AutoCloner

Multiple sequence alignment - TraesCS6A01G060500

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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	TraesCS6A01G060500	chr6A	100.000	3545	0	0	1	3545	32252724	32249180	0.000000e+00	6547
1	TraesCS6A01G060500	chr6A	85.141	1097	138	21	1155	2240	32228259	32229341	0.000000e+00	1099
2	TraesCS6A01G060500	chr6A	80.882	1156	183	21	1236	2366	32412797	32411655	0.000000e+00	876
3	TraesCS6A01G060500	chr6A	94.118	102	6	0	2837	2938	79200357	79200458	4.740000e-34	156
4	TraesCS6A01G060500	chr6D	91.686	1708	114	18	1155	2845	30536350	30534654	0.000000e+00	2342
5	TraesCS6A01G060500	chr6D	95.596	1249	51	2	1155	2402	30483939	30482694	0.000000e+00	1999
6	TraesCS6A01G060500	chr6D	81.513	1163	175	25	1236	2366	31261539	31262693	0.000000e+00	920
7	TraesCS6A01G060500	chr6D	82.515	652	57	32	2942	3545	30531927	30531285	1.460000e-143	520
8	TraesCS6A01G060500	chr6D	94.949	99	5	0	2840	2938	369969453	369969355	4.740000e-34	156
9	TraesCS6A01G060500	chr6D	94.118	102	6	0	2837	2938	370026937	370027038	4.740000e-34	156
10	TraesCS6A01G060500	chr6D	87.313	134	10	3	3302	3434	30533373	30533246	2.850000e-31	147
11	TraesCS6A01G060500	chr2D	96.247	1119	42	0	27	1145	483840585	483841703	0.000000e+00	1834
12	TraesCS6A01G060500	chr6B	93.629	1240	54	10	1155	2388	56915094	56916314	0.000000e+00	1829
13	TraesCS6A01G060500	chr6B	90.799	1152	81	11	2399	3545	56916513	56917644	0.000000e+00	1517
14	TraesCS6A01G060500	chr6B	90.190	1050	75	13	1155	2185	57002247	57001207	0.000000e+00	1343
15	TraesCS6A01G060500	chr6B	84.929	1128	152	14	1155	2272	56993116	56991997	0.000000e+00	1125
16	TraesCS6A01G060500	chr6B	80.846	1159	187	21	1236	2366	56386126	56387277	0.000000e+00	878
17	TraesCS6A01G060500	chr6B	90.940	585	41	5	2178	2754	57001072	57000492	0.000000e+00	776
18	TraesCS6A01G060500	chr6B	86.741	626	50	17	2939	3545	57000366	56999755	0.000000e+00	665
19	TraesCS6A01G060500	chr2A	72.965	1069	270	18	12	1070	683219983	683221042	4.350000e-94	355
20	TraesCS6A01G060500	chr7D	72.272	898	218	23	70	951	476777374	476778256	2.110000e-62	250
21	TraesCS6A01G060500	chr2B	92.169	166	13	0	12	177	20350572	20350737	5.920000e-58	235
22	TraesCS6A01G060500	chr5D	94.949	99	5	0	2840	2938	79996314	79996216	4.740000e-34	156
23	TraesCS6A01G060500	chr4D	94.118	102	6	0	2837	2938	123565498	123565599	4.740000e-34	156
24	TraesCS6A01G060500	chr4B	94.949	99	5	0	2840	2938	309280530	309280432	4.740000e-34	156
25	TraesCS6A01G060500	chr1D	94.118	102	6	0	2837	2938	406712726	406712625	4.740000e-34	156
26	TraesCS6A01G060500	chr1B	94.118	102	6	0	2837	2938	499831490	499831591	4.740000e-34	156

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	TraesCS6A01G060500	chr6A	32249180	32252724	3544	True	6547	6547	100.000000	1	3545	1	chr6A.!!$R1	3544
1	TraesCS6A01G060500	chr6A	32228259	32229341	1082	False	1099	1099	85.141000	1155	2240	1	chr6A.!!$F1	1085
2	TraesCS6A01G060500	chr6A	32411655	32412797	1142	True	876	876	80.882000	1236	2366	1	chr6A.!!$R2	1130
3	TraesCS6A01G060500	chr6D	30482694	30483939	1245	True	1999	1999	95.596000	1155	2402	1	chr6D.!!$R1	1247
4	TraesCS6A01G060500	chr6D	30531285	30536350	5065	True	1003	2342	87.171333	1155	3545	3	chr6D.!!$R3	2390
5	TraesCS6A01G060500	chr6D	31261539	31262693	1154	False	920	920	81.513000	1236	2366	1	chr6D.!!$F1	1130
6	TraesCS6A01G060500	chr2D	483840585	483841703	1118	False	1834	1834	96.247000	27	1145	1	chr2D.!!$F1	1118
7	TraesCS6A01G060500	chr6B	56915094	56917644	2550	False	1673	1829	92.214000	1155	3545	2	chr6B.!!$F2	2390
8	TraesCS6A01G060500	chr6B	56991997	56993116	1119	True	1125	1125	84.929000	1155	2272	1	chr6B.!!$R1	1117
9	TraesCS6A01G060500	chr6B	56999755	57002247	2492	True	928	1343	89.290333	1155	3545	3	chr6B.!!$R2	2390
10	TraesCS6A01G060500	chr6B	56386126	56387277	1151	False	878	878	80.846000	1236	2366	1	chr6B.!!$F1	1130
11	TraesCS6A01G060500	chr2A	683219983	683221042	1059	False	355	355	72.965000	12	1070	1	chr2A.!!$F1	1058
12	TraesCS6A01G060500	chr7D	476777374	476778256	882	False	250	250	72.272000	70	951	1	chr7D.!!$F1	881

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
558	571	0.457853	CCTTCGCTGCTGTACGCTTA	60.458	55.0	10.27	0.0	40.11	3.09	F
992	1005	0.546122	AACCCATTGCAGCTCCGATA	59.454	50.0	0.00	0.0	0.00	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1638	1665	1.278238	CGAAGTCGATGTAGGTTGGC	58.722	55.0	0.0	0.0	43.02	4.52	R
2860	3545	1.516365	ATCCTATCTCGCCACGGTCG	61.516	60.0	0.0	0.0	0.00	4.79	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
24	25	1.330655	GGTCTCCCGGAGCAGAATGA	61.331	60.000	9.87	0.00	39.69	2.57
63	65	3.065648	CAGAGTTTAGACTAGACCGAGCC	59.934	52.174	0.00	0.00	35.88	4.70
162	164	2.861462	TTTCAGCAACAAAGGAACCG	57.139	45.000	0.00	0.00	0.00	4.44
378	391	2.030185	GTCTAGAACGACAACTCCAGCA	60.030	50.000	0.00	0.00	34.11	4.41
389	402	2.283101	TCCAGCAGCGGCCAAAAT	60.283	55.556	4.82	0.00	42.56	1.82
445	458	3.835790	AAAGTACCAAGCGGCGGCA	62.836	57.895	19.21	0.00	43.41	5.69
460	473	2.701780	GGCAGAGGCGACGAAGAGA	61.702	63.158	0.00	0.00	42.47	3.10
473	486	1.735369	CGAAGAGACAGAAGCTGGAGC	60.735	57.143	0.00	0.00	42.49	4.70
479	492	1.071987	CAGAAGCTGGAGCCACACA	59.928	57.895	0.00	0.00	43.38	3.72
510	523	3.815401	CAGAGTCCGGTTTGAAAAGATGT	59.185	43.478	0.00	0.00	0.00	3.06
558	571	0.457853	CCTTCGCTGCTGTACGCTTA	60.458	55.000	10.27	0.00	40.11	3.09
609	622	3.069586	CCACATTACGAGCTTCCCAGATA	59.930	47.826	0.00	0.00	0.00	1.98
696	709	3.065655	CCATTGCTTTGGATTCGCAAAA	58.934	40.909	0.00	0.00	45.46	2.44
722	735	1.695813	CGACACAGCTTGACAGAGAG	58.304	55.000	3.37	0.00	0.00	3.20
732	745	3.324993	CTTGACAGAGAGACAAGCCTTC	58.675	50.000	0.00	0.00	41.62	3.46
837	850	2.432628	CTCGTTGGGACCTGACGC	60.433	66.667	13.15	0.00	36.77	5.19
912	925	3.535561	CACCTTCATCTTATTCGGCACT	58.464	45.455	0.00	0.00	0.00	4.40
942	955	3.945285	TCCACAGTTTCTTCCACAGTTTC	59.055	43.478	0.00	0.00	0.00	2.78
975	988	0.893727	AACCGGAATGCTGACCCAAC	60.894	55.000	9.46	0.00	0.00	3.77
992	1005	0.546122	AACCCATTGCAGCTCCGATA	59.454	50.000	0.00	0.00	0.00	2.92
996	1009	1.143838	ATTGCAGCTCCGATACGCA	59.856	52.632	0.00	0.00	0.00	5.24
1051	1064	1.153901	CGGACAGTGTAATCGCCGT	60.154	57.895	11.20	0.00	34.45	5.68
1066	1079	1.366679	GCCGTACTTAGTGAAAGGCC	58.633	55.000	0.00	0.00	39.73	5.19
1071	1084	0.685097	ACTTAGTGAAAGGCCAGCGA	59.315	50.000	5.01	0.00	39.73	4.93
1116	1129	6.220930	CAAATTTATTGGGATCTGCAGGATG	58.779	40.000	15.13	0.00	40.87	3.51
1134	1147	3.782042	GCGTTAGCCACTTCCTCG	58.218	61.111	0.00	0.00	37.42	4.63
1228	1242	1.508088	CTTGCGTTGATCTTGGCCC	59.492	57.895	0.00	0.00	0.00	5.80
1258	1276	4.802051	GAGCAATGGCGGCCCAGA	62.802	66.667	17.97	0.00	46.24	3.86
1593	1620	1.103803	TCAGGCACGTCAGATACCTC	58.896	55.000	0.00	0.00	0.00	3.85
1638	1665	2.355599	CGCAGCGGCTGGATCTAG	60.356	66.667	29.44	0.86	38.10	2.43
1648	1675	1.762957	GCTGGATCTAGCCAACCTACA	59.237	52.381	19.71	0.00	37.52	2.74
1931	1987	2.664081	CCCTCCAGCTGGTCCAGAC	61.664	68.421	31.58	13.54	32.44	3.51
1995	2054	1.347707	TGCTGTCGGATGGAAGAGTTT	59.652	47.619	0.00	0.00	0.00	2.66
2104	2175	1.103803	CCAGTTAGTCTCTGCGCCTA	58.896	55.000	4.18	0.00	0.00	3.93
2191	2402	1.144298	ACACCACCTACAGGGAAAACC	59.856	52.381	0.00	0.00	40.27	3.27
2604	3246	3.187700	GTTTGATCGTCTATTCTGCCGT	58.812	45.455	0.00	0.00	0.00	5.68
2608	3250	2.273370	TCGTCTATTCTGCCGTGTTC	57.727	50.000	0.00	0.00	0.00	3.18
2618	3260	2.560981	TCTGCCGTGTTCTGATTAGTGA	59.439	45.455	0.00	0.00	0.00	3.41
2642	3284	1.740585	TGTGTTTGGAGGTTGTGTTCG	59.259	47.619	0.00	0.00	0.00	3.95
2702	3352	2.365293	GGCCTTATTATGGGCTGGTTTG	59.635	50.000	13.18	0.00	46.80	2.93
2725	3375	2.237143	AGCTCGATTTCTGATTCCCACA	59.763	45.455	0.00	0.00	0.00	4.17
2726	3376	3.118112	AGCTCGATTTCTGATTCCCACAT	60.118	43.478	0.00	0.00	0.00	3.21
2750	3426	4.571984	AGGAAAGCTTGCATTTTGTTTCAC	59.428	37.500	6.80	0.00	0.00	3.18
2788	3464	0.179161	TTTTGTTTGTGGGTGCGTCG	60.179	50.000	0.00	0.00	0.00	5.12
2791	3467	2.589442	TTTGTGGGTGCGTCGGTC	60.589	61.111	0.00	0.00	0.00	4.79
2829	3514	4.724602	TGCGTGCTCGAGGCTGTC	62.725	66.667	15.58	0.00	42.39	3.51
2860	3545	7.902403	CGAGAAAGATAAAGAGATTGTGCTTTC	59.098	37.037	0.00	0.00	39.90	2.62
2870	3555	4.072088	GTGCTTTCGACCGTGGCG	62.072	66.667	0.00	0.00	0.00	5.69
2892	4746	5.652891	GCGAGATAGGATAGACTTGGGATTA	59.347	44.000	0.00	0.00	0.00	1.75
2921	4775	2.879756	GCCCTTGATTGCCAACACTCTA	60.880	50.000	0.00	0.00	0.00	2.43
3426	6779	3.221771	TGCTTGTGCTAATGTTTCTGGT	58.778	40.909	0.00	0.00	40.48	4.00

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	0.537188	TTCATTCTGCTCCGGGAGAC	59.463	55.000	27.95	18.08	39.59	3.36
7	8	1.275666	TTTCATTCTGCTCCGGGAGA	58.724	50.000	27.95	11.56	38.14	3.71
8	9	2.113860	TTTTCATTCTGCTCCGGGAG	57.886	50.000	19.95	19.95	0.00	4.30
9	10	2.577606	TTTTTCATTCTGCTCCGGGA	57.422	45.000	0.00	0.00	0.00	5.14
10	11	3.694072	TGTATTTTTCATTCTGCTCCGGG	59.306	43.478	0.00	0.00	0.00	5.73
48	50	3.159472	TGTTTTGGCTCGGTCTAGTCTA	58.841	45.455	0.00	0.00	0.00	2.59
50	52	2.450609	TGTTTTGGCTCGGTCTAGTC	57.549	50.000	0.00	0.00	0.00	2.59
63	65	6.598525	TCGTAATGTGTTAGCTCATGTTTTG	58.401	36.000	0.00	0.00	0.00	2.44
378	391	1.747745	GTCCGGTATTTTGGCCGCT	60.748	57.895	0.00	0.00	45.98	5.52
389	402	3.697747	CTGTTGCCCCGTCCGGTA	61.698	66.667	0.00	0.00	0.00	4.02
445	458	0.321741	TCTGTCTCTTCGTCGCCTCT	60.322	55.000	0.00	0.00	0.00	3.69
449	462	0.109504	AGCTTCTGTCTCTTCGTCGC	60.110	55.000	0.00	0.00	0.00	5.19
451	464	1.542030	TCCAGCTTCTGTCTCTTCGTC	59.458	52.381	0.00	0.00	0.00	4.20
460	473	1.072159	GTGTGGCTCCAGCTTCTGT	59.928	57.895	0.00	0.00	41.70	3.41
473	486	3.257393	GACTCTGCATCTAAGTGTGTGG	58.743	50.000	0.00	0.00	0.00	4.17
479	492	1.853963	ACCGGACTCTGCATCTAAGT	58.146	50.000	9.46	0.00	0.00	2.24
510	523	6.712095	GTGCTTATATGGACATGATCTTCCAA	59.288	38.462	13.25	5.95	45.14	3.53
558	571	0.043940	AACCTGATGCTCCTCCTCCT	59.956	55.000	0.00	0.00	0.00	3.69
696	709	0.605083	TCAAGCTGTGTCGCTCATCT	59.395	50.000	0.00	0.00	39.86	2.90
722	735	1.680249	GGGATGAGGTGAAGGCTTGTC	60.680	57.143	3.46	0.00	0.00	3.18
732	745	1.222936	GGCTGTCTGGGATGAGGTG	59.777	63.158	0.00	0.00	0.00	4.00
861	874	1.200716	AGGTTTGCGCATGATTGTCTG	59.799	47.619	12.75	0.00	0.00	3.51
912	925	6.071108	TGTGGAAGAAACTGTGGAAAATCAAA	60.071	34.615	0.00	0.00	0.00	2.69
942	955	2.711922	CGGTTGGTCCTCGGAGGAG	61.712	68.421	26.70	10.45	46.90	3.69
975	988	1.224069	CGTATCGGAGCTGCAATGGG	61.224	60.000	5.91	0.00	0.00	4.00
992	1005	2.326550	CGAGCCGTTTTGTTGCGT	59.673	55.556	0.00	0.00	0.00	5.24
996	1009	0.661020	CAAGGACGAGCCGTTTTGTT	59.339	50.000	1.80	0.00	41.37	2.83
1051	1064	1.897133	TCGCTGGCCTTTCACTAAGTA	59.103	47.619	3.32	0.00	31.56	2.24
1066	1079	1.134995	TGGAGCTGACTATGTTCGCTG	60.135	52.381	0.00	0.00	0.00	5.18
1071	1084	2.171448	GGATGGTGGAGCTGACTATGTT	59.829	50.000	0.00	0.00	0.00	2.71
1145	1158	2.412325	CCAAGTTGGTTAACGCGACATC	60.412	50.000	15.93	0.00	41.71	3.06
1146	1159	1.533731	CCAAGTTGGTTAACGCGACAT	59.466	47.619	15.93	0.13	41.71	3.06
1147	1160	0.938713	CCAAGTTGGTTAACGCGACA	59.061	50.000	15.93	0.00	41.71	4.35
1148	1161	3.740384	CCAAGTTGGTTAACGCGAC	57.260	52.632	15.93	0.00	41.71	5.19
1209	1223	1.508088	GGCCAAGATCAACGCAAGG	59.492	57.895	0.00	0.00	46.39	3.61
1258	1276	1.228154	GCCAGTCCGGTTGTTCCTT	60.228	57.895	0.00	0.00	36.97	3.36
1593	1620	1.734477	CTCCAGGTCGTTGCAGTCG	60.734	63.158	6.98	6.98	0.00	4.18
1638	1665	1.278238	CGAAGTCGATGTAGGTTGGC	58.722	55.000	0.00	0.00	43.02	4.52
1648	1675	2.202623	GCAGTCCGCGAAGTCGAT	60.203	61.111	8.23	0.00	43.02	3.59
1940	1996	4.752879	TGGCGAGGTTAGGCGTGC	62.753	66.667	0.00	0.00	36.92	5.34
1995	2054	4.328536	ACGCAACAAGGTGGACATAATTA	58.671	39.130	0.00	0.00	0.00	1.40
2078	2143	3.194062	GCAGAGACTAACTGGAAGATGC	58.806	50.000	0.00	0.00	37.43	3.91
2281	2728	7.908827	TGTAGACGCATTCCAACTTTTTATA	57.091	32.000	0.00	0.00	0.00	0.98
2604	3246	7.416817	CAAACACACAATCACTAATCAGAACA	58.583	34.615	0.00	0.00	0.00	3.18
2608	3250	6.348786	CCTCCAAACACACAATCACTAATCAG	60.349	42.308	0.00	0.00	0.00	2.90
2618	3260	3.096092	ACACAACCTCCAAACACACAAT	58.904	40.909	0.00	0.00	0.00	2.71
2642	3284	6.663944	AATCGACTAAAGTGAATTACCAGC	57.336	37.500	0.00	0.00	0.00	4.85
2697	3347	5.220681	GGAATCAGAAATCGAGCTACAAACC	60.221	44.000	0.00	0.00	0.00	3.27
2702	3352	3.804873	GTGGGAATCAGAAATCGAGCTAC	59.195	47.826	0.00	0.00	0.00	3.58
2725	3375	6.424812	GTGAAACAAAATGCAAGCTTTCCTAT	59.575	34.615	0.00	0.00	36.32	2.57
2726	3376	5.752955	GTGAAACAAAATGCAAGCTTTCCTA	59.247	36.000	0.00	0.00	36.32	2.94
2737	3387	9.986833	AGAAAATAACAAAGTGAAACAAAATGC	57.013	25.926	0.00	0.00	41.43	3.56
2750	3426	8.731275	AACAAAAGGGGAAGAAAATAACAAAG	57.269	30.769	0.00	0.00	0.00	2.77
2825	3510	3.526931	TTATCTTTCTCGGGCAGACAG	57.473	47.619	0.00	0.00	30.92	3.51
2829	3514	4.392921	TCTCTTTATCTTTCTCGGGCAG	57.607	45.455	0.00	0.00	0.00	4.85
2860	3545	1.516365	ATCCTATCTCGCCACGGTCG	61.516	60.000	0.00	0.00	0.00	4.79
2921	4775	6.698670	TCCCCCATTTAATTAATTTAGCCCT	58.301	36.000	5.91	0.00	0.00	5.19
3290	6641	9.436957	GGTGTAATGAATTAAGGACATCGATAT	57.563	33.333	0.00	0.00	0.00	1.63
3401	6753	3.256631	AGAAACATTAGCACAAGCAAGGG	59.743	43.478	0.00	0.00	45.49	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.