AutoCloner

Multiple sequence alignment - TraesCS7A01G478400

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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	TraesCS7A01G478400	chr7A	100.000	2864	0	0	1	2864	671428317	671425454	0.000000e+00	5289
1	TraesCS7A01G478400	chr7A	81.930	1223	181	23	942	2139	736429553	736428346	0.000000e+00	998
2	TraesCS7A01G478400	chr7A	81.390	1209	203	7	952	2139	735960547	735961754	0.000000e+00	966
3	TraesCS7A01G478400	chr7A	82.143	1092	175	8	998	2070	736060460	736059370	0.000000e+00	918
4	TraesCS7A01G478400	chr7B	93.608	2910	126	25	1	2864	645404223	645401328	0.000000e+00	4289
5	TraesCS7A01G478400	chr7B	82.102	1218	185	9	952	2138	745230107	745231322	0.000000e+00	1011
6	TraesCS7A01G478400	chr7B	81.071	1289	212	21	999	2262	743709479	743710760	0.000000e+00	1000
7	TraesCS7A01G478400	chr7B	82.489	1165	174	9	1005	2139	743999257	743998093	0.000000e+00	994
8	TraesCS7A01G478400	chr7B	80.993	1289	214	20	999	2262	744269346	744270628	0.000000e+00	994
9	TraesCS7A01G478400	chr7B	82.119	1180	179	16	991	2139	744239552	744240730	0.000000e+00	981
10	TraesCS7A01G478400	chr7B	81.895	1182	192	15	998	2163	744330826	744329651	0.000000e+00	977
11	TraesCS7A01G478400	chr7B	93.665	221	14	0	1	221	645579195	645578975	5.910000e-87	331
12	TraesCS7A01G478400	chr7B	81.481	189	24	10	2409	2590	743997822	743997638	8.270000e-31	145
13	TraesCS7A01G478400	chr7D	93.964	2187	114	14	1	2172	579764859	579762676	0.000000e+00	3291
14	TraesCS7A01G478400	chr7D	82.542	1180	179	15	942	2096	632018330	632019507	0.000000e+00	1013
15	TraesCS7A01G478400	chr7D	82.011	1134	163	27	980	2078	555047302	555048429	0.000000e+00	926
16	TraesCS7A01G478400	chr7D	91.289	574	42	7	2164	2732	579762516	579761946	0.000000e+00	776
17	TraesCS7A01G478400	chr1B	82.311	1125	173	13	991	2093	577928805	577927685	0.000000e+00	952

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	TraesCS7A01G478400	chr7A	671425454	671428317	2863	True	5289.0	5289	100.0000	1	2864	1	chr7A.!!$R1	2863
1	TraesCS7A01G478400	chr7A	736428346	736429553	1207	True	998.0	998	81.9300	942	2139	1	chr7A.!!$R3	1197
2	TraesCS7A01G478400	chr7A	735960547	735961754	1207	False	966.0	966	81.3900	952	2139	1	chr7A.!!$F1	1187
3	TraesCS7A01G478400	chr7A	736059370	736060460	1090	True	918.0	918	82.1430	998	2070	1	chr7A.!!$R2	1072
4	TraesCS7A01G478400	chr7B	645401328	645404223	2895	True	4289.0	4289	93.6080	1	2864	1	chr7B.!!$R1	2863
5	TraesCS7A01G478400	chr7B	745230107	745231322	1215	False	1011.0	1011	82.1020	952	2138	1	chr7B.!!$F4	1186
6	TraesCS7A01G478400	chr7B	743709479	743710760	1281	False	1000.0	1000	81.0710	999	2262	1	chr7B.!!$F1	1263
7	TraesCS7A01G478400	chr7B	744269346	744270628	1282	False	994.0	994	80.9930	999	2262	1	chr7B.!!$F3	1263
8	TraesCS7A01G478400	chr7B	744239552	744240730	1178	False	981.0	981	82.1190	991	2139	1	chr7B.!!$F2	1148
9	TraesCS7A01G478400	chr7B	744329651	744330826	1175	True	977.0	977	81.8950	998	2163	1	chr7B.!!$R3	1165
10	TraesCS7A01G478400	chr7B	743997638	743999257	1619	True	569.5	994	81.9850	1005	2590	2	chr7B.!!$R4	1585
11	TraesCS7A01G478400	chr7D	579761946	579764859	2913	True	2033.5	3291	92.6265	1	2732	2	chr7D.!!$R1	2731
12	TraesCS7A01G478400	chr7D	632018330	632019507	1177	False	1013.0	1013	82.5420	942	2096	1	chr7D.!!$F2	1154
13	TraesCS7A01G478400	chr7D	555047302	555048429	1127	False	926.0	926	82.0110	980	2078	1	chr7D.!!$F1	1098
14	TraesCS7A01G478400	chr1B	577927685	577928805	1120	True	952.0	952	82.3110	991	2093	1	chr1B.!!$R1	1102

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
913	936	0.758734	GACATCCATCCATCCGTCCA	59.241	55.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2774	3142	0.111878	CACACGCACAAAGACGTACG	60.112	55.0	15.01	15.01	41.32	3.67	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
146	148	3.054878	ACGACCGTGTAAAACATGAGTC	58.945	45.455	0.00	6.01	37.29	3.36
147	149	3.243636	ACGACCGTGTAAAACATGAGTCT	60.244	43.478	0.00	0.00	37.29	3.24
328	330	1.280998	ACCCCCTGTATTCGACCTTTG	59.719	52.381	0.00	0.00	0.00	2.77
365	367	9.350951	GGGGCTTAGTAAAATACATGTAATCTT	57.649	33.333	10.14	6.22	0.00	2.40
393	395	3.651423	ACCTGTAAAGTTCCACTAAGCCT	59.349	43.478	0.00	0.00	0.00	4.58
493	495	1.760613	ACCTTTCGGCGGATGAATCTA	59.239	47.619	7.21	0.00	0.00	1.98
702	706	2.909006	AGGACAAGATGTGATGTGGTCT	59.091	45.455	0.00	0.00	0.00	3.85
703	707	4.096681	AGGACAAGATGTGATGTGGTCTA	58.903	43.478	0.00	0.00	0.00	2.59
704	708	4.532126	AGGACAAGATGTGATGTGGTCTAA	59.468	41.667	0.00	0.00	0.00	2.10
705	709	4.631813	GGACAAGATGTGATGTGGTCTAAC	59.368	45.833	0.00	0.00	0.00	2.34
706	710	5.482908	GACAAGATGTGATGTGGTCTAACT	58.517	41.667	0.00	0.00	0.00	2.24
709	713	5.269505	AGATGTGATGTGGTCTAACTAGC	57.730	43.478	0.00	0.00	0.00	3.42
711	715	4.882842	TGTGATGTGGTCTAACTAGCAA	57.117	40.909	0.00	0.00	0.00	3.91
712	716	4.566004	TGTGATGTGGTCTAACTAGCAAC	58.434	43.478	0.00	0.00	0.00	4.17
713	717	3.933332	GTGATGTGGTCTAACTAGCAACC	59.067	47.826	0.00	0.00	0.00	3.77
715	719	3.678056	TGTGGTCTAACTAGCAACCTG	57.322	47.619	0.00	0.00	32.82	4.00
716	720	3.236047	TGTGGTCTAACTAGCAACCTGA	58.764	45.455	0.00	0.00	32.82	3.86
717	721	3.006537	TGTGGTCTAACTAGCAACCTGAC	59.993	47.826	0.00	0.00	32.82	3.51
718	722	3.006537	GTGGTCTAACTAGCAACCTGACA	59.993	47.826	0.00	0.00	32.82	3.58
720	724	3.995048	GGTCTAACTAGCAACCTGACAAC	59.005	47.826	0.00	0.00	0.00	3.32
721	725	4.502604	GGTCTAACTAGCAACCTGACAACA	60.503	45.833	0.00	0.00	0.00	3.33
722	726	4.686554	GTCTAACTAGCAACCTGACAACAG	59.313	45.833	0.00	0.00	43.12	3.16
723	727	1.884235	ACTAGCAACCTGACAACAGC	58.116	50.000	0.00	0.00	42.25	4.40
724	728	1.160137	CTAGCAACCTGACAACAGCC	58.840	55.000	0.00	0.00	42.25	4.85
726	730	1.827789	GCAACCTGACAACAGCCCA	60.828	57.895	0.00	0.00	42.25	5.36
767	780	5.990668	AGACAATACTATGACAAGAACCCC	58.009	41.667	0.00	0.00	0.00	4.95
784	797	4.630644	ACCCCAATGCTATGATAGAGTG	57.369	45.455	3.13	0.00	0.00	3.51
788	801	5.471456	CCCCAATGCTATGATAGAGTGAAAC	59.529	44.000	3.13	0.00	0.00	2.78
812	825	9.569122	AACAAATAGTTAGGTAGCTTTCTTTCA	57.431	29.630	0.00	0.00	39.09	2.69
848	864	1.713078	AGCCCCTTCCTCTTCAACATT	59.287	47.619	0.00	0.00	0.00	2.71
884	907	1.067213	GTCCAGTCTCCAGAGCTGAAC	60.067	57.143	15.98	6.67	35.83	3.18
909	932	3.923354	GAGGACATCCATCCATCCG	57.077	57.895	0.00	0.00	41.73	4.18
913	936	0.758734	GACATCCATCCATCCGTCCA	59.241	55.000	0.00	0.00	0.00	4.02
1286	1325	1.120530	GGACCATCCACCGTAGATGT	58.879	55.000	6.26	0.00	36.28	3.06
1352	1391	1.825341	CTCATGAGATCGGCACCCA	59.175	57.895	18.34	0.00	0.00	4.51
1451	1529	2.597455	TGAGGATCATAGCCGTCATGA	58.403	47.619	0.00	0.00	42.56	3.07
1455	1533	5.078411	AGGATCATAGCCGTCATGATAAC	57.922	43.478	0.00	0.00	41.96	1.89
1686	1773	9.059260	GGTGAGTTCAGTAAAAAGTTATGGTTA	57.941	33.333	0.00	0.00	0.00	2.85
1818	1905	0.038744	AGGACACCTTGATTGGCCAG	59.961	55.000	5.11	0.00	45.86	4.85
1856	1943	1.770658	GGATGATGTCTGGGACCATGA	59.229	52.381	0.00	0.00	0.00	3.07
1863	1950	1.065199	GTCTGGGACCATGAAGCATGA	60.065	52.381	8.87	0.00	43.81	3.07
2623	2988	4.105577	TGTTGGGGCTACTACCTATTGAA	58.894	43.478	0.00	0.00	0.00	2.69
2661	3026	5.182380	TGGGAGAAAATAATTTCACGTGACC	59.818	40.000	19.90	11.69	46.03	4.02
2741	3109	1.326328	ATAGCAGCGATGAGAGAGCA	58.674	50.000	4.02	0.00	0.00	4.26
2766	3134	9.406828	CAGTATAAAGTGTATGTACGCATGTAT	57.593	33.333	6.51	3.83	39.08	2.29
2770	3138	7.459394	AAAGTGTATGTACGCATGTATGTAC	57.541	36.000	14.31	14.31	41.00	2.90
2771	3139	5.526115	AGTGTATGTACGCATGTATGTACC	58.474	41.667	16.88	7.31	40.12	3.34
2772	3140	5.301045	AGTGTATGTACGCATGTATGTACCT	59.699	40.000	16.88	12.16	40.12	3.08
2773	3141	6.487668	AGTGTATGTACGCATGTATGTACCTA	59.512	38.462	16.88	11.46	40.12	3.08
2774	3142	6.580041	GTGTATGTACGCATGTATGTACCTAC	59.420	42.308	20.28	20.28	40.27	3.18
2775	3143	4.213596	TGTACGCATGTATGTACCTACG	57.786	45.455	16.88	2.59	40.12	3.51
2776	3144	3.627123	TGTACGCATGTATGTACCTACGT	59.373	43.478	16.88	0.00	40.12	3.57
2777	3145	4.813697	TGTACGCATGTATGTACCTACGTA	59.186	41.667	16.88	0.00	40.12	3.57
2778	3146	4.214980	ACGCATGTATGTACCTACGTAC	57.785	45.455	3.10	7.60	44.80	3.67
2779	3147	3.220773	CGCATGTATGTACCTACGTACG	58.779	50.000	15.01	15.01	46.71	3.67
2780	3148	3.303329	CGCATGTATGTACCTACGTACGT	60.303	47.826	25.98	25.98	46.71	3.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	4.451096	ACACGCTACATAAACAGAGTTTGG	59.549	41.667	5.45	1.05	0.00	3.28
56	57	9.599322	GAACTATAATTACAAAATCATGAGGCG	57.401	33.333	0.09	0.00	0.00	5.52
146	148	9.864034	CATAAGCCGACAAATAAACATAACTAG	57.136	33.333	0.00	0.00	0.00	2.57
147	149	9.386010	ACATAAGCCGACAAATAAACATAACTA	57.614	29.630	0.00	0.00	0.00	2.24
328	330	0.255033	CTAAGCCCCCACCCTACAAC	59.745	60.000	0.00	0.00	0.00	3.32
493	495	6.406177	GCATGATGGATGGTGAAGTATTTGTT	60.406	38.462	0.00	0.00	31.99	2.83
592	594	1.827789	TGGGCTGTTGTCAGGTTGC	60.828	57.895	0.00	0.00	41.57	4.17
646	650	1.535028	CGCAATAACAGTGGCAGACAA	59.465	47.619	0.00	0.00	0.00	3.18
702	706	3.399330	GCTGTTGTCAGGTTGCTAGTTA	58.601	45.455	0.00	0.00	41.57	2.24
703	707	2.222027	GCTGTTGTCAGGTTGCTAGTT	58.778	47.619	0.00	0.00	41.57	2.24
704	708	1.543429	GGCTGTTGTCAGGTTGCTAGT	60.543	52.381	0.00	0.00	41.57	2.57
705	709	1.160137	GGCTGTTGTCAGGTTGCTAG	58.840	55.000	0.00	0.00	41.57	3.42
706	710	0.250727	GGGCTGTTGTCAGGTTGCTA	60.251	55.000	0.00	0.00	41.57	3.49
709	713	0.466189	AGTGGGCTGTTGTCAGGTTG	60.466	55.000	0.00	0.00	41.57	3.77
711	715	1.149174	CAGTGGGCTGTTGTCAGGT	59.851	57.895	0.00	0.00	41.57	4.00
712	716	1.601759	CCAGTGGGCTGTTGTCAGG	60.602	63.158	0.00	0.00	41.02	3.86
713	717	0.466189	AACCAGTGGGCTGTTGTCAG	60.466	55.000	15.21	0.00	41.02	3.51
715	719	1.975660	TAAACCAGTGGGCTGTTGTC	58.024	50.000	15.21	0.00	41.02	3.18
716	720	2.675658	ATAAACCAGTGGGCTGTTGT	57.324	45.000	15.21	0.00	41.02	3.32
717	721	5.659440	ATAAATAAACCAGTGGGCTGTTG	57.341	39.130	15.21	0.00	41.02	3.33
718	722	6.680148	AAATAAATAAACCAGTGGGCTGTT	57.320	33.333	15.21	4.59	41.02	3.16
720	724	8.527810	TCTTTAAATAAATAAACCAGTGGGCTG	58.472	33.333	15.21	0.00	42.22	4.85
721	725	8.528643	GTCTTTAAATAAATAAACCAGTGGGCT	58.471	33.333	15.21	1.96	37.90	5.19
722	726	8.308207	TGTCTTTAAATAAATAAACCAGTGGGC	58.692	33.333	15.21	0.00	37.90	5.36
751	763	3.010584	AGCATTGGGGTTCTTGTCATAGT	59.989	43.478	0.00	0.00	0.00	2.12
758	770	5.624159	TCTATCATAGCATTGGGGTTCTTG	58.376	41.667	0.00	0.00	0.00	3.02
759	771	5.370880	ACTCTATCATAGCATTGGGGTTCTT	59.629	40.000	0.00	0.00	0.00	2.52
812	825	4.870021	GGGGCTCCCATTCTATATGAAT	57.130	45.455	7.34	0.00	44.65	2.57
848	864	3.774766	ACTGGACAGTATGCACCTCAATA	59.225	43.478	2.58	0.00	42.53	1.90
884	907	0.033228	GATGGATGTCCTCCTGCTCG	59.967	60.000	0.09	0.00	45.21	5.03
909	932	3.506067	CCTCACCAACATACCTTTTGGAC	59.494	47.826	7.35	0.00	44.51	4.02
913	936	3.157087	CTGCCTCACCAACATACCTTTT	58.843	45.455	0.00	0.00	0.00	2.27
1352	1391	3.390639	CCTCTGGTTGAGAGCCTTGATAT	59.609	47.826	0.00	0.00	46.36	1.63
1451	1529	1.038280	CGTCTCCCGGCTAAGGTTAT	58.962	55.000	0.00	0.00	0.00	1.89
1455	1533	0.882474	CTATCGTCTCCCGGCTAAGG	59.118	60.000	0.00	0.00	37.11	2.69
1686	1773	4.402155	TCACTGAAGTTTTGGTTGATGCTT	59.598	37.500	0.00	0.00	0.00	3.91
1863	1950	5.184892	AGGGTATTTTGAGCACATTCTCT	57.815	39.130	0.00	0.00	34.29	3.10
2154	2269	7.060421	CCTTCCAAGAGGTAATATTAAGCCAA	58.940	38.462	0.00	0.00	35.89	4.52
2237	2519	4.941263	TGATGTATTTCCTTGTTTAGCGCT	59.059	37.500	17.26	17.26	0.00	5.92
2290	2572	5.412640	TGAACGTGTGTAATGTGGGTATAG	58.587	41.667	0.00	0.00	0.00	1.31
2488	2840	6.430616	CCGTTAGGGGTTAACTGAATTGTTAA	59.569	38.462	5.42	0.00	39.62	2.01
2623	2988	4.993705	TTCTCCCACTCACCTAAAATGT	57.006	40.909	0.00	0.00	0.00	2.71
2636	3001	6.084277	GTCACGTGAAATTATTTTCTCCCAC	58.916	40.000	21.95	0.00	41.54	4.61
2706	3074	6.310467	TCGCTGCTATAAAAACTTGTACTCAG	59.690	38.462	0.00	0.00	0.00	3.35
2720	3088	2.887152	TGCTCTCTCATCGCTGCTATAA	59.113	45.455	0.00	0.00	0.00	0.98
2741	3109	9.406828	CATACATGCGTACATACACTTTATACT	57.593	33.333	0.00	0.00	33.67	2.12
2770	3138	0.979811	CGCACAAAGACGTACGTAGG	59.020	55.000	22.87	13.47	0.00	3.18
2771	3139	1.381100	CACGCACAAAGACGTACGTAG	59.619	52.381	22.87	13.80	41.32	3.51
2772	3140	1.268488	ACACGCACAAAGACGTACGTA	60.268	47.619	22.87	0.00	41.32	3.57
2773	3141	0.526096	ACACGCACAAAGACGTACGT	60.526	50.000	23.04	23.04	41.32	3.57
2774	3142	0.111878	CACACGCACAAAGACGTACG	60.112	55.000	15.01	15.01	41.32	3.67
2775	3143	0.925466	ACACACGCACAAAGACGTAC	59.075	50.000	0.00	0.00	41.32	3.67
2776	3144	2.387185	CTACACACGCACAAAGACGTA	58.613	47.619	0.00	0.00	41.32	3.57
2777	3145	1.205657	CTACACACGCACAAAGACGT	58.794	50.000	0.00	0.00	44.75	4.34
2778	3146	0.506932	CCTACACACGCACAAAGACG	59.493	55.000	0.00	0.00	0.00	4.18
2779	3147	1.792949	CTCCTACACACGCACAAAGAC	59.207	52.381	0.00	0.00	0.00	3.01
2780	3148	1.872237	GCTCCTACACACGCACAAAGA	60.872	52.381	0.00	0.00	0.00	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.