AutoCloner

Multiple sequence alignment - TraesCS1A01G045600

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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	TraesCS1A01G045600	chr1A	100.000	2677	0	0	1	2677	27138258	27135582	0.000000e+00	4944
1	TraesCS1A01G045600	chr1D	93.829	1102	50	9	610	1701	25767333	25766240	0.000000e+00	1642
2	TraesCS1A01G045600	chr1D	91.606	1096	50	17	1314	2404	25784504	25783446	0.000000e+00	1476
3	TraesCS1A01G045600	chr1D	95.616	593	26	0	20	612	25789741	25789149	0.000000e+00	952
4	TraesCS1A01G045600	chr1D	94.032	620	29	2	1	612	25768047	25767428	0.000000e+00	933
5	TraesCS1A01G045600	chr1D	82.309	667	74	20	983	1631	25772553	25771913	3.030000e-149	538
6	TraesCS1A01G045600	chr1D	89.286	364	25	7	610	959	25789059	25788696	6.800000e-121	444
7	TraesCS1A01G045600	chr1D	90.614	277	21	3	2404	2677	25783414	25783140	1.960000e-96	363
8	TraesCS1A01G045600	chr1D	75.598	627	86	47	1	578	25773511	25772903	5.720000e-62	248
9	TraesCS1A01G045600	chr1D	91.304	115	10	0	983	1097	25788710	25788596	9.920000e-35	158
10	TraesCS1A01G045600	chr1B	92.754	897	39	11	983	1862	41413996	41413109	0.000000e+00	1273
11	TraesCS1A01G045600	chr1B	93.443	427	19	6	1	421	41417596	41417173	2.260000e-175	625
12	TraesCS1A01G045600	chr1B	79.095	995	110	49	983	1946	41367372	41366445	1.770000e-166	595
13	TraesCS1A01G045600	chr1B	88.462	364	27	8	610	959	41414344	41413982	2.460000e-115	425
14	TraesCS1A01G045600	chr1B	93.116	276	15	4	2404	2677	41412580	41412307	4.150000e-108	401
15	TraesCS1A01G045600	chr1B	97.449	196	5	0	417	612	41414634	41414439	4.270000e-88	335
16	TraesCS1A01G045600	chr1B	91.111	90	7	1	2092	2180	41412862	41412773	1.300000e-23	121
17	TraesCS1A01G045600	chr1B	88.542	96	1	1	2309	2404	41412693	41412608	1.010000e-19	108

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	TraesCS1A01G045600	chr1A	27135582	27138258	2676	True	4944.000000	4944	100.000000	1	2677	1	chr1A.!!$R1	2676
1	TraesCS1A01G045600	chr1D	25783140	25784504	1364	True	919.500000	1476	91.110000	1314	2677	2	chr1D.!!$R2	1363
2	TraesCS1A01G045600	chr1D	25766240	25773511	7271	True	840.250000	1642	86.442000	1	1701	4	chr1D.!!$R1	1700
3	TraesCS1A01G045600	chr1D	25788596	25789741	1145	True	518.000000	952	92.068667	20	1097	3	chr1D.!!$R3	1077
4	TraesCS1A01G045600	chr1B	41366445	41367372	927	True	595.000000	595	79.095000	983	1946	1	chr1B.!!$R1	963
5	TraesCS1A01G045600	chr1B	41412307	41417596	5289	True	469.714286	1273	92.125286	1	2677	7	chr1B.!!$R2	2676

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
970	9108	2.359531	CCTGTAGTTTCTAGAGGAGGCG	59.64	54.545	12.7	0.0	30.19	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2620	10929	0.322456	TGTCAGCCATTTTCCCCTCG	60.322	55.0	0.0	0.0	0.0	4.63	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	5591	6.015180	AGCACTGAAATGGACATAATTGTGTT	60.015	34.615	9.37	0.00	35.79	3.32
232	5711	9.308000	TCCTAGAATCTGGCTAAAATTTCAAAA	57.692	29.630	0.00	0.00	0.00	2.44
257	5736	6.381133	AGTTTCAGGAGACACTTTGGAAATTT	59.619	34.615	0.00	0.00	30.84	1.82
269	5748	8.103935	ACACTTTGGAAATTTAAAAGAACCCAA	58.896	29.630	23.07	13.46	35.39	4.12
292	5771	2.493278	GGCACCTTTTACATGCATCTGT	59.507	45.455	0.00	0.00	41.27	3.41
369	5848	5.950758	AATGTAATACGTGGAAACAGCAA	57.049	34.783	0.00	0.00	44.46	3.91
439	8461	3.680196	GCATGACCTGTTCTAGAGGGTTC	60.680	52.174	13.04	8.64	34.56	3.62
495	8517	8.242729	AGAAAAGCAATTAATATGGGAGAAGG	57.757	34.615	0.00	0.00	0.00	3.46
524	8546	6.869206	ACTAGCACCACCTTATCTTTTCTA	57.131	37.500	0.00	0.00	0.00	2.10
593	8615	3.208005	AGGAAAAGGGAAAGTTGGGGTTA	59.792	43.478	0.00	0.00	0.00	2.85
656	8792	2.492881	GGTTGTGGACATGATCATGCAA	59.507	45.455	31.17	23.55	42.39	4.08
657	8793	3.056678	GGTTGTGGACATGATCATGCAAA	60.057	43.478	31.17	16.80	42.39	3.68
703	8839	8.330466	ACAATACGAAACCAATATGAAACTGA	57.670	30.769	0.00	0.00	0.00	3.41
714	8850	6.458751	CCAATATGAAACTGACCCTGAAATCG	60.459	42.308	0.00	0.00	0.00	3.34
803	8941	8.506168	TTCTCACAAGAAACAATCAAAGTAGT	57.494	30.769	0.00	0.00	38.58	2.73
810	8948	9.787532	CAAGAAACAATCAAAGTAGTCTTTTGA	57.212	29.630	2.87	2.87	41.31	2.69
853	8991	8.506168	TTGTGCTAAAAATATAAGGAGTGAGG	57.494	34.615	0.00	0.00	0.00	3.86
889	9027	9.457436	TGGTGAAGTTCTCCTATAAATAAAACC	57.543	33.333	21.42	8.46	31.62	3.27
908	9046	6.840780	AAACCCATCATTCTTAAGGTTCTG	57.159	37.500	1.85	0.00	36.61	3.02
962	9100	7.106439	ACAGTGATCATCCTGTAGTTTCTAG	57.894	40.000	15.35	0.00	40.03	2.43
970	9108	2.359531	CCTGTAGTTTCTAGAGGAGGCG	59.640	54.545	12.70	0.00	30.19	5.52
1039	9177	7.465900	AATGAAGATAATTCAGTAAGGGGGA	57.534	36.000	0.00	0.00	0.00	4.81
1188	9328	0.322322	ATACCGTTTGACCGAGGCAA	59.678	50.000	0.00	0.00	0.00	4.52
1342	9484	7.816640	TGAATGCAAAAGAACTAATGGAGTAC	58.183	34.615	0.00	0.00	37.44	2.73
1457	9599	8.524870	TCTTGGAACTTAGTTTATTCGTACAC	57.475	34.615	0.00	0.00	0.00	2.90
1491	9637	8.150945	AGTCTGTATATGTGTGGATCCAATTAC	58.849	37.037	18.20	16.09	0.00	1.89
1584	9751	1.133792	ACAAGAGGACTGGGTTTGGTG	60.134	52.381	0.00	0.00	0.00	4.17
1631	9798	3.389002	TCCACAAGGACGATGATGATGAT	59.611	43.478	0.00	0.00	39.61	2.45
1682	9855	2.025037	TCCTATTGCATGCTGAAGGGTT	60.025	45.455	20.33	0.00	0.00	4.11
1770	9944	5.194432	AGGGCTATCTATGTATCGTGGTAG	58.806	45.833	0.00	0.00	0.00	3.18
1856	10042	6.548622	CCTTGGATCTCATTCCATGTAAATGT	59.451	38.462	14.35	0.75	45.08	2.71
1901	10087	4.227300	AGGTGTCCTATTGTGGAAAGCATA	59.773	41.667	5.82	0.00	42.63	3.14
1912	10098	6.482898	TGTGGAAAGCATATTGCCATATTT	57.517	33.333	0.00	0.00	46.52	1.40
1917	10103	4.261578	AGCATATTGCCATATTTGCCAC	57.738	40.909	0.00	0.00	46.52	5.01
1918	10104	2.988493	GCATATTGCCATATTTGCCACG	59.012	45.455	0.00	0.00	37.42	4.94
1919	10105	2.791383	TATTGCCATATTTGCCACGC	57.209	45.000	0.00	0.00	0.00	5.34
1920	10106	0.248990	ATTGCCATATTTGCCACGCG	60.249	50.000	3.53	3.53	0.00	6.01
1944	10130	7.416101	GCGTACTGTAGGTTCCTCTTAAGTTAT	60.416	40.741	1.63	0.00	0.00	1.89
1985	10171	7.518188	TCCAGAAATAACCTTTTGAGAACTCT	58.482	34.615	3.51	0.00	0.00	3.24
2084	10270	3.502123	TGAGTTCCCAGTTTGGTAAGG	57.498	47.619	0.00	0.00	35.17	2.69
2208	10474	9.587772	ACGATGAGTATGGCTATTAATATGTTC	57.412	33.333	0.00	0.00	0.00	3.18
2213	10479	3.394719	TGGCTATTAATATGTTCGCGCA	58.605	40.909	8.75	0.00	0.00	6.09
2233	10499	4.685628	CGCAATTTTGTTGCTCCAAATACT	59.314	37.500	10.57	0.00	42.87	2.12
2279	10545	0.817229	GCTGAGCCCAGGTAGCAATC	60.817	60.000	0.00	0.00	40.72	2.67
2288	10554	1.135083	CAGGTAGCAATCGTTCGACCT	60.135	52.381	0.00	0.00	38.57	3.85
2348	10614	1.480545	GGCCAAACCACAACAGAAACT	59.519	47.619	0.00	0.00	38.86	2.66
2349	10615	2.691011	GGCCAAACCACAACAGAAACTA	59.309	45.455	0.00	0.00	38.86	2.24
2350	10616	3.131400	GGCCAAACCACAACAGAAACTAA	59.869	43.478	0.00	0.00	38.86	2.24
2351	10617	4.382147	GGCCAAACCACAACAGAAACTAAA	60.382	41.667	0.00	0.00	38.86	1.85
2352	10618	4.565166	GCCAAACCACAACAGAAACTAAAC	59.435	41.667	0.00	0.00	0.00	2.01
2353	10619	5.623596	GCCAAACCACAACAGAAACTAAACT	60.624	40.000	0.00	0.00	0.00	2.66
2354	10620	6.404954	GCCAAACCACAACAGAAACTAAACTA	60.405	38.462	0.00	0.00	0.00	2.24
2355	10621	7.540299	CCAAACCACAACAGAAACTAAACTAA	58.460	34.615	0.00	0.00	0.00	2.24
2356	10622	8.030106	CCAAACCACAACAGAAACTAAACTAAA	58.970	33.333	0.00	0.00	0.00	1.85
2357	10623	8.856247	CAAACCACAACAGAAACTAAACTAAAC	58.144	33.333	0.00	0.00	0.00	2.01
2416	10722	2.410053	GCAGAGCAGAGTGTTAGTTTCG	59.590	50.000	0.00	0.00	0.00	3.46
2476	10782	4.322049	CCGATTCATACTAGCGGGAGATTT	60.322	45.833	0.00	0.00	38.40	2.17
2508	10814	2.888834	TGGTTTGCCAAAGAGAAAGC	57.111	45.000	0.00	0.00	42.83	3.51
2551	10857	9.734620	CAAATTTACAAGAAGTCTGACATTTGA	57.265	29.630	19.00	4.60	0.00	2.69
2604	10913	5.336929	CCTCATGCTCCAAAATCACATTTCA	60.337	40.000	0.00	0.00	0.00	2.69
2617	10926	5.212532	TCACATTTCATCCAAAAACCAGG	57.787	39.130	0.00	0.00	0.00	4.45
2620	10929	5.466393	CACATTTCATCCAAAAACCAGGAAC	59.534	40.000	0.00	0.00	37.48	3.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	5562	7.859377	CACAATTATGTCCATTTCAGTGCTATC	59.141	37.037	0.00	0.00	37.82	2.08
112	5591	3.070446	TCAAGGAAGCTGAAGTTTACGGA	59.930	43.478	0.00	0.00	0.00	4.69
176	5655	3.126343	CGCGTAGTTTCTTGGCCTAAATT	59.874	43.478	3.32	1.78	0.00	1.82
193	5672	2.975732	TCTAGGAGAGAGTTCGCGTA	57.024	50.000	5.77	0.00	0.00	4.42
195	5674	2.875933	AGATTCTAGGAGAGAGTTCGCG	59.124	50.000	0.00	0.00	34.93	5.87
232	5711	4.503714	TTCCAAAGTGTCTCCTGAAACT	57.496	40.909	0.00	0.00	42.28	2.66
257	5736	3.252554	AGGTGCCATTGGGTTCTTTTA	57.747	42.857	4.53	0.00	36.17	1.52
269	5748	3.131577	CAGATGCATGTAAAAGGTGCCAT	59.868	43.478	2.46	0.00	38.06	4.40
342	5821	7.490079	TGCTGTTTCCACGTATTACATTAGTAG	59.510	37.037	0.00	0.00	0.00	2.57
369	5848	7.056006	TGCAGAGTATACAATGATGTTGGATT	58.944	34.615	5.50	0.00	41.05	3.01
495	8517	5.731591	AGATAAGGTGGTGCTAGTTGTTAC	58.268	41.667	0.00	0.00	0.00	2.50
524	8546	1.452108	GCGGTGCTGCCTTATCCTT	60.452	57.895	0.00	0.00	34.25	3.36
593	8615	0.695803	ATTCCTCCTCCCTTCCGCAT	60.696	55.000	0.00	0.00	0.00	4.73
703	8839	4.065789	GAGTTTTCACTCGATTTCAGGGT	58.934	43.478	0.00	0.00	40.30	4.34
889	9027	5.116084	TCCCAGAACCTTAAGAATGATGG	57.884	43.478	3.36	5.51	0.00	3.51
908	9046	2.557056	GGGCTTGTTGTTCTAGTTTCCC	59.443	50.000	0.00	0.00	0.00	3.97
1039	9177	5.484715	CCATGCTTTGAATTCCTTGATGTT	58.515	37.500	2.27	0.00	0.00	2.71
1255	9397	8.430828	CGTATACAGAAATGATGAGCAAGTATG	58.569	37.037	3.32	0.00	0.00	2.39
1312	9454	6.875195	CCATTAGTTCTTTTGCATTCATGGTT	59.125	34.615	0.00	0.00	0.00	3.67
1342	9484	5.560966	ACATATCTTTGTTTGCCTTACCG	57.439	39.130	0.00	0.00	0.00	4.02
1414	9556	7.020827	TCCAAGAAATTGACTAGTGGAGAAT	57.979	36.000	0.00	0.00	0.00	2.40
1415	9557	6.433847	TCCAAGAAATTGACTAGTGGAGAA	57.566	37.500	0.00	0.00	0.00	2.87
1427	9569	9.893305	ACGAATAAACTAAGTTCCAAGAAATTG	57.107	29.630	0.63	0.00	0.00	2.32
1491	9637	8.572855	AGTGGATTCCTTAATCTTGAGAAAAG	57.427	34.615	3.95	0.00	41.18	2.27
1584	9751	6.332630	ACTTCAACATTGCACCTAATATTGC	58.667	36.000	0.00	0.00	39.33	3.56
1599	9766	2.878406	CGTCCTTGTGGAACTTCAACAT	59.122	45.455	0.00	0.00	45.18	2.71
1631	9798	0.107214	GAGGGTTTCCATCGCCATCA	60.107	55.000	0.00	0.00	33.75	3.07
1682	9855	2.297597	CCAATCAAGGCGGGTAACAAAA	59.702	45.455	0.00	0.00	39.74	2.44
1770	9944	3.308866	ACGAACTGCAGACACTTGTTTAC	59.691	43.478	23.35	0.00	0.00	2.01
1912	10098	1.808531	AACCTACAGTACGCGTGGCA	61.809	55.000	24.59	0.00	0.00	4.92
1917	10103	1.093159	AGAGGAACCTACAGTACGCG	58.907	55.000	3.53	3.53	0.00	6.01
1918	10104	4.157472	ACTTAAGAGGAACCTACAGTACGC	59.843	45.833	10.09	0.00	0.00	4.42
1919	10105	5.893897	ACTTAAGAGGAACCTACAGTACG	57.106	43.478	10.09	0.00	0.00	3.67
1994	10180	6.358118	TGAACTGTATGCGCCTAAAAATAG	57.642	37.500	4.18	0.00	0.00	1.73
1996	10182	5.637006	TTGAACTGTATGCGCCTAAAAAT	57.363	34.783	4.18	0.00	0.00	1.82
2006	10192	6.366877	ACAATGAAAGCAATTGAACTGTATGC	59.633	34.615	10.34	0.00	37.28	3.14
2098	10301	6.404734	CCCCAACTTATCTTCCAAAAATCGAG	60.405	42.308	0.00	0.00	0.00	4.04
2101	10304	6.605471	ACCCCAACTTATCTTCCAAAAATC	57.395	37.500	0.00	0.00	0.00	2.17
2213	10479	8.592809	TGGAATAGTATTTGGAGCAACAAAATT	58.407	29.630	9.42	5.54	42.91	1.82
2279	10545	0.512952	CAGCAAGGAAAGGTCGAACG	59.487	55.000	0.00	0.00	0.00	3.95
2288	10554	1.676916	CGATGGAGAGCAGCAAGGAAA	60.677	52.381	0.00	0.00	0.00	3.13
2407	10713	6.368213	CCAACTTTGTATCACCGAAACTAAC	58.632	40.000	0.00	0.00	0.00	2.34
2416	10722	4.023726	TGTACCCCAACTTTGTATCACC	57.976	45.455	0.00	0.00	0.00	4.02
2476	10782	2.025699	GGCAAACCATGGTAGGGTAGAA	60.026	50.000	20.12	0.00	37.77	2.10
2604	10913	2.514803	CCTCGTTCCTGGTTTTTGGAT	58.485	47.619	0.00	0.00	31.76	3.41
2617	10926	0.811281	CAGCCATTTTCCCCTCGTTC	59.189	55.000	0.00	0.00	0.00	3.95
2620	10929	0.322456	TGTCAGCCATTTTCCCCTCG	60.322	55.000	0.00	0.00	0.00	4.63

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.