AutoCloner

Multiple sequence alignment - TraesCS4B01G377200

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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	TraesCS4B01G377200	chr4B	100.000	2816	0	0	1	2816	660297863	660295048	0.000000e+00	5201
1	TraesCS4B01G377200	chr4B	91.106	2867	190	33	1	2816	660252788	660249936	0.000000e+00	3821
2	TraesCS4B01G377200	chr4B	91.780	2360	135	32	1	2331	660322383	660320054	0.000000e+00	3229
3	TraesCS4B01G377200	chr4B	87.401	754	70	14	1	751	660284562	660283831	0.000000e+00	843
4	TraesCS4B01G377200	chr4B	80.932	472	52	22	2352	2789	660320061	660319594	3.470000e-89	339
5	TraesCS4B01G377200	chr5A	92.056	2845	163	37	1	2816	699839832	699842642	0.000000e+00	3943
6	TraesCS4B01G377200	chr5A	92.013	2842	168	34	3	2816	699798487	699801297	0.000000e+00	3936
7	TraesCS4B01G377200	chr5A	92.558	2338	130	19	1	2331	699572322	699574622	0.000000e+00	3314
8	TraesCS4B01G377200	chr5A	93.062	1989	102	13	1	1986	700387904	700389859	0.000000e+00	2876
9	TraesCS4B01G377200	chr5A	93.884	1537	84	5	796	2331	699719394	699720921	0.000000e+00	2309
10	TraesCS4B01G377200	chr5A	85.111	450	54	13	2349	2786	699720911	699721359	5.530000e-122	448
11	TraesCS4B01G377200	chr5A	84.430	456	52	14	2349	2786	699574612	699575066	5.570000e-117	431
12	TraesCS4B01G377200	chr5A	84.245	457	52	15	2349	2786	699642929	699643384	7.210000e-116	427
13	TraesCS4B01G377200	chrUn	91.914	2461	150	31	1	2442	231251589	231254019	0.000000e+00	3397
14	TraesCS4B01G377200	chrUn	92.022	2344	145	23	1	2331	156635253	156637567	0.000000e+00	3254
15	TraesCS4B01G377200	chrUn	93.164	2165	125	17	666	2816	156743161	156745316	0.000000e+00	3157
16	TraesCS4B01G377200	chrUn	91.729	2273	144	27	1	2257	190742403	190744647	0.000000e+00	3116
17	TraesCS4B01G377200	chrUn	92.965	1990	104	13	1	1986	354303507	354305464	0.000000e+00	2867
18	TraesCS4B01G377200	chrUn	88.254	962	77	23	1	950	190749613	190750550	0.000000e+00	1118
19	TraesCS4B01G377200	chrUn	89.362	658	58	10	1	651	156740784	156741436	0.000000e+00	817
20	TraesCS4B01G377200	chrUn	90.750	573	37	10	2257	2816	190746363	190746932	0.000000e+00	750
21	TraesCS4B01G377200	chrUn	84.513	452	55	13	2349	2786	328174904	328175354	1.550000e-117	433

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	TraesCS4B01G377200	chr4B	660295048	660297863	2815	True	5201.000000	5201	100.000000	1	2816	1	chr4B.!!$R3	2815
1	TraesCS4B01G377200	chr4B	660249936	660252788	2852	True	3821.000000	3821	91.106000	1	2816	1	chr4B.!!$R1	2815
2	TraesCS4B01G377200	chr4B	660319594	660322383	2789	True	1784.000000	3229	86.356000	1	2789	2	chr4B.!!$R4	2788
3	TraesCS4B01G377200	chr4B	660283831	660284562	731	True	843.000000	843	87.401000	1	751	1	chr4B.!!$R2	750
4	TraesCS4B01G377200	chr5A	699839832	699842642	2810	False	3943.000000	3943	92.056000	1	2816	1	chr5A.!!$F3	2815
5	TraesCS4B01G377200	chr5A	699798487	699801297	2810	False	3936.000000	3936	92.013000	3	2816	1	chr5A.!!$F2	2813
6	TraesCS4B01G377200	chr5A	700387904	700389859	1955	False	2876.000000	2876	93.062000	1	1986	1	chr5A.!!$F4	1985
7	TraesCS4B01G377200	chr5A	699572322	699575066	2744	False	1872.500000	3314	88.494000	1	2786	2	chr5A.!!$F5	2785
8	TraesCS4B01G377200	chr5A	699719394	699721359	1965	False	1378.500000	2309	89.497500	796	2786	2	chr5A.!!$F6	1990
9	TraesCS4B01G377200	chrUn	231251589	231254019	2430	False	3397.000000	3397	91.914000	1	2442	1	chrUn.!!$F2	2441
10	TraesCS4B01G377200	chrUn	156635253	156637567	2314	False	3254.000000	3254	92.022000	1	2331	1	chrUn.!!$F1	2330
11	TraesCS4B01G377200	chrUn	354303507	354305464	1957	False	2867.000000	2867	92.965000	1	1986	1	chrUn.!!$F4	1985
12	TraesCS4B01G377200	chrUn	156740784	156745316	4532	False	1987.000000	3157	91.263000	1	2816	2	chrUn.!!$F5	2815
13	TraesCS4B01G377200	chrUn	190742403	190750550	8147	False	1661.333333	3116	90.244333	1	2816	3	chrUn.!!$F6	2815

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
119	122	1.019805	GGGCACTTCGTCCACTAAGC	61.02	60.000	0.00	0.00	40.18	3.09	F
374	380	1.069973	TGAAAAGCTCGATTGCACACG	60.07	47.619	5.51	5.51	34.99	4.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1045	2869	0.253044	TTGGCCTGCCATGAGACTAC	59.747	55.0	12.40	0.0	46.64	2.73	R
1843	3672	0.819259	TCCTTCACTTGTGCACTGGC	60.819	55.0	19.41	0.0	41.68	4.85	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
119	122	1.019805	GGGCACTTCGTCCACTAAGC	61.020	60.000	0.00	0.00	40.18	3.09
135	138	2.888051	GCTCGCCGCTTCTTCCTC	60.888	66.667	0.00	0.00	35.14	3.71
326	332	5.856156	TGTTGCTGGATTTCATGACAAATT	58.144	33.333	0.00	0.00	0.00	1.82
333	339	7.537596	TGGATTTCATGACAAATTTACAGGT	57.462	32.000	0.00	0.00	0.00	4.00
374	380	1.069973	TGAAAAGCTCGATTGCACACG	60.070	47.619	5.51	5.51	34.99	4.49
375	381	1.194547	GAAAAGCTCGATTGCACACGA	59.805	47.619	12.61	12.61	37.03	4.35
452	473	2.092267	AGAAGTCATGCATGCACCCATA	60.092	45.455	25.37	3.72	0.00	2.74
453	474	2.670019	AGTCATGCATGCACCCATAT	57.330	45.000	25.37	2.19	0.00	1.78
467	488	2.242043	CCCATATGAATCAAGCCCACC	58.758	52.381	3.65	0.00	0.00	4.61
471	492	4.508943	CCATATGAATCAAGCCCACCCATA	60.509	45.833	3.65	0.00	0.00	2.74
472	493	3.909427	ATGAATCAAGCCCACCCATAT	57.091	42.857	0.00	0.00	0.00	1.78
474	495	4.371624	TGAATCAAGCCCACCCATATAG	57.628	45.455	0.00	0.00	0.00	1.31
475	496	3.721575	TGAATCAAGCCCACCCATATAGT	59.278	43.478	0.00	0.00	0.00	2.12
476	497	4.910913	TGAATCAAGCCCACCCATATAGTA	59.089	41.667	0.00	0.00	0.00	1.82
479	500	5.082633	TCAAGCCCACCCATATAGTAGTA	57.917	43.478	0.00	0.00	0.00	1.82
480	501	5.084519	TCAAGCCCACCCATATAGTAGTAG	58.915	45.833	0.00	0.00	0.00	2.57
481	502	4.761591	AGCCCACCCATATAGTAGTAGT	57.238	45.455	0.00	0.00	0.00	2.73
482	503	4.675038	AGCCCACCCATATAGTAGTAGTC	58.325	47.826	0.00	0.00	0.00	2.59
485	506	5.484290	GCCCACCCATATAGTAGTAGTCATT	59.516	44.000	0.00	0.00	0.00	2.57
488	509	9.096823	CCCACCCATATAGTAGTAGTCATTTTA	57.903	37.037	0.00	0.00	0.00	1.52
539	647	4.761739	CCTTACATGACTTGGCTTTTCTCA	59.238	41.667	0.00	0.00	0.00	3.27
695	2517	9.328845	CAAAATATTTTCCTAAATGGTGATGGG	57.671	33.333	10.53	0.00	35.61	4.00
696	2518	6.670695	ATATTTTCCTAAATGGTGATGGGC	57.329	37.500	0.00	0.00	35.61	5.36
721	2543	1.214175	TGACTTTTCCTGGAACCAGCA	59.786	47.619	9.04	7.92	42.35	4.41
768	2590	5.934625	GGAGAGAGTTTCACATTGCTTCTTA	59.065	40.000	0.00	0.00	0.00	2.10
868	2692	1.601903	GTTGATCGGTTGCACTTGACA	59.398	47.619	0.00	0.00	0.00	3.58
935	2759	1.621107	CTGCATGTTCAAACCATCGC	58.379	50.000	0.00	0.00	0.00	4.58
942	2766	1.197721	GTTCAAACCATCGCCACTCAG	59.802	52.381	0.00	0.00	0.00	3.35
1033	2857	3.772025	CTCTTCCTTTCTCCTCCTTGCTA	59.228	47.826	0.00	0.00	0.00	3.49
1045	2869	0.798776	CCTTGCTACACTTCTTGCGG	59.201	55.000	0.00	0.00	0.00	5.69
1101	2925	2.654863	CCACTCCAGGACTTTTGTGTT	58.345	47.619	5.33	0.00	0.00	3.32
1126	2950	4.253685	CGACATGAATTCACCAGGTACTT	58.746	43.478	11.07	0.00	34.60	2.24
1230	3058	7.520119	TGTAAAATCTGAGCTTACATGTACG	57.480	36.000	4.68	4.88	32.11	3.67
1240	3068	3.060895	GCTTACATGTACGTCTCTTGTGC	59.939	47.826	4.68	11.33	0.00	4.57
1261	3090	2.040544	CCAGTCCGTGTCAATGGGC	61.041	63.158	0.00	0.00	37.34	5.36
1338	3167	0.687757	TCGACAAGCCTAGGATGCCT	60.688	55.000	14.75	0.00	37.71	4.75
1341	3170	2.037772	CGACAAGCCTAGGATGCCTAAT	59.962	50.000	14.75	0.00	35.49	1.73
1368	3197	4.545208	TGGATCCAACGTCACTTTGATA	57.455	40.909	13.46	0.00	0.00	2.15
1491	3320	0.534412	CTGAGATCCTCACGGTGCTT	59.466	55.000	2.51	0.00	35.39	3.91
1509	3338	3.007074	TGCTTGAGGGAACATTGTACGTA	59.993	43.478	0.00	0.00	0.00	3.57
1665	3494	1.861542	TTGCAATTGCCGCGCTAAGT	61.862	50.000	26.94	0.00	41.18	2.24
1701	3530	3.447918	GCTATCACAATTGCCAATGCT	57.552	42.857	5.05	0.00	38.71	3.79
1822	3651	6.334102	AGAACAACCACTACTAAGTCAGAG	57.666	41.667	0.00	0.00	31.97	3.35
1837	3666	8.154856	ACTAAGTCAGAGCTTTGTTAATTACCA	58.845	33.333	3.90	0.00	32.24	3.25
1843	3672	5.946377	AGAGCTTTGTTAATTACCAGGAAGG	59.054	40.000	0.00	0.00	45.67	3.46
1889	3718	4.926238	GGTTGAGTTCCTAGATATGCATCG	59.074	45.833	0.19	0.00	36.20	3.84
2038	3874	8.038351	TCTTTTGGAATCTGATGTGTCGTATTA	58.962	33.333	0.00	0.00	0.00	0.98
2042	3878	7.726216	TGGAATCTGATGTGTCGTATTAATCT	58.274	34.615	0.00	0.00	0.00	2.40
2043	3879	8.856103	TGGAATCTGATGTGTCGTATTAATCTA	58.144	33.333	0.00	0.00	0.00	1.98
2044	3880	9.862371	GGAATCTGATGTGTCGTATTAATCTAT	57.138	33.333	0.00	0.00	0.00	1.98
2091	3927	5.184287	TCATTTCCCCTTGTTCCGAAATAAC	59.816	40.000	0.00	0.00	34.12	1.89
2137	3973	2.307496	TGTTTGATGCTGGGGTGAAT	57.693	45.000	0.00	0.00	0.00	2.57
2175	4011	4.096231	TGCAATACATGTGAAGTATGCCAC	59.904	41.667	9.11	0.00	32.78	5.01
2198	4050	1.303317	GGAACCCGGTTGTGCTCAT	60.303	57.895	7.78	0.00	0.00	2.90
2350	5918	4.458989	AGCTCGATTTTCCAGCATGTTTTA	59.541	37.500	0.00	0.00	35.46	1.52
2398	5997	6.791303	ACACTTGTATGTTTGATTGACGTTT	58.209	32.000	0.00	0.00	0.00	3.60
2438	6037	4.944048	AGGTGGCTTGTTGTATCAAAAAC	58.056	39.130	0.00	0.00	0.00	2.43
2442	6041	5.757808	GTGGCTTGTTGTATCAAAAACCATT	59.242	36.000	8.64	0.00	32.01	3.16
2443	6042	5.757320	TGGCTTGTTGTATCAAAAACCATTG	59.243	36.000	0.00	0.00	0.00	2.82
2607	6243	9.278011	TGAACCCCCAAAAATGATTATTATCTT	57.722	29.630	0.00	0.00	0.00	2.40
2652	6288	6.484643	GCTGGTGATAGAAGCATTTTATCTCA	59.515	38.462	0.00	0.00	36.91	3.27
2669	6305	8.744568	TTTATCTCAAAACAAAATTTTGCCCT	57.255	26.923	26.94	11.85	41.79	5.19
2689	6325	6.120220	GCCCTCTTTATAAAGGAAGCTACAA	58.880	40.000	22.11	2.11	36.67	2.41
2714	6350	3.507786	CGAACGATACATGGTGTTGAGA	58.492	45.455	0.00	0.00	0.00	3.27
2736	6372	8.712103	TGAGAAAATCCTCATACAAGATGATCT	58.288	33.333	0.00	0.00	38.18	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
75	78	3.285484	CAAAAGGAGAGCTGCCACATAT	58.715	45.455	0.00	0.00	0.00	1.78
119	122	0.670546	TTTGAGGAAGAAGCGGCGAG	60.671	55.000	12.98	0.00	0.00	5.03
135	138	5.926542	TCTCTCGAAGTGGTTGAGTATTTTG	59.073	40.000	0.00	0.00	0.00	2.44
452	473	3.909427	ATATGGGTGGGCTTGATTCAT	57.091	42.857	0.00	0.00	0.00	2.57
453	474	3.721575	ACTATATGGGTGGGCTTGATTCA	59.278	43.478	0.00	0.00	0.00	2.57
489	510	8.577296	CCATCAATCGTTTTCTACCTAGAGATA	58.423	37.037	0.00	0.00	33.21	1.98
491	512	6.683110	GCCATCAATCGTTTTCTACCTAGAGA	60.683	42.308	0.00	0.00	33.21	3.10
492	513	5.463724	GCCATCAATCGTTTTCTACCTAGAG	59.536	44.000	0.00	0.00	33.21	2.43
493	514	5.357257	GCCATCAATCGTTTTCTACCTAGA	58.643	41.667	0.00	0.00	0.00	2.43
494	515	4.511826	GGCCATCAATCGTTTTCTACCTAG	59.488	45.833	0.00	0.00	0.00	3.02
495	516	4.163458	AGGCCATCAATCGTTTTCTACCTA	59.837	41.667	5.01	0.00	0.00	3.08
496	517	3.054361	AGGCCATCAATCGTTTTCTACCT	60.054	43.478	5.01	0.00	0.00	3.08
497	518	3.279434	AGGCCATCAATCGTTTTCTACC	58.721	45.455	5.01	0.00	0.00	3.18
499	520	5.492895	TGTAAGGCCATCAATCGTTTTCTA	58.507	37.500	5.01	0.00	0.00	2.10
500	521	4.331968	TGTAAGGCCATCAATCGTTTTCT	58.668	39.130	5.01	0.00	0.00	2.52
501	522	4.695217	TGTAAGGCCATCAATCGTTTTC	57.305	40.909	5.01	0.00	0.00	2.29
502	523	4.704540	TCATGTAAGGCCATCAATCGTTTT	59.295	37.500	5.01	0.00	0.00	2.43
503	524	4.096382	GTCATGTAAGGCCATCAATCGTTT	59.904	41.667	5.01	0.00	0.00	3.60
504	525	3.627577	GTCATGTAAGGCCATCAATCGTT	59.372	43.478	5.01	0.00	0.00	3.85
506	527	3.470709	AGTCATGTAAGGCCATCAATCG	58.529	45.455	5.01	0.00	0.00	3.34
539	647	6.555315	CACAAAGTTAGTCAAAGAGCAGTTT	58.445	36.000	0.00	0.00	0.00	2.66
634	744	9.520204	AAACACTGACAAGATAAACAAATGAAG	57.480	29.630	0.00	0.00	0.00	3.02
695	2517	0.534203	TCCAGGAAAAGTCACCACGC	60.534	55.000	0.00	0.00	0.00	5.34
696	2518	1.602377	GTTCCAGGAAAAGTCACCACG	59.398	52.381	2.45	0.00	0.00	4.94
721	2543	1.972752	TCGCCACAATGCATGCAGT	60.973	52.632	26.69	21.79	0.00	4.40
768	2590	4.820173	CCTTTAAGACACGTTTTCCCTTCT	59.180	41.667	0.00	0.00	0.00	2.85
809	2633	5.065988	TCCCGCTGCTGATTAAACTATTTTC	59.934	40.000	0.00	0.00	0.00	2.29
868	2692	6.233434	TCAGAACTTGTGAGCAATAGACAAT	58.767	36.000	0.00	0.00	33.65	2.71
935	2759	0.179020	TCTGTTTGTGGCCTGAGTGG	60.179	55.000	3.32	0.00	39.35	4.00
942	2766	4.079253	TCTTCCTATTTCTGTTTGTGGCC	58.921	43.478	0.00	0.00	0.00	5.36
1033	2857	1.961394	TGAGACTACCGCAAGAAGTGT	59.039	47.619	0.00	0.00	43.02	3.55
1045	2869	0.253044	TTGGCCTGCCATGAGACTAC	59.747	55.000	12.40	0.00	46.64	2.73
1064	2888	1.419387	GTGGGCTAGGATCAGAAGCAT	59.581	52.381	13.22	0.00	38.01	3.79
1101	2925	1.452110	CTGGTGAATTCATGTCGGCA	58.548	50.000	12.12	0.00	0.00	5.69
1126	2950	6.697892	GGTGAAAACATGATAACAAAACGGAA	59.302	34.615	0.00	0.00	0.00	4.30
1198	3025	9.332502	TGTAAGCTCAGATTTTACAAAGTTGTA	57.667	29.630	0.00	0.00	42.35	2.41
1230	3058	1.003233	GACTGGGGGCACAAGAGAC	60.003	63.158	0.00	0.00	0.00	3.36
1240	3068	1.377202	CATTGACACGGACTGGGGG	60.377	63.158	0.00	0.00	0.00	5.40
1261	3090	4.859326	TCCATCGGGTTCTTGCAAACAAG	61.859	47.826	0.00	0.00	44.08	3.16
1491	3320	2.093869	GCCTACGTACAATGTTCCCTCA	60.094	50.000	0.00	0.00	0.00	3.86
1509	3338	1.133513	TGGTTGGATGTCACAAAGCCT	60.134	47.619	0.00	0.00	0.00	4.58
1539	3368	5.993748	TGGAGAGGAACTTGTTTTTGTTT	57.006	34.783	0.00	0.00	41.55	2.83
1665	3494	3.015145	GCCCCTGGGTTCTGGCTA	61.015	66.667	12.71	0.00	40.77	3.93
1767	3596	5.211973	TGAGCCTGGAGATAGTCTATTGTT	58.788	41.667	0.00	0.00	0.00	2.83
1822	3651	4.381612	GGCCTTCCTGGTAATTAACAAAGC	60.382	45.833	4.45	3.46	38.35	3.51
1837	3666	1.228367	CTTGTGCACTGGCCTTCCT	60.228	57.895	19.41	0.00	40.13	3.36
1843	3672	0.819259	TCCTTCACTTGTGCACTGGC	60.819	55.000	19.41	0.00	41.68	4.85
1989	3824	8.097078	AGAAGCAAATGAGATCATATTAGTGC	57.903	34.615	0.00	3.42	35.10	4.40
2049	3885	9.679661	GGGAAATGAACCCATAATTTTATTTGT	57.320	29.630	0.00	0.00	46.05	2.83
2137	3973	6.508030	TGTATTGCAAGATAATCCTGGGTA	57.492	37.500	4.94	0.00	0.00	3.69
2141	3977	7.500720	TCACATGTATTGCAAGATAATCCTG	57.499	36.000	4.94	0.00	0.00	3.86
2198	4050	9.089601	GCAAATTCAACATTCACATATCAATCA	57.910	29.630	0.00	0.00	0.00	2.57
2350	5918	7.826744	TGTTTTGAACCAAAAGGAAGCTAAAAT	59.173	29.630	5.24	0.00	42.77	1.82
2398	5997	5.163561	GCCACCTCATCGATTTCCATTAAAA	60.164	40.000	0.00	0.00	0.00	1.52
2567	6175	9.548631	TTTTGGGGGTTCATTAATAATCACTTA	57.451	29.630	0.00	0.00	0.00	2.24
2580	6192	9.451206	AGATAATAATCATTTTTGGGGGTTCAT	57.549	29.630	0.00	0.00	34.28	2.57
2607	6243	8.134895	CACCAGCTTGTTAAGAAGAAACAATTA	58.865	33.333	16.08	0.00	43.72	1.40
2620	6256	4.905429	TGCTTCTATCACCAGCTTGTTAA	58.095	39.130	0.00	0.00	34.42	2.01
2669	6305	6.315393	CGGCTTTGTAGCTTCCTTTATAAAGA	59.685	38.462	23.95	9.42	46.90	2.52
2689	6325	1.066430	ACACCATGTATCGTTCGGCTT	60.066	47.619	0.00	0.00	0.00	4.35
2736	6372	4.566360	GCTTGTTTTGCTGTGCTTTTCTTA	59.434	37.500	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.