AutoCloner

Multiple sequence alignment - TraesCS2B01G240500

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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	TraesCS2B01G240500	chr2B	100.000	2460	0	0	1	2460	244871947	244869488	0.000000e+00	4543.0
1	TraesCS2B01G240500	chr2A	92.088	2490	160	17	1	2460	202107547	202105065	0.000000e+00	3472.0
2	TraesCS2B01G240500	chr2A	94.124	1753	83	13	1	1740	202840522	202838777	0.000000e+00	2649.0
3	TraesCS2B01G240500	chr2D	94.481	2156	100	11	308	2456	188553817	188551674	0.000000e+00	3304.0
4	TraesCS2B01G240500	chr2D	93.312	314	18	2	1	311	188588067	188587754	6.200000e-126	460.0
5	TraesCS2B01G240500	chr7B	85.137	767	112	2	1692	2456	604800326	604801092	0.000000e+00	784.0
6	TraesCS2B01G240500	chr7B	72.162	370	84	16	39	397	488709669	488710030	7.240000e-16	95.3
7	TraesCS2B01G240500	chr5D	84.293	764	112	8	1700	2456	546676851	546677613	0.000000e+00	739.0
8	TraesCS2B01G240500	chr7D	83.721	774	122	4	1689	2460	538241640	538240869	0.000000e+00	728.0
9	TraesCS2B01G240500	chr7D	83.528	771	121	6	1687	2455	625029204	625028438	0.000000e+00	715.0
10	TraesCS2B01G240500	chr7D	83.267	753	123	3	1701	2451	233876175	233875424	0.000000e+00	689.0
11	TraesCS2B01G240500	chr7D	72.333	300	68	12	409	703	318024512	318024223	2.030000e-11	80.5
12	TraesCS2B01G240500	chr7A	83.733	750	116	5	1711	2456	667942613	667941866	0.000000e+00	704.0
13	TraesCS2B01G240500	chr6D	82.965	769	128	3	1690	2456	13033352	13032585	0.000000e+00	691.0
14	TraesCS2B01G240500	chr1D	83.444	755	112	8	1706	2456	36532213	36531468	0.000000e+00	689.0
15	TraesCS2B01G240500	chr6A	76.950	282	56	7	406	685	268403560	268403834	4.240000e-33	152.0
16	TraesCS2B01G240500	chr3A	75.972	283	55	12	406	685	330303231	330303503	1.530000e-27	134.0

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	TraesCS2B01G240500	chr2B	244869488	244871947	2459	True	4543	4543	100.000	1	2460	1	chr2B.!!$R1	2459
1	TraesCS2B01G240500	chr2A	202105065	202107547	2482	True	3472	3472	92.088	1	2460	1	chr2A.!!$R1	2459
2	TraesCS2B01G240500	chr2A	202838777	202840522	1745	True	2649	2649	94.124	1	1740	1	chr2A.!!$R2	1739
3	TraesCS2B01G240500	chr2D	188551674	188553817	2143	True	3304	3304	94.481	308	2456	1	chr2D.!!$R1	2148
4	TraesCS2B01G240500	chr7B	604800326	604801092	766	False	784	784	85.137	1692	2456	1	chr7B.!!$F2	764
5	TraesCS2B01G240500	chr5D	546676851	546677613	762	False	739	739	84.293	1700	2456	1	chr5D.!!$F1	756
6	TraesCS2B01G240500	chr7D	538240869	538241640	771	True	728	728	83.721	1689	2460	1	chr7D.!!$R3	771
7	TraesCS2B01G240500	chr7D	625028438	625029204	766	True	715	715	83.528	1687	2455	1	chr7D.!!$R4	768
8	TraesCS2B01G240500	chr7D	233875424	233876175	751	True	689	689	83.267	1701	2451	1	chr7D.!!$R1	750
9	TraesCS2B01G240500	chr7A	667941866	667942613	747	True	704	704	83.733	1711	2456	1	chr7A.!!$R1	745
10	TraesCS2B01G240500	chr6D	13032585	13033352	767	True	691	691	82.965	1690	2456	1	chr6D.!!$R1	766
11	TraesCS2B01G240500	chr1D	36531468	36532213	745	True	689	689	83.444	1706	2456	1	chr1D.!!$R1	750

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
452	457	0.82346	AAATACAATGGCTTGGCGGG	59.177	50.0	2.59	0.0	36.64	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1640	1680	0.394216	CAAGGATTGGATCACCGCCA	60.394	55.0	0.0	0.0	43.94	5.69	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
33	35	9.834628	TTACAATAAAAGCTATGTTGTAAGCAC	57.165	29.630	20.72	0.0	39.16	4.40
137	139	6.510879	TTCATGTACTAGTTGACGAGATGT	57.489	37.500	0.00	0.0	0.00	3.06
170	175	1.445871	GCTAACCTTTGTGTACGGGG	58.554	55.000	0.00	0.0	0.00	5.73
190	195	4.828925	GCCCAGGCGTCAGAGAGC	62.829	72.222	0.00	0.0	0.00	4.09
306	311	1.975680	ACACGATGGAGTTGGTAACCT	59.024	47.619	0.00	0.0	0.00	3.50
378	383	8.889445	TGGTTTGTCTGATATTGGATATATGGA	58.111	33.333	0.00	0.0	0.00	3.41
421	426	5.036117	AGGTTGCTAGAGTTTGTTTCTCA	57.964	39.130	0.00	0.0	34.73	3.27
452	457	0.823460	AAATACAATGGCTTGGCGGG	59.177	50.000	2.59	0.0	36.64	6.13
472	477	6.220201	GCGGGCCACAAAAATAATATACATT	58.780	36.000	4.39	0.0	0.00	2.71
545	550	6.127619	GGTTGAAATTCAATCGAAGGGAGAAT	60.128	38.462	11.87	0.0	38.79	2.40
626	631	6.526325	TGAACAAAGTTCAACACATTTCTTCG	59.474	34.615	9.91	0.0	0.00	3.79
640	645	5.183713	ACATTTCTTCGAGAAAATCCATGCA	59.816	36.000	12.07	0.0	46.08	3.96
757	764	9.665719	ACATTTTTATCCTTAAATTTCCGCAAT	57.334	25.926	0.00	0.0	0.00	3.56
854	886	6.734502	AATGAAATGACCATCAATGCCATA	57.265	33.333	0.00	0.0	0.00	2.74
955	992	3.371168	CGTGCTACAACTTGCAAACATT	58.629	40.909	0.00	0.0	41.10	2.71
1018	1055	8.867112	AATTATGATGAAGAACATGATGCAAC	57.133	30.769	0.00	0.0	39.56	4.17
1021	1058	1.811965	TGAAGAACATGATGCAACCCG	59.188	47.619	0.00	0.0	0.00	5.28
1022	1059	2.083774	GAAGAACATGATGCAACCCGA	58.916	47.619	0.00	0.0	0.00	5.14
1036	1073	2.680841	CAACCCGACAGACTTGTTTTGA	59.319	45.455	0.00	0.0	37.76	2.69
1069	1106	3.243002	GCTTGGATGCTTTACTGCTCATC	60.243	47.826	0.00	0.0	35.74	2.92
1339	1377	4.675063	AAAGATTGTTATCCCACCCTGT	57.325	40.909	0.00	0.0	0.00	4.00
1435	1473	7.132863	GTCTTTGCTACAAAACTAAGGTTGAG	58.867	38.462	0.00	0.0	35.63	3.02
1447	1485	9.574516	AAAACTAAGGTTGAGTGTCAGATAAAT	57.425	29.630	0.00	0.0	35.63	1.40
1538	1577	9.807649	AAAATCTTTGCCACATCTCATTAATAC	57.192	29.630	0.00	0.0	0.00	1.89
1585	1625	2.292016	TGTGGTTTGTTATGCCTCAACG	59.708	45.455	0.00	0.0	0.00	4.10
1586	1626	1.883275	TGGTTTGTTATGCCTCAACGG	59.117	47.619	0.00	0.0	0.00	4.44
1596	1636	1.243902	GCCTCAACGGATGGAAAACA	58.756	50.000	0.00	0.0	33.16	2.83
1599	1639	3.857010	GCCTCAACGGATGGAAAACAAAG	60.857	47.826	0.00	0.0	33.16	2.77
1640	1680	1.412710	TGAACTCAAGTGCTTCGACCT	59.587	47.619	0.00	0.0	0.00	3.85
1718	1759	1.419012	GTAAAGGAGGATTACCCCGGG	59.581	57.143	15.80	15.8	36.73	5.73
1926	1971	1.180029	AGCGTCCCATAACGTGTACT	58.820	50.000	0.00	0.0	44.38	2.73
1971	2016	1.031571	GTTGCCATCTTCCGCCATCA	61.032	55.000	0.00	0.0	0.00	3.07
1981	2026	1.194218	TCCGCCATCACATCTTCAGA	58.806	50.000	0.00	0.0	0.00	3.27
2016	2061	1.707427	AGAACTTGCCAGTCCCATCTT	59.293	47.619	0.00	0.0	30.45	2.40
2136	2181	2.431771	CCGTCGTCAATGCGGTCA	60.432	61.111	0.00	0.0	40.53	4.02
2290	2336	4.470304	GGAACAACTACCACCTAGAGGAAT	59.530	45.833	1.60	0.0	38.94	3.01
2349	2396	1.064003	TGTCCACCACCACATAGCTT	58.936	50.000	0.00	0.0	0.00	3.74
2364	2411	2.126618	CTTGCACGACGACGCCTA	60.127	61.111	7.30	0.0	43.96	3.93
2372	2419	1.403972	CGACGACGCCTACAAGAAGC	61.404	60.000	0.00	0.0	0.00	3.86
2377	2424	0.393077	ACGCCTACAAGAAGCACACT	59.607	50.000	0.00	0.0	0.00	3.55
2379	2426	2.233922	ACGCCTACAAGAAGCACACTAT	59.766	45.455	0.00	0.0	0.00	2.12
2444	2493	0.696501	TGAGGTGGGAAAAGGTAGGC	59.303	55.000	0.00	0.0	0.00	3.93
2456	2505	2.288025	GGTAGGCCAGACCCGAACA	61.288	63.158	14.61	0.0	40.58	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
33	35	2.372172	AGGTCACCACTCCTACCAAAAG	59.628	50.000	0.00	0.00	34.29	2.27
137	139	6.214005	ACAAAGGTTAGCCATACCTGTTACTA	59.786	38.462	0.00	0.00	45.17	1.82
170	175	2.125350	CTCTGACGCCTGGGCTTC	60.125	66.667	10.60	10.60	39.44	3.86
180	185	0.038801	TGTCTTGCAGCTCTCTGACG	60.039	55.000	0.00	0.00	42.95	4.35
184	189	0.252479	CCCATGTCTTGCAGCTCTCT	59.748	55.000	0.00	0.00	0.00	3.10
190	195	6.057533	TCTTAACATATCCCATGTCTTGCAG	58.942	40.000	0.00	0.00	0.00	4.41
248	253	5.997746	TCACTTCATTAAAGTCACCCAGAAG	59.002	40.000	0.00	0.00	45.28	2.85
251	256	5.049405	GTGTCACTTCATTAAAGTCACCCAG	60.049	44.000	0.00	0.00	45.28	4.45
273	278	3.422303	CGTGTCCGTGGGCATGTG	61.422	66.667	4.52	0.00	0.00	3.21
306	311	2.886523	GCATCCATATGTGCTTGGCTTA	59.113	45.455	10.28	0.00	38.30	3.09
378	383	5.893824	ACCTTCTCAAAAGTCCAATCAGTTT	59.106	36.000	0.00	0.00	0.00	2.66
472	477	6.203808	AGTAGTCGTGCATTAGTGTTATCA	57.796	37.500	0.00	0.00	0.00	2.15
481	486	5.488645	TTGTCGATAGTAGTCGTGCATTA	57.511	39.130	0.00	0.00	42.07	1.90
545	550	8.816894	AGAAAATTCTCTGTGTCCTATGAGTTA	58.183	33.333	0.00	0.00	29.94	2.24
626	631	5.633830	TTCACTTCTGCATGGATTTTCTC	57.366	39.130	0.00	0.00	0.00	2.87
640	645	8.375506	TGTGACTTTACCATATCTTTCACTTCT	58.624	33.333	0.00	0.00	34.51	2.85
756	763	3.297134	AGACAAATCCCCACGCATTAT	57.703	42.857	0.00	0.00	0.00	1.28
757	764	2.799126	AGACAAATCCCCACGCATTA	57.201	45.000	0.00	0.00	0.00	1.90
760	767	0.981183	ACTAGACAAATCCCCACGCA	59.019	50.000	0.00	0.00	0.00	5.24
831	863	5.623956	ATGGCATTGATGGTCATTTCATT	57.376	34.783	0.00	0.00	0.00	2.57
911	948	5.529289	GGGAGATGTATATATGGTCCAGGA	58.471	45.833	0.00	0.00	0.00	3.86
1018	1055	4.568152	AAATCAAAACAAGTCTGTCGGG	57.432	40.909	0.00	0.00	33.45	5.14
1021	1058	5.232838	CCAGCAAAATCAAAACAAGTCTGTC	59.767	40.000	0.00	0.00	33.45	3.51
1022	1059	5.111293	CCAGCAAAATCAAAACAAGTCTGT	58.889	37.500	0.00	0.00	37.39	3.41
1036	1073	1.338389	GCATCCAAGCACCAGCAAAAT	60.338	47.619	0.00	0.00	45.49	1.82
1069	1106	9.801873	CCTTATAAATGACCACTTACAATTTGG	57.198	33.333	0.78	0.00	36.39	3.28
1207	1244	0.956633	TGTACCAACGAGTTCTCGCT	59.043	50.000	19.90	7.18	36.44	4.93
1339	1377	4.636648	TGTTTGTCCTTTAAGCAGAAACGA	59.363	37.500	4.58	0.00	0.00	3.85
1435	1473	5.824904	AGCATCCACAATTTATCTGACAC	57.175	39.130	0.00	0.00	0.00	3.67
1447	1485	1.482182	AGCGTCATCTAGCATCCACAA	59.518	47.619	0.00	0.00	35.48	3.33
1494	1532	6.405538	AGATTTTGCCTCAGTTTTGACAAAA	58.594	32.000	9.30	9.30	40.50	2.44
1495	1533	5.976458	AGATTTTGCCTCAGTTTTGACAAA	58.024	33.333	0.00	0.00	31.36	2.83
1555	1595	7.172342	AGGCATAACAAACCACACTAAGAATA	58.828	34.615	0.00	0.00	0.00	1.75
1572	1612	2.325583	TCCATCCGTTGAGGCATAAC	57.674	50.000	0.00	0.00	40.77	1.89
1585	1625	5.561679	AGAGTAGGACTTTGTTTTCCATCC	58.438	41.667	0.00	0.00	33.92	3.51
1586	1626	6.486993	ACAAGAGTAGGACTTTGTTTTCCATC	59.513	38.462	0.00	0.00	30.80	3.51
1596	1636	4.804261	GCCATGTCACAAGAGTAGGACTTT	60.804	45.833	0.00	0.00	0.00	2.66
1599	1639	2.234908	AGCCATGTCACAAGAGTAGGAC	59.765	50.000	0.00	0.00	0.00	3.85
1640	1680	0.394216	CAAGGATTGGATCACCGCCA	60.394	55.000	0.00	0.00	43.94	5.69
1718	1759	3.186001	GTGTACATCATGCTATGCAGAGC	59.814	47.826	26.11	26.11	43.65	4.09
1971	2016	5.809001	TGCAGTTATTCCTTCTGAAGATGT	58.191	37.500	18.68	6.35	36.14	3.06
1981	2026	5.358160	GGCAAGTTCTATGCAGTTATTCCTT	59.642	40.000	0.00	0.00	45.60	3.36
2016	2061	1.918868	CTCGTGGTGACGTCGATGGA	61.919	60.000	11.62	3.70	46.20	3.41
2136	2181	2.233271	CAGGTGGAGCAGTGTTTCATT	58.767	47.619	0.00	0.00	0.00	2.57
2257	2303	0.472352	TAGTTGTTCCGGGGGACACT	60.472	55.000	0.00	2.84	0.00	3.55
2290	2336	0.403655	TTGCAGATTGTGTGCCCCTA	59.596	50.000	0.00	0.00	40.43	3.53
2349	2396	3.196913	TTGTAGGCGTCGTCGTGCA	62.197	57.895	12.77	0.00	39.49	4.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.