AutoCloner

Multiple sequence alignment - TraesCS5B01G197500

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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	TraesCS5B01G197500	chr5B	100.000	2968	0	0	1	2968	356214053	356217020	0.000000e+00	5481.0
1	TraesCS5B01G197500	chr5D	93.647	2865	130	22	139	2968	310257965	310260812	0.000000e+00	4235.0
2	TraesCS5B01G197500	chr5D	92.466	146	4	3	7	150	310257802	310257942	5.020000e-48	202.0
3	TraesCS5B01G197500	chr5A	91.088	3052	151	38	7	2968	403755380	403758400	0.000000e+00	4017.0
4	TraesCS5B01G197500	chr5A	82.222	315	42	7	1348	1655	663769431	663769124	2.930000e-65	259.0
5	TraesCS5B01G197500	chr5A	100.000	29	0	0	878	906	382104453	382104481	1.000000e-03	54.7
6	TraesCS5B01G197500	chr4D	76.801	569	86	31	1107	1655	483837733	483837191	8.100000e-71	278.0
7	TraesCS5B01G197500	chr4B	82.166	314	44	6	1348	1655	614280289	614279982	2.930000e-65	259.0
8	TraesCS5B01G197500	chr4B	84.286	70	7	3	2819	2885	428024891	428024823	6.870000e-07	65.8
9	TraesCS5B01G197500	chr4A	82.812	256	39	4	2715	2968	31611196	31610944	1.070000e-54	224.0
10	TraesCS5B01G197500	chr1B	77.232	224	36	8	2753	2968	662462990	662462774	1.870000e-22	117.0
11	TraesCS5B01G197500	chr6D	81.897	116	18	3	2819	2931	335377911	335378026	8.760000e-16	95.3
12	TraesCS5B01G197500	chr7A	79.851	134	21	4	2752	2884	132577705	132577833	3.150000e-15	93.5
13	TraesCS5B01G197500	chr1A	83.516	91	11	4	2790	2878	514254823	514254911	6.820000e-12	82.4
14	TraesCS5B01G197500	chr2B	81.373	102	11	7	2834	2931	603401674	603401771	3.170000e-10	76.8

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	TraesCS5B01G197500	chr5B	356214053	356217020	2967	False	5481.0	5481	100.0000	1	2968	1	chr5B.!!$F1	2967
1	TraesCS5B01G197500	chr5D	310257802	310260812	3010	False	2218.5	4235	93.0565	7	2968	2	chr5D.!!$F1	2961
2	TraesCS5B01G197500	chr5A	403755380	403758400	3020	False	4017.0	4017	91.0880	7	2968	1	chr5A.!!$F2	2961
3	TraesCS5B01G197500	chr4D	483837191	483837733	542	True	278.0	278	76.8010	1107	1655	1	chr4D.!!$R1	548

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
667	745	0.721718	GCGCTCAGTATTGTGTGGAC	59.278	55.0	0.00	0.0	0.00	4.02	F
843	921	0.950555	CTGCGCTTGCCTCTGTGTTA	60.951	55.0	9.73	0.0	38.03	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1950	2083	0.172803	GGCTACTTCTTCTCCGCGAA	59.827	55.0	8.23	0.0	0.0	4.70	R
2451	2608	0.713883	CGTACTGCAATCGTGTGACC	59.286	55.0	0.00	0.0	0.0	4.02	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
150	154	0.742990	ACGTCGCAGAGAGAGAGAGG	60.743	60.000	0.00	0.00	36.95	3.69
151	155	1.727467	GTCGCAGAGAGAGAGAGGC	59.273	63.158	0.00	0.00	36.95	4.70
152	156	1.817520	TCGCAGAGAGAGAGAGGCG	60.818	63.158	0.00	0.00	45.24	5.52
154	158	2.489275	GCAGAGAGAGAGAGGCGGG	61.489	68.421	0.00	0.00	0.00	6.13
188	227	1.010046	AGAGAATGATGGGGAGGTGGA	59.990	52.381	0.00	0.00	0.00	4.02
227	266	5.572896	CGATTTAGTAGGACGTTTTAACCGT	59.427	40.000	0.00	0.00	42.06	4.83
247	286	6.238648	ACCGTTTAAGAGAATCCAAGACAAT	58.761	36.000	0.00	0.00	33.66	2.71
270	309	9.277783	CAATAATTACTGGAACATAGAAGAGGG	57.722	37.037	0.00	0.00	38.20	4.30
277	316	6.012508	ACTGGAACATAGAAGAGGGAAAATGA	60.013	38.462	0.00	0.00	38.20	2.57
306	345	6.840780	AAATAGCTTTGTTTAGCCACAGAT	57.159	33.333	0.00	0.00	42.20	2.90
353	392	3.737850	GGTCTGATTGGCTCCTCTATTG	58.262	50.000	0.00	0.00	0.00	1.90
362	401	3.131223	TGGCTCCTCTATTGTCTTCTTCG	59.869	47.826	0.00	0.00	0.00	3.79
519	595	7.792374	TCAGAGTTCCATTATTGAGCAATAC	57.208	36.000	2.57	0.00	33.40	1.89
658	736	3.240302	ACTAAATAGGGGCGCTCAGTAT	58.760	45.455	10.74	1.95	0.00	2.12
667	745	0.721718	GCGCTCAGTATTGTGTGGAC	59.278	55.000	0.00	0.00	0.00	4.02
674	752	6.603095	GCTCAGTATTGTGTGGACTTTAAAG	58.397	40.000	13.76	13.76	0.00	1.85
679	757	9.612620	CAGTATTGTGTGGACTTTAAAGAAATC	57.387	33.333	21.92	8.79	0.00	2.17
822	900	5.123344	GCAATCGTTAAGACCACCACTAATT	59.877	40.000	0.00	0.00	0.00	1.40
843	921	0.950555	CTGCGCTTGCCTCTGTGTTA	60.951	55.000	9.73	0.00	38.03	2.41
1697	1829	6.385649	ACAAACGTACCTTGATCAATGTTT	57.614	33.333	19.53	13.85	0.00	2.83
1702	1834	8.506168	AACGTACCTTGATCAATGTTTATCAT	57.494	30.769	19.53	2.38	38.57	2.45
1703	1835	9.607988	AACGTACCTTGATCAATGTTTATCATA	57.392	29.630	19.53	0.00	35.48	2.15
1730	1863	2.916716	CGTTCAATGCAGTACCAATTGC	59.083	45.455	0.00	3.50	38.74	3.56
1736	1869	4.981806	ATGCAGTACCAATTGCGTTAAT	57.018	36.364	0.00	0.00	41.02	1.40
1861	1994	2.594303	CAAGTGCCTGGTGCCGAA	60.594	61.111	0.00	0.00	40.16	4.30
1949	2082	2.049433	CGGTTCACGGAGTCGCTT	60.049	61.111	0.00	0.00	41.61	4.68
1950	2083	1.663702	CGGTTCACGGAGTCGCTTT	60.664	57.895	0.00	0.00	41.61	3.51
1951	2084	1.219522	CGGTTCACGGAGTCGCTTTT	61.220	55.000	0.00	0.00	41.61	2.27
2168	2304	1.202533	CGGTGGATTAGGTGTAGGCAG	60.203	57.143	0.00	0.00	0.00	4.85
2451	2608	3.259064	CGTGTCCCTAAGTACATGGTTG	58.741	50.000	0.00	0.00	0.00	3.77
2560	2717	8.325421	TGCTAATCAGTTCGGTGTTTTTATAA	57.675	30.769	0.00	0.00	0.00	0.98
2561	2718	8.784994	TGCTAATCAGTTCGGTGTTTTTATAAA	58.215	29.630	0.00	0.00	0.00	1.40
2600	2758	6.545666	TGATTCTTGTTTCACTTAGGAAAGCA	59.454	34.615	0.00	0.00	37.44	3.91
2603	2761	6.970484	TCTTGTTTCACTTAGGAAAGCAATC	58.030	36.000	0.00	0.00	37.44	2.67
2620	2779	9.167311	GAAAGCAATCAGTATTTCCTTTAGAGA	57.833	33.333	0.00	0.00	30.21	3.10
2632	2791	5.407407	TCCTTTAGAGAAAAGCAGATCGT	57.593	39.130	0.00	0.00	42.85	3.73
2641	2800	5.297547	AGAAAAGCAGATCGTTTAGTCACA	58.702	37.500	0.00	0.00	0.00	3.58
2723	2896	2.663196	GCCAGTAAGCGGACACCT	59.337	61.111	0.00	0.00	0.00	4.00
2748	2921	0.523968	CAAGGCGGTCATCAAATGCG	60.524	55.000	0.00	0.00	0.00	4.73
2749	2922	2.270297	AAGGCGGTCATCAAATGCGC	62.270	55.000	0.00	0.00	39.80	6.09
2750	2923	2.484662	GCGGTCATCAAATGCGCA	59.515	55.556	14.96	14.96	40.11	6.09
2751	2924	1.064621	GCGGTCATCAAATGCGCAT	59.935	52.632	19.28	19.28	40.11	4.73
2766	2940	3.557908	GCGCATGCATACATTTCAAAC	57.442	42.857	19.57	0.00	42.15	2.93
2783	2957	8.930760	CATTTCAAACCAACTTTTCAACTAACA	58.069	29.630	0.00	0.00	0.00	2.41
2816	2990	1.334288	GCAAACACGGCGGATTTTCG	61.334	55.000	13.24	1.73	0.00	3.46
2903	3077	1.530323	AAAGCGTTGCGACCCTAAAT	58.470	45.000	0.00	0.00	0.00	1.40
2946	3120	2.091588	CGTCCACTTTCGTTGTATTCCG	59.908	50.000	0.00	0.00	0.00	4.30
2952	3126	2.281140	TTCGTTGTATTCCGCATCGA	57.719	45.000	0.00	0.00	36.62	3.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	9.859427	TTTCATGTGAACAATAATCCTGAAATC	57.141	29.630	0.00	0.00	33.13	2.17
151	155	3.750373	CTGTAACCGCCATCCCCCG	62.750	68.421	0.00	0.00	0.00	5.73
152	156	2.192175	CTGTAACCGCCATCCCCC	59.808	66.667	0.00	0.00	0.00	5.40
154	158	0.539986	TTCTCTGTAACCGCCATCCC	59.460	55.000	0.00	0.00	0.00	3.85
188	227	0.611714	AATCGTAGTTCCTGCGGGTT	59.388	50.000	12.43	1.21	39.84	4.11
247	286	8.618240	TTCCCTCTTCTATGTTCCAGTAATTA	57.382	34.615	0.00	0.00	0.00	1.40
270	309	8.607441	AACAAAGCTATTTTCCCTTCATTTTC	57.393	30.769	0.00	0.00	0.00	2.29
277	316	5.542251	TGGCTAAACAAAGCTATTTTCCCTT	59.458	36.000	0.00	0.00	42.37	3.95
306	345	0.931202	CGCGTAATATGCCACGTCGA	60.931	55.000	0.00	0.00	40.25	4.20
334	373	4.293494	AGACAATAGAGGAGCCAATCAGA	58.707	43.478	0.00	0.00	0.00	3.27
353	392	2.808543	ACTGGATTGCAACGAAGAAGAC	59.191	45.455	0.00	0.00	0.00	3.01
362	401	2.134789	ATGGAGGACTGGATTGCAAC	57.865	50.000	0.00	0.00	0.00	4.17
569	646	6.489675	CCAACATTACTACTGATTGATGCAC	58.510	40.000	0.00	0.00	0.00	4.57
637	715	1.497161	ACTGAGCGCCCCTATTTAGT	58.503	50.000	2.29	0.00	0.00	2.24
638	716	3.963428	ATACTGAGCGCCCCTATTTAG	57.037	47.619	2.29	0.00	0.00	1.85
658	736	5.823570	TCCGATTTCTTTAAAGTCCACACAA	59.176	36.000	14.74	0.00	0.00	3.33
667	745	6.349300	TCTCATCCCTCCGATTTCTTTAAAG	58.651	40.000	9.04	9.04	0.00	1.85
674	752	4.342862	TTCATCTCATCCCTCCGATTTC	57.657	45.455	0.00	0.00	0.00	2.17
679	757	2.615912	GCTTTTTCATCTCATCCCTCCG	59.384	50.000	0.00	0.00	0.00	4.63
822	900	1.374631	CACAGAGGCAAGCGCAGTA	60.375	57.895	11.47	0.00	41.24	2.74
843	921	0.759060	GTTTGCTGGGGTGGGTCTTT	60.759	55.000	0.00	0.00	0.00	2.52
1503	1635	0.457851	CCGTCTTCTCGCTGATCCTT	59.542	55.000	0.00	0.00	0.00	3.36
1504	1636	2.010582	GCCGTCTTCTCGCTGATCCT	62.011	60.000	0.00	0.00	0.00	3.24
1697	1829	5.069119	ACTGCATTGAACGAGAGGTATGATA	59.931	40.000	0.00	0.00	0.00	2.15
1702	1834	3.119245	GGTACTGCATTGAACGAGAGGTA	60.119	47.826	0.00	0.00	0.00	3.08
1703	1835	2.353803	GGTACTGCATTGAACGAGAGGT	60.354	50.000	0.00	0.00	0.00	3.85
1730	1863	8.111836	TGGAAAAATCGACGAGAATTATTAACG	58.888	33.333	3.01	0.00	0.00	3.18
1736	1869	5.579511	GTCCTGGAAAAATCGACGAGAATTA	59.420	40.000	3.01	0.00	0.00	1.40
1901	2034	2.048597	TTCACCAGCGCGTTCGAT	60.049	55.556	8.43	0.00	38.10	3.59
1949	2082	1.403780	GGCTACTTCTTCTCCGCGAAA	60.404	52.381	8.23	0.00	0.00	3.46
1950	2083	0.172803	GGCTACTTCTTCTCCGCGAA	59.827	55.000	8.23	0.00	0.00	4.70
1951	2084	0.963856	TGGCTACTTCTTCTCCGCGA	60.964	55.000	8.23	0.00	0.00	5.87
2168	2304	6.534934	GTGGTCTTTCTAAATCAATCGTGAC	58.465	40.000	0.00	0.00	36.31	3.67
2451	2608	0.713883	CGTACTGCAATCGTGTGACC	59.286	55.000	0.00	0.00	0.00	4.02
2600	2758	9.520515	TGCTTTTCTCTAAAGGAAATACTGATT	57.479	29.630	0.00	0.00	40.67	2.57
2603	2761	8.553459	TCTGCTTTTCTCTAAAGGAAATACTG	57.447	34.615	0.00	0.00	42.63	2.74
2612	2771	8.245701	ACTAAACGATCTGCTTTTCTCTAAAG	57.754	34.615	0.00	0.00	44.99	1.85
2620	2779	7.667043	TTATGTGACTAAACGATCTGCTTTT	57.333	32.000	0.00	0.00	0.00	2.27
2707	2880	1.806623	GCATAGGTGTCCGCTTACTGG	60.807	57.143	0.00	0.00	0.00	4.00
2712	2885	2.590092	GGGCATAGGTGTCCGCTT	59.410	61.111	0.00	0.00	40.95	4.68
2748	2921	4.931002	AGTTGGTTTGAAATGTATGCATGC	59.069	37.500	11.82	11.82	35.15	4.06
2749	2922	7.424227	AAAGTTGGTTTGAAATGTATGCATG	57.576	32.000	10.16	0.00	35.15	4.06
2750	2923	7.714377	TGAAAAGTTGGTTTGAAATGTATGCAT	59.286	29.630	3.79	3.79	36.80	3.96
2751	2924	7.044181	TGAAAAGTTGGTTTGAAATGTATGCA	58.956	30.769	0.00	0.00	0.00	3.96
2766	2940	5.130350	TCCTCCTGTTAGTTGAAAAGTTGG	58.870	41.667	0.00	0.00	0.00	3.77
2783	2957	4.082245	CCGTGTTTGCATTAATTTCCTCCT	60.082	41.667	0.00	0.00	0.00	3.69
2816	2990	4.201724	GCATGAATCTCGTCTGGTTTGTAC	60.202	45.833	0.00	0.00	0.00	2.90
2892	3066	3.672781	GCGTAGGATAGATTTAGGGTCGC	60.673	52.174	0.00	0.00	0.00	5.19
2894	3068	3.119566	CGGCGTAGGATAGATTTAGGGTC	60.120	52.174	0.00	0.00	0.00	4.46
2903	3077	2.981909	CCGCCGGCGTAGGATAGA	60.982	66.667	43.12	0.00	37.81	1.98
2934	3108	1.552226	GTCGATGCGGAATACAACGA	58.448	50.000	0.00	0.00	39.56	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.