AutoCloner

Multiple sequence alignment - TraesCS6D01G087900

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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	TraesCS6D01G087900	chr6D	100.000	2728	0	0	1	2728	53309000	53311727	0.000000e+00	5038.0
1	TraesCS6D01G087900	chr6D	89.824	2732	253	16	1	2726	51625067	51622355	0.000000e+00	3482.0
2	TraesCS6D01G087900	chr6A	92.582	2494	167	16	40	2527	62490084	62487603	0.000000e+00	3565.0
3	TraesCS6D01G087900	chr6A	87.090	2014	202	26	610	2609	42389528	42387559	0.000000e+00	2226.0
4	TraesCS6D01G087900	chr6A	86.700	2015	200	28	610	2609	42208617	42206656	0.000000e+00	2174.0
5	TraesCS6D01G087900	chr6A	91.099	573	43	7	1	569	42209181	42208613	0.000000e+00	769.0
6	TraesCS6D01G087900	chr6A	90.925	573	44	7	1	569	42390092	42389524	0.000000e+00	763.0
7	TraesCS6D01G087900	chr6A	85.204	392	53	3	2324	2712	62659928	62659539	5.470000e-107	398.0
8	TraesCS6D01G087900	chr6A	75.000	444	73	24	929	1342	63070637	63071072	1.300000e-38	171.0
9	TraesCS6D01G087900	chr6A	90.110	91	6	3	929	1017	63017906	63017995	6.170000e-22	115.0
10	TraesCS6D01G087900	chr6A	87.368	95	11	1	2635	2728	62487603	62487509	1.030000e-19	108.0
11	TraesCS6D01G087900	chr6B	90.004	2391	219	13	1	2382	118823776	118821397	0.000000e+00	3073.0
12	TraesCS6D01G087900	chr6B	88.581	2417	238	30	13	2411	76599557	76597161	0.000000e+00	2900.0
13	TraesCS6D01G087900	chr6B	87.315	1419	156	15	1003	2411	76733990	76732586	0.000000e+00	1602.0
14	TraesCS6D01G087900	chr6B	89.323	946	92	8	11	949	76742394	76741451	0.000000e+00	1179.0
15	TraesCS6D01G087900	chr6B	75.000	424	91	10	929	1342	118938464	118938882	6.000000e-42	182.0
16	TraesCS6D01G087900	chr6B	86.957	69	9	0	2407	2475	76574718	76574650	8.100000e-11	78.7
17	TraesCS6D01G087900	chrUn	89.381	1761	165	15	860	2609	105245675	105247424	0.000000e+00	2196.0
18	TraesCS6D01G087900	chrUn	90.152	660	52	6	1	655	105245019	105245670	0.000000e+00	846.0
19	TraesCS6D01G087900	chrUn	91.765	425	29	5	1	422	345248701	345248280	1.090000e-163	586.0

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	TraesCS6D01G087900	chr6D	53309000	53311727	2727	False	5038.0	5038	100.0000	1	2728	1	chr6D.!!$F1	2727
1	TraesCS6D01G087900	chr6D	51622355	51625067	2712	True	3482.0	3482	89.8240	1	2726	1	chr6D.!!$R1	2725
2	TraesCS6D01G087900	chr6A	62487509	62490084	2575	True	1836.5	3565	89.9750	40	2728	2	chr6A.!!$R4	2688
3	TraesCS6D01G087900	chr6A	42387559	42390092	2533	True	1494.5	2226	89.0075	1	2609	2	chr6A.!!$R3	2608
4	TraesCS6D01G087900	chr6A	42206656	42209181	2525	True	1471.5	2174	88.8995	1	2609	2	chr6A.!!$R2	2608
5	TraesCS6D01G087900	chr6B	118821397	118823776	2379	True	3073.0	3073	90.0040	1	2382	1	chr6B.!!$R5	2381
6	TraesCS6D01G087900	chr6B	76597161	76599557	2396	True	2900.0	2900	88.5810	13	2411	1	chr6B.!!$R2	2398
7	TraesCS6D01G087900	chr6B	76732586	76733990	1404	True	1602.0	1602	87.3150	1003	2411	1	chr6B.!!$R3	1408
8	TraesCS6D01G087900	chr6B	76741451	76742394	943	True	1179.0	1179	89.3230	11	949	1	chr6B.!!$R4	938
9	TraesCS6D01G087900	chrUn	105245019	105247424	2405	False	1521.0	2196	89.7665	1	2609	2	chrUn.!!$F1	2608

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
758	769	1.069049	ACAGTTTGCCATGTCCTTTGC	59.931	47.619	0.00	0.0	0.0	3.68	F
1592	1606	0.181114	AGTTGGAGCTCAGTGTTGCA	59.819	50.000	17.19	0.0	0.0	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1612	1626	0.540133	ACCCAGATGCATGCACACAA	60.540	50.000	25.37	0.0	0.00	3.33	R
2557	2591	2.120909	CCATGGGCACGATTCCACC	61.121	63.158	2.85	0.0	35.67	4.61	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
116	117	7.661847	TGGAAGATCTTTAAACTTGGAGACTTC	59.338	37.037	9.87	0.00	32.19	3.01
117	118	7.661847	GGAAGATCTTTAAACTTGGAGACTTCA	59.338	37.037	9.87	0.00	33.25	3.02
241	244	8.650143	ATTAGTACATCATTGGTTGTTCCTTT	57.350	30.769	0.00	0.00	37.07	3.11
526	533	2.134346	CACATTCCTTTTTGCCGGTTG	58.866	47.619	1.90	0.00	0.00	3.77
547	555	3.209410	GGAGTGTTCTAGATGCCCATTG	58.791	50.000	0.00	0.00	0.00	2.82
567	575	4.637387	TGCATCCACAATTTTTCCCATT	57.363	36.364	0.00	0.00	0.00	3.16
708	718	7.715265	TCGATCCATAGCTTTCTTACAAATC	57.285	36.000	0.00	0.00	0.00	2.17
758	769	1.069049	ACAGTTTGCCATGTCCTTTGC	59.931	47.619	0.00	0.00	0.00	3.68
825	836	5.835257	TCCATTCTTGCAAAACAAAGAGAG	58.165	37.500	0.00	0.00	37.96	3.20
1054	1065	1.620822	CACTTAGCCCTTGCAACCTT	58.379	50.000	0.00	0.00	41.13	3.50
1198	1209	2.203337	GCACCAGGCACACCAGAA	60.203	61.111	0.00	0.00	43.97	3.02
1297	1308	1.672363	TCTTGCCATCGACATCAATGC	59.328	47.619	0.00	0.00	0.00	3.56
1306	1317	2.755064	CATCAATGCGGTGCCCCA	60.755	61.111	0.00	0.00	0.00	4.96
1307	1318	2.755469	ATCAATGCGGTGCCCCAC	60.755	61.111	0.00	0.00	0.00	4.61
1308	1319	3.582242	ATCAATGCGGTGCCCCACA	62.582	57.895	0.00	0.00	35.86	4.17
1313	1324	3.532155	GCGGTGCCCCACAACAAA	61.532	61.111	0.00	0.00	34.73	2.83
1316	1327	1.739667	GGTGCCCCACAACAAAGAC	59.260	57.895	0.00	0.00	35.37	3.01
1493	1507	3.939740	AAGCAGCTGATGGAGGAAATA	57.060	42.857	20.43	0.00	0.00	1.40
1499	1513	3.324556	AGCTGATGGAGGAAATAGAGCTC	59.675	47.826	5.27	5.27	29.57	4.09
1531	1545	4.259356	CAGTTGGAGAATGAGAAGATGCA	58.741	43.478	0.00	0.00	0.00	3.96
1592	1606	0.181114	AGTTGGAGCTCAGTGTTGCA	59.819	50.000	17.19	0.00	0.00	4.08
1612	1626	1.880941	AGGCCGAAAAGGATCTAGGT	58.119	50.000	0.00	0.00	45.00	3.08
1633	1647	1.271817	TGTGTGCATGCATCTGGGTTA	60.272	47.619	25.64	2.09	0.00	2.85
1639	1653	4.025360	TGCATGCATCTGGGTTATTTTCT	58.975	39.130	18.46	0.00	0.00	2.52
1694	1711	2.242452	AGGGAGGAACAAATAAGAGGCC	59.758	50.000	0.00	0.00	0.00	5.19
1890	1911	1.673767	AGGAGGAGGCTTTCATGGAA	58.326	50.000	0.00	0.00	0.00	3.53
1893	1914	1.283321	GAGGAGGCTTTCATGGAAGGT	59.717	52.381	15.71	0.00	0.00	3.50
1952	1974	1.614241	CCCCCTTCTGTCTACCCGTG	61.614	65.000	0.00	0.00	0.00	4.94
1968	1990	4.337145	ACCCGTGGTTATTGCTTAATTCA	58.663	39.130	0.00	0.00	27.29	2.57
2022	2044	4.754114	GGCATTTGATGACTCTCCATACTC	59.246	45.833	0.00	0.00	34.69	2.59
2211	2236	3.325870	AGATGTTGGTGTATGTCGTGTG	58.674	45.455	0.00	0.00	0.00	3.82
2236	2261	2.288091	CGTGATGCACAATCCAAAACCA	60.288	45.455	0.00	0.00	34.00	3.67
2245	2270	2.801679	CAATCCAAAACCACACACATGC	59.198	45.455	0.00	0.00	0.00	4.06
2250	2275	3.005554	CAAAACCACACACATGCCAAAA	58.994	40.909	0.00	0.00	0.00	2.44
2253	2278	3.557228	ACCACACACATGCCAAAATTT	57.443	38.095	0.00	0.00	0.00	1.82
2260	2285	5.927689	ACACACATGCCAAAATTTAGACATG	59.072	36.000	18.44	18.44	40.48	3.21
2290	2315	7.596248	GTGCATCATATTTGTCTTTTGTGTTCT	59.404	33.333	0.00	0.00	0.00	3.01
2322	2348	8.103948	AGAAAAAGTCTTTGACCAGTATCATG	57.896	34.615	0.00	0.00	29.66	3.07
2370	2400	7.050377	CCATCTGATCACAAAGGTAGTAACAT	58.950	38.462	0.00	0.00	0.00	2.71
2376	2406	6.579666	TCACAAAGGTAGTAACATAGACGT	57.420	37.500	0.00	0.00	0.00	4.34
2463	2493	6.292168	CGGTTTCATTCTTGTACCTATTAGCG	60.292	42.308	0.00	0.00	31.03	4.26
2502	2532	2.435372	TGTGAGGTTTGAACTGCCTT	57.565	45.000	0.00	0.00	31.89	4.35
2531	2565	1.515521	AAAGAAGCCCCTTTGTCGCG	61.516	55.000	0.00	0.00	35.26	5.87
2557	2591	6.153000	ACACTTCCTAGTAGTAGTGTCATTGG	59.847	42.308	21.03	5.17	45.89	3.16
2566	2600	2.113860	AGTGTCATTGGGTGGAATCG	57.886	50.000	0.00	0.00	0.00	3.34
2652	2686	1.557832	TGGCTACCCATGTGAGTTACC	59.442	52.381	0.00	0.00	35.79	2.85
2655	2689	2.737679	GCTACCCATGTGAGTTACCGAC	60.738	54.545	0.00	0.00	0.00	4.79
2657	2691	1.275291	ACCCATGTGAGTTACCGACAG	59.725	52.381	0.00	0.00	0.00	3.51
2663	2697	5.466819	CATGTGAGTTACCGACAGAAACTA	58.533	41.667	0.00	0.00	33.72	2.24
2669	2703	9.148104	GTGAGTTACCGACAGAAACTATTATTT	57.852	33.333	0.00	0.00	33.72	1.40
2726	2760	9.840427	TGTTTCTTTAGATAGTAAAATGCAAGC	57.160	29.630	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	117	0.831288	TTGCCCCAATCACCAACCTG	60.831	55.000	0.00	0.00	0.00	4.00
117	118	0.116940	ATTGCCCCAATCACCAACCT	59.883	50.000	0.00	0.00	26.27	3.50
202	205	4.761975	TGTACTAATCAACCGGATTGGAC	58.238	43.478	9.46	0.67	44.71	4.02
471	477	8.613060	ATCATGCATACTACATCGAAGAATTT	57.387	30.769	0.00	0.00	43.58	1.82
479	485	9.882996	AAAATTTGTATCATGCATACTACATCG	57.117	29.630	16.83	0.00	38.64	3.84
526	533	3.209410	CAATGGGCATCTAGAACACTCC	58.791	50.000	0.00	0.00	0.00	3.85
547	555	4.577875	TCAATGGGAAAAATTGTGGATGC	58.422	39.130	0.00	0.00	36.58	3.91
708	718	8.219105	GCTGCTTATTCTCAAAGTTTTTCAATG	58.781	33.333	0.00	0.00	0.00	2.82
758	769	5.706916	CAATTGACAAGAGATGGGAACTTG	58.293	41.667	0.00	0.00	44.16	3.16
825	836	1.002011	GGCACACTTCCCTTCTCCC	60.002	63.158	0.00	0.00	0.00	4.30
855	866	4.207165	GAGCTAGAATACATTTGGCCCAA	58.793	43.478	0.00	0.00	0.00	4.12
1054	1065	5.178623	GTCGGAATGTGTTGTGATGAAACTA	59.821	40.000	0.00	0.00	0.00	2.24
1140	1151	0.945813	ATACTAGGCTGCTCGTCGTC	59.054	55.000	0.00	0.00	0.00	4.20
1198	1209	1.410153	CTTGCTTGCCCTTGAAAGTGT	59.590	47.619	0.00	0.00	0.00	3.55
1306	1317	1.194495	GTCGTCGTCGTCTTTGTTGT	58.806	50.000	1.33	0.00	38.33	3.32
1307	1318	0.501435	GGTCGTCGTCGTCTTTGTTG	59.499	55.000	1.33	0.00	38.33	3.33
1308	1319	0.383231	AGGTCGTCGTCGTCTTTGTT	59.617	50.000	1.33	0.00	38.33	2.83
1493	1507	3.336468	CAACTGCATCTTCTTGAGCTCT	58.664	45.455	16.19	0.00	0.00	4.09
1499	1513	4.698780	TCATTCTCCAACTGCATCTTCTTG	59.301	41.667	0.00	0.00	0.00	3.02
1531	1545	0.540923	GAGCCTGATGTTCTCCAGCT	59.459	55.000	0.00	0.00	34.80	4.24
1552	1566	1.406069	CCTTACGCTTGATCTGCACCT	60.406	52.381	10.82	0.00	0.00	4.00
1592	1606	2.197465	ACCTAGATCCTTTTCGGCCTT	58.803	47.619	0.00	0.00	0.00	4.35
1612	1626	0.540133	ACCCAGATGCATGCACACAA	60.540	50.000	25.37	0.00	0.00	3.33
1633	1647	5.817816	CCTGATTTCCAGCGTACTAGAAAAT	59.182	40.000	0.00	0.00	37.14	1.82
1639	1653	1.760613	CCCCTGATTTCCAGCGTACTA	59.239	52.381	0.00	0.00	41.57	1.82
1672	1689	3.546724	GCCTCTTATTTGTTCCTCCCTC	58.453	50.000	0.00	0.00	0.00	4.30
1674	1691	2.242452	AGGCCTCTTATTTGTTCCTCCC	59.758	50.000	0.00	0.00	0.00	4.30
1694	1711	7.862512	AGCAGAAATAGGAATCTTTCTTGAG	57.137	36.000	0.00	0.00	39.15	3.02
1857	1877	2.104792	CTCCTCCTTGGTTGTCTCAACA	59.895	50.000	13.34	0.00	37.07	3.33
1890	1911	4.029520	AGTGCAAGAGTGAGATGATACCT	58.970	43.478	0.00	0.00	0.00	3.08
1952	1974	7.945134	ACATGGAGATGAATTAAGCAATAACC	58.055	34.615	0.00	0.00	33.36	2.85
1968	1990	2.885135	TGGTCAAGCAACATGGAGAT	57.115	45.000	0.00	0.00	0.00	2.75
2211	2236	1.155889	TGGATTGTGCATCACGACAC	58.844	50.000	0.00	0.00	37.14	3.67
2236	2261	5.528043	TGTCTAAATTTTGGCATGTGTGT	57.472	34.783	2.70	0.00	0.00	3.72
2245	2270	3.364621	GCACACGCATGTCTAAATTTTGG	59.635	43.478	0.00	0.00	36.72	3.28
2260	2285	3.680642	AGACAAATATGATGCACACGC	57.319	42.857	0.00	0.00	39.24	5.34
2290	2315	8.429641	ACTGGTCAAAGACTTTTTCTACATAGA	58.570	33.333	0.00	0.00	32.51	1.98
2345	2371	6.406370	TGTTACTACCTTTGTGATCAGATGG	58.594	40.000	0.00	3.17	0.00	3.51
2346	2372	9.254133	CTATGTTACTACCTTTGTGATCAGATG	57.746	37.037	0.00	0.00	0.00	2.90
2347	2373	9.201989	TCTATGTTACTACCTTTGTGATCAGAT	57.798	33.333	0.00	0.00	0.00	2.90
2370	2400	7.384932	CCACAATAATTAGATGATGCACGTCTA	59.615	37.037	11.74	11.74	43.62	2.59
2376	2406	7.464273	AGATCCCACAATAATTAGATGATGCA	58.536	34.615	7.77	0.00	0.00	3.96
2463	2493	4.282950	CATGTGCAACCATGTATGAGTC	57.717	45.455	8.73	0.00	37.91	3.36
2502	2532	3.778265	AGGGGCTTCTTTCTTATTGCAA	58.222	40.909	0.00	0.00	0.00	4.08
2557	2591	2.120909	CCATGGGCACGATTCCACC	61.121	63.158	2.85	0.00	35.67	4.61
2669	2703	8.282455	TGTCTTTTGGTTACAAATGAAGTACA	57.718	30.769	9.42	3.59	46.06	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.