AutoCloner

Multiple sequence alignment - TraesCS7B01G351600

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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	TraesCS7B01G351600	chr7B	100.000	2751	0	0	1	2751	608391307	608394057	0.000000e+00	5081.0
1	TraesCS7B01G351600	chr7B	84.984	1878	210	43	884	2744	608379924	608381746	0.000000e+00	1840.0
2	TraesCS7B01G351600	chr7B	84.491	1799	204	41	624	2387	608404960	608406718	0.000000e+00	1707.0
3	TraesCS7B01G351600	chr7B	86.634	1429	133	35	573	1980	608414704	608416095	0.000000e+00	1528.0
4	TraesCS7B01G351600	chr7B	92.754	69	1	3	792	858	608379857	608379923	2.260000e-16	97.1
5	TraesCS7B01G351600	chr7D	91.296	2631	182	25	144	2747	560596423	560599033	0.000000e+00	3546.0
6	TraesCS7B01G351600	chr7D	85.216	2151	248	45	641	2744	560602791	560604918	0.000000e+00	2146.0
7	TraesCS7B01G351600	chr7D	83.494	1969	217	58	16	1937	560682013	560683920	0.000000e+00	1736.0
8	TraesCS7B01G351600	chr7D	83.151	2012	224	64	16	1980	560700978	560702921	0.000000e+00	1731.0
9	TraesCS7B01G351600	chr7D	84.573	1452	160	39	1304	2744	560590253	560591651	0.000000e+00	1382.0
10	TraesCS7B01G351600	chr7A	85.292	2366	247	45	1	2314	644721049	644723365	0.000000e+00	2348.0
11	TraesCS7B01G351600	chr7A	84.819	2154	258	37	624	2744	644768291	644770408	0.000000e+00	2102.0
12	TraesCS7B01G351600	chr7A	87.195	1640	136	34	646	2234	644734770	644736386	0.000000e+00	1797.0
13	TraesCS7B01G351600	chr7A	86.355	1070	107	21	792	1848	644710395	644711438	0.000000e+00	1131.0
14	TraesCS7B01G351600	chr7A	79.412	918	123	41	1843	2744	644715158	644716025	3.050000e-164	588.0
15	TraesCS7B01G351600	chr7A	89.195	472	47	4	2279	2747	644736383	644736853	1.100000e-163	586.0
16	TraesCS7B01G351600	chr7A	85.856	403	52	4	2345	2744	644723487	644723887	9.110000e-115	424.0
17	TraesCS7B01G351600	chr7A	78.558	527	95	12	16	539	644779046	644779557	5.680000e-87	331.0
18	TraesCS7B01G351600	chr7A	83.660	153	17	6	624	768	644710253	644710405	1.330000e-28	137.0

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	TraesCS7B01G351600	chr7B	608391307	608394057	2750	False	5081.000000	5081	100.000000	1	2751	1	chr7B.!!$F1	2750
1	TraesCS7B01G351600	chr7B	608404960	608406718	1758	False	1707.000000	1707	84.491000	624	2387	1	chr7B.!!$F2	1763
2	TraesCS7B01G351600	chr7B	608414704	608416095	1391	False	1528.000000	1528	86.634000	573	1980	1	chr7B.!!$F3	1407
3	TraesCS7B01G351600	chr7B	608379857	608381746	1889	False	968.550000	1840	88.869000	792	2744	2	chr7B.!!$F4	1952
4	TraesCS7B01G351600	chr7D	560596423	560604918	8495	False	2846.000000	3546	88.256000	144	2747	2	chr7D.!!$F4	2603
5	TraesCS7B01G351600	chr7D	560682013	560683920	1907	False	1736.000000	1736	83.494000	16	1937	1	chr7D.!!$F2	1921
6	TraesCS7B01G351600	chr7D	560700978	560702921	1943	False	1731.000000	1731	83.151000	16	1980	1	chr7D.!!$F3	1964
7	TraesCS7B01G351600	chr7D	560590253	560591651	1398	False	1382.000000	1382	84.573000	1304	2744	1	chr7D.!!$F1	1440
8	TraesCS7B01G351600	chr7A	644768291	644770408	2117	False	2102.000000	2102	84.819000	624	2744	1	chr7A.!!$F1	2120
9	TraesCS7B01G351600	chr7A	644721049	644723887	2838	False	1386.000000	2348	85.574000	1	2744	2	chr7A.!!$F4	2743
10	TraesCS7B01G351600	chr7A	644734770	644736853	2083	False	1191.500000	1797	88.195000	646	2747	2	chr7A.!!$F5	2101
11	TraesCS7B01G351600	chr7A	644710253	644716025	5772	False	618.666667	1131	83.142333	624	2744	3	chr7A.!!$F3	2120
12	TraesCS7B01G351600	chr7A	644779046	644779557	511	False	331.000000	331	78.558000	16	539	1	chr7A.!!$F2	523

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
120	122	0.616111	TGGCCCGCCATTGGTATTTT	60.616	50.0	3.74	0.0	41.89	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2052	11872	0.107703	CTCATTTGCGAGGGCCACTA	60.108	55.0	6.18	0.0	38.85	2.74	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
53	54	2.418368	TAACAGTGATGGGCATGGAC	57.582	50.000	0.00	0.00	0.00	4.02
63	64	2.203070	GCATGGACTACCGCCCAG	60.203	66.667	0.00	0.00	39.42	4.45
68	70	2.056223	GGACTACCGCCCAGCACTA	61.056	63.158	0.00	0.00	0.00	2.74
69	71	1.400530	GGACTACCGCCCAGCACTAT	61.401	60.000	0.00	0.00	0.00	2.12
88	90	9.014297	AGCACTATTATTCTAAATACCAATGGC	57.986	33.333	0.00	0.00	0.00	4.40
89	91	8.792633	GCACTATTATTCTAAATACCAATGGCA	58.207	33.333	0.00	0.00	0.00	4.92
94	96	8.995027	TTATTCTAAATACCAATGGCAGATGT	57.005	30.769	0.00	0.00	0.00	3.06
108	110	2.539476	CAGATGTTATTTTTGGCCCGC	58.461	47.619	0.00	0.00	0.00	6.13
111	113	1.270907	TGTTATTTTTGGCCCGCCAT	58.729	45.000	9.70	0.00	46.64	4.40
113	115	2.006169	GTTATTTTTGGCCCGCCATTG	58.994	47.619	9.70	0.00	46.64	2.82
120	122	0.616111	TGGCCCGCCATTGGTATTTT	60.616	50.000	3.74	0.00	41.89	1.82
197	199	1.327303	GCATTAAATCCCGATGGGCA	58.673	50.000	0.00	0.00	43.94	5.36
216	218	2.011617	AAGGAAAGCCTGCACCCACT	62.012	55.000	0.00	0.00	46.28	4.00
324	327	2.776072	CGTCGTTTTAGGCAGCCG	59.224	61.111	5.55	0.00	0.00	5.52
451	470	9.866936	AATGTTTTGATTTCACATTTCATTTCG	57.133	25.926	0.00	0.00	37.79	3.46
452	471	8.640091	TGTTTTGATTTCACATTTCATTTCGA	57.360	26.923	0.00	0.00	0.00	3.71
453	472	9.091784	TGTTTTGATTTCACATTTCATTTCGAA	57.908	25.926	0.00	0.00	0.00	3.71
456	475	9.913451	TTTGATTTCACATTTCATTTCGAAAAC	57.087	25.926	15.66	0.00	46.48	2.43
457	476	8.870160	TGATTTCACATTTCATTTCGAAAACT	57.130	26.923	15.66	0.00	46.48	2.66
458	477	9.958234	TGATTTCACATTTCATTTCGAAAACTA	57.042	25.926	15.66	0.23	46.48	2.24
567	612	9.533253	GCAACCTAGCATATGTATTTCAAATTT	57.467	29.630	4.29	0.00	0.00	1.82
649	695	1.667724	CGATGGCATGTTCTCTTGGAC	59.332	52.381	3.81	0.00	0.00	4.02
769	823	7.010460	CGTCCCATGCATATTATACATACACAG	59.990	40.741	0.00	0.00	0.00	3.66
977	1073	4.181578	TCGACTGCTTGCTAATTTACTCC	58.818	43.478	0.00	0.00	0.00	3.85
1146	1242	9.745880	GGTACAATACGCATACTGCTATATAAT	57.254	33.333	0.00	0.00	42.25	1.28
1576	1681	1.692519	GGCCTCGTCCATTACCAGTAT	59.307	52.381	0.00	0.00	0.00	2.12
1618	1723	2.016393	TAGCTATTGCGGCGCTGAGT	62.016	55.000	33.26	17.45	45.42	3.41
1666	1771	2.203153	AACGCGGTGTTTGGAGCT	60.203	55.556	12.47	0.00	37.59	4.09
1692	1797	2.038863	TCCATCCCGGCTGGTATTAT	57.961	50.000	17.91	0.00	35.19	1.28
1696	1801	3.259064	CATCCCGGCTGGTATTATTACG	58.741	50.000	11.58	0.00	34.77	3.18
1711	1816	2.467566	TTACGAAAGCCTTCCAGGTC	57.532	50.000	0.00	0.00	37.80	3.85
1766	1872	6.879458	ACAGTTCTAAGTTATGTTCCCATGAC	59.121	38.462	0.00	0.00	37.73	3.06
1780	1887	2.292016	CCCATGACTGCGTTTGTTTGTA	59.708	45.455	0.00	0.00	0.00	2.41
1881	11615	3.706594	GTCAGGGATATTGTCTCCTCACA	59.293	47.826	0.00	0.00	33.05	3.58
1943	11689	4.338379	GGACACACCCCTATTGACTATC	57.662	50.000	0.00	0.00	0.00	2.08
2017	11767	6.377327	GGACACATCCCTATTGTTTGTATG	57.623	41.667	0.00	0.00	39.39	2.39
2052	11872	6.694447	TGTTCTTTTCCTACGTAACTAGCAT	58.306	36.000	0.00	0.00	0.00	3.79
2070	11890	0.546122	ATAGTGGCCCTCGCAAATGA	59.454	50.000	0.00	0.00	36.38	2.57
2072	11892	1.675641	GTGGCCCTCGCAAATGAGT	60.676	57.895	0.00	0.00	36.38	3.41
2078	11898	1.033746	CCTCGCAAATGAGTGGGCAT	61.034	55.000	0.00	0.00	34.04	4.40
2079	11899	0.099968	CTCGCAAATGAGTGGGCATG	59.900	55.000	0.00	0.00	0.00	4.06
2080	11900	1.517694	CGCAAATGAGTGGGCATGC	60.518	57.895	9.90	9.90	0.00	4.06
2082	11902	1.610554	GCAAATGAGTGGGCATGCCT	61.611	55.000	34.70	17.16	36.10	4.75
2083	11903	0.174845	CAAATGAGTGGGCATGCCTG	59.825	55.000	34.70	19.22	36.10	4.85
2165	11999	8.836413	CATAAGAAATCGGACTTATTAAAGGCA	58.164	33.333	0.00	0.00	43.19	4.75
2170	12004	7.497925	AATCGGACTTATTAAAGGCATCTTC	57.502	36.000	0.00	0.00	43.19	2.87
2173	12008	5.276868	CGGACTTATTAAAGGCATCTTCGTG	60.277	44.000	0.00	0.00	43.19	4.35
2177	12012	6.430000	ACTTATTAAAGGCATCTTCGTGTGTT	59.570	34.615	0.00	0.00	37.01	3.32
2189	12024	7.116233	GCATCTTCGTGTGTTGGATTTTAAAAT	59.884	33.333	13.24	13.24	0.00	1.82
2192	12027	9.834628	TCTTCGTGTGTTGGATTTTAAAATATC	57.165	29.630	13.34	9.49	0.00	1.63
2234	12070	0.250338	AGAGGACCGGAAAGCACAAC	60.250	55.000	9.46	0.00	0.00	3.32
2364	12308	8.715191	TTGTAAACTTTGACCTAAGTTCGTAA	57.285	30.769	9.33	4.09	45.13	3.18
2414	12358	6.238374	CCAAACCATTACCGTTAGATCATGAC	60.238	42.308	0.00	0.00	0.00	3.06
2481	12425	8.363029	GTCAAACTTTACGAAACTTGACTTTTG	58.637	33.333	5.69	0.00	0.00	2.44
2507	12454	8.433421	AGAAAACAATCACACTATATTACGGG	57.567	34.615	0.00	0.00	0.00	5.28
2511	12458	7.062749	ACAATCACACTATATTACGGGATGT	57.937	36.000	0.00	0.00	0.00	3.06
2662	12611	5.863935	TCTCACATCATGTCTTTTCGTACAG	59.136	40.000	0.00	0.00	0.00	2.74
2705	12654	5.582665	CCTCTAGAGAACCTTTTGAAATCCG	59.417	44.000	21.76	0.00	0.00	4.18
2711	12660	4.459337	AGAACCTTTTGAAATCCGTGATCC	59.541	41.667	0.00	0.00	0.00	3.36
2721	12670	8.810652	TTGAAATCCGTGATCCTTTTAAAAAG	57.189	30.769	1.66	0.00	0.00	2.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	0.107410	CTAAATACCAGTGGCGGCCA	60.107	55.000	19.77	19.77	0.00	5.36
14	15	0.107361	ACCTAAATACCAGTGGCGGC	60.107	55.000	9.78	0.00	0.00	6.53
42	43	2.510906	GCGGTAGTCCATGCCCAT	59.489	61.111	0.00	0.00	0.00	4.00
43	44	3.792736	GGCGGTAGTCCATGCCCA	61.793	66.667	0.00	0.00	41.70	5.36
53	54	3.006967	AGAATAATAGTGCTGGGCGGTAG	59.993	47.826	0.00	0.00	0.00	3.18
63	64	8.792633	TGCCATTGGTATTTAGAATAATAGTGC	58.207	33.333	4.26	0.00	0.00	4.40
68	70	9.592196	ACATCTGCCATTGGTATTTAGAATAAT	57.408	29.630	4.26	0.00	0.00	1.28
69	71	8.995027	ACATCTGCCATTGGTATTTAGAATAA	57.005	30.769	4.26	0.00	0.00	1.40
88	90	2.539476	GCGGGCCAAAAATAACATCTG	58.461	47.619	4.39	0.00	0.00	2.90
89	91	1.480545	GGCGGGCCAAAAATAACATCT	59.519	47.619	4.39	0.00	35.81	2.90
120	122	1.303724	CGCCCACCATTGGTAACCA	60.304	57.895	8.31	0.00	42.10	3.67
140	142	1.667510	CATTGGCGGGCACAAAACC	60.668	57.895	2.73	0.00	0.00	3.27
197	199	1.531602	GTGGGTGCAGGCTTTCCTT	60.532	57.895	0.00	0.00	41.93	3.36
332	335	0.688487	ACAACAACTAGCGGGGCTTA	59.312	50.000	0.00	0.00	40.44	3.09
333	336	0.605589	GACAACAACTAGCGGGGCTT	60.606	55.000	0.00	0.00	40.44	4.35
453	472	9.396022	CCCTGTGAATTGACATAGTATTAGTTT	57.604	33.333	0.00	0.00	0.00	2.66
454	473	8.768397	TCCCTGTGAATTGACATAGTATTAGTT	58.232	33.333	0.00	0.00	0.00	2.24
455	474	8.319057	TCCCTGTGAATTGACATAGTATTAGT	57.681	34.615	0.00	0.00	0.00	2.24
456	475	9.046296	GTTCCCTGTGAATTGACATAGTATTAG	57.954	37.037	0.00	0.00	34.90	1.73
457	476	8.544622	TGTTCCCTGTGAATTGACATAGTATTA	58.455	33.333	0.00	0.00	34.90	0.98
458	477	7.402054	TGTTCCCTGTGAATTGACATAGTATT	58.598	34.615	0.00	0.00	34.90	1.89
459	478	6.957631	TGTTCCCTGTGAATTGACATAGTAT	58.042	36.000	0.00	0.00	34.90	2.12
460	479	6.367374	TGTTCCCTGTGAATTGACATAGTA	57.633	37.500	0.00	0.00	34.90	1.82
469	488	2.964464	TGTTGCATGTTCCCTGTGAATT	59.036	40.909	0.00	0.00	34.90	2.17
649	695	7.374272	ACATATCTACATCGATTGACCAAGAG	58.626	38.462	0.00	0.00	0.00	2.85
769	823	1.884926	GGACAGCCTGCTACGCATC	60.885	63.158	0.00	0.00	38.13	3.91
977	1073	3.185391	GTCTCTTTGTTTTCTCCTCGCTG	59.815	47.826	0.00	0.00	0.00	5.18
1146	1242	2.496070	CTCAACTACGGTTCCATGGAGA	59.504	50.000	15.53	4.48	32.73	3.71
1576	1681	4.647853	ACTGCATCGGTAGTCCTGTTATTA	59.352	41.667	0.00	0.00	34.66	0.98
1666	1771	3.797353	GCCGGGATGGAAGGCTCA	61.797	66.667	2.18	0.00	46.83	4.26
1711	1816	0.108615	AATCCACCGTGCTCTTCTCG	60.109	55.000	0.00	0.00	0.00	4.04
1766	1872	3.059868	ACTCGACATACAAACAAACGCAG	60.060	43.478	0.00	0.00	0.00	5.18
1813	1927	7.686519	TGTAATGCAATGCAAATTTGAATAGC	58.313	30.769	22.31	17.90	43.62	2.97
1858	11592	3.706594	GTGAGGAGACAATATCCCTGACA	59.293	47.826	0.00	0.00	37.57	3.58
1862	11596	4.271807	TCTGTGAGGAGACAATATCCCT	57.728	45.455	0.00	0.00	37.57	4.20
1863	11597	4.346418	ACATCTGTGAGGAGACAATATCCC	59.654	45.833	0.00	0.00	37.57	3.85
1971	11718	6.889177	TCCCACAACACATCAATATTACACAT	59.111	34.615	0.00	0.00	0.00	3.21
2017	11767	8.347771	ACGTAGGAAAAGAACAATTTACCTTTC	58.652	33.333	0.00	0.00	0.00	2.62
2040	11860	1.411612	GGGCCACTATGCTAGTTACGT	59.588	52.381	4.39	0.00	36.76	3.57
2052	11872	0.107703	CTCATTTGCGAGGGCCACTA	60.108	55.000	6.18	0.00	38.85	2.74
2070	11890	0.251922	ACAATTCAGGCATGCCCACT	60.252	50.000	33.14	12.66	36.58	4.00
2072	11892	0.609151	CAACAATTCAGGCATGCCCA	59.391	50.000	33.14	17.75	36.58	5.36
2078	11898	7.222872	ACATTATTTTTCCAACAATTCAGGCA	58.777	30.769	0.00	0.00	0.00	4.75
2079	11899	7.671495	ACATTATTTTTCCAACAATTCAGGC	57.329	32.000	0.00	0.00	0.00	4.85
2150	11984	5.585047	ACACGAAGATGCCTTTAATAAGTCC	59.415	40.000	0.00	0.00	31.62	3.85
2151	11985	6.092259	ACACACGAAGATGCCTTTAATAAGTC	59.908	38.462	0.00	0.00	31.62	3.01
2197	12032	6.096001	GGTCCTCTATTTGAACTTGCATCAAT	59.904	38.462	2.22	0.00	36.72	2.57
2246	12084	7.011857	TGGCTTGACAATTATTGAACCAAAAAC	59.988	33.333	12.28	6.44	0.00	2.43
2262	12103	9.116067	GTACCTATTGTTATTATGGCTTGACAA	57.884	33.333	0.00	0.00	0.00	3.18
2387	12331	5.180271	TGATCTAACGGTAATGGTTTGGTC	58.820	41.667	0.00	0.00	33.02	4.02
2453	12397	4.959757	GTCAAGTTTCGTAAAGTTTGACCG	59.040	41.667	16.39	0.00	38.70	4.79
2466	12410	7.561237	TTGTTTTCTCAAAAGTCAAGTTTCG	57.439	32.000	0.00	0.00	0.00	3.46
2481	12425	8.548721	CCCGTAATATAGTGTGATTGTTTTCTC	58.451	37.037	0.00	0.00	0.00	2.87
2504	12451	9.706691	AATCATAATTGTACTTACTACATCCCG	57.293	33.333	0.00	0.00	35.18	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.