AutoCloner

Multiple sequence alignment - TraesCS1B01G041800

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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	TraesCS1B01G041800	chr1B	100.000	2543	0	0	1	2543	21537454	21534912	0.000000e+00	4697.0
1	TraesCS1B01G041800	chr6B	96.592	2553	60	7	3	2543	9928631	9931168	0.000000e+00	4207.0
2	TraesCS1B01G041800	chr6B	88.750	160	17	1	2380	2538	259286344	259286503	7.180000e-46	195.0
3	TraesCS1B01G041800	chr6B	82.895	152	20	5	1733	1881	295982919	295982771	5.710000e-27	132.0
4	TraesCS1B01G041800	chr4D	92.806	139	8	2	2380	2517	479044960	479044823	1.540000e-47	200.0
5	TraesCS1B01G041800	chr4D	89.172	157	17	0	2121	2277	75266904	75266748	2.000000e-46	196.0
6	TraesCS1B01G041800	chr4D	90.476	42	4	0	111	152	442219440	442219481	3.530000e-04	56.5
7	TraesCS1B01G041800	chr2D	88.608	158	18	0	2120	2277	549021010	549020853	2.580000e-45	193.0
8	TraesCS1B01G041800	chr3A	88.199	161	17	2	2380	2540	602923441	602923283	9.290000e-45	191.0
9	TraesCS1B01G041800	chr3A	86.420	162	22	0	2116	2277	607058411	607058572	7.230000e-41	178.0
10	TraesCS1B01G041800	chr3A	90.476	105	7	2	177	278	429624344	429624240	4.410000e-28	135.0
11	TraesCS1B01G041800	chr5B	86.628	172	22	1	2115	2285	539314444	539314273	3.340000e-44	189.0
12	TraesCS1B01G041800	chr2A	87.349	166	16	3	2380	2540	189206852	189206687	4.320000e-43	185.0
13	TraesCS1B01G041800	chr7A	86.667	165	20	2	2116	2280	719336336	719336174	5.590000e-42	182.0
14	TraesCS1B01G041800	chr7A	88.679	106	7	5	177	278	50806493	50806597	9.550000e-25	124.0
15	TraesCS1B01G041800	chr5A	87.037	162	19	2	2116	2277	636415293	636415134	5.590000e-42	182.0
16	TraesCS1B01G041800	chr5A	86.957	161	17	4	2380	2537	343081665	343081506	7.230000e-41	178.0
17	TraesCS1B01G041800	chr5A	89.524	105	8	2	177	278	595917078	595916974	2.050000e-26	130.0
18	TraesCS1B01G041800	chr4B	87.037	162	19	2	2116	2277	142521060	142520901	5.590000e-42	182.0
19	TraesCS1B01G041800	chr4A	86.957	161	17	4	2380	2539	319817601	319817444	7.230000e-41	178.0
20	TraesCS1B01G041800	chr7D	85.380	171	23	2	2109	2278	55414250	55414081	2.600000e-40	176.0
21	TraesCS1B01G041800	chr7D	86.875	160	18	2	2383	2540	128859622	128859780	2.600000e-40	176.0
22	TraesCS1B01G041800	chr3D	86.076	158	20	2	2380	2536	266387747	266387903	4.350000e-38	169.0
23	TraesCS1B01G041800	chr6A	83.125	160	25	2	1714	1873	417629113	417628956	7.330000e-31	145.0
24	TraesCS1B01G041800	chr6D	82.099	162	24	5	1714	1874	299902784	299902941	1.590000e-27	134.0
25	TraesCS1B01G041800	chr3B	82.667	150	21	5	1717	1865	776039204	776039349	7.380000e-26	128.0

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	TraesCS1B01G041800	chr1B	21534912	21537454	2542	True	4697	4697	100.000	1	2543	1	chr1B.!!$R1	2542
1	TraesCS1B01G041800	chr6B	9928631	9931168	2537	False	4207	4207	96.592	3	2543	1	chr6B.!!$F1	2540

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
596	605	1.227973	CTTGCCCCTCCCGCTTATC	60.228	63.158	0.0	0.0	0.0	1.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1781	1790	0.250381	ATGCTCAGCCTCTGCATAGC	60.25	55.0	0.0	4.73	44.37	2.97	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
112	113	2.116125	GGTGGTTGGCTCCTTGCT	59.884	61.111	0.00	0.00	42.39	3.91
166	167	3.958018	TCCCAACCAAATAATGCGTACT	58.042	40.909	0.00	0.00	0.00	2.73
170	171	5.929415	CCCAACCAAATAATGCGTACTTTTT	59.071	36.000	0.00	0.00	0.00	1.94
204	205	1.813513	AAGATGGTCTGGCTGAAACG	58.186	50.000	0.00	0.00	0.00	3.60
215	217	6.483640	GGTCTGGCTGAAACGATATTATTTCT	59.516	38.462	11.69	0.00	36.09	2.52
278	280	5.178623	CGCACTTGTGTTTTAGTCCATTCTA	59.821	40.000	2.61	0.00	0.00	2.10
279	281	6.603095	GCACTTGTGTTTTAGTCCATTCTAG	58.397	40.000	2.61	0.00	0.00	2.43
318	327	2.291741	TGCAACGCACATACATGTTTGA	59.708	40.909	21.17	0.00	39.39	2.69
345	354	4.698201	TGTCCTAACACAAAGTGATGGA	57.302	40.909	3.88	5.51	36.96	3.41
441	450	3.463944	ACCACCATGCGTAGTAATAAGC	58.536	45.455	0.99	0.99	0.00	3.09
576	585	7.148407	CGTATGGTTTCTTACTCTGCTGATTTT	60.148	37.037	0.00	0.00	0.00	1.82
596	605	1.227973	CTTGCCCCTCCCGCTTATC	60.228	63.158	0.00	0.00	0.00	1.75
682	691	5.048224	ACAACTTCGTAGCCTGCGTATATAT	60.048	40.000	1.31	0.00	0.00	0.86
693	702	4.917998	CCTGCGTATATATATGGACATCGC	59.082	45.833	12.81	12.51	41.17	4.58
946	955	1.884075	CGACTCCCCGGTGATGACAA	61.884	60.000	0.00	0.00	0.00	3.18
1026	1035	2.154798	ATCTGGTGTCGGTGTCCACG	62.155	60.000	0.00	0.00	32.30	4.94
1125	1134	1.667830	CGGCTTCGAGAAAGTGCCA	60.668	57.895	12.85	0.00	43.38	4.92
1183	1192	0.469331	TCCATCGCTTATCCCTCCGT	60.469	55.000	0.00	0.00	0.00	4.69
1431	1440	3.833645	TATGTCGCCGCGGCTTCT	61.834	61.111	43.60	27.95	39.32	2.85
1439	1448	3.423154	CGCGGCTTCTTTCGGCTT	61.423	61.111	0.00	0.00	0.00	4.35
1573	1582	6.435430	TCACAGTTCCATATGCATGTTTAC	57.565	37.500	10.16	0.47	0.00	2.01
1628	1637	3.691575	TCTCAAGGTAGGTCAGTGAGAG	58.308	50.000	0.00	0.00	39.73	3.20
1635	1644	7.502895	TCAAGGTAGGTCAGTGAGAGTATAATC	59.497	40.741	0.00	0.00	0.00	1.75
1737	1746	2.584835	TGACTTTGCTATTGGCTGGT	57.415	45.000	0.00	0.00	42.39	4.00
1781	1790	2.095567	GTGTTGGCTGTGTGCATCTTAG	60.096	50.000	0.00	0.00	45.15	2.18
1798	1807	0.678395	TAGCTATGCAGAGGCTGAGC	59.322	55.000	10.92	0.00	44.05	4.26
1799	1808	1.145598	GCTATGCAGAGGCTGAGCA	59.854	57.895	10.92	12.19	43.54	4.26
1900	1909	0.811281	AGCTAGCAACCGAAATTGGC	59.189	50.000	18.83	0.00	0.00	4.52
1933	1942	2.242926	TGATTGCCAACGGAAAATGGA	58.757	42.857	0.00	0.00	39.12	3.41
2020	2033	9.848710	ACATATTTCTGAATTCTGATCATCTGT	57.151	29.630	14.89	14.31	0.00	3.41
2102	2115	6.969473	GCATCCTTAGTTTTGTATTCAGCTTC	59.031	38.462	0.00	0.00	0.00	3.86
2118	2131	3.077359	AGCTTCAGCACAAACATCTACC	58.923	45.455	0.75	0.00	45.16	3.18
2184	2197	4.623167	GGACTACATACGCAGCAATATGAG	59.377	45.833	17.01	12.63	33.73	2.90
2206	2219	9.737427	ATGAGTCAATCTACAGTCTAAAATACG	57.263	33.333	0.00	0.00	0.00	3.06
2316	2329	5.351465	CCAGCAATTAACGACAACTAGATGT	59.649	40.000	5.17	5.17	35.90	3.06
2336	2349	1.100510	CAATGCCAGTGGAGTGATGG	58.899	55.000	15.20	0.00	37.15	3.51
2390	2403	8.945481	AAACTTTGTCTAGAGATGATGATGAG	57.055	34.615	0.00	0.00	0.00	2.90
2406	2419	5.003692	TGATGAGTGAATGAGTGCTCTAC	57.996	43.478	0.68	0.00	0.00	2.59
2408	2421	5.128335	TGATGAGTGAATGAGTGCTCTACAT	59.872	40.000	0.68	0.00	0.00	2.29
2418	2431	5.269991	TGAGTGCTCTACATACTAAACCCT	58.730	41.667	0.68	0.00	0.00	4.34
2419	2432	5.360144	TGAGTGCTCTACATACTAAACCCTC	59.640	44.000	0.68	0.00	0.00	4.30
2420	2433	5.520751	AGTGCTCTACATACTAAACCCTCT	58.479	41.667	0.00	0.00	0.00	3.69
2421	2434	5.361285	AGTGCTCTACATACTAAACCCTCTG	59.639	44.000	0.00	0.00	0.00	3.35
2422	2435	4.649674	TGCTCTACATACTAAACCCTCTGG	59.350	45.833	0.00	0.00	37.80	3.86
2454	2467	2.633481	CACTAGGGGTATCTAGGGTTGC	59.367	54.545	0.00	0.00	40.63	4.17
2501	2514	3.610040	ACATGCCGAATCTAACAGACA	57.390	42.857	0.00	0.00	0.00	3.41
2504	2517	5.050490	ACATGCCGAATCTAACAGACATAC	58.950	41.667	0.00	0.00	0.00	2.39

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.611757	TCATGTTAGGTCATTTATCATCAAACG	58.388	33.333	0.00	0.00	0.00	3.60
1	2	9.722056	GTCATGTTAGGTCATTTATCATCAAAC	57.278	33.333	0.00	0.00	0.00	2.93
4	5	7.572814	TGGTCATGTTAGGTCATTTATCATCA	58.427	34.615	0.00	0.00	0.00	3.07
5	6	7.716998	ACTGGTCATGTTAGGTCATTTATCATC	59.283	37.037	0.00	0.00	0.00	2.92
57	58	6.409810	GCCTGAACCTCTCCCTAATTTATCTT	60.410	42.308	0.00	0.00	0.00	2.40
141	142	3.322254	ACGCATTATTTGGTTGGGAAACA	59.678	39.130	0.00	0.00	0.00	2.83
170	171	8.748412	CCAGACCATCTTTACAAAATGGATAAA	58.252	33.333	16.20	0.00	42.13	1.40
185	186	1.347707	TCGTTTCAGCCAGACCATCTT	59.652	47.619	0.00	0.00	0.00	2.40
215	217	8.811017	ACATCCCACATTAATTATTCACAACAA	58.189	29.630	0.00	0.00	0.00	2.83
278	280	3.129638	TGCAACGTAAGGAAAACAAAGCT	59.870	39.130	0.00	0.00	46.39	3.74
279	281	3.440228	TGCAACGTAAGGAAAACAAAGC	58.560	40.909	0.00	0.00	46.39	3.51
309	318	7.446931	TGTGTTAGGACAATACATCAAACATGT	59.553	33.333	0.00	0.00	37.57	3.21
318	327	7.121168	CCATCACTTTGTGTTAGGACAATACAT	59.879	37.037	0.00	0.00	37.57	2.29
345	354	0.872388	GCGTTGTTGATCCGGTCTTT	59.128	50.000	0.00	0.00	0.00	2.52
398	407	1.764723	AGACCGAGCCAATCATCATCA	59.235	47.619	0.00	0.00	0.00	3.07
576	585	1.279025	ATAAGCGGGAGGGGCAAGAA	61.279	55.000	0.00	0.00	0.00	2.52
596	605	8.715998	CCGAGATATTTATTCATTCCAGACAAG	58.284	37.037	0.00	0.00	0.00	3.16
682	691	5.301805	TGATGTTTCTAGAGCGATGTCCATA	59.698	40.000	0.00	0.00	0.00	2.74
693	702	8.659925	AGCTAATTGTGATGATGTTTCTAGAG	57.340	34.615	0.00	0.00	0.00	2.43
946	955	1.705997	AAAGCCTGGGAACTGTCCGT	61.706	55.000	0.00	0.00	46.04	4.69
949	958	2.861147	AGTAAAGCCTGGGAACTGTC	57.139	50.000	0.00	0.00	0.00	3.51
995	1004	4.552365	CCAGATCCGGCATGGCGT	62.552	66.667	35.39	21.60	37.80	5.68
1001	1010	3.770040	CCGACACCAGATCCGGCA	61.770	66.667	0.00	0.00	35.29	5.69
1108	1117	0.320771	TCTGGCACTTTCTCGAAGCC	60.321	55.000	0.00	0.00	45.41	4.35
1125	1134	3.181434	TGGGGACTTGTACAATTTGCTCT	60.181	43.478	9.13	0.00	0.00	4.09
1139	1148	1.539124	GGTGGAGGACTGGGGACTT	60.539	63.158	0.00	0.00	0.00	3.01
1183	1192	8.225416	AGGCGGTATAGTTGGATCTGATATATA	58.775	37.037	0.00	0.00	0.00	0.86
1305	1314	0.686224	GCAGGATGATGGAGAGGGAG	59.314	60.000	0.00	0.00	39.69	4.30
1431	1440	2.203337	AGCTGCACCAAGCCGAAA	60.203	55.556	1.02	0.00	44.68	3.46
1439	1448	1.071987	CAGACCAAGAGCTGCACCA	59.928	57.895	1.02	0.00	0.00	4.17
1518	1527	5.104776	TCAGAGTCCATCCCAGAAGTAATTG	60.105	44.000	0.00	0.00	0.00	2.32
1635	1644	7.624549	ACACAAGCCTCCATAATATATACTGG	58.375	38.462	7.02	7.02	0.00	4.00
1653	1662	8.437742	CAATCATTCTTATTTGGAAACACAAGC	58.562	33.333	0.00	0.00	42.67	4.01
1686	1695	7.934855	AGATTCATACAAGCAACAAGATTCT	57.065	32.000	0.00	0.00	0.00	2.40
1689	1698	7.458409	ACAAGATTCATACAAGCAACAAGAT	57.542	32.000	0.00	0.00	0.00	2.40
1690	1699	6.882610	ACAAGATTCATACAAGCAACAAGA	57.117	33.333	0.00	0.00	0.00	3.02
1696	1705	9.836864	AGTCATATAACAAGATTCATACAAGCA	57.163	29.630	0.00	0.00	0.00	3.91
1729	1738	3.449018	ACACATAAAAACACACCAGCCAA	59.551	39.130	0.00	0.00	0.00	4.52
1737	1746	5.089411	CGAACACACACACATAAAAACACA	58.911	37.500	0.00	0.00	0.00	3.72
1781	1790	0.250381	ATGCTCAGCCTCTGCATAGC	60.250	55.000	0.00	4.73	44.37	2.97
1798	1807	8.039538	AGGATACAGATACATAATGAGCACATG	58.960	37.037	0.00	0.00	36.32	3.21
1799	1808	8.143673	AGGATACAGATACATAATGAGCACAT	57.856	34.615	0.00	0.00	37.42	3.21
1831	1840	5.067805	GGATTTTATTGGCTCGAAATGGAGT	59.932	40.000	0.00	0.00	36.41	3.85
1900	1909	5.850557	TTGGCAATCAACAATATACCCTG	57.149	39.130	0.00	0.00	0.00	4.45
2013	2026	1.648504	CGCATGCTTCAGACAGATGA	58.351	50.000	17.13	0.00	0.00	2.92
2102	2115	1.004745	AGGGGGTAGATGTTTGTGCTG	59.995	52.381	0.00	0.00	0.00	4.41
2118	2131	4.941873	GGCGTATATTTAGAAATGGAGGGG	59.058	45.833	0.00	0.00	0.00	4.79
2316	2329	1.340308	CCATCACTCCACTGGCATTGA	60.340	52.381	6.39	0.00	0.00	2.57
2336	2349	4.453478	TGATCTCAAGACTTGCAACATCAC	59.547	41.667	10.50	0.00	0.00	3.06
2390	2403	7.222999	GGTTTAGTATGTAGAGCACTCATTCAC	59.777	40.741	0.00	0.00	0.00	3.18
2418	2431	5.091552	CCCCTAGTGCCTATATAAACCAGA	58.908	45.833	0.00	0.00	0.00	3.86
2419	2432	4.844655	ACCCCTAGTGCCTATATAAACCAG	59.155	45.833	0.00	0.00	0.00	4.00
2420	2433	4.834852	ACCCCTAGTGCCTATATAAACCA	58.165	43.478	0.00	0.00	0.00	3.67
2421	2434	6.901857	AGATACCCCTAGTGCCTATATAAACC	59.098	42.308	0.00	0.00	0.00	3.27
2422	2435	7.974730	AGATACCCCTAGTGCCTATATAAAC	57.025	40.000	0.00	0.00	0.00	2.01
2423	2436	8.287350	CCTAGATACCCCTAGTGCCTATATAAA	58.713	40.741	0.00	0.00	35.51	1.40
2501	2514	4.021368	AGACTTGGCGTGTACTTCAAGTAT	60.021	41.667	17.04	13.67	46.46	2.12
2504	2517	2.755650	AGACTTGGCGTGTACTTCAAG	58.244	47.619	12.78	12.78	41.46	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.