AutoCloner

Multiple sequence alignment - TraesCS4B01G367800

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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	TraesCS4B01G367800	chr4B	100.000	2432	0	0	1	2432	654594027	654591596	0.000000e+00	4492.0
1	TraesCS4B01G367800	chr4B	95.188	2452	78	13	1	2432	654721114	654718683	0.000000e+00	3838.0
2	TraesCS4B01G367800	chr4B	87.437	987	86	19	793	1763	654794104	654793140	0.000000e+00	1101.0
3	TraesCS4B01G367800	chr4B	90.940	585	35	9	793	1362	654676599	654676018	0.000000e+00	771.0
4	TraesCS4B01G367800	chr4B	91.429	490	27	3	1945	2432	654781233	654780757	0.000000e+00	658.0
5	TraesCS4B01G367800	chr4B	90.408	490	32	3	1945	2432	654649507	654649031	4.410000e-177	630.0
6	TraesCS4B01G367800	chr4B	84.101	673	76	18	790	1443	654752245	654751585	2.660000e-174	621.0
7	TraesCS4B01G367800	chr4B	83.804	673	78	18	790	1443	654762484	654761824	5.750000e-171	610.0
8	TraesCS4B01G367800	chr4B	83.655	673	79	18	790	1443	654774690	654774030	2.670000e-169	604.0
9	TraesCS4B01G367800	chr4B	88.587	184	18	3	441	622	654794299	654794117	1.130000e-53	220.0
10	TraesCS4B01G367800	chr4B	89.595	173	15	3	452	622	654676783	654676612	1.460000e-52	217.0
11	TraesCS4B01G367800	chr4B	96.774	31	1	0	1666	1696	654560726	654560696	4.000000e-03	52.8
12	TraesCS4B01G367800	chrUn	85.133	1547	134	42	439	1913	154586302	154587824	0.000000e+00	1495.0
13	TraesCS4B01G367800	chrUn	88.406	621	65	4	986	1604	154617347	154617962	0.000000e+00	741.0
14	TraesCS4B01G367800	chrUn	87.342	474	43	9	1960	2431	154619219	154619677	5.960000e-146	527.0
15	TraesCS4B01G367800	chrUn	87.560	418	38	10	2021	2430	154588472	154588883	2.830000e-129	472.0
16	TraesCS4B01G367800	chrUn	85.321	218	19	5	104	313	154585918	154586130	1.890000e-51	213.0
17	TraesCS4B01G367800	chr5A	88.217	1273	90	25	724	1947	692180082	692178821	0.000000e+00	1465.0
18	TraesCS4B01G367800	chr5A	90.654	214	14	3	2224	2432	692178573	692178361	1.840000e-71	279.0
19	TraesCS4B01G367800	chr5A	91.061	179	13	2	1945	2121	692178764	692178587	3.130000e-59	239.0
20	TraesCS4B01G367800	chr1B	79.710	138	18	9	475	604	65708914	65708779	9.260000e-15	91.6

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	TraesCS4B01G367800	chr4B	654591596	654594027	2431	True	4492.000000	4492	100.000000	1	2432	1	chr4B.!!$R2	2431
1	TraesCS4B01G367800	chr4B	654718683	654721114	2431	True	3838.000000	3838	95.188000	1	2432	1	chr4B.!!$R4	2431
2	TraesCS4B01G367800	chr4B	654793140	654794299	1159	True	660.500000	1101	88.012000	441	1763	2	chr4B.!!$R10	1322
3	TraesCS4B01G367800	chr4B	654751585	654752245	660	True	621.000000	621	84.101000	790	1443	1	chr4B.!!$R5	653
4	TraesCS4B01G367800	chr4B	654761824	654762484	660	True	610.000000	610	83.804000	790	1443	1	chr4B.!!$R6	653
5	TraesCS4B01G367800	chr4B	654774030	654774690	660	True	604.000000	604	83.655000	790	1443	1	chr4B.!!$R7	653
6	TraesCS4B01G367800	chr4B	654676018	654676783	765	True	494.000000	771	90.267500	452	1362	2	chr4B.!!$R9	910
7	TraesCS4B01G367800	chrUn	154585918	154588883	2965	False	726.666667	1495	86.004667	104	2430	3	chrUn.!!$F1	2326
8	TraesCS4B01G367800	chrUn	154617347	154619677	2330	False	634.000000	741	87.874000	986	2431	2	chrUn.!!$F2	1445
9	TraesCS4B01G367800	chr5A	692178361	692180082	1721	True	661.000000	1465	89.977333	724	2432	3	chr5A.!!$R1	1708

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
885	1001	2.35361	CGTTACACCCCGGCCTAGT	61.354	63.158	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1799	2027	2.566833	ACATGAAGTAGCAGCCAACA	57.433	45.0	0.0	0.0	0.0	3.33	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
30	31	5.298276	GTGTATTTCCTTTGTCAGTGTTGGA	59.702	40.000	0.00	0.00	0.00	3.53
269	278	4.094294	GCGCTGCCGGATATATTTCAATTA	59.906	41.667	5.05	0.00	34.32	1.40
638	709	3.511540	CCGGGCTAGAATATCATGTCTCA	59.488	47.826	0.00	0.00	0.00	3.27
674	745	4.522405	TGTCGAATTTGTGAACCCATCAAT	59.478	37.500	0.00	0.00	40.50	2.57
675	746	5.707764	TGTCGAATTTGTGAACCCATCAATA	59.292	36.000	0.00	0.00	40.50	1.90
676	747	6.207614	TGTCGAATTTGTGAACCCATCAATAA	59.792	34.615	0.00	0.00	40.50	1.40
713	788	9.747898	ATTGGAGTACATGGAAATTAGTTAACA	57.252	29.630	8.61	0.00	0.00	2.41
760	837	7.007725	ACGCACGTAATATCGTACAATTATAGC	59.992	37.037	0.00	0.47	42.27	2.97
761	838	7.007636	CGCACGTAATATCGTACAATTATAGCA	59.992	37.037	0.00	0.00	42.27	3.49
762	839	8.311822	GCACGTAATATCGTACAATTATAGCAG	58.688	37.037	0.00	0.00	42.27	4.24
763	840	9.338291	CACGTAATATCGTACAATTATAGCAGT	57.662	33.333	0.00	0.00	42.27	4.40
799	879	2.997315	AGCAGCGCTAGTGGTGGA	60.997	61.111	30.56	0.00	36.99	4.02
885	1001	2.353610	CGTTACACCCCGGCCTAGT	61.354	63.158	0.00	0.00	0.00	2.57
1051	1175	0.549950	CATGAACCTGGCCATCCTCT	59.450	55.000	5.51	0.00	0.00	3.69
1476	1619	7.090808	GCATTTCATACTTGCATCATCATCAT	58.909	34.615	0.00	0.00	36.40	2.45
1477	1620	7.273598	GCATTTCATACTTGCATCATCATCATC	59.726	37.037	0.00	0.00	36.40	2.92
1478	1621	7.811117	TTTCATACTTGCATCATCATCATCA	57.189	32.000	0.00	0.00	0.00	3.07
1482	1625	3.188667	ACTTGCATCATCATCATCATCGC	59.811	43.478	0.00	0.00	0.00	4.58
1491	1634	1.193203	CATCATCATCGCCGTACTTGC	59.807	52.381	0.00	0.00	0.00	4.01
1625	1773	5.885230	TCAGGCATTCAGTTAGTCATTTG	57.115	39.130	0.00	0.00	0.00	2.32
1632	1780	5.600908	TTCAGTTAGTCATTTGCCGTTAC	57.399	39.130	0.00	0.00	0.00	2.50
1799	2027	4.221482	TCAGATACACAGCTCTTCACATGT	59.779	41.667	0.00	0.00	0.00	3.21
1938	2961	3.998341	GGCTACGAAGGTATTTCACAACA	59.002	43.478	0.00	0.00	35.43	3.33
2037	3211	6.147656	TGCATACCTATTTATGTTGAGCATCG	59.852	38.462	0.00	0.00	38.94	3.84
2084	3263	0.530870	GCTCTCGTTGGCTGGGTATC	60.531	60.000	0.00	0.00	0.00	2.24
2339	3526	6.550843	TGCAACTTTATGAATATGTTGGTCG	58.449	36.000	0.00	0.00	38.57	4.79
2340	3527	5.971202	GCAACTTTATGAATATGTTGGTCGG	59.029	40.000	0.00	0.00	38.57	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	5.930837	AATTCCAACACTGACAAAGGAAA	57.069	34.783	0.00	0.00	38.50	3.13
30	31	2.283298	CAGCGGTGCTCACAGATAATT	58.717	47.619	0.00	0.00	36.40	1.40
59	60	8.086522	GCCGTCTAATTATTAGTTGATCCTACA	58.913	37.037	11.23	0.00	34.81	2.74
277	286	7.101652	TCATTCTCCTAGAAGACACACATAC	57.898	40.000	0.00	0.00	37.69	2.39
351	388	8.909708	TGAAACAAGATAAGTTTTGACAACAG	57.090	30.769	0.00	0.00	39.15	3.16
607	674	5.905331	TGATATTCTAGCCCGGGATATCATT	59.095	40.000	26.58	14.23	0.00	2.57
638	709	8.465999	TCACAAATTCGACAATAATTTAGGCAT	58.534	29.630	0.00	0.00	35.35	4.40
674	745	9.230122	CCATGTACTCCAATATGCATGTATTTA	57.770	33.333	10.16	0.00	33.85	1.40
675	746	7.944000	TCCATGTACTCCAATATGCATGTATTT	59.056	33.333	10.16	0.00	33.85	1.40
676	747	7.460910	TCCATGTACTCCAATATGCATGTATT	58.539	34.615	10.16	0.00	33.85	1.89
713	788	7.971722	GTGCGTACCATTATTGGAGTTTAAAAT	59.028	33.333	10.62	0.00	46.92	1.82
760	837	8.604640	TGCTGCTACTATTAGTACTACTACTG	57.395	38.462	0.91	0.00	34.79	2.74
761	838	7.388500	GCTGCTGCTACTATTAGTACTACTACT	59.612	40.741	8.53	0.00	35.32	2.57
762	839	7.520686	GCTGCTGCTACTATTAGTACTACTAC	58.479	42.308	8.53	0.00	36.03	2.73
763	840	6.368243	CGCTGCTGCTACTATTAGTACTACTA	59.632	42.308	14.03	0.72	36.97	1.82
764	841	5.179742	CGCTGCTGCTACTATTAGTACTACT	59.820	44.000	14.03	0.00	36.97	2.57
765	842	5.383958	CGCTGCTGCTACTATTAGTACTAC	58.616	45.833	14.03	0.00	36.97	2.73
774	854	1.000827	CACTAGCGCTGCTGCTACTAT	60.001	52.381	22.90	7.71	45.14	2.12
885	1001	4.957327	GGTTGCTTGGGGTGGTATTTATAA	59.043	41.667	0.00	0.00	0.00	0.98
1010	1134	1.608717	GAGGAAGAGGGCGAGCTTGA	61.609	60.000	4.70	0.00	0.00	3.02
1476	1619	1.732941	AATTGCAAGTACGGCGATGA	58.267	45.000	16.62	0.00	35.57	2.92
1477	1620	2.350192	TGTAATTGCAAGTACGGCGATG	59.650	45.455	26.48	8.15	35.57	3.84
1478	1621	2.623535	TGTAATTGCAAGTACGGCGAT	58.376	42.857	26.48	8.88	36.95	4.58
1482	1625	6.861055	AGAAAACATTGTAATTGCAAGTACGG	59.139	34.615	26.48	21.09	32.52	4.02
1491	1634	7.900864	TGCGTATACGAGAAAACATTGTAATTG	59.099	33.333	28.66	0.00	43.02	2.32
1551	1699	2.570442	TGCACGCGACTGACATATAA	57.430	45.000	15.93	0.00	0.00	0.98
1607	1755	3.119849	ACGGCAAATGACTAACTGAATGC	60.120	43.478	0.00	0.00	0.00	3.56
1608	1756	4.685169	ACGGCAAATGACTAACTGAATG	57.315	40.909	0.00	0.00	0.00	2.67
1609	1757	5.163893	CGTAACGGCAAATGACTAACTGAAT	60.164	40.000	0.00	0.00	0.00	2.57
1610	1758	4.150980	CGTAACGGCAAATGACTAACTGAA	59.849	41.667	0.00	0.00	0.00	3.02
1611	1759	3.676172	CGTAACGGCAAATGACTAACTGA	59.324	43.478	0.00	0.00	0.00	3.41
1612	1760	3.181524	CCGTAACGGCAAATGACTAACTG	60.182	47.826	0.00	0.00	41.17	3.16
1613	1761	2.997986	CCGTAACGGCAAATGACTAACT	59.002	45.455	0.00	0.00	41.17	2.24
1614	1762	3.378959	CCGTAACGGCAAATGACTAAC	57.621	47.619	0.00	0.00	41.17	2.34
1632	1780	6.600427	ACCCTTTTACAAATACTGGAATACCG	59.400	38.462	0.00	0.00	39.42	4.02
1640	1833	8.067784	CGCACATATACCCTTTTACAAATACTG	58.932	37.037	0.00	0.00	0.00	2.74
1799	2027	2.566833	ACATGAAGTAGCAGCCAACA	57.433	45.000	0.00	0.00	0.00	3.33
1861	2096	5.342433	GTGGCAAGTTTAAAAACGTTACCT	58.658	37.500	0.00	0.00	43.51	3.08
2084	3263	9.971744	ATTTCATTTTTCAAACTTTTTCGAGTG	57.028	25.926	0.00	0.00	0.00	3.51
2121	3303	6.387220	AGGGCTTTGTAGGATATTGTTCTACT	59.613	38.462	1.16	0.00	35.63	2.57
2140	3322	8.829373	AGTAATTCATTCATCTAAAAGGGCTT	57.171	30.769	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.