AutoCloner

Multiple sequence alignment - TraesCS1A01G293500

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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	TraesCS1A01G293500	chr1A	100.000	4314	0	0	1	4314	488624316	488620003	0.000000e+00	7967
1	TraesCS1A01G293500	chr1A	96.065	2719	95	4	692	3400	525042600	525039884	0.000000e+00	4418
2	TraesCS1A01G293500	chr1A	98.656	1860	23	2	692	2550	590651066	590652924	0.000000e+00	3295
3	TraesCS1A01G293500	chr1A	97.685	1771	36	3	2544	4314	590671440	590673205	0.000000e+00	3038
4	TraesCS1A01G293500	chr1A	99.630	541	2	0	1	541	590650534	590651074	0.000000e+00	989
5	TraesCS1A01G293500	chr1A	97.782	541	12	0	1	541	525043132	525042592	0.000000e+00	933
6	TraesCS1A01G293500	chr1A	84.321	759	102	10	3559	4314	525031290	525030546	0.000000e+00	726
7	TraesCS1A01G293500	chr1A	88.053	226	27	0	3820	4045	525031087	525030862	7.110000e-68	268
8	TraesCS1A01G293500	chr1A	94.891	137	6	1	4179	4314	590649614	590649478	3.380000e-51	213
9	TraesCS1A01G293500	chr1A	91.912	136	11	0	4179	4314	525043987	525044122	1.580000e-44	191
10	TraesCS1A01G293500	chr7A	97.985	3623	68	3	692	4314	92421938	92425555	0.000000e+00	6281
11	TraesCS1A01G293500	chr7A	98.706	541	7	0	1	541	92421406	92421946	0.000000e+00	961
12	TraesCS1A01G293500	chr7A	100.000	155	0	0	541	695	226759194	226759040	1.960000e-73	287
13	TraesCS1A01G293500	chr7A	99.338	151	1	0	542	692	219852982	219852832	1.530000e-69	274
14	TraesCS1A01G293500	chr7A	92.701	137	9	1	4179	4314	92420486	92420350	3.400000e-46	196
15	TraesCS1A01G293500	chr3A	92.301	3234	184	29	692	3920	732977112	732973939	0.000000e+00	4532
16	TraesCS1A01G293500	chr3A	93.939	825	42	2	3490	4314	26152562	26151746	0.000000e+00	1240
17	TraesCS1A01G293500	chr3A	96.104	539	21	0	3	541	732977642	732977104	0.000000e+00	880
18	TraesCS1A01G293500	chr3A	91.515	165	6	5	3351	3508	26153836	26153673	2.020000e-53	220
19	TraesCS1A01G293500	chr5A	98.310	1716	28	1	1494	3209	41388046	41389760	0.000000e+00	3007
20	TraesCS1A01G293500	chr5A	93.611	1127	55	3	3204	4314	41389959	41391084	0.000000e+00	1666
21	TraesCS1A01G293500	chr5A	93.611	1127	55	3	3204	4314	41392119	41393244	0.000000e+00	1666
22	TraesCS1A01G293500	chr5A	97.229	794	20	1	2416	3209	41391129	41391920	0.000000e+00	1343
23	TraesCS1A01G293500	chr5A	99.074	540	5	0	2	541	41382584	41383123	0.000000e+00	970
24	TraesCS1A01G293500	chr4A	95.508	1781	62	5	692	2471	723795928	723794165	0.000000e+00	2830
25	TraesCS1A01G293500	chr4A	96.111	540	20	1	3	541	723796459	723795920	0.000000e+00	880
26	TraesCS1A01G293500	chr2A	92.503	1894	123	5	692	2581	88741182	88739304	0.000000e+00	2693
27	TraesCS1A01G293500	chr2A	83.448	580	74	16	2803	3370	88732329	88731760	1.780000e-143	520
28	TraesCS1A01G293500	chr2A	93.367	196	12	1	4120	4314	4908360	4908165	5.460000e-74	289
29	TraesCS1A01G293500	chr2A	100.000	152	0	0	542	693	118674024	118674175	9.130000e-72	281
30	TraesCS1A01G293500	chr6B	92.733	1500	87	12	1734	3226	351230068	351228584	0.000000e+00	2146
31	TraesCS1A01G293500	chr6B	97.036	1046	29	2	692	1736	351231417	351230373	0.000000e+00	1759
32	TraesCS1A01G293500	chr6B	84.844	1313	191	6	692	1998	707504305	707502995	0.000000e+00	1315
33	TraesCS1A01G293500	chr6B	96.455	536	18	1	6	541	351231943	351231409	0.000000e+00	883
34	TraesCS1A01G293500	chr6B	81.766	872	119	26	3061	3911	351228806	351227954	0.000000e+00	693
35	TraesCS1A01G293500	chr6B	99.342	152	1	0	542	693	164031989	164032140	4.250000e-70	276
36	TraesCS1A01G293500	chr6B	89.899	198	19	1	3830	4026	351228152	351227955	1.990000e-63	254
37	TraesCS1A01G293500	chr6B	84.211	247	37	2	3724	3969	351228199	351227954	5.580000e-59	239
38	TraesCS1A01G293500	chr2B	97.251	1164	31	1	694	1856	748163062	748164225	0.000000e+00	1971
39	TraesCS1A01G293500	chr2B	97.032	539	16	0	3	541	748162530	748163068	0.000000e+00	907
40	TraesCS1A01G293500	chr4B	96.475	539	19	0	3	541	562693716	562693178	0.000000e+00	891
41	TraesCS1A01G293500	chr4B	92.281	583	36	5	2594	3170	562692280	562691701	0.000000e+00	819
42	TraesCS1A01G293500	chr4B	86.921	604	67	5	3082	3676	562691897	562691297	0.000000e+00	667
43	TraesCS1A01G293500	chr4B	90.870	230	20	1	4085	4313	562686702	562686473	1.510000e-79	307
44	TraesCS1A01G293500	chr4B	99.342	152	1	0	540	691	189153187	189153338	4.250000e-70	276
45	TraesCS1A01G293500	chr5D	84.307	822	96	21	2670	3474	228504036	228504841	0.000000e+00	773
46	TraesCS1A01G293500	chr6A	99.351	154	1	0	541	694	600302201	600302048	3.290000e-71	279
47	TraesCS1A01G293500	chr3B	99.346	153	1	0	542	694	100968457	100968305	1.180000e-70	278
48	TraesCS1A01G293500	chr3B	98.693	153	2	0	539	691	817065039	817065191	5.500000e-69	272
49	TraesCS1A01G293500	chr4D	99.333	150	1	0	542	691	498575152	498575301	5.500000e-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	TraesCS1A01G293500	chr1A	488620003	488624316	4313	True	7967.000000	7967	100.000000	1	4314	1	chr1A.!!$R1	4313
1	TraesCS1A01G293500	chr1A	590671440	590673205	1765	False	3038.000000	3038	97.685000	2544	4314	1	chr1A.!!$F2	1770
2	TraesCS1A01G293500	chr1A	525039884	525043132	3248	True	2675.500000	4418	96.923500	1	3400	2	chr1A.!!$R4	3399
3	TraesCS1A01G293500	chr1A	590650534	590652924	2390	False	2142.000000	3295	99.143000	1	2550	2	chr1A.!!$F3	2549
4	TraesCS1A01G293500	chr1A	525030546	525031290	744	True	497.000000	726	86.187000	3559	4314	2	chr1A.!!$R3	755
5	TraesCS1A01G293500	chr7A	92421406	92425555	4149	False	3621.000000	6281	98.345500	1	4314	2	chr7A.!!$F1	4313
6	TraesCS1A01G293500	chr3A	732973939	732977642	3703	True	2706.000000	4532	94.202500	3	3920	2	chr3A.!!$R2	3917
7	TraesCS1A01G293500	chr3A	26151746	26153836	2090	True	730.000000	1240	92.727000	3351	4314	2	chr3A.!!$R1	963
8	TraesCS1A01G293500	chr5A	41388046	41393244	5198	False	1920.500000	3007	95.690250	1494	4314	4	chr5A.!!$F2	2820
9	TraesCS1A01G293500	chr5A	41382584	41383123	539	False	970.000000	970	99.074000	2	541	1	chr5A.!!$F1	539
10	TraesCS1A01G293500	chr4A	723794165	723796459	2294	True	1855.000000	2830	95.809500	3	2471	2	chr4A.!!$R1	2468
11	TraesCS1A01G293500	chr2A	88739304	88741182	1878	True	2693.000000	2693	92.503000	692	2581	1	chr2A.!!$R3	1889
12	TraesCS1A01G293500	chr2A	88731760	88732329	569	True	520.000000	520	83.448000	2803	3370	1	chr2A.!!$R2	567
13	TraesCS1A01G293500	chr6B	707502995	707504305	1310	True	1315.000000	1315	84.844000	692	1998	1	chr6B.!!$R1	1306
14	TraesCS1A01G293500	chr6B	351227954	351231943	3989	True	995.666667	2146	90.350000	6	4026	6	chr6B.!!$R2	4020
15	TraesCS1A01G293500	chr2B	748162530	748164225	1695	False	1439.000000	1971	97.141500	3	1856	2	chr2B.!!$F1	1853
16	TraesCS1A01G293500	chr4B	562691297	562693716	2419	True	792.333333	891	91.892333	3	3676	3	chr4B.!!$R2	3673
17	TraesCS1A01G293500	chr5D	228504036	228504841	805	False	773.000000	773	84.307000	2670	3474	1	chr5D.!!$F1	804

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
689	691	0.039074	GTCGTCTGTGTAGCAGCACT	60.039	55.000	11.09	0.0	44.66	4.40	F
690	692	0.241213	TCGTCTGTGTAGCAGCACTC	59.759	55.000	11.09	0.0	44.66	3.51	F
2294	2627	1.816074	TGCAGACCCGAACATTAACC	58.184	50.000	0.00	0.0	0.00	2.85	F
2925	3275	5.014858	CCTTTGGTACTACTACTCACAGGA	58.985	45.833	0.00	0.0	30.24	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2356	2689	2.224066	ACTTGACCCTCGAACAGTCTTG	60.224	50.000	9.68	5.89	0.00	3.02	R
2925	3275	3.433306	TTGTCGGAACTCCCAAATGAT	57.567	42.857	0.00	0.00	34.14	2.45	R
3234	5947	0.038021	TGGCTGCAGTGGAGCATTTA	59.962	50.000	33.67	16.47	44.68	1.40	R
3728	7594	1.654220	CTTCGTGGCCCTGTTTGTG	59.346	57.895	0.00	0.00	0.00	3.33	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
100	101	8.865090	TGCATTTTTAGATGGGACTAAGAAAAA	58.135	29.630	0.00	0.00	32.85	1.94
536	538	7.410120	AGGTTTCAGAAGATGTCAAGTTTTT	57.590	32.000	0.00	0.00	0.00	1.94
559	561	8.922738	TTTTTATCGAAACTACTTAGCAAACG	57.077	30.769	0.00	0.00	0.00	3.60
560	562	7.872163	TTTATCGAAACTACTTAGCAAACGA	57.128	32.000	0.00	0.00	0.00	3.85
561	563	5.758570	ATCGAAACTACTTAGCAAACGAC	57.241	39.130	0.00	0.00	0.00	4.34
562	564	4.609947	TCGAAACTACTTAGCAAACGACA	58.390	39.130	0.00	0.00	0.00	4.35
563	565	4.442073	TCGAAACTACTTAGCAAACGACAC	59.558	41.667	0.00	0.00	0.00	3.67
564	566	4.207635	CGAAACTACTTAGCAAACGACACA	59.792	41.667	0.00	0.00	0.00	3.72
565	567	5.399604	AAACTACTTAGCAAACGACACAC	57.600	39.130	0.00	0.00	0.00	3.82
567	569	0.580104	ACTTAGCAAACGACACACGC	59.420	50.000	0.00	0.00	46.94	5.34
568	570	0.859232	CTTAGCAAACGACACACGCT	59.141	50.000	0.00	0.00	46.94	5.07
569	571	0.579630	TTAGCAAACGACACACGCTG	59.420	50.000	0.00	0.00	46.94	5.18
570	572	1.218875	TAGCAAACGACACACGCTGG	61.219	55.000	0.00	0.00	46.94	4.85
571	573	2.052237	CAAACGACACACGCTGGC	60.052	61.111	0.00	0.00	46.94	4.85
572	574	3.276846	AAACGACACACGCTGGCC	61.277	61.111	0.00	0.00	46.94	5.36
576	578	2.742372	GACACACGCTGGCCGATT	60.742	61.111	0.00	0.00	41.02	3.34
577	579	2.281484	ACACACGCTGGCCGATTT	60.281	55.556	0.00	0.00	41.02	2.17
578	580	2.176546	CACACGCTGGCCGATTTG	59.823	61.111	0.00	0.00	41.02	2.32
579	581	3.055719	ACACGCTGGCCGATTTGG	61.056	61.111	0.00	0.00	41.02	3.28
580	582	2.745884	CACGCTGGCCGATTTGGA	60.746	61.111	0.00	0.00	42.00	3.53
581	583	2.436646	ACGCTGGCCGATTTGGAG	60.437	61.111	0.00	0.00	42.00	3.86
582	584	2.125147	CGCTGGCCGATTTGGAGA	60.125	61.111	0.00	0.00	42.00	3.71
583	585	2.464459	CGCTGGCCGATTTGGAGAC	61.464	63.158	0.00	0.00	42.00	3.36
584	586	2.464459	GCTGGCCGATTTGGAGACG	61.464	63.158	0.00	0.00	42.00	4.18
585	587	1.218047	CTGGCCGATTTGGAGACGA	59.782	57.895	0.00	0.00	42.00	4.20

Showing 1 to 25 of 138 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
536	538	7.381948	TGTCGTTTGCTAAGTAGTTTCGATAAA	59.618	33.333	0.00	0.00	0.00	1.40
537	539	6.862608	TGTCGTTTGCTAAGTAGTTTCGATAA	59.137	34.615	0.00	0.00	0.00	1.75
538	540	6.306356	GTGTCGTTTGCTAAGTAGTTTCGATA	59.694	38.462	0.00	0.00	0.00	2.92
539	541	5.118203	GTGTCGTTTGCTAAGTAGTTTCGAT	59.882	40.000	0.00	0.00	0.00	3.59
540	542	4.442073	GTGTCGTTTGCTAAGTAGTTTCGA	59.558	41.667	0.00	0.00	0.00	3.71
541	543	4.207635	TGTGTCGTTTGCTAAGTAGTTTCG	59.792	41.667	0.00	0.00	0.00	3.46
542	544	5.429615	GTGTGTCGTTTGCTAAGTAGTTTC	58.570	41.667	0.00	0.00	0.00	2.78
543	545	4.026310	CGTGTGTCGTTTGCTAAGTAGTTT	60.026	41.667	0.00	0.00	34.52	2.66
544	546	3.488310	CGTGTGTCGTTTGCTAAGTAGTT	59.512	43.478	0.00	0.00	34.52	2.24
545	547	3.047796	CGTGTGTCGTTTGCTAAGTAGT	58.952	45.455	0.00	0.00	34.52	2.73
546	548	2.160013	GCGTGTGTCGTTTGCTAAGTAG	60.160	50.000	0.00	0.00	42.13	2.57
547	549	1.788308	GCGTGTGTCGTTTGCTAAGTA	59.212	47.619	0.00	0.00	42.13	2.24
548	550	0.580104	GCGTGTGTCGTTTGCTAAGT	59.420	50.000	0.00	0.00	42.13	2.24
549	551	0.859232	AGCGTGTGTCGTTTGCTAAG	59.141	50.000	0.00	0.00	42.13	2.18
550	552	0.579630	CAGCGTGTGTCGTTTGCTAA	59.420	50.000	0.00	0.00	42.13	3.09
551	553	1.218875	CCAGCGTGTGTCGTTTGCTA	61.219	55.000	0.00	0.00	42.13	3.49
552	554	2.534019	CCAGCGTGTGTCGTTTGCT	61.534	57.895	0.00	0.00	42.13	3.91
553	555	2.052237	CCAGCGTGTGTCGTTTGC	60.052	61.111	0.00	0.00	42.13	3.68
554	556	2.052237	GCCAGCGTGTGTCGTTTG	60.052	61.111	0.00	0.00	42.13	2.93
555	557	3.276846	GGCCAGCGTGTGTCGTTT	61.277	61.111	0.00	0.00	42.13	3.60
559	561	2.325082	AAATCGGCCAGCGTGTGTC	61.325	57.895	2.24	0.00	0.00	3.67
560	562	2.281484	AAATCGGCCAGCGTGTGT	60.281	55.556	2.24	0.00	0.00	3.72
561	563	2.176546	CAAATCGGCCAGCGTGTG	59.823	61.111	2.24	0.00	0.00	3.82
562	564	3.055719	CCAAATCGGCCAGCGTGT	61.056	61.111	2.24	0.00	0.00	4.49
563	565	2.745884	TCCAAATCGGCCAGCGTG	60.746	61.111	2.24	0.00	33.14	5.34

Showing 1 to 25 of 138 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.