AutoCloner

Multiple sequence alignment - TraesCS5D01G401400

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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	TraesCS5D01G401400	chr5D	100.000	3823	0	0	681	4503	466594650	466598472	0.000000e+00	7060.0
1	TraesCS5D01G401400	chr5D	100.000	192	0	0	1	192	466593970	466594161	5.540000e-94	355.0
2	TraesCS5D01G401400	chr5B	94.068	3220	122	28	681	3853	573494778	573497975	0.000000e+00	4824.0
3	TraesCS5D01G401400	chr5B	88.158	76	3	2	1	75	573490803	573490873	8.030000e-13	86.1
4	TraesCS5D01G401400	chr5A	93.612	2442	94	25	681	3096	586723370	586725775	0.000000e+00	3589.0
5	TraesCS5D01G401400	chr5A	88.706	788	54	18	3094	3853	586725833	586726613	0.000000e+00	929.0
6	TraesCS5D01G401400	chr5A	92.857	154	2	3	1	152	586722616	586722762	9.810000e-52	215.0
7	TraesCS5D01G401400	chr6A	94.504	655	29	5	3853	4503	580272130	580271479	0.000000e+00	1003.0
8	TraesCS5D01G401400	chr1B	96.477	511	12	4	3998	4503	77552628	77552119	0.000000e+00	839.0
9	TraesCS5D01G401400	chr7A	96.471	510	13	4	3998	4503	18539969	18540477	0.000000e+00	837.0
10	TraesCS5D01G401400	chr7A	95.211	522	20	3	3985	4503	670156858	670156339	0.000000e+00	821.0
11	TraesCS5D01G401400	chr4D	87.700	626	69	7	3880	4503	100774943	100774324	0.000000e+00	723.0
12	TraesCS5D01G401400	chr4D	87.540	626	70	7	3880	4503	448178377	448177758	0.000000e+00	717.0
13	TraesCS5D01G401400	chr3D	87.700	626	69	7	3880	4503	29215108	29214489	0.000000e+00	723.0
14	TraesCS5D01G401400	chr7D	87.540	626	71	6	3880	4503	534463988	534463368	0.000000e+00	717.0
15	TraesCS5D01G401400	chr3B	88.321	411	45	3	3880	4289	143541131	143540723	1.460000e-134	490.0
16	TraesCS5D01G401400	chr3B	97.872	47	1	0	3849	3895	633387781	633387827	1.040000e-11	82.4
17	TraesCS5D01G401400	chr3B	97.826	46	1	0	3851	3896	145839618	145839663	3.730000e-11	80.5
18	TraesCS5D01G401400	chr3B	93.878	49	2	1	3852	3900	677425596	677425643	6.250000e-09	73.1
19	TraesCS5D01G401400	chr2D	89.508	305	30	2	4199	4503	392362059	392362361	7.070000e-103	385.0
20	TraesCS5D01G401400	chr2D	100.000	44	0	0	3853	3896	476916295	476916338	1.040000e-11	82.4
21	TraesCS5D01G401400	chr7B	88.583	254	17	10	3855	4107	449514176	449514418	9.470000e-77	298.0
22	TraesCS5D01G401400	chr2A	100.000	44	0	0	3853	3896	509971435	509971478	1.040000e-11	82.4
23	TraesCS5D01G401400	chr2A	100.000	42	0	0	3853	3894	624975584	624975543	1.340000e-10	78.7
24	TraesCS5D01G401400	chr2B	92.727	55	2	2	3841	3894	106014317	106014370	1.340000e-10	78.7

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	TraesCS5D01G401400	chr5D	466593970	466598472	4502	False	3707.500000	7060	100.000	1	4503	2	chr5D.!!$F1	4502
1	TraesCS5D01G401400	chr5B	573490803	573497975	7172	False	2455.050000	4824	91.113	1	3853	2	chr5B.!!$F1	3852
2	TraesCS5D01G401400	chr5A	586722616	586726613	3997	False	1577.666667	3589	91.725	1	3853	3	chr5A.!!$F1	3852
3	TraesCS5D01G401400	chr6A	580271479	580272130	651	True	1003.000000	1003	94.504	3853	4503	1	chr6A.!!$R1	650
4	TraesCS5D01G401400	chr1B	77552119	77552628	509	True	839.000000	839	96.477	3998	4503	1	chr1B.!!$R1	505
5	TraesCS5D01G401400	chr7A	18539969	18540477	508	False	837.000000	837	96.471	3998	4503	1	chr7A.!!$F1	505
6	TraesCS5D01G401400	chr7A	670156339	670156858	519	True	821.000000	821	95.211	3985	4503	1	chr7A.!!$R1	518
7	TraesCS5D01G401400	chr4D	100774324	100774943	619	True	723.000000	723	87.700	3880	4503	1	chr4D.!!$R1	623
8	TraesCS5D01G401400	chr4D	448177758	448178377	619	True	717.000000	717	87.540	3880	4503	1	chr4D.!!$R2	623
9	TraesCS5D01G401400	chr3D	29214489	29215108	619	True	723.000000	723	87.700	3880	4503	1	chr3D.!!$R1	623
10	TraesCS5D01G401400	chr7D	534463368	534463988	620	True	717.000000	717	87.540	3880	4503	1	chr7D.!!$R1	623

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
740	4536	0.543749	GATCCATCCATCGATCCCCC	59.456	60.0	0.0	0.0	30.64	5.40	F
1736	5562	0.393132	GGCCCTTCTTCAGTGCCTAC	60.393	60.0	0.0	0.0	39.05	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2271	6106	0.667993	CACGGCCGCCAATTATCATT	59.332	50.0	28.58	0.0	0.0	2.57	R
3706	7636	0.106894	CCTCTAAACATCTCCCCGGC	59.893	60.0	0.00	0.0	0.0	6.13	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
60	61	1.371558	GCCGCTTCGAATATCCCCT	59.628	57.895	0.00	0.00	0.00	4.79
88	1143	3.541713	GCGCCAAACCCAAACCCA	61.542	61.111	0.00	0.00	0.00	4.51
740	4536	0.543749	GATCCATCCATCGATCCCCC	59.456	60.000	0.00	0.00	30.64	5.40
868	4669	1.977009	CCCCGCCTTTGTTTCTCCC	60.977	63.158	0.00	0.00	0.00	4.30
1124	4929	0.802607	GAGGATGAGGACGACGTTGC	60.803	60.000	0.13	0.00	0.00	4.17
1126	4931	1.080093	GATGAGGACGACGTTGCCA	60.080	57.895	15.74	0.61	0.00	4.92
1223	5049	2.371658	AGCAAGAAAGGGAACAGCTT	57.628	45.000	0.00	0.00	0.00	3.74
1225	5051	3.832527	AGCAAGAAAGGGAACAGCTTTA	58.167	40.909	0.00	0.00	0.00	1.85
1260	5086	8.927721	GTGATCAACATAGAAGATGATGATGAG	58.072	37.037	13.12	0.00	40.20	2.90
1359	5185	2.028112	TGTGCGTGCTTCTCCTAGAAAT	60.028	45.455	0.00	0.00	33.19	2.17
1389	5215	3.065925	GGCTGGATTATGTTTCTGACAGC	59.934	47.826	0.00	0.00	46.71	4.40
1509	5335	0.679321	GGGAGAAGGCTGCTTCAAGG	60.679	60.000	2.39	0.00	35.91	3.61
1517	5343	2.165998	GGCTGCTTCAAGGAGAACAAT	58.834	47.619	10.67	0.00	35.49	2.71
1520	5346	2.555325	CTGCTTCAAGGAGAACAATGCA	59.445	45.455	0.00	0.00	35.49	3.96
1599	5425	5.968261	CGAGTCAAGTACACACTATGATGAG	59.032	44.000	0.00	0.00	33.48	2.90
1736	5562	0.393132	GGCCCTTCTTCAGTGCCTAC	60.393	60.000	0.00	0.00	39.05	3.18
1751	5577	0.618968	CCTACTGCCCAGGAAGGTCT	60.619	60.000	0.00	0.00	34.91	3.85
1861	5696	3.652869	TCCTCCAGAAAGAAGTCACCATT	59.347	43.478	0.00	0.00	0.00	3.16
1927	5762	4.026356	AGCTTTGTCTCTGCAAATAGGT	57.974	40.909	0.00	0.00	37.66	3.08
2175	6010	5.131642	TGGCTTGAGACAATCTGGAGAATAT	59.868	40.000	0.00	0.00	0.00	1.28
2260	6095	7.889873	TTGGTTGAAGATCCTGAAAAGTTAA	57.110	32.000	0.00	0.00	0.00	2.01
2271	6106	8.924511	ATCCTGAAAAGTTAAGACAATCTTCA	57.075	30.769	0.00	0.00	37.89	3.02
2490	6326	5.444744	TTTAAGGACCAGCAGGCTTATAA	57.555	39.130	0.00	0.00	39.06	0.98
2493	6329	2.436173	AGGACCAGCAGGCTTATAAGAC	59.564	50.000	16.85	13.87	39.06	3.01
2811	6651	6.817184	TCCTTTGTAGTATCTAGGTCATTGC	58.183	40.000	0.00	0.00	0.00	3.56
2837	6677	5.743026	TTTTCTTTGCGTGATCTTGTGTA	57.257	34.783	0.00	0.00	0.00	2.90
2942	6782	5.723295	TGGAGCTTGAAATTATTGAAAGGC	58.277	37.500	0.00	0.00	0.00	4.35
3009	6849	1.306654	AAGGGGGCGAGGTATGTCA	60.307	57.895	0.00	0.00	0.00	3.58
3045	6885	2.205074	CTGACACACACAACCTGTCTC	58.795	52.381	0.00	0.00	36.15	3.36
3049	6889	0.249489	ACACACAACCTGTCTCGAGC	60.249	55.000	7.81	3.58	0.00	5.03
3050	6890	0.032678	CACACAACCTGTCTCGAGCT	59.967	55.000	7.81	0.00	0.00	4.09
3051	6891	0.753262	ACACAACCTGTCTCGAGCTT	59.247	50.000	7.81	0.00	0.00	3.74
3102	7002	7.762159	GCTCTTACCTCTGCTATGTAATATTCC	59.238	40.741	0.00	0.00	0.00	3.01
3162	7068	4.946478	AGTACAGATACCAATGGCTCTC	57.054	45.455	0.00	0.00	30.88	3.20
3260	7189	9.836864	TGTTATGATGCAAATCTACAGATAGTT	57.163	29.630	0.00	0.00	33.73	2.24
3282	7211	6.491403	AGTTCTGAATGTAAGCACTGGAAAAT	59.509	34.615	0.00	0.00	0.00	1.82
3343	7272	9.995003	AATGTTCTATCTCCTAATGACTGATTC	57.005	33.333	0.00	0.00	0.00	2.52
3409	7338	0.548510	CCCTCCTGAAGTTCCATCCC	59.451	60.000	0.00	0.00	0.00	3.85
3714	7644	1.102978	CCAAGTTTAATGCCGGGGAG	58.897	55.000	2.18	0.00	0.00	4.30
3757	7687	3.045601	AGGGTCGTTTTCACTGATGAG	57.954	47.619	0.00	0.00	35.83	2.90
3758	7688	2.368875	AGGGTCGTTTTCACTGATGAGT	59.631	45.455	0.00	0.00	35.83	3.41
3771	7701	3.956848	ACTGATGAGTGATAGCAGTAGCA	59.043	43.478	0.00	0.00	42.40	3.49
3772	7702	4.202101	ACTGATGAGTGATAGCAGTAGCAC	60.202	45.833	0.00	0.00	42.40	4.40
3784	7717	3.019564	GCAGTAGCACTTTTCCCATGAT	58.980	45.455	0.00	0.00	41.58	2.45
3786	7719	4.823989	GCAGTAGCACTTTTCCCATGATAT	59.176	41.667	0.00	0.00	41.58	1.63
3864	7797	7.489574	ACTATACCTGTAACTAGTAGAACGC	57.510	40.000	3.59	0.00	0.00	4.84
3866	7799	2.757314	ACCTGTAACTAGTAGAACGCCC	59.243	50.000	3.59	0.00	0.00	6.13
3913	7846	9.790344	ATGCATATACTTTAAGAAGCATCTCTT	57.210	29.630	0.00	0.00	36.86	2.85
3941	7874	5.103728	TGAACTCCTAATCCAATTATGCCCA	60.104	40.000	0.00	0.00	0.00	5.36
4122	8062	6.055588	TCGCCCTTCCTCTATCAATAAAAAG	58.944	40.000	0.00	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	1143	1.102809	GTCCGGGGTCGTTTTGGTTT	61.103	55.000	0.00	0.00	33.95	3.27
868	4669	2.106683	GGTTTGACGGCGATCCTGG	61.107	63.158	16.62	0.00	0.00	4.45
994	4799	3.770040	CCTCCACGACATCGGGCA	61.770	66.667	6.21	0.00	42.34	5.36
997	4802	1.364171	GATCCCTCCACGACATCGG	59.636	63.158	6.21	0.00	44.95	4.18
1124	4929	2.778299	TGAAAACCTCAGATTCCGTGG	58.222	47.619	0.00	0.00	0.00	4.94
1126	4931	6.884295	TCAATAATGAAAACCTCAGATTCCGT	59.116	34.615	0.00	0.00	37.52	4.69
1166	4992	1.345741	CACGGGCTATCTCCACATCAT	59.654	52.381	0.00	0.00	0.00	2.45
1167	4993	0.752658	CACGGGCTATCTCCACATCA	59.247	55.000	0.00	0.00	0.00	3.07
1168	4994	0.753262	ACACGGGCTATCTCCACATC	59.247	55.000	0.00	0.00	0.00	3.06
1169	4995	0.465705	CACACGGGCTATCTCCACAT	59.534	55.000	0.00	0.00	0.00	3.21
1170	4996	0.613572	TCACACGGGCTATCTCCACA	60.614	55.000	0.00	0.00	0.00	4.17
1171	4997	0.179108	GTCACACGGGCTATCTCCAC	60.179	60.000	0.00	0.00	0.00	4.02
1223	5049	9.317936	CTTCTATGTTGATCACATTGCTACTAA	57.682	33.333	13.57	4.54	44.40	2.24
1225	5051	7.559486	TCTTCTATGTTGATCACATTGCTACT	58.441	34.615	13.57	0.00	44.40	2.57
1248	5074	3.502672	CCTCCTCCTCCTCATCATCATCT	60.503	52.174	0.00	0.00	0.00	2.90
1260	5086	0.105709	CCTCCTCTTCCTCCTCCTCC	60.106	65.000	0.00	0.00	0.00	4.30
1359	5185	7.237471	TCAGAAACATAATCCAGCCCATATCTA	59.763	37.037	0.00	0.00	0.00	1.98
1509	5335	3.255149	GGGGATGATGATGCATTGTTCTC	59.745	47.826	0.00	0.00	0.00	2.87
1517	5343	0.854908	ATGTGGGGGATGATGATGCA	59.145	50.000	0.00	0.00	0.00	3.96
1520	5346	1.733385	TCGATGTGGGGGATGATGAT	58.267	50.000	0.00	0.00	0.00	2.45
1599	5425	3.161866	AGTGAAGAGGTTCTCTGGAGTC	58.838	50.000	0.00	0.00	40.28	3.36
1751	5577	3.204831	TCCATGGGAATCATTGTCCATCA	59.795	43.478	13.02	0.00	37.86	3.07
1861	5696	6.173339	GTTTCATGGTTTCATCTAGGTGAGA	58.827	40.000	5.69	0.00	39.01	3.27
1942	5777	6.073331	GGACTATCATCTTTACAATCAGCTGC	60.073	42.308	9.47	0.00	0.00	5.25
2260	6095	6.238842	CCGCCAATTATCATTGAAGATTGTCT	60.239	38.462	17.17	0.00	42.35	3.41
2271	6106	0.667993	CACGGCCGCCAATTATCATT	59.332	50.000	28.58	0.00	0.00	2.57
2310	6145	2.480419	CTCTTGTGCCCTTTTGTACTCG	59.520	50.000	0.00	0.00	0.00	4.18
2416	6251	2.566833	ACCTGTATTGCTGTTGCTGA	57.433	45.000	0.00	0.00	40.48	4.26
2476	6312	3.201290	CACAGTCTTATAAGCCTGCTGG	58.799	50.000	20.60	5.03	35.53	4.85
2490	6326	1.242076	GCATGCCAAAGACACAGTCT	58.758	50.000	6.36	0.00	45.64	3.24
2493	6329	1.470098	GTAGGCATGCCAAAGACACAG	59.530	52.381	37.18	0.00	38.92	3.66
2546	6384	5.534278	TGTGCCAGTGTGAGATTTTGAATTA	59.466	36.000	0.00	0.00	0.00	1.40
2824	6664	9.435802	GAATAGTAAGTACTACACAAGATCACG	57.564	37.037	0.00	0.00	41.18	4.35
2888	6728	0.534412	CCTCGACACTGCTCCTTCAT	59.466	55.000	0.00	0.00	0.00	2.57
2942	6782	8.385858	CAATATTGAAGCCATATCAGTGTATCG	58.614	37.037	10.04	0.00	0.00	2.92
3009	6849	8.770828	GTGTGTGTCAGTAATGTTAGTAATGTT	58.229	33.333	0.00	0.00	0.00	2.71
3029	6869	1.491670	CTCGAGACAGGTTGTGTGTG	58.508	55.000	6.58	0.00	40.56	3.82
3045	6885	3.577649	TTGTCACTAGGAAGAAGCTCG	57.422	47.619	0.00	0.00	0.00	5.03
3051	6891	9.547753	GCAAATAATCTATTGTCACTAGGAAGA	57.452	33.333	0.00	0.00	0.00	2.87
3083	6923	6.036517	GCAATCGGAATATTACATAGCAGAGG	59.963	42.308	0.00	0.00	0.00	3.69
3102	7002	9.515020	AAATAAACATAACCAATACAGCAATCG	57.485	29.630	0.00	0.00	0.00	3.34
3181	7105	6.573664	AATGTTGTGCATTTAGAAGCTACA	57.426	33.333	0.00	0.00	44.82	2.74
3199	7123	7.451255	TGAAATTCAGGTAGTGATCCAAATGTT	59.549	33.333	0.00	0.00	34.17	2.71
3260	7189	9.679661	TTATATTTTCCAGTGCTTACATTCAGA	57.320	29.630	0.00	0.00	0.00	3.27
3343	7272	8.041829	CCTGAAAGAATAAGCATGATATCAGG	57.958	38.462	12.98	12.98	42.80	3.86
3409	7338	3.653256	TCGTTTCTCGATACTCTGTCG	57.347	47.619	0.00	0.00	44.01	4.35
3624	7554	2.129363	TGATGGATGAGGAATGCTCCA	58.871	47.619	0.00	0.00	45.24	3.86
3706	7636	0.106894	CCTCTAAACATCTCCCCGGC	59.893	60.000	0.00	0.00	0.00	6.13
3714	7644	1.340017	TGCCTGCCACCTCTAAACATC	60.340	52.381	0.00	0.00	0.00	3.06
3757	7687	3.623510	GGGAAAAGTGCTACTGCTATCAC	59.376	47.826	0.00	0.00	40.48	3.06
3758	7688	3.263170	TGGGAAAAGTGCTACTGCTATCA	59.737	43.478	0.00	0.00	40.48	2.15
3759	7689	3.873910	TGGGAAAAGTGCTACTGCTATC	58.126	45.455	0.00	0.00	40.48	2.08
3762	7692	2.040278	TCATGGGAAAAGTGCTACTGCT	59.960	45.455	0.00	0.00	40.48	4.24
3763	7693	2.436417	TCATGGGAAAAGTGCTACTGC	58.564	47.619	0.00	0.00	40.20	4.40
3765	7695	6.041637	TCGTATATCATGGGAAAAGTGCTACT	59.958	38.462	0.00	0.00	0.00	2.57
3766	7696	6.220930	TCGTATATCATGGGAAAAGTGCTAC	58.779	40.000	0.00	0.00	0.00	3.58
3768	7698	5.290493	TCGTATATCATGGGAAAAGTGCT	57.710	39.130	0.00	0.00	0.00	4.40
3771	7701	6.099845	AGTCCTTCGTATATCATGGGAAAAGT	59.900	38.462	0.00	0.00	0.00	2.66
3772	7702	6.425114	CAGTCCTTCGTATATCATGGGAAAAG	59.575	42.308	0.00	0.00	0.00	2.27
3784	7717	2.829720	ACAACCAGCAGTCCTTCGTATA	59.170	45.455	0.00	0.00	0.00	1.47
3786	7719	1.045407	ACAACCAGCAGTCCTTCGTA	58.955	50.000	0.00	0.00	0.00	3.43
3913	7846	8.103305	GGCATAATTGGATTAGGAGTTCAGATA	58.897	37.037	0.00	0.00	0.00	1.98
4122	8062	5.386958	TGTAAGTACACATGAGAGGTGTC	57.613	43.478	0.00	0.00	45.89	3.67
4148	8088	1.409427	ACTCTTAGAGGGAATTCGGCG	59.591	52.381	14.24	0.00	33.35	6.46
4205	8147	5.822519	TGAAGGAATGTATACCATTGACTGC	59.177	40.000	0.00	1.88	43.87	4.40
4457	8400	3.531538	TCCATAGGTCTTTCGCAATCAC	58.468	45.455	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.