AutoCloner

Multiple sequence alignment - TraesCS7A01G290400

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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	TraesCS7A01G290400	chr7A	100.000	2821	0	0	1	2821	352624667	352621847	0.000000e+00	5210
1	TraesCS7A01G290400	chr5D	95.807	2838	101	7	1	2821	503225677	503222841	0.000000e+00	4566
2	TraesCS7A01G290400	chr5D	95.458	2840	109	7	1	2821	503235993	503233155	0.000000e+00	4512
3	TraesCS7A01G290400	chr5D	95.191	1414	57	2	1419	2821	503272837	503274250	0.000000e+00	2224
4	TraesCS7A01G290400	chr2B	95.666	2838	105	7	1	2821	449213745	449210909	0.000000e+00	4543
5	TraesCS7A01G290400	chr2B	95.520	2835	113	3	1	2821	474915899	474913065	0.000000e+00	4519
6	TraesCS7A01G290400	chr3A	95.559	2837	108	7	2	2821	66010165	66013000	0.000000e+00	4525
7	TraesCS7A01G290400	chr3A	95.486	1573	59	3	1261	2821	495095692	495094120	0.000000e+00	2501
8	TraesCS7A01G290400	chrUn	95.487	2836	111	5	1	2821	216511149	216513982	0.000000e+00	4512
9	TraesCS7A01G290400	chrUn	95.487	2836	111	5	1	2821	286272234	286269401	0.000000e+00	4512
10	TraesCS7A01G290400	chr6D	95.418	2837	114	5	1	2821	458922773	458919937	0.000000e+00	4505
11	TraesCS7A01G290400	chr4D	95.349	2838	112	7	1	2821	177441984	177444818	0.000000e+00	4492
12	TraesCS7A01G290400	chr3B	95.282	2840	115	6	1	2821	201534488	201531649	0.000000e+00	4484
13	TraesCS7A01G290400	chr6A	95.106	2840	116	6	1	2821	84403959	84401124	0.000000e+00	4453
14	TraesCS7A01G290400	chr7D	94.609	2838	135	5	1	2821	307141037	307138201	0.000000e+00	4377
15	TraesCS7A01G290400	chr7D	94.603	2835	127	6	1	2821	307045645	307048467	0.000000e+00	4364
16	TraesCS7A01G290400	chr5A	93.146	321	12	1	2511	2821	510135551	510135871	1.980000e-126	462
17	TraesCS7A01G290400	chr6B	96.875	256	8	0	2566	2821	450089864	450089609	2.010000e-116	429

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	TraesCS7A01G290400	chr7A	352621847	352624667	2820	True	5210	5210	100.000	1	2821	1	chr7A.!!$R1	2820
1	TraesCS7A01G290400	chr5D	503222841	503225677	2836	True	4566	4566	95.807	1	2821	1	chr5D.!!$R1	2820
2	TraesCS7A01G290400	chr5D	503233155	503235993	2838	True	4512	4512	95.458	1	2821	1	chr5D.!!$R2	2820
3	TraesCS7A01G290400	chr5D	503272837	503274250	1413	False	2224	2224	95.191	1419	2821	1	chr5D.!!$F1	1402
4	TraesCS7A01G290400	chr2B	449210909	449213745	2836	True	4543	4543	95.666	1	2821	1	chr2B.!!$R1	2820
5	TraesCS7A01G290400	chr2B	474913065	474915899	2834	True	4519	4519	95.520	1	2821	1	chr2B.!!$R2	2820
6	TraesCS7A01G290400	chr3A	66010165	66013000	2835	False	4525	4525	95.559	2	2821	1	chr3A.!!$F1	2819
7	TraesCS7A01G290400	chr3A	495094120	495095692	1572	True	2501	2501	95.486	1261	2821	1	chr3A.!!$R1	1560
8	TraesCS7A01G290400	chrUn	216511149	216513982	2833	False	4512	4512	95.487	1	2821	1	chrUn.!!$F1	2820
9	TraesCS7A01G290400	chrUn	286269401	286272234	2833	True	4512	4512	95.487	1	2821	1	chrUn.!!$R1	2820
10	TraesCS7A01G290400	chr6D	458919937	458922773	2836	True	4505	4505	95.418	1	2821	1	chr6D.!!$R1	2820
11	TraesCS7A01G290400	chr4D	177441984	177444818	2834	False	4492	4492	95.349	1	2821	1	chr4D.!!$F1	2820
12	TraesCS7A01G290400	chr3B	201531649	201534488	2839	True	4484	4484	95.282	1	2821	1	chr3B.!!$R1	2820
13	TraesCS7A01G290400	chr6A	84401124	84403959	2835	True	4453	4453	95.106	1	2821	1	chr6A.!!$R1	2820
14	TraesCS7A01G290400	chr7D	307138201	307141037	2836	True	4377	4377	94.609	1	2821	1	chr7D.!!$R1	2820
15	TraesCS7A01G290400	chr7D	307045645	307048467	2822	False	4364	4364	94.603	1	2821	1	chr7D.!!$F1	2820

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
245	250	0.101579	TTCACGCTCTTGTCACGTCA	59.898	50.0	0.00	0.0	38.09	4.35	F
1635	1656	0.541863	GGGGGAGATCGAGCTTCAAA	59.458	55.0	11.82	0.0	0.00	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1762	1783	1.204941	ACCACACTCCTTCATAGACGC	59.795	52.381	0.0	0.0	0.00	5.19	R
2483	2505	0.836400	GACTGGAGTGGGGGAGTCAA	60.836	60.000	0.0	0.0	35.82	3.18	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
112	113	9.976364	CGTATTCGATGAAAGTCGTACGTACGA	62.976	44.444	38.86	38.86	46.73	3.43
140	141	5.604650	GGAGGGAGATCTTTCCTATCTTTCA	59.395	44.000	15.78	0.00	37.40	2.69
235	240	2.365617	TCTTGAACCTCTTTCACGCTCT	59.634	45.455	0.00	0.00	44.28	4.09
245	250	0.101579	TTCACGCTCTTGTCACGTCA	59.898	50.000	0.00	0.00	38.09	4.35
316	321	6.677781	ATCGATTAGTTAACATGGTGGTTG	57.322	37.500	8.61	0.00	32.29	3.77
525	539	8.826765	TGAAATAGGATCTAAACAAGGAAGAGT	58.173	33.333	0.00	0.00	0.00	3.24
615	629	4.950050	AGTTCCGAATTAGTAGATGCTGG	58.050	43.478	0.00	0.00	0.00	4.85
633	647	2.440599	CAAAGGGAGTGGGGGTGG	59.559	66.667	0.00	0.00	0.00	4.61
665	679	5.344743	AAAGGAAGCGACTCATAGAATGA	57.655	39.130	0.00	0.00	37.76	2.57
688	702	1.596727	GAGGCAAATAGAGCTCTTGCG	59.403	52.381	25.20	13.19	45.09	4.85
711	725	5.570973	CGCATTTTCGTTAATCCATGAACAA	59.429	36.000	0.00	0.00	0.00	2.83
745	759	5.134661	TGTAGACACATGGATCCGTACATA	58.865	41.667	6.04	0.00	0.00	2.29
748	762	4.832823	AGACACATGGATCCGTACATATCA	59.167	41.667	6.04	0.00	0.00	2.15
848	862	6.182627	ACAGAAATCATGATCAACTAAGCCA	58.817	36.000	9.06	0.00	0.00	4.75
863	877	2.586245	CCATCTCGAGGGCTTGCA	59.414	61.111	13.56	0.00	0.00	4.08
912	926	7.346751	TGGAAATAGCATGGAATAAGGTTTC	57.653	36.000	0.00	0.00	0.00	2.78
1157	1172	4.877823	TCTGATGATCGATTCAACCTTTGG	59.122	41.667	0.00	0.00	38.03	3.28
1199	1214	8.690203	TGGTTCTATTTCATCTCTTCAACAAA	57.310	30.769	0.00	0.00	0.00	2.83
1508	1524	9.615660	ATGTTCCTACCTATTGTCTGGATATAA	57.384	33.333	0.00	0.00	32.16	0.98
1516	1532	9.386122	ACCTATTGTCTGGATATAACAAGAGAT	57.614	33.333	9.86	1.34	42.12	2.75
1607	1623	5.065914	TCATGGTTTCTCTTGGCTATATGC	58.934	41.667	0.00	0.00	41.94	3.14
1635	1656	0.541863	GGGGGAGATCGAGCTTCAAA	59.458	55.000	11.82	0.00	0.00	2.69
1708	1729	6.822667	TTCAATTGCGCTTATATCCATCAT	57.177	33.333	9.73	0.00	0.00	2.45
1761	1782	4.079787	CCCCTTTTCATCAATGGACTCCTA	60.080	45.833	0.00	0.00	32.27	2.94
1762	1783	5.128919	CCCTTTTCATCAATGGACTCCTAG	58.871	45.833	0.00	0.00	32.27	3.02
1883	1904	2.857744	GCTATCCCCACTCCGACCG	61.858	68.421	0.00	0.00	0.00	4.79
1884	1905	1.455217	CTATCCCCACTCCGACCGT	60.455	63.158	0.00	0.00	0.00	4.83
1958	1979	0.329596	GGTGAAGCAGGGTCAGGAAT	59.670	55.000	0.00	0.00	0.00	3.01
1962	1983	4.273318	GTGAAGCAGGGTCAGGAATAATT	58.727	43.478	0.00	0.00	0.00	1.40
2061	2082	8.655651	TGACGTATACAATGCTTGAATTATCA	57.344	30.769	3.32	0.00	0.00	2.15
2094	2115	4.494091	ACATAGTGGGTTCTCATCCTTG	57.506	45.455	0.00	0.00	0.00	3.61
2158	2179	5.798125	TCACCCTAAGATGATCATCTCAC	57.202	43.478	33.00	10.97	46.75	3.51
2186	2207	8.365647	GCTATTGGGAATGAATCAAATCAGATT	58.634	33.333	0.00	0.00	40.75	2.40
2234	2255	1.447314	CCTACGGAACCAAGGTCGC	60.447	63.158	0.00	0.00	0.00	5.19
2237	2258	0.600782	TACGGAACCAAGGTCGCAAC	60.601	55.000	0.00	0.00	0.00	4.17
2273	2294	4.153655	CAGTCATTCACAACCACTGATGAG	59.846	45.833	0.00	0.00	37.28	2.90
2275	2296	3.327464	TCATTCACAACCACTGATGAGGA	59.673	43.478	0.00	0.00	0.00	3.71
2304	2325	7.282675	TCCTCGAGAAGTTAAGGATTAGTAGTG	59.717	40.741	15.71	0.00	33.00	2.74
2345	2367	5.001232	TCGAAAAAGAATGGATTCGGTCTT	58.999	37.500	6.88	0.00	43.46	3.01
2463	2485	4.261741	GGTTTTGCATGAGAGAAAGAAGCA	60.262	41.667	0.00	0.00	0.00	3.91
2483	2505	3.753797	GCAAGGAATCCTCTTTTCGACTT	59.246	43.478	0.56	0.00	30.89	3.01
2506	2528	0.995024	CTCCCCCACTCCAGTCATTT	59.005	55.000	0.00	0.00	0.00	2.32
2516	2538	6.490040	CCCACTCCAGTCATTTCTTTTCTTTA	59.510	38.462	0.00	0.00	0.00	1.85
2551	2573	3.993535	CTGCTTCAGCTTCACCCC	58.006	61.111	0.00	0.00	42.66	4.95
2617	2649	9.213777	TCTTCTGGAAATCCTAGCTATTCTTAA	57.786	33.333	0.00	0.00	36.82	1.85
2691	2724	3.557054	GCTTGCATATTCGTCCATAGGGA	60.557	47.826	0.00	0.00	42.29	4.20
2708	2741	8.046708	TCCATAGGGAAAATCGGATATGTAATG	58.953	37.037	0.00	0.00	41.32	1.90
2800	2833	7.257790	TCTCCATGATTCTAGGAACTTTTGA	57.742	36.000	0.00	0.00	41.75	2.69
2809	2842	5.713025	TCTAGGAACTTTTGATTGCATTGC	58.287	37.500	0.46	0.46	41.75	3.56

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
106	107	1.334243	GATCTCCCTCCAAGTCGTACG	59.666	57.143	9.53	9.53	0.00	3.67
112	113	3.213160	AGGAAAGATCTCCCTCCAAGT	57.787	47.619	16.69	0.00	35.95	3.16
140	141	3.657727	CCCCATATTGTAGGGTGGATCTT	59.342	47.826	0.00	0.00	43.89	2.40
207	212	4.315803	TGAAAGAGGTTCAAGAATCCGTC	58.684	43.478	0.00	0.00	43.43	4.79
235	240	1.137282	TGCAGTACCTTGACGTGACAA	59.863	47.619	0.00	0.00	0.00	3.18
485	499	4.763279	TCCTATTTCAACCGGAACTTTTCC	59.237	41.667	9.46	0.00	46.62	3.13
487	501	6.246163	AGATCCTATTTCAACCGGAACTTTT	58.754	36.000	9.46	0.00	34.56	2.27
497	511	9.449719	TCTTCCTTGTTTAGATCCTATTTCAAC	57.550	33.333	0.00	0.00	0.00	3.18
615	629	2.283173	CACCCCCACTCCCTTTGC	60.283	66.667	0.00	0.00	0.00	3.68
633	647	1.259316	CGCTTCCTTTTTGCGTATGC	58.741	50.000	0.00	0.00	44.00	3.14
665	679	3.871485	CAAGAGCTCTATTTGCCTCTGT	58.129	45.455	18.59	0.00	0.00	3.41
688	702	6.942886	TTGTTCATGGATTAACGAAAATGC	57.057	33.333	0.00	0.00	0.00	3.56
711	725	9.935241	GATCCATGTGTCTACATACATAGATTT	57.065	33.333	0.00	0.00	45.53	2.17
745	759	8.844244	CCTTCTATTGATTCTTTTCCGATTGAT	58.156	33.333	0.00	0.00	0.00	2.57
748	762	8.267894	TCTCCTTCTATTGATTCTTTTCCGATT	58.732	33.333	0.00	0.00	0.00	3.34
848	862	2.540265	CTTATGCAAGCCCTCGAGAT	57.460	50.000	15.71	0.00	0.00	2.75
884	898	9.605951	AACCTTATTCCATGCTATTTCCATAAT	57.394	29.630	0.00	0.00	0.00	1.28
912	926	3.009473	ACGGAATCCCCATGAATAGGATG	59.991	47.826	0.00	0.00	39.53	3.51
975	989	7.568349	TGAATTAGTAACTGCATCCAATCTCT	58.432	34.615	0.00	0.00	0.00	3.10
1129	1144	6.590068	AGGTTGAATCGATCATCAGAAGAAT	58.410	36.000	0.00	0.00	38.03	2.40
1157	1172	8.794335	ATAGAACCAAGGTCTATCTTTTTGAC	57.206	34.615	0.00	0.00	0.00	3.18
1199	1214	6.540083	AGGGCCGTTATGCTTATTACTAAAT	58.460	36.000	0.00	0.00	0.00	1.40
1263	1278	8.743085	TGAAATTGTTCATTTGGAAATTTCCA	57.257	26.923	31.75	31.75	45.76	3.53
1405	1420	7.184022	ACATAAAAACATTCCCCCTAGAGTAGT	59.816	37.037	0.00	0.00	0.00	2.73
1508	1524	7.392113	CCTCATTAGACCGTAGATATCTCTTGT	59.608	40.741	8.95	4.61	32.66	3.16
1516	1532	6.124316	AGTAGCCTCATTAGACCGTAGATA	57.876	41.667	0.00	0.00	0.00	1.98
1635	1656	8.788806	TGTATTGATAAGACCGTTCACAATTTT	58.211	29.630	0.00	0.00	0.00	1.82
1708	1729	4.717279	AGCTTAAACCCAAGTCCTACAA	57.283	40.909	0.00	0.00	0.00	2.41
1761	1782	1.478510	CCACACTCCTTCATAGACGCT	59.521	52.381	0.00	0.00	0.00	5.07
1762	1783	1.204941	ACCACACTCCTTCATAGACGC	59.795	52.381	0.00	0.00	0.00	5.19
1827	1848	9.818526	GCATGTCTATGGAGTTTTGCAAAACCT	62.819	40.741	38.50	28.91	40.50	3.50
1908	1929	9.574458	TTGTTATTCGAACAAAAAGATCACAAA	57.426	25.926	0.00	0.00	37.22	2.83
1926	1947	6.152831	ACCCTGCTTCACCTTAATTGTTATTC	59.847	38.462	0.00	0.00	0.00	1.75
2061	2082	3.958798	ACCCACTATGTAGCGTCTACATT	59.041	43.478	26.34	14.14	38.84	2.71
2069	2090	3.553096	GGATGAGAACCCACTATGTAGCG	60.553	52.174	0.00	0.00	0.00	4.26
2094	2115	6.712998	TGCTCCTATTACACTCATAGTCTCTC	59.287	42.308	0.00	0.00	0.00	3.20
2158	2179	4.916983	TTTGATTCATTCCCAATAGCCG	57.083	40.909	0.00	0.00	0.00	5.52
2186	2207	7.509546	AGTCAGAAAGGTTGAGAAATAGAACA	58.490	34.615	0.00	0.00	0.00	3.18
2234	2255	6.912051	TGAATGACTGACTTTTTCAATCGTTG	59.088	34.615	0.00	0.00	39.31	4.10
2237	2258	6.429624	TGTGAATGACTGACTTTTTCAATCG	58.570	36.000	0.00	0.00	32.82	3.34
2273	2294	5.340439	TCCTTAACTTCTCGAGGAATTCC	57.660	43.478	17.31	17.31	35.45	3.01
2275	2296	8.080363	ACTAATCCTTAACTTCTCGAGGAATT	57.920	34.615	13.56	1.75	41.33	2.17
2345	2367	5.706833	TGATTACCTTCCTCGCGTATGTATA	59.293	40.000	5.77	0.00	0.00	1.47
2397	2419	3.119495	GCACGGCTCCAAAGTGATAAAAT	60.119	43.478	0.00	0.00	38.06	1.82
2409	2431	2.166130	TTTCATCTCGCACGGCTCCA	62.166	55.000	0.00	0.00	0.00	3.86
2463	2485	5.470437	GTCAAAGTCGAAAAGAGGATTCCTT	59.530	40.000	6.68	0.00	31.76	3.36
2483	2505	0.836400	GACTGGAGTGGGGGAGTCAA	60.836	60.000	0.00	0.00	35.82	3.18
2516	2538	4.822026	AGCAGCTACTTTCGAAGTAACAT	58.178	39.130	0.00	0.00	42.99	2.71
2548	2570	3.402628	AATATCGAGAATTCGTGGGGG	57.597	47.619	0.00	0.00	46.72	5.40
2551	2573	8.520835	TGATTAGAAATATCGAGAATTCGTGG	57.479	34.615	2.39	0.00	46.72	4.94
2572	2604	5.416952	AGAAGAAGATGCCATTCGTTTGATT	59.583	36.000	0.00	0.00	0.00	2.57
2617	2649	4.614967	AGGAGATTCCCCAAAATCATGT	57.385	40.909	0.00	0.00	37.19	3.21
2708	2741	7.630242	TGAGTCTCCAACAATTATTCCAATC	57.370	36.000	0.00	0.00	0.00	2.67
2785	2818	6.158598	GCAATGCAATCAAAAGTTCCTAGAA	58.841	36.000	0.00	0.00	0.00	2.10

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.