AutoCloner

Multiple sequence alignment - TraesCS3B01G085900

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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	TraesCS3B01G085900	chr3B	100.000	2894	0	0	860	3753	54499819	54502712	0.000000e+00	5345.0
1	TraesCS3B01G085900	chr3B	79.300	1628	249	52	1487	3051	54304813	54303211	0.000000e+00	1059.0
2	TraesCS3B01G085900	chr3B	78.609	1697	279	57	1410	3051	53952025	53950358	0.000000e+00	1046.0
3	TraesCS3B01G085900	chr3B	100.000	537	0	0	1	537	54498960	54499496	0.000000e+00	992.0
4	TraesCS3B01G085900	chr3B	94.234	607	27	6	3150	3753	53960410	53961011	0.000000e+00	920.0
5	TraesCS3B01G085900	chr3B	90.219	593	54	4	3150	3741	54315849	54316438	0.000000e+00	771.0
6	TraesCS3B01G085900	chr3B	86.667	360	41	6	2697	3051	54068976	54069333	3.510000e-105	392.0
7	TraesCS3B01G085900	chr3B	86.351	359	43	5	2697	3051	54145171	54145527	1.630000e-103	387.0
8	TraesCS3B01G085900	chr3B	85.644	202	25	4	2697	2895	53996102	53996302	3.800000e-50	209.0
9	TraesCS3B01G085900	chr3B	85.294	102	9	6	2567	2667	54070938	54071034	2.390000e-17	100.0
10	TraesCS3B01G085900	chr3B	85.294	102	9	6	2567	2667	54147174	54147270	2.390000e-17	100.0
11	TraesCS3B01G085900	chr3B	93.023	43	0	2	943	985	54499873	54499912	4.050000e-05	60.2
12	TraesCS3B01G085900	chr3B	93.023	43	0	2	914	953	54499902	54499944	4.050000e-05	60.2
13	TraesCS3B01G085900	chr3D	95.067	2372	79	13	929	3268	31846166	31848531	0.000000e+00	3698.0
14	TraesCS3B01G085900	chr3D	79.953	1706	259	47	1410	3051	31776854	31775168	0.000000e+00	1179.0
15	TraesCS3B01G085900	chr3D	95.033	604	30	0	3150	3753	31803231	31803834	0.000000e+00	950.0
16	TraesCS3B01G085900	chr3D	92.611	609	31	7	3150	3753	31966151	31965552	0.000000e+00	863.0
17	TraesCS3B01G085900	chr3D	95.939	394	6	2	3	396	31842682	31843065	6.840000e-177	630.0
18	TraesCS3B01G085900	chr3D	92.308	117	5	3	398	510	31845954	31846070	3.000000e-36	163.0
19	TraesCS3B01G085900	chr3D	96.364	55	2	0	891	945	31846109	31846163	1.440000e-14	91.6
20	TraesCS3B01G085900	chr3D	90.566	53	2	2	904	953	31846173	31846225	2.420000e-07	67.6
21	TraesCS3B01G085900	chr3D	100.000	31	0	0	943	973	31846132	31846162	1.460000e-04	58.4
22	TraesCS3B01G085900	chr2A	95.515	602	26	1	3150	3751	528108033	528107433	0.000000e+00	961.0
23	TraesCS3B01G085900	chr2B	90.306	196	16	2	3472	3667	227312082	227311890	1.730000e-63	254.0

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	TraesCS3B01G085900	chr3B	54498960	54502712	3752	False	1614.350000	5345	96.511500	1	3753	4	chr3B.!!$F6	3752
1	TraesCS3B01G085900	chr3B	54303211	54304813	1602	True	1059.000000	1059	79.300000	1487	3051	1	chr3B.!!$R2	1564
2	TraesCS3B01G085900	chr3B	53950358	53952025	1667	True	1046.000000	1046	78.609000	1410	3051	1	chr3B.!!$R1	1641
3	TraesCS3B01G085900	chr3B	53960410	53961011	601	False	920.000000	920	94.234000	3150	3753	1	chr3B.!!$F1	603
4	TraesCS3B01G085900	chr3B	54315849	54316438	589	False	771.000000	771	90.219000	3150	3741	1	chr3B.!!$F3	591
5	TraesCS3B01G085900	chr3B	54068976	54071034	2058	False	246.000000	392	85.980500	2567	3051	2	chr3B.!!$F4	484
6	TraesCS3B01G085900	chr3B	54145171	54147270	2099	False	243.500000	387	85.822500	2567	3051	2	chr3B.!!$F5	484
7	TraesCS3B01G085900	chr3D	31775168	31776854	1686	True	1179.000000	1179	79.953000	1410	3051	1	chr3D.!!$R1	1641
8	TraesCS3B01G085900	chr3D	31803231	31803834	603	False	950.000000	950	95.033000	3150	3753	1	chr3D.!!$F1	603
9	TraesCS3B01G085900	chr3D	31965552	31966151	599	True	863.000000	863	92.611000	3150	3753	1	chr3D.!!$R2	603
10	TraesCS3B01G085900	chr3D	31842682	31848531	5849	False	784.766667	3698	95.040667	3	3268	6	chr3D.!!$F2	3265
11	TraesCS3B01G085900	chr2A	528107433	528108033	600	True	961.000000	961	95.515000	3150	3751	1	chr2A.!!$R1	601

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
54	55	0.321653	AGCAACGGAGGCGAAATCTT	60.322	50.0	0.0	0.0	36.08	2.40	F
1067	3996	0.616395	TTCATCTACCACAGGGGCGA	60.616	55.0	0.0	0.0	42.05	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1408	4337	0.693049	ATTGCCTCCGTGTCTTCCTT	59.307	50.0	0.0	0.0	0.0	3.36	R
2795	5783	0.031314	ACATCGCCACTCTATGCTCG	59.969	55.0	0.0	0.0	0.0	5.03	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
21	22	3.826524	TCCACTACCTGCATGTGAAAAA	58.173	40.909	4.73	0.00	33.95	1.94
32	33	5.858381	TGCATGTGAAAAAGAGACTAGAGT	58.142	37.500	0.00	0.00	0.00	3.24
54	55	0.321653	AGCAACGGAGGCGAAATCTT	60.322	50.000	0.00	0.00	36.08	2.40
186	187	3.061260	GACCCCCGACGACAGTAGC	62.061	68.421	0.00	0.00	0.00	3.58
207	208	4.008933	GAGCCGCACAGGACCACT	62.009	66.667	0.00	0.00	45.00	4.00
208	209	3.941657	GAGCCGCACAGGACCACTC	62.942	68.421	0.00	0.00	45.00	3.51
209	210	4.314440	GCCGCACAGGACCACTCA	62.314	66.667	0.00	0.00	45.00	3.41
210	211	2.047844	CCGCACAGGACCACTCAG	60.048	66.667	0.00	0.00	45.00	3.35
211	212	2.740055	CGCACAGGACCACTCAGC	60.740	66.667	0.00	0.00	0.00	4.26
212	213	2.427320	GCACAGGACCACTCAGCA	59.573	61.111	0.00	0.00	0.00	4.41
213	214	1.670406	GCACAGGACCACTCAGCAG	60.670	63.158	0.00	0.00	0.00	4.24
240	241	0.981943	ACAAGCACCTACTACCACCC	59.018	55.000	0.00	0.00	0.00	4.61
424	3314	1.069765	ATAAGCAGCCCATCGACCG	59.930	57.895	0.00	0.00	0.00	4.79
462	3352	1.169661	ACCGCACAATCGAAAAGCCA	61.170	50.000	0.00	0.00	0.00	4.75
498	3388	3.314553	GTCATCGTCGAAACTTGGAAGA	58.685	45.455	0.00	0.00	0.00	2.87
499	3389	3.927142	GTCATCGTCGAAACTTGGAAGAT	59.073	43.478	0.00	0.00	35.34	2.40
502	3392	6.916387	GTCATCGTCGAAACTTGGAAGATATA	59.084	38.462	0.00	0.00	33.85	0.86
503	3393	7.595502	GTCATCGTCGAAACTTGGAAGATATAT	59.404	37.037	0.00	0.00	33.85	0.86
504	3394	8.789762	TCATCGTCGAAACTTGGAAGATATATA	58.210	33.333	0.00	0.00	33.85	0.86
505	3395	9.066939	CATCGTCGAAACTTGGAAGATATATAG	57.933	37.037	0.00	0.00	33.85	1.31
506	3396	8.387190	TCGTCGAAACTTGGAAGATATATAGA	57.613	34.615	0.00	0.00	0.00	1.98
507	3397	9.011095	TCGTCGAAACTTGGAAGATATATAGAT	57.989	33.333	0.00	0.00	0.00	1.98
508	3398	9.279904	CGTCGAAACTTGGAAGATATATAGATC	57.720	37.037	0.00	0.00	0.00	2.75
897	3787	0.735471	TCTCAATCTCTCCTCGCGTG	59.265	55.000	5.77	2.75	0.00	5.34
1067	3996	0.616395	TTCATCTACCACAGGGGCGA	60.616	55.000	0.00	0.00	42.05	5.54
1141	4070	2.261671	CCACTTCGTCCACCTCCG	59.738	66.667	0.00	0.00	0.00	4.63
1288	4217	2.486472	TCTCTTCCGGTTCGTCTACT	57.514	50.000	0.00	0.00	0.00	2.57
1304	4233	3.056749	GTCTACTTTGACCTCCACGTCAT	60.057	47.826	0.00	0.00	42.20	3.06
1408	4337	1.314730	GGTCTTGCCTCCGTTTTTCA	58.685	50.000	0.00	0.00	0.00	2.69
1424	4353	0.034896	TTCAAGGAAGACACGGAGGC	59.965	55.000	0.00	0.00	0.00	4.70
1441	4370	1.476891	AGGCAATCACTACACGTCGAT	59.523	47.619	0.00	0.00	0.00	3.59
1447	4376	5.740569	GCAATCACTACACGTCGATACTTTA	59.259	40.000	0.00	0.00	0.00	1.85
1598	4527	1.537638	CCGCTCTCGTGTATCAGCTAT	59.462	52.381	0.00	0.00	0.00	2.97
1661	4590	3.064958	CAGCACAAGGAGCATCAATACTG	59.935	47.826	0.00	0.00	36.25	2.74
1813	4742	0.976073	ACCTACCCATCACCGTCCTG	60.976	60.000	0.00	0.00	0.00	3.86
1908	4843	0.232303	CTTCTGTTGTTCGCACCGAC	59.768	55.000	0.00	0.00	34.89	4.79
1909	4844	1.155424	TTCTGTTGTTCGCACCGACC	61.155	55.000	0.00	0.00	34.89	4.79
1950	4885	2.572556	TGAACCTCGCCAGGGTTATAAA	59.427	45.455	1.31	0.00	41.40	1.40
2295	5230	4.720649	TCTCAAGTCCTTCCTTACATCG	57.279	45.455	0.00	0.00	0.00	3.84
2394	5339	6.605471	AGATACAAGTCAGTGATGGTGTAA	57.395	37.500	14.00	3.30	0.00	2.41
2427	5381	3.730215	TTAGTTTGAAGCAGCCCCATA	57.270	42.857	0.00	0.00	0.00	2.74
2433	5387	1.496001	TGAAGCAGCCCCATATGACAT	59.504	47.619	3.65	0.00	0.00	3.06
2628	5587	7.281549	TGCCTTATTAAGAAATTCGTAAGGTCC	59.718	37.037	19.86	11.56	32.82	4.46
2696	5676	7.370383	ACAATTAGCATTTGGTGACTAAAGTG	58.630	34.615	0.00	0.91	33.39	3.16
2727	5715	3.699413	TCATGGATTGCTGAACATCCAA	58.301	40.909	5.01	0.00	45.18	3.53
2795	5783	6.088749	CGATTGCTATACTATGTTCTGCTGTC	59.911	42.308	0.00	0.00	0.00	3.51
2799	5787	2.285827	ACTATGTTCTGCTGTCGAGC	57.714	50.000	0.00	0.00	46.44	5.03
2812	5800	0.312416	GTCGAGCATAGAGTGGCGAT	59.688	55.000	0.00	0.00	34.54	4.58
2861	5849	1.905215	CTTGGTGAGGAGATGGTCTGT	59.095	52.381	0.00	0.00	0.00	3.41
2873	5862	4.973168	AGATGGTCTGTAGTTTGCTGAAA	58.027	39.130	0.00	0.00	0.00	2.69
2931	5922	6.469275	GTCAGTCTTGTTAGTTTTGCAAACTC	59.531	38.462	12.39	8.34	0.00	3.01
2933	5924	6.806249	CAGTCTTGTTAGTTTTGCAAACTCAA	59.194	34.615	12.39	11.84	0.00	3.02
2938	5929	5.293079	TGTTAGTTTTGCAAACTCAAATGGC	59.707	36.000	12.39	0.00	36.04	4.40
2953	5944	0.893727	ATGGCACCCCAGTTTCGTTC	60.894	55.000	0.00	0.00	46.24	3.95
2960	5951	2.170985	CAGTTTCGTTCGGCGCTG	59.829	61.111	10.86	10.86	41.07	5.18
3326	7424	2.549754	CACCTCTGTCATCGTTGCTTTT	59.450	45.455	0.00	0.00	0.00	2.27
3370	7614	1.096967	TCATTCATGATGCGCCGCTT	61.097	50.000	11.67	3.10	35.64	4.68
3443	7687	2.287915	GACGCTGTCGCCATAATCAAAT	59.712	45.455	0.00	0.00	39.84	2.32
3444	7688	2.032054	ACGCTGTCGCCATAATCAAATG	59.968	45.455	0.00	0.00	39.84	2.32
3566	7811	5.840243	CATGAATGCTGTAGGGAAATTGA	57.160	39.130	0.00	0.00	0.00	2.57
3706	7951	5.245751	TGTCCCTGTATTTCAAATTGCATGT	59.754	36.000	0.00	0.00	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.500448	TTTTCACATGCAGGTAGTGGA	57.500	42.857	2.51	0.00	34.17	4.02
1	2	3.820467	TCTTTTTCACATGCAGGTAGTGG	59.180	43.478	2.51	0.00	34.17	4.00
21	22	4.333690	TCCGTTGCTTTACTCTAGTCTCT	58.666	43.478	0.00	0.00	0.00	3.10
32	33	1.735571	GATTTCGCCTCCGTTGCTTTA	59.264	47.619	0.00	0.00	35.54	1.85
54	55	2.494059	GTCTGCTGCACTTTCTTGGTA	58.506	47.619	0.00	0.00	0.00	3.25
186	187	4.767255	GTCCTGTGCGGCTCCCTG	62.767	72.222	0.00	0.00	0.00	4.45
207	208	1.162181	GCTTGTGTGCTGACTGCTGA	61.162	55.000	5.87	0.00	43.37	4.26
208	209	1.281960	GCTTGTGTGCTGACTGCTG	59.718	57.895	5.87	0.00	43.37	4.41
209	210	1.153107	TGCTTGTGTGCTGACTGCT	60.153	52.632	5.87	0.00	43.37	4.24
210	211	1.009222	GTGCTTGTGTGCTGACTGC	60.009	57.895	0.00	0.00	43.25	4.40
211	212	0.816825	AGGTGCTTGTGTGCTGACTG	60.817	55.000	0.00	0.00	0.00	3.51
212	213	0.758734	TAGGTGCTTGTGTGCTGACT	59.241	50.000	0.00	0.00	0.00	3.41
213	214	0.868406	GTAGGTGCTTGTGTGCTGAC	59.132	55.000	0.00	0.00	0.00	3.51
240	241	3.020026	CTTGCTTCTGGACGCGCTG	62.020	63.158	5.73	1.02	0.00	5.18
361	362	2.823196	TGCGTTTGTGTTTGTCTCAG	57.177	45.000	0.00	0.00	0.00	3.35
362	363	3.433709	CAATGCGTTTGTGTTTGTCTCA	58.566	40.909	0.00	0.00	0.00	3.27
363	364	2.216263	GCAATGCGTTTGTGTTTGTCTC	59.784	45.455	0.00	0.00	37.65	3.36
462	3352	0.110486	ATGACGTGTGGGCCTTTCTT	59.890	50.000	4.53	0.00	0.00	2.52
897	3787	2.335011	GGTGCGGTGGCTGTTTTC	59.665	61.111	0.00	0.00	40.82	2.29
1090	4019	2.582436	GGATTCGTCCGGGAAGCA	59.418	61.111	0.00	0.00	34.12	3.91
1408	4337	0.693049	ATTGCCTCCGTGTCTTCCTT	59.307	50.000	0.00	0.00	0.00	3.36
1424	4353	7.565252	GCATAAAGTATCGACGTGTAGTGATTG	60.565	40.741	0.00	0.00	0.00	2.67
1441	4370	4.163458	CCCTAGAGTGTTGGGCATAAAGTA	59.837	45.833	0.00	0.00	33.88	2.24
1598	4527	1.479757	CCCATGTGCCATCATCATCCA	60.480	52.381	0.00	0.00	0.00	3.41
1661	4590	3.626154	GACCAATCGACGAGTCTCC	57.374	57.895	3.01	0.00	0.00	3.71
1684	4613	2.661866	GAACGTGGTGACAGCGCT	60.662	61.111	2.64	2.64	44.46	5.92
1813	4742	3.451540	AGGAAACCTCTTTCTCGGTATCC	59.548	47.826	0.00	0.00	36.71	2.59
1908	4843	4.767255	GGGCCACAGAGCTGACGG	62.767	72.222	4.39	5.54	0.00	4.79
1909	4844	4.007644	TGGGCCACAGAGCTGACG	62.008	66.667	0.00	0.00	0.00	4.35
1950	4885	7.230849	TGCCTTCAAAACATCAGTGATAATT	57.769	32.000	5.03	0.56	0.00	1.40
2295	5230	2.951229	TCAGAAACTTGGGGAACTCC	57.049	50.000	0.00	0.00	0.00	3.85
2382	5322	6.362248	ACTTTACAAAGGTTACACCATCACT	58.638	36.000	6.66	0.00	41.95	3.41
2388	5333	9.292846	CAAACTAAACTTTACAAAGGTTACACC	57.707	33.333	7.89	0.00	43.71	4.16
2394	5339	7.832769	TGCTTCAAACTAAACTTTACAAAGGT	58.167	30.769	6.66	0.00	40.31	3.50
2427	5381	6.957920	ATAGCGCTAGAGATATCATGTCAT	57.042	37.500	23.37	0.00	0.00	3.06
2628	5587	9.519191	TGGATTTGGACCTGAACATATATATTG	57.481	33.333	0.00	0.00	0.00	1.90
2634	5593	5.195940	CACTGGATTTGGACCTGAACATAT	58.804	41.667	0.00	0.00	0.00	1.78
2709	5695	3.306225	GCTTTTGGATGTTCAGCAATCCA	60.306	43.478	0.23	0.23	41.05	3.41
2727	5715	2.867624	TGCACAGAATCCTCAAGCTTT	58.132	42.857	0.00	0.00	0.00	3.51
2795	5783	0.031314	ACATCGCCACTCTATGCTCG	59.969	55.000	0.00	0.00	0.00	5.03
2799	5787	4.449068	GGATTAACACATCGCCACTCTATG	59.551	45.833	0.00	0.00	0.00	2.23
2812	5800	6.652053	TGTGATCATCAGATGGATTAACACA	58.348	36.000	10.67	9.18	37.25	3.72
2861	5849	6.756074	CACAAAGTCCAAATTTCAGCAAACTA	59.244	34.615	0.00	0.00	0.00	2.24
2873	5862	4.949856	AGAGAACACACACAAAGTCCAAAT	59.050	37.500	0.00	0.00	0.00	2.32
2931	5922	0.038343	CGAAACTGGGGTGCCATTTG	60.038	55.000	0.00	0.00	0.00	2.32
2933	5924	0.469144	AACGAAACTGGGGTGCCATT	60.469	50.000	0.00	0.00	0.00	3.16
2938	5929	2.613506	GCCGAACGAAACTGGGGTG	61.614	63.158	0.00	0.00	0.00	4.61
2953	5944	1.000827	AGTTCATATCTCTCAGCGCCG	60.001	52.381	2.29	0.00	0.00	6.46
3047	6039	7.740805	TGGCCTTAAAACACCTAATGAAATTT	58.259	30.769	3.32	0.00	37.87	1.82
3326	7424	2.926242	AACTTCCGGGAAGGGCGA	60.926	61.111	33.73	2.72	43.25	5.54
3370	7614	3.377485	GCTCAACGAGTATAGTCCTGACA	59.623	47.826	1.88	0.00	31.39	3.58
3443	7687	2.026356	TCCAATACTAAGCAAGCTGCCA	60.026	45.455	0.00	0.00	46.52	4.92
3444	7688	2.643551	TCCAATACTAAGCAAGCTGCC	58.356	47.619	0.00	0.00	46.52	4.85
3566	7811	8.138712	GTCGATGAAGAAGATAAGGTGTCTATT	58.861	37.037	0.00	0.00	0.00	1.73
3706	7951	3.784845	GAAAATCCTTTTCGCGCCA	57.215	47.368	0.00	0.00	39.56	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.