AutoCloner

Multiple sequence alignment - TraesCS4D01G335800

Loading Multiple Alignment...

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	TraesCS4D01G335800	chr4D	100.000	2287	0	0	1	2287	493971116	493968830	0.000000e+00	4224.0
1	TraesCS4D01G335800	chr4D	93.268	1738	110	5	1	1736	116524564	116522832	0.000000e+00	2555.0
2	TraesCS4D01G335800	chr4D	92.997	1742	108	8	3	1736	421048641	421046906	0.000000e+00	2529.0
3	TraesCS4D01G335800	chr4D	78.986	138	11	5	1742	1864	494060110	494059976	6.770000e-11	78.7
4	TraesCS4D01G335800	chr3A	93.707	1732	98	6	3	1727	418765665	418763938	0.000000e+00	2584.0
5	TraesCS4D01G335800	chr1A	93.125	1731	111	6	1	1727	327011925	327010199	0.000000e+00	2531.0
6	TraesCS4D01G335800	chr1A	92.134	1729	128	6	1	1727	387995194	387996916	0.000000e+00	2433.0
7	TraesCS4D01G335800	chr4A	92.622	1735	116	8	2	1729	327748380	327746651	0.000000e+00	2484.0
8	TraesCS4D01G335800	chr7D	92.524	1739	116	10	1	1732	432740550	432738819	0.000000e+00	2479.0
9	TraesCS4D01G335800	chr5B	91.915	1744	130	4	1	1737	375712252	375710513	0.000000e+00	2429.0
10	TraesCS4D01G335800	chr5A	91.988	1735	126	7	1	1728	604232067	604230339	0.000000e+00	2422.0
11	TraesCS4D01G335800	chr5A	90.335	538	45	6	1753	2284	673443221	673442685	0.000000e+00	699.0
12	TraesCS4D01G335800	chr4B	89.485	485	36	2	1803	2287	632863180	632862711	1.170000e-167	599.0
13	TraesCS4D01G335800	chr4B	93.750	80	5	0	1728	1807	632863604	632863525	1.110000e-23	121.0

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	TraesCS4D01G335800	chr4D	493968830	493971116	2286	True	4224	4224	100.0000	1	2287	1	chr4D.!!$R3	2286
1	TraesCS4D01G335800	chr4D	116522832	116524564	1732	True	2555	2555	93.2680	1	1736	1	chr4D.!!$R1	1735
2	TraesCS4D01G335800	chr4D	421046906	421048641	1735	True	2529	2529	92.9970	3	1736	1	chr4D.!!$R2	1733
3	TraesCS4D01G335800	chr3A	418763938	418765665	1727	True	2584	2584	93.7070	3	1727	1	chr3A.!!$R1	1724
4	TraesCS4D01G335800	chr1A	327010199	327011925	1726	True	2531	2531	93.1250	1	1727	1	chr1A.!!$R1	1726
5	TraesCS4D01G335800	chr1A	387995194	387996916	1722	False	2433	2433	92.1340	1	1727	1	chr1A.!!$F1	1726
6	TraesCS4D01G335800	chr4A	327746651	327748380	1729	True	2484	2484	92.6220	2	1729	1	chr4A.!!$R1	1727
7	TraesCS4D01G335800	chr7D	432738819	432740550	1731	True	2479	2479	92.5240	1	1732	1	chr7D.!!$R1	1731
8	TraesCS4D01G335800	chr5B	375710513	375712252	1739	True	2429	2429	91.9150	1	1737	1	chr5B.!!$R1	1736
9	TraesCS4D01G335800	chr5A	604230339	604232067	1728	True	2422	2422	91.9880	1	1728	1	chr5A.!!$R1	1727
10	TraesCS4D01G335800	chr5A	673442685	673443221	536	True	699	699	90.3350	1753	2284	1	chr5A.!!$R2	531
11	TraesCS4D01G335800	chr4B	632862711	632863604	893	True	360	599	91.6175	1728	2287	2	chr4B.!!$R1	559

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
774	784	0.398522	ATGAGATGGGCACGGAGGTA	60.399	55.0	0.0	0.0	0.0	3.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1998	2374	0.03601	CGTCCCCTGACTTTGATGCT	60.036	55.0	0.0	0.0	39.47	3.79	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
81	82	2.804090	GGTTGTCGTCGTCCTCGC	60.804	66.667	0.00	0.00	36.96	5.03
104	105	4.590487	TCGAGGTCGATTTGCCAC	57.410	55.556	0.00	0.00	44.22	5.01
108	109	1.278238	GAGGTCGATTTGCCACGTAG	58.722	55.000	0.00	0.00	0.00	3.51
180	181	0.625849	CTTAGGCTCCCCACCAATGT	59.374	55.000	0.00	0.00	0.00	2.71
212	213	2.933495	CGATTGTCGTCTCCCAGTAA	57.067	50.000	0.00	0.00	34.72	2.24
536	539	2.525592	CAAGGGAAGGGGTTGGCA	59.474	61.111	0.00	0.00	0.00	4.92
576	585	2.667470	CGATGGAGAGGAGGAAGGTTA	58.333	52.381	0.00	0.00	0.00	2.85
605	615	1.153565	AGAAGAGAGGGGGTGGGTAAA	59.846	52.381	0.00	0.00	0.00	2.01
645	655	4.106197	GAGTAAATATAGGCGCGATGGAG	58.894	47.826	12.10	0.00	0.00	3.86
646	656	3.762288	AGTAAATATAGGCGCGATGGAGA	59.238	43.478	12.10	0.00	0.00	3.71
647	657	2.949451	AATATAGGCGCGATGGAGAG	57.051	50.000	12.10	0.00	0.00	3.20
665	675	2.110899	AGAGGAGGAGGAAGAGTGACAA	59.889	50.000	0.00	0.00	0.00	3.18
683	693	6.205853	AGTGACAATCATGCCGTTTTAACTAA	59.794	34.615	0.00	0.00	0.00	2.24
709	719	4.260538	GCTCTTCAATAAGCCATGAACTCG	60.261	45.833	0.00	0.00	32.46	4.18
774	784	0.398522	ATGAGATGGGCACGGAGGTA	60.399	55.000	0.00	0.00	0.00	3.08
897	907	2.419198	GACGAGCGCATGGAGGAT	59.581	61.111	11.47	0.00	0.00	3.24
947	957	1.573108	CACTACCATGAGGAGGGTGT	58.427	55.000	0.00	0.00	36.73	4.16
1223	1235	3.381590	TCAAGGTCATCATCTTCGACGAT	59.618	43.478	0.00	0.00	0.00	3.73
1237	1249	0.590195	GACGATGATGGCATTGAGGC	59.410	55.000	0.00	0.00	38.02	4.70
1428	1446	3.495753	TGATGCTCTGTTTATGCTATGCG	59.504	43.478	0.00	0.00	0.00	4.73
1445	1463	0.590732	GCGCTGCTTATGATGTGTGC	60.591	55.000	0.00	0.00	0.00	4.57
1468	1486	0.179032	ATGGTTGTGCCGAAGTGTGA	60.179	50.000	0.00	0.00	41.21	3.58
1512	1530	0.763035	GAGGTTACCACACACCAGGT	59.237	55.000	3.51	0.00	41.89	4.00
1704	1725	3.876914	GCTATACAATGCAGCCACTGTAA	59.123	43.478	0.00	0.00	37.24	2.41
1705	1726	4.260784	GCTATACAATGCAGCCACTGTAAC	60.261	45.833	0.00	0.00	37.24	2.50
1745	1767	2.986479	CCCTTAGTGTTTGCGCAATTTC	59.014	45.455	25.64	17.18	0.00	2.17
1753	1775	2.982470	GTTTGCGCAATTTCTCCTTCAG	59.018	45.455	25.64	0.00	0.00	3.02
1801	2172	6.425114	GGACAATTGCAGAGTATAACGATCAT	59.575	38.462	5.05	0.00	0.00	2.45
1824	2195	4.136341	TCCCTCCTTCCTTGTAGTACAA	57.864	45.455	14.85	14.85	36.54	2.41
1923	2297	3.143211	ACGTCTGAACTAGGTCTGTCT	57.857	47.619	9.68	0.00	0.00	3.41
1946	2320	6.424509	TCTGAACGTATTTTGTTATCCAACGT	59.575	34.615	0.00	0.00	37.48	3.99
1981	2357	1.267121	AGCAGACATACCTGGACGTT	58.733	50.000	0.00	0.00	34.82	3.99
1992	2368	1.539827	CCTGGACGTTTGAAATCCCAC	59.460	52.381	0.00	0.00	0.00	4.61
2016	2392	2.237392	ACTAGCATCAAAGTCAGGGGAC	59.763	50.000	0.00	0.00	44.66	4.46
2061	2437	2.933906	TCAAGTTTGAGTCCGACAACAC	59.066	45.455	0.40	0.00	32.50	3.32
2062	2438	2.675844	CAAGTTTGAGTCCGACAACACA	59.324	45.455	0.40	0.00	0.00	3.72
2091	2467	4.077108	CCCAAAACCTTCCTACACCTTAC	58.923	47.826	0.00	0.00	0.00	2.34
2116	2492	0.949105	AGAAACCTCGTCGCGCATTT	60.949	50.000	8.75	0.00	0.00	2.32
2164	2540	3.375299	GCATTGATGTTGGGTAGACAGAC	59.625	47.826	0.00	0.00	0.00	3.51
2206	2582	1.079197	AGCATTCACACCGATGCGA	60.079	52.632	3.03	0.00	44.08	5.10
2207	2583	0.462581	AGCATTCACACCGATGCGAT	60.463	50.000	3.03	0.00	44.08	4.58
2212	2588	1.153568	CACACCGATGCGATGACCT	60.154	57.895	0.00	0.00	0.00	3.85
2226	2602	3.318557	CGATGACCTAGAAACCTACTCCC	59.681	52.174	0.00	0.00	0.00	4.30
2239	2615	4.529219	CTCCCGCATGCTACGCCA	62.529	66.667	17.13	0.00	0.00	5.69
2249	2625	1.155889	TGCTACGCCACATTGAAGTG	58.844	50.000	0.00	0.00	39.21	3.16
2269	2645	1.462432	TGTTGGTCTGCCTACCCCA	60.462	57.895	2.36	0.00	39.30	4.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
104	105	4.208686	GAGCCAGGCCGTCCTACG	62.209	72.222	8.22	0.00	41.93	3.51
212	213	2.591715	GACTGCCGTGCCACAGTT	60.592	61.111	0.00	0.00	46.82	3.16
360	361	3.144506	CCACTGCACAAGAGTTGAAGAT	58.855	45.455	0.00	0.00	0.00	2.40
576	585	3.273618	ACCCCCTCTCTTCTCTCACTATT	59.726	47.826	0.00	0.00	0.00	1.73
605	615	2.158445	ACTCACTCTGACCACCACTACT	60.158	50.000	0.00	0.00	0.00	2.57
645	655	2.223803	TGTCACTCTTCCTCCTCCTC	57.776	55.000	0.00	0.00	0.00	3.71
646	656	2.704190	TTGTCACTCTTCCTCCTCCT	57.296	50.000	0.00	0.00	0.00	3.69
647	657	2.834549	TGATTGTCACTCTTCCTCCTCC	59.165	50.000	0.00	0.00	0.00	4.30
665	675	6.095440	AGAGCATTTAGTTAAAACGGCATGAT	59.905	34.615	0.00	0.76	34.65	2.45
683	693	5.655532	AGTTCATGGCTTATTGAAGAGCATT	59.344	36.000	5.83	0.00	40.63	3.56
709	719	0.250901	ATGGAGTCAGGCACAACACC	60.251	55.000	0.00	0.00	0.00	4.16
774	784	3.552384	TTGTCAACGGCCGGGAGT	61.552	61.111	31.76	4.77	0.00	3.85
947	957	2.158475	ACCTTGCAGAAGTGATTTGGGA	60.158	45.455	0.00	0.00	0.00	4.37
953	963	2.575279	AGGATGACCTTGCAGAAGTGAT	59.425	45.455	0.00	0.00	45.36	3.06
1121	1132	4.419921	CGTAGGTGGCCCAACCCC	62.420	72.222	8.63	0.00	41.54	4.95
1151	1162	4.302455	CACCATGTAGTCGATCTTGATCC	58.698	47.826	5.18	0.00	0.00	3.36
1223	1235	1.451927	GACCGCCTCAATGCCATCA	60.452	57.895	0.00	0.00	0.00	3.07
1237	1249	1.841663	CTTCCCGCACTTGTTGACCG	61.842	60.000	0.00	0.00	0.00	4.79
1428	1446	2.938451	TGTAGCACACATCATAAGCAGC	59.062	45.455	0.00	0.00	30.04	5.25
1445	1463	1.464608	CACTTCGGCACAACCATGTAG	59.535	52.381	0.00	0.00	37.82	2.74
1535	1554	2.242708	TGTTAGTGGACAAACCCAAGGT	59.757	45.455	0.00	0.00	38.06	3.50
1745	1767	1.592223	GTGGACCCGACTGAAGGAG	59.408	63.158	0.00	0.00	0.00	3.69
1801	2172	5.476950	TGTACTACAAGGAAGGAGGGATA	57.523	43.478	0.00	0.00	0.00	2.59
1824	2195	6.665992	TCCAGTAGTACTTGAAAGATGTGT	57.334	37.500	0.00	0.00	0.00	3.72
1875	2247	4.399303	GGGAGATTTGGTGATTAGTGTTGG	59.601	45.833	0.00	0.00	0.00	3.77
1923	2297	6.542574	ACGTTGGATAACAAAATACGTTCA	57.457	33.333	0.00	0.00	41.58	3.18
1946	2320	2.557924	TCTGCTAACGTTTAAGGGACGA	59.442	45.455	5.91	0.00	42.82	4.20
1981	2357	5.076182	TGATGCTAGTTTGTGGGATTTCAA	58.924	37.500	0.00	0.00	0.00	2.69
1992	2368	3.441572	CCCCTGACTTTGATGCTAGTTTG	59.558	47.826	0.00	0.00	0.00	2.93
1998	2374	0.036010	CGTCCCCTGACTTTGATGCT	60.036	55.000	0.00	0.00	39.47	3.79
2061	2437	1.459348	AAGGTTTTGGGTGGGCCTG	60.459	57.895	4.53	0.00	34.45	4.85
2062	2438	1.152333	GAAGGTTTTGGGTGGGCCT	60.152	57.895	4.53	0.00	34.45	5.19
2091	2467	1.801913	CGACGAGGTTTCTGGAGCG	60.802	63.158	0.00	0.00	0.00	5.03
2116	2492	2.501128	GGTGCTCTGAGCGGCATA	59.499	61.111	23.35	3.84	46.26	3.14
2164	2540	2.048503	GTCAACCCTCCGGTCACG	60.049	66.667	0.00	0.00	43.71	4.35
2187	2563	1.061411	CGCATCGGTGTGAATGCTG	59.939	57.895	2.15	0.00	38.10	4.41
2206	2582	3.297736	CGGGAGTAGGTTTCTAGGTCAT	58.702	50.000	0.00	0.00	0.00	3.06
2207	2583	2.731572	CGGGAGTAGGTTTCTAGGTCA	58.268	52.381	0.00	0.00	0.00	4.02
2212	2588	1.138266	GCATGCGGGAGTAGGTTTCTA	59.862	52.381	0.00	0.00	0.00	2.10
2239	2615	2.951642	CAGACCAACACCACTTCAATGT	59.048	45.455	0.00	0.00	0.00	2.71
2249	2625	1.002502	GGGTAGGCAGACCAACACC	60.003	63.158	10.37	0.00	41.73	4.16
2251	2627	1.063070	TTGGGGTAGGCAGACCAACA	61.063	55.000	10.37	6.14	41.73	3.33
2252	2628	1.765074	TTGGGGTAGGCAGACCAAC	59.235	57.895	10.37	3.88	41.73	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.