AutoCloner

Multiple sequence alignment - TraesCS3A01G363200

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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	TraesCS3A01G363200	chr3A	100.000	3049	0	0	1	3049	611708524	611705476	0.000000e+00	5631.0
1	TraesCS3A01G363200	chr3A	80.389	1698	270	49	272	1939	611707975	611706311	0.000000e+00	1232.0
2	TraesCS3A01G363200	chr3A	80.366	1696	274	45	550	2214	611708253	611706586	0.000000e+00	1232.0
3	TraesCS3A01G363200	chr3A	82.115	1409	218	24	264	1654	611707703	611706311	0.000000e+00	1175.0
4	TraesCS3A01G363200	chr3A	81.344	1131	178	23	264	1377	611707425	611706311	0.000000e+00	889.0
5	TraesCS3A01G363200	chr3A	81.344	1131	178	23	1100	2214	611708261	611707148	0.000000e+00	889.0
6	TraesCS3A01G363200	chr3A	82.840	845	130	13	264	1100	611707148	611706311	0.000000e+00	743.0
7	TraesCS3A01G363200	chr3A	82.840	845	130	13	1377	2214	611708261	611707425	0.000000e+00	743.0
8	TraesCS3A01G363200	chr3D	94.799	3057	119	19	1	3049	469161225	469158201	0.000000e+00	4728.0
9	TraesCS3A01G363200	chr3D	81.372	1691	265	39	272	1939	469160687	469159024	0.000000e+00	1332.0
10	TraesCS3A01G363200	chr3D	80.812	1699	270	42	542	2213	469160972	469159303	0.000000e+00	1280.0
11	TraesCS3A01G363200	chr3D	82.194	1404	224	21	264	1654	469160414	469159024	0.000000e+00	1184.0
12	TraesCS3A01G363200	chr3D	82.140	1411	217	25	822	2214	469160972	469159579	0.000000e+00	1177.0
13	TraesCS3A01G363200	chr3D	81.673	1124	185	16	264	1377	469160136	469159024	0.000000e+00	915.0
14	TraesCS3A01G363200	chr3D	83.097	846	126	16	1377	2214	469160972	469160136	0.000000e+00	754.0
15	TraesCS3A01G363200	chr3D	83.577	274	41	3	1944	2214	469160967	469160695	1.400000e-63	254.0
16	TraesCS3A01G363200	chr3D	88.496	113	13	0	2381	2493	523902680	523902568	1.470000e-28	137.0
17	TraesCS3A01G363200	chr3D	91.111	90	8	0	2404	2493	523846709	523846620	4.130000e-24	122.0
18	TraesCS3A01G363200	chr3B	94.178	584	33	1	2466	3049	623154346	623153764	0.000000e+00	889.0
19	TraesCS3A01G363200	chr3B	85.886	666	65	13	140	800	623156468	623155827	0.000000e+00	682.0
20	TraesCS3A01G363200	chr3B	82.364	533	65	15	551	1078	623156335	623155827	1.300000e-118	436.0
21	TraesCS3A01G363200	chr3B	84.985	333	48	2	264	595	623155361	623155030	1.350000e-88	337.0
22	TraesCS3A01G363200	chr7D	82.353	153	18	8	2405	2552	133313601	133313453	1.150000e-24	124.0
23	TraesCS3A01G363200	chr4D	88.608	79	8	1	2184	2262	301730973	301730896	9.000000e-16	95.3
24	TraesCS3A01G363200	chr4B	83.168	101	13	4	2188	2286	376136971	376136873	4.190000e-14	89.8
25	TraesCS3A01G363200	chr4A	84.524	84	7	4	2184	2262	179144445	179144527	9.060000e-11	78.7
26	TraesCS3A01G363200	chr4A	91.071	56	3	2	2553	2607	692044233	692044287	1.170000e-09	75.0
27	TraesCS3A01G363200	chr7A	89.091	55	6	0	2552	2606	547564325	547564379	5.450000e-08	69.4

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	TraesCS3A01G363200	chr3A	611705476	611708524	3048	True	1566.75	5631	83.90475	1	3049	8	chr3A.!!$R1	3048
1	TraesCS3A01G363200	chr3D	469158201	469161225	3024	True	1453.00	4728	83.70800	1	3049	8	chr3D.!!$R3	3048
2	TraesCS3A01G363200	chr3B	623153764	623156468	2704	True	586.00	889	86.85325	140	3049	4	chr3B.!!$R1	2909

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
547	558	0.108851	CTGTTTTTACCATGGCGGCC	60.109	55.0	13.04	13.32	39.03	6.13	F
1681	1863	0.521735	GGGCATGGTGAAAAGACGAC	59.478	55.0	0.00	0.00	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1876	2063	0.178975	TGGCTGTTCCACCGGAAAAT	60.179	50.0	9.46	0.0	43.86	1.82	R
2771	2963	1.557443	GCGTACAGGTGCACACACTC	61.557	60.0	20.43	0.0	46.57	3.51	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
54	55	1.205655	TCGAGACTGAGCTTGAATGGG	59.794	52.381	0.00	0.00	0.00	4.00
99	100	1.993653	CATGGAAGGAGCAGGGACA	59.006	57.895	0.00	0.00	0.00	4.02
100	101	0.329261	CATGGAAGGAGCAGGGACAA	59.671	55.000	0.00	0.00	0.00	3.18
122	123	1.298014	GACCTGGGTGAGGAAGCAG	59.702	63.158	0.00	0.00	46.33	4.24
161	162	2.352715	GGCATTGGAAGTAAGGTGCAAC	60.353	50.000	0.00	0.00	34.45	4.17
235	246	4.162690	GCCGGTGGCTGGAGTAGG	62.163	72.222	1.90	0.00	46.69	3.18
306	317	4.680237	CGTTGGCGTCCCTGAGCA	62.680	66.667	0.00	0.00	34.54	4.26
309	320	2.818169	TTGGCGTCCCTGAGCAAGT	61.818	57.895	0.00	0.00	34.54	3.16
458	469	7.386573	GGAAACCAAAACGGAATATTGTGAAAT	59.613	33.333	0.00	0.00	38.63	2.17
473	484	7.690952	ATTGTGAAATGGAAATTGAAATGGG	57.309	32.000	0.00	0.00	0.00	4.00
492	503	2.394545	GAAAACGTTTTCCGGTGGAG	57.605	50.000	33.63	0.00	40.41	3.86
516	527	2.093500	TCCATGGAAACGGATCTGTGAG	60.093	50.000	13.46	0.00	0.00	3.51
547	558	0.108851	CTGTTTTTACCATGGCGGCC	60.109	55.000	13.04	13.32	39.03	6.13
568	579	2.430367	GGCGGGGTGAAGACAACT	59.570	61.111	0.00	0.00	33.68	3.16
569	580	1.966451	GGCGGGGTGAAGACAACTG	60.966	63.158	0.00	0.00	33.68	3.16
588	599	4.802051	GGCATCCCCAAGCGAGCA	62.802	66.667	0.00	0.00	0.00	4.26
666	678	8.862325	ACTATGACAAAATGAAATGGACACTA	57.138	30.769	0.00	0.00	0.00	2.74
694	706	5.051973	GGATTTTCCACGAAAAACAGAAACG	60.052	40.000	3.85	0.00	43.32	3.60
701	713	3.685756	ACGAAAAACAGAAACGGAGTGAA	59.314	39.130	0.00	0.00	45.00	3.18
708	720	2.093783	CAGAAACGGAGTGAAATACGGC	59.906	50.000	0.00	0.00	45.00	5.68
717	729	4.443063	GGAGTGAAATACGGCAACAAAAAC	59.557	41.667	0.00	0.00	0.00	2.43
750	762	6.314896	TGCGAAACAGAAACAAAAATGGAAAT	59.685	30.769	0.00	0.00	0.00	2.17
755	767	8.572855	AACAGAAACAAAAATGGAAATGGAAA	57.427	26.923	0.00	0.00	0.00	3.13
762	774	7.984391	ACAAAAATGGAAATGGAAAAGTGTTC	58.016	30.769	0.00	0.00	0.00	3.18
790	802	3.222603	GGAATAGCCACGGAAATGGATT	58.777	45.455	0.00	0.00	43.02	3.01
791	803	3.253432	GGAATAGCCACGGAAATGGATTC	59.747	47.826	0.00	0.00	43.02	2.52
845	857	4.388499	CGGGGTGGGGTGAAGACG	62.388	72.222	0.00	0.00	0.00	4.18
950	962	5.009310	GGATGAAAACGGAGTGGTAACTTTT	59.991	40.000	0.00	0.00	45.00	2.27
1070	1083	5.711506	TGGAATATCCATGGAAATTGATCCG	59.288	40.000	20.67	0.00	42.67	4.18
1071	1084	5.711976	GGAATATCCATGGAAATTGATCCGT	59.288	40.000	20.67	0.00	38.22	4.69
1146	1159	3.695606	GGTGTCCCTGAGCGAGCA	61.696	66.667	0.00	0.00	0.00	4.26
1163	1176	1.523711	CAGCCGCGATAATGGGTGT	60.524	57.895	8.23	0.00	46.15	4.16
1225	1239	5.003096	AGGATGAAAATGGAGTGGAAACT	57.997	39.130	0.00	0.00	0.00	2.66
1304	1485	1.771291	GTTGCGAAACGAAAACGGAAG	59.229	47.619	0.00	0.00	37.92	3.46
1370	1551	6.801862	CCGTGAATGTGAAACTTCCTATTTTC	59.198	38.462	0.00	0.00	38.04	2.29
1402	1583	3.728373	GGGCGGGGTGAAGATGGT	61.728	66.667	0.00	0.00	0.00	3.55
1504	1685	6.552008	AGGATGAAAATGGAGTGGAAACTTA	58.448	36.000	0.00	0.00	0.00	2.24
1587	1769	7.077050	TGTGAAAGGGAAATTGAAATGGAAT	57.923	32.000	0.00	0.00	0.00	3.01
1636	1818	7.067008	ACGAAAACGGATCCTTGAATATGAAAT	59.933	33.333	10.75	0.00	0.00	2.17
1674	1856	4.652131	ACGCGGGGCATGGTGAAA	62.652	61.111	12.47	0.00	0.00	2.69
1676	1858	2.573340	GCGGGGCATGGTGAAAAG	59.427	61.111	0.00	0.00	0.00	2.27
1677	1859	1.976474	GCGGGGCATGGTGAAAAGA	60.976	57.895	0.00	0.00	0.00	2.52
1678	1860	1.883021	CGGGGCATGGTGAAAAGAC	59.117	57.895	0.00	0.00	0.00	3.01
1679	1861	1.883021	GGGGCATGGTGAAAAGACG	59.117	57.895	0.00	0.00	0.00	4.18
1681	1863	0.521735	GGGCATGGTGAAAAGACGAC	59.478	55.000	0.00	0.00	0.00	4.34
1801	1984	5.391312	AATTGTCCGGATTTTCCAGAAAG	57.609	39.130	7.81	0.00	35.91	2.62
1811	1994	6.067412	GGATTTTCCAGAAAGAACGGAAACG	61.067	44.000	2.42	0.00	45.93	3.60
1835	2018	7.008538	ACGGAGTGAAAATACGAAAACAAAAAC	59.991	33.333	0.00	0.00	42.51	2.43
1845	2028	5.885194	ACGAAAACAAAAACGAATATTGCG	58.115	33.333	0.00	0.00	0.00	4.85
1846	2029	5.681982	ACGAAAACAAAAACGAATATTGCGA	59.318	32.000	12.27	0.00	0.00	5.10
1847	2030	6.129561	ACGAAAACAAAAACGAATATTGCGAG	60.130	34.615	12.27	0.00	0.00	5.03
1848	2031	6.085718	CGAAAACAAAAACGAATATTGCGAGA	59.914	34.615	12.27	0.00	0.00	4.04
1849	2032	7.201232	CGAAAACAAAAACGAATATTGCGAGAT	60.201	33.333	12.27	0.00	0.00	2.75
1850	2033	6.853279	AACAAAAACGAATATTGCGAGATG	57.147	33.333	12.27	8.64	0.00	2.90
1938	2125	8.712285	ATATGAATCTTTCTGTTTTTGCCATG	57.288	30.769	0.00	0.00	0.00	3.66
2117	2306	7.981142	AGAGTGAAAATACTGAAACGAAAACA	58.019	30.769	0.00	0.00	0.00	2.83
2182	2372	0.250901	AACAGCCACGGAAGCAGATT	60.251	50.000	0.00	0.00	0.00	2.40
2269	2459	1.815613	TCACGTTGTGGCCAATAATGG	59.184	47.619	21.05	12.80	39.99	3.16
2372	2564	1.218316	CCACCGGCTTAGGAGTCAC	59.782	63.158	0.00	0.00	34.73	3.67
2477	2669	4.655963	ACATCTGGTTTTGTATCTGCTGT	58.344	39.130	0.00	0.00	0.00	4.40
2478	2670	5.804639	ACATCTGGTTTTGTATCTGCTGTA	58.195	37.500	0.00	0.00	0.00	2.74
2490	2682	3.945981	TCTGCTGTACACCGTATTTGA	57.054	42.857	0.00	0.00	0.00	2.69
2493	2685	5.242434	TCTGCTGTACACCGTATTTGATTT	58.758	37.500	0.00	0.00	0.00	2.17
2559	2751	7.961325	AGGTTTTTGCATTCGTTATGAAAAT	57.039	28.000	7.09	0.00	40.65	1.82
2853	3045	6.293698	AGTCTGTAACGGGTTTCTAACATTT	58.706	36.000	0.00	0.00	0.00	2.32
2950	3142	1.206371	GACAAGCCACACGGGTAGTAT	59.794	52.381	0.00	0.00	44.22	2.12
2979	3171	8.539770	AGAACTATTATCTTGTTCTGTGTGTG	57.460	34.615	6.78	0.00	44.70	3.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	100	2.204151	CCTCACCCAGGTCCCCTT	60.204	66.667	0.00	0.00	37.53	3.95
100	101	2.772594	CTTCCTCACCCAGGTCCCCT	62.773	65.000	0.00	0.00	43.95	4.79
161	162	2.543012	CCAAGCTAGCATCATTCGTGAG	59.457	50.000	18.83	0.00	0.00	3.51
235	246	1.825622	GTCCCCTAGGCAATGCAGC	60.826	63.158	7.79	0.00	0.00	5.25
236	247	0.465097	CTGTCCCCTAGGCAATGCAG	60.465	60.000	7.79	3.17	0.00	4.41
237	248	1.609239	CTGTCCCCTAGGCAATGCA	59.391	57.895	7.79	0.00	0.00	3.96
238	249	1.152881	CCTGTCCCCTAGGCAATGC	60.153	63.158	2.05	0.00	0.00	3.56
306	317	1.122227	ACCCATTGTTGCAGCAACTT	58.878	45.000	32.99	20.56	43.85	2.66
309	320	1.069427	GCACCCATTGTTGCAGCAA	59.931	52.632	18.67	18.67	0.00	3.91
458	469	5.283457	ACGTTTTCCCATTTCAATTTCCA	57.717	34.783	0.00	0.00	0.00	3.53
473	484	1.598676	GCTCCACCGGAAAACGTTTTC	60.599	52.381	35.04	35.04	44.38	2.29
547	558	4.410400	GTCTTCACCCCGCCCCAG	62.410	72.222	0.00	0.00	0.00	4.45
568	579	3.626996	CTCGCTTGGGGATGCCACA	62.627	63.158	5.30	0.00	33.67	4.17
569	580	2.825836	CTCGCTTGGGGATGCCAC	60.826	66.667	5.30	0.00	0.00	5.01
583	594	2.398429	CATTGTCGCAGCTGCTCG	59.602	61.111	34.22	21.04	39.32	5.03
586	597	3.058160	ACCCATTGTCGCAGCTGC	61.058	61.111	29.12	29.12	37.78	5.25
588	599	3.058160	GCACCCATTGTCGCAGCT	61.058	61.111	0.00	0.00	0.00	4.24
694	706	3.907894	TTTGTTGCCGTATTTCACTCC	57.092	42.857	0.00	0.00	0.00	3.85
701	713	3.712091	TTCCGTTTTTGTTGCCGTATT	57.288	38.095	0.00	0.00	0.00	1.89
708	720	5.814314	TTCGCAATATTCCGTTTTTGTTG	57.186	34.783	0.00	0.00	0.00	3.33
717	729	4.717991	TGTTTCTGTTTCGCAATATTCCG	58.282	39.130	0.00	0.00	0.00	4.30
750	762	1.476110	CCACCGGAGAACACTTTTCCA	60.476	52.381	9.46	0.00	0.00	3.53
755	767	2.354805	GCTATTCCACCGGAGAACACTT	60.355	50.000	9.46	0.00	31.21	3.16
1146	1159	1.523711	CACACCCATTATCGCGGCT	60.524	57.895	6.13	0.00	0.00	5.52
1154	1167	2.353189	CGCCCCACACACCCATTA	59.647	61.111	0.00	0.00	0.00	1.90
1255	1436	8.030106	TCTGTTTTTGTTTCCGTATTTTCACTT	58.970	29.630	0.00	0.00	0.00	3.16
1304	1485	0.734309	ACCGGAAAACGTTGTTCCAC	59.266	50.000	26.97	12.35	44.14	4.02
1402	1583	2.099652	CTCACTCAGGGACGGCAACA	62.100	60.000	0.00	0.00	0.00	3.33
1448	1629	0.976641	TCTCACCTTCCGCAATGAGT	59.023	50.000	0.00	0.00	39.68	3.41
1504	1685	1.762471	TTCCCGTGGAAAATCCGGT	59.238	52.632	0.00	0.00	38.93	5.28
1587	1769	2.623878	TGTTCCACCAGAAAACGCTA	57.376	45.000	0.00	0.00	35.85	4.26
1636	1818	5.583495	CGTCACCATGGTAAAAACAGAAAA	58.417	37.500	19.28	0.00	0.00	2.29
1801	1984	3.891056	ATTTTCACTCCGTTTCCGTTC	57.109	42.857	0.00	0.00	0.00	3.95
1811	1994	7.218583	TCGTTTTTGTTTTCGTATTTTCACTCC	59.781	33.333	0.00	0.00	0.00	3.85
1835	2018	3.362986	CCGTTTCCATCTCGCAATATTCG	60.363	47.826	0.00	0.00	0.00	3.34
1845	2028	2.088950	TCCGTTTCCGTTTCCATCTC	57.911	50.000	0.00	0.00	0.00	2.75
1846	2029	2.554370	TTCCGTTTCCGTTTCCATCT	57.446	45.000	0.00	0.00	0.00	2.90
1847	2030	3.498082	CATTTCCGTTTCCGTTTCCATC	58.502	45.455	0.00	0.00	0.00	3.51
1848	2031	2.230266	CCATTTCCGTTTCCGTTTCCAT	59.770	45.455	0.00	0.00	0.00	3.41
1849	2032	1.609555	CCATTTCCGTTTCCGTTTCCA	59.390	47.619	0.00	0.00	0.00	3.53
1850	2033	1.881324	TCCATTTCCGTTTCCGTTTCC	59.119	47.619	0.00	0.00	0.00	3.13
1876	2063	0.178975	TGGCTGTTCCACCGGAAAAT	60.179	50.000	9.46	0.00	43.86	1.82
1920	2107	3.703556	TCACCATGGCAAAAACAGAAAGA	59.296	39.130	13.04	0.00	0.00	2.52
1960	2147	3.530260	CGGGGATGCCAATGCCAC	61.530	66.667	5.30	0.00	45.91	5.01
2137	2327	2.287308	CGGAAAACGCTGTTCCATTTCA	60.287	45.455	11.58	0.00	44.14	2.69
2171	2361	3.843426	GTATTCACGAATCTGCTTCCG	57.157	47.619	0.00	0.00	32.50	4.30
2281	2471	5.982391	AGGATGGGTGAGGATTCTATTAGA	58.018	41.667	0.00	0.00	0.00	2.10
2286	2476	3.051803	AGTGAGGATGGGTGAGGATTCTA	60.052	47.826	0.00	0.00	0.00	2.10
2372	2564	6.083098	TGATATGACCACAACAACTTTTGG	57.917	37.500	0.00	0.00	35.06	3.28
2477	2669	8.780846	AACAGATACAAATCAAATACGGTGTA	57.219	30.769	0.00	0.00	34.28	2.90
2478	2670	7.681939	AACAGATACAAATCAAATACGGTGT	57.318	32.000	0.00	0.00	34.28	4.16
2518	2710	7.416777	GCAAAAACCTAGGAAATGAATAGGGAG	60.417	40.741	17.98	0.00	40.40	4.30
2559	2751	2.566833	ACTGAGTGCTGCCACATTTA	57.433	45.000	0.00	0.00	44.53	1.40
2687	2879	4.705507	TCCTCATGTACCTCTCAAGTGTAC	59.294	45.833	0.00	0.00	36.30	2.90
2771	2963	1.557443	GCGTACAGGTGCACACACTC	61.557	60.000	20.43	0.00	46.57	3.51
2776	2968	3.918977	ACGGCGTACAGGTGCACA	61.919	61.111	20.43	0.00	0.00	4.57
2853	3045	4.072131	GCACAAGAAGGGTCAAGTGATTA	58.928	43.478	0.00	0.00	34.50	1.75
2898	3090	8.508883	TTTTACTTAACAGACTGGCAAGTTTA	57.491	30.769	21.81	12.29	36.52	2.01
2979	3171	6.479001	TCGTCATTAAAAGGCTGTTAGCTATC	59.521	38.462	0.00	0.00	41.99	2.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.