AutoCloner

Multiple sequence alignment - TraesCS6D01G295400

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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	TraesCS6D01G295400	chr6D	100.000	3281	0	0	1	3281	406220811	406217531	0.000000e+00	6059.0
1	TraesCS6D01G295400	chr6D	75.518	531	113	10	1	519	388266942	388267467	9.090000e-61	244.0
2	TraesCS6D01G295400	chr6A	93.958	2400	82	29	748	3121	552751326	552748964	0.000000e+00	3570.0
3	TraesCS6D01G295400	chr6A	88.667	750	60	11	1	726	552753005	552752257	0.000000e+00	891.0
4	TraesCS6D01G295400	chr6A	96.364	165	5	1	3117	3280	552748894	552748730	1.500000e-68	270.0
5	TraesCS6D01G295400	chr6B	95.395	1607	56	7	673	2273	610262317	610260723	0.000000e+00	2542.0
6	TraesCS6D01G295400	chr6B	90.732	615	55	2	3	615	610303130	610302516	0.000000e+00	819.0
7	TraesCS6D01G295400	chr6B	76.710	541	107	16	6	538	486570257	486569728	1.930000e-72	283.0
8	TraesCS6D01G295400	chr6B	92.727	165	9	1	2903	3064	610259426	610259262	5.470000e-58	235.0
9	TraesCS6D01G295400	chr6B	100.000	30	0	0	3069	3098	610259239	610259210	4.570000e-04	56.5
10	TraesCS6D01G295400	chr3D	82.732	1413	150	49	965	2346	581974871	581976220	0.000000e+00	1171.0
11	TraesCS6D01G295400	chr3D	77.852	447	82	16	84	521	529828628	529829066	9.030000e-66	261.0
12	TraesCS6D01G295400	chr3B	81.151	1459	167	52	929	2346	779582425	779581034	0.000000e+00	1072.0
13	TraesCS6D01G295400	chr3B	79.412	374	70	5	1	369	689697667	689698038	1.170000e-64	257.0
14	TraesCS6D01G295400	chr5D	80.460	609	107	10	3	603	462451505	462450901	3.860000e-124	455.0
15	TraesCS6D01G295400	chr2D	76.160	625	111	29	3	615	49890100	49889502	8.900000e-76	294.0
16	TraesCS6D01G295400	chr3A	76.701	485	107	6	123	603	641786052	641786534	6.980000e-67	265.0
17	TraesCS6D01G295400	chr2B	72.895	380	94	9	1	376	18970191	18969817	4.450000e-24	122.0
18	TraesCS6D01G295400	chr2B	80.000	145	28	1	472	615	77182543	77182399	4.480000e-19	106.0
19	TraesCS6D01G295400	chr1B	78.472	144	17	8	1	143	487656138	487656008	7.550000e-12	82.4

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	TraesCS6D01G295400	chr6D	406217531	406220811	3280	True	6059.0	6059	100.000000	1	3281	1	chr6D.!!$R1	3280
1	TraesCS6D01G295400	chr6D	388266942	388267467	525	False	244.0	244	75.518000	1	519	1	chr6D.!!$F1	518
2	TraesCS6D01G295400	chr6A	552748730	552753005	4275	True	1577.0	3570	92.996333	1	3280	3	chr6A.!!$R1	3279
3	TraesCS6D01G295400	chr6B	610259210	610262317	3107	True	944.5	2542	96.040667	673	3098	3	chr6B.!!$R3	2425
4	TraesCS6D01G295400	chr6B	610302516	610303130	614	True	819.0	819	90.732000	3	615	1	chr6B.!!$R2	612
5	TraesCS6D01G295400	chr6B	486569728	486570257	529	True	283.0	283	76.710000	6	538	1	chr6B.!!$R1	532
6	TraesCS6D01G295400	chr3D	581974871	581976220	1349	False	1171.0	1171	82.732000	965	2346	1	chr3D.!!$F2	1381
7	TraesCS6D01G295400	chr3B	779581034	779582425	1391	True	1072.0	1072	81.151000	929	2346	1	chr3B.!!$R1	1417
8	TraesCS6D01G295400	chr5D	462450901	462451505	604	True	455.0	455	80.460000	3	603	1	chr5D.!!$R1	600
9	TraesCS6D01G295400	chr2D	49889502	49890100	598	True	294.0	294	76.160000	3	615	1	chr2D.!!$R1	612

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	Hairpin	End Stability	Orientation
111	122	0.178891	AAGACCTTGGAGGAGCTGGA	60.179	55.0	37.67	3.86	F
666	713	0.461961	GGGCAGATTAGTCAGACGCT	59.538	55.0	0.00	5.07	F
1773	2774	0.838987	TTAGGGAGGCGTGGGAGTTT	60.839	55.0	0.00	2.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1972	2989	0.467474	TCGCCGTACATCTCCTGGAT	60.467	55.000	34.51	3.41	R
2259	3282	1.303236	CCGGCAATCTTGGTCCACA	60.303	57.895	0.00	4.17	R
2895	3931	3.173151	GGAAATTCCCCCTGATTGTTGT	58.827	45.455	0.00	3.32	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
66	67	1.339929	TGCTAAGTCGTTGTCAGAGCA	59.660	47.619	0.00	0.00	36.17	4.26
111	122	0.178891	AAGACCTTGGAGGAGCTGGA	60.179	55.000	0.00	0.00	37.67	3.86
222	236	1.821061	CTCCCACAGAGCGTTCCTGT	61.821	60.000	0.00	0.00	44.92	4.00
321	336	2.949644	GCCGCCTTTAAATAGTGGATGT	59.050	45.455	17.72	0.00	32.75	3.06
324	339	4.116961	CGCCTTTAAATAGTGGATGTCGA	58.883	43.478	0.00	0.00	0.00	4.20
416	435	2.722201	GGCAGACGAAGGGACCGAT	61.722	63.158	0.00	0.00	0.00	4.18
547	567	1.013596	TCACTTCAATATTGGCGCCG	58.986	50.000	23.90	6.13	0.00	6.46
577	597	2.347490	GTCCTCTTTGAGCGGGCA	59.653	61.111	0.00	0.00	0.00	5.36
649	696	0.608308	GAGAGGGGTTTTTGGTCGGG	60.608	60.000	0.00	0.00	0.00	5.14
664	711	0.738975	TCGGGCAGATTAGTCAGACG	59.261	55.000	0.00	0.00	0.00	4.18
666	713	0.461961	GGGCAGATTAGTCAGACGCT	59.538	55.000	0.00	0.00	0.00	5.07
685	732	4.373116	GCGTTGGCAGAGGTCCGA	62.373	66.667	0.00	0.00	39.62	4.55
882	1838	9.088512	GAAACCCTTTCTTTTTCTTCTCTTTTC	57.911	33.333	0.00	0.00	36.73	2.29
883	1839	7.962995	ACCCTTTCTTTTTCTTCTCTTTTCT	57.037	32.000	0.00	0.00	0.00	2.52
884	1840	8.367660	ACCCTTTCTTTTTCTTCTCTTTTCTT	57.632	30.769	0.00	0.00	0.00	2.52
923	1879	1.905637	ACGTCAAATCTGAAACCCCC	58.094	50.000	0.00	0.00	31.88	5.40
1110	2075	2.355481	GACGTCACCGCGGAGTTT	60.355	61.111	35.90	12.71	37.70	2.66
1281	2258	4.286320	GAGCCCGTCCGCGATGAT	62.286	66.667	8.23	0.00	41.33	2.45
1426	2409	3.373565	TCCTCGCGCTGCTCTTCA	61.374	61.111	5.56	0.00	0.00	3.02
1431	2414	2.939022	GCGCTGCTCTTCAACGTT	59.061	55.556	0.00	0.00	36.69	3.99
1650	2645	2.722487	GCCACGATCCGAGTCGAT	59.278	61.111	15.64	5.62	44.06	3.59
1773	2774	0.838987	TTAGGGAGGCGTGGGAGTTT	60.839	55.000	0.00	0.00	0.00	2.66
1992	3009	1.101635	TCCAGGAGATGTACGGCGAG	61.102	60.000	16.62	0.00	0.00	5.03
2259	3282	0.976641	TGTCCGAGACCAAGATTGCT	59.023	50.000	2.23	0.00	0.00	3.91
2260	3283	1.338105	TGTCCGAGACCAAGATTGCTG	60.338	52.381	2.23	0.00	0.00	4.41
2274	3297	0.961019	TTGCTGTGGACCAAGATTGC	59.039	50.000	0.00	0.00	0.00	3.56
2307	3330	1.883084	GCGTGATGTAGCTTCGGGG	60.883	63.158	0.00	0.00	0.00	5.73
2321	3344	1.699730	TCGGGGAATCGATGCTCTTA	58.300	50.000	2.49	0.00	33.92	2.10
2366	3389	2.171448	GGATAGAGGTGTGTGCCAAGAT	59.829	50.000	0.00	0.00	0.00	2.40
2398	3421	4.853924	ATGAGTGCTCCAAAATTCGTTT	57.146	36.364	0.00	0.00	0.00	3.60
2457	3482	4.398319	ACGGATGTCTTTTCAAGGTGAAT	58.602	39.130	0.00	0.00	36.11	2.57
2466	3491	5.290643	TCTTTTCAAGGTGAATTTTTGCACG	59.709	36.000	0.00	0.00	36.11	5.34
2485	3518	5.107104	TGCACGATGTTAGTTGAAGTTCATC	60.107	40.000	6.36	6.10	0.00	2.92
2486	3519	5.671329	GCACGATGTTAGTTGAAGTTCATCC	60.671	44.000	6.36	0.66	0.00	3.51
2554	3587	7.087409	TGTTTATGTGGATGTATTTGAGCTG	57.913	36.000	0.00	0.00	0.00	4.24
2617	3651	9.213799	TGTAAGAAACAACTTTTGAAGCATTTT	57.786	25.926	0.00	0.00	34.29	1.82
2663	3698	3.743396	CAGACTACTCTTGGTTCTTGTGC	59.257	47.826	0.00	0.00	0.00	4.57
2676	3711	4.502950	GGTTCTTGTGCATCATCCCAAAAA	60.503	41.667	0.00	0.00	0.00	1.94
2690	3725	5.486735	TCCCAAAAATCATGCTCACAAAT	57.513	34.783	0.00	0.00	0.00	2.32
2764	3799	9.511272	CAATTATATTCATTGAGTCAGATCCCA	57.489	33.333	0.00	0.00	34.05	4.37
2847	3882	0.734942	TCGCTCCCGTTCGATTTGTC	60.735	55.000	0.00	0.00	35.54	3.18
2886	3922	4.668431	GCTCGTCTCGTGGGTTTTTATTTC	60.668	45.833	0.00	0.00	0.00	2.17
2895	3931	8.179509	TCGTGGGTTTTTATTTCCTTTGATAA	57.820	30.769	0.00	0.00	0.00	1.75
3098	5151	9.573133	TTCTTTGATTTCTTTCTTCAGTGTTTC	57.427	29.630	0.00	0.00	0.00	2.78
3103	5156	8.906867	TGATTTCTTTCTTCAGTGTTTCAGATT	58.093	29.630	0.00	0.00	0.00	2.40
3141	5268	7.234355	AGTTTCAGTCCTATTTGTTCCTCATT	58.766	34.615	0.00	0.00	0.00	2.57
3147	5274	8.206867	CAGTCCTATTTGTTCCTCATTATCTCA	58.793	37.037	0.00	0.00	0.00	3.27
3170	5297	8.575649	TCAGTTTTAGTTTCAGTCTTTTCCTT	57.424	30.769	0.00	0.00	0.00	3.36
3262	5390	0.035317	AGCAGTCAGGCATTCAACGA	59.965	50.000	0.00	0.00	35.83	3.85
3280	5408	4.783959	ACGACACTTTACCGTTTTCTTC	57.216	40.909	0.00	0.00	32.03	2.87

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	1.725557	CGATCCCACGACGGAGACAT	61.726	60.000	0.00	0.00	36.56	3.06
174	187	1.596727	GACGAAGATGAAGCATGAGGC	59.403	52.381	0.00	0.00	45.30	4.70
222	236	1.750018	CATCTGCCATGACCGCCAA	60.750	57.895	0.00	0.00	0.00	4.52
321	336	4.415332	GACGCTTGGCCTCGTCGA	62.415	66.667	22.63	0.00	44.18	4.20
416	435	6.217280	TGGATATCTACCATGCCCATTCAATA	59.783	38.462	2.05	0.00	32.03	1.90
526	546	1.742831	GGCGCCAATATTGAAGTGACA	59.257	47.619	24.80	0.00	0.00	3.58
564	584	1.097232	CATTGATGCCCGCTCAAAGA	58.903	50.000	5.92	0.00	36.30	2.52
649	696	1.565305	CCAGCGTCTGACTAATCTGC	58.435	55.000	6.21	0.71	32.44	4.26
666	713	4.329545	GGACCTCTGCCAACGCCA	62.330	66.667	0.00	0.00	0.00	5.69
671	718	1.377202	GCATTCGGACCTCTGCCAA	60.377	57.895	0.00	0.00	0.00	4.52
685	732	1.722011	CGGGAACAACTCGTAGCATT	58.278	50.000	0.00	0.00	37.75	3.56
882	1838	7.425915	CGTTCTCGTCACTTATAGAAAGAAG	57.574	40.000	0.00	0.00	31.66	2.85
1426	2409	1.271656	CTTGACCTCCGACCTAACGTT	59.728	52.381	5.88	5.88	0.00	3.99
1431	2414	1.030488	CGAGCTTGACCTCCGACCTA	61.030	60.000	0.00	0.00	0.00	3.08
1773	2774	1.287815	CTTGGTGTACGCGGTCTCA	59.712	57.895	12.47	0.37	0.00	3.27
1972	2989	0.467474	TCGCCGTACATCTCCTGGAT	60.467	55.000	0.00	0.00	34.51	3.41
2259	3282	1.303236	CCGGCAATCTTGGTCCACA	60.303	57.895	0.00	0.00	0.00	4.17
2260	3283	1.303317	ACCGGCAATCTTGGTCCAC	60.303	57.895	0.00	0.00	0.00	4.02
2307	3330	5.973651	TCAACACATAAGAGCATCGATTC	57.026	39.130	0.00	0.00	42.67	2.52
2321	3344	6.150641	CCACTCAATGAATCTCTTCAACACAT	59.849	38.462	0.00	0.00	44.29	3.21
2334	3357	5.190528	ACACACCTCTATCCACTCAATGAAT	59.809	40.000	0.00	0.00	0.00	2.57
2376	3399	4.853924	AACGAATTTTGGAGCACTCATT	57.146	36.364	0.00	0.00	0.00	2.57
2377	3400	4.853924	AAACGAATTTTGGAGCACTCAT	57.146	36.364	0.00	0.00	0.00	2.90
2457	3482	5.885881	ACTTCAACTAACATCGTGCAAAAA	58.114	33.333	0.00	0.00	0.00	1.94
2554	3587	3.913163	AGGACATGGATTATCTTCTCCCC	59.087	47.826	0.00	0.00	0.00	4.81
2663	3698	5.047847	GTGAGCATGATTTTTGGGATGATG	58.952	41.667	0.00	0.00	0.00	3.07
2676	3711	9.926158	TTTGTGTAATTTATTTGTGAGCATGAT	57.074	25.926	0.00	0.00	0.00	2.45
2847	3882	3.508840	GCGCCAAGATTCGGGGTG	61.509	66.667	0.00	6.01	38.67	4.61
2886	3922	4.160252	CCCCCTGATTGTTGTTATCAAAGG	59.840	45.833	0.00	0.00	35.20	3.11
2895	3931	3.173151	GGAAATTCCCCCTGATTGTTGT	58.827	45.455	0.00	0.00	0.00	3.32
3098	5151	8.997323	ACTGAAACTAATTGAACTGAGAATCTG	58.003	33.333	0.00	0.00	40.23	2.90
3103	5156	7.067496	AGGACTGAAACTAATTGAACTGAGA	57.933	36.000	0.00	0.00	0.00	3.27
3177	5305	4.380233	GCACTGAAAATGAGACAATGAGGG	60.380	45.833	0.00	0.00	0.00	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.