AutoCloner

Multiple sequence alignment - TraesCS5D01G535200

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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	TraesCS5D01G535200	chr5D	100.000	3773	0	0	1	3773	549263167	549259395	0.000000e+00	6968
1	TraesCS5D01G535200	chr5D	92.176	3106	147	37	665	3728	549230170	549227119	0.000000e+00	4301
2	TraesCS5D01G535200	chr5D	82.875	1635	223	35	1148	2773	549548153	549546567	0.000000e+00	1415
3	TraesCS5D01G535200	chr5D	82.127	1617	229	35	1148	2755	549430068	549428503	0.000000e+00	1330
4	TraesCS5D01G535200	chr5D	77.023	309	63	8	2127	2431	380695156	380694852	1.800000e-38	171
5	TraesCS5D01G535200	chr4A	92.416	2901	182	19	58	2938	620705699	620702817	0.000000e+00	4104
6	TraesCS5D01G535200	chr4A	90.482	788	50	12	2935	3717	620657557	620656790	0.000000e+00	1016
7	TraesCS5D01G535200	chr4A	87.059	255	28	4	3481	3733	620647381	620647130	2.220000e-72	283
8	TraesCS5D01G535200	chr5B	91.110	2261	131	22	624	2845	700857025	700854796	0.000000e+00	2998
9	TraesCS5D01G535200	chr5B	82.508	1635	231	37	1148	2773	701051702	701050114	0.000000e+00	1384
10	TraesCS5D01G535200	chr5B	88.753	898	62	12	2842	3728	700845755	700844886	0.000000e+00	1062
11	TraesCS5D01G535200	chr5B	76.774	310	64	8	2126	2431	456637949	456637644	2.330000e-37	167
12	TraesCS5D01G535200	chr7D	85.977	870	107	11	1142	1998	162823654	162822787	0.000000e+00	917
13	TraesCS5D01G535200	chr7A	85.780	872	103	15	1142	1998	163617765	163616900	0.000000e+00	904
14	TraesCS5D01G535200	chr2D	84.936	863	106	12	1148	2008	110843195	110842355	0.000000e+00	852
15	TraesCS5D01G535200	chr2B	84.820	863	107	13	1148	2008	159971028	159970188	0.000000e+00	846
16	TraesCS5D01G535200	chr2A	84.571	862	111	11	1148	2008	107182762	107181922	0.000000e+00	835
17	TraesCS5D01G535200	chr3D	78.404	639	121	15	2125	2756	426048494	426049122	2.110000e-107	399
18	TraesCS5D01G535200	chr3B	78.233	634	123	14	2129	2756	556350152	556349528	3.530000e-105	392

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	TraesCS5D01G535200	chr5D	549259395	549263167	3772	True	6968	6968	100.000	1	3773	1	chr5D.!!$R3	3772
1	TraesCS5D01G535200	chr5D	549227119	549230170	3051	True	4301	4301	92.176	665	3728	1	chr5D.!!$R2	3063
2	TraesCS5D01G535200	chr5D	549546567	549548153	1586	True	1415	1415	82.875	1148	2773	1	chr5D.!!$R5	1625
3	TraesCS5D01G535200	chr5D	549428503	549430068	1565	True	1330	1330	82.127	1148	2755	1	chr5D.!!$R4	1607
4	TraesCS5D01G535200	chr4A	620702817	620705699	2882	True	4104	4104	92.416	58	2938	1	chr4A.!!$R3	2880
5	TraesCS5D01G535200	chr4A	620656790	620657557	767	True	1016	1016	90.482	2935	3717	1	chr4A.!!$R2	782
6	TraesCS5D01G535200	chr5B	700854796	700857025	2229	True	2998	2998	91.110	624	2845	1	chr5B.!!$R3	2221
7	TraesCS5D01G535200	chr5B	701050114	701051702	1588	True	1384	1384	82.508	1148	2773	1	chr5B.!!$R4	1625
8	TraesCS5D01G535200	chr5B	700844886	700845755	869	True	1062	1062	88.753	2842	3728	1	chr5B.!!$R2	886
9	TraesCS5D01G535200	chr7D	162822787	162823654	867	True	917	917	85.977	1142	1998	1	chr7D.!!$R1	856
10	TraesCS5D01G535200	chr7A	163616900	163617765	865	True	904	904	85.780	1142	1998	1	chr7A.!!$R1	856
11	TraesCS5D01G535200	chr2D	110842355	110843195	840	True	852	852	84.936	1148	2008	1	chr2D.!!$R1	860
12	TraesCS5D01G535200	chr2B	159970188	159971028	840	True	846	846	84.820	1148	2008	1	chr2B.!!$R1	860
13	TraesCS5D01G535200	chr2A	107181922	107182762	840	True	835	835	84.571	1148	2008	1	chr2A.!!$R1	860
14	TraesCS5D01G535200	chr3D	426048494	426049122	628	False	399	399	78.404	2125	2756	1	chr3D.!!$F1	631
15	TraesCS5D01G535200	chr3B	556349528	556350152	624	True	392	392	78.233	2129	2756	1	chr3B.!!$R1	627

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
25	26	0.027586	AACTCGAGCAAAACACACGC	59.972	50.0	13.61	0.00	0.00	5.34	F
218	220	0.235404	CTTGCCCAAATTTGCGCAAC	59.765	50.0	30.04	10.16	44.32	4.17	F
1080	1135	0.242825	CCTTCACAATGCTGGTGCTG	59.757	55.0	0.00	0.00	40.48	4.41	F
1663	1727	0.464036	ATTCGGCAGGCGATACTTCA	59.536	50.0	21.13	4.05	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1064	1119	1.879380	GTAACAGCACCAGCATTGTGA	59.121	47.619	4.67	45.49	3.58	R
1695	1762	2.204136	TGCTCCACCTCCATGGGT	60.204	61.111	13.02	40.49	4.51	R
2394	2474	0.623723	GGCTTCCCTTGGGTATGTGA	59.376	55.000	5.51	0.00	3.58	R
3409	3506	0.539051	CCCTGAGAATCTTCGCCAGT	59.461	55.000	11.56	33.79	4.00	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	4.654015	GTGTAAAACTCGAGCAAAACACA	58.346	39.130	24.91	15.05	36.77	3.72
23	24	4.494410	GTGTAAAACTCGAGCAAAACACAC	59.506	41.667	24.91	20.29	36.77	3.82
24	25	2.452006	AAACTCGAGCAAAACACACG	57.548	45.000	13.61	0.00	0.00	4.49
25	26	0.027586	AACTCGAGCAAAACACACGC	59.972	50.000	13.61	0.00	0.00	5.34
26	27	1.087202	ACTCGAGCAAAACACACGCA	61.087	50.000	13.61	0.00	0.00	5.24
27	28	0.383491	CTCGAGCAAAACACACGCAG	60.383	55.000	0.00	0.00	0.00	5.18
28	29	2.005537	CGAGCAAAACACACGCAGC	61.006	57.895	0.00	0.00	0.00	5.25
29	30	1.658409	GAGCAAAACACACGCAGCC	60.658	57.895	0.00	0.00	0.00	4.85
30	31	2.658268	GCAAAACACACGCAGCCC	60.658	61.111	0.00	0.00	0.00	5.19
31	32	2.027460	CAAAACACACGCAGCCCC	59.973	61.111	0.00	0.00	0.00	5.80
32	33	2.441164	AAAACACACGCAGCCCCA	60.441	55.556	0.00	0.00	0.00	4.96
33	34	2.055042	AAAACACACGCAGCCCCAA	61.055	52.632	0.00	0.00	0.00	4.12
34	35	2.291457	AAAACACACGCAGCCCCAAC	62.291	55.000	0.00	0.00	0.00	3.77
35	36	3.714487	AACACACGCAGCCCCAACT	62.714	57.895	0.00	0.00	0.00	3.16
36	37	3.357079	CACACGCAGCCCCAACTC	61.357	66.667	0.00	0.00	0.00	3.01
37	38	4.643387	ACACGCAGCCCCAACTCC	62.643	66.667	0.00	0.00	0.00	3.85
46	47	4.323477	CCCAACTCCCACGCGGAA	62.323	66.667	12.47	0.00	41.40	4.30
47	48	3.047877	CCAACTCCCACGCGGAAC	61.048	66.667	12.47	0.00	41.40	3.62
48	49	2.280524	CAACTCCCACGCGGAACA	60.281	61.111	12.47	0.00	41.40	3.18
49	50	1.671054	CAACTCCCACGCGGAACAT	60.671	57.895	12.47	0.00	41.40	2.71
50	51	1.072505	AACTCCCACGCGGAACATT	59.927	52.632	12.47	0.00	41.40	2.71
51	52	0.953960	AACTCCCACGCGGAACATTC	60.954	55.000	12.47	0.00	41.40	2.67
52	53	1.079127	CTCCCACGCGGAACATTCT	60.079	57.895	12.47	0.00	41.40	2.40
53	54	1.079405	TCCCACGCGGAACATTCTC	60.079	57.895	12.47	0.00	37.88	2.87
54	55	2.452813	CCCACGCGGAACATTCTCG	61.453	63.158	12.47	5.66	0.00	4.04

Showing 1 to 25 of 134 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.494410	GTGTGTTTTGCTCGAGTTTTACAC	59.506	41.667	23.67	23.67	36.19	2.90
1	2	4.654015	GTGTGTTTTGCTCGAGTTTTACA	58.346	39.130	15.13	10.84	0.00	2.41
2	3	3.717404	CGTGTGTTTTGCTCGAGTTTTAC	59.283	43.478	15.13	8.40	0.00	2.01
3	4	3.786161	GCGTGTGTTTTGCTCGAGTTTTA	60.786	43.478	15.13	0.00	0.00	1.52
4	5	2.780993	CGTGTGTTTTGCTCGAGTTTT	58.219	42.857	15.13	0.00	0.00	2.43
5	6	1.531058	GCGTGTGTTTTGCTCGAGTTT	60.531	47.619	15.13	0.00	0.00	2.66
6	7	0.027586	GCGTGTGTTTTGCTCGAGTT	59.972	50.000	15.13	0.00	0.00	3.01
7	8	1.087202	TGCGTGTGTTTTGCTCGAGT	61.087	50.000	15.13	0.00	0.00	4.18
8	9	0.383491	CTGCGTGTGTTTTGCTCGAG	60.383	55.000	8.45	8.45	0.00	4.04
9	10	1.641140	CTGCGTGTGTTTTGCTCGA	59.359	52.632	0.00	0.00	0.00	4.04
10	11	2.005537	GCTGCGTGTGTTTTGCTCG	61.006	57.895	0.00	0.00	0.00	5.03
11	12	1.658409	GGCTGCGTGTGTTTTGCTC	60.658	57.895	0.00	0.00	0.00	4.26
12	13	2.412937	GGCTGCGTGTGTTTTGCT	59.587	55.556	0.00	0.00	0.00	3.91
13	14	2.658268	GGGCTGCGTGTGTTTTGC	60.658	61.111	0.00	0.00	0.00	3.68
14	15	2.027460	GGGGCTGCGTGTGTTTTG	59.973	61.111	0.00	0.00	0.00	2.44
15	16	2.055042	TTGGGGCTGCGTGTGTTTT	61.055	52.632	0.00	0.00	0.00	2.43
16	17	2.441164	TTGGGGCTGCGTGTGTTT	60.441	55.556	0.00	0.00	0.00	2.83
17	18	3.216292	GTTGGGGCTGCGTGTGTT	61.216	61.111	0.00	0.00	0.00	3.32
18	19	4.189580	AGTTGGGGCTGCGTGTGT	62.190	61.111	0.00	0.00	0.00	3.72
19	20	3.357079	GAGTTGGGGCTGCGTGTG	61.357	66.667	0.00	0.00	0.00	3.82
20	21	4.643387	GGAGTTGGGGCTGCGTGT	62.643	66.667	0.00	0.00	0.00	4.49
35	36	1.079405	GAGAATGTTCCGCGTGGGA	60.079	57.895	16.49	2.36	45.40	4.37
36	37	2.452813	CGAGAATGTTCCGCGTGGG	61.453	63.158	16.49	1.03	35.24	4.61
37	38	3.081133	CGAGAATGTTCCGCGTGG	58.919	61.111	9.28	9.28	0.00	4.94
38	39	2.395690	GCGAGAATGTTCCGCGTG	59.604	61.111	4.92	0.00	37.22	5.34

Showing 1 to 25 of 126 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.