AutoCloner

Multiple sequence alignment - TraesCS2D01G438500

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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	TraesCS2D01G438500	chr2D	100.000	2318	0	0	1	2318	547952868	547950551	0.000000e+00	4281
1	TraesCS2D01G438500	chr2D	95.054	2325	100	9	1	2317	547807430	547805113	0.000000e+00	3642
2	TraesCS2D01G438500	chr2D	83.519	1796	215	53	333	2075	547791942	547790175	0.000000e+00	1602
3	TraesCS2D01G438500	chr2D	81.364	220	23	11	2099	2315	547790038	547789834	1.840000e-36	163
4	TraesCS2D01G438500	chr2A	89.280	2360	177	32	1	2317	691115091	691117417	0.000000e+00	2887
5	TraesCS2D01G438500	chr2A	87.256	973	76	20	1367	2317	691134199	691135145	0.000000e+00	1066
6	TraesCS2D01G438500	chr2A	86.056	251	35	0	79	329	69311213	69310963	1.060000e-68	270
7	TraesCS2D01G438500	chr2A	82.700	237	26	10	2082	2316	691170267	691170490	1.820000e-46	196
8	TraesCS2D01G438500	chr2B	92.665	1677	103	10	647	2317	654653562	654651900	0.000000e+00	2398
9	TraesCS2D01G438500	chr2B	92.546	1677	105	10	647	2317	654703665	654702003	0.000000e+00	2386
10	TraesCS2D01G438500	chr2B	92.431	1678	106	11	647	2317	654681833	654680170	0.000000e+00	2375
11	TraesCS2D01G438500	chr2B	91.892	1184	75	11	1141	2317	654730650	654729481	0.000000e+00	1635
12	TraesCS2D01G438500	chr2B	83.298	1413	162	44	333	1693	654649920	654648530	0.000000e+00	1234
13	TraesCS2D01G438500	chr2B	89.579	499	33	5	1	483	654656741	654656246	1.180000e-172	616
14	TraesCS2D01G438500	chr2B	89.379	499	33	6	1	483	654735772	654735278	5.480000e-171	610
15	TraesCS2D01G438500	chr2B	89.178	499	35	5	1	483	654685013	654684518	2.550000e-169	604
16	TraesCS2D01G438500	chr2B	89.178	499	35	5	1	483	654706847	654706352	2.550000e-169	604
17	TraesCS2D01G438500	chr2B	89.444	180	10	7	470	645	654705119	654704945	3.880000e-53	219
18	TraesCS2D01G438500	chr2B	88.889	180	11	7	470	645	654683287	654683113	1.800000e-51	213
19	TraesCS2D01G438500	chr2B	88.333	180	12	7	470	645	654655016	654654842	8.390000e-50	207
20	TraesCS2D01G438500	chrUn	92.546	1677	105	11	647	2317	248126996	248125334	0.000000e+00	2386
21	TraesCS2D01G438500	chrUn	83.439	1413	160	44	333	1693	248123355	248121965	0.000000e+00	1245
22	TraesCS2D01G438500	chrUn	89.579	499	33	5	1	483	248130176	248129681	1.180000e-172	616
23	TraesCS2D01G438500	chrUn	88.889	180	11	7	470	645	248128450	248128276	1.800000e-51	213
24	TraesCS2D01G438500	chr5B	85.938	256	34	2	75	329	527760360	527760614	2.930000e-69	272

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	TraesCS2D01G438500	chr2D	547950551	547952868	2317	True	4281.000000	4281	100.000000	1	2318	1	chr2D.!!$R2	2317
1	TraesCS2D01G438500	chr2D	547805113	547807430	2317	True	3642.000000	3642	95.054000	1	2317	1	chr2D.!!$R1	2316
2	TraesCS2D01G438500	chr2D	547789834	547791942	2108	True	882.500000	1602	82.441500	333	2315	2	chr2D.!!$R3	1982
3	TraesCS2D01G438500	chr2A	691115091	691117417	2326	False	2887.000000	2887	89.280000	1	2317	1	chr2A.!!$F1	2316
4	TraesCS2D01G438500	chr2A	691134199	691135145	946	False	1066.000000	1066	87.256000	1367	2317	1	chr2A.!!$F2	950
5	TraesCS2D01G438500	chr2B	654729481	654730650	1169	True	1635.000000	1635	91.892000	1141	2317	1	chr2B.!!$R1	1176
6	TraesCS2D01G438500	chr2B	654648530	654656741	8211	True	1113.750000	2398	88.468750	1	2317	4	chr2B.!!$R3	2316
7	TraesCS2D01G438500	chr2B	654702003	654706847	4844	True	1069.666667	2386	90.389333	1	2317	3	chr2B.!!$R5	2316
8	TraesCS2D01G438500	chr2B	654680170	654685013	4843	True	1064.000000	2375	90.166000	1	2317	3	chr2B.!!$R4	2316
9	TraesCS2D01G438500	chrUn	248121965	248130176	8211	True	1115.000000	2386	88.613250	1	2317	4	chrUn.!!$R1	2316

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
532	1811	0.525761	TGCTTGCCTTAATCGTTGGC	59.474	50.0	0.0	0.0	46.26	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1898	4527	0.694444	TCCTGGTAGGATGCTTCCCC	60.694	60.0	14.77	10.45	40.06	4.81	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
532	1811	0.525761	TGCTTGCCTTAATCGTTGGC	59.474	50.000	0.00	0.00	46.26	4.52
601	1887	9.986833	TTCTCTTTTGCAAAATTCTTTTAAAGC	57.013	25.926	24.06	0.00	0.00	3.51
643	1930	4.385748	GTGGGCAAATCGAAAAATCACTTC	59.614	41.667	0.00	0.00	0.00	3.01
662	3229	6.042777	CACTTCCTATCATTGCGAAGAACTA	58.957	40.000	2.86	0.00	36.16	2.24
755	3350	3.416119	TGGTAGTCGTTATCGCTCAAG	57.584	47.619	0.00	0.00	36.96	3.02
874	3470	7.566760	AAATACACACTTCATGAACACAGAA	57.433	32.000	3.38	0.00	0.00	3.02
886	3483	1.078143	CACAGAAGCCTGCCCCTAC	60.078	63.158	0.00	0.00	44.16	3.18
887	3484	1.229658	ACAGAAGCCTGCCCCTACT	60.230	57.895	0.00	0.00	44.16	2.57
942	3539	4.100808	ACATTTCCAAAGCAAAACCTAGCA	59.899	37.500	0.00	0.00	0.00	3.49
947	3544	4.588528	TCCAAAGCAAAACCTAGCAAAGAT	59.411	37.500	0.00	0.00	0.00	2.40
1252	3851	2.637382	TGGCTGAGAAAGTACCACATCA	59.363	45.455	0.00	0.00	0.00	3.07
1260	3859	4.518970	AGAAAGTACCACATCAACGCAAAT	59.481	37.500	0.00	0.00	0.00	2.32
1313	3912	0.760189	ACCATGCCCAACAACTGCTT	60.760	50.000	0.00	0.00	0.00	3.91
1353	3954	3.928754	ACCCATAAGCATCTAGGAGTCA	58.071	45.455	0.00	0.00	0.00	3.41
1519	4142	2.811431	CGAAGTGTAAGGATGGCAAACA	59.189	45.455	0.00	0.00	0.00	2.83
1592	4215	5.406780	TCGTGTCAAAAAGTTGCATGTTTTT	59.593	32.000	11.58	11.58	36.51	1.94
1619	4242	6.146184	AGTGAACAAGTAAATGACGATCACAG	59.854	38.462	0.00	0.00	0.00	3.66
1640	4265	4.154195	CAGTTTTTCCCTATTGGTCACTCG	59.846	45.833	0.00	0.00	34.77	4.18
1651	4276	7.713507	CCCTATTGGTCACTCGTAAATAAATCA	59.286	37.037	0.00	0.00	0.00	2.57
1652	4277	8.765219	CCTATTGGTCACTCGTAAATAAATCAG	58.235	37.037	0.00	0.00	0.00	2.90
1758	4384	5.104374	AGAAAATGCAGCCAATGTTTATCG	58.896	37.500	0.00	0.00	0.00	2.92
1760	4386	3.698029	ATGCAGCCAATGTTTATCGTC	57.302	42.857	0.00	0.00	0.00	4.20
1781	4407	8.301730	TCGTCAGAAAACATAAACGTCTTATT	57.698	30.769	0.00	0.00	0.00	1.40
1797	4423	7.434492	ACGTCTTATTGTATCTAATGGACTGG	58.566	38.462	0.00	0.00	0.00	4.00
1898	4527	7.307493	TCATTCAGAATTTCAAGGTGATACG	57.693	36.000	0.00	0.00	0.00	3.06
1940	4571	4.822026	ACTAGTAAACAGACATGTGCTCC	58.178	43.478	1.15	0.00	40.39	4.70
1961	4592	3.999663	CCAATACTAGCAGATAAGGCAGC	59.000	47.826	0.00	0.00	0.00	5.25
1980	4611	4.276678	GCAGCACTCCTGATTTGCATAATA	59.723	41.667	0.00	0.00	44.64	0.98
2097	4842	6.912426	TCATCTATAGGTACTTGTGAGGACT	58.088	40.000	0.00	0.00	41.75	3.85
2138	4897	2.244695	CCCATGCCATGTGCTCATATT	58.755	47.619	3.63	0.00	42.00	1.28
2192	4951	3.298686	TGGTTGTTGGGTCACACAATA	57.701	42.857	0.00	0.00	0.00	1.90
2193	4952	3.838565	TGGTTGTTGGGTCACACAATAT	58.161	40.909	0.00	0.00	0.00	1.28
2194	4953	4.219115	TGGTTGTTGGGTCACACAATATT	58.781	39.130	0.00	0.00	0.00	1.28
2195	4954	4.651503	TGGTTGTTGGGTCACACAATATTT	59.348	37.500	0.00	0.00	0.00	1.40
2196	4955	5.833667	TGGTTGTTGGGTCACACAATATTTA	59.166	36.000	0.00	0.00	0.00	1.40
2197	4956	6.323996	TGGTTGTTGGGTCACACAATATTTAA	59.676	34.615	0.00	0.00	0.00	1.52
2198	4957	7.015682	TGGTTGTTGGGTCACACAATATTTAAT	59.984	33.333	0.00	0.00	0.00	1.40
2199	4958	8.524487	GGTTGTTGGGTCACACAATATTTAATA	58.476	33.333	0.00	0.00	0.00	0.98
2229	4990	1.577736	AGTGTGGGAAGAGAGATGGG	58.422	55.000	0.00	0.00	0.00	4.00
2284	5045	1.819903	AGGAGTGGAGCTTAGTCGTTC	59.180	52.381	0.00	0.00	0.00	3.95
2317	5078	6.712179	TTTCAGCATGCCACATATTCAATA	57.288	33.333	15.66	0.00	34.76	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
302	304	9.275398	TCCGTTTTTATTTACTCCGCATATTAT	57.725	29.630	0.00	0.00	0.00	1.28
643	1930	5.837437	AGACTAGTTCTTCGCAATGATAGG	58.163	41.667	0.00	0.00	0.00	2.57
662	3229	4.822026	AGAGTACGCTGCAAATTAAGACT	58.178	39.130	0.00	0.00	0.00	3.24
755	3350	5.429957	AAAATCTGCACTTGAACTCACTC	57.570	39.130	0.00	0.00	0.00	3.51
874	3470	2.896039	CTCTATTAGTAGGGGCAGGCT	58.104	52.381	0.00	0.00	0.00	4.58
886	3483	7.498900	TGAATGTTTGGTGTATGGCTCTATTAG	59.501	37.037	0.00	0.00	0.00	1.73
887	3484	7.342581	TGAATGTTTGGTGTATGGCTCTATTA	58.657	34.615	0.00	0.00	0.00	0.98
942	3539	7.501892	GGATTGCTAGAGGAGATTTTGATCTTT	59.498	37.037	0.00	0.00	0.00	2.52
947	3544	5.190528	AGTGGATTGCTAGAGGAGATTTTGA	59.809	40.000	0.00	0.00	0.00	2.69
1285	3884	4.101448	GGGCATGGTGAGACCGCT	62.101	66.667	0.00	0.00	42.58	5.52
1313	3912	3.572682	GGGTAGTACATCCGATCATCACA	59.427	47.826	2.06	0.00	0.00	3.58
1353	3954	2.428530	TCGATGCAGATGTAGAGCAACT	59.571	45.455	0.00	0.00	42.15	3.16
1498	4121	2.811431	TGTTTGCCATCCTTACACTTCG	59.189	45.455	0.00	0.00	0.00	3.79
1519	4142	7.880577	ATTCATGGGAATAACATGCAAGGCAT	61.881	38.462	0.00	0.00	44.95	4.40
1556	4179	1.934589	TGACACGAAAGACACCACTG	58.065	50.000	0.00	0.00	0.00	3.66
1566	4189	4.489810	ACATGCAACTTTTTGACACGAAA	58.510	34.783	0.00	0.00	34.24	3.46
1592	4215	7.654116	TGTGATCGTCATTTACTTGTTCACTAA	59.346	33.333	0.00	0.00	0.00	2.24
1619	4242	4.070009	ACGAGTGACCAATAGGGAAAAAC	58.930	43.478	0.00	0.00	41.15	2.43
1651	4276	9.606631	GGACAATCTTCTTGATAGTTGATTACT	57.393	33.333	0.00	0.00	41.04	2.24
1652	4277	8.543774	CGGACAATCTTCTTGATAGTTGATTAC	58.456	37.037	0.00	0.00	34.45	1.89
1770	4396	9.314321	CAGTCCATTAGATACAATAAGACGTTT	57.686	33.333	0.00	0.00	30.91	3.60
1781	4407	4.019771	TGTTGTGCCAGTCCATTAGATACA	60.020	41.667	0.00	0.00	0.00	2.29
1787	4413	1.073763	AGCTGTTGTGCCAGTCCATTA	59.926	47.619	0.00	0.00	34.84	1.90
1797	4423	2.232452	TCTAGAAGGAGAGCTGTTGTGC	59.768	50.000	0.00	0.00	0.00	4.57
1844	4473	8.230486	GCGATGCTATATGTTTGCTAATAAGTT	58.770	33.333	0.00	0.00	0.00	2.66
1898	4527	0.694444	TCCTGGTAGGATGCTTCCCC	60.694	60.000	14.77	10.45	40.06	4.81
1940	4571	4.450419	GTGCTGCCTTATCTGCTAGTATTG	59.550	45.833	0.00	0.00	32.95	1.90
1953	4584	2.715046	CAAATCAGGAGTGCTGCCTTA	58.285	47.619	6.80	0.00	32.12	2.69
2097	4842	4.083003	GGGCATTTTCGTATTGTTGTGAGA	60.083	41.667	0.00	0.00	0.00	3.27
2196	4955	9.853177	CTCTTCCCACACTTAAATAGGAATATT	57.147	33.333	0.00	0.00	33.17	1.28
2197	4956	9.225682	TCTCTTCCCACACTTAAATAGGAATAT	57.774	33.333	0.00	0.00	33.17	1.28
2198	4957	8.618240	TCTCTTCCCACACTTAAATAGGAATA	57.382	34.615	0.00	0.00	33.17	1.75
2199	4958	7.403231	TCTCTCTTCCCACACTTAAATAGGAAT	59.597	37.037	0.00	0.00	33.17	3.01
2229	4990	2.991250	TGGCTTCTTAGAGTCATTGCC	58.009	47.619	0.00	0.00	39.53	4.52
2284	5045	2.360165	GGCATGCTGAAATGAACCTAGG	59.640	50.000	18.92	7.41	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.