AutoCloner

Multiple sequence alignment - TraesCS3B01G207400

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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	TraesCS3B01G207400	chr3B	100.000	3295	0	0	1	3295	242888706	242885412	0.000000e+00	6085.0
1	TraesCS3B01G207400	chr3B	95.000	100	5	0	28	127	89177692	89177791	1.220000e-34	158.0
2	TraesCS3B01G207400	chr3B	94.737	38	1	1	1	37	749737440	749737477	1.280000e-04	58.4
3	TraesCS3B01G207400	chr3D	94.667	2550	93	20	753	3295	167791826	167789313	0.000000e+00	3916.0
4	TraesCS3B01G207400	chr3A	97.238	1557	40	1	780	2333	201474838	201476394	0.000000e+00	2634.0
5	TraesCS3B01G207400	chr3A	93.625	549	25	6	208	752	691993113	691992571	0.000000e+00	811.0
6	TraesCS3B01G207400	chr3A	90.317	630	42	11	2669	3295	201478580	201479193	0.000000e+00	808.0
7	TraesCS3B01G207400	chr3A	94.565	184	9	1	2398	2581	201478399	201478581	1.940000e-72	283.0
8	TraesCS3B01G207400	chr3A	97.222	36	1	0	753	788	201474393	201474428	9.870000e-06	62.1
9	TraesCS3B01G207400	chr2B	96.203	632	18	5	125	752	166878039	166878668	0.000000e+00	1029.0
10	TraesCS3B01G207400	chr4A	93.417	638	26	10	125	752	634511237	634511868	0.000000e+00	931.0
11	TraesCS3B01G207400	chr4A	92.031	640	33	8	125	751	22220461	22221095	0.000000e+00	883.0
12	TraesCS3B01G207400	chr4A	82.188	320	20	23	28	314	634510808	634511123	1.180000e-59	241.0
13	TraesCS3B01G207400	chr1A	92.913	635	31	9	125	751	72553341	72553969	0.000000e+00	911.0
14	TraesCS3B01G207400	chr1A	82.188	320	20	23	28	314	72552912	72553227	1.180000e-59	241.0
15	TraesCS3B01G207400	chr1A	94.737	38	1	1	1	37	159520706	159520669	1.280000e-04	58.4
16	TraesCS3B01G207400	chr6A	92.019	639	37	7	125	754	34553638	34554271	0.000000e+00	885.0
17	TraesCS3B01G207400	chr6A	80.870	345	27	23	28	336	34553209	34553550	5.500000e-58	235.0
18	TraesCS3B01G207400	chr6A	80.938	320	25	22	28	314	610191525	610191841	1.540000e-53	220.0
19	TraesCS3B01G207400	chr1B	90.694	634	49	9	125	752	590501811	590502440	0.000000e+00	835.0
20	TraesCS3B01G207400	chr1B	92.268	582	34	10	125	698	590518892	590518314	0.000000e+00	815.0
21	TraesCS3B01G207400	chr1B	95.876	97	3	1	32	127	409280602	409280698	4.400000e-34	156.0
22	TraesCS3B01G207400	chr1B	95.833	96	4	0	32	127	590519295	590519200	4.400000e-34	156.0
23	TraesCS3B01G207400	chr5B	91.214	626	34	13	125	739	463971240	463970625	0.000000e+00	832.0
24	TraesCS3B01G207400	chr5A	82.500	320	19	23	28	314	400571400	400571715	2.540000e-61	246.0
25	TraesCS3B01G207400	chr6B	94.845	97	5	0	31	127	640331410	640331314	5.690000e-33	152.0
26	TraesCS3B01G207400	chr7A	94.737	38	1	1	1	37	23251004	23251041	1.280000e-04	58.4

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	TraesCS3B01G207400	chr3B	242885412	242888706	3294	True	6085.000	6085	100.0000	1	3295	1	chr3B.!!$R1	3294
1	TraesCS3B01G207400	chr3D	167789313	167791826	2513	True	3916.000	3916	94.6670	753	3295	1	chr3D.!!$R1	2542
2	TraesCS3B01G207400	chr3A	201474393	201479193	4800	False	946.775	2634	94.8355	753	3295	4	chr3A.!!$F1	2542
3	TraesCS3B01G207400	chr3A	691992571	691993113	542	True	811.000	811	93.6250	208	752	1	chr3A.!!$R1	544
4	TraesCS3B01G207400	chr2B	166878039	166878668	629	False	1029.000	1029	96.2030	125	752	1	chr2B.!!$F1	627
5	TraesCS3B01G207400	chr4A	22220461	22221095	634	False	883.000	883	92.0310	125	751	1	chr4A.!!$F1	626
6	TraesCS3B01G207400	chr4A	634510808	634511868	1060	False	586.000	931	87.8025	28	752	2	chr4A.!!$F2	724
7	TraesCS3B01G207400	chr1A	72552912	72553969	1057	False	576.000	911	87.5505	28	751	2	chr1A.!!$F1	723
8	TraesCS3B01G207400	chr6A	34553209	34554271	1062	False	560.000	885	86.4445	28	754	2	chr6A.!!$F2	726
9	TraesCS3B01G207400	chr1B	590501811	590502440	629	False	835.000	835	90.6940	125	752	1	chr1B.!!$F2	627
10	TraesCS3B01G207400	chr1B	590518314	590519295	981	True	485.500	815	94.0505	32	698	2	chr1B.!!$R1	666
11	TraesCS3B01G207400	chr5B	463970625	463971240	615	True	832.000	832	91.2140	125	739	1	chr5B.!!$R1	614

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
878	1654	1.201429	TCCCTCCCTGCAGTTTCTCC	61.201	60.0	13.81	0.0	0.0	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2753	5475	0.321387	ACTGACATGGCAGTGCTGAG	60.321	55.0	33.39	6.8	46.72	3.35	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
235	573	7.505585	TCTGAAACTAGTGAAATGGGTGAAATT	59.494	33.333	0.00	0.00	0.00	1.82
252	591	7.272731	GGGTGAAATTTATCTTTTGTAACGAGC	59.727	37.037	0.00	0.00	0.00	5.03
256	598	9.109533	GAAATTTATCTTTTGTAACGAGCGAAA	57.890	29.630	0.00	0.00	0.00	3.46
562	910	3.067320	TGCGTCATTCATCTCCACTCTAG	59.933	47.826	0.00	0.00	0.00	2.43
678	1036	1.704641	TATACGGAGCCAGACAGCAT	58.295	50.000	0.00	0.00	34.23	3.79
795	1571	8.394121	GGAGATTGCTCTAATAAACACTCTTTG	58.606	37.037	0.00	0.00	41.06	2.77
878	1654	1.201429	TCCCTCCCTGCAGTTTCTCC	61.201	60.000	13.81	0.00	0.00	3.71
944	1721	3.187227	CACTTAATTTGCTCTCGTGTGCT	59.813	43.478	12.13	0.00	34.18	4.40
1307	2084	1.450312	CTCCTTCATGACCGTGCCC	60.450	63.158	0.00	0.00	0.00	5.36
1784	2561	1.112113	GCTACGAGATGGACCTGGAA	58.888	55.000	0.00	0.00	0.00	3.53
2110	2887	1.535462	CGATGTCAGTGGGTTTGGAAC	59.465	52.381	0.00	0.00	0.00	3.62
2151	2928	0.179081	CCGGGTTCCTAGCTAAGCAC	60.179	60.000	0.00	0.00	0.00	4.40
2217	2995	8.310406	ACTAGCTTTTTATTTTGTCAAATGGC	57.690	30.769	0.00	0.00	34.29	4.40
2312	3093	7.339212	CACCATATCCACTCAACCATCTTTTAA	59.661	37.037	0.00	0.00	0.00	1.52
2333	4940	0.688487	CCCGGTGTGAAAACCCTAGA	59.312	55.000	0.00	0.00	36.84	2.43
2339	4946	4.868734	CGGTGTGAAAACCCTAGATCTAAC	59.131	45.833	3.57	0.00	36.84	2.34
2392	4999	7.688989	TGTATAATGATGTTTTTGCGTCGTTAC	59.311	33.333	0.00	0.00	38.15	2.50
2519	5240	2.197283	AAAGGCCTTGAGCTTCTCTG	57.803	50.000	21.33	0.00	43.05	3.35
2527	5248	4.142513	GCCTTGAGCTTCTCTGGTTATTTG	60.143	45.833	0.00	0.00	38.99	2.32
2534	5255	5.471456	AGCTTCTCTGGTTATTTGAGTTGTG	59.529	40.000	0.00	0.00	0.00	3.33
2582	5303	7.225538	AGAGTGACTAACAACATCTTCAACTTG	59.774	37.037	0.00	0.00	0.00	3.16
2616	5338	2.938838	ACATCTTCAACGGTTTCCCAA	58.061	42.857	0.00	0.00	0.00	4.12
2619	5341	2.510613	TCTTCAACGGTTTCCCAATCC	58.489	47.619	0.00	0.00	0.00	3.01
2621	5343	1.611519	TCAACGGTTTCCCAATCCAC	58.388	50.000	0.00	0.00	0.00	4.02
2637	5359	6.275335	CCAATCCACACCAATATGATGTTTC	58.725	40.000	0.00	0.00	0.00	2.78
2753	5475	1.165270	ACTTCACTTTGTATGGCGCC	58.835	50.000	22.73	22.73	0.00	6.53
2795	5517	1.540267	CGGGAGCTCGAGAATAGGAT	58.460	55.000	18.75	0.00	0.00	3.24
2799	5521	2.814919	GGAGCTCGAGAATAGGATCGAA	59.185	50.000	18.75	0.00	46.34	3.71
2820	5542	5.635280	CGAATAGCACGATTTGGATGAGTAT	59.365	40.000	0.00	0.00	0.00	2.12
2854	5576	2.284625	ACCGGATCAGCCTGTCCA	60.285	61.111	9.46	0.00	34.05	4.02
2863	5585	3.368571	GCCTGTCCAGCTTGGTGC	61.369	66.667	0.00	0.00	39.03	5.01
2968	5691	9.903682	TCTATACCTACTAATATTGAACAACGC	57.096	33.333	0.00	0.00	0.00	4.84
2976	5699	8.895932	ACTAATATTGAACAACGCATTTCTTC	57.104	30.769	0.00	0.00	0.00	2.87
2977	5700	8.511321	ACTAATATTGAACAACGCATTTCTTCA	58.489	29.630	0.00	0.00	0.00	3.02
2979	5702	8.761575	AATATTGAACAACGCATTTCTTCAAT	57.238	26.923	12.74	12.74	41.89	2.57
2983	5706	7.301068	TGAACAACGCATTTCTTCAATTTTT	57.699	28.000	0.00	0.00	0.00	1.94
3007	5730	1.472878	GTCCATCTCGTGTAGCTGACA	59.527	52.381	0.00	0.00	34.94	3.58
3010	5733	3.195610	TCCATCTCGTGTAGCTGACAAAT	59.804	43.478	0.00	0.00	40.66	2.32
3024	5747	5.300286	AGCTGACAAATATTACCCTCAATGC	59.700	40.000	0.00	0.00	0.00	3.56
3027	5750	5.359576	TGACAAATATTACCCTCAATGCCAC	59.640	40.000	0.00	0.00	0.00	5.01
3028	5751	5.518865	ACAAATATTACCCTCAATGCCACT	58.481	37.500	0.00	0.00	0.00	4.00
3033	5756	5.589367	ATTACCCTCAATGCCACTCATAT	57.411	39.130	0.00	0.00	34.33	1.78
3079	5802	4.855531	ACATGAAGACAAAAGCCGTAAAC	58.144	39.130	0.00	0.00	0.00	2.01
3080	5803	4.336993	ACATGAAGACAAAAGCCGTAAACA	59.663	37.500	0.00	0.00	0.00	2.83
3113	5837	5.642919	TGGTTTTACATGTACGATAACCCAC	59.357	40.000	22.73	7.41	34.17	4.61
3125	5849	2.713863	TAACCCACGTGAACCAACTT	57.286	45.000	19.30	0.00	0.00	2.66
3138	5862	1.266178	CCAACTTGATTTCCACCCCC	58.734	55.000	0.00	0.00	0.00	5.40
3209	5934	5.525378	GCATGATACCTGTCGAAAGAGATTT	59.475	40.000	3.47	0.00	43.49	2.17
3280	6005	6.431543	CACGTATCATAGGATCAGGAAGTAGT	59.568	42.308	0.00	0.00	34.89	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
235	573	6.201425	AGTGTTTCGCTCGTTACAAAAGATAA	59.799	34.615	0.00	0.00	0.00	1.75
494	838	8.030692	CACACACTCACATGGATTAATTTCATT	58.969	33.333	0.00	0.00	0.00	2.57
562	910	2.418368	TCACAGAGGAGAGAGAGAGC	57.582	55.000	0.00	0.00	0.00	4.09
678	1036	6.406512	CCATCCATCAATTTTCTCAAGATGCA	60.407	38.462	0.00	0.00	35.84	3.96
783	1141	6.035650	CGACAAACAGAGACAAAGAGTGTTTA	59.964	38.462	0.00	0.00	41.96	2.01
795	1571	1.711206	GGCCTACGACAAACAGAGAC	58.289	55.000	0.00	0.00	0.00	3.36
878	1654	1.137479	GCAACAATGGGGATCACATGG	59.863	52.381	0.00	0.00	0.00	3.66
1307	2084	4.477975	GAGCCCACGACGGACGAG	62.478	72.222	6.90	0.00	45.77	4.18
1650	2427	1.694696	GGGGATGTTTCGGCTATCTCT	59.305	52.381	0.00	0.00	0.00	3.10
1784	2561	4.760047	GGCATCCGCAGTGTCCGT	62.760	66.667	0.00	0.00	41.24	4.69
1909	2686	1.815421	CTTCTAGCGCCGGCAATGT	60.815	57.895	28.98	9.77	43.41	2.71
1965	2742	2.125512	CTGCTTCCTTACGCCGCT	60.126	61.111	0.00	0.00	0.00	5.52
1973	2750	2.031120	CTCCTCGATCTCTGCTTCCTT	58.969	52.381	0.00	0.00	0.00	3.36
2110	2887	4.404098	CCCAACCTTCCCCGTCCG	62.404	72.222	0.00	0.00	0.00	4.79
2151	2928	5.869753	ATCGGAAAGACTGAACTGAAATG	57.130	39.130	0.00	0.00	37.44	2.32
2202	2980	9.645059	TGATAAAATTCGCCATTTGACAAAATA	57.355	25.926	4.41	0.00	35.09	1.40
2217	2995	9.740239	ATGTCCTCATTGAATTGATAAAATTCG	57.260	29.630	6.38	0.00	38.99	3.34
2283	3064	5.428457	AGATGGTTGAGTGGATATGGTGTTA	59.572	40.000	0.00	0.00	0.00	2.41
2312	3093	1.061324	TAGGGTTTTCACACCGGGGT	61.061	55.000	1.51	1.51	37.76	4.95
2365	4972	6.781138	ACGACGCAAAAACATCATTATACAT	58.219	32.000	0.00	0.00	0.00	2.29
2373	4980	2.873472	AGGTAACGACGCAAAAACATCA	59.127	40.909	0.00	0.00	46.39	3.07
2392	4999	4.318332	TCCGAGCAATGCATTCTATAAGG	58.682	43.478	9.53	8.67	0.00	2.69
2469	5190	6.048732	TGTACATTCCTGAATAGCAGTCAA	57.951	37.500	0.00	0.00	43.33	3.18
2485	5206	8.588290	TCAAGGCCTTTAACATAATGTACATT	57.412	30.769	23.80	23.80	34.93	2.71
2519	5240	7.444487	AGGTAAAGTCTCACAACTCAAATAACC	59.556	37.037	0.00	0.00	0.00	2.85
2527	5248	4.868067	TCGAAGGTAAAGTCTCACAACTC	58.132	43.478	0.00	0.00	0.00	3.01
2534	5255	4.175787	TGAAGCTCGAAGGTAAAGTCTC	57.824	45.455	0.00	0.00	0.00	3.36
2612	5334	4.217510	ACATCATATTGGTGTGGATTGGG	58.782	43.478	0.00	0.00	40.78	4.12
2616	5338	7.503566	CCTAAGAAACATCATATTGGTGTGGAT	59.496	37.037	0.00	0.00	41.60	3.41
2619	5341	6.828273	TCCCTAAGAAACATCATATTGGTGTG	59.172	38.462	0.00	0.00	41.60	3.82
2621	5343	7.201821	GGTTCCCTAAGAAACATCATATTGGTG	60.202	40.741	0.00	0.00	42.22	4.17
2637	5359	3.832527	CACCATATTGGGGTTCCCTAAG	58.167	50.000	11.99	1.98	45.70	2.18
2753	5475	0.321387	ACTGACATGGCAGTGCTGAG	60.321	55.000	33.39	6.80	46.72	3.35
2795	5517	4.051237	CTCATCCAAATCGTGCTATTCGA	58.949	43.478	0.00	0.00	41.45	3.71
2799	5521	5.180117	GCAATACTCATCCAAATCGTGCTAT	59.820	40.000	0.00	0.00	0.00	2.97
2820	5542	1.339631	CGGTGGACTAAGGATTGGCAA	60.340	52.381	0.68	0.68	0.00	4.52
2959	5682	6.900568	AAAATTGAAGAAATGCGTTGTTCA	57.099	29.167	11.06	11.06	45.15	3.18
2983	5706	1.816835	AGCTACACGAGATGGACGAAA	59.183	47.619	0.00	0.00	34.70	3.46
3007	5730	5.765510	TGAGTGGCATTGAGGGTAATATTT	58.234	37.500	0.00	0.00	0.00	1.40
3010	5733	6.044287	ACATATGAGTGGCATTGAGGGTAATA	59.956	38.462	10.38	0.00	38.44	0.98
3027	5750	9.350357	CTTTTCAGATTTGTTTCCACATATGAG	57.650	33.333	10.38	0.54	32.38	2.90
3028	5751	8.306038	CCTTTTCAGATTTGTTTCCACATATGA	58.694	33.333	10.38	0.00	29.60	2.15
3033	5756	4.161189	TGCCTTTTCAGATTTGTTTCCACA	59.839	37.500	0.00	0.00	0.00	4.17
3038	5761	6.347696	TCATGTTGCCTTTTCAGATTTGTTT	58.652	32.000	0.00	0.00	0.00	2.83
3041	5764	6.145048	GTCTTCATGTTGCCTTTTCAGATTTG	59.855	38.462	0.00	0.00	0.00	2.32
3045	5768	4.206375	TGTCTTCATGTTGCCTTTTCAGA	58.794	39.130	0.00	0.00	0.00	3.27
3079	5802	8.714179	TCGTACATGTAAAACCAATCTACTTTG	58.286	33.333	7.25	0.00	0.00	2.77
3080	5803	8.836268	TCGTACATGTAAAACCAATCTACTTT	57.164	30.769	7.25	0.00	0.00	2.66
3113	5837	3.550030	GGTGGAAATCAAGTTGGTTCACG	60.550	47.826	16.92	0.00	0.00	4.35
3125	5849	1.003812	CTTACGTGGGGGTGGAAATCA	59.996	52.381	0.00	0.00	0.00	2.57
3138	5862	4.456222	AGGACTCGATGGATATCTTACGTG	59.544	45.833	0.00	8.92	0.00	4.49
3164	5888	4.202202	TGCATGGAGTGAAAACGGAATTTT	60.202	37.500	0.00	0.00	43.44	1.82
3168	5892	1.974265	TGCATGGAGTGAAAACGGAA	58.026	45.000	0.00	0.00	0.00	4.30
3172	5896	4.641989	AGGTATCATGCATGGAGTGAAAAC	59.358	41.667	25.97	10.01	0.00	2.43
3209	5934	8.483758	GTGGGTTAGGAGAGAGTTGATTTTATA	58.516	37.037	0.00	0.00	0.00	0.98
3216	5941	3.254093	TGTGGGTTAGGAGAGAGTTGA	57.746	47.619	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.