AutoCloner

Multiple sequence alignment - TraesCS7B01G419400

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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	TraesCS7B01G419400	chr7B	100.000	3085	0	0	1	3085	688162090	688165174	0.000000e+00	5698.0
1	TraesCS7B01G419400	chr7B	91.534	1441	86	20	717	2139	686966720	686965298	0.000000e+00	1953.0
2	TraesCS7B01G419400	chr7B	91.688	1179	70	17	966	2118	686850026	686851202	0.000000e+00	1609.0
3	TraesCS7B01G419400	chr7B	85.500	1131	121	22	968	2074	686888458	686887347	0.000000e+00	1140.0
4	TraesCS7B01G419400	chr7B	85.020	494	63	7	2410	2898	686965079	686964592	2.760000e-135	492.0
5	TraesCS7B01G419400	chr7B	77.285	722	121	31	28	717	686967504	686966794	4.830000e-103	385.0
6	TraesCS7B01G419400	chr7B	91.176	136	11	1	583	717	686889011	686888876	1.890000e-42	183.0
7	TraesCS7B01G419400	chr7B	88.806	134	7	5	723	848	686849694	686849827	1.150000e-34	158.0
8	TraesCS7B01G419400	chr7B	82.184	174	13	7	542	709	686849444	686849605	1.930000e-27	134.0
9	TraesCS7B01G419400	chr7A	89.669	1481	92	26	717	2139	696723789	696722312	0.000000e+00	1831.0
10	TraesCS7B01G419400	chr7A	92.229	1171	72	9	962	2118	696552635	696553800	0.000000e+00	1640.0
11	TraesCS7B01G419400	chr7A	86.192	1195	115	30	907	2074	696623565	696622394	0.000000e+00	1247.0
12	TraesCS7B01G419400	chr7A	91.401	721	55	6	1	717	696724580	696723863	0.000000e+00	981.0
13	TraesCS7B01G419400	chr7A	87.549	257	32	0	2410	2666	696722124	696721868	6.470000e-77	298.0
14	TraesCS7B01G419400	chr7A	92.701	137	9	1	581	717	696624026	696623891	2.430000e-46	196.0
15	TraesCS7B01G419400	chr7A	85.965	171	17	4	542	709	696552113	696552279	3.160000e-40	176.0
16	TraesCS7B01G419400	chr7A	91.589	107	5	2	723	825	696552368	696552474	8.920000e-31	145.0
17	TraesCS7B01G419400	chr7A	96.774	62	2	0	908	969	696552545	696552606	1.510000e-18	104.0
18	TraesCS7B01G419400	chr7D	93.723	1147	72	0	966	2112	603847872	603849018	0.000000e+00	1720.0
19	TraesCS7B01G419400	chr7D	89.608	1328	98	21	840	2136	604530907	604532225	0.000000e+00	1652.0
20	TraesCS7B01G419400	chr7D	90.571	1262	85	11	962	2198	604475310	604476562	0.000000e+00	1640.0
21	TraesCS7B01G419400	chr7D	85.380	1197	117	27	908	2074	603982471	603983639	0.000000e+00	1188.0
22	TraesCS7B01G419400	chr7D	94.231	676	36	2	2410	3085	604476856	604477528	0.000000e+00	1029.0
23	TraesCS7B01G419400	chr7D	89.833	718	59	11	1	713	604471696	604472404	0.000000e+00	909.0
24	TraesCS7B01G419400	chr7D	87.860	486	54	5	2414	2895	604532361	604532845	1.610000e-157	566.0
25	TraesCS7B01G419400	chr7D	94.203	207	11	1	2201	2407	604476608	604476813	6.420000e-82	315.0
26	TraesCS7B01G419400	chr7D	93.617	188	10	1	2900	3085	603853471	603853658	2.340000e-71	279.0
27	TraesCS7B01G419400	chr7D	82.900	269	13	5	717	967	604475019	604475272	8.670000e-51	211.0
28	TraesCS7B01G419400	chr7D	92.969	128	9	0	581	708	603982010	603982137	1.460000e-43	187.0
29	TraesCS7B01G419400	chr7D	92.079	101	8	0	2566	2666	603852620	603852720	3.210000e-30	143.0
30	TraesCS7B01G419400	chr7D	98.387	62	1	0	908	969	603847779	603847840	3.250000e-20	110.0
31	TraesCS7B01G419400	chr7D	96.491	57	2	0	661	717	604530609	604530665	9.110000e-16	95.3

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	TraesCS7B01G419400	chr7B	688162090	688165174	3084	False	5698.000000	5698	100.000000	1	3085	1	chr7B.!!$F1	3084
1	TraesCS7B01G419400	chr7B	686964592	686967504	2912	True	943.333333	1953	84.613000	28	2898	3	chr7B.!!$R2	2870
2	TraesCS7B01G419400	chr7B	686887347	686889011	1664	True	661.500000	1140	88.338000	583	2074	2	chr7B.!!$R1	1491
3	TraesCS7B01G419400	chr7B	686849444	686851202	1758	False	633.666667	1609	87.559333	542	2118	3	chr7B.!!$F2	1576
4	TraesCS7B01G419400	chr7A	696721868	696724580	2712	True	1036.666667	1831	89.539667	1	2666	3	chr7A.!!$R2	2665
5	TraesCS7B01G419400	chr7A	696622394	696624026	1632	True	721.500000	1247	89.446500	581	2074	2	chr7A.!!$R1	1493
6	TraesCS7B01G419400	chr7A	696552113	696553800	1687	False	516.250000	1640	91.639250	542	2118	4	chr7A.!!$F1	1576
7	TraesCS7B01G419400	chr7D	604471696	604477528	5832	False	820.800000	1640	90.347600	1	3085	5	chr7D.!!$F3	3084
8	TraesCS7B01G419400	chr7D	604530609	604532845	2236	False	771.100000	1652	91.319667	661	2895	3	chr7D.!!$F4	2234
9	TraesCS7B01G419400	chr7D	603982010	603983639	1629	False	687.500000	1188	89.174500	581	2074	2	chr7D.!!$F2	1493
10	TraesCS7B01G419400	chr7D	603847779	603853658	5879	False	563.000000	1720	94.451500	908	3085	4	chr7D.!!$F1	2177

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
398	424	1.000731	CCAAATTTCTTCCTTGGCGCA	59.999	47.619	10.83	0.0	33.65	6.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2244	8247	0.97064	TGTCGCCTTAGGTGCAAGTA	59.029	50.0	6.99	0.0	32.51	2.24	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
116	120	9.811995	GTAAAGGTTTTCTTTATGAAACCTTGT	57.188	29.630	25.32	18.97	46.10	3.16
135	139	1.000938	GTCAAGAGGGCAAAGTGCTTG	60.001	52.381	0.00	0.00	44.28	4.01
162	166	8.659527	TGATTATGTTTCATATAGAAGGCTGGA	58.340	33.333	0.00	0.00	37.57	3.86
170	174	2.743636	TAGAAGGCTGGACTCGTTTG	57.256	50.000	0.00	0.00	0.00	2.93
230	235	1.678101	AGGCGCAATTGATTAAGGAGC	59.322	47.619	10.83	0.89	0.00	4.70
275	281	5.499139	TCACAACTTGAGTCATCCAAAAC	57.501	39.130	0.00	0.00	0.00	2.43
311	317	9.781834	TTGGTATATTGCGTCTTTAATTTTCAG	57.218	29.630	0.00	0.00	0.00	3.02
318	324	8.560576	TTGCGTCTTTAATTTTCAGAAAGAAG	57.439	30.769	8.40	8.40	40.04	2.85
389	415	3.363341	TTCGGTGTGCCAAATTTCTTC	57.637	42.857	0.00	0.00	34.09	2.87
398	424	1.000731	CCAAATTTCTTCCTTGGCGCA	59.999	47.619	10.83	0.00	33.65	6.09
455	482	5.957771	ATCTAAGTCCATTCTACAAGGCA	57.042	39.130	0.00	0.00	0.00	4.75
466	493	8.659527	TCCATTCTACAAGGCATCTTATATTCA	58.340	33.333	0.00	0.00	0.00	2.57
490	517	3.628008	TCTCAACTAGGCGACATAGGAA	58.372	45.455	0.00	0.00	0.00	3.36
499	527	2.694109	GGCGACATAGGAAGACTTAGGT	59.306	50.000	0.00	0.00	0.00	3.08
544	574	8.655935	AATCCAGGTGACTTAGATTTTGAAAT	57.344	30.769	0.00	0.00	37.51	2.17
717	3290	1.581447	CCCAAGGAAACAAGCGCTC	59.419	57.895	12.06	0.00	0.00	5.03
719	3292	1.172180	CCAAGGAAACAAGCGCTCCA	61.172	55.000	12.06	0.00	0.00	3.86
794	3462	4.217118	CACTTCTTGCCAGCTTCACTAAAT	59.783	41.667	0.00	0.00	0.00	1.40
812	3480	8.248253	TCACTAAATATATTGTATCGCGGTCAT	58.752	33.333	6.13	0.00	0.00	3.06
831	3506	4.736631	GCGACCAAAAGGCGACGC	62.737	66.667	12.43	12.43	39.33	5.19
886	3608	1.003442	CTCTCATGTCCCCTCCCCA	59.997	63.158	0.00	0.00	0.00	4.96
901	3626	5.104409	CCCTCCCCATCCTCTCTATAAATT	58.896	45.833	0.00	0.00	0.00	1.82
902	3627	5.045286	CCCTCCCCATCCTCTCTATAAATTG	60.045	48.000	0.00	0.00	0.00	2.32
903	3628	5.787494	CCTCCCCATCCTCTCTATAAATTGA	59.213	44.000	0.00	0.00	0.00	2.57
904	3629	6.446434	CCTCCCCATCCTCTCTATAAATTGAT	59.554	42.308	0.00	0.00	0.00	2.57
905	3630	7.262990	TCCCCATCCTCTCTATAAATTGATG	57.737	40.000	0.00	0.00	0.00	3.07
1424	4263	1.283793	CCGTAAGTGTCACCGTCGT	59.716	57.895	0.00	0.00	0.00	4.34
1425	4264	0.318107	CCGTAAGTGTCACCGTCGTT	60.318	55.000	0.00	0.00	0.00	3.85
1547	4386	2.355986	CCGACCCCTCCGACATCAA	61.356	63.158	0.00	0.00	0.00	2.57
1869	4730	4.999939	CGCCGCCCAAGCAACAAC	63.000	66.667	0.00	0.00	39.83	3.32
2151	5024	2.302733	TCAAGATAGTTGTGCTGCTGGA	59.697	45.455	0.00	0.00	0.00	3.86
2152	5025	2.676839	CAAGATAGTTGTGCTGCTGGAG	59.323	50.000	0.00	0.00	0.00	3.86
2153	5026	1.905215	AGATAGTTGTGCTGCTGGAGT	59.095	47.619	0.00	0.00	0.00	3.85
2154	5027	2.304180	AGATAGTTGTGCTGCTGGAGTT	59.696	45.455	0.00	0.00	0.00	3.01
2155	5028	1.882912	TAGTTGTGCTGCTGGAGTTG	58.117	50.000	0.00	0.00	0.00	3.16
2157	5030	1.453562	TTGTGCTGCTGGAGTTGCA	60.454	52.632	0.00	0.00	38.81	4.08
2167	5040	2.512515	GAGTTGCAGCTAGCCCGG	60.513	66.667	12.13	2.38	44.83	5.73
2241	8244	2.464796	TAAAGATAGAGGGCCGGTGA	57.535	50.000	1.90	0.00	0.00	4.02
2244	8247	1.807814	AGATAGAGGGCCGGTGAATT	58.192	50.000	1.90	0.00	0.00	2.17
2407	8410	4.849310	TAGGGAATGCCGCCACGC	62.849	66.667	0.00	0.00	33.83	5.34
2460	8503	3.875023	TCGCCACCCCGAAACCAA	61.875	61.111	0.00	0.00	33.77	3.67
2521	8567	1.000827	CTGATCCGAGGAAGATCACGG	60.001	57.143	0.00	0.00	43.96	4.94
2522	8568	0.315568	GATCCGAGGAAGATCACGGG	59.684	60.000	0.00	0.00	44.57	5.28
2555	8604	1.196808	ACGACGTTTGCATTCATCCAC	59.803	47.619	0.00	0.00	0.00	4.02
2603	8867	8.103305	AGTTCATCTACATGTAAACTGGTGAAT	58.897	33.333	16.91	7.73	0.00	2.57
2641	8905	4.994217	TGAGCGTATGAACTGATGTTGAAA	59.006	37.500	0.00	0.00	36.39	2.69
2707	8972	4.264253	TGTCTTCAACATATGCTTCTGGG	58.736	43.478	1.58	0.00	31.20	4.45
2745	9011	4.217118	GGATGAATTTTGATATCTGCGGCT	59.783	41.667	3.98	0.00	0.00	5.52
2767	9033	0.296642	CTTAACGTATCGCACACGGC	59.703	55.000	6.67	0.00	43.59	5.68
2783	9049	1.335935	CGGCTTACAACCGCAAATTG	58.664	50.000	0.00	0.00	44.90	2.32
2824	9091	6.446909	TGGGAATATTCATAGGTATGCACA	57.553	37.500	17.07	0.00	33.76	4.57
3014	9840	7.709947	TGAAAATGCAAAACAAATTGGCATAA	58.290	26.923	7.63	0.00	31.47	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
26	27	7.803279	TTTCTGAGGAGGAGAAAGTTAAAAC	57.197	36.000	0.00	0.00	35.07	2.43
116	120	1.321474	CAAGCACTTTGCCCTCTTGA	58.679	50.000	0.00	0.00	46.52	3.02
135	139	8.725148	CCAGCCTTCTATATGAAACATAATCAC	58.275	37.037	0.00	0.00	33.79	3.06
157	161	3.955771	TGTTTTACAAACGAGTCCAGC	57.044	42.857	0.00	0.00	0.00	4.85
162	166	5.865013	CCCAACTTTTGTTTTACAAACGAGT	59.135	36.000	13.51	8.96	46.53	4.18
170	174	6.183360	GGTTTTCGACCCAACTTTTGTTTTAC	60.183	38.462	0.00	0.00	43.06	2.01
226	231	4.280174	TGGTATATTTGTCGTAGAGGCTCC	59.720	45.833	11.71	0.00	36.95	4.70
230	235	7.169308	GTGAATGTGGTATATTTGTCGTAGAGG	59.831	40.741	0.00	0.00	36.95	3.69
311	317	7.430992	ACTATTTACAACCGAACCTTCTTTC	57.569	36.000	0.00	0.00	0.00	2.62
318	324	4.685628	TGTCGAACTATTTACAACCGAACC	59.314	41.667	0.00	0.00	0.00	3.62
389	415	0.734889	ATCTTTTCGATGCGCCAAGG	59.265	50.000	4.18	0.00	0.00	3.61
398	424	8.177119	AGAGAGATAGCTTACATCTTTTCGAT	57.823	34.615	0.00	0.00	32.86	3.59
433	460	5.957771	TGCCTTGTAGAATGGACTTAGAT	57.042	39.130	0.00	0.00	0.00	1.98
455	482	9.429359	CGCCTAGTTGAGATTTGAATATAAGAT	57.571	33.333	0.00	0.00	0.00	2.40
466	493	4.649674	TCCTATGTCGCCTAGTTGAGATTT	59.350	41.667	0.00	0.00	0.00	2.17
477	504	2.959707	CCTAAGTCTTCCTATGTCGCCT	59.040	50.000	0.00	0.00	0.00	5.52
524	552	5.106157	CGGCATTTCAAAATCTAAGTCACCT	60.106	40.000	0.00	0.00	0.00	4.00
527	555	4.380444	GCCGGCATTTCAAAATCTAAGTCA	60.380	41.667	24.80	0.00	0.00	3.41
717	3290	1.878088	CAGCATGAGGGAATCGATTGG	59.122	52.381	16.96	0.00	39.69	3.16
794	3462	3.517602	GCCATGACCGCGATACAATATA	58.482	45.455	8.23	0.00	0.00	0.86
812	3480	2.975799	GTCGCCTTTTGGTCGCCA	60.976	61.111	0.00	0.00	42.99	5.69
886	3608	6.479884	GTGGGCATCAATTTATAGAGAGGAT	58.520	40.000	0.00	0.00	0.00	3.24
901	3626	1.003839	GAAGTGGTCGTGGGCATCA	60.004	57.895	0.00	0.00	0.00	3.07
902	3627	0.741221	GAGAAGTGGTCGTGGGCATC	60.741	60.000	0.00	0.00	0.00	3.91
903	3628	1.194781	AGAGAAGTGGTCGTGGGCAT	61.195	55.000	0.00	0.00	0.00	4.40
904	3629	0.541063	TAGAGAAGTGGTCGTGGGCA	60.541	55.000	0.00	0.00	0.00	5.36
905	3630	0.173708	CTAGAGAAGTGGTCGTGGGC	59.826	60.000	0.00	0.00	0.00	5.36
1256	4086	2.443016	GGTGGTGGTTGTTGGCCA	60.443	61.111	0.00	0.00	0.00	5.36
1410	4249	1.068585	GGGAACGACGGTGACACTT	59.931	57.895	5.39	0.00	0.00	3.16
1450	4289	2.674380	GTTGCAGGGCTGGTGGAG	60.674	66.667	0.00	0.00	0.00	3.86
1616	4461	2.169769	AGCTAATTGGCGGCTACAACTA	59.830	45.455	11.43	0.00	37.29	2.24
1869	4730	2.435586	CTTCCTGCCACCAGAGCG	60.436	66.667	0.00	0.00	41.77	5.03
1929	4790	2.749044	CCGCTGCTGCTGGACAAT	60.749	61.111	17.20	0.00	35.80	2.71
2151	5024	4.785453	GCCGGGCTAGCTGCAACT	62.785	66.667	15.72	0.00	45.15	3.16
2183	8052	4.863925	GCTCCGCGAGTGAGAGCC	62.864	72.222	19.57	5.76	45.83	4.70
2223	8226	1.580059	TTCACCGGCCCTCTATCTTT	58.420	50.000	0.00	0.00	0.00	2.52
2241	8244	3.007635	GTCGCCTTAGGTGCAAGTAATT	58.992	45.455	6.99	0.00	32.51	1.40
2244	8247	0.970640	TGTCGCCTTAGGTGCAAGTA	59.029	50.000	6.99	0.00	32.51	2.24
2298	8301	2.184167	CAGGGTTGCGTCCGTTGTT	61.184	57.895	0.00	0.00	0.00	2.83
2384	8387	2.203209	CGGCATTCCCTAGGGCAC	60.203	66.667	24.42	11.48	34.68	5.01
2448	8491	0.999712	ATCTCCATTGGTTTCGGGGT	59.000	50.000	1.86	0.00	0.00	4.95
2460	8503	1.533299	CGTCGAGTCGATGATCTCCAT	59.467	52.381	27.02	0.00	44.49	3.41
2521	8567	4.077184	TCGTGCCACCATCGTCCC	62.077	66.667	0.00	0.00	0.00	4.46
2522	8568	2.813908	GTCGTGCCACCATCGTCC	60.814	66.667	0.00	0.00	0.00	4.79
2573	8837	6.149308	CCAGTTTACATGTAGATGAACTGCAA	59.851	38.462	27.80	8.33	43.69	4.08
2603	8867	8.312896	TCATACGCTCACTATTTTACAAACAA	57.687	30.769	0.00	0.00	0.00	2.83
2641	8905	8.611654	AAATTGTCTAATTTTGCAGCAGAAAT	57.388	26.923	1.88	6.16	42.33	2.17
2683	8948	5.181009	CCAGAAGCATATGTTGAAGACAGA	58.819	41.667	4.29	0.00	42.62	3.41
2707	8972	5.741388	ATTCATCCTAAATTCTCACACGC	57.259	39.130	0.00	0.00	0.00	5.34
2745	9011	3.170505	CCGTGTGCGATACGTTAAGTAA	58.829	45.455	0.00	0.00	41.33	2.24
2767	9033	2.470999	GCACACAATTTGCGGTTGTAAG	59.529	45.455	0.00	0.13	37.69	2.34
2783	9049	3.814842	TCCCATGATTTATCATCGCACAC	59.185	43.478	2.27	0.00	45.23	3.82
2817	9084	8.720562	CGATATTTCCAGAACATTATGTGCATA	58.279	33.333	6.06	0.00	0.00	3.14
2831	9098	6.096673	TCGGATTCATTCGATATTTCCAGA	57.903	37.500	0.00	0.00	0.00	3.86
2891	9162	1.672881	CCCATGCGAAATGAAGGACTC	59.327	52.381	0.44	0.00	0.00	3.36
3014	9840	8.865090	TCAGTCACCACATACCATTTTAATTTT	58.135	29.630	0.00	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.