AutoCloner

Multiple sequence alignment - TraesCS5B01G110800

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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	TraesCS5B01G110800	chr5B	100.000	4958	0	0	801	5758	162775892	162770935	0.000000e+00	9156
1	TraesCS5B01G110800	chr5B	100.000	410	0	0	1	410	162776692	162776283	0.000000e+00	758
2	TraesCS5B01G110800	chr5D	96.305	4871	113	35	808	5649	170381257	170376425	0.000000e+00	7936
3	TraesCS5B01G110800	chr5D	97.500	360	9	0	1	360	170381699	170381340	2.950000e-172	616
4	TraesCS5B01G110800	chr5D	95.556	90	4	0	3832	3921	509426471	509426560	1.670000e-30	145
5	TraesCS5B01G110800	chr5D	94.521	73	3	1	5687	5758	170376425	170376353	1.700000e-20	111
6	TraesCS5B01G110800	chr5A	96.704	3064	52	10	812	3833	175832413	175835469	0.000000e+00	5053
7	TraesCS5B01G110800	chr5A	95.043	1513	37	13	3915	5408	175835468	175836961	0.000000e+00	2344
8	TraesCS5B01G110800	chr5A	96.620	355	10	2	9	362	175832014	175832367	6.430000e-164	588
9	TraesCS5B01G110800	chr5A	95.950	321	11	1	5440	5758	175836960	175837280	2.380000e-143	520
10	TraesCS5B01G110800	chr5A	81.343	134	23	2	5477	5608	494224356	494224223	2.190000e-19	108
11	TraesCS5B01G110800	chr6B	97.727	88	2	0	3829	3916	713960523	713960610	9.990000e-33	152
12	TraesCS5B01G110800	chr3A	96.703	91	3	0	3830	3920	642160657	642160747	9.990000e-33	152
13	TraesCS5B01G110800	chr3A	92.929	99	4	2	3818	3916	710277979	710277884	2.160000e-29	141
14	TraesCS5B01G110800	chr2B	94.792	96	5	0	3830	3925	28631534	28631629	3.590000e-32	150
15	TraesCS5B01G110800	chr2B	94.667	75	4	0	3915	3989	446046915	446046989	3.650000e-22	117
16	TraesCS5B01G110800	chr3D	95.604	91	4	0	3829	3919	497908041	497907951	4.650000e-31	147
17	TraesCS5B01G110800	chr3B	95.604	91	4	0	3832	3922	551513972	551513882	4.650000e-31	147
18	TraesCS5B01G110800	chr4B	90.566	106	8	2	3815	3919	423051097	423050993	7.780000e-29	139
19	TraesCS5B01G110800	chr1A	98.571	70	1	0	3917	3986	469589921	469589990	2.180000e-24	124
20	TraesCS5B01G110800	chr1D	98.551	69	1	0	3915	3983	233084864	233084796	7.840000e-24	122
21	TraesCS5B01G110800	chr1D	94.737	76	3	1	3915	3989	74276328	74276253	3.650000e-22	117
22	TraesCS5B01G110800	chr7D	97.183	71	2	0	3915	3985	620699455	620699525	2.820000e-23	121
23	TraesCS5B01G110800	chr4D	91.463	82	7	0	3900	3981	49514676	49514757	4.720000e-21	113
24	TraesCS5B01G110800	chr2D	94.366	71	4	0	3915	3985	461087353	461087283	6.100000e-20	110
25	TraesCS5B01G110800	chr6A	80.741	135	22	4	5477	5608	613628513	613628380	1.020000e-17	102

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	TraesCS5B01G110800	chr5B	162770935	162776692	5757	True	4957.000000	9156	100.000000	1	5758	2	chr5B.!!$R1	5757
1	TraesCS5B01G110800	chr5D	170376353	170381699	5346	True	2887.666667	7936	96.108667	1	5758	3	chr5D.!!$R1	5757
2	TraesCS5B01G110800	chr5A	175832014	175837280	5266	False	2126.250000	5053	96.079250	9	5758	4	chr5A.!!$F1	5749

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
208	209	2.671396	CTCGTTTTGATCCGGTTACCTG	59.329	50.0	0.00	0.0	0.00	4.00	F
1017	1027	0.469494	TCATGGACATGGTGGGATCG	59.531	55.0	11.98	0.0	39.24	3.69	F
1311	1321	0.472925	TGCCTCAGGGTGTAGGTTCA	60.473	55.0	0.00	0.0	35.16	3.18	F
2039	2049	1.237285	ATCAACGGCAAGAGTGGTGC	61.237	55.0	0.00	0.0	41.45	5.01	F
3599	3636	0.256752	CATGGATTCAGCCACCTGGA	59.743	55.0	0.00	0.0	41.56	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1231	1241	1.071471	CACCACGGAAGCAGTCCTT	59.929	57.895	5.06	0.0	45.36	3.36	R
2691	2701	2.104967	ACCTTGGCATCACATCCAATG	58.895	47.619	0.00	0.0	41.10	2.82	R
3227	3240	2.236146	CAACACCACCCATGTAGCTAGA	59.764	50.000	0.00	0.0	0.00	2.43	R
3985	4032	0.037232	GCTAAGACAAGCCACCGAGT	60.037	55.000	0.00	0.0	36.45	4.18	R
5073	5134	2.624838	CCCAAAGCTATGCCTATTGTGG	59.375	50.000	0.00	0.0	0.00	4.17	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
208	209	2.671396	CTCGTTTTGATCCGGTTACCTG	59.329	50.000	0.00	0.00	0.00	4.00
283	285	5.888161	GGTGAATCCAAGGTGATCAATTAGT	59.112	40.000	0.00	0.00	35.97	2.24
311	313	2.938756	GCCAGAGAGGAGACCACAATTG	60.939	54.545	3.24	3.24	41.22	2.32
365	367	9.699106	TTTTTCTCCCCTTATATATTACTCCCT	57.301	33.333	0.00	0.00	0.00	4.20
367	369	7.865347	TCTCCCCTTATATATTACTCCCTCT	57.135	40.000	0.00	0.00	0.00	3.69
369	371	7.244239	TCTCCCCTTATATATTACTCCCTCTGT	59.756	40.741	0.00	0.00	0.00	3.41
370	372	8.486556	TCCCCTTATATATTACTCCCTCTGTA	57.513	38.462	0.00	0.00	0.00	2.74
371	373	8.918601	TCCCCTTATATATTACTCCCTCTGTAA	58.081	37.037	0.00	0.00	34.87	2.41
372	374	9.556772	CCCCTTATATATTACTCCCTCTGTAAA	57.443	37.037	0.00	0.00	34.20	2.01
377	379	4.820894	ATTACTCCCTCTGTAAAAGCGT	57.179	40.909	0.00	0.00	34.20	5.07
379	381	3.487120	ACTCCCTCTGTAAAAGCGTTT	57.513	42.857	2.53	2.53	0.00	3.60
380	382	4.612264	ACTCCCTCTGTAAAAGCGTTTA	57.388	40.909	0.33	0.33	0.00	2.01
381	383	4.566987	ACTCCCTCTGTAAAAGCGTTTAG	58.433	43.478	5.01	0.00	29.74	1.85
382	384	4.040095	ACTCCCTCTGTAAAAGCGTTTAGT	59.960	41.667	5.01	0.00	29.74	2.24
383	385	4.964593	TCCCTCTGTAAAAGCGTTTAGTT	58.035	39.130	5.01	0.00	29.74	2.24
385	387	6.523840	TCCCTCTGTAAAAGCGTTTAGTTAA	58.476	36.000	5.01	0.00	29.74	2.01
386	388	7.163441	TCCCTCTGTAAAAGCGTTTAGTTAAT	58.837	34.615	5.01	0.00	29.74	1.40
387	389	7.332678	TCCCTCTGTAAAAGCGTTTAGTTAATC	59.667	37.037	5.01	0.00	29.74	1.75
388	390	7.333672	CCCTCTGTAAAAGCGTTTAGTTAATCT	59.666	37.037	5.01	0.00	29.74	2.40
843	845	5.640732	ACTGATGTCCGAAAATTATTGTGC	58.359	37.500	0.00	0.00	0.00	4.57
847	849	4.804108	TGTCCGAAAATTATTGTGCAAGG	58.196	39.130	0.00	0.00	0.00	3.61
1006	1016	4.819783	GGCCAACTGTCATGGACA	57.180	55.556	0.00	0.00	45.90	4.02
1017	1027	0.469494	TCATGGACATGGTGGGATCG	59.531	55.000	11.98	0.00	39.24	3.69
1231	1241	0.911769	CTCAAGCCATACCTGGACCA	59.088	55.000	0.00	0.00	46.37	4.02
1308	1318	1.201429	CCTTGCCTCAGGGTGTAGGT	61.201	60.000	0.00	0.00	35.16	3.08
1311	1321	0.472925	TGCCTCAGGGTGTAGGTTCA	60.473	55.000	0.00	0.00	35.16	3.18
1687	1697	3.283751	TCGGTGAAACAAGTTGGTCAAT	58.716	40.909	7.96	0.00	39.98	2.57
1815	1825	2.813754	GTCTGGCATTAAGACAACTGCA	59.186	45.455	0.21	0.00	42.98	4.41
1875	1885	4.500499	AGGATTTGCTAGACTGCAGAAT	57.500	40.909	23.35	10.77	44.27	2.40
1958	1968	6.484643	ACATGTGGATCTGACATTACTAATGC	59.515	38.462	0.00	3.35	42.69	3.56
2039	2049	1.237285	ATCAACGGCAAGAGTGGTGC	61.237	55.000	0.00	0.00	41.45	5.01
2155	2165	6.194235	ACACCTTATATTTTGCAATGGAGGA	58.806	36.000	0.00	0.00	0.00	3.71
2609	2619	3.519913	AGACTATCCTTCAACTTCCACCC	59.480	47.826	0.00	0.00	0.00	4.61
2691	2701	9.162764	TGATTTAGTTTCTATTGACTTGTAGGC	57.837	33.333	0.00	0.00	0.00	3.93
2772	2782	6.203723	CAGATAAATTTAGCAGTCAGGTAGGC	59.796	42.308	15.37	0.00	0.00	3.93
2822	2835	7.925483	ACAGCTTAAATCTATCTTACTGCAGAG	59.075	37.037	23.35	8.59	0.00	3.35
2893	2906	7.032377	AGAACAGTTTCTTGTGAAATTCCTC	57.968	36.000	0.00	0.00	43.14	3.71
3227	3240	8.032045	AGAAGGTGTGATCATTCTGAATATCT	57.968	34.615	8.21	0.40	37.14	1.98
3432	3469	7.340122	TCGCTTCTATATAATGCTATCAGCT	57.660	36.000	0.00	0.00	42.97	4.24
3599	3636	0.256752	CATGGATTCAGCCACCTGGA	59.743	55.000	0.00	0.00	41.56	3.86
3639	3676	3.257624	CCGTGGACAGGTACTTTACTTCT	59.742	47.826	0.00	0.00	34.60	2.85
3793	3837	1.664649	CTTCGAACTCCACGCAGCA	60.665	57.895	0.00	0.00	0.00	4.41
3812	3856	2.359900	CAAAGGGATTCCGTTCTCCAG	58.640	52.381	10.89	0.00	38.33	3.86
3952	3996	1.880271	CATCGATTGATGCAGAGGCT	58.120	50.000	10.05	0.00	45.06	4.58
4589	4647	1.205064	CGTTTCTGACGCTGCCTTG	59.795	57.895	0.00	0.00	45.86	3.61
4590	4648	1.081840	GTTTCTGACGCTGCCTTGC	60.082	57.895	0.00	0.00	0.00	4.01
4591	4649	1.227943	TTTCTGACGCTGCCTTGCT	60.228	52.632	0.00	0.00	0.00	3.91
4592	4650	1.509644	TTTCTGACGCTGCCTTGCTG	61.510	55.000	0.00	0.00	0.00	4.41
4771	4829	3.528078	TCCTCCTGACAGTCCATACTACT	59.472	47.826	0.93	0.00	33.48	2.57
5066	5127	6.671614	TTTTGTAACTGGAGTGTGTGTTAG	57.328	37.500	0.00	0.00	0.00	2.34
5067	5128	5.347620	TTGTAACTGGAGTGTGTGTTAGT	57.652	39.130	0.00	0.00	0.00	2.24
5068	5129	4.689071	TGTAACTGGAGTGTGTGTTAGTG	58.311	43.478	0.00	0.00	0.00	2.74
5069	5130	3.906720	AACTGGAGTGTGTGTTAGTGT	57.093	42.857	0.00	0.00	0.00	3.55
5070	5131	3.454371	ACTGGAGTGTGTGTTAGTGTC	57.546	47.619	0.00	0.00	0.00	3.67
5071	5132	3.031736	ACTGGAGTGTGTGTTAGTGTCT	58.968	45.455	0.00	0.00	0.00	3.41
5072	5133	3.451178	ACTGGAGTGTGTGTTAGTGTCTT	59.549	43.478	0.00	0.00	0.00	3.01
5073	5134	4.051922	CTGGAGTGTGTGTTAGTGTCTTC	58.948	47.826	0.00	0.00	0.00	2.87
5074	5135	3.181469	TGGAGTGTGTGTTAGTGTCTTCC	60.181	47.826	0.00	0.00	0.00	3.46
5075	5136	3.181469	GGAGTGTGTGTTAGTGTCTTCCA	60.181	47.826	0.00	0.00	0.00	3.53
5183	5244	4.454678	TCTTGATGTATGTCTGCAATCCC	58.545	43.478	0.00	0.00	0.00	3.85
5288	5350	7.062848	CACGAAATGAAAATAAAACAAGGTGC	58.937	34.615	0.00	0.00	0.00	5.01
5363	5426	6.238759	GGTCTTCATTCATATAGCCACAAACC	60.239	42.308	0.00	0.00	0.00	3.27
5452	5515	6.700352	TCATTCCCCACAATTTTCATTCTTC	58.300	36.000	0.00	0.00	0.00	2.87
5577	5641	6.867662	ACTATGGTGAAACAGAAGAACAAG	57.132	37.500	0.00	0.00	39.98	3.16
5620	5684	4.559862	AACCCTCTCAACCTTCATACAG	57.440	45.455	0.00	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
167	168	2.036862	AGACAAGGAAACCGGAGTACAC	59.963	50.000	9.46	0.00	0.00	2.90
171	172	0.317479	CGAGACAAGGAAACCGGAGT	59.683	55.000	9.46	0.00	0.00	3.85
208	209	2.679996	AACCAAATCGGGGCCAGC	60.680	61.111	4.39	0.00	40.22	4.85
311	313	6.483640	ACAGCATATAGGAAAATTCTCGTTCC	59.516	38.462	0.00	0.00	43.17	3.62
363	365	8.252964	AGATTAACTAAACGCTTTTACAGAGG	57.747	34.615	0.00	0.00	0.00	3.69
804	806	9.040939	CGGACATCAGTATATTATTCACAACAA	57.959	33.333	0.00	0.00	0.00	2.83
805	807	8.417884	TCGGACATCAGTATATTATTCACAACA	58.582	33.333	0.00	0.00	0.00	3.33
806	808	8.812147	TCGGACATCAGTATATTATTCACAAC	57.188	34.615	0.00	0.00	0.00	3.32
807	809	9.825109	TTTCGGACATCAGTATATTATTCACAA	57.175	29.630	0.00	0.00	0.00	3.33
808	810	9.825109	TTTTCGGACATCAGTATATTATTCACA	57.175	29.630	0.00	0.00	0.00	3.58
843	845	3.181479	TGGCGCTACTGTATCTTACCTTG	60.181	47.826	7.64	0.00	0.00	3.61
847	849	3.431922	TGTGGCGCTACTGTATCTTAC	57.568	47.619	24.82	0.00	0.00	2.34
987	997	0.184692	TGTCCATGACAGTTGGCCAA	59.815	50.000	16.05	16.05	37.67	4.52
1006	1016	1.703014	ATCAGCAGCGATCCCACCAT	61.703	55.000	0.00	0.00	0.00	3.55
1017	1027	1.331756	CGGGTCATGTTTATCAGCAGC	59.668	52.381	0.00	0.00	0.00	5.25
1231	1241	1.071471	CACCACGGAAGCAGTCCTT	59.929	57.895	5.06	0.00	45.36	3.36
1311	1321	2.606587	ATCAGCGTCAAGGGCCCTT	61.607	57.895	32.48	32.48	36.60	3.95
1368	1378	2.185350	CCCTGCGAGCAGTACCAG	59.815	66.667	21.73	7.65	42.15	4.00
1687	1697	3.164977	TCCACTGGTTGCCGGACA	61.165	61.111	5.05	0.00	33.36	4.02
1815	1825	4.520492	AGAATTGAACTGTCTGCGGAAATT	59.480	37.500	0.00	0.00	0.00	1.82
1875	1885	5.425217	TGCCAGAGTATACTTTCCATTCAGA	59.575	40.000	6.88	0.00	0.00	3.27
1958	1968	5.936956	ACAAGCTCATACTTCTTTTCCTCTG	59.063	40.000	0.00	0.00	0.00	3.35
2155	2165	7.398024	AGGTTAGAGCATCAAATCTGTTACTT	58.602	34.615	0.00	0.00	37.82	2.24
2609	2619	9.229784	GCAATACATCAAATGTTGACTAAGATG	57.770	33.333	0.00	0.00	43.48	2.90
2691	2701	2.104967	ACCTTGGCATCACATCCAATG	58.895	47.619	0.00	0.00	41.10	2.82
2796	2809	7.786030	TCTGCAGTAAGATAGATTTAAGCTGT	58.214	34.615	14.67	0.00	0.00	4.40
2843	2856	9.810870	TCATGTGGGAATATGATAAATTCATGA	57.189	29.630	0.00	0.00	44.90	3.07
2893	2906	9.763465	GCATTGTCTGAAATGGAAAAATTATTG	57.237	29.630	11.68	0.00	37.89	1.90
2902	2915	6.647334	TGTTTAGCATTGTCTGAAATGGAA	57.353	33.333	11.68	0.00	37.89	3.53
3227	3240	2.236146	CAACACCACCCATGTAGCTAGA	59.764	50.000	0.00	0.00	0.00	2.43
3432	3469	9.953697	AGTTAACGCTAACATTATTGTTGAAAA	57.046	25.926	11.07	0.00	45.56	2.29
3658	3695	6.484818	TGTGTGTGTGTGAATTCTATCATG	57.515	37.500	7.05	0.00	0.00	3.07
3793	3837	1.282157	CCTGGAGAACGGAATCCCTTT	59.718	52.381	0.00	0.00	34.47	3.11
3853	3897	9.088512	CACTAAAGTATTGATCTAAACGCTCTT	57.911	33.333	0.00	0.00	0.00	2.85
3856	3900	9.250624	GATCACTAAAGTATTGATCTAAACGCT	57.749	33.333	7.85	0.00	40.02	5.07
3903	3947	4.282703	GCCATCTTTATTACTCCCTCCGTA	59.717	45.833	0.00	0.00	0.00	4.02
3904	3948	3.071167	GCCATCTTTATTACTCCCTCCGT	59.929	47.826	0.00	0.00	0.00	4.69
3905	3949	3.325135	AGCCATCTTTATTACTCCCTCCG	59.675	47.826	0.00	0.00	0.00	4.63
3906	3950	4.646572	CAGCCATCTTTATTACTCCCTCC	58.353	47.826	0.00	0.00	0.00	4.30
3952	3996	2.518834	TGAAAAGGAGGTTAAACCCCCA	59.481	45.455	0.00	0.00	39.75	4.96
3985	4032	0.037232	GCTAAGACAAGCCACCGAGT	60.037	55.000	0.00	0.00	36.45	4.18
4037	4084	2.288961	TAACGATTCGCTCCCTGTTC	57.711	50.000	5.86	0.00	0.00	3.18
4086	4133	1.070175	CGTTCATGACCACCAAACGTC	60.070	52.381	0.00	0.00	38.24	4.34
4202	4249	2.363680	GAGCTGAGCCAGAGCATAGTAA	59.636	50.000	0.00	0.00	43.56	2.24
4203	4250	1.959985	GAGCTGAGCCAGAGCATAGTA	59.040	52.381	0.00	0.00	43.56	1.82
4208	4255	3.767806	CGGAGCTGAGCCAGAGCA	61.768	66.667	0.00	0.00	43.56	4.26
4549	4607	5.133264	CGATTTCGCTATGTATTTGCACTC	58.867	41.667	0.00	0.00	0.00	3.51
4771	4829	4.281182	GTGTTAGGTTTCTGAGTGGAGAGA	59.719	45.833	0.00	0.00	0.00	3.10
5042	5103	5.968528	AACACACACTCCAGTTACAAAAA	57.031	34.783	0.00	0.00	0.00	1.94
5067	5128	3.455910	AGCTATGCCTATTGTGGAAGACA	59.544	43.478	0.00	0.00	0.00	3.41
5068	5129	4.078639	AGCTATGCCTATTGTGGAAGAC	57.921	45.455	0.00	0.00	0.00	3.01
5069	5130	4.778213	AAGCTATGCCTATTGTGGAAGA	57.222	40.909	0.00	0.00	0.00	2.87
5070	5131	4.037208	CCAAAGCTATGCCTATTGTGGAAG	59.963	45.833	0.00	0.00	0.00	3.46
5071	5132	3.953612	CCAAAGCTATGCCTATTGTGGAA	59.046	43.478	0.00	0.00	0.00	3.53
5072	5133	3.554934	CCAAAGCTATGCCTATTGTGGA	58.445	45.455	0.00	0.00	0.00	4.02
5073	5134	2.624838	CCCAAAGCTATGCCTATTGTGG	59.375	50.000	0.00	0.00	0.00	4.17
5074	5135	2.624838	CCCCAAAGCTATGCCTATTGTG	59.375	50.000	0.00	0.00	0.00	3.33
5075	5136	2.949447	CCCCAAAGCTATGCCTATTGT	58.051	47.619	0.00	0.00	0.00	2.71
5183	5244	4.853196	CACACAAATTTTCAGCACGGATAG	59.147	41.667	0.00	0.00	0.00	2.08
5237	5299	5.816777	CACACAATTTTCCAGTTTTCACCAT	59.183	36.000	0.00	0.00	0.00	3.55
5332	5395	7.661437	GTGGCTATATGAATGAAGACCACAATA	59.339	37.037	0.00	0.00	43.52	1.90
5589	5653	5.953571	AGGTTGAGAGGGTTATTTTTCAGT	58.046	37.500	0.00	0.00	0.00	3.41
5620	5684	0.469144	TCCTTTGGCTTTGGGACCAC	60.469	55.000	0.00	0.00	35.10	4.16
5675	5741	3.127548	ACGCAGCCTGAAGTTCAAATATG	59.872	43.478	7.06	5.07	0.00	1.78
5682	5748	1.347817	CGAGACGCAGCCTGAAGTTC	61.348	60.000	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.