0.00	2.01
888	906	0.730834	CGTCTCGTCCTCTGTTGCTG	60.731	60.000	0.00	0.00	0.00	4.41
892	918	0.750249	TCGTCCTCTGTTGCTGTTGA	59.250	50.000	0.00	0.00	0.00	3.18
893	919	1.344438	TCGTCCTCTGTTGCTGTTGAT	59.656	47.619	0.00	0.00	0.00	2.57
910	936	0.040958	GATTCCCGCGATGCATTGAC	60.041	55.000	18.58	8.06	0.00	3.18
955	981	4.755614	GCTCGACGTCTCGCCGTT	62.756	66.667	14.70	0.00	41.98	4.44
1355	1983	2.434359	CCCTCGGGTCGTTTGCTC	60.434	66.667	0.00	0.00	0.00	4.26
1482	2110	1.446966	GCTGCTCTCCTTCCACGAC	60.447	63.158	0.00	0.00	0.00	4.34
1510	2459	2.328099	CGGCTTGTTCCTGTCCAGC	61.328	63.158	0.00	0.00	0.00	4.85
1794	3084	2.456119	CGGCCTTGCACTCATCGAC	61.456	63.158	0.00	0.00	0.00	4.20
1914	3351	1.146358	GCTTCGATGTACTGGGCGTC	61.146	60.000	0.00	0.00	0.00	5.19
1918	3355	1.807886	GATGTACTGGGCGTCGAGT	59.192	57.895	10.24	10.24	36.02	4.18
2088	3525	1.487976	GATCTTGACTCCCCTGATGCA	59.512	52.381	0.00	0.00	0.00	3.96
2167	3604	3.310501	TGCACGCAGAATTCTACATCATG	59.689	43.478	7.86	2.74	0.00	3.07
2268	3705	7.493971	CACCAGGTTTTCTCTGAGTTATATGAG	59.506	40.741	4.32	0.00	34.36	2.90
2426	3863	9.586435	AAGAAAAGTTGAAATTCCAAGTTAGTG	57.414	29.630	0.00	0.00	38.37	2.74
2450	3887	4.065088	TGCTGTTTGAAGTCATGACCTAC	58.935	43.478	22.21	13.71	0.00	3.18
2682	4121	6.126863	ACCTGAACTTCATATTGTCTTCCA	57.873	37.500	0.00	0.00	0.00	3.53
2715	4154	5.070685	ACTTTAGGAGGAGCGACAATTTTT	58.929	37.500	0.00	0.00	0.00	1.94
2744	4183	2.075355	AATGGTGGAAAGTGCCGGGA	62.075	55.000	2.18	0.00	0.00	5.14
2876	4316	2.957402	TTCAGGGTGCAACAAGATCT	57.043	45.000	3.06	0.00	39.98	2.75
2918	4358	7.114754	TGCTCTTTATCCTTCATCAACTGATT	58.885	34.615	0.00	0.00	32.72	2.57
2928	4368	6.183360	CCTTCATCAACTGATTGGTGCATATT	60.183	38.462	0.00	0.00	45.22	1.28
2979	4419	5.818857	ACCATTGTACGACAGTAAAGTGTTT	59.181	36.000	0.00	0.00	34.16	2.83
3071	4512	5.234972	ACTTCGTTTTTCTTTACGTTCCGAT	59.765	36.000	0.00	0.00	38.79	4.18
3078	4519	1.927174	CTTTACGTTCCGATGAGCAGG	59.073	52.381	0.00	0.00	0.00	4.85
3248	4691	9.362151	CCTTTTATGGGGTATAAAAATGCTCTA	57.638	33.333	0.00	0.00	45.63	2.43
3315	4758	4.154195	AGCGTGATTTGAGTAACACAATCC	59.846	41.667	0.00	0.00	33.56	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	9.959721	TTTACTTGACTCCTAAGCAAATAAGAT	57.040	29.630	0.00	0.00	0.00	2.40
2	3	9.216117	GTTTACTTGACTCCTAAGCAAATAAGA	57.784	33.333	0.00	0.00	0.00	2.10
3	4	8.451748	GGTTTACTTGACTCCTAAGCAAATAAG	58.548	37.037	0.00	0.00	0.00	1.73
4	5	8.161425	AGGTTTACTTGACTCCTAAGCAAATAA	58.839	33.333	0.00	0.00	0.00	1.40
5	6	7.686434	AGGTTTACTTGACTCCTAAGCAAATA	58.314	34.615	0.00	0.00	0.00	1.40
6	7	6.543735	AGGTTTACTTGACTCCTAAGCAAAT	58.456	36.000	0.00	0.00	0.00	2.32
82	83	2.507407	AAGGGAAGCCGAGCAAATAA	57.493	45.000	0.00	0.00	0.00	1.40
201	202	1.215679	AAGAGGGAGGAGGACGAGGA	61.216	60.000	0.00	0.00	0.00	3.71
209	210	1.008449	TGTAGGGGAAAGAGGGAGGAG	59.992	57.143	0.00	0.00	0.00	3.69
216	217	3.198872	GCGAAGATTGTAGGGGAAAGAG	58.801	50.000	0.00	0.00	0.00	2.85
333	334	5.307196	TGCTTAGGAGTCAAGTAAACCTCTT	59.693	40.000	0.00	0.00	32.90	2.85
343	344	6.100004	TCTTATCGTTTGCTTAGGAGTCAAG	58.900	40.000	0.00	0.00	0.00	3.02
396	397	0.808755	GGTTGTGGCCCAAGTTATCG	59.191	55.000	0.00	0.00	32.51	2.92
476	477	2.476854	GGAAGACATGTGCATTTCGCTC	60.477	50.000	1.15	0.00	43.06	5.03
477	478	1.470098	GGAAGACATGTGCATTTCGCT	59.530	47.619	1.15	0.00	43.06	4.93
511	512	1.070289	GCTAGAATTACGGAGGGTGGG	59.930	57.143	0.00	0.00	0.00	4.61
516	517	3.118738	AGTGTTGGCTAGAATTACGGAGG	60.119	47.826	0.00	0.00	0.00	4.30
519	520	6.715464	CATTTAGTGTTGGCTAGAATTACGG	58.285	40.000	0.00	0.00	0.00	4.02
550	551	4.454717	GCGGTAGCCCAAAACGCG	62.455	66.667	3.53	3.53	40.84	6.01
554	555	2.034999	CCCTGCGGTAGCCCAAAA	59.965	61.111	0.00	0.00	44.33	2.44
597	598	8.217799	CCATATTACAAAAGGATTACTCTCCCA	58.782	37.037	0.00	0.00	35.79	4.37
680	682	4.457834	TTTTCTGAAACCGAGGCAAAAA	57.542	36.364	1.58	0.00	0.00	1.94
769	787	9.515020	GTTCTGATTTCATTCTTGTGTTGTTTA	57.485	29.630	0.00	0.00	0.00	2.01
888	906	0.381801	AATGCATCGCGGGAATCAAC	59.618	50.000	6.13	0.00	0.00	3.18
892	918	0.747644	TGTCAATGCATCGCGGGAAT	60.748	50.000	6.13	0.00	0.00	3.01
893	919	1.368345	CTGTCAATGCATCGCGGGAA	61.368	55.000	6.13	0.00	0.00	3.97
910	936	2.834638	ATGGTGGGGATTTTCCTCTG	57.165	50.000	0.00	0.00	38.07	3.35
1510	2459	2.432628	GACAGGACCGGCGACAAG	60.433	66.667	9.30	0.00	0.00	3.16
1648	2722	1.974875	CAGCAGCAGACATTGGCCA	60.975	57.895	0.00	0.00	0.00	5.36
1794	3084	1.539929	GCATTCTCCTCCACCGATGAG	60.540	57.143	0.00	0.00	33.37	2.90
1852	3289	0.329596	GGAAGAGCTCCACCACCAAT	59.670	55.000	10.93	0.00	44.67	3.16
1914	3351	3.032017	AGGACAACACAATCAGACTCG	57.968	47.619	0.00	0.00	0.00	4.18
1918	3355	3.572682	ACGTCTAGGACAACACAATCAGA	59.427	43.478	0.00	0.00	32.09	3.27
2088	3525	1.785041	GCGCACTGACACCACACATT	61.785	55.000	0.30	0.00	0.00	2.71
2167	3604	3.201290	CATTCAGTACCAGCACTCCATC	58.799	50.000	0.00	0.00	0.00	3.51
2426	3863	3.316308	AGGTCATGACTTCAAACAGCAAC	59.684	43.478	24.50	3.98	0.00	4.17
2450	3887	1.265236	AGTCTGGAACAGCCTCTCTG	58.735	55.000	0.00	0.00	43.12	3.35
2682	4121	4.141597	GCTCCTCCTAAAGTATTCAGCCTT	60.142	45.833	0.00	0.00	0.00	4.35
2715	4154	5.526846	GCACTTTCCACCATTGATTTTCAAA	59.473	36.000	0.00	0.00	40.12	2.69
2729	4168	1.743394	CTTTATCCCGGCACTTTCCAC	59.257	52.381	0.00	0.00	0.00	4.02
2918	4358	7.172868	ACAATCTTCATGAAAATATGCACCA	57.827	32.000	9.88	0.00	0.00	4.17
2928	4368	5.048504	GCAGGACAGAACAATCTTCATGAAA	60.049	40.000	9.88	1.39	31.83	2.69
3020	4460	7.175104	TCAAATGGCTAAACTAGAATTCTGGT	58.825	34.615	17.94	17.94	39.47	4.00
3071	4512	6.096141	TGACAGTAAAACAAAATTCCTGCTCA	59.904	34.615	0.00	0.00	0.00	4.26
3108	4549	5.304778	TGCTTTGAGCTAAATCACTACACA	58.695	37.500	1.29	0.00	42.97	3.72
3222	4665	8.250143	AGAGCATTTTTATACCCCATAAAAGG	57.750	34.615	3.27	0.00	45.39	3.11
3248	4691	8.539544	ACAAGGCAACCTTAAAAGCATATTTAT	58.460	29.630	0.00	0.00	42.67	1.40
3315	4758	9.887629	AAGGAGAGATCAATTGTATATGCTATG	57.112	33.333	5.13	0.00	0.00	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.