AutoCloner

Multiple sequence alignment - TraesCS3B01G185800

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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	TraesCS3B01G185800	chr3B	100.000	2363	0	0	1	2363	201494049	201491687	0.000000e+00	4327
1	TraesCS3B01G185800	chr3B	98.529	340	5	0	502	841	201493898	201493559	3.360000e-168	601
2	TraesCS3B01G185800	chr3B	96.078	153	6	0	577	729	374245160	374245312	1.400000e-62	250
3	TraesCS3B01G185800	chr1A	98.871	1860	20	1	504	2363	554447403	554449261	0.000000e+00	3317
4	TraesCS3B01G185800	chr1A	99.389	491	3	0	1	491	554445442	554445932	0.000000e+00	891
5	TraesCS3B01G185800	chr1A	99.389	491	3	0	1	491	554447250	554447740	0.000000e+00	891
6	TraesCS3B01G185800	chr1D	98.497	1863	26	2	502	2363	254477543	254475682	0.000000e+00	3284
7	TraesCS3B01G185800	chr1D	96.455	1862	62	2	502	2363	244201835	244199978	0.000000e+00	3070
8	TraesCS3B01G185800	chr1D	96.296	1863	57	7	502	2363	244769023	244767172	0.000000e+00	3048
9	TraesCS3B01G185800	chr1D	97.216	1688	46	1	676	2363	180356024	180357710	0.000000e+00	2856
10	TraesCS3B01G185800	chr1D	99.593	491	2	0	1	491	180355197	180355687	0.000000e+00	896
11	TraesCS3B01G185800	chr1D	98.982	491	4	1	1	491	254477693	254477204	0.000000e+00	878
12	TraesCS3B01G185800	chr5D	98.013	1862	35	1	502	2363	6235356	6237215	0.000000e+00	3232
13	TraesCS3B01G185800	chr5D	98.318	1665	26	2	700	2363	503331258	503329595	0.000000e+00	2918
14	TraesCS3B01G185800	chr5D	97.967	492	9	1	1	491	6235204	6235695	0.000000e+00	852
15	TraesCS3B01G185800	chr2D	98.532	1567	21	2	502	2067	648662758	648664323	0.000000e+00	2765
16	TraesCS3B01G185800	chr2D	99.187	492	3	1	1	491	648660267	648660758	0.000000e+00	885
17	TraesCS3B01G185800	chr2D	99.185	491	4	0	1	491	648662607	648663097	0.000000e+00	885
18	TraesCS3B01G185800	chr7A	95.108	1533	71	3	502	2033	352295901	352297430	0.000000e+00	2412
19	TraesCS3B01G185800	chr7A	95.563	293	13	0	1951	2243	647115792	647116084	9.890000e-129	470
20	TraesCS3B01G185800	chr7A	97.761	268	6	0	2071	2338	352297429	352297696	1.650000e-126	462
21	TraesCS3B01G185800	chrUn	99.389	491	3	0	1	491	457255746	457255256	0.000000e+00	891
22	TraesCS3B01G185800	chrUn	99.389	491	3	0	1	491	462818728	462819218	0.000000e+00	891
23	TraesCS3B01G185800	chr4A	97.556	491	11	1	1	491	309288143	309288632	0.000000e+00	839

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	TraesCS3B01G185800	chr3B	201491687	201494049	2362	True	2464.000000	4327	99.264500	1	2363	2	chr3B.!!$R1	2362
1	TraesCS3B01G185800	chr1A	554445442	554449261	3819	False	1699.666667	3317	99.216333	1	2363	3	chr1A.!!$F1	2362
2	TraesCS3B01G185800	chr1D	244199978	244201835	1857	True	3070.000000	3070	96.455000	502	2363	1	chr1D.!!$R1	1861
3	TraesCS3B01G185800	chr1D	244767172	244769023	1851	True	3048.000000	3048	96.296000	502	2363	1	chr1D.!!$R2	1861
4	TraesCS3B01G185800	chr1D	254475682	254477693	2011	True	2081.000000	3284	98.739500	1	2363	2	chr1D.!!$R3	2362
5	TraesCS3B01G185800	chr1D	180355197	180357710	2513	False	1876.000000	2856	98.404500	1	2363	2	chr1D.!!$F1	2362
6	TraesCS3B01G185800	chr5D	503329595	503331258	1663	True	2918.000000	2918	98.318000	700	2363	1	chr5D.!!$R1	1663
7	TraesCS3B01G185800	chr5D	6235204	6237215	2011	False	2042.000000	3232	97.990000	1	2363	2	chr5D.!!$F1	2362
8	TraesCS3B01G185800	chr2D	648660267	648664323	4056	False	1511.666667	2765	98.968000	1	2067	3	chr2D.!!$F1	2066
9	TraesCS3B01G185800	chr7A	352295901	352297696	1795	False	1437.000000	2412	96.434500	502	2338	2	chr7A.!!$F2	1836

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
472	475	1.287739	GGGAGTTGGGATTCCATTGGA	59.712	52.381	0.0	0.0	43.63	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1575	5730	5.65648	TCCATAACGATCAAAGTCGAATCA	58.344	37.5	3.09	0.0	44.06	2.57	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
369	372	5.751243	AGAGATTCTAGAGAAAGCGAGAC	57.249	43.478	0.00	0.00	37.61	3.36
370	373	5.189928	AGAGATTCTAGAGAAAGCGAGACA	58.810	41.667	0.00	0.00	37.61	3.41
371	374	5.650266	AGAGATTCTAGAGAAAGCGAGACAA	59.350	40.000	0.00	0.00	37.61	3.18
372	375	6.151985	AGAGATTCTAGAGAAAGCGAGACAAA	59.848	38.462	0.00	0.00	37.61	2.83
373	376	6.329496	AGATTCTAGAGAAAGCGAGACAAAG	58.671	40.000	0.00	0.00	37.61	2.77
374	377	5.455056	TTCTAGAGAAAGCGAGACAAAGT	57.545	39.130	0.00	0.00	0.00	2.66
375	378	4.799678	TCTAGAGAAAGCGAGACAAAGTG	58.200	43.478	0.00	0.00	0.00	3.16
376	379	3.735237	AGAGAAAGCGAGACAAAGTGA	57.265	42.857	0.00	0.00	0.00	3.41
377	380	4.060038	AGAGAAAGCGAGACAAAGTGAA	57.940	40.909	0.00	0.00	0.00	3.18
378	381	4.442706	AGAGAAAGCGAGACAAAGTGAAA	58.557	39.130	0.00	0.00	0.00	2.69
379	382	4.271291	AGAGAAAGCGAGACAAAGTGAAAC	59.729	41.667	0.00	0.00	0.00	2.78
380	383	3.001330	AGAAAGCGAGACAAAGTGAAACG	59.999	43.478	0.00	0.00	45.86	3.60
381	384	2.218953	AGCGAGACAAAGTGAAACGA	57.781	45.000	0.00	0.00	45.86	3.85
382	385	2.128035	AGCGAGACAAAGTGAAACGAG	58.872	47.619	0.00	0.00	45.86	4.18
383	386	2.124903	GCGAGACAAAGTGAAACGAGA	58.875	47.619	0.00	0.00	45.86	4.04
384	387	2.538449	GCGAGACAAAGTGAAACGAGAA	59.462	45.455	0.00	0.00	45.86	2.87
385	388	3.000925	GCGAGACAAAGTGAAACGAGAAA	59.999	43.478	0.00	0.00	45.86	2.52
386	389	4.752224	CGAGACAAAGTGAAACGAGAAAG	58.248	43.478	0.00	0.00	45.86	2.62
387	390	4.267928	CGAGACAAAGTGAAACGAGAAAGT	59.732	41.667	0.00	0.00	45.86	2.66
388	391	5.220416	CGAGACAAAGTGAAACGAGAAAGTT	60.220	40.000	0.00	0.00	45.86	2.66
389	392	6.496338	AGACAAAGTGAAACGAGAAAGTTT	57.504	33.333	0.00	0.00	45.86	2.66
390	393	6.909909	AGACAAAGTGAAACGAGAAAGTTTT	58.090	32.000	0.00	0.00	45.86	2.43
391	394	7.021790	AGACAAAGTGAAACGAGAAAGTTTTC	58.978	34.615	0.00	0.00	45.86	2.29
393	396	7.368059	ACAAAGTGAAACGAGAAAGTTTTCTT	58.632	30.769	8.41	0.30	46.84	2.52
394	397	7.865889	ACAAAGTGAAACGAGAAAGTTTTCTTT	59.134	29.630	8.41	14.36	46.84	2.52
395	398	9.337091	CAAAGTGAAACGAGAAAGTTTTCTTTA	57.663	29.630	8.41	0.00	46.84	1.85
457	460	4.814967	TGGAAATCCAAAAGAAAGGGAGT	58.185	39.130	0.00	0.00	44.35	3.85
458	461	5.215845	TGGAAATCCAAAAGAAAGGGAGTT	58.784	37.500	0.00	0.00	44.35	3.01
459	462	5.070313	TGGAAATCCAAAAGAAAGGGAGTTG	59.930	40.000	0.00	0.00	44.35	3.16
460	463	5.511373	GGAAATCCAAAAGAAAGGGAGTTGG	60.511	44.000	0.00	0.00	38.93	3.77
461	464	2.957474	TCCAAAAGAAAGGGAGTTGGG	58.043	47.619	0.00	0.00	39.39	4.12
462	465	2.516277	TCCAAAAGAAAGGGAGTTGGGA	59.484	45.455	0.00	0.00	39.39	4.37
463	466	3.142028	TCCAAAAGAAAGGGAGTTGGGAT	59.858	43.478	0.00	0.00	39.39	3.85
464	467	3.903714	CCAAAAGAAAGGGAGTTGGGATT	59.096	43.478	0.00	0.00	36.00	3.01
465	468	4.021104	CCAAAAGAAAGGGAGTTGGGATTC	60.021	45.833	0.00	0.00	36.00	2.52
466	469	3.458044	AAGAAAGGGAGTTGGGATTCC	57.542	47.619	0.00	0.00	0.00	3.01
467	470	2.358258	AGAAAGGGAGTTGGGATTCCA	58.642	47.619	4.80	0.00	42.25	3.53
468	471	2.929043	AGAAAGGGAGTTGGGATTCCAT	59.071	45.455	4.80	0.00	43.63	3.41
469	472	3.337909	AGAAAGGGAGTTGGGATTCCATT	59.662	43.478	4.80	0.00	43.63	3.16
470	473	2.834638	AGGGAGTTGGGATTCCATTG	57.165	50.000	4.80	0.00	43.63	2.82
471	474	1.288932	AGGGAGTTGGGATTCCATTGG	59.711	52.381	4.80	0.00	43.63	3.16
472	475	1.287739	GGGAGTTGGGATTCCATTGGA	59.712	52.381	0.00	0.00	43.63	3.53
473	476	2.091111	GGGAGTTGGGATTCCATTGGAT	60.091	50.000	6.15	0.00	43.63	3.41
474	477	2.961062	GGAGTTGGGATTCCATTGGATG	59.039	50.000	6.15	0.00	43.63	3.51
475	478	3.373001	GGAGTTGGGATTCCATTGGATGA	60.373	47.826	6.15	0.00	43.63	2.92
476	479	4.280819	GAGTTGGGATTCCATTGGATGAA	58.719	43.478	6.15	0.00	43.63	2.57
477	480	4.887367	AGTTGGGATTCCATTGGATGAAT	58.113	39.130	6.15	0.00	43.63	2.57
478	481	4.897670	AGTTGGGATTCCATTGGATGAATC	59.102	41.667	6.15	6.76	43.63	2.52
479	482	4.819702	TGGGATTCCATTGGATGAATCT	57.180	40.909	6.15	0.00	38.32	2.40
480	483	5.146868	TGGGATTCCATTGGATGAATCTT	57.853	39.130	6.15	0.00	38.32	2.40
481	484	5.531198	TGGGATTCCATTGGATGAATCTTT	58.469	37.500	6.15	0.00	38.32	2.52
482	485	6.681538	TGGGATTCCATTGGATGAATCTTTA	58.318	36.000	6.15	0.00	38.32	1.85
483	486	7.131451	TGGGATTCCATTGGATGAATCTTTAA	58.869	34.615	6.15	0.00	38.32	1.52
484	487	7.622878	TGGGATTCCATTGGATGAATCTTTAAA	59.377	33.333	6.15	0.00	38.32	1.52
485	488	8.146412	GGGATTCCATTGGATGAATCTTTAAAG	58.854	37.037	6.15	9.04	35.20	1.85
486	489	8.917088	GGATTCCATTGGATGAATCTTTAAAGA	58.083	33.333	19.83	19.83	39.78	2.52
489	492	9.532494	TTCCATTGGATGAATCTTTAAAGAAGA	57.468	29.630	21.26	8.96	38.77	2.87
490	493	9.705103	TCCATTGGATGAATCTTTAAAGAAGAT	57.295	29.630	21.26	12.97	38.77	2.40
808	811	4.832823	TGGAAATCCAAAAGAAAGGGAGTC	59.167	41.667	0.00	0.00	44.35	3.36
1226	5379	7.748241	CGTTTTTGTTGTTTTTGATGTGGAAAT	59.252	29.630	0.00	0.00	0.00	2.17
1543	5698	5.360714	CCCTTCTATACGGTACCAGTTGTTA	59.639	44.000	13.54	3.95	0.00	2.41
1575	5730	8.241497	TGAATTTGCTTCATTAATAGGCTCAT	57.759	30.769	0.00	0.00	38.97	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
345	348	6.481976	TGTCTCGCTTTCTCTAGAATCTCTAG	59.518	42.308	4.59	4.59	45.99	2.43
346	349	6.350103	TGTCTCGCTTTCTCTAGAATCTCTA	58.650	40.000	0.00	0.00	33.54	2.43
347	350	5.189928	TGTCTCGCTTTCTCTAGAATCTCT	58.810	41.667	0.00	0.00	33.54	3.10
348	351	5.493133	TGTCTCGCTTTCTCTAGAATCTC	57.507	43.478	0.00	0.00	33.54	2.75
349	352	5.906113	TTGTCTCGCTTTCTCTAGAATCT	57.094	39.130	0.00	0.00	33.54	2.40
350	353	6.034470	CACTTTGTCTCGCTTTCTCTAGAATC	59.966	42.308	0.00	0.00	33.54	2.52
351	354	5.866633	CACTTTGTCTCGCTTTCTCTAGAAT	59.133	40.000	0.00	0.00	33.54	2.40
352	355	5.009710	TCACTTTGTCTCGCTTTCTCTAGAA	59.990	40.000	0.00	0.00	0.00	2.10
353	356	4.519350	TCACTTTGTCTCGCTTTCTCTAGA	59.481	41.667	0.00	0.00	0.00	2.43
354	357	4.799678	TCACTTTGTCTCGCTTTCTCTAG	58.200	43.478	0.00	0.00	0.00	2.43
355	358	4.848562	TCACTTTGTCTCGCTTTCTCTA	57.151	40.909	0.00	0.00	0.00	2.43
356	359	3.735237	TCACTTTGTCTCGCTTTCTCT	57.265	42.857	0.00	0.00	0.00	3.10
357	360	4.519147	GTTTCACTTTGTCTCGCTTTCTC	58.481	43.478	0.00	0.00	0.00	2.87
358	361	3.001330	CGTTTCACTTTGTCTCGCTTTCT	59.999	43.478	0.00	0.00	0.00	2.52
359	362	3.000925	TCGTTTCACTTTGTCTCGCTTTC	59.999	43.478	0.00	0.00	0.00	2.62
360	363	2.933906	TCGTTTCACTTTGTCTCGCTTT	59.066	40.909	0.00	0.00	0.00	3.51
361	364	2.540101	CTCGTTTCACTTTGTCTCGCTT	59.460	45.455	0.00	0.00	0.00	4.68
362	365	2.128035	CTCGTTTCACTTTGTCTCGCT	58.872	47.619	0.00	0.00	0.00	4.93
363	366	2.124903	TCTCGTTTCACTTTGTCTCGC	58.875	47.619	0.00	0.00	0.00	5.03
364	367	4.267928	ACTTTCTCGTTTCACTTTGTCTCG	59.732	41.667	0.00	0.00	0.00	4.04
365	368	5.720261	ACTTTCTCGTTTCACTTTGTCTC	57.280	39.130	0.00	0.00	0.00	3.36
366	369	6.496338	AAACTTTCTCGTTTCACTTTGTCT	57.504	33.333	0.00	0.00	31.87	3.41
367	370	7.021790	AGAAAACTTTCTCGTTTCACTTTGTC	58.978	34.615	0.00	0.00	43.72	3.18
368	371	6.909909	AGAAAACTTTCTCGTTTCACTTTGT	58.090	32.000	0.00	0.00	43.72	2.83
369	372	7.796958	AAGAAAACTTTCTCGTTTCACTTTG	57.203	32.000	5.21	0.00	46.22	2.77
427	430	9.948964	CCTTTCTTTTGGATTTCCATTCTATTT	57.051	29.630	0.00	0.00	46.97	1.40
428	431	8.542926	CCCTTTCTTTTGGATTTCCATTCTATT	58.457	33.333	0.00	0.00	46.97	1.73
429	432	7.900784	TCCCTTTCTTTTGGATTTCCATTCTAT	59.099	33.333	0.00	0.00	46.97	1.98
430	433	7.245292	TCCCTTTCTTTTGGATTTCCATTCTA	58.755	34.615	0.00	0.00	46.97	2.10
431	434	6.084060	TCCCTTTCTTTTGGATTTCCATTCT	58.916	36.000	0.00	0.00	46.97	2.40
432	435	6.014242	ACTCCCTTTCTTTTGGATTTCCATTC	60.014	38.462	0.00	0.00	46.97	2.67
433	436	5.846164	ACTCCCTTTCTTTTGGATTTCCATT	59.154	36.000	0.00	0.00	46.97	3.16
434	437	5.406163	ACTCCCTTTCTTTTGGATTTCCAT	58.594	37.500	0.00	0.00	46.97	3.41
435	438	4.814967	ACTCCCTTTCTTTTGGATTTCCA	58.185	39.130	0.00	0.00	45.94	3.53
436	439	5.511373	CCAACTCCCTTTCTTTTGGATTTCC	60.511	44.000	0.00	0.00	39.33	3.13
437	440	5.511373	CCCAACTCCCTTTCTTTTGGATTTC	60.511	44.000	0.12	0.00	39.33	2.17
438	441	4.347876	CCCAACTCCCTTTCTTTTGGATTT	59.652	41.667	0.12	0.00	39.33	2.17
439	442	3.903714	CCCAACTCCCTTTCTTTTGGATT	59.096	43.478	0.12	0.00	39.33	3.01
440	443	3.142028	TCCCAACTCCCTTTCTTTTGGAT	59.858	43.478	0.12	0.00	39.33	3.41
441	444	2.516277	TCCCAACTCCCTTTCTTTTGGA	59.484	45.455	0.12	0.00	39.33	3.53
442	445	2.957474	TCCCAACTCCCTTTCTTTTGG	58.043	47.619	0.00	0.00	37.13	3.28
443	446	4.021104	GGAATCCCAACTCCCTTTCTTTTG	60.021	45.833	0.00	0.00	0.00	2.44
444	447	4.160329	GGAATCCCAACTCCCTTTCTTTT	58.840	43.478	0.00	0.00	0.00	2.27
445	448	3.142028	TGGAATCCCAACTCCCTTTCTTT	59.858	43.478	0.00	0.00	40.09	2.52
446	449	2.721906	TGGAATCCCAACTCCCTTTCTT	59.278	45.455	0.00	0.00	40.09	2.52
447	450	2.358258	TGGAATCCCAACTCCCTTTCT	58.642	47.619	0.00	0.00	40.09	2.52
448	451	2.899303	TGGAATCCCAACTCCCTTTC	57.101	50.000	0.00	0.00	40.09	2.62
453	456	9.986871	AGATTCATCCAATGGAATCCCAACTCC	62.987	44.444	5.89	0.00	46.69	3.85
454	457	7.143975	AGATTCATCCAATGGAATCCCAACTC	61.144	42.308	5.89	0.00	46.69	3.01
455	458	5.341454	AGATTCATCCAATGGAATCCCAACT	60.341	40.000	5.89	0.00	46.69	3.16
456	459	4.897670	AGATTCATCCAATGGAATCCCAAC	59.102	41.667	5.89	0.00	46.69	3.77
457	460	5.146868	AGATTCATCCAATGGAATCCCAA	57.853	39.130	5.89	0.00	46.69	4.12
458	461	4.819702	AGATTCATCCAATGGAATCCCA	57.180	40.909	5.89	0.00	46.69	4.37
459	462	7.601705	TTAAAGATTCATCCAATGGAATCCC	57.398	36.000	5.89	0.00	46.69	3.85
460	463	8.917088	TCTTTAAAGATTCATCCAATGGAATCC	58.083	33.333	13.99	0.00	46.69	3.01
463	466	9.532494	TCTTCTTTAAAGATTCATCCAATGGAA	57.468	29.630	18.37	0.00	32.79	3.53
464	467	9.705103	ATCTTCTTTAAAGATTCATCCAATGGA	57.295	29.630	18.37	3.67	33.47	3.41
703	706	5.533482	TCACTTTGTCTCACTTTCTCTAGC	58.467	41.667	0.00	0.00	0.00	3.42
808	811	3.759581	AGATTCATCCAATGGAATCCCG	58.240	45.455	5.89	0.00	46.69	5.14
1226	5379	2.433239	GCCCAAGGGTATAGAAAGACGA	59.567	50.000	7.05	0.00	37.65	4.20
1575	5730	5.656480	TCCATAACGATCAAAGTCGAATCA	58.344	37.500	3.09	0.00	44.06	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.