AutoCloner

Multiple sequence alignment - TraesCS6A01G073100

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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	TraesCS6A01G073100	chr6A	100.000	2336	0	0	1	2336	39879021	39876686	0.000000e+00	4314.0
1	TraesCS6A01G073100	chr6A	79.065	1347	205	54	1010	2332	39670773	39669480	0.000000e+00	854.0
2	TraesCS6A01G073100	chr6A	78.741	1350	207	54	1010	2332	39628984	39627688	0.000000e+00	830.0
3	TraesCS6A01G073100	chr6A	72.670	633	126	37	1020	1636	45066223	45065622	1.440000e-37	167.0
4	TraesCS6A01G073100	chr6D	92.272	2368	105	23	3	2336	36107105	36104782	0.000000e+00	3288.0
5	TraesCS6A01G073100	chr6D	81.315	1338	184	42	1019	2336	35667512	35666221	0.000000e+00	1026.0
6	TraesCS6A01G073100	chr6D	79.452	949	132	38	1401	2332	36084580	36083678	4.270000e-172	614.0
7	TraesCS6A01G073100	chr6D	79.632	653	101	19	1695	2336	35717377	35716746	7.660000e-120	440.0
8	TraesCS6A01G073100	chr6D	86.557	305	32	8	1021	1322	36074173	36073875	6.220000e-86	327.0
9	TraesCS6A01G073100	chr6D	79.167	192	29	7	2148	2336	36073835	36073652	3.150000e-24	122.0
10	TraesCS6A01G073100	chr6D	97.436	39	1	0	2187	2225	36073772	36073734	1.500000e-07	67.6
11	TraesCS6A01G073100	chr6B	81.528	1348	175	49	1020	2336	75514585	75513281	0.000000e+00	1042.0
12	TraesCS6A01G073100	chr6B	80.670	1283	200	29	1016	2287	75510369	75509124	0.000000e+00	952.0
13	TraesCS6A01G073100	chr6B	79.691	1359	185	58	1003	2332	75526328	75525032	0.000000e+00	896.0
14	TraesCS6A01G073100	chr6B	83.614	653	82	17	996	1642	75423508	75422875	7.190000e-165	590.0
15	TraesCS6A01G073100	chr6B	79.876	646	86	24	1013	1655	76153366	76152762	1.280000e-117	433.0
16	TraesCS6A01G073100	chr6B	76.398	644	101	33	1019	1649	75990630	75990025	1.360000e-77	300.0
17	TraesCS6A01G073100	chr6B	72.828	633	134	27	1021	1636	77764764	77764153	5.130000e-42	182.0
18	TraesCS6A01G073100	chr6B	85.088	114	14	3	2184	2295	51560351	51560463	1.900000e-21	113.0
19	TraesCS6A01G073100	chr1D	82.638	599	74	22	1022	1616	37880021	37880593	9.640000e-139	503.0
20	TraesCS6A01G073100	chr1D	81.197	117	20	1	1	115	131629109	131628993	2.470000e-15	93.5
21	TraesCS6A01G073100	chr1A	84.545	330	40	7	988	1313	36785342	36785664	1.350000e-82	316.0
22	TraesCS6A01G073100	chr1A	78.623	276	41	8	1349	1616	36789149	36789414	1.440000e-37	167.0

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	TraesCS6A01G073100	chr6A	39876686	39879021	2335	True	4314.0	4314	100.000	1	2336	1	chr6A.!!$R3	2335
1	TraesCS6A01G073100	chr6A	39669480	39670773	1293	True	854.0	854	79.065	1010	2332	1	chr6A.!!$R2	1322
2	TraesCS6A01G073100	chr6A	39627688	39628984	1296	True	830.0	830	78.741	1010	2332	1	chr6A.!!$R1	1322
3	TraesCS6A01G073100	chr6D	36104782	36107105	2323	True	3288.0	3288	92.272	3	2336	1	chr6D.!!$R4	2333
4	TraesCS6A01G073100	chr6D	35666221	35667512	1291	True	1026.0	1026	81.315	1019	2336	1	chr6D.!!$R1	1317
5	TraesCS6A01G073100	chr6D	36083678	36084580	902	True	614.0	614	79.452	1401	2332	1	chr6D.!!$R3	931
6	TraesCS6A01G073100	chr6D	35716746	35717377	631	True	440.0	440	79.632	1695	2336	1	chr6D.!!$R2	641
7	TraesCS6A01G073100	chr6B	75509124	75514585	5461	True	997.0	1042	81.099	1016	2336	2	chr6B.!!$R6	1320
8	TraesCS6A01G073100	chr6B	75525032	75526328	1296	True	896.0	896	79.691	1003	2332	1	chr6B.!!$R2	1329
9	TraesCS6A01G073100	chr6B	75422875	75423508	633	True	590.0	590	83.614	996	1642	1	chr6B.!!$R1	646
10	TraesCS6A01G073100	chr6B	76152762	76153366	604	True	433.0	433	79.876	1013	1655	1	chr6B.!!$R4	642
11	TraesCS6A01G073100	chr6B	75990025	75990630	605	True	300.0	300	76.398	1019	1649	1	chr6B.!!$R3	630
12	TraesCS6A01G073100	chr1D	37880021	37880593	572	False	503.0	503	82.638	1022	1616	1	chr1D.!!$F1	594
13	TraesCS6A01G073100	chr1A	36785342	36789414	4072	False	241.5	316	81.584	988	1616	2	chr1A.!!$F1	628

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
528	544	0.033601	TGCAACACCCAAGGTCTTGT	60.034	50.0	9.51	0.0	34.76	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1898	8606	1.035923	TGGGCGCTGAATTTTGACAA	58.964	45.0	7.64	0.0	0.0	3.18	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	40	2.546778	GGATGATTTTCCACTCGCGTA	58.453	47.619	5.77	0.00	35.72	4.42
58	60	3.254654	CCACGTGCTATGGACGCG	61.255	66.667	10.91	3.53	46.03	6.01
61	63	2.202557	CGTGCTATGGACGCGACA	60.203	61.111	15.93	12.47	43.44	4.35
136	152	4.794439	TCGTGCCCGCACATCTCG	62.794	66.667	19.14	5.55	46.47	4.04
147	163	3.285215	CATCTCGCCCATGCCTGC	61.285	66.667	0.00	0.00	0.00	4.85
155	171	3.129502	CCATGCCTGCTGTGTCCG	61.130	66.667	0.00	0.00	0.00	4.79
162	178	3.907260	CTGCTGTGTCCGCCATGGT	62.907	63.158	14.67	0.00	39.52	3.55
169	185	2.203408	TCCGCCATGGTTGCACAA	60.203	55.556	14.67	0.00	39.52	3.33
228	244	3.935872	GCGTGCTGCGACACAACA	61.936	61.111	9.30	0.00	44.77	3.33
237	253	0.861837	GCGACACAACACTCCTTGAG	59.138	55.000	0.00	0.00	35.52	3.02
244	260	2.289072	ACAACACTCCTTGAGATCGGTG	60.289	50.000	0.00	0.00	33.32	4.94
258	274	3.188786	GGTGCTCCGATGCGACAC	61.189	66.667	0.00	0.00	35.36	3.67
284	300	1.020861	CGGCTGCTATGCAACACTCA	61.021	55.000	0.00	0.00	38.41	3.41
289	305	3.268330	CTGCTATGCAACACTCATGAGT	58.732	45.455	22.89	22.89	39.34	3.41
320	336	3.857038	ACGACCGTTGGTGGCTGT	61.857	61.111	0.00	0.00	35.25	4.40
333	349	2.353839	GCTGTTGGTGCTGCAACG	60.354	61.111	13.71	0.00	34.30	4.10
365	381	1.236616	CGGTGCAATGCAGGACTTCA	61.237	55.000	8.73	0.00	40.08	3.02
368	384	1.236616	TGCAATGCAGGACTTCACGG	61.237	55.000	2.72	0.00	33.32	4.94
491	507	2.359850	TGTGCCCACGGATCTTGC	60.360	61.111	0.00	0.00	0.00	4.01
492	508	3.134127	GTGCCCACGGATCTTGCC	61.134	66.667	0.00	0.00	0.00	4.52
515	531	3.120385	CGGAGCTGCGATGCAACA	61.120	61.111	24.56	0.00	38.41	3.33
528	544	0.033601	TGCAACACCCAAGGTCTTGT	60.034	50.000	9.51	0.00	34.76	3.16
531	547	2.374184	CAACACCCAAGGTCTTGTTGA	58.626	47.619	15.22	0.00	38.53	3.18
543	559	1.227823	TTGTTGAGTGGCGGAGTGG	60.228	57.895	0.00	0.00	0.00	4.00
567	583	1.847798	TACAAGCTGGGGCGGTGATT	61.848	55.000	0.00	0.00	44.37	2.57
572	588	1.250840	GCTGGGGCGGTGATTTTTCT	61.251	55.000	0.00	0.00	0.00	2.52
574	590	1.743394	CTGGGGCGGTGATTTTTCTAC	59.257	52.381	0.00	0.00	0.00	2.59
673	690	3.904136	GTTGACTCATCCAACAACCAG	57.096	47.619	0.00	0.00	42.40	4.00
676	693	2.441375	TGACTCATCCAACAACCAGGAA	59.559	45.455	0.00	0.00	37.48	3.36
686	703	3.329929	ACAACCAGGAAAGACGTATCC	57.670	47.619	0.00	6.44	35.88	2.59
700	717	1.849097	GTATCCGACGGTTCATGACC	58.151	55.000	14.79	0.00	45.55	4.02
702	719	2.292794	ATCCGACGGTTCATGACCCG	62.293	60.000	27.94	27.94	46.35	5.28
708	725	1.224592	GGTTCATGACCCGGCTGAT	59.775	57.895	0.00	0.00	43.06	2.90
709	726	0.394352	GGTTCATGACCCGGCTGATT	60.394	55.000	0.00	0.00	43.06	2.57
710	727	1.463674	GTTCATGACCCGGCTGATTT	58.536	50.000	0.00	0.00	0.00	2.17
711	728	1.401905	GTTCATGACCCGGCTGATTTC	59.598	52.381	0.00	0.00	0.00	2.17
713	730	1.281867	TCATGACCCGGCTGATTTCTT	59.718	47.619	0.00	0.00	0.00	2.52
736	753	2.589540	AATCGGCCGGCTGATTCA	59.410	55.556	44.10	24.90	45.79	2.57
894	914	1.063867	TCTCTCCCGAAGTAGGAAGGG	60.064	57.143	0.00	0.00	45.10	3.95
940	960	2.740055	CAGTGGCAGCCGTGACTC	60.740	66.667	7.03	0.00	30.05	3.36
941	961	2.919856	AGTGGCAGCCGTGACTCT	60.920	61.111	7.03	0.00	30.18	3.24
946	966	4.291047	CAGCCGTGACTCTGCAAT	57.709	55.556	0.00	0.00	0.00	3.56
947	967	2.084844	CAGCCGTGACTCTGCAATC	58.915	57.895	0.00	0.00	0.00	2.67
950	970	0.390340	GCCGTGACTCTGCAATCTCA	60.390	55.000	0.00	0.00	0.00	3.27
953	973	1.723542	CGTGACTCTGCAATCTCACAC	59.276	52.381	14.42	7.75	33.94	3.82
961	981	3.450096	TCTGCAATCTCACACTCTGCTAT	59.550	43.478	0.00	0.00	34.10	2.97
1080	4298	0.961358	AGGACGACAACCTCCTCTCG	60.961	60.000	0.00	0.00	30.37	4.04
1334	4565	2.880879	CGACGACCGCATCTGGTG	60.881	66.667	0.00	0.00	44.01	4.17
1335	4566	2.571757	GACGACCGCATCTGGTGA	59.428	61.111	0.00	0.00	44.01	4.02
1465	8167	2.010497	GAGTTCGATTTGGAGAAGGCC	58.990	52.381	0.00	0.00	0.00	5.19
1466	8168	1.095600	GTTCGATTTGGAGAAGGCCC	58.904	55.000	0.00	0.00	0.00	5.80
1467	8169	0.991920	TTCGATTTGGAGAAGGCCCT	59.008	50.000	0.00	0.00	0.00	5.19
1468	8170	0.253044	TCGATTTGGAGAAGGCCCTG	59.747	55.000	0.00	0.00	0.00	4.45
1469	8171	0.749454	CGATTTGGAGAAGGCCCTGG	60.749	60.000	0.00	0.00	0.00	4.45
1470	8172	0.332972	GATTTGGAGAAGGCCCTGGT	59.667	55.000	0.00	0.00	0.00	4.00
1471	8173	0.332972	ATTTGGAGAAGGCCCTGGTC	59.667	55.000	0.00	0.00	0.00	4.02
1472	8174	1.065410	TTTGGAGAAGGCCCTGGTCA	61.065	55.000	0.00	0.00	0.00	4.02
1473	8175	1.492133	TTGGAGAAGGCCCTGGTCAG	61.492	60.000	0.00	0.00	0.00	3.51
1670	8378	7.120923	TCTAGTTCTACTATGGGCGAATTTT	57.879	36.000	0.00	0.00	29.08	1.82
1677	8385	1.864669	ATGGGCGAATTTTCCACCAT	58.135	45.000	7.31	7.31	36.17	3.55
1691	8399	5.559427	TTCCACCATGATTACAATGTTCG	57.441	39.130	0.00	0.00	0.00	3.95
1825	8533	0.821517	CTGTGATACCGGTGCCAGTA	59.178	55.000	19.93	0.00	0.00	2.74
1852	8560	4.623932	TGCCAATAATAGTCTAGCCCAG	57.376	45.455	0.00	0.00	0.00	4.45
1898	8606	2.239907	GGTGGCCTTGGTATTCTCTCTT	59.760	50.000	3.32	0.00	0.00	2.85
1986	8694	6.409704	TGCTGCAAAGAACTATCAATCTAGT	58.590	36.000	0.00	0.00	33.34	2.57
2112	8822	0.247460	CACGATCCAGCTTGAGTCCA	59.753	55.000	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	6.751888	GGAAAATCATCCGATTGAAAATCGTT	59.248	34.615	18.08	6.71	41.12	3.85
7	8	7.260603	AGTGGAAAATCATCCGATTGAAAATC	58.739	34.615	0.00	0.00	41.12	2.17
10	12	5.163764	CGAGTGGAAAATCATCCGATTGAAA	60.164	40.000	0.00	0.00	41.12	2.69
38	40	1.296056	GCGTCCATAGCACGTGGTTT	61.296	55.000	26.96	15.72	39.54	3.27
58	60	2.668550	GCCCCACCAAGACGTGTC	60.669	66.667	0.00	0.00	31.47	3.67
78	80	0.250510	GATAAGGCTAGCAGGTGGGC	60.251	60.000	18.24	0.73	0.00	5.36
126	142	3.945434	GCATGGGCGAGATGTGCG	61.945	66.667	0.00	0.00	0.00	5.34
136	152	3.446570	GACACAGCAGGCATGGGC	61.447	66.667	0.00	0.00	40.13	5.36
147	163	2.981560	GCAACCATGGCGGACACAG	61.982	63.158	13.04	0.00	38.63	3.66
155	171	1.080298	GAGCTTGTGCAACCATGGC	60.080	57.895	13.04	0.00	42.74	4.40
162	178	0.764890	AGTAGGTGGAGCTTGTGCAA	59.235	50.000	0.00	0.00	42.74	4.08
228	244	0.820871	GAGCACCGATCTCAAGGAGT	59.179	55.000	0.00	0.00	0.00	3.85
284	300	0.466007	TGTGGCAGTGCAACACTCAT	60.466	50.000	21.71	0.00	43.43	2.90
289	305	2.124942	TCGTGTGGCAGTGCAACA	60.125	55.556	21.71	21.71	40.51	3.33
348	364	0.110056	CGTGAAGTCCTGCATTGCAC	60.110	55.000	7.38	0.00	33.79	4.57
352	368	0.108585	ACACCGTGAAGTCCTGCATT	59.891	50.000	5.28	0.00	0.00	3.56
359	375	2.244651	AGCGCAACACCGTGAAGTC	61.245	57.895	11.47	0.00	0.00	3.01
368	384	3.788766	CCTACGGCAGCGCAACAC	61.789	66.667	11.47	0.00	0.00	3.32
451	467	2.203552	TTGGGGGTTGCATCGCAA	60.204	55.556	13.17	11.15	46.80	4.85
476	492	4.776322	CGGCAAGATCCGTGGGCA	62.776	66.667	0.00	0.00	44.18	5.36
499	515	2.482374	GTGTTGCATCGCAGCTCC	59.518	61.111	3.45	0.00	40.35	4.70
515	531	1.133792	CCACTCAACAAGACCTTGGGT	60.134	52.381	13.58	4.93	44.45	4.51
528	544	3.555324	TGCCACTCCGCCACTCAA	61.555	61.111	0.00	0.00	0.00	3.02
543	559	2.751837	GCCCCAGCTTGTAGGTGC	60.752	66.667	0.51	0.00	42.05	5.01
567	583	1.342555	CATGCGTCGTCGGTAGAAAA	58.657	50.000	3.90	0.00	37.56	2.29
572	588	1.153726	AATGCATGCGTCGTCGGTA	60.154	52.632	13.95	0.00	37.56	4.02
574	590	2.021793	CAATGCATGCGTCGTCGG	59.978	61.111	13.95	0.00	37.56	4.79
617	633	4.620332	CGATCTCCTCTTGCTTTGTTCTCT	60.620	45.833	0.00	0.00	0.00	3.10
705	722	3.126858	CGGCCGATTTTCTGAAGAAATCA	59.873	43.478	24.07	0.00	42.83	2.57
708	725	1.810151	CCGGCCGATTTTCTGAAGAAA	59.190	47.619	30.73	1.31	41.77	2.52
709	726	1.448985	CCGGCCGATTTTCTGAAGAA	58.551	50.000	30.73	0.00	0.00	2.52
710	727	1.024579	GCCGGCCGATTTTCTGAAGA	61.025	55.000	30.73	0.00	0.00	2.87
711	728	1.026718	AGCCGGCCGATTTTCTGAAG	61.027	55.000	30.73	6.52	0.00	3.02
713	730	1.745115	CAGCCGGCCGATTTTCTGA	60.745	57.895	30.73	0.00	0.00	3.27
716	733	0.029433	GAATCAGCCGGCCGATTTTC	59.971	55.000	32.76	21.38	32.05	2.29
723	740	1.227943	TGCTATGAATCAGCCGGCC	60.228	57.895	26.15	7.94	38.29	6.13
757	774	7.106439	TCTTTGAAGCTAACAAAAATGGTCA	57.894	32.000	16.10	0.00	36.91	4.02
762	779	9.435688	AACTGTTTCTTTGAAGCTAACAAAAAT	57.564	25.926	16.10	0.00	36.91	1.82
830	850	5.583061	CCCTCAAATACAAACAGTATACGCA	59.417	40.000	0.00	0.00	42.56	5.24
832	852	7.039882	ACTCCCTCAAATACAAACAGTATACG	58.960	38.462	0.00	0.00	42.56	3.06
940	960	2.096220	AGCAGAGTGTGAGATTGCAG	57.904	50.000	0.00	0.00	37.24	4.41
941	961	3.431346	GGATAGCAGAGTGTGAGATTGCA	60.431	47.826	0.00	0.00	37.24	4.08
944	964	4.099266	GTGAGGATAGCAGAGTGTGAGATT	59.901	45.833	0.00	0.00	0.00	2.40
946	966	3.020274	GTGAGGATAGCAGAGTGTGAGA	58.980	50.000	0.00	0.00	0.00	3.27
947	967	2.757314	TGTGAGGATAGCAGAGTGTGAG	59.243	50.000	0.00	0.00	0.00	3.51
950	970	2.360483	CGATGTGAGGATAGCAGAGTGT	59.640	50.000	0.00	0.00	0.00	3.55
953	973	2.288091	CCACGATGTGAGGATAGCAGAG	60.288	54.545	0.00	0.00	35.23	3.35
961	981	1.003839	GCAACCCACGATGTGAGGA	60.004	57.895	10.21	0.00	35.23	3.71
1334	4565	2.595754	GCGGGATCCAAGGGCATC	60.596	66.667	15.23	0.00	0.00	3.91
1335	4566	4.209866	GGCGGGATCCAAGGGCAT	62.210	66.667	15.23	0.00	0.00	4.40
1337	4568	4.209866	ATGGCGGGATCCAAGGGC	62.210	66.667	15.23	14.51	39.96	5.19
1465	8167	4.421515	CTGGCCCAGCTGACCAGG	62.422	72.222	32.48	20.60	45.97	4.45
1512	8214	1.152756	ACCACCTGGAAGTGTTGGC	60.153	57.895	0.00	0.00	38.94	4.52
1670	8378	4.584874	ACGAACATTGTAATCATGGTGGA	58.415	39.130	0.00	0.00	0.00	4.02
1677	8385	9.083080	CACTGATAGTTACGAACATTGTAATCA	57.917	33.333	0.00	0.00	34.59	2.57
1825	8533	7.182749	TGGGCTAGACTATTATTGGCAATATCT	59.817	37.037	19.88	19.63	0.00	1.98
1852	8560	1.376609	CTGCCCGCATAACCTGGAAC	61.377	60.000	0.00	0.00	0.00	3.62
1898	8606	1.035923	TGGGCGCTGAATTTTGACAA	58.964	45.000	7.64	0.00	0.00	3.18
1986	8694	6.761312	TCTGAATCCGTGGAAAGTAGTTTAA	58.239	36.000	0.00	0.00	0.00	1.52
2035	8743	7.859325	TTATTGTACTCAGCAAACCCTAATC	57.141	36.000	0.00	0.00	0.00	1.75
2112	8822	5.596836	TTGGAAACTTTCTTGAACTGCAT	57.403	34.783	1.57	0.00	0.00	3.96

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.