AutoCloner

Multiple sequence alignment - TraesCS7B01G261500

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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	TraesCS7B01G261500	chr7B	100.000	2990	0	0	1	2990	482079396	482076407	0.000000e+00	5522.0
1	TraesCS7B01G261500	chr7B	86.821	1897	242	7	1099	2990	481856891	481854998	0.000000e+00	2111.0
2	TraesCS7B01G261500	chr7B	83.570	1899	298	13	1100	2990	482684530	482686422	0.000000e+00	1766.0
3	TraesCS7B01G261500	chr7B	100.000	28	0	0	3	30	376441054	376441081	5.000000e-03	52.8
4	TraesCS7B01G261500	chr7D	97.008	1905	48	4	1095	2990	459790071	459788167	0.000000e+00	3193.0
5	TraesCS7B01G261500	chr7D	86.977	1889	237	8	1107	2990	459752630	459750746	0.000000e+00	2117.0
6	TraesCS7B01G261500	chr7D	83.544	1896	298	14	1103	2990	460279887	460281776	0.000000e+00	1760.0
7	TraesCS7B01G261500	chr7D	96.255	534	20	0	556	1089	459791002	459790469	0.000000e+00	876.0
8	TraesCS7B01G261500	chr7D	89.759	498	31	12	3	491	459791491	459791005	1.180000e-173	619.0
9	TraesCS7B01G261500	chr7D	83.730	252	38	3	34	283	363904013	363904263	4.980000e-58	235.0
10	TraesCS7B01G261500	chr7A	83.175	1896	305	14	1103	2990	539325806	539323917	0.000000e+00	1722.0
11	TraesCS7B01G261500	chr7A	88.909	1118	118	5	1877	2990	539928022	539929137	0.000000e+00	1373.0
12	TraesCS7B01G261500	chr7A	98.039	510	10	0	2481	2990	539848157	539848666	0.000000e+00	887.0
13	TraesCS7B01G261500	chr7A	86.285	751	56	13	74	794	539847408	539848141	0.000000e+00	773.0
14	TraesCS7B01G261500	chr7A	81.892	740	132	2	1096	1834	539927121	539927859	9.100000e-175	623.0
15	TraesCS7B01G261500	chr7A	80.843	261	42	7	34	290	16125047	16124791	6.540000e-47	198.0
16	TraesCS7B01G261500	chr3B	84.496	258	37	3	43	298	790199381	790199125	4.950000e-63	252.0
17	TraesCS7B01G261500	chr3A	82.353	289	43	7	34	317	205566635	205566920	8.280000e-61	244.0
18	TraesCS7B01G261500	chr6A	81.100	291	43	9	35	316	136886326	136886039	3.880000e-54	222.0
19	TraesCS7B01G261500	chr6A	87.500	56	7	0	228	283	153681845	153681900	6.920000e-07	65.8
20	TraesCS7B01G261500	chr1A	81.034	290	45	9	34	316	153586888	153587174	3.880000e-54	222.0
21	TraesCS7B01G261500	chr5A	80.903	288	43	9	34	316	444955405	444955125	1.800000e-52	217.0
22	TraesCS7B01G261500	chr2D	82.787	244	39	3	53	295	596000461	596000220	6.490000e-52	215.0
23	TraesCS7B01G261500	chr4D	79.612	206	34	8	322	521	6713136	6712933	1.120000e-29	141.0
24	TraesCS7B01G261500	chr2A	87.755	98	12	0	1100	1197	208167086	208167183	6.770000e-22	115.0

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	TraesCS7B01G261500	chr7B	482076407	482079396	2989	True	5522.000000	5522	100.000000	1	2990	1	chr7B.!!$R2	2989
1	TraesCS7B01G261500	chr7B	481854998	481856891	1893	True	2111.000000	2111	86.821000	1099	2990	1	chr7B.!!$R1	1891
2	TraesCS7B01G261500	chr7B	482684530	482686422	1892	False	1766.000000	1766	83.570000	1100	2990	1	chr7B.!!$F2	1890
3	TraesCS7B01G261500	chr7D	459750746	459752630	1884	True	2117.000000	2117	86.977000	1107	2990	1	chr7D.!!$R1	1883
4	TraesCS7B01G261500	chr7D	460279887	460281776	1889	False	1760.000000	1760	83.544000	1103	2990	1	chr7D.!!$F2	1887
5	TraesCS7B01G261500	chr7D	459788167	459791491	3324	True	1562.666667	3193	94.340667	3	2990	3	chr7D.!!$R2	2987
6	TraesCS7B01G261500	chr7A	539323917	539325806	1889	True	1722.000000	1722	83.175000	1103	2990	1	chr7A.!!$R2	1887
7	TraesCS7B01G261500	chr7A	539927121	539929137	2016	False	998.000000	1373	85.400500	1096	2990	2	chr7A.!!$F2	1894
8	TraesCS7B01G261500	chr7A	539847408	539848666	1258	False	830.000000	887	92.162000	74	2990	2	chr7A.!!$F1	2916

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
897	935	0.389296	CCACTGATACGCCGTTCACA	60.389	55.0	0.0	0.0	0.0	3.58	F
1097	1135	0.630673	CCTCACCATCCCAATTCCCA	59.369	55.0	0.0	0.0	0.0	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1712	2142	0.807667	CGCAGAAGGAATCTCACCGG	60.808	60.000	0.00	0.0	35.73	5.28	R
2310	2890	3.220940	TGTGTGCAATTGGTCAATGAGA	58.779	40.909	7.72	0.0	0.00	3.27	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
38	39	9.802039	TTGGGTAAATAACTCAAGAATAAGTGT	57.198	29.630	0.00	0.00	43.85	3.55
118	120	3.896888	TGCAAACCACCATCTCTTTCATT	59.103	39.130	0.00	0.00	0.00	2.57
142	144	5.742562	TTAATTACCCCACCCTCAATGAT	57.257	39.130	0.00	0.00	0.00	2.45
143	145	4.625225	AATTACCCCACCCTCAATGATT	57.375	40.909	0.00	0.00	0.00	2.57
160	162	9.961265	CTCAATGATTTATGTGCATGTAGAAAT	57.039	29.630	0.00	0.00	0.00	2.17
181	183	7.492344	AGAAATTGAAAAGACCATGTGTTGAAC	59.508	33.333	0.00	0.00	0.00	3.18
206	209	3.665745	TTGGTCTTAGTTACCGGTGAC	57.334	47.619	21.25	21.25	40.08	3.67
226	229	4.926238	TGACGAGAGAGAAGCATTTTCTTC	59.074	41.667	0.00	0.00	42.01	2.87
291	294	6.748333	TGAACAAATTTTGAATGCCAAACA	57.252	29.167	15.81	0.77	43.82	2.83
329	335	7.208064	AGGAGGGAGTAAACTGCAATTAATA	57.792	36.000	3.97	0.00	35.89	0.98
360	366	4.757799	TTGTAATTTGGTCACCATGTCG	57.242	40.909	0.00	0.00	31.53	4.35
367	378	1.673400	TGGTCACCATGTCGTGTTTTG	59.327	47.619	0.00	0.00	35.18	2.44
372	383	5.506649	GGTCACCATGTCGTGTTTTGTTATT	60.507	40.000	0.00	0.00	35.18	1.40
403	414	4.098196	GTCACTAGCGAAACTAAGGATCCT	59.902	45.833	9.02	9.02	0.00	3.24
509	539	6.757237	TGCAATTATCACTTCCAAACACAAT	58.243	32.000	0.00	0.00	0.00	2.71
513	543	7.656707	ATTATCACTTCCAAACACAATTTGC	57.343	32.000	0.00	0.00	0.00	3.68
520	550	6.650390	ACTTCCAAACACAATTTGCATTATCC	59.350	34.615	0.00	0.00	0.00	2.59
524	554	5.343307	AACACAATTTGCATTATCCCCTC	57.657	39.130	0.00	0.00	0.00	4.30
674	708	6.928492	GCCAGATTATTCAAGACTAAGAGAGG	59.072	42.308	0.00	0.00	0.00	3.69
719	753	5.012328	AGGTGAGAACCAGATTCGTTATC	57.988	43.478	0.00	0.00	42.69	1.75
792	830	1.226746	AAACGTCAAGTGGCTAGCAC	58.773	50.000	18.24	12.66	0.00	4.40
793	831	0.393077	AACGTCAAGTGGCTAGCACT	59.607	50.000	18.24	14.74	33.80	4.40
890	928	3.608707	CGTACATAGACCACTGATACGCC	60.609	52.174	0.00	0.00	31.43	5.68
897	935	0.389296	CCACTGATACGCCGTTCACA	60.389	55.000	0.00	0.00	0.00	3.58
937	975	5.403246	CAAGTGGATCACTACTCTACACAC	58.597	45.833	0.67	0.00	44.62	3.82
944	982	2.093941	CACTACTCTACACACGACGGAG	59.906	54.545	0.00	0.00	0.00	4.63
1031	1069	1.373873	GCGGGCGCCCTATAAGTAC	60.374	63.158	41.01	16.91	34.56	2.73
1065	1103	6.317893	TGAATCACATCCATCACAGATTCAAG	59.682	38.462	11.81	0.00	44.65	3.02
1076	1114	3.681417	CACAGATTCAAGCGTCTCAATCA	59.319	43.478	10.95	0.00	0.00	2.57
1089	1127	2.239654	TCTCAATCAACCTCACCATCCC	59.760	50.000	0.00	0.00	0.00	3.85
1091	1129	2.378208	TCAATCAACCTCACCATCCCAA	59.622	45.455	0.00	0.00	0.00	4.12
1092	1130	3.011595	TCAATCAACCTCACCATCCCAAT	59.988	43.478	0.00	0.00	0.00	3.16
1093	1131	3.763557	ATCAACCTCACCATCCCAATT	57.236	42.857	0.00	0.00	0.00	2.32
1094	1132	3.085952	TCAACCTCACCATCCCAATTC	57.914	47.619	0.00	0.00	0.00	2.17
1097	1135	0.630673	CCTCACCATCCCAATTCCCA	59.369	55.000	0.00	0.00	0.00	4.37
1104	1534	2.459644	CATCCCAATTCCCAAGCTTCA	58.540	47.619	0.00	0.00	0.00	3.02
1168	1598	4.436448	GCAGCAAGAGACACGCGC	62.436	66.667	5.73	0.00	0.00	6.86
1261	1691	2.549754	ACTTTCCTCACAAGAATGCACG	59.450	45.455	0.00	0.00	0.00	5.34
1284	1714	1.604604	CCAACAATCAACTCGGTGGT	58.395	50.000	0.00	0.00	0.00	4.16
1357	1787	6.214191	TCAGCTCAAACTATCTTAGTGGAG	57.786	41.667	10.16	10.16	40.84	3.86
1474	1904	2.169978	TGTTCAGATATGCAGCAGCTCT	59.830	45.455	0.00	2.23	42.74	4.09
1494	1924	1.283793	CTTGGGTCGCAACAAGCTG	59.716	57.895	0.00	0.00	42.61	4.24
1509	1939	0.757188	AGCTGAGTGGAGGTATCCCG	60.757	60.000	0.00	0.00	46.04	5.14
1540	1970	2.811317	CGCTCCGCAACCTCTCAC	60.811	66.667	0.00	0.00	0.00	3.51
1543	1973	1.016653	GCTCCGCAACCTCTCACTTC	61.017	60.000	0.00	0.00	0.00	3.01
1550	1980	3.526534	GCAACCTCTCACTTCTACATCC	58.473	50.000	0.00	0.00	0.00	3.51
1593	2023	1.746615	CATCCCGACTGCACTTGGG	60.747	63.158	11.57	11.57	43.36	4.12
1712	2142	6.734137	TGGACTTAACAAACAATCACATGAC	58.266	36.000	0.00	0.00	0.00	3.06
1716	2146	2.582052	ACAAACAATCACATGACCGGT	58.418	42.857	6.92	6.92	0.00	5.28
1771	2208	7.552687	TGTCGCTTCAAAAATTATCACTAGGAT	59.447	33.333	0.00	0.00	40.14	3.24
2071	2651	4.036734	GGCATGGGTATGAACATACTTGTG	59.963	45.833	19.71	16.23	42.42	3.33
2116	2696	5.070685	GGATATACCCTTCCAAACATCCAC	58.929	45.833	0.00	0.00	32.65	4.02
2146	2726	3.733443	ATGCAAGGAAACAACTTCACC	57.267	42.857	0.00	0.00	35.55	4.02
2165	2745	2.175202	CCGGACAAATCCCCATTTCAA	58.825	47.619	0.00	0.00	42.83	2.69
2310	2890	6.072199	AGCAGGAGATTGGTCTTTCTTATT	57.928	37.500	0.00	0.00	33.97	1.40
2686	3266	0.547712	TCCCAGGAGCTTTAGCAGGT	60.548	55.000	4.33	0.00	45.16	4.00
2703	3283	4.290969	GCAGGTTGCAAGAAGTTAGAAAC	58.709	43.478	0.00	0.00	44.26	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.201242	AGTTATTTACCCAAAACCATCACAAT	57.799	30.769	0.00	0.00	0.00	2.71
1	2	7.287927	TGAGTTATTTACCCAAAACCATCACAA	59.712	33.333	0.00	0.00	0.00	3.33
4	5	7.726291	TCTTGAGTTATTTACCCAAAACCATCA	59.274	33.333	0.00	0.00	0.00	3.07
5	6	8.117813	TCTTGAGTTATTTACCCAAAACCATC	57.882	34.615	0.00	0.00	0.00	3.51
6	7	8.485578	TTCTTGAGTTATTTACCCAAAACCAT	57.514	30.769	0.00	0.00	0.00	3.55
118	120	5.905088	TCATTGAGGGTGGGGTAATTAAAA	58.095	37.500	0.00	0.00	0.00	1.52
143	145	9.624697	GTCTTTTCAATTTCTACATGCACATAA	57.375	29.630	0.00	0.00	0.00	1.90
160	162	4.156922	ACGTTCAACACATGGTCTTTTCAA	59.843	37.500	0.00	0.00	0.00	2.69
164	166	6.205784	CAATAACGTTCAACACATGGTCTTT	58.794	36.000	2.82	0.00	0.00	2.52
181	183	4.563976	CACCGGTAACTAAGACCAATAACG	59.436	45.833	6.87	0.00	36.72	3.18
291	294	3.757493	CTCCCTCCTACGAATAAGCGTAT	59.243	47.826	0.00	0.00	44.65	3.06
329	335	7.450014	TGGTGACCAAATTACAATTGTGTATCT	59.550	33.333	21.42	0.00	39.96	1.98
360	366	7.865707	AGTGACATCTCTCAATAACAAAACAC	58.134	34.615	0.00	0.00	0.00	3.32
367	378	5.822278	TCGCTAGTGACATCTCTCAATAAC	58.178	41.667	0.70	0.00	0.00	1.89
372	383	3.759086	AGTTTCGCTAGTGACATCTCTCA	59.241	43.478	5.23	0.00	0.00	3.27
403	414	2.785269	AGCAATAGGGATGAATGGTCCA	59.215	45.455	0.00	0.00	37.49	4.02
497	527	5.936956	GGGATAATGCAAATTGTGTTTGGAA	59.063	36.000	0.00	0.00	33.62	3.53
501	531	5.338300	GGAGGGGATAATGCAAATTGTGTTT	60.338	40.000	0.00	0.00	0.00	2.83
509	539	0.923358	ACGGGAGGGGATAATGCAAA	59.077	50.000	0.00	0.00	0.00	3.68
513	543	1.214424	ACCAAACGGGAGGGGATAATG	59.786	52.381	0.00	0.00	41.15	1.90
520	550	0.251608	AAATCCACCAAACGGGAGGG	60.252	55.000	0.00	0.00	46.63	4.30
524	554	4.461081	TCTCATAAAAATCCACCAAACGGG	59.539	41.667	0.00	0.00	44.81	5.28
719	753	4.026475	GCGGAATCGTAGAGAAAATGTGAG	60.026	45.833	0.00	0.00	43.63	3.51
792	830	0.669318	TTGAAACTGGCTACGCGGAG	60.669	55.000	15.88	15.88	0.00	4.63
793	831	0.249953	TTTGAAACTGGCTACGCGGA	60.250	50.000	12.47	0.00	0.00	5.54
890	928	5.492854	CGTCCATTTGATCTAATGTGAACG	58.507	41.667	22.69	22.32	34.42	3.95
897	935	4.336433	CCACTTGCGTCCATTTGATCTAAT	59.664	41.667	0.00	0.00	0.00	1.73
937	975	0.172578	TCCATGCAAGTACTCCGTCG	59.827	55.000	0.00	0.00	0.00	5.12
944	982	4.566004	TCAGTAGTGTTCCATGCAAGTAC	58.434	43.478	0.00	0.00	0.00	2.73
955	993	9.856488	TGAATAGTAAGTTGATCAGTAGTGTTC	57.144	33.333	14.18	14.18	0.00	3.18
1031	1069	2.162921	GATGTGATTCATCCGGCGCG	62.163	60.000	0.00	0.00	45.05	6.86
1051	1089	3.256558	TGAGACGCTTGAATCTGTGATG	58.743	45.455	0.00	0.00	0.00	3.07
1065	1103	1.079503	GGTGAGGTTGATTGAGACGC	58.920	55.000	0.00	0.00	0.00	5.19
1076	1114	1.007118	GGGAATTGGGATGGTGAGGTT	59.993	52.381	0.00	0.00	0.00	3.50
1089	1127	3.765511	TCTTCCATGAAGCTTGGGAATTG	59.234	43.478	18.87	11.64	39.29	2.32
1091	1129	3.744940	TCTTCCATGAAGCTTGGGAAT	57.255	42.857	18.87	0.77	39.29	3.01
1092	1130	3.157087	GTTCTTCCATGAAGCTTGGGAA	58.843	45.455	17.99	17.99	39.29	3.97
1093	1131	2.795329	GTTCTTCCATGAAGCTTGGGA	58.205	47.619	2.10	5.24	39.29	4.37
1094	1132	1.470098	CGTTCTTCCATGAAGCTTGGG	59.530	52.381	2.10	2.46	39.29	4.12
1097	1135	3.244215	TGAGTCGTTCTTCCATGAAGCTT	60.244	43.478	0.00	0.00	39.29	3.74
1104	1534	1.344438	TGCAGTGAGTCGTTCTTCCAT	59.656	47.619	0.00	0.00	0.00	3.41
1168	1598	3.767230	CAGCGCAACGACACGAGG	61.767	66.667	11.47	0.00	0.00	4.63
1261	1691	1.165270	CCGAGTTGATTGTTGGGGAC	58.835	55.000	0.00	0.00	0.00	4.46
1284	1714	3.007831	GGCCAATTTCAGGTGGAATTTGA	59.992	43.478	0.00	0.00	44.12	2.69
1357	1787	1.277557	AGACAGAGTGCTTGGGATCAC	59.722	52.381	0.00	0.00	0.00	3.06
1474	1904	2.624169	GCTTGTTGCGACCCAAGTA	58.376	52.632	0.45	0.00	40.13	2.24
1509	1939	2.044946	AGCGTCCCCAATCCTTGC	60.045	61.111	0.00	0.00	0.00	4.01
1540	1970	5.403766	CGCTATTTGTAGCAGGATGTAGAAG	59.596	44.000	8.04	0.00	42.95	2.85
1543	1973	4.445718	CACGCTATTTGTAGCAGGATGTAG	59.554	45.833	8.04	0.00	42.95	2.74
1550	1980	1.588404	CCGTCACGCTATTTGTAGCAG	59.412	52.381	8.04	3.77	42.95	4.24
1585	2015	1.303155	AAGAGCTGCTCCCAAGTGC	60.303	57.895	25.09	0.00	0.00	4.40
1593	2023	0.173255	AGCGAAGAGAAGAGCTGCTC	59.827	55.000	21.72	21.72	38.67	4.26
1712	2142	0.807667	CGCAGAAGGAATCTCACCGG	60.808	60.000	0.00	0.00	35.73	5.28
1716	2146	1.002430	AGCAACGCAGAAGGAATCTCA	59.998	47.619	0.00	0.00	35.73	3.27
1771	2208	2.018515	GGACCCGACAAAGTTGTTCAA	58.981	47.619	0.00	0.00	42.43	2.69
2071	2651	4.705023	CCGATGTTATATGGAATTTCCCCC	59.295	45.833	12.90	0.00	35.03	5.40
2116	2696	6.925165	AGTTGTTTCCTTGCATAATCAAAGTG	59.075	34.615	0.00	0.00	0.00	3.16
2146	2726	4.499696	GCTATTGAAATGGGGATTTGTCCG	60.500	45.833	0.00	0.00	0.00	4.79
2165	2745	4.406456	TGAAGATTGGTTGTGTTGGCTAT	58.594	39.130	0.00	0.00	0.00	2.97
2310	2890	3.220940	TGTGTGCAATTGGTCAATGAGA	58.779	40.909	7.72	0.00	0.00	3.27
2686	3266	7.338449	AGGTTTAGTGTTTCTAACTTCTTGCAA	59.662	33.333	0.00	0.00	38.22	4.08
2703	3283	6.619801	AGCTGTTACAAGAAAGGTTTAGTG	57.380	37.500	0.00	0.00	0.00	2.74
2964	3544	3.282885	CCTCCCAAACTTATGAAGGAGC	58.717	50.000	0.00	0.00	39.68	4.70

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.