AutoCloner

Multiple sequence alignment - TraesCS5D01G164100

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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	TraesCS5D01G164100	chr5D	100.000	3113	0	0	1	3113	255597758	255594646	0.000000e+00	5749
1	TraesCS5D01G164100	chr5D	93.863	717	39	5	1	712	528874647	528875363	0.000000e+00	1075
2	TraesCS5D01G164100	chr5A	95.812	2340	80	11	1	2336	338926758	338924433	0.000000e+00	3762
3	TraesCS5D01G164100	chr5A	95.072	345	14	2	2336	2678	338924391	338924048	9.820000e-150	540
4	TraesCS5D01G164100	chr5A	91.421	373	22	5	2743	3111	338923083	338922717	1.290000e-138	503
5	TraesCS5D01G164100	chr5A	97.222	72	2	0	2677	2748	338923190	338923119	4.220000e-24	122
6	TraesCS5D01G164100	chr5B	94.459	1534	66	11	810	2337	289259297	289257777	0.000000e+00	2344
7	TraesCS5D01G164100	chr5B	95.204	417	16	2	2336	2748	289257736	289257320	0.000000e+00	656
8	TraesCS5D01G164100	chr5B	97.059	374	8	3	2743	3113	289257283	289256910	7.330000e-176	627
9	TraesCS5D01G164100	chr6A	92.479	718	46	8	2	712	569966544	569965828	0.000000e+00	1020
10	TraesCS5D01G164100	chr6B	92.490	719	39	14	1	712	640672561	640671851	0.000000e+00	1014
11	TraesCS5D01G164100	chr6B	91.108	731	47	12	1	724	300963440	300964159	0.000000e+00	974
12	TraesCS5D01G164100	chr6B	90.575	626	54	4	1	622	367972332	367971708	0.000000e+00	824
13	TraesCS5D01G164100	chr7B	91.771	717	53	6	1	713	54786527	54787241	0.000000e+00	992
14	TraesCS5D01G164100	chr6D	93.559	621	31	7	1	618	403036590	403037204	0.000000e+00	917
15	TraesCS5D01G164100	chr4A	86.778	658	57	16	88	715	679261806	679261149	0.000000e+00	706
16	TraesCS5D01G164100	chr2A	82.615	719	70	25	974	1686	713367032	713366363	4.470000e-163	584
17	TraesCS5D01G164100	chr7D	91.864	295	21	3	1	293	177874735	177874442	2.890000e-110	409

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	TraesCS5D01G164100	chr5D	255594646	255597758	3112	True	5749.00	5749	100.00000	1	3113	1	chr5D.!!$R1	3112
1	TraesCS5D01G164100	chr5D	528874647	528875363	716	False	1075.00	1075	93.86300	1	712	1	chr5D.!!$F1	711
2	TraesCS5D01G164100	chr5A	338922717	338926758	4041	True	1231.75	3762	94.88175	1	3111	4	chr5A.!!$R1	3110
3	TraesCS5D01G164100	chr5B	289256910	289259297	2387	True	1209.00	2344	95.57400	810	3113	3	chr5B.!!$R1	2303
4	TraesCS5D01G164100	chr6A	569965828	569966544	716	True	1020.00	1020	92.47900	2	712	1	chr6A.!!$R1	710
5	TraesCS5D01G164100	chr6B	640671851	640672561	710	True	1014.00	1014	92.49000	1	712	1	chr6B.!!$R2	711
6	TraesCS5D01G164100	chr6B	300963440	300964159	719	False	974.00	974	91.10800	1	724	1	chr6B.!!$F1	723
7	TraesCS5D01G164100	chr6B	367971708	367972332	624	True	824.00	824	90.57500	1	622	1	chr6B.!!$R1	621
8	TraesCS5D01G164100	chr7B	54786527	54787241	714	False	992.00	992	91.77100	1	713	1	chr7B.!!$F1	712
9	TraesCS5D01G164100	chr6D	403036590	403037204	614	False	917.00	917	93.55900	1	618	1	chr6D.!!$F1	617
10	TraesCS5D01G164100	chr4A	679261149	679261806	657	True	706.00	706	86.77800	88	715	1	chr4A.!!$R1	627
11	TraesCS5D01G164100	chr2A	713366363	713367032	669	True	584.00	584	82.61500	974	1686	1	chr2A.!!$R1	712

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
916	968	1.118965	TCGGCCACTCCTCTTTGACA	61.119	55.0	2.24	0.0	0.0	3.58	F
1845	1900	0.470268	ATAGGAAGAGGCGGAGGACC	60.470	60.0	0.00	0.0	0.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1968	2023	1.153539	TTCTTCCATGTGGGGGTTCA	58.846	50.0	0.0	0.0	37.22	3.18	R
2994	3999	0.252197	AATGTACCTCCCAAGTCCGC	59.748	55.0	0.0	0.0	0.00	5.54	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
120	124	6.581171	ATTTCTTTGACCAACTTCAGGATC	57.419	37.500	0.00	0.00	0.00	3.36
141	145	9.258629	AGGATCATGTTTTCCTCAATTCATTAA	57.741	29.630	8.27	0.00	37.89	1.40
603	647	4.022068	TCAATGTTGGTGCTCAAGAATTCC	60.022	41.667	0.65	0.00	35.80	3.01
629	673	7.290813	GGAAAGTTCTATTATGTCCCCATTCT	58.709	38.462	0.00	0.00	32.29	2.40
771	819	6.705863	ATTTCTGCTCATTTCCTATGAACC	57.294	37.500	0.00	0.00	0.00	3.62
786	834	1.162698	GAACCGAACTGGGCCTAAAC	58.837	55.000	4.53	0.00	44.64	2.01
837	889	3.253432	GCCCAAATAGAATTCGGCCTAAG	59.747	47.826	0.00	0.00	0.00	2.18
874	926	4.457466	TCCGCATATGACGCCTATAGATA	58.543	43.478	6.97	0.00	0.00	1.98
916	968	1.118965	TCGGCCACTCCTCTTTGACA	61.119	55.000	2.24	0.00	0.00	3.58
929	981	1.665679	CTTTGACATCCACCCGATTCG	59.334	52.381	0.00	0.00	0.00	3.34
1124	1176	2.652095	CCTACGCCCCCGAGAACAA	61.652	63.158	0.00	0.00	38.29	2.83
1125	1177	1.447314	CTACGCCCCCGAGAACAAC	60.447	63.158	0.00	0.00	38.29	3.32
1126	1178	2.162338	CTACGCCCCCGAGAACAACA	62.162	60.000	0.00	0.00	38.29	3.33
1596	1648	2.975799	GAACGGGAGCGTGCCAAA	60.976	61.111	0.00	0.00	0.00	3.28
1682	1737	1.139853	GGGAAGATCGAAGCACAGGAT	59.860	52.381	0.00	0.00	0.00	3.24
1805	1860	4.016444	GAGAGTGACTCTGACAGGAAGAT	58.984	47.826	21.45	0.00	41.35	2.40
1845	1900	0.470268	ATAGGAAGAGGCGGAGGACC	60.470	60.000	0.00	0.00	0.00	4.46
1968	2023	1.276421	GGTAGTGACAGTGATGGCAGT	59.724	52.381	0.00	0.00	34.37	4.40
1972	2027	1.532868	GTGACAGTGATGGCAGTGAAC	59.467	52.381	7.64	2.67	46.24	3.18
1982	2037	1.978617	GCAGTGAACCCCCACATGG	60.979	63.158	0.00	0.00	39.42	3.66
1986	2041	0.404040	GTGAACCCCCACATGGAAGA	59.596	55.000	0.00	0.00	37.04	2.87
1998	2053	1.332997	CATGGAAGAAAGCGATCCAGC	59.667	52.381	0.00	0.00	45.82	4.85
2002	2057	2.350522	GAAGAAAGCGATCCAGCAAGA	58.649	47.619	0.00	0.00	40.15	3.02
2028	2083	1.771255	AGCCACAAGAGGTCAGAAAGT	59.229	47.619	0.00	0.00	0.00	2.66
2033	2088	4.384056	CACAAGAGGTCAGAAAGTCATGT	58.616	43.478	0.00	0.00	0.00	3.21
2091	2146	1.319614	GCCGCTCTGGAGAGAAGAGT	61.320	60.000	7.89	0.00	44.74	3.24
2093	2148	2.370349	CCGCTCTGGAGAGAAGAGTAA	58.630	52.381	7.89	0.00	44.74	2.24
2150	2205	3.555547	CGGTAAATTGCACTCATCGATGA	59.444	43.478	25.80	25.80	35.16	2.92
2165	2220	8.097811	CTCATCGATGATTGCAACAGTGCTTA	62.098	42.308	27.43	0.11	42.91	3.09
2264	2319	0.819259	TGCTTGTCAGTGGCTGAACC	60.819	55.000	0.00	0.00	42.46	3.62
2352	2449	7.611213	TCTTTCAAAGGTAGCTTTAGCATAC	57.389	36.000	18.94	4.14	45.16	2.39
2433	2532	4.944317	GGCCTTGTATAAAGCTCTTCAGTT	59.056	41.667	0.00	0.00	0.00	3.16
2450	2549	6.271391	TCTTCAGTTATCAGGTGGTAAAAGGA	59.729	38.462	0.00	0.00	0.00	3.36
2541	2640	1.135431	TGCAAATTCATGTGCCGTAGC	60.135	47.619	3.81	0.00	40.14	3.58
2548	2647	0.738063	CATGTGCCGTAGCCACGTAA	60.738	55.000	3.55	0.00	46.96	3.18
2579	2680	5.063438	CGGTACTGACACATATTTGGTCAAG	59.937	44.000	0.00	0.00	40.67	3.02
2722	3682	9.959749	TTTGTACCAATTTCTTTGATGTCTAAC	57.040	29.630	0.00	0.00	37.53	2.34
2799	3801	7.088905	GCATGACAAGAATTTGATCTTCTGTT	58.911	34.615	0.00	0.00	37.56	3.16
2924	3929	7.011482	AGTGACTTTAGTCTGCAGTTTAACTTG	59.989	37.037	14.67	6.39	44.99	3.16
2930	3935	3.004734	GTCTGCAGTTTAACTTGCATGGT	59.995	43.478	14.67	0.00	33.91	3.55
2977	3982	2.626840	GGAGTGATCTCTTTCCTGCAC	58.373	52.381	0.00	0.00	40.29	4.57
3048	4053	2.234143	AGCCTTCTTTTGCACCTCTTC	58.766	47.619	0.00	0.00	0.00	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	8.215736	TCACATCATTCCATGAGAAGTTGATAT	58.784	33.333	0.00	0.00	43.53	1.63
43	45	6.656632	TTTGCCCACATTGTAAACATCTAA	57.343	33.333	0.00	0.00	0.00	2.10
141	145	6.092944	TGTGATATTTTTGTTCCGAGCGTATT	59.907	34.615	0.00	0.00	0.00	1.89
383	425	0.105964	TCACAGGACCGAGGTTGTTG	59.894	55.000	0.00	0.00	0.00	3.33
603	647	5.031066	TGGGGACATAATAGAACTTTCCG	57.969	43.478	0.00	0.00	33.40	4.30
686	734	2.591129	AAATATGCCCGTGCGTTGCG	62.591	55.000	0.00	0.00	41.78	4.85
743	791	8.668510	TCATAGGAAATGAGCAGAAATAAGAC	57.331	34.615	0.00	0.00	0.00	3.01
771	819	2.736682	CGCGTTTAGGCCCAGTTCG	61.737	63.158	0.00	0.00	0.00	3.95
874	926	4.193090	CTCGTGTACTACTCTCTGGACAT	58.807	47.826	0.00	0.00	0.00	3.06
929	981	1.626388	GATGTCTTTCGAGCGACGC	59.374	57.895	13.03	13.03	42.26	5.19
935	987	2.474816	GAATCGGGGATGTCTTTCGAG	58.525	52.381	0.00	0.00	33.32	4.04
1124	1176	2.914097	GGGCCTGCTGCTTGTTGT	60.914	61.111	0.84	0.00	40.92	3.32
1125	1177	3.688159	GGGGCCTGCTGCTTGTTG	61.688	66.667	0.84	0.00	40.92	3.33
1287	1339	0.323087	TCTCGTCGGAGTTGGATCCA	60.323	55.000	11.44	11.44	41.26	3.41
1596	1648	4.394712	CGCTTCCCTCCACGGCTT	62.395	66.667	0.00	0.00	0.00	4.35
1682	1737	1.342496	CACTGTCACTCTTCCTGCTCA	59.658	52.381	0.00	0.00	0.00	4.26
1805	1860	3.239449	TCTTTCCTACTCTTCCTGTGCA	58.761	45.455	0.00	0.00	0.00	4.57
1845	1900	2.608970	AATCATCCTTCCGGCGGTGG	62.609	60.000	27.32	26.67	0.00	4.61
1872	1927	3.064773	TCCCCTCCAGATTCATCATCA	57.935	47.619	0.00	0.00	33.75	3.07
1968	2023	1.153539	TTCTTCCATGTGGGGGTTCA	58.846	50.000	0.00	0.00	37.22	3.18
1972	2027	1.315257	CGCTTTCTTCCATGTGGGGG	61.315	60.000	0.00	0.00	37.22	5.40
1982	2037	2.350522	TCTTGCTGGATCGCTTTCTTC	58.649	47.619	0.00	0.00	0.00	2.87
1986	2041	2.479566	TCTTCTTGCTGGATCGCTTT	57.520	45.000	0.00	0.00	0.00	3.51
1998	2053	3.072944	CCTCTTGTGGCTCTTCTTCTTG	58.927	50.000	0.00	0.00	0.00	3.02
2002	2057	2.038295	CTGACCTCTTGTGGCTCTTCTT	59.962	50.000	0.00	0.00	0.00	2.52
2028	2083	3.181451	GCTCATCCTCACCCAATACATGA	60.181	47.826	0.00	0.00	0.00	3.07
2033	2088	1.412710	GTCGCTCATCCTCACCCAATA	59.587	52.381	0.00	0.00	0.00	1.90
2091	2146	2.496679	AGCCCCTCTTATGCTCCTTA	57.503	50.000	0.00	0.00	0.00	2.69
2093	2148	2.496679	TTAGCCCCTCTTATGCTCCT	57.503	50.000	0.00	0.00	36.57	3.69
2165	2220	9.480053	CATTTGACAAGACAAATAACAAAGGAT	57.520	29.630	9.47	0.00	45.00	3.24
2247	2302	3.402186	TGGTTCAGCCACTGACAAG	57.598	52.632	0.00	0.00	43.61	3.16
2264	2319	7.490079	GCAACACCATTTATGCATATATGGATG	59.510	37.037	40.19	34.53	41.52	3.51
2352	2449	8.939929	CCATCACTGCAATATTATAGTTAGTGG	58.060	37.037	11.33	6.53	36.03	4.00
2433	2532	6.391649	ACCCAATATCCTTTTACCACCTGATA	59.608	38.462	0.00	0.00	0.00	2.15
2450	2549	6.212840	TGCATAAGTTATCCCACCCAATAT	57.787	37.500	0.00	0.00	0.00	1.28
2541	2640	5.806502	TGTCAGTACCGATTTTATTACGTGG	59.193	40.000	0.00	0.00	0.00	4.94
2548	2647	8.836413	CCAAATATGTGTCAGTACCGATTTTAT	58.164	33.333	0.00	0.00	0.00	1.40
2589	2690	9.788889	ATAAATCAGCTGATATCAAATCAGACA	57.211	29.630	28.92	0.00	46.25	3.41
2722	3682	4.885907	ACCCAATGCTACATTGATTCAGAG	59.114	41.667	19.24	3.46	0.00	3.35
2799	3801	5.298989	AGCCGTAACATATACCAAATCCA	57.701	39.130	0.00	0.00	0.00	3.41
2924	3929	3.343941	TGGTGGAGTAACTTACCATGC	57.656	47.619	0.00	0.00	38.23	4.06
2930	3935	5.989477	CCATGAGATTGGTGGAGTAACTTA	58.011	41.667	0.00	0.00	34.94	2.24
2977	3982	2.032377	TCCGCACTTCAAACGCTTAAAG	60.032	45.455	0.00	0.00	0.00	1.85
2994	3999	0.252197	AATGTACCTCCCAAGTCCGC	59.748	55.000	0.00	0.00	0.00	5.54
3048	4053	3.260884	TCTTAGGCAAGTAGTGGAACCTG	59.739	47.826	0.00	0.00	32.77	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.