AutoCloner

Multiple sequence alignment - TraesCS3B01G437400

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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	TraesCS3B01G437400	chr3B	100.000	6063	0	0	1	6063	676276774	676270712	0.000000e+00	11197.0
1	TraesCS3B01G437400	chr3D	93.066	5408	201	70	629	5917	513953571	513948219	0.000000e+00	7749.0
2	TraesCS3B01G437400	chr3D	87.821	624	66	7	1	617	513954176	513953556	0.000000e+00	723.0
3	TraesCS3B01G437400	chr3D	97.500	40	1	0	5760	5799	513948337	513948298	1.090000e-07	69.4
4	TraesCS3B01G437400	chr3A	94.782	2319	88	13	2830	5131	648870447	648868145	0.000000e+00	3581.0
5	TraesCS3B01G437400	chr3A	90.771	1972	96	33	638	2561	648872702	648870769	0.000000e+00	2555.0
6	TraesCS3B01G437400	chr3A	85.667	900	48	34	5085	5931	648868150	648867279	0.000000e+00	872.0
7	TraesCS3B01G437400	chr3A	82.835	635	88	13	1	617	648874410	648873779	3.190000e-152	549.0
8	TraesCS3B01G437400	chr3A	96.694	242	5	2	2591	2831	648870768	648870529	3.400000e-107	399.0
9	TraesCS3B01G437400	chr3A	80.897	513	84	8	109	609	648873511	648873001	5.700000e-105	392.0
10	TraesCS3B01G437400	chr3A	95.918	49	2	0	5760	5808	648867407	648867359	5.040000e-11	80.5
11	TraesCS3B01G437400	chr6B	89.157	83	9	0	2446	2528	10313869	10313787	2.990000e-18	104.0
12	TraesCS3B01G437400	chr1D	92.000	75	5	1	4325	4398	356154912	356154838	2.990000e-18	104.0
13	TraesCS3B01G437400	chr1A	92.000	75	5	1	4325	4398	456941372	456941298	2.990000e-18	104.0
14	TraesCS3B01G437400	chr1A	91.837	49	3	1	2445	2492	45840206	45840254	3.920000e-07	67.6
15	TraesCS3B01G437400	chr5A	92.453	53	4	0	2445	2497	505496758	505496810	6.520000e-10	76.8
16	TraesCS3B01G437400	chr2D	86.154	65	5	4	2477	2539	291859396	291859334	3.920000e-07	67.6
17	TraesCS3B01G437400	chr6D	89.130	46	5	0	2495	2540	150786062	150786017	2.360000e-04	58.4
18	TraesCS3B01G437400	chr6D	88.889	45	5	0	2445	2489	157659514	157659470	8.490000e-04	56.5
19	TraesCS3B01G437400	chr7B	100.000	28	0	0	2442	2469	693954271	693954298	1.100000e-02	52.8
20	TraesCS3B01G437400	chr7A	100.000	28	0	0	2445	2472	716231985	716231958	1.100000e-02	52.8
21	TraesCS3B01G437400	chr4A	100.000	28	0	0	2441	2468	546196560	546196587	1.100000e-02	52.8

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	TraesCS3B01G437400	chr3B	676270712	676276774	6062	True	11197.000000	11197	100.000	1	6063	1	chr3B.!!$R1	6062
1	TraesCS3B01G437400	chr3D	513948219	513953571	5352	True	7749.000000	7749	93.066	629	5917	1	chr3D.!!$R1	5288
2	TraesCS3B01G437400	chr3D	513953556	513954176	620	True	723.000000	723	87.821	1	617	1	chr3D.!!$R3	616
3	TraesCS3B01G437400	chr3A	648867279	648874410	7131	True	1204.071429	3581	89.652	1	5931	7	chr3A.!!$R1	5930

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	Hairpin	End Stability	Orientation
856	1955	1.027357	CTCCATCTTGGCATTTCCGG	58.973	55.0	0.00	37.47	5.14	F
1224	2337	0.108992	GGAAGTACGTGGTCGATGCA	60.109	55.0	0.00	40.62	3.96	F
2339	3491	0.396435	CCCGGGTGCTATTGCTATCA	59.604	55.0	14.18	40.48	2.15	F
2713	3866	1.059098	TGTGATTGTGGTCCTGCTCT	58.941	50.0	0.00	0.00	4.09	F
4280	5529	0.033504	TCTGACTGTGGTCCTTTCGC	59.966	55.0	0.00	41.47	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2049	3197	2.009774	CCTGCAGCCATAGTGTGTAAC	58.990	52.381	8.66	0.00	37.35	2.50	R
3146	4380	1.215647	GGTGCGAGTTGAGGTCGAT	59.784	57.895	0.00	0.00	39.92	3.59	R
3611	4851	0.106708	GCACAACAGACCTCACCTGA	59.893	55.000	0.00	0.00	35.69	3.86	R
4537	5788	0.038801	GCTTTGCTTGGTCCTTGAGC	60.039	55.000	5.76	5.76	36.95	4.26	R
5992	7414	0.036105	GGGGTGTATTTCGACCGGTT	60.036	55.000	9.42	0.00	32.48	4.44	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	2.045926	GACCCTCTTGGCGTGCAT	60.046	61.111	0.00	0.00	37.83	3.96
42	43	1.675641	GACCCTCTTGGCGTGCATT	60.676	57.895	0.00	0.00	37.83	3.56
64	67	3.300388	TGCTCATCTCTCCCTCGTAAAT	58.700	45.455	0.00	0.00	0.00	1.40
128	131	4.799949	TGCGTGTATTATCGTGTTAACTCC	59.200	41.667	7.22	0.00	0.00	3.85
132	135	6.634436	CGTGTATTATCGTGTTAACTCCCTAC	59.366	42.308	7.22	0.00	0.00	3.18
134	137	2.573941	ATCGTGTTAACTCCCTACGC	57.426	50.000	7.22	0.00	34.98	4.42
259	262	1.450312	CACCATCCCGAGGAGCAAC	60.450	63.158	0.00	0.00	34.05	4.17
291	294	5.407387	TGTAAAGATAGTGGCGTTTCAACTC	59.593	40.000	0.00	0.00	0.00	3.01
294	297	2.922740	TAGTGGCGTTTCAACTCCTT	57.077	45.000	0.61	0.00	34.89	3.36
313	318	2.588027	TGTGTCTGTAGCGTTCACAA	57.412	45.000	0.00	0.00	36.34	3.33
315	320	2.799978	TGTGTCTGTAGCGTTCACAATG	59.200	45.455	0.00	0.00	36.34	2.82
327	338	3.241773	CGTTCACAATGTCGCACTAGATG	60.242	47.826	0.00	0.00	0.00	2.90
382	394	8.732531	TCTTTATAAACTTTCAATAACCACCGG	58.267	33.333	0.00	0.00	0.00	5.28
403	415	2.006888	CGCGTGGATTCCAGTAACAAT	58.993	47.619	5.39	0.00	32.34	2.71
409	421	5.123936	GTGGATTCCAGTAACAATCTACCC	58.876	45.833	5.39	0.00	35.51	3.69
410	422	4.785914	TGGATTCCAGTAACAATCTACCCA	59.214	41.667	0.00	0.00	30.85	4.51
414	426	3.262405	TCCAGTAACAATCTACCCACCAC	59.738	47.826	0.00	0.00	0.00	4.16
417	429	4.454504	CAGTAACAATCTACCCACCACAAC	59.545	45.833	0.00	0.00	0.00	3.32
425	437	5.353394	TCTACCCACCACAACTATTCATC	57.647	43.478	0.00	0.00	0.00	2.92
438	450	2.532531	ATTCATCGCGTGCAAGAAAG	57.467	45.000	5.77	0.00	0.00	2.62
441	453	2.409012	TCATCGCGTGCAAGAAAGTAA	58.591	42.857	5.77	0.00	0.00	2.24
450	462	5.275741	GCGTGCAAGAAAGTAAGTTTTCAAC	60.276	40.000	2.99	0.00	39.08	3.18
454	466	4.205323	AGAAAGTAAGTTTTCAACCGCG	57.795	40.909	0.00	0.00	39.08	6.46
460	472	3.757745	AAGTTTTCAACCGCGGATATG	57.242	42.857	35.90	25.84	0.00	1.78
462	474	2.676342	AGTTTTCAACCGCGGATATGTC	59.324	45.455	35.90	15.65	0.00	3.06

Showing 1 to 25 of 229 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.142097	GCCAAGAGGGTCGTCTAGC	59.858	63.158	0.00	0.00	39.65	3.42
30	31	0.108992	ATGAGCAAATGCACGCCAAG	60.109	50.000	8.28	0.00	45.16	3.61
41	42	1.561643	ACGAGGGAGAGATGAGCAAA	58.438	50.000	0.00	0.00	0.00	3.68
42	43	2.437085	TACGAGGGAGAGATGAGCAA	57.563	50.000	0.00	0.00	0.00	3.91
64	67	2.517402	GCCGGTGGTTGTTGGACA	60.517	61.111	1.90	0.00	0.00	4.02
147	150	3.127376	GGGTAGTGTGACAACAAAAACGT	59.873	43.478	0.00	0.00	38.27	3.99
259	262	3.242739	GCCACTATCTTTACACGCAATGG	60.243	47.826	0.00	0.00	0.00	3.16
291	294	1.792949	GTGAACGCTACAGACACAAGG	59.207	52.381	0.00	0.00	0.00	3.61
294	297	2.588027	TTGTGAACGCTACAGACACA	57.412	45.000	0.00	0.00	39.22	3.72
313	318	2.752121	CATGCTCATCTAGTGCGACAT	58.248	47.619	0.00	0.00	39.54	3.06
315	320	0.857935	GCATGCTCATCTAGTGCGAC	59.142	55.000	11.37	0.00	39.54	5.19
319	324	1.227639	GCCAGCATGCTCATCTAGTG	58.772	55.000	19.68	4.63	31.97	2.74
357	368	7.486870	GCCGGTGGTTATTGAAAGTTTATAAAG	59.513	37.037	1.90	0.00	0.00	1.85
358	369	7.314393	GCCGGTGGTTATTGAAAGTTTATAAA	58.686	34.615	1.90	0.00	0.00	1.40
359	370	6.403418	CGCCGGTGGTTATTGAAAGTTTATAA	60.403	38.462	7.26	0.00	0.00	0.98
360	371	5.064962	CGCCGGTGGTTATTGAAAGTTTATA	59.935	40.000	7.26	0.00	0.00	0.98
361	372	4.142556	CGCCGGTGGTTATTGAAAGTTTAT	60.143	41.667	7.26	0.00	0.00	1.40
366	377	0.179174	GCGCCGGTGGTTATTGAAAG	60.179	55.000	18.41	0.00	0.00	2.62
369	381	2.816083	CGCGCCGGTGGTTATTGA	60.816	61.111	18.41	0.00	0.00	2.57
382	394	1.017177	TGTTACTGGAATCCACGCGC	61.017	55.000	5.73	0.00	0.00	6.86
403	415	4.142026	CGATGAATAGTTGTGGTGGGTAGA	60.142	45.833	0.00	0.00	0.00	2.59
409	421	1.999735	ACGCGATGAATAGTTGTGGTG	59.000	47.619	15.93	0.00	0.00	4.17
410	422	1.999735	CACGCGATGAATAGTTGTGGT	59.000	47.619	15.93	0.00	0.00	4.16
414	426	2.348362	TCTTGCACGCGATGAATAGTTG	59.652	45.455	15.93	0.00	0.00	3.16
417	429	3.062639	ACTTTCTTGCACGCGATGAATAG	59.937	43.478	15.93	10.96	0.00	1.73

Showing 1 to 25 of 255 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.