AutoCloner

Multiple sequence alignment - TraesCS6D01G298300

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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	TraesCS6D01G298300	chr6D	100.000	3255	0	0	1	3255	409294585	409291331	0.000000e+00	6011.0
1	TraesCS6D01G298300	chr6D	80.207	773	145	5	61	832	433502900	433503665	1.010000e-159	573.0
2	TraesCS6D01G298300	chr6D	96.774	62	2	0	2	63	358492373	358492434	1.600000e-18	104.0
3	TraesCS6D01G298300	chr6A	94.511	2405	86	22	881	3255	554792941	554790553	0.000000e+00	3668.0
4	TraesCS6D01G298300	chr6B	94.583	1569	48	12	1700	3255	614132419	614130875	0.000000e+00	2392.0
5	TraesCS6D01G298300	chr6B	94.166	857	40	6	850	1704	614133292	614132444	0.000000e+00	1297.0
6	TraesCS6D01G298300	chr3D	98.588	779	10	1	63	841	143157633	143156856	0.000000e+00	1376.0
7	TraesCS6D01G298300	chr3D	96.825	63	2	0	2	64	498758754	498758692	4.440000e-19	106.0
8	TraesCS6D01G298300	chr1D	98.203	779	12	2	63	841	466100503	466099727	0.000000e+00	1360.0
9	TraesCS6D01G298300	chr2D	97.946	779	15	1	63	841	575333628	575334405	0.000000e+00	1349.0
10	TraesCS6D01G298300	chr2D	92.647	68	4	1	4	71	563985672	563985738	2.670000e-16	97.1
11	TraesCS6D01G298300	chr5D	97.818	779	16	1	63	841	35661128	35661905	0.000000e+00	1343.0
12	TraesCS6D01G298300	chr5D	96.721	61	2	0	2	62	135588639	135588699	5.750000e-18	102.0
13	TraesCS6D01G298300	chr4A	96.662	779	24	2	63	841	675794641	675793865	0.000000e+00	1293.0
14	TraesCS6D01G298300	chr5B	96.205	448	7	3	63	510	325799646	325800083	0.000000e+00	725.0
15	TraesCS6D01G298300	chr4B	93.388	484	26	2	301	784	652396453	652395976	0.000000e+00	712.0
16	TraesCS6D01G298300	chr4B	90.991	444	40	0	398	841	63220447	63220890	1.670000e-167	599.0
17	TraesCS6D01G298300	chr7A	81.267	742	136	3	71	811	672230391	672229652	6.010000e-167	597.0
18	TraesCS6D01G298300	chr4D	95.588	68	2	1	2	69	250167621	250167687	1.230000e-19	108.0
19	TraesCS6D01G298300	chr4D	96.721	61	2	0	2	62	382559927	382559987	5.750000e-18	102.0
20	TraesCS6D01G298300	chr4D	96.721	61	2	0	2	62	428820160	428820220	5.750000e-18	102.0
21	TraesCS6D01G298300	chr7D	96.774	62	2	0	1	62	200706036	200706097	1.600000e-18	104.0
22	TraesCS6D01G298300	chr7D	98.276	58	1	0	5	62	200700371	200700428	5.750000e-18	102.0

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	TraesCS6D01G298300	chr6D	409291331	409294585	3254	True	6011.0	6011	100.0000	1	3255	1	chr6D.!!$R1	3254
1	TraesCS6D01G298300	chr6D	433502900	433503665	765	False	573.0	573	80.2070	61	832	1	chr6D.!!$F2	771
2	TraesCS6D01G298300	chr6A	554790553	554792941	2388	True	3668.0	3668	94.5110	881	3255	1	chr6A.!!$R1	2374
3	TraesCS6D01G298300	chr6B	614130875	614133292	2417	True	1844.5	2392	94.3745	850	3255	2	chr6B.!!$R1	2405
4	TraesCS6D01G298300	chr3D	143156856	143157633	777	True	1376.0	1376	98.5880	63	841	1	chr3D.!!$R1	778
5	TraesCS6D01G298300	chr1D	466099727	466100503	776	True	1360.0	1360	98.2030	63	841	1	chr1D.!!$R1	778
6	TraesCS6D01G298300	chr2D	575333628	575334405	777	False	1349.0	1349	97.9460	63	841	1	chr2D.!!$F2	778
7	TraesCS6D01G298300	chr5D	35661128	35661905	777	False	1343.0	1343	97.8180	63	841	1	chr5D.!!$F1	778
8	TraesCS6D01G298300	chr4A	675793865	675794641	776	True	1293.0	1293	96.6620	63	841	1	chr4A.!!$R1	778
9	TraesCS6D01G298300	chr7A	672229652	672230391	739	True	597.0	597	81.2670	71	811	1	chr7A.!!$R1	740

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
19	20	0.327924	TGCTGGGTCATCGGTGAAAT	59.672	50.0	0.00	0.00	35.80	2.17	F
41	42	0.462047	CAAGTCTGGCCGGGTCATAC	60.462	60.0	12.87	8.96	0.00	2.39	F
1737	1776	0.175760	TGCCGGATAGTGCTGAACTC	59.824	55.0	5.05	0.00	40.56	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1384	1389	1.421410	GGCTACACGACCAATGCTCG	61.421	60.000	37.17	5.03	R
1780	1819	1.942776	TGGGATGCTTCTGAGACTGA	58.057	50.000	0.00	3.41	R
2667	2716	3.189080	GCACAGTTGAGCATAATCACACA	59.811	43.478	0.00	3.72	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
17	18	3.477582	TGCTGGGTCATCGGTGAA	58.522	55.556	0.00	0.00	35.80	3.18
18	19	1.757949	TGCTGGGTCATCGGTGAAA	59.242	52.632	0.00	0.00	35.80	2.69
19	20	0.327924	TGCTGGGTCATCGGTGAAAT	59.672	50.000	0.00	0.00	35.80	2.17
20	21	0.734889	GCTGGGTCATCGGTGAAATG	59.265	55.000	0.00	0.00	35.80	2.32
21	22	0.734889	CTGGGTCATCGGTGAAATGC	59.265	55.000	0.00	0.00	35.80	3.56
22	23	0.679640	TGGGTCATCGGTGAAATGCC	60.680	55.000	0.00	0.00	35.80	4.40
23	24	0.679640	GGGTCATCGGTGAAATGCCA	60.680	55.000	0.00	0.00	35.80	4.92
24	25	1.173043	GGTCATCGGTGAAATGCCAA	58.827	50.000	0.00	0.00	35.80	4.52
25	26	1.133025	GGTCATCGGTGAAATGCCAAG	59.867	52.381	0.00	0.00	35.80	3.61
26	27	1.812571	GTCATCGGTGAAATGCCAAGT	59.187	47.619	0.00	0.00	35.80	3.16
27	28	2.083774	TCATCGGTGAAATGCCAAGTC	58.916	47.619	0.00	0.00	0.00	3.01
28	29	2.086869	CATCGGTGAAATGCCAAGTCT	58.913	47.619	0.00	0.00	0.00	3.24
29	30	1.522668	TCGGTGAAATGCCAAGTCTG	58.477	50.000	0.00	0.00	0.00	3.51
30	31	0.523072	CGGTGAAATGCCAAGTCTGG	59.477	55.000	0.00	0.00	46.65	3.86
38	39	3.636231	CCAAGTCTGGCCGGGTCA	61.636	66.667	12.87	0.00	35.39	4.02
39	40	2.671070	CAAGTCTGGCCGGGTCAT	59.329	61.111	12.87	0.00	0.00	3.06
40	41	1.622607	CCAAGTCTGGCCGGGTCATA	61.623	60.000	12.87	0.00	35.39	2.15
41	42	0.462047	CAAGTCTGGCCGGGTCATAC	60.462	60.000	12.87	8.96	0.00	2.39
42	43	1.623542	AAGTCTGGCCGGGTCATACC	61.624	60.000	12.87	0.00	37.60	2.73
518	519	7.682787	ACTCTTGTGATCACTATATTTCCCT	57.317	36.000	25.55	0.00	0.00	4.20
616	617	4.223923	CCTACTCTCCAAATGTGTCCTCTT	59.776	45.833	0.00	0.00	0.00	2.85
680	681	5.733620	TGAACTACCCTTCTTCAACGTAT	57.266	39.130	0.00	0.00	0.00	3.06
684	685	6.448207	ACTACCCTTCTTCAACGTATAGTC	57.552	41.667	0.00	0.00	0.00	2.59
756	757	4.927978	ATGATTCCGGTTCACACAAAAA	57.072	36.364	11.21	0.00	0.00	1.94
873	874	6.757897	TTTAGTGGAAAAGATGCATTCGAT	57.242	33.333	0.00	0.00	0.00	3.59
874	875	6.757897	TTAGTGGAAAAGATGCATTCGATT	57.242	33.333	0.00	0.00	0.00	3.34
875	876	5.649782	AGTGGAAAAGATGCATTCGATTT	57.350	34.783	0.00	0.08	0.00	2.17
876	877	5.644644	AGTGGAAAAGATGCATTCGATTTC	58.355	37.500	0.00	9.35	35.78	2.17
882	883	3.444916	AGATGCATTCGATTTCGTACGT	58.555	40.909	16.05	0.00	40.80	3.57
1284	1289	2.588989	GGGGAGCTCTTCCTGCTG	59.411	66.667	14.64	0.00	45.98	4.41
1384	1389	0.175989	CCTTCCTCGGTTACTGCTCC	59.824	60.000	0.00	0.00	0.00	4.70
1417	1422	1.757118	TGTAGCCTTTATCTCTGCGCT	59.243	47.619	9.73	0.00	0.00	5.92
1432	1437	0.436531	GCGCTATATTGCTGTCTCGC	59.563	55.000	0.00	0.00	34.61	5.03
1473	1481	3.099905	TGGTGGAAATGTTGTGACCAAA	58.900	40.909	0.00	0.00	30.54	3.28
1569	1578	5.065988	TGTTCAGCTTACAGACTTTTTCACC	59.934	40.000	0.00	0.00	0.00	4.02
1592	1601	7.224753	CACCGAATTCTGCTCTAAGCTAAAATA	59.775	37.037	3.52	0.00	42.97	1.40
1594	1603	7.307455	CCGAATTCTGCTCTAAGCTAAAATACC	60.307	40.741	3.52	0.00	42.97	2.73
1676	1685	2.878406	GGTAGAGCAGTCACTTGCAAAA	59.122	45.455	0.00	0.00	46.47	2.44
1701	1710	3.445096	GCTAGTTGGATGTTTGCCTGATT	59.555	43.478	0.00	0.00	0.00	2.57
1704	1713	4.406456	AGTTGGATGTTTGCCTGATTGTA	58.594	39.130	0.00	0.00	0.00	2.41
1737	1776	0.175760	TGCCGGATAGTGCTGAACTC	59.824	55.000	5.05	0.00	40.56	3.01
1780	1819	2.440409	CTTATGCTGCTGGGACAACTT	58.560	47.619	0.00	0.00	38.70	2.66
1812	1858	3.450904	AGCATCCCAACAGTAGTCCTTA	58.549	45.455	0.00	0.00	0.00	2.69
1833	1879	6.311935	CCTTAACATTTGCAGGTTTCATGATG	59.688	38.462	0.00	0.00	0.00	3.07
1842	1888	4.811908	CAGGTTTCATGATGCAATGTTCA	58.188	39.130	0.00	0.00	0.00	3.18
2062	2108	1.857965	TCAGATGCCTCAGTAGCAGT	58.142	50.000	0.00	0.00	44.90	4.40
2167	2213	7.790823	AATTGAACAAGGAATCAACAAAAGG	57.209	32.000	0.00	0.00	38.29	3.11
2251	2297	1.290732	AGGGAGAAGAAGGAGGAGGAG	59.709	57.143	0.00	0.00	0.00	3.69
2912	2963	2.554032	CCAGCTTAACTGTCCAAACTGG	59.446	50.000	9.02	9.02	45.68	4.00
3036	3089	3.941483	AGATTGCTCACTTTATTGGACCG	59.059	43.478	0.00	0.00	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	0.327924	ATTTCACCGATGACCCAGCA	59.672	50.000	0.00	0.00	33.38	4.41
2	3	0.734889	GCATTTCACCGATGACCCAG	59.265	55.000	0.00	0.00	33.38	4.45
3	4	0.679640	GGCATTTCACCGATGACCCA	60.680	55.000	0.00	0.00	33.38	4.51
4	5	0.679640	TGGCATTTCACCGATGACCC	60.680	55.000	0.00	0.00	33.38	4.46
6	7	1.812571	ACTTGGCATTTCACCGATGAC	59.187	47.619	0.00	0.00	33.38	3.06
7	8	2.083774	GACTTGGCATTTCACCGATGA	58.916	47.619	0.00	0.00	0.00	2.92
8	9	2.086869	AGACTTGGCATTTCACCGATG	58.913	47.619	0.00	0.00	0.00	3.84
9	10	2.086869	CAGACTTGGCATTTCACCGAT	58.913	47.619	0.00	0.00	0.00	4.18
10	11	1.522668	CAGACTTGGCATTTCACCGA	58.477	50.000	0.00	0.00	0.00	4.69
11	12	0.523072	CCAGACTTGGCATTTCACCG	59.477	55.000	0.00	0.00	37.73	4.94
22	23	0.462047	GTATGACCCGGCCAGACTTG	60.462	60.000	2.24	0.00	0.00	3.16
23	24	1.623542	GGTATGACCCGGCCAGACTT	61.624	60.000	15.97	0.00	30.04	3.01
24	25	2.064581	GGTATGACCCGGCCAGACT	61.065	63.158	15.97	0.00	30.04	3.24
25	26	2.504519	GGTATGACCCGGCCAGAC	59.495	66.667	2.24	10.26	30.04	3.51
26	27	3.151710	CGGTATGACCCGGCCAGA	61.152	66.667	2.24	0.00	44.32	3.86
33	34	2.839162	TACCCCGCGGTATGACCC	60.839	66.667	26.12	0.00	42.18	4.46
47	48	0.320697	GTGCCTGTCGGGGATATACC	59.679	60.000	0.00	0.00	37.86	2.73
48	49	1.000955	CTGTGCCTGTCGGGGATATAC	59.999	57.143	0.00	0.00	37.86	1.47
49	50	1.133294	TCTGTGCCTGTCGGGGATATA	60.133	52.381	0.00	0.00	37.86	0.86
50	51	0.398522	TCTGTGCCTGTCGGGGATAT	60.399	55.000	0.00	0.00	37.86	1.63
51	52	0.616395	TTCTGTGCCTGTCGGGGATA	60.616	55.000	0.00	0.00	37.86	2.59
52	53	1.488705	TTTCTGTGCCTGTCGGGGAT	61.489	55.000	0.00	0.00	37.86	3.85
53	54	2.144078	TTTCTGTGCCTGTCGGGGA	61.144	57.895	0.00	0.00	35.12	4.81
54	55	1.966451	GTTTCTGTGCCTGTCGGGG	60.966	63.158	0.00	0.00	35.12	5.73
55	56	0.606401	ATGTTTCTGTGCCTGTCGGG	60.606	55.000	0.00	0.00	38.36	5.14
56	57	2.002586	CTATGTTTCTGTGCCTGTCGG	58.997	52.381	0.00	0.00	0.00	4.79
57	58	1.394917	GCTATGTTTCTGTGCCTGTCG	59.605	52.381	0.00	0.00	0.00	4.35
58	59	2.426522	TGCTATGTTTCTGTGCCTGTC	58.573	47.619	0.00	0.00	0.00	3.51
59	60	2.566833	TGCTATGTTTCTGTGCCTGT	57.433	45.000	0.00	0.00	0.00	4.00
220	221	3.584406	TGGCGTACCATTTGGAAATTG	57.416	42.857	3.01	0.00	42.67	2.32
518	519	3.056035	ACCCGCAAAGTTTTTACACCAAA	60.056	39.130	0.00	0.00	0.00	3.28
680	681	3.455910	CCCAATGATGACCTTCTGGACTA	59.544	47.826	0.00	0.00	37.04	2.59
684	685	1.565759	TCCCCAATGATGACCTTCTGG	59.434	52.381	0.00	0.00	39.83	3.86
756	757	1.111277	GGCAAAACAGTGTTGGAGGT	58.889	50.000	9.79	0.00	0.00	3.85
841	842	8.735315	TGCATCTTTTCCACTAAATAAATCGAA	58.265	29.630	0.00	0.00	0.00	3.71
842	843	8.275015	TGCATCTTTTCCACTAAATAAATCGA	57.725	30.769	0.00	0.00	0.00	3.59
843	844	9.520204	AATGCATCTTTTCCACTAAATAAATCG	57.480	29.630	0.00	0.00	0.00	3.34
845	846	9.520204	CGAATGCATCTTTTCCACTAAATAAAT	57.480	29.630	0.00	0.00	0.00	1.40
846	847	8.735315	TCGAATGCATCTTTTCCACTAAATAAA	58.265	29.630	0.00	0.00	0.00	1.40
847	848	8.275015	TCGAATGCATCTTTTCCACTAAATAA	57.725	30.769	0.00	0.00	0.00	1.40
848	849	7.857734	TCGAATGCATCTTTTCCACTAAATA	57.142	32.000	0.00	0.00	0.00	1.40
873	874	1.111667	CGTGTGAACGACGTACGAAA	58.888	50.000	24.41	0.00	45.77	3.46
874	875	2.769564	CGTGTGAACGACGTACGAA	58.230	52.632	24.41	0.00	45.77	3.85
875	876	4.495091	CGTGTGAACGACGTACGA	57.505	55.556	24.41	0.00	45.77	3.43
882	883	2.048498	CGAATCTTCACGTGTGAACGA	58.952	47.619	16.51	12.54	43.90	3.85
1384	1389	1.421410	GGCTACACGACCAATGCTCG	61.421	60.000	0.00	0.00	37.17	5.03
1417	1422	2.698274	TCCCAAGCGAGACAGCAATATA	59.302	45.455	0.00	0.00	40.15	0.86
1432	1437	2.954318	CAATAGGATGCTGGTTCCCAAG	59.046	50.000	0.00	0.00	33.45	3.61
1448	1454	4.522405	TGGTCACAACATTTCCACCAATAG	59.478	41.667	0.00	0.00	30.86	1.73
1569	1578	7.307455	GGGTATTTTAGCTTAGAGCAGAATTCG	60.307	40.741	0.00	0.00	45.56	3.34
1592	1601	7.101054	CAGACAATCATTTCAAAATCATGGGT	58.899	34.615	0.00	0.00	0.00	4.51
1594	1603	6.816640	AGCAGACAATCATTTCAAAATCATGG	59.183	34.615	0.00	0.00	0.00	3.66
1676	1685	3.194116	CAGGCAAACATCCAACTAGCAAT	59.806	43.478	0.00	0.00	0.00	3.56
1701	1710	5.870706	TCCGGCAACATTCCATAATATACA	58.129	37.500	0.00	0.00	0.00	2.29
1704	1713	6.599244	CACTATCCGGCAACATTCCATAATAT	59.401	38.462	0.00	0.00	0.00	1.28
1737	1776	4.380867	GCACAAACCATCCCTAAATGACTG	60.381	45.833	0.00	0.00	0.00	3.51
1780	1819	1.942776	TGGGATGCTTCTGAGACTGA	58.057	50.000	0.00	0.00	0.00	3.41
1789	1828	2.237392	AGGACTACTGTTGGGATGCTTC	59.763	50.000	0.00	0.00	0.00	3.86
1812	1858	3.998341	GCATCATGAAACCTGCAAATGTT	59.002	39.130	12.97	0.00	34.77	2.71
1833	1879	4.149396	GCAAGTGTCAAAGATGAACATTGC	59.851	41.667	0.00	0.00	37.30	3.56
1842	1888	4.194640	AGCATATCGCAAGTGTCAAAGAT	58.805	39.130	0.00	0.00	46.13	2.40
2167	2213	5.091261	TCCTGTCAAGCTTCCTAGAATTC	57.909	43.478	0.00	0.00	0.00	2.17
2251	2297	4.429108	TGCCTGTTTTTGCTGTTTTCTAC	58.571	39.130	0.00	0.00	0.00	2.59
2666	2715	4.320421	GCACAGTTGAGCATAATCACACAA	60.320	41.667	0.00	0.00	0.00	3.33
2667	2716	3.189080	GCACAGTTGAGCATAATCACACA	59.811	43.478	0.00	0.00	0.00	3.72
2668	2717	3.725895	CGCACAGTTGAGCATAATCACAC	60.726	47.826	2.66	0.00	0.00	3.82
2912	2963	7.602517	AGCAATGTTAAGTGAGTAGAATGAC	57.397	36.000	0.00	0.00	0.00	3.06
3036	3089	8.515414	AGGTAAATCAGTTCTTTTTAGCATCAC	58.485	33.333	0.00	0.00	36.35	3.06
3116	3169	8.571336	AGCACCATAATTCACAAAGCTATTATC	58.429	33.333	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.