AutoCloner

Multiple sequence alignment - TraesCS5D01G139600

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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	TraesCS5D01G139600	chr5D	100.000	4829	0	0	1	4829	222736823	222741651	0.000000e+00	8918.0
1	TraesCS5D01G139600	chr5B	95.327	4537	146	29	1	4504	250236963	250232460	0.000000e+00	7143.0
2	TraesCS5D01G139600	chr5B	88.218	331	32	4	4502	4829	250232115	250231789	5.860000e-104	388.0
3	TraesCS5D01G139600	chr5B	83.436	326	45	5	4502	4825	657394579	657394897	1.310000e-75	294.0
4	TraesCS5D01G139600	chr5A	96.963	4083	94	8	449	4505	304541307	304537229	0.000000e+00	6826.0
5	TraesCS5D01G139600	chr5A	91.630	454	27	4	1	453	304541773	304541330	6.870000e-173	617.0
6	TraesCS5D01G139600	chr3D	79.652	747	121	27	2506	3238	581114580	581113851	4.310000e-140	508.0
7	TraesCS5D01G139600	chr3D	92.000	150	12	0	1138	1287	581116131	581115982	1.360000e-50	211.0
8	TraesCS5D01G139600	chr3D	84.579	214	28	5	4294	4504	571507703	571507492	1.760000e-49	207.0
9	TraesCS5D01G139600	chr3D	85.128	195	27	2	4304	4498	600540362	600540554	1.060000e-46	198.0
10	TraesCS5D01G139600	chr3D	87.143	70	8	1	6	74	30666171	30666240	1.440000e-10	78.7
11	TraesCS5D01G139600	chr3A	79.095	751	127	28	2506	3238	716758250	716758988	1.560000e-134	490.0
12	TraesCS5D01G139600	chr3A	84.195	329	41	7	4502	4828	43639331	43639650	4.690000e-80	309.0
13	TraesCS5D01G139600	chr3A	83.891	329	42	7	4502	4828	43016083	43016402	2.180000e-78	303.0
14	TraesCS5D01G139600	chr3A	90.566	159	15	0	1129	1287	716756679	716756837	1.360000e-50	211.0
15	TraesCS5D01G139600	chr3B	78.828	751	129	28	2506	3238	777580272	777581010	3.380000e-131	479.0
16	TraesCS5D01G139600	chr3B	89.937	159	16	0	1129	1287	777578686	777578844	6.340000e-49	206.0
17	TraesCS5D01G139600	chr1D	85.580	319	35	9	4513	4828	370334764	370335074	1.680000e-84	324.0
18	TraesCS5D01G139600	chr7B	84.242	330	40	8	4502	4826	179960625	179960303	1.310000e-80	311.0
19	TraesCS5D01G139600	chr7B	83.030	330	45	9	4502	4828	736089039	736089360	6.120000e-74	289.0
20	TraesCS5D01G139600	chr6B	82.979	329	48	6	4502	4828	193283	192961	1.700000e-74	291.0
21	TraesCS5D01G139600	chr4A	82.727	330	47	8	4502	4828	731341303	731340981	7.910000e-73	285.0
22	TraesCS5D01G139600	chr1A	87.817	197	21	2	4298	4491	437164688	437164884	1.350000e-55	228.0
23	TraesCS5D01G139600	chr4B	86.935	199	22	3	4303	4498	481492139	481491942	2.260000e-53	220.0
24	TraesCS5D01G139600	chr4D	92.763	152	9	2	4354	4505	479683278	479683427	8.140000e-53	219.0
25	TraesCS5D01G139600	chr4D	85.644	202	24	4	4296	4493	53788925	53789125	1.760000e-49	207.0
26	TraesCS5D01G139600	chr6A	84.615	208	28	2	4302	4505	158306475	158306682	2.280000e-48	204.0

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	TraesCS5D01G139600	chr5D	222736823	222741651	4828	False	8918.0	8918	100.0000	1	4829	1	chr5D.!!$F1	4828
1	TraesCS5D01G139600	chr5B	250231789	250236963	5174	True	3765.5	7143	91.7725	1	4829	2	chr5B.!!$R1	4828
2	TraesCS5D01G139600	chr5A	304537229	304541773	4544	True	3721.5	6826	94.2965	1	4505	2	chr5A.!!$R1	4504
3	TraesCS5D01G139600	chr3D	581113851	581116131	2280	True	359.5	508	85.8260	1138	3238	2	chr3D.!!$R2	2100
4	TraesCS5D01G139600	chr3A	716756679	716758988	2309	False	350.5	490	84.8305	1129	3238	2	chr3A.!!$F3	2109
5	TraesCS5D01G139600	chr3B	777578686	777581010	2324	False	342.5	479	84.3825	1129	3238	2	chr3B.!!$F1	2109

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	Hairpin	End Stability	Orientation
407	413	1.355720	AGATGACCACCTTTTCCCCTG	59.644	52.381	0.00	4.45	F
867	901	1.421646	GGAGAGGGAGAGAGAGAGAGG	59.578	61.905	0.00	3.69	F
2116	2605	0.801251	CTTTTTCCTCGCTCCTGCTG	59.199	55.000	36.97	4.41	F
3420	4224	0.036306	GAGGCGAGGAACAAAGGGAA	59.964	55.000	0.00	3.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1851	2202	3.129287	GCAGACGTCCATGGATTTGATTT	59.871	43.478	19.62	0.00	2.17	R
3031	3835	0.263468	TATCCGGGGACACCATCTCA	59.737	55.000	0.00	40.22	3.27	R
3521	4325	1.471501	GCATGTGTGATAGGAGCGACA	60.472	52.381	0.00	0.00	4.35	R
4512	5663	0.698818	AATCAGACTGGGGGAACACC	59.301	55.000	1.81	39.11	4.16	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
68	72	4.019321	GGCCTTCCCTGATGTATTATGCTA	60.019	45.833	0.00	0.00	0.00	3.49
69	73	5.514834	GGCCTTCCCTGATGTATTATGCTAA	60.515	44.000	0.00	0.00	0.00	3.09
71	75	6.490040	GCCTTCCCTGATGTATTATGCTAAAA	59.510	38.462	0.00	0.00	0.00	1.52
72	76	7.014230	GCCTTCCCTGATGTATTATGCTAAAAA	59.986	37.037	0.00	0.00	0.00	1.94
117	121	3.624777	CATAGTCATTTGGTCCTTGCCT	58.375	45.455	0.00	0.00	0.00	4.75
118	122	2.683211	AGTCATTTGGTCCTTGCCTT	57.317	45.000	0.00	0.00	0.00	4.35
159	165	9.393512	TCAGATGTTTCCAAAATGAAAACAAAT	57.606	25.926	0.00	0.00	36.09	2.32
231	237	2.765699	GCACACCCATCCCACAATAAAT	59.234	45.455	0.00	0.00	0.00	1.40
246	252	7.123247	CCCACAATAAATCTGAATTCTTGGACT	59.877	37.037	7.05	0.00	0.00	3.85
259	265	8.539544	TGAATTCTTGGACTGATGATGTACTTA	58.460	33.333	7.05	0.00	0.00	2.24
265	271	7.107639	TGGACTGATGATGTACTTATTCGAA	57.892	36.000	0.00	0.00	0.00	3.71
324	330	8.734386	AGTTGAGTTTCAAAACATCCATAGATC	58.266	33.333	8.23	0.00	38.22	2.75
326	332	8.868522	TGAGTTTCAAAACATCCATAGATCTT	57.131	30.769	0.00	0.00	41.30	2.40
407	413	1.355720	AGATGACCACCTTTTCCCCTG	59.644	52.381	0.00	0.00	0.00	4.45
565	599	3.735746	CCAATCGCAAACTCCACTTTTTC	59.264	43.478	0.00	0.00	0.00	2.29
601	635	2.988570	ACCACACACGAAAACCTAACA	58.011	42.857	0.00	0.00	0.00	2.41
604	638	3.304391	CCACACACGAAAACCTAACATGG	60.304	47.826	0.00	0.00	0.00	3.66
770	804	1.912001	CACAGCAAACAACACAGTGG	58.088	50.000	5.31	0.00	0.00	4.00
867	901	1.421646	GGAGAGGGAGAGAGAGAGAGG	59.578	61.905	0.00	0.00	0.00	3.69
1081	1144	3.320626	GTGCAAAAGCTGGGATCTTTTC	58.679	45.455	0.00	0.00	40.57	2.29
1851	2202	1.072173	TGCAAGCTAGCAGGTCAGAAA	59.928	47.619	18.83	0.00	40.11	2.52
2116	2605	0.801251	CTTTTTCCTCGCTCCTGCTG	59.199	55.000	0.00	0.00	36.97	4.41
2768	3548	1.278127	CGTTCCTCACCCACCACTATT	59.722	52.381	0.00	0.00	0.00	1.73
3420	4224	0.036306	GAGGCGAGGAACAAAGGGAA	59.964	55.000	0.00	0.00	0.00	3.97
3521	4325	1.338579	GCCTCAGTGTTCTAGCTGCTT	60.339	52.381	7.79	0.00	33.09	3.91
4060	4864	1.851304	GAATGAATGGCCACAGGGAA	58.149	50.000	8.16	0.00	35.59	3.97
4109	4913	5.882557	ACTGTGACAATATTTCTGTCCATCC	59.117	40.000	4.05	0.00	42.13	3.51
4264	5068	7.040617	TGCGGGAACAATACAAATACTTTAACA	60.041	33.333	0.00	0.00	0.00	2.41
4301	5105	8.506437	CAAATGTTCATTCCACATAGCGTATAT	58.494	33.333	0.00	0.00	33.54	0.86
4313	5117	7.095187	CCACATAGCGTATATTTCTTTCTTCCC	60.095	40.741	0.00	0.00	0.00	3.97
4329	5133	1.573108	TCCCATCGAAGAAAGAGGCT	58.427	50.000	0.00	0.00	43.58	4.58
4332	5136	3.711704	TCCCATCGAAGAAAGAGGCTATT	59.288	43.478	0.00	0.00	43.58	1.73
4335	5139	5.118990	CCATCGAAGAAAGAGGCTATTTCA	58.881	41.667	29.88	14.33	43.58	2.69
4359	5163	2.960688	GCCGCCAGGGAGTTTCTCT	61.961	63.158	0.00	0.00	38.47	3.10
4532	5683	1.075536	GGTGTTCCCCCAGTCTGATTT	59.924	52.381	0.00	0.00	0.00	2.17
4552	5703	6.865726	TGATTTGTTCAATGGTAATGGTTTCG	59.134	34.615	0.00	0.00	0.00	3.46
4574	5725	0.181587	TTCGGTGAGCCACTTTGGAA	59.818	50.000	0.00	2.97	40.96	3.53
4584	5735	1.001378	CCACTTTGGAAGTCCGCAAAG	60.001	52.381	0.00	0.00	40.96	2.77
4617	5768	4.872485	GGAGTCGCGTCGAGCTCG	62.872	72.222	30.03	30.03	45.59	5.03
4624	5775	2.865308	CGTCGAGCTCGGTGTGTA	59.135	61.111	33.98	12.67	40.29	2.90
4635	5786	1.182667	CGGTGTGTAGAGGTGATCCA	58.817	55.000	0.00	0.00	35.89	3.41
4637	5788	2.168521	CGGTGTGTAGAGGTGATCCATT	59.831	50.000	0.00	0.00	35.89	3.16
4642	5793	6.828785	GGTGTGTAGAGGTGATCCATTATTTT	59.171	38.462	0.00	0.00	35.89	1.82
4665	5816	1.108727	TCTTTTGGTGGCTGCTGTGG	61.109	55.000	0.00	0.00	0.00	4.17
4691	5842	3.066814	GAGGTAGGTGACGGGCGT	61.067	66.667	0.00	0.00	0.00	5.68
4706	5857	1.444119	GGCGTTGGTGTCAAGCTCAA	61.444	55.000	0.00	0.00	32.92	3.02
4712	5864	4.498009	CGTTGGTGTCAAGCTCAAAGATTT	60.498	41.667	0.00	0.00	32.92	2.17
4755	5909	8.925161	TTTACTTCTTGGATGTTGTTTCTTTG	57.075	30.769	0.00	0.00	0.00	2.77
4763	5917	4.270808	GGATGTTGTTTCTTTGTGCAAAGG	59.729	41.667	20.39	6.38	45.80	3.11
4764	5918	2.999355	TGTTGTTTCTTTGTGCAAAGGC	59.001	40.909	20.39	13.17	45.80	4.35
4765	5919	3.261580	GTTGTTTCTTTGTGCAAAGGCT	58.738	40.909	20.39	0.00	45.80	4.58
4766	5920	4.081972	TGTTGTTTCTTTGTGCAAAGGCTA	60.082	37.500	20.39	7.55	45.80	3.93
4767	5921	4.305989	TGTTTCTTTGTGCAAAGGCTAG	57.694	40.909	20.39	0.54	45.80	3.42
4801	5955	6.862209	TGCTATTTGTTCAGTTTTGTCAGTT	58.138	32.000	0.00	0.00	0.00	3.16
4802	5956	6.972328	TGCTATTTGTTCAGTTTTGTCAGTTC	59.028	34.615	0.00	0.00	0.00	3.01
4808	5962	5.007234	TGTTCAGTTTTGTCAGTTCGGTATG	59.993	40.000	0.00	0.00	0.00	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
82	86	6.610075	AATGACTATGGGCAATTGTCTTTT	57.390	33.333	15.80	8.18	40.45	2.27
102	106	3.807553	ACAAAAAGGCAAGGACCAAATG	58.192	40.909	0.00	0.00	0.00	2.32
103	107	4.198530	CAACAAAAAGGCAAGGACCAAAT	58.801	39.130	0.00	0.00	0.00	2.32
118	122	9.474920	GGAAACATCTGAATATTGACAACAAAA	57.525	29.630	0.00	0.00	39.54	2.44
231	237	6.058553	ACATCATCAGTCCAAGAATTCAGA	57.941	37.500	8.44	0.00	0.00	3.27
246	252	7.784633	TGCAATTCGAATAAGTACATCATCA	57.215	32.000	11.83	0.00	0.00	3.07
435	441	6.806739	GGGCAAAGATGTATTTACAACTTGTC	59.193	38.462	12.27	8.90	44.93	3.18
565	599	2.227194	GTGGTAAAAGTGTGAGGGTGG	58.773	52.381	0.00	0.00	0.00	4.61
601	635	4.033776	CGGGTGACTGTGGCCCAT	62.034	66.667	14.29	0.00	42.44	4.00
604	638	3.315949	TACCGGGTGACTGTGGCC	61.316	66.667	10.66	0.00	33.66	5.36
770	804	1.080025	GGTGGTGTACAGTCGAGCC	60.080	63.158	0.00	0.00	0.00	4.70
867	901	1.304464	CTTTTGTGGCTCCCCTCCC	60.304	63.158	0.00	0.00	0.00	4.30
1610	1794	4.012811	AGCAAGGCGAGCTGCTCA	62.013	61.111	27.46	0.00	45.79	4.26
1695	1891	4.273318	AGAAAAGGGGAATATGAGTGCAC	58.727	43.478	9.40	9.40	0.00	4.57
1851	2202	3.129287	GCAGACGTCCATGGATTTGATTT	59.871	43.478	19.62	0.00	0.00	2.17
3028	3832	2.659063	CGGGGACACCATCTCAGCA	61.659	63.158	0.00	0.00	40.22	4.41
3031	3835	0.263468	TATCCGGGGACACCATCTCA	59.737	55.000	0.00	0.00	40.22	3.27
3521	4325	1.471501	GCATGTGTGATAGGAGCGACA	60.472	52.381	0.00	0.00	0.00	4.35
4142	4946	5.382616	AGTTAGATCGTTTTGGGGAAGTTT	58.617	37.500	0.00	0.00	0.00	2.66
4279	5083	7.931407	AGAAATATACGCTATGTGGAATGAACA	59.069	33.333	0.00	0.00	0.00	3.18
4284	5088	9.561069	AAGAAAGAAATATACGCTATGTGGAAT	57.439	29.630	0.00	0.00	0.00	3.01
4313	5117	5.007136	GGTGAAATAGCCTCTTTCTTCGATG	59.993	44.000	4.48	0.00	34.43	3.84
4329	5133	2.822255	GGCGGCGCTGGTGAAATA	60.822	61.111	32.30	0.00	0.00	1.40
4433	5237	1.669265	GGCCTAAAACTATCCACACGC	59.331	52.381	0.00	0.00	0.00	5.34
4512	5663	0.698818	AATCAGACTGGGGGAACACC	59.301	55.000	1.81	0.00	39.11	4.16
4513	5664	2.162681	CAAATCAGACTGGGGGAACAC	58.837	52.381	1.81	0.00	0.00	3.32
4518	5669	2.584835	TGAACAAATCAGACTGGGGG	57.415	50.000	1.81	0.00	33.04	5.40
4519	5670	3.194116	CCATTGAACAAATCAGACTGGGG	59.806	47.826	1.81	0.00	39.77	4.96
4523	5674	6.721208	ACCATTACCATTGAACAAATCAGACT	59.279	34.615	0.00	0.00	39.77	3.24
4532	5683	5.067273	AGACGAAACCATTACCATTGAACA	58.933	37.500	0.00	0.00	0.00	3.18
4552	5703	0.868406	CAAAGTGGCTCACCGAAGAC	59.132	55.000	2.18	0.00	39.70	3.01
4574	5725	1.303309	GATATGCAGCTTTGCGGACT	58.697	50.000	0.00	0.00	37.69	3.85
4584	5735	1.270518	ACTCCATCACGGATATGCAGC	60.271	52.381	0.00	0.00	45.19	5.25
4596	5747	2.791927	CTCGACGCGACTCCATCA	59.208	61.111	15.93	0.00	0.00	3.07
4617	5768	3.914426	AATGGATCACCTCTACACACC	57.086	47.619	0.00	0.00	37.04	4.16
4642	5793	2.235898	ACAGCAGCCACCAAAAGAAAAA	59.764	40.909	0.00	0.00	0.00	1.94
4648	5799	1.381056	ACCACAGCAGCCACCAAAA	60.381	52.632	0.00	0.00	0.00	2.44
4660	5811	1.480212	TACCTCTGGCACCACCACAG	61.480	60.000	0.00	0.00	46.36	3.66
4665	5816	1.192146	TCACCTACCTCTGGCACCAC	61.192	60.000	0.00	0.00	0.00	4.16
4671	5822	2.722201	GCCCGTCACCTACCTCTGG	61.722	68.421	0.00	0.00	0.00	3.86
4691	5842	5.596836	AAAATCTTTGAGCTTGACACCAA	57.403	34.783	0.00	0.00	0.00	3.67
4750	5904	4.422712	GCTAGCTAGCCTTTGCACAAAGA	61.423	47.826	31.67	4.18	45.52	2.52
4755	5909	0.741221	ACGCTAGCTAGCCTTTGCAC	60.741	55.000	34.27	9.97	46.34	4.57
4801	5955	0.889994	ACAAGCCACGTACATACCGA	59.110	50.000	0.00	0.00	0.00	4.69
4802	5956	2.159338	AGTACAAGCCACGTACATACCG	60.159	50.000	9.73	0.00	41.40	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.