AutoCloner

Multiple sequence alignment - TraesCS5D01G214300

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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	TraesCS5D01G214300	chr5D	100.000	3747	0	0	639	4385	323914618	323910872	0.000000e+00	6920.0
1	TraesCS5D01G214300	chr5D	100.000	348	0	0	1	348	323915256	323914909	1.030000e-180	643.0
2	TraesCS5D01G214300	chr5A	97.231	3756	70	12	639	4385	421831497	421827767	0.000000e+00	6329.0
3	TraesCS5D01G214300	chr5A	97.989	348	7	0	1	348	421831873	421831526	4.850000e-169	604.0
4	TraesCS5D01G214300	chr5B	97.571	2882	67	3	861	3742	375641459	375638581	0.000000e+00	4931.0
5	TraesCS5D01G214300	chr5B	95.977	348	14	0	1	348	375642187	375641840	2.290000e-157	566.0
6	TraesCS5D01G214300	chr5B	94.311	334	14	4	3891	4224	375638567	375638239	1.410000e-139	507.0
7	TraesCS5D01G214300	chr5B	94.248	226	11	2	639	863	375641813	375641589	1.170000e-90	344.0
8	TraesCS5D01G214300	chr5B	89.941	169	13	3	4218	4385	375620415	375620250	9.550000e-52	215.0
9	TraesCS5D01G214300	chr3D	90.843	2632	219	13	941	3553	340890827	340888199	0.000000e+00	3506.0
10	TraesCS5D01G214300	chr3D	86.747	83	8	1	3606	3685	340888196	340888114	6.040000e-14	89.8
11	TraesCS5D01G214300	chr3D	94.872	39	2	0	3557	3595	69500642	69500680	1.320000e-05	62.1
12	TraesCS5D01G214300	chr3A	91.135	2572	209	9	941	3494	462332822	462335392	0.000000e+00	3469.0
13	TraesCS5D01G214300	chr3B	89.680	2655	230	21	941	3553	439859263	439856611	0.000000e+00	3345.0
14	TraesCS5D01G214300	chr3B	85.714	84	8	3	3606	3685	439856608	439856525	7.810000e-13	86.1
15	TraesCS5D01G214300	chr2D	82.609	207	24	7	639	838	308021576	308021777	5.830000e-39	172.0
16	TraesCS5D01G214300	chr1B	83.422	187	20	8	702	881	402171201	402171019	3.510000e-36	163.0
17	TraesCS5D01G214300	chr4A	78.571	252	43	10	639	886	618675658	618675902	5.870000e-34	156.0
18	TraesCS5D01G214300	chrUn	81.325	166	25	5	647	811	79373929	79374089	3.560000e-26	130.0
19	TraesCS5D01G214300	chrUn	81.325	166	25	5	647	811	79400553	79400713	3.560000e-26	130.0
20	TraesCS5D01G214300	chrUn	90.698	43	4	0	3549	3591	155025677	155025635	1.700000e-04	58.4
21	TraesCS5D01G214300	chr6B	78.818	203	36	7	639	840	679395643	679395839	3.560000e-26	130.0
22	TraesCS5D01G214300	chr6B	97.619	42	1	0	3554	3595	494088511	494088552	6.080000e-09	73.1
23	TraesCS5D01G214300	chr6A	82.353	153	24	3	639	790	594607682	594607832	3.560000e-26	130.0
24	TraesCS5D01G214300	chr4B	72.441	381	94	10	2591	2966	660195944	660195570	1.290000e-20	111.0
25	TraesCS5D01G214300	chr7D	95.745	47	1	1	3550	3595	634214349	634214303	1.690000e-09	75.0
26	TraesCS5D01G214300	chr1D	89.286	56	4	2	3541	3595	296168370	296168316	7.870000e-08	69.4
27	TraesCS5D01G214300	chr1D	92.857	42	3	0	3554	3595	450055840	450055881	1.320000e-05	62.1
28	TraesCS5D01G214300	chr6D	93.182	44	3	0	3552	3595	10677228	10677271	1.020000e-06	65.8

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	TraesCS5D01G214300	chr5D	323910872	323915256	4384	True	3781.50	6920	100.00000	1	4385	2	chr5D.!!$R1	4384
1	TraesCS5D01G214300	chr5A	421827767	421831873	4106	True	3466.50	6329	97.61000	1	4385	2	chr5A.!!$R1	4384
2	TraesCS5D01G214300	chr5B	375638239	375642187	3948	True	1587.00	4931	95.52675	1	4224	4	chr5B.!!$R2	4223
3	TraesCS5D01G214300	chr3D	340888114	340890827	2713	True	1797.90	3506	88.79500	941	3685	2	chr3D.!!$R1	2744
4	TraesCS5D01G214300	chr3A	462332822	462335392	2570	False	3469.00	3469	91.13500	941	3494	1	chr3A.!!$F1	2553
5	TraesCS5D01G214300	chr3B	439856525	439859263	2738	True	1715.55	3345	87.69700	941	3685	2	chr3B.!!$R1	2744

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
887	1020	2.361438	GGGACAGAGGGAGTAATACACG	59.639	54.545	0.0	0.0	0.0	4.49	F
1251	1394	1.742750	GCAAATCCCTACTCCACGGTC	60.743	57.143	0.0	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1791	1935	1.203050	ACCACCCAATTCCCTGTTGAG	60.203	52.381	0.0	0.0	0.00	3.02	R
3495	3668	7.661847	ACTGCTACACTTTACAATAGCTTCTTT	59.338	33.333	0.0	0.0	40.59	2.52	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
40	41	7.947890	ACTGGGAATAACTTGGAATTAAAGACA	59.052	33.333	7.24	0.00	0.00	3.41
266	267	4.957759	AATAGTAATTGGCGGTGTCAAC	57.042	40.909	0.00	0.00	26.97	3.18
887	1020	2.361438	GGGACAGAGGGAGTAATACACG	59.639	54.545	0.00	0.00	0.00	4.49
1251	1394	1.742750	GCAAATCCCTACTCCACGGTC	60.743	57.143	0.00	0.00	0.00	4.79
1347	1490	5.018809	ACAGATAACAATGGCTCAATGGTT	58.981	37.500	0.00	0.00	0.00	3.67
1501	1644	2.223157	TGGCAAAACTTGACGAAAGACG	60.223	45.455	9.13	0.00	43.38	4.18
1620	1764	5.625197	GCCAAGTCCAGATTACAATGCATTT	60.625	40.000	9.83	4.36	0.00	2.32
1621	1765	5.808540	CCAAGTCCAGATTACAATGCATTTG	59.191	40.000	9.83	8.18	41.36	2.32
1726	1870	5.707066	AATAGAGGCTTCAGATTCAGGTT	57.293	39.130	0.00	0.00	0.00	3.50
1791	1935	4.507710	TCAGAATGTACAGCTTGGATGTC	58.492	43.478	0.33	0.00	37.40	3.06
1878	2022	3.763897	GTGGTAAGAATGGGCTTTGTGAT	59.236	43.478	0.00	0.00	0.00	3.06
1921	2065	0.033796	ATGCCCTCCAGAACATGTGG	60.034	55.000	0.00	0.00	36.28	4.17
2820	2969	2.312390	GGTTGGAGCCAAAGGTACAAA	58.688	47.619	3.05	0.00	45.68	2.83
3601	3775	4.020839	TCGTAGTTTTAGTTCAAGGAGGGG	60.021	45.833	0.00	0.00	0.00	4.79
3619	3793	3.910627	AGGGGGTGTGATGGACTAATATC	59.089	47.826	0.00	0.00	0.00	1.63
3710	3891	0.178891	AGAGAGAAGGGGGCAACTCA	60.179	55.000	0.00	0.00	41.13	3.41
3711	3892	0.251634	GAGAGAAGGGGGCAACTCAG	59.748	60.000	0.00	0.00	41.13	3.35
3712	3893	0.474660	AGAGAAGGGGGCAACTCAGT	60.475	55.000	0.00	0.00	41.13	3.41
3723	3904	3.561725	GGGCAACTCAGTTACATCTATGC	59.438	47.826	0.00	0.00	0.00	3.14
3826	4009	8.073768	CAGACGAAAATAAACACCACATTAAGT	58.926	33.333	0.00	0.00	0.00	2.24
3886	4069	1.814793	TAAACGCACCAGCTATTGCA	58.185	45.000	16.65	0.00	42.74	4.08
3887	4070	0.240945	AAACGCACCAGCTATTGCAC	59.759	50.000	16.65	0.00	42.74	4.57
3946	4129	2.084546	GTTGGTCACCCATTAGTCTGC	58.915	52.381	0.00	0.00	41.49	4.26
3950	4133	0.249120	TCACCCATTAGTCTGCACCG	59.751	55.000	0.00	0.00	0.00	4.94
3981	4164	3.305629	CCAAACCAAATGTGTTGACAACG	59.694	43.478	13.46	0.21	35.11	4.10
3995	4178	5.639931	TGTTGACAACGCATTGCTATAGTTA	59.360	36.000	13.46	0.00	39.66	2.24
4088	4278	4.065088	GGCAGACAAAACAGACATGACTA	58.935	43.478	0.00	0.00	0.00	2.59
4089	4279	4.697352	GGCAGACAAAACAGACATGACTAT	59.303	41.667	0.00	0.00	0.00	2.12
4149	4339	1.207329	ACATCACGGGAAGTAGGAAGC	59.793	52.381	0.00	0.00	0.00	3.86
4206	4396	4.557205	TCTCTAGTTTCCGTTTGAGCTTC	58.443	43.478	0.00	0.00	0.00	3.86
4207	4397	4.281182	TCTCTAGTTTCCGTTTGAGCTTCT	59.719	41.667	0.00	0.00	0.00	2.85
4227	4417	4.139786	TCTATTGAGAGGGATGCAAATGC	58.860	43.478	0.00	0.00	42.50	3.56
4240	4430	1.604593	AAATGCTGCAGCCCGTCTT	60.605	52.632	34.64	17.36	41.18	3.01
4241	4431	1.181098	AAATGCTGCAGCCCGTCTTT	61.181	50.000	34.64	21.35	41.18	2.52
4242	4432	1.870055	AATGCTGCAGCCCGTCTTTG	61.870	55.000	34.64	0.00	41.18	2.77
4254	4444	2.359531	CCCGTCTTTGTGTAAAAAGGCA	59.640	45.455	0.63	0.00	40.96	4.75
4258	4448	5.390613	CGTCTTTGTGTAAAAAGGCATAGG	58.609	41.667	0.63	0.00	40.96	2.57
4358	4548	3.921119	AGCTCATTGAATCGCAACAAA	57.079	38.095	0.02	0.00	39.78	2.83
4359	4549	4.241590	AGCTCATTGAATCGCAACAAAA	57.758	36.364	0.02	0.00	39.78	2.44
4360	4550	4.619973	AGCTCATTGAATCGCAACAAAAA	58.380	34.783	0.02	0.00	39.78	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	2.024414	GGTTCACACCACAAGCTCTTT	58.976	47.619	0.00	0.00	43.61	2.52
163	164	6.049790	GGAATGGGAGTACTTGACTGAATAC	58.950	44.000	0.00	0.00	39.06	1.89
266	267	3.190079	CGGATCCAGAGTGTACACATTG	58.810	50.000	27.06	21.85	0.00	2.82
887	1020	4.025647	GCCTTGCTGTAATTAGATGACGAC	60.026	45.833	0.00	0.00	0.00	4.34
1251	1394	1.561542	ACTGGGGAGAAGTAGCCATTG	59.438	52.381	0.00	0.00	0.00	2.82
1347	1490	3.822735	CTGAAGATGTCTTGCTTTCCCAA	59.177	43.478	0.00	0.00	36.11	4.12
1501	1644	3.007614	TGGTAACCAGAGACTAACCTTGC	59.992	47.826	0.00	0.00	0.00	4.01
1620	1764	8.669946	TGTTATATCTATTGCGTCCATTTTCA	57.330	30.769	0.00	0.00	0.00	2.69
1621	1765	7.746475	GCTGTTATATCTATTGCGTCCATTTTC	59.254	37.037	0.00	0.00	0.00	2.29
1726	1870	4.227197	GTGATCCTCCTCTTTATCCCAGA	58.773	47.826	0.00	0.00	0.00	3.86
1791	1935	1.203050	ACCACCCAATTCCCTGTTGAG	60.203	52.381	0.00	0.00	0.00	3.02
1878	2022	2.923629	ACATTTAAGGCCCCCTGAGTAA	59.076	45.455	0.00	0.00	32.13	2.24
3495	3668	7.661847	ACTGCTACACTTTACAATAGCTTCTTT	59.338	33.333	0.00	0.00	40.59	2.52
3536	3710	5.240844	AGGGAGTACTGTTTATTTGTTGCAC	59.759	40.000	0.00	0.00	0.00	4.57
3601	3775	8.421784	TGTAAGAAGATATTAGTCCATCACACC	58.578	37.037	0.00	0.00	0.00	4.16
3619	3793	7.383102	ACACTTGATGCCTTTATGTAAGAAG	57.617	36.000	0.00	0.00	35.80	2.85
3723	3904	3.093574	CAATTGTGCGTGATAAGCGAAG	58.906	45.455	0.00	0.00	37.44	3.79
3853	4036	5.456173	TGGTGCGTTTAACGAAATTTCTTTC	59.544	36.000	22.15	0.00	46.05	2.62
3871	4054	2.400798	CGTGCAATAGCTGGTGCG	59.599	61.111	16.02	2.50	43.93	5.34
3886	4069	2.851263	TCATTCCAGCTAAACACCGT	57.149	45.000	0.00	0.00	0.00	4.83
3887	4070	4.701956	AAATCATTCCAGCTAAACACCG	57.298	40.909	0.00	0.00	0.00	4.94
3946	4129	2.623535	TGGTTTGGATAATCGTCGGTG	58.376	47.619	0.00	0.00	0.00	4.94
3950	4133	5.949735	ACACATTTGGTTTGGATAATCGTC	58.050	37.500	0.00	0.00	0.00	4.20
3981	4164	8.997323	AGATGTTGATTCTAACTATAGCAATGC	58.003	33.333	0.00	0.00	0.00	3.56
4088	4278	1.327303	TGCTTCCGCCTTTGACAAAT	58.673	45.000	0.05	0.00	34.43	2.32
4089	4279	1.000385	CATGCTTCCGCCTTTGACAAA	60.000	47.619	0.00	0.00	34.43	2.83
4149	4339	3.063510	TCCTGAACTTCCTGCAGAATG	57.936	47.619	17.39	0.00	40.87	2.67
4206	4396	4.023107	CAGCATTTGCATCCCTCTCAATAG	60.023	45.833	5.20	0.00	45.16	1.73
4207	4397	3.887110	CAGCATTTGCATCCCTCTCAATA	59.113	43.478	5.20	0.00	45.16	1.90
4227	4417	0.602638	TACACAAAGACGGGCTGCAG	60.603	55.000	10.11	10.11	0.00	4.41
4236	4426	6.149633	CACCTATGCCTTTTTACACAAAGAC	58.850	40.000	0.00	0.00	36.03	3.01
4240	4430	4.513198	GCACCTATGCCTTTTTACACAA	57.487	40.909	0.00	0.00	46.97	3.33
4275	4465	1.005215	CAGCAAGGAAAGGAGGGATGT	59.995	52.381	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.