AutoCloner

Multiple sequence alignment - TraesCS6D01G095200

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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	TraesCS6D01G095200	chr6D	100.000	2767	0	0	1	2767	59413782	59411016	0.000000e+00	5110.0
1	TraesCS6D01G095200	chr6B	96.449	1943	46	12	490	2417	139443837	139445771	0.000000e+00	3184.0
2	TraesCS6D01G095200	chr6B	97.072	444	10	1	1	441	139442525	139442968	0.000000e+00	745.0
3	TraesCS6D01G095200	chr3D	95.883	1943	48	12	490	2419	166289181	166291104	0.000000e+00	3116.0
4	TraesCS6D01G095200	chr3D	95.982	448	11	1	1	441	166287876	166288323	0.000000e+00	721.0
5	TraesCS6D01G095200	chr3D	91.477	352	24	4	2417	2767	319128304	319128650	1.930000e-131	479.0
6	TraesCS6D01G095200	chr3D	91.453	351	26	4	2417	2767	339177488	339177142	1.930000e-131	479.0
7	TraesCS6D01G095200	chr3D	91.292	356	23	5	2417	2767	375493544	375493896	1.930000e-131	479.0
8	TraesCS6D01G095200	chr3D	91.268	355	23	5	2417	2767	119744111	119744461	6.930000e-131	477.0
9	TraesCS6D01G095200	chr3D	100.000	30	0	0	437	466	166288250	166288279	3.850000e-04	56.5
10	TraesCS6D01G095200	chrUn	95.724	1941	49	12	490	2417	75467106	75469025	0.000000e+00	3094.0
11	TraesCS6D01G095200	chrUn	97.059	442	10	1	3	441	75465796	75466237	0.000000e+00	741.0
12	TraesCS6D01G095200	chrUn	100.000	30	0	0	437	466	75466164	75466193	3.850000e-04	56.5
13	TraesCS6D01G095200	chr2D	95.675	1896	55	15	490	2379	121214078	121212204	0.000000e+00	3022.0
14	TraesCS6D01G095200	chr2D	96.622	444	12	1	1	441	121215389	121214946	0.000000e+00	734.0
15	TraesCS6D01G095200	chr2D	100.000	30	0	0	437	466	121215019	121214990	3.850000e-04	56.5
16	TraesCS6D01G095200	chr7A	95.003	1941	65	11	490	2417	450568927	450567006	0.000000e+00	3018.0
17	TraesCS6D01G095200	chr7A	96.833	442	11	1	3	441	450570237	450569796	0.000000e+00	736.0
18	TraesCS6D01G095200	chr7A	87.037	54	3	4	437	490	450569869	450569820	1.070000e-04	58.4
19	TraesCS6D01G095200	chr7B	94.401	1268	50	12	725	1980	515049126	515050384	0.000000e+00	1929.0
20	TraesCS6D01G095200	chr7B	94.322	1268	51	13	725	1980	515069093	515070351	0.000000e+00	1923.0
21	TraesCS6D01G095200	chr7B	96.847	444	11	3	1	441	515067578	515068021	0.000000e+00	739.0
22	TraesCS6D01G095200	chr7B	96.171	444	14	3	1	441	515047611	515048054	0.000000e+00	723.0
23	TraesCS6D01G095200	chr3B	96.691	1118	33	3	725	1840	62880256	62879141	0.000000e+00	1857.0
24	TraesCS6D01G095200	chr3B	93.092	1216	68	9	725	1934	15665473	15664268	0.000000e+00	1766.0
25	TraesCS6D01G095200	chr3B	97.484	477	10	2	1941	2417	62878225	62877751	0.000000e+00	813.0
26	TraesCS6D01G095200	chr3B	97.059	476	13	1	1941	2416	15741814	15741340	0.000000e+00	800.0
27	TraesCS6D01G095200	chr3B	94.867	487	23	2	1941	2425	15664308	15663822	0.000000e+00	760.0
28	TraesCS6D01G095200	chr3B	95.495	444	17	3	1	441	62881770	62881327	0.000000e+00	706.0
29	TraesCS6D01G095200	chr3B	95.485	443	16	4	1	440	15749701	15749260	0.000000e+00	704.0
30	TraesCS6D01G095200	chr3B	87.037	54	3	4	437	490	15749332	15749283	1.070000e-04	58.4
31	TraesCS6D01G095200	chr5A	95.690	1137	29	6	1298	2427	672814169	672813046	0.000000e+00	1810.0
32	TraesCS6D01G095200	chr5A	97.073	820	14	7	490	1303	672816735	672815920	0.000000e+00	1373.0
33	TraesCS6D01G095200	chr1A	80.228	1401	221	36	490	1867	134968812	134967445	0.000000e+00	1002.0
34	TraesCS6D01G095200	chr1A	95.082	610	17	7	658	1259	42887825	42888429	0.000000e+00	948.0
35	TraesCS6D01G095200	chr1A	100.000	30	0	0	437	466	42882407	42882436	3.850000e-04	56.5
36	TraesCS6D01G095200	chr2B	92.534	509	33	5	1912	2417	213956302	213956808	0.000000e+00	725.0
37	TraesCS6D01G095200	chr5D	87.316	544	59	6	2230	2767	494518080	494518619	5.060000e-172	614.0
38	TraesCS6D01G095200	chr5D	91.761	352	24	5	2417	2767	45442941	45442594	4.140000e-133	484.0
39	TraesCS6D01G095200	chr5D	90.935	353	27	5	2417	2767	190082866	190083215	1.160000e-128	470.0
40	TraesCS6D01G095200	chr5D	100.000	30	0	0	437	466	529819230	529819201	3.850000e-04	56.5
41	TraesCS6D01G095200	chr7D	91.268	355	22	7	2417	2767	157723291	157723640	2.490000e-130	475.0
42	TraesCS6D01G095200	chr1D	91.168	351	28	3	2417	2767	241357271	241356924	8.970000e-130	473.0

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	TraesCS6D01G095200	chr6D	59411016	59413782	2766	True	5110.000000	5110	100.000000	1	2767	1	chr6D.!!$R1	2766
1	TraesCS6D01G095200	chr6B	139442525	139445771	3246	False	1964.500000	3184	96.760500	1	2417	2	chr6B.!!$F1	2416
2	TraesCS6D01G095200	chr3D	166287876	166291104	3228	False	1297.833333	3116	97.288333	1	2419	3	chr3D.!!$F4	2418
3	TraesCS6D01G095200	chrUn	75465796	75469025	3229	False	1297.166667	3094	97.594333	3	2417	3	chrUn.!!$F1	2414
4	TraesCS6D01G095200	chr2D	121212204	121215389	3185	True	1270.833333	3022	97.432333	1	2379	3	chr2D.!!$R1	2378
5	TraesCS6D01G095200	chr7A	450567006	450570237	3231	True	1270.800000	3018	92.957667	3	2417	3	chr7A.!!$R1	2414
6	TraesCS6D01G095200	chr7B	515067578	515070351	2773	False	1331.000000	1923	95.584500	1	1980	2	chr7B.!!$F2	1979
7	TraesCS6D01G095200	chr7B	515047611	515050384	2773	False	1326.000000	1929	95.286000	1	1980	2	chr7B.!!$F1	1979
8	TraesCS6D01G095200	chr3B	15663822	15665473	1651	True	1263.000000	1766	93.979500	725	2425	2	chr3B.!!$R2	1700
9	TraesCS6D01G095200	chr3B	62877751	62881770	4019	True	1125.333333	1857	96.556667	1	2417	3	chr3B.!!$R4	2416
10	TraesCS6D01G095200	chr5A	672813046	672816735	3689	True	1591.500000	1810	96.381500	490	2427	2	chr5A.!!$R1	1937
11	TraesCS6D01G095200	chr1A	134967445	134968812	1367	True	1002.000000	1002	80.228000	490	1867	1	chr1A.!!$R1	1377
12	TraesCS6D01G095200	chr1A	42887825	42888429	604	False	948.000000	948	95.082000	658	1259	1	chr1A.!!$F2	601
13	TraesCS6D01G095200	chr2B	213956302	213956808	506	False	725.000000	725	92.534000	1912	2417	1	chr2B.!!$F1	505
14	TraesCS6D01G095200	chr5D	494518080	494518619	539	False	614.000000	614	87.316000	2230	2767	1	chr5D.!!$F2	537

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
459	710	1.616374	TGCGTATGAAGTGTGGTCTGA	59.384	47.619	0.0	0.0	0.0	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1796	4509	0.394762	TGTGCATGGGAAGCTCCATC	60.395	55.0	3.96	1.61	45.08	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
147	155	6.693113	CGAAGAGAACAAAAGAAGAAAAAGGG	59.307	38.462	0.00	0.00	0.00	3.95
284	292	8.144478	TGATATGTTCATAGGAAGTACTTGCTC	58.856	37.037	30.08	17.19	40.47	4.26
389	397	3.006003	TGTTGCGTATGAAGTGTGGTCTA	59.994	43.478	0.00	0.00	0.00	2.59
427	435	5.984725	TGTCACTGTAGAAGAAAAGGTTGA	58.015	37.500	0.00	0.00	0.00	3.18
441	449	7.147976	AGAAAAGGTTGATATGTTCTTGTTGC	58.852	34.615	0.00	0.00	0.00	4.17
442	450	4.685169	AGGTTGATATGTTCTTGTTGCG	57.315	40.909	0.00	0.00	0.00	4.85
443	451	4.072131	AGGTTGATATGTTCTTGTTGCGT	58.928	39.130	0.00	0.00	0.00	5.24
444	452	5.242434	AGGTTGATATGTTCTTGTTGCGTA	58.758	37.500	0.00	0.00	0.00	4.42
446	454	5.965334	GGTTGATATGTTCTTGTTGCGTATG	59.035	40.000	0.00	0.00	0.00	2.39
447	455	6.183360	GGTTGATATGTTCTTGTTGCGTATGA	60.183	38.462	0.00	0.00	0.00	2.15
448	456	6.976636	TGATATGTTCTTGTTGCGTATGAA	57.023	33.333	0.00	0.00	0.00	2.57
449	457	7.003939	TGATATGTTCTTGTTGCGTATGAAG	57.996	36.000	0.00	0.00	0.00	3.02
450	458	6.593770	TGATATGTTCTTGTTGCGTATGAAGT	59.406	34.615	0.00	0.00	0.00	3.01
451	459	4.466567	TGTTCTTGTTGCGTATGAAGTG	57.533	40.909	0.00	0.00	0.00	3.16
456	464	2.139917	TGTTGCGTATGAAGTGTGGTC	58.860	47.619	0.00	0.00	0.00	4.02
459	710	1.616374	TGCGTATGAAGTGTGGTCTGA	59.384	47.619	0.00	0.00	0.00	3.27
483	734	9.815306	TGAAAGATATGCCTACTAATAGTCTCT	57.185	33.333	0.00	0.00	0.00	3.10
688	1558	5.184479	AGTTGATGGTGGATGTCTCATTTTG	59.816	40.000	0.00	0.00	0.00	2.44
794	1702	3.022607	AGCTTGCTGATTGTCTTTTGC	57.977	42.857	0.00	0.00	0.00	3.68
1158	2074	6.347725	GCAATAAGGATATCGCGAAGAACAAT	60.348	38.462	15.24	0.00	0.00	2.71
1458	4133	1.372087	GAAGCACTGGGAAGCCATCG	61.372	60.000	0.00	0.00	0.00	3.84
1528	4215	0.176219	GCTGAGACTGCTGCTGAGAT	59.824	55.000	13.69	0.00	0.00	2.75
1761	4472	0.370273	CATGTTGCGCTCTTACGGAC	59.630	55.000	9.73	0.00	31.24	4.79
1765	4476	0.883153	TTGCGCTCTTACGGACAGTA	59.117	50.000	9.73	0.00	31.24	2.74
1796	4509	0.590195	AGCGCTTGTTTGAAGCTCTG	59.410	50.000	2.64	0.00	37.00	3.35
1893	5472	6.403855	CCGTGTCTTGTTAAACTTCTTGGAAA	60.404	38.462	0.00	0.00	0.00	3.13
2051	5652	5.639506	ACTATGTGTCGTTGAGAATTTGAGG	59.360	40.000	0.00	0.00	0.00	3.86
2471	6078	5.336849	CCTTAGTTGTGGGTGAAACAAACAA	60.337	40.000	0.00	0.00	40.09	2.83
2472	6079	4.608948	AGTTGTGGGTGAAACAAACAAA	57.391	36.364	0.00	0.00	42.66	2.83
2473	6080	4.962155	AGTTGTGGGTGAAACAAACAAAA	58.038	34.783	0.00	0.00	42.66	2.44
2474	6081	5.368989	AGTTGTGGGTGAAACAAACAAAAA	58.631	33.333	0.00	0.00	42.66	1.94
2475	6082	5.237561	AGTTGTGGGTGAAACAAACAAAAAC	59.762	36.000	0.00	0.00	42.66	2.43
2476	6083	4.703897	TGTGGGTGAAACAAACAAAAACA	58.296	34.783	0.00	0.00	39.98	2.83
2479	6086	6.934645	TGTGGGTGAAACAAACAAAAACATTA	59.065	30.769	0.00	0.00	39.98	1.90
2531	6140	5.897377	TGCCTCTTATGCCTAAAAACTTC	57.103	39.130	0.00	0.00	0.00	3.01
2533	6142	5.648092	TGCCTCTTATGCCTAAAAACTTCTC	59.352	40.000	0.00	0.00	0.00	2.87
2534	6143	5.648092	GCCTCTTATGCCTAAAAACTTCTCA	59.352	40.000	0.00	0.00	0.00	3.27
2614	6223	3.921119	TGTGTTCATGCTCATGGAAAC	57.079	42.857	9.69	7.19	39.24	2.78
2720	6329	8.986477	CCAAGTTTTGGTTTTAGGATGATTAG	57.014	34.615	0.00	0.00	45.93	1.73
2735	6344	6.154021	AGGATGATTAGATTGCTTGTTTGCTT	59.846	34.615	0.00	0.00	0.00	3.91
2752	6361	0.297230	CTTTGTGCGGTGCAAAAACG	59.703	50.000	3.10	0.00	40.32	3.60
2761	6370	3.423776	GCGGTGCAAAAACGAAAACTTTT	60.424	39.130	5.67	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
147	155	5.879223	ACATCACTGTCAAGATGATCCTTTC	59.121	40.000	17.38	0.00	43.28	2.62
284	292	6.573664	TCTGACCCATTGTACATTTCTTTG	57.426	37.500	0.00	0.00	0.00	2.77
389	397	8.847196	TCTACAGTGACATATACGCTATCTTTT	58.153	33.333	0.00	0.00	0.00	2.27
427	435	6.371548	ACACTTCATACGCAACAAGAACATAT	59.628	34.615	0.00	0.00	0.00	1.78
441	449	4.556233	TCTTTCAGACCACACTTCATACG	58.444	43.478	0.00	0.00	0.00	3.06
442	450	7.254590	GCATATCTTTCAGACCACACTTCATAC	60.255	40.741	0.00	0.00	0.00	2.39
443	451	6.763135	GCATATCTTTCAGACCACACTTCATA	59.237	38.462	0.00	0.00	0.00	2.15
444	452	5.587844	GCATATCTTTCAGACCACACTTCAT	59.412	40.000	0.00	0.00	0.00	2.57
446	454	4.333926	GGCATATCTTTCAGACCACACTTC	59.666	45.833	0.00	0.00	0.00	3.01
447	455	4.018960	AGGCATATCTTTCAGACCACACTT	60.019	41.667	0.00	0.00	0.00	3.16
448	456	3.521126	AGGCATATCTTTCAGACCACACT	59.479	43.478	0.00	0.00	0.00	3.55
449	457	3.878778	AGGCATATCTTTCAGACCACAC	58.121	45.455	0.00	0.00	0.00	3.82
450	458	4.716784	AGTAGGCATATCTTTCAGACCACA	59.283	41.667	0.00	0.00	0.00	4.17
451	459	5.283457	AGTAGGCATATCTTTCAGACCAC	57.717	43.478	0.00	0.00	0.00	4.16
467	718	9.198837	GCAATTCTTTAGAGACTATTAGTAGGC	57.801	37.037	0.00	0.00	36.09	3.93
470	721	9.751542	GCAGCAATTCTTTAGAGACTATTAGTA	57.248	33.333	0.00	0.00	0.00	1.82
478	729	5.869753	TCTTGCAGCAATTCTTTAGAGAC	57.130	39.130	8.67	0.00	0.00	3.36
479	730	6.000219	ACTTCTTGCAGCAATTCTTTAGAGA	59.000	36.000	8.67	0.00	0.00	3.10
482	733	6.441274	TCAACTTCTTGCAGCAATTCTTTAG	58.559	36.000	8.67	0.00	0.00	1.85
483	734	6.389830	TCAACTTCTTGCAGCAATTCTTTA	57.610	33.333	8.67	0.00	0.00	1.85
484	735	5.266733	TCAACTTCTTGCAGCAATTCTTT	57.733	34.783	8.67	0.00	0.00	2.52
485	736	4.924305	TCAACTTCTTGCAGCAATTCTT	57.076	36.364	8.67	0.00	0.00	2.52
486	737	4.806330	CATCAACTTCTTGCAGCAATTCT	58.194	39.130	8.67	0.00	0.00	2.40
487	738	3.367025	GCATCAACTTCTTGCAGCAATTC	59.633	43.478	8.67	0.00	36.40	2.17
488	739	3.006537	AGCATCAACTTCTTGCAGCAATT	59.993	39.130	8.67	0.00	38.84	2.32
688	1558	0.249398	CCACCACCTAGGCACTACAC	59.751	60.000	9.30	0.00	43.14	2.90
794	1702	0.108186	TGGTCAGCCAAGCTATCACG	60.108	55.000	0.00	0.00	42.83	4.35
1158	2074	7.727186	TCGAAAGTCCTAAGCCTTCCTAATATA	59.273	37.037	0.00	0.00	0.00	0.86
1458	4133	7.907045	CGCATGATCTTTTGAATATATGGTAGC	59.093	37.037	0.00	0.00	0.00	3.58
1528	4215	4.898320	TGTTTCTTCTAGATCTGCAGCAA	58.102	39.130	9.47	0.00	0.00	3.91
1732	4443	3.444034	AGAGCGCAACATGTCTACTTCTA	59.556	43.478	11.47	0.00	0.00	2.10
1761	4472	5.521735	ACAAGCGCTCATTAAGAATCTACTG	59.478	40.000	12.06	1.00	0.00	2.74
1765	4476	5.412594	TCAAACAAGCGCTCATTAAGAATCT	59.587	36.000	12.06	0.00	0.00	2.40
1796	4509	0.394762	TGTGCATGGGAAGCTCCATC	60.395	55.000	3.96	1.61	45.08	3.51
2448	6055	5.317733	TGTTTGTTTCACCCACAACTAAG	57.682	39.130	0.00	0.00	33.81	2.18
2503	6110	5.950544	TTTAGGCATAAGAGGCAAGTAGA	57.049	39.130	0.00	0.00	36.37	2.59
2504	6111	6.599638	AGTTTTTAGGCATAAGAGGCAAGTAG	59.400	38.462	0.00	0.00	36.37	2.57
2546	6155	4.608269	TCCAATGCATAACCTTCCAATCA	58.392	39.130	0.00	0.00	0.00	2.57
2700	6309	9.034800	AGCAATCTAATCATCCTAAAACCAAAA	57.965	29.630	0.00	0.00	0.00	2.44
2706	6315	9.859427	CAAACAAGCAATCTAATCATCCTAAAA	57.141	29.630	0.00	0.00	0.00	1.52
2720	6329	2.347846	CGCACAAAGCAAACAAGCAATC	60.348	45.455	0.00	0.00	46.13	2.67
2735	6344	0.109272	TTCGTTTTTGCACCGCACAA	60.109	45.000	0.00	0.00	38.71	3.33

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.