AutoCloner

Multiple sequence alignment - TraesCS5D01G122800

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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	TraesCS5D01G122800	chr5D	100.000	5827	0	0	1	5827	177685314	177679488	0.000000e+00	10761.0
1	TraesCS5D01G122800	chr5D	79.476	458	80	13	1147	1597	489905900	489906350	4.380000e-81	313.0
2	TraesCS5D01G122800	chr5A	95.614	5860	156	23	23	5827	191035270	191041083	0.000000e+00	9304.0
3	TraesCS5D01G122800	chr5A	85.802	162	21	2	5311	5471	684656742	684656902	2.790000e-38	171.0
4	TraesCS5D01G122800	chr5A	92.727	55	3	1	1814	1867	332288484	332288538	1.740000e-10	78.7
5	TraesCS5D01G122800	chr5B	95.511	3319	78	20	2079	5392	192382298	192379046	0.000000e+00	5238.0
6	TraesCS5D01G122800	chr5B	95.574	2056	45	8	1	2042	192384323	192382300	0.000000e+00	3251.0
7	TraesCS5D01G122800	chr5B	90.293	443	32	7	5388	5827	192352994	192352560	2.360000e-158	569.0
8	TraesCS5D01G122800	chr5B	79.476	458	80	13	1147	1597	604065331	604065781	4.380000e-81	313.0
9	TraesCS5D01G122800	chr5B	78.099	484	95	10	1124	1601	604164075	604163597	4.420000e-76	296.0
10	TraesCS5D01G122800	chr5B	78.444	450	83	14	1144	1586	153503427	153502985	1.240000e-71	281.0
11	TraesCS5D01G122800	chr4D	90.416	553	47	4	1051	1597	85579264	85579816	0.000000e+00	723.0
12	TraesCS5D01G122800	chr4B	90.625	544	47	2	1054	1597	122520587	122521126	0.000000e+00	719.0
13	TraesCS5D01G122800	chr4A	90.441	544	48	2	1054	1597	499341600	499342139	0.000000e+00	713.0
14	TraesCS5D01G122800	chr4A	92.593	135	8	2	3492	3626	499343375	499343507	5.960000e-45	193.0
15	TraesCS5D01G122800	chr7B	86.782	174	23	0	5301	5474	743393180	743393007	1.660000e-45	195.0
16	TraesCS5D01G122800	chr7B	92.857	56	2	2	1801	1856	482485048	482484995	4.840000e-11	80.5
17	TraesCS5D01G122800	chr2B	91.045	67	3	3	1793	1857	622914128	622914063	2.890000e-13	87.9
18	TraesCS5D01G122800	chr2B	94.231	52	3	0	1814	1865	358674792	358674741	4.840000e-11	80.5
19	TraesCS5D01G122800	chr3B	96.078	51	1	1	1807	1857	628472956	628473005	1.350000e-11	82.4
20	TraesCS5D01G122800	chr2A	100.000	43	0	0	1814	1856	373868958	373869000	4.840000e-11	80.5
21	TraesCS5D01G122800	chr6B	91.379	58	3	1	1800	1857	164040166	164040221	1.740000e-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	TraesCS5D01G122800	chr5D	177679488	177685314	5826	True	10761.0	10761	100.0000	1	5827	1	chr5D.!!$R1	5826
1	TraesCS5D01G122800	chr5A	191035270	191041083	5813	False	9304.0	9304	95.6140	23	5827	1	chr5A.!!$F1	5804
2	TraesCS5D01G122800	chr5B	192379046	192384323	5277	True	4244.5	5238	95.5425	1	5392	2	chr5B.!!$R4	5391
3	TraesCS5D01G122800	chr4D	85579264	85579816	552	False	723.0	723	90.4160	1051	1597	1	chr4D.!!$F1	546
4	TraesCS5D01G122800	chr4B	122520587	122521126	539	False	719.0	719	90.6250	1054	1597	1	chr4B.!!$F1	543
5	TraesCS5D01G122800	chr4A	499341600	499343507	1907	False	453.0	713	91.5170	1054	3626	2	chr4A.!!$F1	2572

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
732	759	1.000496	AAACCTCCCCTAAAGCTCCC	59.000	55.000	0.00	0.00	0.00	4.30	F
981	1008	1.469423	GGTTCTTGATCCCGTCGAGAC	60.469	57.143	0.00	0.00	45.16	3.36	F
2467	2676	1.279840	GTGTTGCAGGACGTTGCTC	59.720	57.895	13.05	7.24	44.38	4.26	F
2734	2943	3.392947	TGAGGACATGTGGGACAACTTAA	59.607	43.478	1.15	0.00	44.16	1.85	F
3204	3418	4.543590	TTTCTCCTCTCAGAAAGCGAAT	57.456	40.909	0.00	0.00	37.45	3.34	F
3645	3859	4.829064	TTTTGTCCTGTTAGTGACATGC	57.171	40.909	0.00	0.00	40.88	4.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2234	2437	2.669364	CACTGAACTTTGGCATTCTGC	58.331	47.619	6.23	44.08	4.26	R
2898	3112	3.955771	TGTCAACGAACTTTTAGTGCC	57.044	42.857	0.00	0.00	5.01	R
3880	4094	1.067295	AGGCCCACTGACAAGATTGA	58.933	50.000	0.00	0.00	2.57	R
3942	4156	1.131638	TGCCACTTCACCAAGAGTCT	58.868	50.000	0.00	33.34	3.24	R
4261	4475	1.691976	ACCGATGGACTCAACAAGACA	59.308	47.619	0.00	0.00	3.41	R
5215	5431	0.175989	TATTCATGTGGGTGCGCGTA	59.824	50.000	8.43	0.00	4.42	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
211	220	2.816411	TCCACCGAGTCCTGTTTCTAT	58.184	47.619	0.00	0.00	0.00	1.98
334	349	8.548880	AGTAGTAACAATATGTGACATACCCT	57.451	34.615	7.55	1.06	34.07	4.34
335	350	9.650714	AGTAGTAACAATATGTGACATACCCTA	57.349	33.333	7.55	0.21	34.07	3.53
514	529	2.440796	ACATGCCCATGCCCGAAG	60.441	61.111	8.11	0.00	42.39	3.79
732	759	1.000496	AAACCTCCCCTAAAGCTCCC	59.000	55.000	0.00	0.00	0.00	4.30
981	1008	1.469423	GGTTCTTGATCCCGTCGAGAC	60.469	57.143	0.00	0.00	45.16	3.36
1686	1742	9.573133	CTTGGTGTTAAATTGATCTTGGTATTC	57.427	33.333	0.00	0.00	0.00	1.75
1733	1789	7.066645	CCATTTGAATAGATTGCTCAGTTGAGA	59.933	37.037	13.13	0.00	44.74	3.27
1866	2052	3.389925	TTTAGTACAACGGTGGGAGTG	57.610	47.619	4.97	0.00	0.00	3.51
1956	2154	9.998106	ACAGAGGTATGTTACATAACCATATTC	57.002	33.333	15.89	7.48	35.37	1.75
1991	2190	7.344093	TGTTGCCCAATAATCTGATGGAAATTA	59.656	33.333	0.00	0.00	36.27	1.40
2398	2607	1.738700	GCTGCAGACAGGAGAGCTTAC	60.739	57.143	20.43	0.00	44.63	2.34
2467	2676	1.279840	GTGTTGCAGGACGTTGCTC	59.720	57.895	13.05	7.24	44.38	4.26
2707	2916	3.682858	GCTTCACGGAGCTGTTAAATGTA	59.317	43.478	0.00	0.00	39.57	2.29
2734	2943	3.392947	TGAGGACATGTGGGACAACTTAA	59.607	43.478	1.15	0.00	44.16	1.85
3204	3418	4.543590	TTTCTCCTCTCAGAAAGCGAAT	57.456	40.909	0.00	0.00	37.45	3.34
3645	3859	4.829064	TTTTGTCCTGTTAGTGACATGC	57.171	40.909	0.00	0.00	40.88	4.06
3942	4156	7.609760	ATGATTGTACAATCTTGTTCGCTTA	57.390	32.000	36.15	20.06	45.55	3.09
4261	4475	1.191535	TGGATGCGGTTAGTGCTACT	58.808	50.000	0.00	0.00	0.00	2.57
4712	4926	1.517242	CGGCTATGATGAGAAAGGGC	58.483	55.000	0.00	0.00	0.00	5.19
4834	5048	3.518590	GTGGAACCACCTAACTCGTATG	58.481	50.000	12.42	0.00	40.79	2.39
4852	5066	2.435372	TGTGAGAGGGTTGTGCTTTT	57.565	45.000	0.00	0.00	0.00	2.27
4861	5075	4.074970	AGGGTTGTGCTTTTCAGATACTG	58.925	43.478	0.00	0.00	0.00	2.74
4882	5096	2.483714	GCTGTCTGAAGTGTTCACCTGA	60.484	50.000	0.00	0.00	35.46	3.86
4943	5157	7.756722	GGACGCTGTTGAATTTTACTAGTAGTA	59.243	37.037	5.90	5.90	0.00	1.82
4982	5196	9.665264	GCAAAGCATACTATGGTATTTTTAGTC	57.335	33.333	0.00	0.00	40.65	2.59
5215	5431	4.640771	ATACACAGGTGAACATGGTTCT	57.359	40.909	6.40	0.00	30.95	3.01
5237	5453	1.870402	CGCGCACCCACATGAATAATA	59.130	47.619	8.75	0.00	0.00	0.98
5238	5454	2.289274	CGCGCACCCACATGAATAATAA	59.711	45.455	8.75	0.00	0.00	1.40
5239	5455	3.058293	CGCGCACCCACATGAATAATAAT	60.058	43.478	8.75	0.00	0.00	1.28
5450	5666	5.496133	AACATCATGCTCAAGTAGAATGC	57.504	39.130	0.00	0.00	40.72	3.56
5455	5671	2.881074	TGCTCAAGTAGAATGCTCGAC	58.119	47.619	0.00	0.00	0.00	4.20
5556	5789	3.070734	TGTGGAACCATGTCCCAAATTTG	59.929	43.478	11.40	11.40	36.80	2.32
5569	5802	8.556213	TGTCCCAAATTTGTACTATTAGTGTC	57.444	34.615	16.73	1.09	0.00	3.67
5636	5869	3.312404	GCTCTTGAAGCCAGTGTGA	57.688	52.632	0.00	0.00	45.92	3.58
5638	5871	1.949525	GCTCTTGAAGCCAGTGTGAAA	59.050	47.619	0.00	0.00	45.92	2.69
5651	5884	5.445845	CCAGTGTGAAATTGTAACCGTAAC	58.554	41.667	0.00	0.00	0.00	2.50
5653	5886	6.133392	CAGTGTGAAATTGTAACCGTAACTG	58.867	40.000	0.00	0.00	0.00	3.16
5657	5890	4.214545	TGAAATTGTAACCGTAACTGCAGG	59.785	41.667	19.93	2.50	0.00	4.85
5670	5903	2.292267	ACTGCAGGTTTTGTGAGTCAG	58.708	47.619	19.93	0.00	0.00	3.51
5733	5966	8.600625	CATTCATTAAGGATTGAAATGTTGCAG	58.399	33.333	6.22	0.00	35.63	4.41
5804	6037	9.288576	CCCATATGAATAGAGAATGCAGTTTTA	57.711	33.333	3.65	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	50	6.015940	CCCTTTTGTCTGAAGCTGTTCTATTT	60.016	38.462	0.00	0.00	33.38	1.40
113	122	5.069318	TGCTGTGAATCAAACAACTATCCA	58.931	37.500	0.00	0.00	0.00	3.41
182	191	2.375509	AGGACTCGGTGGAATTCCTTTT	59.624	45.455	24.73	3.92	33.03	2.27
186	195	0.613777	ACAGGACTCGGTGGAATTCC	59.386	55.000	18.17	18.17	0.00	3.01
292	307	9.231297	TGTTACTACTTATGGAGTACGTACTTT	57.769	33.333	27.96	17.97	39.86	2.66
514	529	1.662044	GGCGCATGGGGATGAATTC	59.338	57.895	10.83	0.00	0.00	2.17
732	759	6.103330	CAGATGATGATCAGAGGCTAATGAG	58.897	44.000	0.09	0.00	0.00	2.90
1686	1742	3.242739	GGCGTATTGATAAGGTTGCTGTG	60.243	47.826	0.00	0.00	0.00	3.66
1866	2052	5.095490	GTCAAACCACATAGCATTTACAGC	58.905	41.667	0.00	0.00	0.00	4.40
1956	2154	8.034215	TCAGATTATTGGGCAACATTACAAAAG	58.966	33.333	0.00	0.00	39.74	2.27
2082	2283	4.718961	ACCACTCATAGCCCACAATATTC	58.281	43.478	0.00	0.00	0.00	1.75
2234	2437	2.669364	CACTGAACTTTGGCATTCTGC	58.331	47.619	6.23	0.00	44.08	4.26
2398	2607	5.180492	TCTTTAAAGTGCAACCCTATGAACG	59.820	40.000	14.74	0.00	37.80	3.95
2597	2806	4.114073	CTGTTTCACATTCTTTTGCTGCA	58.886	39.130	0.00	0.00	0.00	4.41
2707	2916	4.860802	TGTCCCACATGTCCTCAAATAT	57.139	40.909	0.00	0.00	0.00	1.28
2876	3085	9.547753	GTGCCAGTTCTATTAATCATTTCTAGA	57.452	33.333	0.00	0.00	0.00	2.43
2898	3112	3.955771	TGTCAACGAACTTTTAGTGCC	57.044	42.857	0.00	0.00	0.00	5.01
3170	3384	8.762645	TCTGAGAGGAGAAAAGCAGATTTTATA	58.237	33.333	0.00	0.00	41.24	0.98
3819	4033	5.834169	TCCTTCGTTACATATGCGTGATAA	58.166	37.500	1.58	0.00	0.00	1.75
3880	4094	1.067295	AGGCCCACTGACAAGATTGA	58.933	50.000	0.00	0.00	0.00	2.57
3942	4156	1.131638	TGCCACTTCACCAAGAGTCT	58.868	50.000	0.00	0.00	33.34	3.24
4261	4475	1.691976	ACCGATGGACTCAACAAGACA	59.308	47.619	0.00	0.00	0.00	3.41
4589	4803	5.300286	AGAAGAATGGAGTGGTGAAAAACAG	59.700	40.000	0.00	0.00	0.00	3.16
4834	5048	2.291741	CTGAAAAGCACAACCCTCTCAC	59.708	50.000	0.00	0.00	0.00	3.51
4861	5075	1.869767	CAGGTGAACACTTCAGACAGC	59.130	52.381	4.96	0.00	41.01	4.40
4882	5096	7.067496	ACTATATCACTTGTTCCGATGGATT	57.933	36.000	0.00	0.00	0.00	3.01
4943	5157	9.838339	ATAGTATGCTTTGCTCAACTATTTAGT	57.162	29.630	0.00	0.00	38.39	2.24
4992	5206	9.640952	ACTTATATGGCATGTTAAACACCTAAT	57.359	29.630	10.98	0.00	0.00	1.73
5078	5294	7.284034	ACCAAAAATCCAACAATAATTTGTGCA	59.716	29.630	0.00	0.00	45.30	4.57
5102	5318	8.464404	GGAACAAAATCAATACCTACCTTAACC	58.536	37.037	0.00	0.00	0.00	2.85
5103	5319	9.016438	TGGAACAAAATCAATACCTACCTTAAC	57.984	33.333	0.00	0.00	31.92	2.01
5215	5431	0.175989	TATTCATGTGGGTGCGCGTA	59.824	50.000	8.43	0.00	0.00	4.42
5286	5502	5.532406	CCCCAATGTCAGTTTGATATACCAG	59.468	44.000	0.00	0.00	27.79	4.00
5290	5506	8.723365	AGAATACCCCAATGTCAGTTTGATATA	58.277	33.333	0.00	0.00	27.79	0.86
5434	5650	3.452474	GTCGAGCATTCTACTTGAGCAT	58.548	45.455	0.00	0.00	0.00	3.79
5436	5652	2.197577	GGTCGAGCATTCTACTTGAGC	58.802	52.381	10.30	0.00	38.49	4.26
5506	5724	8.154856	GCACCCACTATGAATAGTAAATAGGAA	58.845	37.037	2.71	0.00	41.44	3.36
5507	5725	7.291416	TGCACCCACTATGAATAGTAAATAGGA	59.709	37.037	2.71	0.00	41.44	2.94
5508	5726	7.450074	TGCACCCACTATGAATAGTAAATAGG	58.550	38.462	2.71	0.76	41.44	2.57
5509	5727	8.939929	CATGCACCCACTATGAATAGTAAATAG	58.060	37.037	2.71	0.00	41.44	1.73
5510	5728	8.436778	ACATGCACCCACTATGAATAGTAAATA	58.563	33.333	2.71	0.00	41.44	1.40
5569	5802	7.308589	CCACCCTTTCAACTCAAGTAATAACTG	60.309	40.741	0.00	0.00	35.62	3.16
5623	5856	4.037446	GGTTACAATTTCACACTGGCTTCA	59.963	41.667	0.00	0.00	0.00	3.02
5624	5857	4.546570	GGTTACAATTTCACACTGGCTTC	58.453	43.478	0.00	0.00	0.00	3.86
5636	5869	4.139038	ACCTGCAGTTACGGTTACAATTT	58.861	39.130	13.81	0.00	0.00	1.82
5638	5871	3.412237	ACCTGCAGTTACGGTTACAAT	57.588	42.857	13.81	0.00	0.00	2.71
5651	5884	2.564771	TCTGACTCACAAAACCTGCAG	58.435	47.619	6.78	6.78	0.00	4.41
5653	5886	4.036734	TGATTTCTGACTCACAAAACCTGC	59.963	41.667	0.00	0.00	0.00	4.85
5694	5927	9.750783	ATCCTTAATGAATGCAATATTAGCTCT	57.249	29.630	0.00	0.00	0.00	4.09
5733	5966	2.128771	TTTGGGCTGACTAATGCTCC	57.871	50.000	0.00	0.00	0.00	4.70
5770	6003	9.075678	CATTCTCTATTCATATGGGCTTTTCTT	57.924	33.333	2.13	0.00	0.00	2.52
5772	6005	7.040201	TGCATTCTCTATTCATATGGGCTTTTC	60.040	37.037	2.13	0.00	0.00	2.29
5776	6009	5.013913	ACTGCATTCTCTATTCATATGGGCT	59.986	40.000	2.13	0.00	0.00	5.19
5804	6037	5.486297	AGATGGCCTCTGAGGATATATCT	57.514	43.478	27.53	21.87	37.67	1.98

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.